diff --git a/CMakeLists.txt b/CMakeLists.txt index 0c9e8604..3f5d2bdc 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -2,37 +2,11 @@ cmake_minimum_required(VERSION 3.0) # Set the name of the project -project(ThermoFun VERSION 0.2.0 LANGUAGES CXX) +project(ThermoFun VERSION 0.2.2 LANGUAGES CXX) # Set the cmake module path of the project set(CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake/modules") -if (CMAKE_CXX_COMPILER_ID MATCHES "MSVC") - -include_directories("${CMAKE_SOURCE_DIR}/../dependencies/include") - -else() # build for linux - -endif() - -if (BUILD_WINDOWS) -set(CMAKE_CXX_STANDARD 11) -# the name of the target operating system -SET(CMAKE_SYSTEM_NAME Windows) - -# which compilers to use for C and C++ -SET(CMAKE_C_COMPILER x86_64-w64-mingw32-gcc) -SET(CMAKE_CXX_COMPILER x86_64-w64-mingw32-g++) - -# here is the target environment located -SET(CMAKE_FIND_ROOT_PATH /usr/x86_64-w64-mingw32) - -include_directories("/usr/local/include") -link_directories("/usr/local/lib") - -else() # build for linux -endif() - # Use ccache to speed up repeated compilations include(CCache) @@ -46,27 +20,16 @@ include(CondaAware) option(TFUN_BUILD_SHARED_LIBS "Build shared libraries." ON) option(TFUN_BUILD_STATIC_LIBS "Build static libraries." ON) #option(TFUN_BUILD_TESTS "Build tests." OFF) -option(TFUN_BUILD_GUI "Build ThermoFunGui library." OFF) -option(TFUN_BUILD_HUBCLIENT "Build ThermoFun with ThermoHubClient." OFF) -option(TFUN_BUILD_GUIDEMO "Build ThermoFunGui demo." OFF) option(TFUN_BUILD_PYTHON "Build the python wrappers and python package thermofun." ON) -#option(REFRESH_THIRDPARTY "Refresh thirdparty libraries." OFF) # Modify the TFUN_BUILD_* variables accordingly to BUILD_ALL if(TFUN_BUILD_ALL MATCHES ON) set(TFUN_BUILD_SHARED_LIBS ON) set(TFUN_BUILD_STATIC_LIBS ON) # set(TFUN_BUILD_TESTS ON) - set(TFUN_BUILD_GUI ON) - set(TFUN_BUILD_HUBCLIENT ON) - set(TFUN_BUILD_GUIDEMO ON) set(TFUN_BUILD_PYTHON ON) endif() -# DBClient is necessary when building the GUI DEMO -if(TFUN_BUILD_GUI MATCHES ON OR TFUN_BUILD_GUIDEMO MATCHES ON) - set(TFUN_BUILD_HUBCLIENT ON) -endif() # Set the default build type to Release if(NOT CMAKE_BUILD_TYPE) @@ -126,21 +89,9 @@ file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/Resources # add_subdirectory(tests EXCLUDE_FROM_ALL) #endif() -# Build ThermoFunGui library -if(TFUN_BUILD_HUBCLIENT) - add_subdirectory(ThermoHubClient) -endif() - -# Build ThermoFunGui library -if(TFUN_BUILD_GUI) - add_subdirectory(ThermoFunGui) -endif() - # Build python wraper if(TFUN_BUILD_PYTHON) add_subdirectory(python) -else() - add_subdirectory(python EXCLUDE_FROM_ALL) endif() # Install the cmake config files that permit users to use find_package(ThermoFun) diff --git a/README.md b/README.md index 9fe0fff3..d9c399fc 100644 --- a/README.md +++ b/README.md @@ -1,282 +1,17 @@ # ThermoFun -[![Build Status](https://travis-ci.com/thermomod/thermofun.svg?branch=master)](https://travis-ci.com/thermomod/thermofun) +[![Build Status](https://travis-ci.com/thermohub/thermofun.svg?branch=master)](https://travis-ci.com/thermohub/thermofun) [![Build status](https://ci.appveyor.com/api/projects/status/13098q3j713uo06v/branch/master?svg=true)](https://ci.appveyor.com/project/gdmiron/thermofun-44e8m/branch/master) A code for calculating the standard state thermodynamic properties at a given temperature and pressure. ## Try ThermoFun in your browser using Jupyter Notebooks and Binder -[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/thermomod/thermofun-jupyter/master) +[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/thermohub/thermofun-jupyter/master) Please wait until the Jupyter Notebook server starts (~1 min) then click on `tutorial-thermo-batch-calculations.ipynb ` More information on Jupyter Notebooks: [Jupyter Documentation](https://jupyter.readthedocs.io/en/latest/index.html) -## Prepare building tools - -* Make sure you have g++, cmake and git installed. If not, install them (on Ubuntu Linux): - -``` -#!bash -sudo apt-get install g++ cmake git -``` - -## Download ThermoFun source code using git clone - -* In a terminal, at the home directory level e.g. ```@ubuntu:~$``` copy-paste and run the following code: - -``` -#!bash -git clone https://bitbucket.org/gems4/thermofun.git && cd thermofun -``` - -* In the terminal you should be in ```~/thermofun$```. - -## (A) Build and install ThermoFun library (working with json database files) - -This option allows the user to build thermofun library that works with a user provided thermodynamic database file in json format and has only one thirdpary library dependency. To build thermofun with access to the thermohub thermodynamic database cloud and local server see bellow. - -### Install Dependencies - -The thermofun library uses nlohmann/json.hpp as thirdparty dependency to parse database files in json format. To install the header only json library in a terminal ```~/thermofun$``` execute the following: - -``` -#!bash -sudo ./install-dependencies.sh -``` - -### Compiling the C++ library - -In the terminal ```~/thermofun$```, execute the following commands: - -``` -#!bash -mkdir build && \ -cd build && \ -cmake .. && \ -make -``` - -To take advantage of parallel compilation use ```make -j3```. 3 representing the number of threads. - -For a global installation of the compiled libraries in your system, execute: - -``` -#!bash -sudo make install -``` - -This will install Thermofun library and header files in the default installation directory of your system (e.g, ```/usr/local/``` ). - -For a local installation, you can specify a directory path for the installed files as follows: - -``` -#!bash -cmake .. -DCMAKE_INSTALL_PREFIX=/home/username/local/ -``` -then execute: - -``` -sudo make install -``` - -To compile ThermoFun library in debug mode: - -``` -#!bash -cmake .. -DCMAKE_BUILD_TYPE=Debug -``` -then execute: - -``` -sudo make install -``` - -## (B) Build and install ThermoFun library (working with access to the local and cloud ThemroHub database) - -This option builds thermofun library together with the dbclient, which provides access to the local and cloud thermohub databases, allowing specific a ThermoDataSet to be used or a selection on elements of the thermodynamic data. - -### Install Dependencies - -Installing dependencies needed to build ThermoFun/dbclient on (k)ubuntu linux 16.04 or 18.04, in a terminal ```~/thermofun/build$``` execute the following: - -``` -#!bash -sudo ./install-dependencies-dbclient.sh -``` - -### Compiling the C++ library - -In the terminal ```~/thermofun/build$```, execute the following commands: - -``` -#!bash -cmake .. -DTFUN_BUILD_HUBCLIENT=ON && \ -make -``` - -To take advantage of parallel compilation use ```make -j3```. 3 representing the number of threads. - -For a global installation of the compiled libraries in your system, execute: - -``` -#!bash -sudo make install -``` - -### Install the current version of ArangoDB server locally (if not yet installed) - -For using ThermoFun with a local arangodb client. If only the remote db.thermohub.net database will be used, the installation of a local arangodb client is not necessary. Proceed to the next section Install Dependencies -In a terminal copy-paste and run to flowing code: (for possibly newer versions of arangodb check [click here](https://www.arangodb.com/download-major/ubuntu/). In the arangodb packedge configuration we recommend to leave ```root``` password empty, and click enter for the following questions, using default selections. For Backup database files before upgrading select "Yes". - -On (K)Ubuntu linux, install the current version of ArangoDB server locally [from here](https://www.arangodb.com/download-major/ubuntu/) by using a terminal to copy-paste and run the following commands: - -~~~ -curl -OL https://download.arangodb.com/arangodb34/DEBIAN/Release.key -sudo apt-key add - < Release.key -echo 'deb https://download.arangodb.com/arangodb34/DEBIAN/ /' | sudo tee /etc/apt/sources.list.d/arangodb.list -sudo apt-get install apt-transport-https -sudo apt-get update -sudo apt-get install arangodb3=3.4.4-1 -~~~ - -The updates will come together with other ubuntu packages that you have installed. - - -## (C) Build and run ThermoFun GUI Demo - -To be able to build and run the ThemroFun GUI (graphical user batch) application demo, Qt needs to be installed. - -* Download and install Qt 5.12.2 (https://www1.qt.io/download/) in your home directory ```~/Qt```. In the "Select components to install" menu select: Qt 5.12.2 with Desktop gcc 64-bit, Qt Charts, and Qt WebEngine - -### Install Dependencies - -Installing dependencies needed to build ThermoFun on (k)ubuntu linux 16.04 or 18.04, in the terminal go in ```~/thermofun$``` and execute the following: - -``` -#!bash -sudo ./install-dependencies-gui.sh $HOME/Qt/5.12.2/gcc_64 -``` - -This step will download, configure, build, and install all dependencies: `lua5.3-dev`, `libboost-all-dev`, `libcurl4-openssl-dev`, `libboost-test-dev`, `automake`, `flex`, `bison`, `libssl-dev`, `pugixml`, `yaml-cpp`, `thrift`, `velocypack`, `jsonio`, `jsonimpex`, `jsonui`. The script will check if the dependencies are not already present at the default installation path ```/usr/local/``` and will only install them if not found. -To reinstall dependencies open `install-dependencies.sh` and/or `install-dependencies-gui.sh` files with a text editor. At the beginning of the script file commands for removing dependency library files are present but they are commented out with `#` symbol. Remove `#` for each dependency you wish to be reinstalled. - -### Compiling the ThermoFun GUI demo - -In the terminal at ```~/thermofun/build$```, execute the following commands: - -``` -#!bash -cmake .. -DTFUN_BUILD_HUBCLIENT=ON -DTFUN_BUILD_GUI=ON -DTFUN_BUILD_GUIDEMO=ON -DCMAKE_PREFIX_PATH=$HOME/Qt/5.11.2/gcc_64 && \ -make -``` - --DTFUN_BUILD_GUI=ON -DTFUN_BUILD_GUIDEMO=ON options trigger the compilation of ThermoFunGui library and the gui demo widget. - -The build script will also copy into the build folder the necessary /Resources folder. In the Resources folder a file named "fun-hubclient-config.json" is present and contains the arangodb database connection preferences. - -To run the ThermoFun GUI demo in the terminal at ```~/build$``` execute: - -``` -./guidemo.sh -``` - -You can change the arango database connection setup using the preferences icon on the start widget, or by making changes in ```Resources/fun-hubclient-config.json``` file. - -* For building using Qt Creator, use the ThermoFunDemoGUI.pro project file found in ```~/thermofun/fungui```. - -## (D) Build and install the Python interface - -### Install Dependencies - -The thermofun python api uses pybind11 as thirdparty dependency. To install the header only json library in a terminal ```~/thermofun$``` execute the following: - -``` -#!bash -sudo ./install-dependencies-py.sh -``` - -## Compiling the Python interface - -In the terminal ~/thermofun/build$, execute the following commands: - -``` -#!bash -cmake .. -DTFUN_BUILD_PYTHON=ON -``` - -with DBClient - -``` -#!bash -cmake .. -DTFUN_BUILD_HUBCLIENT=ON -DTFUN_BUILD_PYTHON=ON -``` - -then execute: - -``` -#!bash -make -``` - -After compilation, you should find the shared library PyThermoFun inside the directory ```lib``` in the build directory. This library is also a Python module, which can be imported from Python as: - -``` -from thermofun import * -``` - -In the build folder a test file text.py can be found, this can be run by executing ```python test.py``` and ```python test-dbc.py``` . If successful in addition to on screen output, two files, results.csv and results_dbc.csv files containing calculation results will be created. - -If compilation was successful the /Resources folder will be copied to the build folder. In this folder the necessary test files, connection to the arangodb database preferences, and data schemas are present. To change database connection without using the GUI, make changes in the ```Resources/fun-hubclient-config.json``` file. - - -## Build and Run ThermoFun GUI on Windows 10 - -* Make sure you have git installed. If not, install it on Windows: https://git-scm.com/download/win. -* To download ThermoFun source code, using Windows Command Prompt go to C:/git/THERMOFUN and execute - -``` -git clone https://bitbucket.org/gems4/thermofun.git -``` - -## Prepare building tools - -* ThermoFun GUI dependencies will be compiled using MSVC 2017 64 bit compiler. For this Visual Studio Community (2017) needs to be installed: -https://docs.microsoft.com/en-us/visualstudio/install/install-visual-studio?view=vs-2017 -At Step 4 - Select workloads, select Desktop development with C++ to be installed. On the individual components page check that also Windows 10 SDK is selected to be installed. -* In addition to MSVC 2017, Qt needs to be installed: https://www.qt.io/download in C:/Qt folder (Qt installation folder is used in further scripts, please use C:/Qt)! -Select with Qt 5.12.0 MSVC 2017 64-bit with Qt Charts, and Qt WebEngine. - -### Install Dependencies - -* For compiling the libraries that ThermoFun GUI is dependent on, three .bat scripts can be found in /thermofun. The process will several minutes. In a windows Command Prompt terminal go to C:/git/THERMOFUN/thermofun and run: - -``` -C:\git\THERMOFUN\thermofun>a-build-win-dependencies.bat -``` - -* This script builds curl and velocypack libraries, copies then in the C:\git\THERMOFUN\dependencies folder, creates buil-fun-gui folder and copies there the necessary resources files - -``` -C:\git\THERMOFUN\thermofun>b-build-win-boost.bat -``` - -* This script builds the necessary boost libraries and copies then in the C:\git\THERMOFUN\dependencies folder - -``` -C:\git\THERMOFUN\thermofun>c-build-win-jsonio-jsonui.bat C:\Qt\5.12.3\msvc2017_64\bin -``` - -* This script builds jsonio and jsonui libraries, copies then in the C:\git\THERMOFUN\dependencies folder. Don't forget to use the corect Qt installation path. - -### Compiling and the ThermoFun GUI demo in Qt Creator - -* In Qt Creator open C:\git\THERMOFUN\thermofun\fungui\ThermoFunDemoGUI.pro -* Set the build folder to C:\git\THERMOFUN\build-fun-gui (release mode). NOT! C:\git\THERMOFUN\build-fun-gui\release -* After the successful compilation try to run ThermoFun GUI from Qt Creator. All necessary dependencies and Resources should be already set in the right place. - -* Unsuccessful attempts could be due to unsuccesful compilation of dependences, missing or not correctly copied lib or Resources files, etc. - ## Simple C++ API example * Using a json database file @@ -339,9 +74,9 @@ int main() // Optional set calculation and output preferences ThermoFun::OutputSettings op; op.isFixed = true; - op.outSolventProp = true; - op.calcReactFromSubst = false; - op.calcSubstFromReact = false; + op.outputSolventProperties = true; + op.reactionPropertiesFromReactants = false; + op.substancePropertiesFromReaction = false; batch.setOutputSettings(op); // Optional set units and significant digits @@ -364,8 +99,8 @@ int main() ``` #!Python -import PyThermoFun -import PyThermoDBClient +import thermofun.PyThermoFun as PyThermoFun +import thermofbclient.PyThermoDBClient as PyThermoDBClient properties = PyThermoFun.ThermoPropertiesSubstance @@ -428,9 +163,9 @@ batch2.setSolventSymbol("H2O@") print("\n# Optional set calculation and output preferences\n") op = PyThermoFun.BatchPreferences() op.isFixed = True -op.outSolventProp = True -op.calcReactFromSubst = False -op.calcSubstFromReact = False +op.outputSolventProperties = True +op.reactionPropertiesFromReactants = False +op.substancePropertiesFromReaction = False batch2.setBatchPreferences(op) print("\n# Optional set units and significant digits\n") @@ -443,3 +178,156 @@ print("\n# Do calculations and write output\n") batch2.thermoPropertiesSubstance([[25,1]], ["Na(CO3)-", "Mg+2"], ["gibbs_energy", "entropy", "volume", "enthalpy"]).toCSV("results_dbc.csv") ``` + +## Installation using Conda + +ThaemroFun can be easily installed using [Conda](https://conda.io/docs/) package manager. If you have Conda installed, install ThermoFun by executing the following command: + +``` +#!bash +conda install thermofun +``` +Conda can be installed by installing [Miniconda](https://conda.io/miniconda.html). + +## Install ThermoFun using CMake + +* Make sure you have g++, cmake and git installed. If not, install them (on Ubuntu Linux): + +``` +#!bash +sudo apt-get install g++ cmake git +``` + +## Download ThermoFun source code using git clone + +* In a terminal, at the home directory level e.g. ```@ubuntu:~$``` copy-paste and run the following code: + +``` +#!bash +git clone https://github.com/thermohub/thermofun.git && cd thermofun +``` + +* In the terminal you should be in ```~/thermofun$```. + +## (A) Build and install ThermoFun library (working with json database files) + +This option allows the user to build thermofun library that works with a user provided thermodynamic database file in json format and has only one thirdpary library dependency. To build thermofun with access to the thermohub thermodynamic database cloud and local server see bellow. + +### Install Dependencies (if not using Conda environment) + +The thermofun library uses nlohmann/json.hpp as thirdparty dependency to parse database files in json format. To install the header only json library in a terminal ```~/thermofun$``` execute the following: + +``` +#!bash +sudo ./install-dependencies.sh +``` + +### Compiling the C++ library + +In the terminal ```~/thermofun$```, execute the following commands: + +``` +#!bash +mkdir build && \ +cd build && \ +cmake .. && \ +make +``` + +To take advantage of parallel compilation use ```make -j3```. 3 representing the number of threads. + +For a global installation of the compiled libraries in your system, execute: + +``` +#!bash +sudo make install +``` + +This will install Thermofun library and header files in the default installation directory of your system (e.g, ```/usr/local/``` ). + +For a local installation, you can specify a directory path for the installed files as follows: + +``` +#!bash +cmake .. -DCMAKE_INSTALL_PREFIX=/home/username/local/ +``` +then execute: + +``` +sudo make install +``` + +To compile ThermoFun library in debug mode: + +``` +#!bash +cmake .. -DCMAKE_BUILD_TYPE=Debug +``` +then execute: + +``` +sudo make install +``` + +## (B) Build and install ThermoFun library (working with access to the local and cloud ThemroHub database) + +This option builds thermofun library together with the dbclient, which provides access to the local and cloud thermohub databases, allowing specific a ThermoDataSet to be used or a selection on elements of the thermodynamic data. + +### Install ThermoHubClient + +Clone and install ThermoHubClient library + +``` +#!bash +git clone https://bitbucket.org/gems4/thermohubclient.git +cd thermohubclient +sudo ./install-dependencies.sh +mkdir build +cd build +cmake .. +make +``` + +For a global installation of the compiled library in your system, execute: + +``` +#!bash +sudo make install +``` + +## Install ThermoFun using CMake and Conda + +This procedure uses Conda for handling all the dependencies of ThermoFun and builds ThermoFun for Windows, Mac OS X, and Linux. + +Once you have conda installed execute: + +``` +#!bash +conda install -n base conda-devenv +``` +This installs conda-devenv, a conda tool used to define and initialize conda environments. + +Download ThermoFun from github + +``` +#!bash +git clone https://github.com/thermohub/thermofun.git && cd thermofun +``` + +In the next step we create a clean environment with all dependencies necessary to build ThermoFun, executing: + +``` +#!bash +conda devenv +``` + +In the next step we need to activate the thermofun environment + +``` +#!bash +conda activate thermofun +``` + +Remember to always activate thermofun environment whenever you use ThermoFun from C++ or Python. This is because conda will adjust some environment variables in your system. + +Now we can proceed and [build ThermoFun using CMake.](#install-thermofun-using-cmake) diff --git a/Resources/aq17new-format.json b/Resources/aq17new-format.json deleted file mode 100644 index 0928c65a..00000000 --- a/Resources/aq17new-format.json +++ /dev/null @@ -1,16589 +0,0 @@ -[ - { - "_id" : "substances/Akermanite_0:SC_COMPONENT_19:AQ17", - "_key" : "Akermanite_0:SC_COMPONENT_19:AQ17", - "_rev" : "_Xy-gWuS---", - "_type" : "vertex", - "_label" : "substance", - "properties" : { - "symbol" : "Akermanite", - "sourcetdb" : { - "19" : "AQ17" - }, - "formula" : "Ca2MgSi2O7", - "name" : "Akermanite (ak)", - "class_" : { - "0" : "SC_COMPONENT" - }, - "aggregate_state" : { - "3" : "AS_CRYSTAL" - }, - "Tst" : 298.15, - "Pst" : 100000, - "formula_charge" : 0, - "mass_per_mole" : 272.62780761719, - "sm_volume" : { - "values" : [ - 9.253999710083 - ], - "errors" : [ - 0 - ] - }, - "sm_gibbs_energy" : { - "values" : [ - -3669893 - ] - }, - "sm_enthalpy" : { - "values" : [ - -3866360 - ] - }, - "sm_entropy_abs" : { - "values" : [ - 212.5 - ] - }, - "sm_heat_capacity_p" : { - "values" : [ - 216.20722961426 - ], - "errors" : [ - 0 - ] - }, - "m_compressibility" : { - "values" : [ - 1420 - ] - }, - "m_expansivity" : { - "values" : [ - 5.080000119051e-05 - ] - }, - "TPMethods" : [ - { - "method" : { - "0" : "cp_ft_equation" - }, - "m_heat_capacity_ft_coeffs" : { - "values" : [ - 385.39999389648, - 0.0032089999876916, - -247500, - -2889.8999023438, - 0, - 0, - 0, - 0, - 0, - 0, - 0, - 0 - ] - } - }, - { - "method" : { - "38" : "mv_eos_murnaghan_hp98" - } - } - ], - "comment" : "", - "datasources" : [ - "Holland and Powell (2002)" - ], - "time_stamp" : { - "year" : 2018, - "month" : 11, - "day" : 23, - "hour" : 11, - "minute" : 34, - "second" : 14 - } - } - }, - { - "_id" : "substances/Al(OH)2+_2:SC_AQSOLUTE_19:AQ17", - "_key" : "Al(OH)2+_2:SC_AQSOLUTE_19:AQ17", - "_rev" : "_Xy-gUs6---", - "_type" : "vertex", - "_label" : "substance", - "properties" : { - "symbol" : "Al(OH)2+", - "sourcetdb" : { - "19" : "AQ17" - }, - "formula" : "Al(OH)2+", - "name" : "Al(OH)2+", - "class_" : { - "2" : "SC_AQSOLUTE" - }, - "aggregate_state" : { - "4" : "AS_AQUEOUS" - }, - "Tst" : 298.15, - "Pst" : 100000, - "formula_charge" : 1, - "mass_per_mole" : 60.996200561523, - "sm_volume" : { - "values" : [ - 0.38507527112961 - ], - "errors" : [ - 0 - ] - }, - "sm_gibbs_energy" : { - "values" : [ - -898292 - ] - }, - "sm_enthalpy" : { - "values" : [ - -995581 - ] - }, - "sm_entropy_abs" : { - "values" : [ - -27.530000686646 - ] - }, - "sm_heat_capacity_p" : { - "values" : [ - 40.865230560303 - ], - "errors" : [ - 0 - ] - }, - "TPMethods" : [ - { - "method" : { - "3" : "solute_hkf88_reaktoro" - }, - "eos_hkf_coeffs" : { - "values" : [ - 0.24940000474453, - -169.08999633789, - 6.4145998954773, - -27091, - 16.743900299072, - -10465, - 53240, - 0 - ] - } - } - ], - "aq_edh_props" : { - "values" : [ - 4.5, - 0 - ] - }, - "comment" : "GF global R01", - 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diff --git a/Resources/files/README.md b/Resources/files/README.md deleted file mode 100644 index e75ab309..00000000 --- a/Resources/files/README.md +++ /dev/null @@ -1,2 +0,0 @@ -This folder contains test input/output files with structured data. - diff --git a/Resources/files/TestDataSource/README.md b/Resources/files/TestDataSource/README.md deleted file mode 100644 index 5f8ac72c..00000000 --- a/Resources/files/TestDataSource/README.md +++ /dev/null @@ -1,2 +0,0 @@ -This folder is for DataSource files. - diff --git a/Resources/files/TestDataSource/science.bib b/Resources/files/TestDataSource/science.bib deleted file mode 100644 index 04644f46..00000000 --- a/Resources/files/TestDataSource/science.bib +++ /dev/null @@ -1,68 +0,0 @@ -# Comment 1 -@article{Wang20161, -# Comment 2 -title = "pH effect on Re(VII) and Se(IV) diffusion in compacted \{GMZ\} bentonite ", -journal = "Applied Geochemistry ", -volume = "73", -number = # Comment 6 -"", -pages = "1 - 7", -year = "2016", -note = "", -issn = "0883-2927", -doi = "http://dx.doi.org/10.1016/j.apgeochem.2016.07.015", -url = "http://www.sciencedirect.com/science/article/pii/S0883292716301664", -author = "Zhifen Wang and Hai Wang and Qingmei Li and Minhong Xu and Yuhua Guo and Jinying Li and Tao Wu", -keywords = "Diffusion",#comment 7 -keywords = "Se(IV)", -#comment8 -keywords = "Re(VII)", -keywords = "pH", -keywords = "GMZ bentonite ", -abstract = "Abstract In a high-level radioactive waste (HLW) repository, pH has an impact on the solubility, migration, and adsorption of radionuclides. Thus, understanding the effects of pH on the diffusion of radionuclides is essential for long-term disposal of HLW. In this work, the diffusion behaviors of Re(VII) and Se(IV) in compacted Gaomiaozi (GMZ) bentonite at different pH have been investigated by a through-diffusion method. The effective diffusion coefficient, i.e., De values of Re(VII) and Se(IV) were in the range of (1.0–2.4) × 10−11 m2/s at pH 3.0–10.0 and (0.38–2.3) × 10−11 m2/s at pH 3.0–9.0. In the case of Re(VII), the De values remained almost unchanged probably because ReO4− was the dominant species in the pH range of 3.0–10.0. In the case of Se(IV), whose predominant species were HSeO3− at pH < 9.0 and SeO32− at pH ≥ 9.0, the De values decreased by a factor of 3–6 at pH 9.0, i.e., De (pH < 9.0)/De (pH 9.0) ≈ 3–6, implying that the species with a higher valence state had a stronger anion exclusion effect. The decrease in De values can be explained by the diffusion species of Se(IV). Additionally, the rock capacity factor α decreased with the increase of pH. HSeO3− was absorbed on \{GMZ\} bentonite with distribution coefficient Kd values in the range of (1.0–2.5) × 10−4 m3/kg at pH ≤ 8.0, whereas SeO32− was negligibly sorbed at pH > 8.0. " -# Comment 3 -} -# Comment 4 -@article{Peiffer20168, -title = "Reaction time scales for sulphate reduction in sediments of acidic pit lakes and its relation to in-lake acidity neutralisation ", -journal = "Applied Geochemistry ", -volume = "73", -number = "", -pages = "8 - 12", -year = "2016", -note = "", -issn = "0883-2927", -doi = "http://dx.doi.org/10.1016/j.apgeochem.2016.07.009", -url = "http://www.sciencedirect.com/science/article/pii/S0883292716301524", -author = "Stefan Peiffer", -keywords = "Sulphate reduction rates", -keywords = "Acid pit lakes", -keywords = "Monod kinetics", -keywords = "Modelling", -keywords = "Acidity", -keywords = "Internal neutralisation", -keywords = "Residence time", -keywords = "Sediments ", -abstract = "Abstract Sulphate reduction is a key reaction to remove acidity from water bodies affected by acid mine drainage. In this study, 35SSO42− reduction rates determined in sediments from a variety of acidic lignite pit lakes have been compiled. The rates decreased with pH and are strongly dependent on carbon substrate. The rates were fitted to a Monod model adapted to the specific conditions of acidic pit lakes (APL) sediments: i) sulphate reduction rate is independent from sulphate concentration due to the high concentration typically observed in \{APL\} systems (10–30 mM), ii) the observed pH dependency of sulphate reduction was accounted for by an inhibition function Finihibt which considers the occurrence of low cell numbers of sulphate reducing bacteria at pH values < 4.75. Simulated steady-state sulphate reduction rates are predicting measured rates at carbon substrate concentrations of <10 μM. Estimated steady-state reaction time scales range between 2.4 h at pH 7 and 41 h at pH 3 at a carbon half-saturation constant of KC−S = 100 μM and are increasing with increasing KC−S values. Time scales at low pH are too long to allow for significant generation of alkalinity during the time of residence of groundwater passing through the top and hence most reactive zone of \{APL\} sediments which has important implications for the remediation of acidic pit lakes. " -} -@article{Rakotonimaro201613, -title = "Effectiveness of various dispersed alkaline substrates for the pre-treatment of ferriferous acid mine drainage ", -journal = "Applied Geochemistry ", -volume = "73", -number = "", -pages = "13 - 23", -year = "2016", -note = "", -issn = "0883-2927", -doi = "http://dx.doi.org/10.1016/j.apgeochem.2016.07.014", -url = "http://www.sciencedirect.com/science/article/pii/S0883292716301615", -author = "Tsiverihasina V. Rakotonimaro and Carmen Mihaela Neculita and Bruno Bussière and Gérald J. Zagury", -keywords = "Ferriferous acid mine drainage", -keywords = "Iron pre-treatment", -keywords = "Dispersed alkaline substrate", -keywords = "Calcite", -keywords = "Dolomite ", -abstract = "Abstract Dispersed alkaline substrates (DAS) have been successfully used in passive treatment of highly contaminated acid mine drainage (AMD) to limit coating and clogging issues. However, further optimization of \{DAS\} systems is still needed, especially for their long-term efficiency during the treatment of ferriferous AMD. In the present study, three types of \{DAS\} comprised of natural alkaline materials (wood ash, calcite, dolomite), in different proportions (20%v/v, 50%v/v, 80%v/v), and a substrate with high surface area (wood chips) were tested in 9 batch reactors. The testing was carried out, in duplicate, for a period of 91 days, to evaluate the comparative performance of the mixtures for iron pre-treatment in ferriferous \{AMD\} (2500 mg/L Fe, at pH 4). Results showed increasing of pH (between 4.15 and 7.12), regardless of the proportion of alkaline materials in the \{DAS\} mixtures. Among the tested mixtures, wood ash type \{DAS\} were more effective for Fe removal (99.9%) than calcite or dolomite type \{DAS\} (up to 66%). All tested \{DAS\} had limited efficiency for sulfate removal and an additional treatment unit, such as a sulfate-reducing biochemical reactor, is needed. Moreover, due to the similar performances of the calcite and dolomite DAS, they could be potentially substituted and rather be used in a polishing treatment unit. Based on these findings, the most promising mixture was the 50% wood ash type \{DAS\} (WA50-DAS). " -} -# Comment 5 - diff --git a/Resources/files/TestDataSource/scienceb33f8877.ris b/Resources/files/TestDataSource/scienceb33f8877.ris deleted file mode 100644 index 29c70dfd..00000000 --- a/Resources/files/TestDataSource/scienceb33f8877.ris +++ /dev/null @@ -1,39 +0,0 @@ -TY - JOUR -T1 - Preface: SI: Geochemical speciation codes and databases -JO - Applied Geochemistry -VL - 55 -IS - -SP - 1 -EP - 2 -PY - 2015/4// -T2 - Geochemical Speciation Codes and Databases -AU - Kulik, Dmitrii A. -AU - Hummel, Wolfgang -AU - Lützenkirchen, Johannes -AU - Lefèvre, Grégory -SN - 0883-2927 -DO - http://dx.doi.org/10.1016/j.apgeochem.2014.12.019 -UR - http://www.sciencedirect.com/science/article/pii/S0883292714003321 -ER - - -TY - JOUR -T1 - GEMSFITS: Code package for optimization of geochemical model parameters and inverse modeling -JO - Applied Geochemistry -VL - 55 -IS - -SP - 28 -EP - 45 -PY - 2015/4// -T2 - Geochemical Speciation Codes and Databases -AU - Miron, George D. -AU - Kulik, Dmitrii A. -AU - Dmytrieva, Svitlana V. -AU - Wagner, Thomas -SN - 0883-2927 -DO - http://dx.doi.org/10.1016/j.apgeochem.2014.10.013 -UR - http://www.sciencedirect.com/science/article/pii/S088329271400256X -AB - Abstract -GEMSFITS is a new code package for fitting internally consistent input parameters of GEM (Gibbs Energy Minimization) geochemical–thermodynamic models against various types of experimental or geochemical data, and for performing inverse modeling tasks. It consists of the gemsfit2 (parameter optimizer) and gfshell2 (graphical user interface) programs both accessing a NoSQL database, all developed with flexibility, generality, efficiency, and user friendliness in mind. The parameter optimizer gemsfit2 includes the GEMS3K chemical speciation solver (http://gems.web.psi.ch/GEMS3K), which features a comprehensive suite of non-ideal activity- and equation-of-state models of solution phases (aqueous electrolyte, gas and fluid mixtures, solid solutions, (ad)sorption. The gemsfit2 code uses the robust open-source NLopt library for parameter fitting, which provides a selection between several nonlinear optimization algorithms (global, local, gradient-based), and supports large-scale parallelization. The gemsfit2 code can also perform comprehensive statistical analysis of the fitted parameters (basic statistics, sensitivity, Monte Carlo confidence intervals), thus supporting the user with powerful tools for evaluating the quality of the fits and the physical significance of the model parameters. The gfshell2 code provides menu-driven setup of optimization options (data selection, properties to fit and their constraints, measured properties to compare with computed counterparts, and statistics). The practical utility, efficiency, and geochemical relevance of GEMSFITS is demonstrated by examples of typical classes of problems that include fitting of parameters of thermodynamic mixing models, optimization of standard state Gibbs energies of aqueous species and solid-solution end-members, thermobarometry, inverse titrations, and optimization problems that combine several parameter- and property types. -ER - - - diff --git a/Resources/files/TestDataSource/test_Citations.ris b/Resources/files/TestDataSource/test_Citations.ris deleted file mode 100644 index 151b2d61..00000000 --- a/Resources/files/TestDataSource/test_Citations.ris +++ /dev/null @@ -1,1000 +0,0 @@ -TY - JOUR -AU - Aberle, N. -AU - Witte, U. -PY - 2003// -TI - Deep-sea macrofauna exposed to a simulated sedimentation event in the abyssal NE Atlantic: _in situ_ pulse-chase experiments using [super:13]C-labelled phytodetritus -T2 - Mar Ecol Prog Ser -JO - Marine Ecology Progress Series -SP - 37 -EP - 47 -VL - 251 -PB - Inter-Research -CY - Oldendorf/Luhe -KW - Deep-sea -KW - Pulse-chase experiment -KW - [delta][super:13]C -KW - Benthic carbon remineralisation -KW - Macrofauna -KW - Porcupine Abyssal Plain -AB - Tracer experiments with [super:13]C-labelled diatoms _Thalassiosira rotula_ (Bacillariophycea, 98% [super:13]C-labelled) were conducted at the Porcupine Abyssal Plain (PAP) in the NE Atlantic (BENGAL Station; 48°50'N, 16°30'W, 4850 m depth) during May/June 2000. _In situ_ enrichment experiments were carried out using deep-sea benthic chamber landers: within the chambers a spring bloom was simulated and the fate of this food-pulse within the abyssal macrobenthic community was followed. In focus was the role of different macrofauna taxa and their vertical distribution within the sediment column in consuming and reworking the freshly deposited material. _T. rotula_ is one of the most abundant pelagic diatoms in the NE Atlantic and therefore 0.2 g of freeze dried _T. rotula_, equivalent to 1 g algal C m[super:-2] yr[super:-1], was injected into each incubation chamber. Three different incubation times of 2.5, 8 and 23 d were chosen in order to follow the uptake of [super:13]C-labelled phytodetritus by macrofauna. After only 2.5 d, 77% of all macrofauna organisms showed tracer uptake. After 23 d the highest degree of enrichment was measured and 95% of the individuals had taken up [super:13]C from the introduced algal material. In addition to that a downward transport of organic matter was observed, even though the mixing was not very intense. The initial processing of carbon was dominated by polychaetes that made up a percentage of 52% of total macrofauna. In general macrofauna organisms that lived close to the sediment surface had higher access to the simulated food-pulse, confirming the hypothesis that individuals close to the sediment surface have the strongest impact on the decomposition of phytodetritus. In our study we observed only modest vertical entrainment of [super:13]C tracers into the sediment. With regard to contradictory results from former [super:13]C-enrichment experiments in bathyal regions, compared to results from our study site in the abyssal plain, we thus propose pronounced differences in feeding strategies between macrofauna communities from continental margins and abyssal plains. -SN - 0171-8630 -UR - http://www.int-res.com/abstracts/meps/v251/p37-47/ -ID - Aberle+Witte2003 -ER - -TY - CHAP -AU - Arntz, WE -AU - Gutt, J. -AU - Klages, M. -ED - Battaglia, B. -ED - Valencia, J. -ED - Walton, DWH -PY - 1997// -TI - Antarctic marine biodiversity: an overview -BT - Antarctic Communities: Species, Structure and Survival -SP - 3 -EP - 14 -PB - Cambridge University Press (UK) -CY - Cambridge -KW - Species diversity -KW - Antarctic zone -KW - Community composition -KW - Taxonomy -KW - Geographical distribution -AB - The unique Antarctic marine environment, its evolutionary history, its biotic peculiarities and its (hitherto) comparatively low degree of human impact make a biodiversity approach and a comparison with other areas particularly worth while. Current knowledge seems to indicate that there is no common pattern for species richness in the various Antarctic subsystems (e.g. pelagic/benthic, shallow/deep) or for different taxonomic groups. Some assemblages appear to be fairly rich in species, others consist of only a few, and the same pattern applies to the various taxa at a higher taxonomic level. The Antarctic marine ecosystem as a whole seems to have a lower percentage of species known to date in most higher taxa than would be expected from its share of the area of the world's oceans. However, comparison with other marine ecosystems is difficult because of differences in area, environment, sampling and processing, and taxonomic knowledge. Comparison with the Arctic Ocean indicates that species numbers of most groups are much higher in Antarctic waters, but many more comparable data are needed to judge whether this also holds generally true for diversity, and whether large-scale latitudinal gradients exist for more than a few groups. Few authors have calculated diversity and evenness indices, and these, too, are often of very limited comparability. High species numbers do not necessarily imply high values of diversity and evenness. -SN - 0-521-48033-7 -ID - Arntz++1997 -ER - -TY - CHAP -AU - Arrigo, KR -ED - Thomas, DN -ED - Dieckmann, GS -PY - 2003// -TI - Primary production in sea ice -BT - Sea ice - an introduction to its physics, chemistry, biology and geology -SP - 143 -EP - 183 -PB - Blackwell Science Ltd -CY - Oxford -SN - 0-632-05808-0 -ID - Arrigo2003 -ER - -TY - JOUR -AU - Auel, H. -AU - Klages, M. -AU - Werner, I. -PY - 2003// -TI - Respiration and lipid content of the Arctic copepod _Calanus hyperboreus_ overwintering 1 m above the seafloor at 2,300 m water depth in the Fram Strait -T2 - Mar Biol -JO - Marine Biology -SP - 275 -EP - 282 -VL - 143 -IS - 2 -PB - Springer-Verlag -CY - Heidelberg -AB - In August 2000 high concentrations of the dominant herbivorous copepod _Calanus hyperboreus_ were detected in the Arctic Fram Strait, west of Spitsbergen, 1 m above the seafloor at 2,290 m water depth. Individuals from that layer were sampled by a hyper-benthic net attached to the frame of an epi-benthic sledge. For comparison, the vertical distribution of _C. hyperboreus_ in the water column was studied simultaneously by a multiple opening/closing net haul from 2,250 m depth to the surface. Maximum abundance was found close to the surface with 6.6 and 10.0 ind. m[super:-3] at 0-50 m and 50-100 m depth, respectively. However, the major fraction of the population (>40%) occurred between 1,000 and 1,500 m depth. In the deepest layer (2,000-2,250 m) abundance measured 2.2 ind. m[super:-3] and was twice as high as between 100 and 1,000 m depth. In comparison to individuals from surface waters, copepods from the hyper-benthic layer were torpid and did not react to mechanical stimuli. Stage CV copepodids and females from the deep sample contained 4-10% less lipid and showed significantly reduced respiration rates of 0.24 and 0.26 ml O[sub:2] h[super:-1] g[super:-1] dry mass (DM) as compared to surface samples (0.49 and 0.43 ml O[sub:2] h[super:-1] g[super:-1] DM). All these observations indicate that the hyper-benthic part of the population had already started a dormant overwintering phase at great depth. Based on the lipid deposits and energy demands, the potential maximum duration of the non-feeding dormant phase was estimated at 76-110 days for females and at 98-137 days for CV copepodids, depending on what indispensable minimum lipid content was assumed. In any case, the estimated times could not meet the necessary requirements for a starvation period of >6 months until the next phytoplankton bloom in the following spring. The ecological implications of these results are discussed with respect to the life cycle and eco-physiological adaptations of _C. hyperboreus_ to its high-Arctic habitat. -SN - 0025-3162 -UR - http://www.springerlink.com/openurl.asp?genre=article&issn=0025-3162&volume=143&issue=2&spage=275 -ID - Auel++2003 -ER - -TY - THES -AU - Benthien, A. -PY - 1994// -TI - Echographiekartierung und physikalische Eigenschaften der oberflächennahen Sedimente in der Laptevsee -PB - Universität Kiel -CY - Kiel -N1 - Diplomarbeit (Teil II, Laborarbeit), Studiengang Geologie/Paläontologie an der Universität Kiel -ID - Benthien1994 -ER - -TY - THES -AU - Bochert, A. -PY - 1996// -TI - Klassifikation von Radarsatellitendaten zur Meereiserkennung mit Hilfe von Line-Scanner-Messungen -T2 - Ber Polarforsch -BT - Berichte zur Polarforschung -VL - 209 -PB - Alfred-Wegener Institut für Meeres- und Polarforschung -CY - Bremerhaven -SN - 0176-5027 -N1 - Dissertation 1996, FB Physik/Elektrotechnik Univ. Bremen; English title: Classification of radar satellite data for sea ice identification by means of line scanner measurements -ID - Bochert1996 -ER - -TY - THES -AU - Haas, C. -PY - 1997// -TI - Bestimmung der Meereisdicke mit seismischen und elektromagnetisch-induktiven Verfahren -T2 - Ber Polarforsch -BT - Berichte zur Polarforschung -VL - 223 -PB - Alfred-Wegener Institut für Meeres- und Polarforschung -CY - Bremerhaven -SN - 0176-5027 -N1 - Dissertation 1996, FB Geowissenschaften Univ. Bremen -ID - Haas1997 -ER - -TY - JOUR -AU - Krell, A. -AU - Ummenhofer, C. -AU - Kattner, G. -AU - Naumov, A. -AU - Evans, D. -AU - Dieckmann, GS -AU - Thomas, DN -PY - 2003// -TI - The biology and chemistry of land fast ice in the White Sea, Russia - A comparison of winter and spring conditions -T2 - Polar Biol -JO - Polar Biology -SP - 707 -EP - 719 -VL - 26 -IS - 11 -PB - Springer-Verlag -CY - Heidelberg -AB - Various abiotic and biotic parameters, including phytoplankton distribution, were studied to investigate seasonal changes within the fast-ice cover in Chupa Inlet, a freshwater-influenced Arctic-like fjord in Kandalaksha Bay (White Sea). Sea ice and under-ice water were collected along transects in the inlet in February and April 2002. Ice-texture analysis, salinity and [delta][super:18]O values indicated that the complete ice sheet had transformed within 2 months. This resulted from an upward growth of snow ice and subsequent melting at the underside of the ice, which makes a comparison between the two sampling periods difficult in terms of defining temporal developments within the ice. Nutrients, DOC and DON concentrations in the under-ice water were typical for Russian Arctic rivers. Concentrations of nitrate, silicate and DOC in the ice were lower, which is attributed to a loss as the ice forms. The concentrations were also modified by biological activity. In February, there was a strong correspondence between the distribution of biological parameters, including particulate and dissolved organic carbon and nitrogen (POC and PON, DOC and DON) and inorganic nutrients (nitrate, nitrite, phosphate and silicate), which was not the case in April. The correlation between both DOC and DON with ammonium indicates heterotrophic activity within the winter ice collected in February. Sea-ice organisms were distributed throughout the ice, and several assemblages were found in surface layers of the ice. In April, a more typical distribution of biomass in the ice was measured, with low values in the upper part and high algal concentrations in the lower sections of the ice, characteristic of a spring ice-algal bloom. In contrast to the February sampling, there was evidence that the ice-algal assemblage in April was nitrogen-limited, with total inorganic nitrogen concentrations being <1 µ mand a mean inorganic nitrogen to phosphorus ratio of 2.8. The ice assemblages were dominated by diatoms (in particular, _Nitzschia_ spp.). There were temporal shifts in the assemblage composition: in February, diatoms accounted for 40% and in April for >98% of all organisms counted. -SN - 0722-4060 -UR - http://www.springerlink.com/openurl.asp?genre=article&issn=0722-4060&volume=26&issue=11&spage=707 -ID - Krell++2003 -ER - -TY - CHAP -AU - McMinn, A. -AU - Heijnis, H. -AU - Hodgson, D. -ED - Battaglia, B. -ED - Valencia, J. -ED - Walton, DWH -PY - 1997// -TI - Preliminary sediment core evidence against short-term UV-B induced changes in Antarctic coastal diatom communities -BT - Antarctic Communities: Species, Structure and Survival -SP - 381 -EP - 387 -PB - Cambridge University Press -CY - Cambridge -KW - Ozone -KW - Ultraviolet radiation -KW - Environmental effects -KW - Phytoplankton -AB - Springtime UV-B levels have been increasing in Antarctic marine ecosystems since the 1970s. Effects on natural phytoplankton and sea-ice algal communities, however, remain unresolved. At the Marginal Ice Edge Zone, enhanced springtime UV-B levels coincide with a shallow, stratified water column and a major phytoplankton bloom. In these areas it is possible that phytoplankton growth and survival is adversely impacted by enhanced UV-B. In coastal areas, however, the sea ice, which attenuates most of the UV-B before it reaches the water column, remains until December/January, by which time UV-B levels have returned to long-term seasonal averages. Phytoplankton from these areas are unlikely to show long-term changes resulting from the hole in the ozone layer. Fjords of the Vestfold Hills, eastern Antarctica, have anoxic basins which contain high-resolution, unbioturbated sedimentary sequences. Diatom assemblages from these sequences reflect the diatom component of the phytoplankton and sea-ice algal assemblages at the time of deposition. Twenty-year records from these sequences show no consistent record of change in species composition, diversity or species richness. Six-hundred-year records from the same area also show changes in species abundance greater than those seen in the last 20 years. From these records it can be seen that recent changes in diatom abundances generally fall within the limits of natural variability and there is little evidence of recent changes that might be associated with UV-B-induced change. -SN - 0-521-48033-7 -ID - McMinn++1997 -ER - -TY - BOOK -ED - Medlin, LK -ED - Priddle, J. -PY - 1990// -TI - Polar marine diatoms -PB - British Antarctic Survey -CY - Cambridge -SN - 0-85665-140-0 -N1 - Review -ID - Medlin+Priddle1990 -ER - -TY - JOUR -AU - Mock, T. -AU - Kruse, M. -AU - Dieckmann, GS -PY - 2003// -TI - A new microcosm to investigate oxygen dynamics at the sea ice water interface -T2 - Aquat Microb Ecol -JO - Aquatic Microbial Ecology -SP - 197 -EP - 205 -VL - 30 -IS - 2 -PB - Inter-Research -CY - Oldendorf/Luhe -KW - _Fragilariopsis cylindrus_ -KW - Methods -KW - Microcosm -KW - Micro-optodes -KW - Oxygen exchange -KW - Photosynthesis -KW - Sea ice -KW - Ice -KW - Water -KW - Diatoms -KW - Epontic environment -KW - Gas exchange -KW - Diffusion -KW - Boundary layers -KW - Oxygen -KW - Patchiness -KW - Epontic organisms -KW - Laminar boundary layer -KW - Ice-water interface -KW - Methodology -KW - Bacillariophyceae -AB - A laboratory sea ice microcosm was developed to enable the cultivation of the ice diatom _Fragilariopsis cylindrus_ in the skeletal layer and bottom 10 cm of sea ice. Growth of diatoms was ensured by continuous flow of new medium beneath the ice. Light was provided from above by a metal halide lamp to simulate a typical natural daylight irradiance spectrum. Oxygen micro-optodes were deployed in the microcosm to measure micro-profiles through the ice water interface and between the ice lamellae of the skeletal layer. Net oxygen production at the ice water interface, at an irradiance of 40 µmol photons m[super:-2] s[super:-1] and -1.9 °C, ranged between 0.0064 and 0.0225 nmol O[sub:2] cm[super:-2] s[super:-1]. Algal biomass increased from 0.03 µg chlorophyll _a_ (chl _a_) l[super:-1] in the column interior to 42 µg chl a l[super:-1] within 5 mm of the ice water interface. Oxygen micro-profiles revealed diffusive boundary layers (DBLs) which varied between ca. 460 and 1000 µm. DBLs were detected between ice lamellae, the periphery of the ice water interface and extending from the water below the ice through the ice water interface into the spaces between ice lamellae. An additional small-scale horizontal variability of DBLs was also reflected in the net photosynthetic activity. The small-scale patchiness of algae and the differences in DBL thickness were caused by physico-chemical processes (e.g. turbulence, water flow velocity), which in turn were influenced by ice lamellar structure at the ice water interface. These factors were the grounds for the observed variability in net-photosynthesis. -SN - 0948-3055 -UR - http://int-res.com/abstracts/ame/v30/n2/p197-205.html -N1 - Marine -ID - Mock++2003 -ER - -TY - JOUR -AU - Schewe, I. -AU - Soltwedel, T. -PY - 2003// -TI - Benthic response to ice-edge-induced particle flux in the Arctic Ocean -T2 - Polar Biol -JO - Polar Biology -SP - 610 -EP - 620 -VL - 26 -IS - 9 -PB - Springer-Verlag -CY - Heidelberg -AB - With the aims of investigating the response of the smallest benthic biota to a strong ice-edge-related input of phytodetritus, and of registering supposed lateral transportation processes of phytodetrital matter with northerly direction under the ice, we analysed a number of abiotic and biotic parameters in surface sediments from the northern Fram Strait. Two transects of 14 stations in total were made. One transect, crossing the Fram Strait from the east to the west, followed mainly the ice edge. The second transect extended latitudinally in a northerly direction, starting in ice-free areas, passing the ice edge, and ending in heavy ice-covered areas, approximately 100 nm north of the ice edge. Stations along this transect were sampled at almost constant water depths to avoid depth-related influences in our investigations. Results showed the expected high phytodetritus concentrations in the ice-edge vicinity. Concentrations of sediment-bound plant pigments were approximately 5 times higher than in ice-covered areas, indicating a very strong phytodetritus input. With increasing distance from the highly productive areas at the ice edge, we found significantly decreasing concentrations of phytodetrital input to the seafloor in a northerly direction. Within the foraminiferans, generic diversity was clearly reduced in the area of strong phytodetritus deposition. Along the latitudinal transect, out of the direct ice-edge influence, foraminiferal diversities slowly increased within increasing distance from the ice edge. The integration of results from earlier foraminiferal investigations, from stations further to the north, indicates a once more decreasing diversity with continually decreasing food supply. -SN - 0722-4060 -UR - http://www.springerlink.com/openurl.asp?genre=article&issn=0722-4060&volume=26&issue=9&spage=610 -ID - Schewe+Soltwedel2003 -ER - -TY - BOOK -ED - Thomas, DN -ED - Dieckmann, GS -PY - 2003// -TI - Sea ice - an introduction to its physics, chemistry, biology and geology -PB - Blackwell Science Ltd -CY - Oxford -KW - zoology -KW - sea ice -AB - Sea ice, which covers up to 7% of the planet's surface, is a major component of the world's oceans, partly driving ocean circulation and global climate patterns. It provides a habitat for a rich diversity of marine organisms, and is a valuable source of information in studies of global climate change and the evolution of present day life forms. Increasingly, sea ice is being used as a proxy for extraterrestrial ice covered systems._Sea Ice_ provides a comprehensive review of our current available knowledge of polar pack ice, the study of which is severely constrained by the logistic difficulties of working in such harsh and remote regions of the earth. The book's editors, Drs Thomas and Dieckmann have drawn together an impressive group of international contributing authors, providing a well-edited and integrated volume, which will stand for many years as the standard work on the subject. Contents of the book include details of the growth, microstructure and properties of sea ice, large-scale variations in thickness and characteristics, its primary production, micro-and macrobiology, sea ice as a habitat for birds and mammals, sea ice biogeochemistry, particulate flux, and the distribution and significance of palaeo sea ice. -SN - 0-632-05808-0 -UR - http://www.blackwellpublishing.com/book.asp?ref=0632058080&site=1 -ID - Thomas+Dieckmann2003 -ER - -TY - JOUR -AU - Zhukov, YuN -AU - Fedorov, VD -PY - 2003// -TI - Ice planktonic algae of the strand White Sea -T2 - Vestn Mosk Univ (Biol) -JO - Vestnik Moskovskogo universiteta -SP - 24 -EP - 31 -IS - 1 -KW - Phytoplankton -KW - Cryoplankton -KW - Biomass -KW - Sea ice -KW - Bays -KW - Ecological distribution -KW - Quantitative distribution -KW - PNE -KW - White Sea -KW - Kandalakshskiy Bay -AB - The species composition and abundance of algae at the upper and bottom layers of ice were investigated in the Kandalakshskiy Bay of the White Sea (Russia). The samples were collected on four stations with the different distance from the shore (depth 2-10 m). The number of littoral species decreased and the number of ice planktonic species increased with distance from the shore. The abundance of ice algae was maximal (about 1x10[super:6] cells/l) in April, with the greatest value on the station located far from the shore. The abundance of algae at the upper layer of ice was in two times lower than at the bottom ice layer. The maximum value of biomass (4 mg/l) was found at the lower layer of ice on the near shore station in April. -SN - 0137-0952 -N1 - Marine -ID - Zhukov+Fedorov2003 -ER - - -TY - JOUR -T1 - Organic and organo-mineral colloids in discontinuous permafrost zone -JO - Geochimica et Cosmochimica Acta -VL - 188 -IS - -SP - 1 -EP - 20 -PY - 2016/9/1/ -T2 - -AU - Pokrovsky, Oleg S. -AU - Manasypov, Rinat M. -AU - Loiko, Sergey V. -AU - Shirokova, Liudmila S. -SN - 0016-7037 -DO - http://dx.doi.org/10.1016/j.gca.2016.05.035 -UR - http://www.sciencedirect.com/science/article/pii/S0016703716302782 -KW - peat -KW - thaw -KW - ponds -KW - lakes -KW - trace elements -KW - metals -KW - organic carbon -AB - Abstract -On-going permafrost thaw in discontinuous permafrost regions produces significant amounts of small permafrost subsidence and depressions, while large lakes are likely to drain into streams and rivers. The intensification of permafrost thaw may alter the size distribution and chemical composition of organo-Fe–Al colloids in lakes and rivers. We used a continuum of surface water bodies, from permafrost subsidence, small depressions and thaw ponds to large lakes and rivers that drain the Western Siberia Lowland (WSL), to assess OC, major and the trace element size distribution between the 20-μm, 5-μm, 1.2-μm, 0.45-μm, 0.22-μm, 0.025-μm and 1-kDa (∼1.4 nm) size fractions. This approach allowed us to distinguish the organic and organo-ferric colloids that were responsible for the transport of trace elements in surface waters and address their evolution during possible physico-chemical and biological processes. Both conventionally dissolved (<0.22 μm) and low-molecular-weight (<1 kDa) fractions exhibited an order of magnitude decrease in DOC/Fe in the landscape continuum “depressions and permafrost subsidence → thaw ponds → thermokarst lakes → streams → riversâ€. Thermodynamic modeling and on-site size separation suggested that a number of trace elements (TEs), including alkaline earth elements and several micronutrients (Zn, Ba, Mn, and Ni), decreased the degree of their binding to DOM along the landscape continuum, whereas the majority of insoluble TEs (Al, Fe, Co, Cd, Cu, Pb, REEs, Th, and U) remained complexed with DOM in the LMW<1 kDa fraction. Two primary sites of colloid generation included (i) ground vegetation and peat leaching, which supplied DOM complexes of divalent metals and organo-Al entities to thaw ponds and lakes; and (ii) Fe2+ oxidation and TE co-precipitation with Fe hydroxides in the presence of surface DOM at groundwater discharge sites within the riparian/hyporheic zones of rivers. Under a warming climate scenario, an increase in the thickness of the thawing depth will intensify the input of inorganic components from deep mineral horizons and possibly underground waters thus producing the enrichment of large lakes in Fe-rich colloids and particles. The speciation of divalent metal micronutrients (Cu, Ni, and Co) and toxic metals (Al, Cd, Pb, and U) that are complexed within DOM will most likely remain conservative. Overall, the WSL’s surface water colloidal composition may shift from DOM-rich and DOM-Al-rich to Fe-rich, and the export of low-soluble trivalent and tetravalent hydrolysates from the soil to rivers will increase. -ER - - -TY - JOUR -T1 - Variable helium diffusion characteristics in fluorite -JO - Geochimica et Cosmochimica Acta -VL - 188 -IS - -SP - 21 -EP - 34 -PY - 2016/9/1/ -T2 - -AU - Wolff, R. -AU - Dunkl, I. -AU - Kempe, U. -AU - Stockli, D. -AU - Wiedenbeck, M. -AU - von Eynatten, H. -SN - 0016-7037 -DO - http://dx.doi.org/10.1016/j.gca.2016.05.029 -UR - http://www.sciencedirect.com/science/article/pii/S0016703716302721 -KW - Fluorite -KW - Helium -KW - Diffusion -KW - Thermochronology -AB - Abstract -Precise analysis of the diffusion characteristics of helium in fluorite is crucial for establishing the new fluorite (U–Th–Sm)/He thermochronometer (FHe), which potentially provides a powerful tool for dating ore deposits unsuitable for the application of conventional geochronometers. Incremental helium outgassing experiments performed on fluorites derived from a spectrum of geological environments suggest a thermally activated volume diffusion mechanism. The diffusion behaviour is highly variable and the parameters range between log D0/a2 = 0.30 ± 0.27–7.27 ± 0.46 s−1 and Ea = 96 ± 3.5–182 ± 3.8 kJ/mol. Despite the fact that the CaF2 content of natural fluorites in most cases exceeds 99 weight percent, the closure temperature (Tc) of the fluorite (U–Th–Sm)/He thermochronometer as calculated from these diffusion parameters varies between 46 ± 14 °C and 169 ± 9 °C, considering a 125 μm fragment size. Here we establish that minor substitutions of calcium by rare earth elements and yttrium (REE + Y) and related charge compensation by sodium, fluorine, oxygen and/or vacancies in the fluorite crystal lattice have a significant impact on the diffusivity of helium in the mineral. With increasing REE + Y concentrations F vacancies are reduced and key diffusion pathways are narrowed. Consequently, a higher closure temperature is to be expected. An empirical case study confirms this variability: two fluorite samples from the same deposit (Horni Krupka, Czech Republic) with ca. 170 °C and ca. 43 °C Tc yield highly different (U–Th–Sm)/He ages of 290 ± 10 Ma and 79 ± 10 Ma, respectively. Accordingly, the fluorite sample with the high Tc could have quantitatively retained helium since the formation of the fluorite-bearing ores in the Permian, despite subsequent Mesozoic burial and associated regional hydrothermal heating. In contrast, the fluorite with the low Tc yields a Late Cretaceous age close to the apatite fission track (AFT) and apatite (U–Th)/He ages (AHe) from the same locality. Remarkably, thermal modelling of FHe yields comparable results to the well-established modelling based on AFT and AHe. -ER - - -TY - JOUR -T1 - Factors influencing 14C concentrations of algal and archaeal lipids and their associated sea surface temperature proxies in the Black Sea -JO - Geochimica et Cosmochimica Acta -VL - 188 -IS - -SP - 35 -EP - 57 -PY - 2016/9/1/ -T2 - -AU - Kusch, Stephanie -AU - Rethemeyer, Janet -AU - Hopmans, Ellen C. -AU - Wacker, Lukas -AU - Mollenhauer, Gesine -SN - 0016-7037 -DO - http://dx.doi.org/10.1016/j.gca.2016.05.025 -UR - http://www.sciencedirect.com/science/article/pii/S001670371630268X -KW - Compound-specific radiocarbon analysis -KW - Alkenones, GDGTs, low molecular weight n-fatty acids -KW - Preferential preservation -KW - Redox-regime -KW - Uk′37, Uk37, TEX86, sea surface temperature proxies -AB - Abstract -Understanding the preservation and deposition history of organic molecules is crucial for the understanding of paleoenvironmental information contained in their abundance ratios such as Uk′37 and TEX86 used as proxies for sea surface temperature (SST). Based on their relatively high refractivity, alkenones and glycerol dialkyl glycerol tetraethers (GDGTs) can survive postdepositional processes like lateral transport, potentially causing inferred SSTs to be misleading. Likewise, selective preservation of alkenones and GDGTs may cause biases of the SST proxies themselves and can lead to decoupling of both proxy records. Here we report compound-specific radiocarbon data of marine biomarkers including alkenones, GDGTs, and low molecular weight (LMW) n-fatty acids from Black Sea sediments deposited under different redox regimes to evaluate the potentially differential preservation of both biomarker classes and its effect on the SST indices Uk′37 and TEX86. The decadal Δ14C values of alkenones, GDGTs, and LMW n-fatty acids indicate similar preservation under oxic, suboxic, and anoxic redox regimes and no contribution of pre-aged compounds, e.g., by lateral supply. Moreover, similar 14C concentrations of crenarchaeol, alkenones, and LMW n-fatty acids imply that the thaumarchaeotal GDGTs preserved in these sediments are produced in the euphotic zone rather than in subsurface/thermocline waters. However, we observe biomarker-based SSTs that strongly deviate (ΔSST up to 8.4 °C) from in situ measured mean annual SSTs in the Black Sea. This is not due to redox-dependent differential biomarker preservation as implied by their Δ14C values and spatial SST pattern. Since contributions from different sources can largely be excluded, the deviation of the Uk′37 and TEX86 proxy-derived SSTs from in situ SSTs requires further study of phylogenetic and other yet unknown environmental controls on alkenone and GDGT lipid distributions in the Black Sea. -ER - - -TY - JOUR -T1 - Analysis of the site-specific carbon isotope composition of propane by gas source isotope ratio mass spectrometer -JO - Geochimica et Cosmochimica Acta -VL - 188 -IS - -SP - 58 -EP - 72 -PY - 2016/9/1/ -T2 - -AU - Piasecki, Alison -AU - Sessions, Alex -AU - Lawson, Michael -AU - Ferreira, A.A. -AU - Neto, E.V. Santos -AU - Eiler, John M. -SN - 0016-7037 -DO - http://dx.doi.org/10.1016/j.gca.2016.04.048 -UR - http://www.sciencedirect.com/science/article/pii/S0016703716302174 -KW - Stable isotopes -KW - Site-specific isotopes -KW - Natural gas -KW - Mass spectrometry -AB - Abstract -Site-specific isotope ratio measurements potentially provide valuable information about the formation and degradation of complex molecules—information that is lost in conventional bulk isotopic measurements. Here we discuss the background and possible applications of such measurements, and present a technique for studying the site-specific carbon isotope composition of propane at natural abundance based on mass spectrometric analysis of the intact propane molecule and its fragment ions. We demonstrate the feasibility of this approach through measurements of mixtures of natural propane and propane synthesized with site-specific 13C enrichment, and we document the limits of precision of our technique. We show that mass balance calculations of the bulk δ13C of propane based on our site-specific measurements is generally consistent with independent constraints on bulk δ13C. We further demonstrate the accuracy of the technique, and illustrate one of its simpler applications by documenting the site-specific carbon isotope signature associated with gas phase diffusion of propane, confirming that our measurements conform to the predictions of the kinetic theory of gases. This method can be applied to propane samples of moderate size (tens of micromoles) isolated from natural gases. Thus, it provides a means of studying the site-specific stable isotope systematics of propane at natural isotope abundances on sample sizes that are readily recovered from many natural environments. This method may also serve as a model for future techniques that apply high-resolution mass spectrometry to study the site-specific isotopic distributions of larger organic molecules, with potential applications to biosynthesis, forensics and other geochemical subjects. -ER - - -TY - JOUR -T1 - Study of thermochemical sulfate reduction mechanism using compound specific sulfur isotope analysis -JO - Geochimica et Cosmochimica Acta -VL - 188 -IS - -SP - 73 -EP - 92 -PY - 2016/9/1/ -T2 - -AU - Meshoulam, Alexander -AU - Ellis, Geoffrey S. -AU - Said Ahmad, Ward -AU - Deev, Andrei -AU - Sessions, Alex L. -AU - Tang, Yongchun -AU - Adkins, Jess F. -AU - Liu, Jinzhong -AU - Gilhooly III, William P. -AU - Aizenshtat, Zeev -AU - Amrani, Alon -SN - 0016-7037 -DO - http://dx.doi.org/10.1016/j.gca.2016.05.026 -UR - http://www.sciencedirect.com/science/article/pii/S0016703716302691 -KW - Thermochemical alteration -KW - Organic matter -KW - Sulfur compounds -KW - Sulfate dissolution -KW - Isotopes -AB - Abstract -The sulfur isotopic fractionation associated with the formation of organic sulfur compounds (OSCs) during thermochemical sulfate reduction (TSR) was studied using gold-tube pyrolysis experiments to simulate TSR. The reactants used included n-hexadecane (n-C16) as a model organic compound with sulfate, sulfite, or elemental sulfur as the sulfur source. At the end of each experiment, the S-isotopic composition and concentration of remaining sulfate, H2S, benzothiophene, dibenzothiophene, and 2-phenylthiophene (PT) were measured. The observed S-isotopic fractionations between sulfate and BT, DBT, and H2S in experimental simulations of TSR correlate well with a multi-stage model of the overall TSR process. Large kinetic isotope fractionations occur during the first, uncatalyzed stage of TSR, 12.4‰ for H2S and as much as 22.2‰ for BT. The fractionations decrease as the H2S concentration increases and the reaction enters the second, catalyzed stage. Once all of the oxidizable hydrocarbons have been consumed, sulfate reduction ceases and equilibrium partitioning then dictates the fractionation between H2S and sulfate (∼17‰). - -Experiments involving sparingly soluble CaSO4 show that during the second catalytic phase of TSR the rate of sulfate reduction exceeds that of sulfate dissolution. In this case, there is no apparent isotopic fractionation between source sulfate and generated H2S, as all of the available sulfate is effectively reduced at all reaction times. When CaSO4 is replaced with fully soluble Na2SO4, sulfate dissolution is no longer rate limiting and significant S-isotopic fractionation is observed. This supports the notion that CaSO4 dissolution can lead to the apparent lack of fractionation between H2S and sulfate produced by TSR in nature. The S-isotopic composition of individual OSCs record information related to geochemical reactions that cannot be discerned from the δ34S values obtained from bulk phases such as H2S, oil, and sulfate minerals, and provide important mechanistic details about the overall TSR process. -ER - - -TY - JOUR -T1 - Origin of low δ26Mg basalts with EM-I component: Evidence for interaction between enriched lithosphere and carbonated asthenosphere -JO - Geochimica et Cosmochimica Acta -VL - 188 -IS - -SP - 93 -EP - 105 -PY - 2016/9/1/ -T2 - -AU - Tian, Heng-Ci -AU - Yang, Wei -AU - Li, Shu-Guang -AU - Ke, Shan -AU - Chu, Zhu-Yin -SN - 0016-7037 -DO - http://dx.doi.org/10.1016/j.gca.2016.05.021 -UR - http://www.sciencedirect.com/science/article/pii/S0016703716302642 -KW - Magnesium isotopes -KW - Continental basalts -KW - Asthenosphere–lithosphere interaction -KW - Recycled carbonates -KW - Pacific slab subduction -AB - Abstract -This study presents stable Mg isotopic data for Cenozoic potassic basalts from Wudalianchi and Erkeshan in northeastern China to determine the interactions between upwelling carbonated asthenosphere and enriched lithospheric mantle. Although the Wudalianchi and Erkeshan basalts have variable MgO contents of 4.45 to 9.47 wt.%, they exhibit a homogeneous Mg isotopic composition with δ26Mg values ranging from −0.57‰ to −0.46‰ and averaging −0.51 ± 0.06‰ (2SD, n = 18). This Mg isotopic composition is lighter than that of the average mantle (δ26Mg = −0.25 ± 0.07‰) but similar to late Cretaceous (<110 Ma) and Cenozoic basalts from the North China Craton and the South China Block (δ26Mg = −0.60 to −0.35‰). The high CaO/Al2O3 and Ba/Rb, and low Hf/Hf∗ ratios of the Wudalianchi and Erkeshan basalts are typical characteristics of carbonatitic metasomatism, suggesting that the light Mg isotopic composition could derive from involvement of recycled sedimentary carbonates in the mantle source. The high Dy/Er ratios (2.55 to 2.75) and excess of 230Th (230Th/238U = 1.24 to 1.33) suggest presence of garnet in a relatively deep mantle source. Additionally, the seismic tomographic observations show the existence of the stagnant Pacific slab in the mantle transition zone (410–660 km) under eastern China. This carbonated mantle source should be located in the asthenosphere. However, compared to other low δ26Mg basalts from eastern China with MORB-like Sr–Nd–Pb isotopic compositions and OIB-like trace element features, the Wudalianchi and Erkeshan basalts exhibit EM-I Sr–Nd–Pb isotopic compositions combined with high SiO2, Ba, K, Pb and LREE contents, high Ba/Th and low Ce/Pb ratios. These geochemical features require a contribution from another mantle source, most likely an EM-I lithospheric mantle. Therefore, an asthenosphere-lithosphere interaction model is proposed for determine the origin of the Wudalianchi and Erkeshan basalts. The original melt was derived from partial melting of the carbonated asthenospheric mantle that was metasomatized by carbonate melt from the stagnant Pacific slab in the mantle transition zone. This ascending melt with a low δ26Mg signature subsequently interacted with the EM-I lithospheric mantle. The interaction dissolved pyroxene and crystallized olivine, releasing LILE, REE, Sr and Pb from dissolved minerals into the melt. Simultaneously, Mg was inherited by newly formed olivine. Therefore, this interaction modified the trace elements and the Sr–Nd–Pb isotopic compositions of the melt toward EM-I geochemical features but preserved the light Mg isotope signatures. -ER - - -TY - JOUR -T1 - The CO chondrites: Major recent Antarctic finds, their thermal and radiation history, and describing the metamorphic history of members of the class -JO - Geochimica et Cosmochimica Acta -VL - 188 -IS - -SP - 106 -EP - 124 -PY - 2016/9/1/ -T2 - -AU - Sears, Derek W.G. -SN - 0016-7037 -DO - http://dx.doi.org/10.1016/j.gca.2016.05.033 -UR - http://www.sciencedirect.com/science/article/pii/S0016703716302769 -KW - CO chondrites -KW - Metamorphism -KW - Thermoluminescence -KW - Antarctic meteorites -AB - Abstract -Thermoluminescence (TL) properties of 29 CO chondrites from the Miller Range (MIL) and five chondrites from the Dominion Range (DOM) have been measured. MIL has a relatively strong natural TL signal (19.6 ± 14.7 krad), while some of the DOM samples have a very weak natural TL signal (<1 krad) whereas others resemble the MIL meteorites. I argue that MIL and some of the DOM samples had a normal perihelion (∼1.0 AU) and terrestrial age of ∼450–700 ka, while some of the DOM samples have a terrestrial age of ∼100 ka but a perihelion of ∼0.8 AU. The DOM meteorites also show considerable heterogeneity in their induced TL properties, also suggesting that the DOM fragments represent more than one fall. The induced TL data for the MIL samples studied here are consistent with them all being from a single fragmented meteorite. Small (50 mg) chips have TL properties similar to 500 mg chips, so that the smaller chips are representative, although samples taken from original masses less than ∼2 g have low natural TL suggesting that they were heated during atmospheric fall. The properties of CO chondrites are reviewed in terms of their petrologic types. Correlations between TL sensitivity, the most quantitative technique for evaluating metamorphic alteration in CO chondrites, and data for olivine composition and heterogeneity, matrix composition, inert gas content, metal composition (Ni, Co, and Cr in the kamacite), bulk carbon, C and O isotopes, graphite ordering, spectral reflectance at 0.8 μm, and textural characteristics of the ameboid olivine and Ca-rich inclusions are examined. The petrographic types appear to be largely metamorphic in origin with perhaps a minor role for metasomatism. Contrary to recent proposals it is here argued that petrologic type definitions should (1) be specific enough to be meaningful, but broad enough to be simple in application and robust to new developments, (2) be descriptive and not interpretative, (3) should not oversimplify and obscure important class-to-class differences, and (4) take account of all the available information, while avoiding reliance on any one technique or single observation whose application is based on interpretation. With these considerations in mind the petrographic type definitions for CO chondrites are restated and the petrologic type of 3.2 assigned to both the MIL and DOM CO chondrites. -ER - - -TY - JOUR -T1 - Diagenetic regimes in Arctic Ocean sediments: Implications for sediment geochemistry and core correlation -JO - Geochimica et Cosmochimica Acta -VL - 188 -IS - -SP - 125 -EP - 146 -PY - 2016/9/1/ -T2 - -AU - Meinhardt, A.-K. -AU - März, C. -AU - Schuth, S. -AU - Lettmann, K.A. -AU - Schnetger, B. -AU - Wolff, J.-O. -AU - Brumsack, H.-J. -SN - 0016-7037 -DO - http://dx.doi.org/10.1016/j.gca.2016.05.032 -UR - http://www.sciencedirect.com/science/article/pii/S0016703716302757 -KW - Arctic Ocean -KW - Sediment -KW - Pore water -KW - Diagenesis -KW - Manganese -KW - Iron isotopes -KW - Budget -AB - Abstract -Dark brown sediment layers are a potential stratigraphic tool in Quaternary Arctic Ocean sediments. They are rich in Mn, Fe, and trace metals scavenged from the water column and were most likely deposited during interglacial intervals. In this study, we combine sediment and pore water data from sediment cores taken in different parts of the Arctic Ocean to investigate the influence of early diagenetic processes on sediment geochemistry. In most studied cores, Mn, Co, and Mo are released into the pore waters from Mn oxide dissolution in deeper (>1.5 m) sediment layers. The relationship between sedimentary Mn, Co, and Mo contents in excess of the lithogenic background (elementxs) shows that Coxs/Moxs values are a diagnostic tool to distinguish between layers with diagenetic metal addition from the pore waters (Coxs/Moxs < 1), layers affected by Mn oxide dissolution and metal release (Coxs/Moxs > 10), and unaffected layers (Coxs/Moxs from 1 to 10). Steady-state calculations based on current pore water profiles reveal that in the studied cores, the diagenetic addition of these metals from the pore water pool alone is not sufficient to produce the sedimentary metal enrichments. However, it seems evident that dissolution of Mn oxides in the Mn reduction zone can permanently alter the primary geochemical signature of the dark brown layers. Therefore, pore water data and Coxs/Moxs values should be considered before core correlation when this correlation is solely based on Mn contents and dark sediment color. In contrast to the mostly non-lithogenic origin of Mn in the dark brown layers, sedimentary Fe consists of a large lithogenic (80%) and a small non-lithogenic fraction (20%). Our pore water data show that diagenetic Fe remobilization is not currently occurring in the sediment. The dominant Fe sources are coastal erosion and river input. Budget calculations show that Fe seems to be trapped in the modern Arctic Ocean and accumulates in shelf and basin sediments. - -The Fe isotopic signal δ56Fe of the solid phase is positive (∼0.2–0.3‰) in samples defined as the lithogenic background without significant Fe enrichments. With increasing non-lithogenic Fe contents in the sediment, δ56Fe becomes more negative, which indicates a shelf-to-basin export of an isotopically lighter Fe fraction. We assume that the same transport process is true for Mn. -ER - - -TY - JOUR -T1 - Bioalteration of synthetic Fe(III)-, Fe(II)-bearing basaltic glasses and Fe-free glass in the presence of the heterotrophic bacteria strain Pseudomonas aeruginosa: Impact of siderophores -JO - Geochimica et Cosmochimica Acta -VL - 188 -IS - -SP - 147 -EP - 162 -PY - 2016/9/1/ -T2 - -AU - Perez, Anne -AU - Rossano, Stéphanie -AU - Trcera, Nicolas -AU - Huguenot, David -AU - Fourdrin, Chloé -AU - Verney-Carron, Aurélie -AU - van Hullebusch, Eric D. -AU - Guyot, François -SN - 0016-7037 -DO - http://dx.doi.org/10.1016/j.gca.2016.05.028 -UR - http://www.sciencedirect.com/science/article/pii/S001670371630271X -KW - Basaltic glass -KW - Pseudomonas aeruginosa -KW - Siderophore -KW - Bioalteration -KW - Dissolution kinetics -AB - Abstract -This study aims to evaluate the role of micro-organisms and their siderophores in the first steps of the alteration processes of basaltic glasses in aqueous media. In this regard, three different types of glasses – with or without iron, in the reduced Fe(II) or oxidized Fe(III) states – were prepared on the basis of a simplified basaltic glass composition. Control and Pseudomonas aeruginosa inoculated experiments were performed in a buffered (pH 6.5) nutrient depleted medium to stimulate the production of the pyoverdine siderophore. Results show that the presence of P. aeruginosa has an effect on the dissolution kinetics of all glasses as most of the calculated elemental release rates are increased compared to sterile conditions. Reciprocally, the composition of the glass in contact with P. aeruginosa has an impact on the bacterial growth and siderophore production. As an essential nutrient for this microbial strain, Fe notably appears to play a central role during biotic experiments. Its presence in the glass stimulates the bacterial growth and minimizes the synthesis of pyoverdine. Moreover the initial Fe2+/Fe3+ ratio in the glasses modulates this synthesis, as pyoverdine is not detected at all in the system in contact with Fe(III)-bearing glass. Finally, the dissolution rates appear to be correlated to siderophore concentrations as they increase with respect to sterile experiments in the order Fe(III)-bearing glass < Fe(II)-bearing glass < Fe-free glass. This increase is attributed to complexation reactions between siderophores and Fe or Al for Fe(II)-bearing glass or Fe-free glass, respectively. The dissolution of an Fe-free glass is significantly improved in the presence of bacteria, as initial dissolution rates are increased by a factor of 3. This study attests to the essential role of siderophores in the P. aeruginosa-promoted dissolution processes of basaltic glasses as well as to the complex relationships between the nutritional potential of the glass and its dissolution rates. -ER - - -TY - JOUR -T1 - Diverse origins of Arctic and Subarctic methane point source emissions identified with multiply-substituted isotopologues -JO - Geochimica et Cosmochimica Acta -VL - 188 -IS - -SP - 163 -EP - 188 -PY - 2016/9/1/ -T2 - -AU - Douglas, P.M.J. -AU - Stolper, D.A. -AU - Smith, D.A. -AU - Walter Anthony, K.M. -AU - Paull, C.K. -AU - Dallimore, S. -AU - Wik, M. -AU - Crill, P.M. -AU - Winterdahl, M. -AU - Eiler, J.M. -AU - Sessions, A.L. -SN - 0016-7037 -DO - http://dx.doi.org/10.1016/j.gca.2016.05.031 -UR - http://www.sciencedirect.com/science/article/pii/S0016703716302745 -KW - Methane -KW - Clumped isotope geochemistry -KW - Arctic -KW - Carbon cycle -KW - Greenhouse gases -AB - Abstract -Methane is a potent greenhouse gas, and there are concerns that its natural emissions from the Arctic could act as a substantial positive feedback to anthropogenic global warming. Determining the sources of methane emissions and the biogeochemical processes controlling them is important for understanding present and future Arctic contributions to atmospheric methane budgets. Here we apply measurements of multiply-substituted isotopologues, or clumped isotopes, of methane as a new tool to identify the origins of ebullitive fluxes in Alaska, Sweden and the Arctic Ocean. When methane forms in isotopic equilibrium, clumped isotope measurements indicate the formation temperature. In some microbial methane, however, non-equilibrium isotope effects, probably related to the kinetics of methanogenesis, lead to low clumped isotope values. We identify four categories of emissions in the studied samples: thermogenic methane, deep subsurface or marine microbial methane formed in isotopic equilibrium, freshwater microbial methane with non-equilibrium clumped isotope values, and mixtures of deep and shallow methane (i.e., combinations of the first three end members). Mixing between deep and shallow methane sources produces a non-linear variation in clumped isotope values with mixing proportion that provides new constraints for the formation environment of the mixing end-members. Analyses of microbial methane emitted from lakes, as well as a methanol-consuming methanogen pure culture, support the hypothesis that non-equilibrium clumped isotope values are controlled, in part, by kinetic isotope effects induced during enzymatic reactions involved in methanogenesis. Our results indicate that these kinetic isotope effects vary widely in microbial methane produced in Arctic lake sediments, with non-equilibrium Δ18 values spanning a range of more than 5‰. -ER - - - - -TY - CHAP -TI - Front Matter -PB - John Wiley & Sons, Ltd -SN - 9781118622179 -UR - http://dx.doi.org/10.1002/9781118622179.fmatter -DO - 10.1002/9781118622179.fmatter -SP - i -EP - xiv -T2 - Sustainable Carbon Materials from Hydrothermal Processes -PY - 2013 -ER - - -TY - CHAP -TI - Green Carbon -AU - Titirici, Maria-Magdalena -PB - John Wiley & Sons, Ltd -SN - 9781118622179 -UR - http://dx.doi.org/10.1002/9781118622179.ch1 -DO - 10.1002/9781118622179.ch1 -SP - 1 -EP - 36 -KW - green carbon -KW - hydrothermal carbonization (HTC) -T2 - Sustainable Carbon Materials from Hydrothermal Processes -PY - 2013 -ER - - -TY - CHAP -TI - Porous Hydrothermal Carbons -AU - White, Robin J. -AU - Fellinger, Tim-Patrick -AU - Kubo, Shiori -AU - Brun, Nicolas -AU - Titirici, Maria-Magdalena -PB - John Wiley & Sons, Ltd -SN - 9781118622179 -UR - http://dx.doi.org/10.1002/9781118622179.ch2 -DO - 10.1002/9781118622179.ch2 -SP - 37 -EP - 73 -KW - carbon aerogels -KW - HTC-derived carbogels -KW - pore morphology control -KW - porous hydrothermal carbonization (HTC) -T2 - Sustainable Carbon Materials from Hydrothermal Processes -PY - 2013 -ER - - -TY - CHAP -TI - Porous Biomass-Derived Carbons: Activated Carbons -AU - Dolores, Lozano-Castell -AU - Juan, Pablo Marco-Lozar -AU - Falco, Camillo -AU - Titirici, Maria-Magdalena -AU - Diego, Cazorla-Amorós -PB - John Wiley & Sons, Ltd -SN - 9781118622179 -UR - http://dx.doi.org/10.1002/9781118622179.ch3 -DO - 10.1002/9781118622179.ch3 -SP - 75 -EP - 100 -KW - activated carbons -KW - hydrothermal carbonization (HTC) -KW - lignocellulosic biomass -KW - microporosity -T2 - Sustainable Carbon Materials from Hydrothermal Processes -PY - 2013 -ER - - -TY - CHAP -TI - Hydrothermally Synthesized Carbonaceous Nanocomposites -AU - Hu, Bo -AU - Zhu, Hai-Zhou -AU - Yu, Shu-Hong -PB - John Wiley & Sons, Ltd -SN - 9781118622179 -UR - http://dx.doi.org/10.1002/9781118622179.ch4 -DO - 10.1002/9781118622179.ch4 -SP - 101 -EP - 124 -KW - carbonaceous nanocomposites -KW - carbonaceous nanomaterials -KW - hydrothermal carbonization (HTC) synthesis -T2 - Sustainable Carbon Materials from Hydrothermal Processes -PY - 2013 -ER - - -TY - CHAP -TI - Chemical Modification of Hydrothermal Carbon Materials -AU - Wohlgemuth, Stephanie -AU - Urakami, Hiromitsu -AU - Zhao, Li -AU - Titirici, Maria-Magdalena -PB - John Wiley & Sons, Ltd -SN - 9781118622179 -UR - http://dx.doi.org/10.1002/9781118622179.ch5 -DO - 10.1002/9781118622179.ch5 -SP - 125 -EP - 149 -KW - chemical modification -KW - hydrothermal carbon materials -KW - in situ doping procedures -T2 - Sustainable Carbon Materials from Hydrothermal Processes -PY - 2013 -ER - - -TY - CHAP -TI - Characterization of Hydrothermal Carbonization Materials -AU - Baccile, Niki -AU - Weber, Jens -AU - Falco, Camillo -AU - Titirici, Maria-Magdalena -PB - John Wiley & Sons, Ltd -SN - 9781118622179 -UR - http://dx.doi.org/10.1002/9781118622179.ch6 -DO - 10.1002/9781118622179.ch6 -SP - 151 -EP - 211 -KW - Fourier transform infrared spectroscopy (FTIR) -KW - hydrothermal carbonization (HTC) materials -KW - X-ray diffraction (XRD) -KW - X-ray photoelectron spectroscopy (XPS) -KW - zeta potential -T2 - Sustainable Carbon Materials from Hydrothermal Processes -PY - 2013 -ER - - -TY - CHAP -TI - Applications of Hydrothermal Carbon in Modern Nanotechnology -AU - Sevilla, Marta -AU - Fuertes, Antonio B. -AU - Rezan, Demir-Cakan -AU - Titirici, Maria-Magdalena -PB - John Wiley & Sons, Ltd -SN - 9781118622179 -UR - http://dx.doi.org/10.1002/9781118622179.ch7 -DO - 10.1002/9781118622179.ch7 -SP - 213 -EP - 294 -KW - energy storage -KW - gas storage -KW - hydrothermal carbonization (HTC) -KW - nanotechnology -KW - photocatalysis -KW - water purification -T2 - Sustainable Carbon Materials from Hydrothermal Processes -PY - 2013 -ER - - -TY - CHAP -TI - Environmental Applications of Hydrothermal Carbonization Technology: Biochar Production, Carbon Sequestration, and Waste Conversion -AU - Berge, Nicole D. -AU - Kammann, Claudia -AU - Ro, Kyoung -AU - Libra, Judy -PB - John Wiley & Sons, Ltd -SN - 9781118622179 -UR - http://dx.doi.org/10.1002/9781118622179.ch8 -DO - 10.1002/9781118622179.ch8 -SP - 295 -EP - 340 -KW - biochar production -KW - carbon sequestration -KW - hydrothermal carbonization (HTC) -KW - soil amendment -KW - waste conversion -T2 - Sustainable Carbon Materials from Hydrothermal Processes -PY - 2013 -ER - - -TY - CHAP -TI - Scale-Up in Hydrothermal Carbonization -AU - Kruse, Andrea -AU - Baris, Daniela -AU - Tröger, Nicole -AU - Wieczorek, Peter -PB - John Wiley & Sons, Ltd -SN - 9781118622179 -UR - http://dx.doi.org/10.1002/9781118622179.ch9 -DO - 10.1002/9781118622179.ch9 -SP - 341 -EP - 353 -KW - hydrothermal carbonization (HTC) -KW - scale-up -T2 - Sustainable Carbon Materials from Hydrothermal Processes -PY - 2013 -ER - - -TY - CHAP -TI - Index -PB - John Wiley & Sons, Ltd -SN - 9781118622179 -UR - http://dx.doi.org/10.1002/9781118622179.index -DO - 10.1002/9781118622179.index -SP - 355 -EP - 357 -T2 - Sustainable Carbon Materials from Hydrothermal Processes -PY - 2013 -ER - - -TY - JOUR -TI - Issue Information -JO - Geoscience Data Journal -JA - Geosci. Data J. -VL - 1 -IS - 2 -SN - 2049-6060 -UR - http://dx.doi.org/10.1002/gdj3.16 -DO - 10.1002/gdj3.16 -SP - i -EP - iii -PY - 2014 -ER - - -TY - JOUR -AU - Rennie, J. J. -AU - Lawrimore, J. H. -AU - Gleason, B. E. -AU - Thorne, P. W. -AU - Morice, C. P. -AU - Menne, M. J. -AU - Williams, C. N. -AU - de Almeida, W. Gambi -AU - Christy, J.R. -AU - Flannery, M. -AU - Ishihara, M. -AU - Kamiguchi, K. -AU - Klein-Tank, A. M. G. -AU - Mhanda, A. -AU - Lister, D. H. -AU - Razuvaev, V. -AU - Renom, M. -AU - Rusticucci, M. -AU - Tandy, J. -AU - Worley, S. J. -AU - Venema, V. -AU - Angel, W. -AU - Brunet, M. -AU - Dattore, B. -AU - Diamond, H. -AU - Lazzara, M. A. -AU - Le Blancq, F. -AU - Luterbacher, J. -AU - Mächel, H. -AU - Revadekar, J. -AU - Vose, R. S. -AU - Yin, X. -TI - The international surface temperature initiative global land surface databank: monthly temperature data release description and methods -JO - Geoscience Data Journal -JA - Geosci. Data J. -VL - 1 -IS - 2 -SN - 2049-6060 -UR - http://dx.doi.org/10.1002/gdj3.8 -DO - 10.1002/gdj3.8 -SP - 75 -EP - 102 -KW - global climate -KW - surface land temperature -KW - statistical analysis -PY - 2014 -AB - Described herein is the first version release of monthly temperature holdings of a new Global Land Surface Meteorological Databank. Organized under the auspices of the International Surface Temperature Initiative (ISTI), an international group of scientists have spent three years collating and merging data from numerous sources to create a merged holding. This release in its recommended form consists of over 30 000 individual station records, some of which extend over the past 300 years. This article describes the sources, the chosen merge methodology, and the resulting databank characteristics. Several variants of the databank have also been released that reflect the structural uncertainty in merging datasets. Variants differ in, for example, the order in which sources are considered and the degree of congruence required in station geolocation for consideration as a merged or unique record. Also described is a version control protocol that will be applied in the event of updates. Future updates are envisaged with the addition of new data sources, and with changes in processing, where public feedback is always welcomed. Major updates, when necessary, will always be accompanied by a new journal paper. This databank release forms the foundation for the construction of new global land surface air temperature analyses by the global research community and their assessment by the ISTI's benchmarking and assessment working group. -ER - - -TY - JOUR -AU - Slonosky, Victoria -TI - Historical climate observations in Canada: 18th and 19th century daily temperature from the St. Lawrence Valley, Quebec -JO - Geoscience Data Journal -JA - Geosci. Data J. -VL - 1 -IS - 2 -SN - 2049-6060 -UR - http://dx.doi.org/10.1002/gdj3.11 -DO - 10.1002/gdj3.11 -SP - 103 -EP - 120 -KW - historical climatology -KW - daily temperature -KW - early meteorological instruments -KW - 18th and 19th century climate -KW - Quebec -KW - Canada -PY - 2014 -AB - Daily observations of weather and climate for the province of Québec, Canada, start in the 18th century and continue to the present day. Daily temperature observations from 12 observers ranging from 1742 to 1873 are described here. The frequency distributions of the temperature observations from each of the historical weather journals are examined for data quality and consistency. Adjustments for differing types of exposures, particularly north wall exposures, are developed. It is shown that examination of the daily data distribution can be used to infer information concerning the instruments used and likely exposure in the absence of metadata. Comparisons of the relative frequency distributions of historical and modern hourly observations are used to assess the reliability of the daily historical temperature data, and are able to detect problems with instrument exposure or sampling biases. Historical observations of temperature from the 18th and 19th centuries are shown to be comparable to modern temperature data. These daily observations will be used in further studies to analyse changes in climate and extreme conditions on a decadal to centennial time frame, and will form part of international data sets for the reconstruction and analysis of past climate events. -ER - - -TY - JOUR -AU - Brunet, Manola -AU - Gilabert, Alba -AU - Jones, Phil -AU - Efthymiadis, Dimitrios -TI - A historical surface climate dataset from station observations in Mediterranean North Africa and Middle East areas -JO - Geoscience Data Journal -JA - Geosci. Data J. -VL - 1 -IS - 2 -SN - 2049-6060 -UR - http://dx.doi.org/10.1002/gdj3.12 -DO - 10.1002/gdj3.12 -SP - 121 -EP - 128 -KW - historical climate observations -KW - data rescue -KW - Mediterranean -KW - North Africa -KW - Middle East -PY - 2014 -AB - Historical climatic data from station observations taken in North African and Middle East Mediterranean countries since the second half of the 19th century have been digitized and quality-controlled in the framework of the EU-funded European Reanalysis and Observations for Monitoring (EURO4M) project. Daily maximum and minimum temperatures and precipitation totals, along with sub-daily data for surface air pressure have been recovered by using historical data sources involving book/logbook collections archived in national and international data centres. The new dataset produced comprises climatic time series for 79 stations that have operated in southern and eastern Mediterranean countries. While the developed time series have data gaps, every effort has been made to infill these gaps, to improve assessments of the long-term changes in climate variability in the region. -ER - - -TY - JOUR -AU - Montabone, L. -AU - Marsh, K. -AU - Lewis, S. R. -AU - Read, P. L. -AU - Smith, M. D. -AU - Holmes, J. -AU - Spiga, A. -AU - Lowe, D. -AU - Pamment, A. -TI - The Mars Analysis Correction Data Assimilation (MACDA) Dataset V1.0 -JO - Geoscience Data Journal -JA - Geosci. Data J. -VL - 1 -IS - 2 -SN - 2049-6060 -UR - http://dx.doi.org/10.1002/gdj3.13 -DO - 10.1002/gdj3.13 -SP - 129 -EP - 139 -KW - mars atmosphere -KW - mars reanalysis -KW - mars Global Surveyor -KW - global climate model (GCM) -KW - data assimilation -PY - 2014 -AB - The Mars Analysis Correction Data Assimilation (MACDA) dataset version 1.0 contains the reanalysis of fundamental atmospheric and surface variables for the planet Mars covering a period of about three Martian years (a Martian year is about 1.88 terrestrial years). This has been produced by data assimilation of observations from NASA's Mars Global Surveyor (MGS) spacecraft during its science mapping phase (February 1999–August 2004). In particular, we have used retrieved thermal profiles and total dust optical depths from the Thermal Emission Spectrometer (TES) on board MGS. Data have been assimilated into a Mars global climate model (MGCM) using the Analysis Correction scheme developed at the UK Meteorological Office. The MGCM used is the UK spectral version of the Laboratoire de Météorologie Dynamique (LMD, Paris, France) MGCM. MACDA is a joint project of the University of Oxford and The Open University in the UK. -ER - - -TY - JOUR -AU - Locci, F. -AU - Melis, M. T. -AU - Dessì, F. -AU - Stocchi, P. -AU - Akinde, M. O. -AU - Bønes, V. -AU - Bonasoni, P. -AU - Vuillermoz, E. -TI - Implementation of a webGIS service platform for high mountain climate research: the SHARE GeoNetwork project -JO - Geoscience Data Journal -JA - Geosci. Data J. -VL - 1 -IS - 2 -SN - 2049-6060 -UR - http://dx.doi.org/10.1002/gdj3.14 -DO - 10.1002/gdj3.14 -SP - 140 -EP - 157 -KW - weather database -KW - spatial database -KW - open source -KW - high mountains -KW - SHARE -KW - GeoNetwork -PY - 2014 -AB - The implementation of a webGIS service platform dedicated to the management and sharing of climatological data acquired by high elevation stations is the core of the Station at High Altitude for Research on the Environment (SHARE) GeoNetwork project, promoted by the Ev-K2 CNR Committee. The web platform basically will provide three types of services: structured metadata archive, data and results from high-altitude environments research and projects; access to high-altitude Ev-K2 CNR stations and creation of a network of existing stations; dedicated webGIS for geo-referenced data collected during the research. High elevation environmental and territorial data and metadata are catalogued in a single integrated platform to get access to the information heritage of the SHARE project, using open-source tools: Geonetwork for the metadata catalogue and webGIS resources, and the open-source Weather and Water Database (WDB), developed by the Norwegian Meteorological Institute, for the database information system implementation. The information system is designed to have a main node, with the possibility to install relocated subsystems based on the same technology, named focal point of SHARE, which will contain metadata and data connected to the main node. In this study, a new structure of metadata for the description of the climatological stations is proposed and WDB adaptation and data preprocessing are described in detail, giving code and script samples. -ER - - -TY - JOUR -AU - Ashcroft, Linden -AU - Gergis, Joëlle -AU - Karoly, David John -TI - A historical climate dataset for southeastern Australia, 1788–1859 -JO - Geoscience Data Journal -JA - Geosci. Data J. -VL - 1 -IS - 2 -SN - 2049-6060 -UR - http://dx.doi.org/10.1002/gdj3.19 -DO - 10.1002/gdj3.19 -SP - 158 -EP - 178 -KW - early instrumental data -KW - Australia -KW - temperature -KW - pressure -KW - rainfall -KW - Southern Hemisphere -KW - historical climatology -KW - 19th century climate -PY - 2014 -AB - There is a significant lack of historical climate data in the Southern Hemisphere compared to the northern latitudes. To address this data scarcity and to improve understanding of regional climate variability, historical instrumental observations were recovered for southeastern Australian (SEA) for the 1788–1859 period. Instrumental observations of temperature, atmospheric pressure, rainfall and raindays were rescued from 39 archival sources, and examined to identify observer biases and inhomogeneities. The rescued data provide continuous information on SEA climate variability from 1826 to 1859, with short periods of observations identified between 1788–1791, 1803–1805 and 1821–1824. Quality control and homogenization of each data source indicates that the historical observations successfully capture regional interannual climate variability. The historical records exhibit high correlations between neighbouring observations and related climate variables. The instrumental observations also display very good agreement with documentary climate reconstructions, further verifying their quality. As an example of how this new historical dataset may be used, regional averages of the observations were calculated to estimate interannual climate variability across SEA from 1826 to 1859. Prolonged dry conditions were identified in various parts of the region during 1837–1843 and 1845–1852, while wet conditions were noted from 1836 to 1838, primarily in southern SEA. Anomalously cold periods were also identified in 1835–1836 and 1848–1849, in general agreement with temperature reconstructions from other regions of the Southern Hemisphere. This new dataset provides a valuable source of subdaily to monthly information on SEA climate variability for future climate analysis, palaeoclimate reconstruction verification and historical studies. -ER - - -TY - JOUR -AU - Merchant, Christopher J. -AU - Embury, Owen -AU - Roberts-Jones, Jonah -AU - Fiedler, Emma -AU - Bulgin, Claire E. -AU - Corlett, Gary K. -AU - Good, Simon -AU - McLaren, Alison -AU - Rayner, Nick -AU - Morak-Bozzo, Simone -AU - Donlon, Craig -TI - Sea surface temperature datasets for climate applications from Phase 1 of the European Space Agency Climate Change Initiative (SST CCI) -JO - Geoscience Data Journal -JA - Geosci. Data J. -VL - 1 -IS - 2 -SN - 2049-6060 -UR - http://dx.doi.org/10.1002/gdj3.20 -DO - 10.1002/gdj3.20 -SP - 179 -EP - 191 -KW - sea surface temperature -KW - climate data record -KW - remote sensing -KW - oceanography -KW - infra-red radiometer -PY - 2014 -AB - Sea surface temperature (SST) datasets have been generated from satellite observations for the period 1991–2010, intended for use in climate science applications. Attributes of the datasets specifically relevant to climate applications are: first, independence from in situ observations; second, effort to ensure homogeneity and stability through the time-series; third, context-specific uncertainty estimates attached to each SST value; and, fourth, provision of estimates of both skin SST (the fundamental measurement, relevant to air-sea fluxes) and SST at standard depth and local time (partly model mediated, enabling comparison with historical in situ datasets). These attributes in part reflect requirements solicited from climate data users prior to and during the project. Datasets consisting of SSTs on satellite swaths are derived from the Along-Track Scanning Radiometers (ATSRs) and Advanced Very High Resolution Radiometers (AVHRRs). These are then used as sole SST inputs to a daily, spatially complete, analysis SST product, with a latitude-longitude resolution of 0.05°C and good discrimination of ocean surface thermal features. A product user guide is available, linking to reports describing the datasets' algorithmic basis, validation results, format, uncertainty information and experimental use in trial climate applications. Future versions of the datasets will span at least 1982–2015, better addressing the need in many climate applications for stable records of global SST that are at least 30 years in length. -ER - - -TY - JOUR -AU - Jansen, J. D. -AU - Fonseca, R. M. -AU - Kahrobaei, S. -AU - Siraj, M. M. -AU - Van Essen, G. M. -AU - Van den Hof, P. M. J. -TI - The egg model – a geological ensemble for reservoir simulation -JO - Geoscience Data Journal -JA - Geosci. Data J. -VL - 1 -IS - 2 -SN - 2049-6060 -UR - http://dx.doi.org/10.1002/gdj3.21 -DO - 10.1002/gdj3.21 -SP - 192 -EP - 195 -KW - reservoir -KW - simulation -KW - channelized -KW - geological -KW - ensemble -PY - 2014 -AB - The ‘Egg Model’ is a synthetic reservoir model consisting of an ensemble of 101 relatively small three-dimensional realizations of a channelized oil reservoir produced under water flooding conditions with eight water injectors and four oil producers. It has been used in numerous publications to demonstrate a variety of aspects related to computer-assisted flooding optimization and history matching. Unfortunately the details of the parameter settings are not always identical and not always fully documented in several of these publications. We present a ‘standard version’ of the Egg Model which is meant to serve as a test case in future publications, and a dataset of 100 permeability realizations in addition to the permeability field used for the standard model. We implemented and tested the model in four reservoir simulators: Dynamo/Mores (Shell), Eclipse (Schlumberger), AD-GPRS (Stanford University) and MRST (Sintef), which produced near-identical output. This article describes the input parameters of the standard model. Together with the input files for the various simulators, it has been be uploaded in the 3TU.Datacentrum repository with free access to external users. -ER - diff --git a/Resources/files/TestDataSource/testbib2.FormatKeyValueFile.json b/Resources/files/TestDataSource/testbib2.FormatKeyValueFile.json deleted file mode 100644 index 607300ae..00000000 --- a/Resources/files/TestDataSource/testbib2.FormatKeyValueFile.json +++ /dev/null @@ -1,63 +0,0 @@ -{ - "block" : { - "defaults" : { - "properties.bibliographic_type" : "3" - }, - "pairs" : { - "author" : { - "datatype" : "string", - "organization" : "list" - } - }, - "matches" : { - "title" : { - "field" : "properties.title" - }, - "head0" : { - "field" : "properties.bibliographic_type", - "convert" : { - "@article" : "0", - "@book" : "1", - "@booklet" : "2", - "@conference" : "3" - } - }, - "head1" : { - "field" : "properties.shortname" - }, - "journal" : { - "field" : "properties.journal" - }, - "volume" : { - "field" : "properties.volume" - 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"block" : { - "defaults" : { - "properties.sourcetdb" : "15", - "properties.datasources" : "[\"PSI-Nagra-12-07\"]", - "properties.reactyp" : "1" - }, - "pairs" : { - - }, - "matches" : { - "dod.30.val" : { - "field" : "properties.comment" - }, - "key.2.fv" : { - "field" : "properties.symbol" - }, - "dod.16.val" : { - "field" : "properties.name" - }, - "key.0.fv" : { - "field" : "properties.aggregate_state", - "convert" : { - "a" : "4", - "g" : "0", - "s" : "3", - "c" : "5", - "l" : "1" - } - }, - "dod.1.val.0" : { - "field" : "properties.class_", - "convert" : { - "d" : "---", - "r" : "---", - "n" : "---", - "i" : "---", - "f" : "---", - "T" : "---", - "E" : "---", - "S" : "2", - "K" : "4", - "W" : "3", - "L" : "---", - "G" : "1", - "V" : "---", - "C" : "---", - "H" : "---", - "N" : "---", - "I" : "---", - "J" : "---", - "M" : "---", - "F" : "---", - "D" : "---", - "Q" : "---", - "P" : "---", - "R" : "---", - "0" : "---", - "2" : "---", - "4" : "---", - "6" : "---", - "8" : "---", - "1" : "---", - 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"F" : "319", - "A" : "320", - "P" : "321", - "Z" : "322" - } - }, - "dod.17.val" : { - "field" : "properties.formula" - }, - "dod.7.val.1" : { - "field" : "properties.sm_gibbs_energy.values" - }, - "dod.8.val.1" : { - "field" : "properties.sm_enthalpy.values" - }, - "dod.9.val.1" : { - "field" : "properties.sm_entropy_abs.values" - }, - "dod.10.val.1" : { - "field" : "properties.sm_heat_capacity_p.values" - }, - "dod.11.val.1" : { - "field" : "properties.sm_volume.values" - } - } - }, - "renderer" : "JSON", - "label" : "VertexSubstance", - "comment" : "test" -} diff --git a/Resources/files/TestReaction/PSI-Nagra/Reaction2.PSI-Nagra-12-07.FormatStructDataFile.json b/Resources/files/TestReaction/PSI-Nagra/Reaction2.PSI-Nagra-12-07.FormatStructDataFile.json deleted file mode 100644 index ae09abbc..00000000 --- a/Resources/files/TestReaction/PSI-Nagra/Reaction2.PSI-Nagra-12-07.FormatStructDataFile.json +++ /dev/null @@ -1,142 +0,0 @@ -{ - "block" : { - "defaults" : { - "properties.sourcetdb" : "15", - "properties.datasources" : "[\"PSI-Nagra-12-07\"]", - "properties.reactyp" : "1", - "properties.level" : "0" - }, - "pairs" : { - - }, - "matches" : { - "dod.30.val" : { - "field" : "properties.comment" - }, - "key.2.fv" : { - "field" : "properties.symbol" - }, - "dod.16.val" : { - "field" : "properties.name" - }, - "dod.0.val.0" : { - "field" : "4.18", - "convert" : { - "C" : "100", - "H" : "101", - "K" : "102", - "S" : "103", - "I" : "104", - "X" : "105", - "N" : "106" - } - }, - "dod.0.val.1" : { - "field" : "properties.method_corrT", - "convert" : { - "S" : "200", - "H" : "201", - "B" : "202", - "F" : "203", - "X" : "204", - "K" : "205", - "W" : "206", - "V" : "207", - "L" : "208", - "0" : "209", - "1" : "210", - "2" : "211", - "3" : "212", - "Z" : "213", - "R" : "214", - "E" : "215", - "Y" : "216", - "C" : "217", - "G" : "218" - } - }, - "dod.0.val.2" : { - "field" : "4.20", - "convert" : { - "N" : "300", - "0" : "301", - "1" : "302", - "2" : "303", - "3" : "304", - "C" : "305", - "K" : "306", - "V" : "307", - "B" : "308", - "E" : "309", - "H" : "310", - "G" : "311", - "R" : "312", - "S" : "313", - "T" : "314", - "6" : "315", - "7" : "316", - "8" : "317", - "9" : "318", - "F" : "319", - "A" : "320", - "P" : "321", - "Z" : "322" - } - }, - "dod.6.val.1" : { - "field" : "properties.logKr.values" - }, - "dod.7.val.0" : { - "field" : "properties.drsm_gibbs_energy.values" - }, - "dod.8.val.0" : { - "field" : "properties.drsm_enthalpy.values" - }, - "dod.9.val.0" : { - "field" : "properties.drsm_entropy.values" - }, - "dod.10.val.0" : { - "field" : "properties.drsm_heat_capacity_p.values" - }, - "dod.11.val.0" : { - "field" : "properties.drsm_volume.values" - }, - "dod.13.val.0" : { - "field" : "properties.Pst", - "script" : "field = field * 1e05" - }, - "dod.13.val.1" : { - "field" : "properties.Tst", - "script" : "field = field + 273.15" - }, - "dod.22.val.0" : { - "field" : "properties.limitsTP.lowerT", - "script" : "field = field + 273.15" - }, - "dod.22.val.1" : { - "field" : "properties.limitsTP.upperT", - "script" : "field = field + 273.15" - }, - "dod.23.val.0" : { - "field" : "properties.limitsTP.lowerP", - "script" : "field = field * 1e05" - }, - "dod.23.val.1" : { - "field" : "properties.limitsTP.upperP", - "script" : "field = field * 1e05" - }, - "dod.28.val" : { - "field" : "properties.logk_ft_coeffs.values" - }, - "dod.26.val" : { - "field" : "properties.dr_volume_pt_coeffs.values" - }, - "dod.24.val" : { - "field" : "properties.dr_heat_aapacity_p_t_coeffs.values" - } - } - }, - "renderer" : "JSON", - "label" : "VertexReaction", - "comment" : "test" -} diff --git a/Resources/files/TestReaction/PSI-Nagra/ReactionEdge.PSI-Nagra-12-07.FormatStructDataFile.json b/Resources/files/TestReaction/PSI-Nagra/ReactionEdge.PSI-Nagra-12-07.FormatStructDataFile.json deleted file mode 100644 index f8d78c07..00000000 --- a/Resources/files/TestReaction/PSI-Nagra/ReactionEdge.PSI-Nagra-12-07.FormatStructDataFile.json +++ /dev/null @@ -1,26 +0,0 @@ -{ - "block" : { - "defaults" : { - "properties.level" : "0" - }, - "pairs" : { - - }, - "matches" : { - "dod.21.val.%" : { - "field" : "properties.stoi_coeff" - }, - "dod.18.val.%" : { - "field" : "@key", - "script" : "field = string.sub(field, 13, -5); field = string.match(field,\"(%S*)\");" - } - }, - "script" : "if rintable.properties.stoi_coeff < 0 then rintable.properties.rct = 0 end; if rintable.properties.stoi_coeff > 0 then rintable.properties.rct = 1 end;" - }, - "renderer" : "JSON", - "label" : "EdgeTakes", - "comment" : "", - "fname" : "", - "Nblocks" : 0, - "Nlines" : 0 -} diff --git a/Resources/files/TestReaction/PSI-Nagra/ReactionEdge.PSI-Nagra-12-07___.FormatStructDataFile.json b/Resources/files/TestReaction/PSI-Nagra/ReactionEdge.PSI-Nagra-12-07___.FormatStructDataFile.json deleted file mode 100644 index 43442116..00000000 --- a/Resources/files/TestReaction/PSI-Nagra/ReactionEdge.PSI-Nagra-12-07___.FormatStructDataFile.json +++ /dev/null @@ -1,27 +0,0 @@ -{ - "block" : { - "defaults" : { - "properties.rct" : "1", - "properties.level" : "0" - }, - "pairs" : { - - }, - "matches" : { - "dod.21.val.%" : { - "field" : "properties.stoi_coeff" - }, - "dod.18.val.%" : { - "field" : "@key", - "script" : "field = string.sub(field, 13, -5); field = string.match(field,\"(%S*)\");" - } - }, - "script" : "if rintable.properties.stoi_coeff < 0 then rintable.properties.rct = 0 end; if rintable.properties.stoi_coeff > 0 then rintable.properties.rct = 1 end;" - }, - "renderer" : "JSON", - "label" : "EdgeTakes", - "comment" : "", - "fname" : "", - "Nblocks" : 0, - "Nlines" : 0 -} diff --git a/Resources/files/TestReaction/README.md b/Resources/files/TestReaction/README.md deleted file mode 100644 index 6cd82b80..00000000 --- a/Resources/files/TestReaction/README.md +++ /dev/null @@ -1,3 +0,0 @@ -This folder is for Reaction files. - - diff --git a/Resources/files/TestReaction/mines-reactions.json b/Resources/files/TestReaction/mines-reactions.json deleted file mode 100644 index 58c0beb4..00000000 --- a/Resources/files/TestReaction/mines-reactions.json +++ /dev/null @@ -1,1713 +0,0 @@ -[ -{ - 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{ - "id": 618, - "label": "RDform", - "dot": 0, - "dN": 1, - "dM": 72, - "dyn": false, - "val": "SiO3-2" - }, - { - "id": 619, - "label": "REsDC", - "dot": 32, - "dN": 4, - "dM": 1, - "dyn": true, - "val": [ - "a Si SiO2@ cem ", - "a w_ H+ an_ ", - "a w_ H2O@ an_ ", - "a Si SiO3-2 cem " - ] - }, - { - "id": 620, - "label": "REmDC", - "dot": -9, - "dN": 4, - "dM": 1, - "dyn": true, - "val": [ - "d", - "d", - "d", - "n" - ] - }, - { - "id": 621, - "label": "RE_dim", - "dot": -1, - "dN": 1, - "dM": 8, - "dyn": false, - "val": [ - 4, - 0, - 0, - 0, - 0, - 0, - 0, - 2 - ] - }, - { - "id": 625, - "label": "SC_DC", - "dot": -6, - "dN": 4, - "dM": 1, - "dyn": true, - "val": [ - -1, - 2, - -1, - 1 - ] - }, - { - "id": 626, - "label": "TCint_", - "dot": -5, - "dN": 2, - "dM": 1, - "dyn": true, - "val": [ - 0, - 150 - ] - }, - { - "id": 627, - "label": "P_int", - "dot": -5, - "dN": 2, - "dM": 1, - "dyn": true, - "val": [ - 0, - 1000 - ] - }, - { - "id": 628, - "label": "adCpT", - "dot": -5, - "dN": 12, - "dM": 0, - "dyn": true, - "val": null - }, - { - "id": 629, - "label": "adHKF", - "dot": -5, - "dN": 8, - "dM": 0, - "dyn": true, - "val": null - }, - { - "id": 630, - "label": "adVTP", - "dot": -5, - "dN": 5, - "dM": 0, - "dyn": true, - "val": null - }, - { - "id": 631, - "label": "a_dST", - "dot": -5, - "dN": 12, - "dM": 0, - "dyn": true, - "val": null - }, - { - "id": 632, - "label": "aiLgKr", - "dot": -5, - "dN": 12, - "dM": 1, - "dyn": true, - "val": [ - -10.0006437301636, - 0, - -3917.49926757812, - 0, - 0, - 0, - 0, - 0, - 0, - 0, - 0, - 0 - ] - }, - { - "id": 633, - "label": "logKTP", - "dot": -5, - "dN": 0, - "dM": 0, - "dyn": true, - "val": null - }, - { - "id": 634, - "label": "rSDref", - "dot": 32, - "dN": 2, - "dM": 1, - "dyn": true, - "val": [ - "AUG20_GEMS:2001:dat: ", - "Matschei_ea:2007:pap:" - ] - }, - { - "id": 635, - "label": "rSDval", - "dot": 24, - "dN": 2, - "dM": 1, - "dyn": true, - "val": [ - "logK, H0r ", - "corrected Cp,S0 (SiO2)" - ] - } - ], - "mtime": "Sat, 01 Mar 2014 09:22:18 +0100" -} -] \ No newline at end of file diff --git a/Resources/files/TestReactionSet/README,md b/Resources/files/TestReactionSet/README,md deleted file mode 100644 index 6bad8b25..00000000 --- a/Resources/files/TestReactionSet/README,md +++ /dev/null @@ -1,3 +0,0 @@ -This folder is for ReactionSet files. - - diff --git a/Resources/files/TestRealLip/cheminode.0000001.json b/Resources/files/TestRealLip/cheminode.0000001.json deleted file mode 100644 index 0ff1861f..00000000 --- a/Resources/files/TestRealLip/cheminode.0000001.json +++ /dev/null @@ -1,216 +0,0 @@ -{ - "label": "cheminode", - "symbol" : "", - "chemisystem": "TestRealLip", - "csalgorithm": "GEMIPM3", - "initialguess": "unknown", - "eqstatus": "calculated", - "errorcodes": [ "none" ], - - "Nelements": 6, - "Nspecies": 27, - "Nphases": 6, - "Nsolutions": 4, - - "T": 298.15, - "P": 100000, - "V": 0, - "Veq": 0.00138226725453406, - "Vinert": 0, - "Meq": 2.2386560395697, - "Minert": 0, - "Heq": 0, - "Hinert": 0, - "Geq": -9897.62347664476, - - "IS": 0.00280594071459541, - "pH": 7.80171639329603, - "pe": 12.9446491209147, - "Eh": 0.764256669530329, - - "t": 0, - "dtt": 0, - "dtk": 0, - - "nElements": [ 10.0010001413112, 5, 111.016746657646, 85.5123733288231, 5.00000014131116, 0 ], - "mbrElements": [ 5.709422e-16, 0, 0, -2.367307e-14, 5.709422e-16, 7.846143e-20 ], - "uElements": [ -165.12674904613, -289.967954370153, -47.7702720641779, -0.136873269306601, - -296.269294541616, 29.806156161848 ], - - "nbSolid": [ - 9.99904926402201, 4.9991787747544, 0, 29.997147792066, 4.99987048926762, 0 ], - - "nSpecies": [ - 5.53027059733272e-06, - 1.50195274040463e-05, - 0.000800668384082946, - 7.06352024600843e-09, - 3.32831108300117e-07, - 2.84560871254645e-06, - 0.000126473258923506, - 3.44796374624969e-10, - 6.22271778485187e-05, - 6.57907238248883e-06, - 0.00185834280109027, - 0, - 0, - 0.000999788033267764, - 6.71614738208874e-07, - 1.67301473374758e-08, - 55.5074348769779, - 0, - 0, - 0, - 0, - 0.172047686718185, - 4.98293311364154, - 4.82713108803621, - 0.0169373756260739, - 0, - 0 - ], - "gammas": [ - 0.999999997559069, - 0.943495669819756, - 0.791442161704231, - 0.943495669819756, - 0.999999997559069, - 0.943495669819756, - 0.791442161704231, - 0.943495669819756, - 0.999999997559069, - 0.791442161704231, - 0.943495669819756, - 0.999999997559069, - 0.999999997559069, - 0.999999997559069, - 0.943495669819756, - 0.943495669819756, - 0.999999995118025, - 1, - 1, - 1, - 1, - 21.4410980466502, - 1.00556184025244, - 1.00005042819509, - 7.01832482353092, - 1, - 1 - ], - "cSpecies": [ - 5.5303641e-06, - 1.5019781e-05, - 0.00080068192, - 7.0636397e-09, - 3.3283674e-07, - 2.8456568e-06, - 0.0001264754, - 3.448022e-10, - 6.222823e-05, - 6.5791836e-06, - 0.0018583742, - 0, - 0, - 0.00099980494, - 6.7162609e-07, - 1.673043e-08, - 0, - 0, - 0, - 0, - 0.033375039, - 0.96662496, - 0.99650348, - 0.0034965186, - 0, - 0 - ], - - "kinrSpecies": [ - -1, - -1, - -1, - -1, - -1, - -1, - -1, - -1, - -1, - -1, - -1, - -1, - -1, - -1, - -1, - -1, - -1, - -1, - -1, - -1, - -1, - -1, - -1, - -1, - -1, - -1, - -1 - ], - - "ssaPhases": [ - 0, - 0, - 0, - 0, - 0, - 0 - ], - "nPhases": [ - 55.5113133796965, - 0, - 5.15498080035973, - 4.84406846366228, - 0, - 0 - ], - "mPhases": [ - 1.0001773359913, - 0, - 0.752845186999718, - 0.485633516578689, - 0, - 0 - ], - "vPhases": [ - 0.00100299100473657, - 0, - 0.00020025963886941, - 0.000179016610928072, - 0, - 0 - ], - "saPhases": [ - 55.5074348769779, - 0, - 0, - 0, - 0, - 0 - ], - "kinrPhases": [ - -1, - -1, - -1, - -1, - -1, - -1 - ], - "nbPhases": [ - [ 0.0019508772891435, 0.000821225245604571, 111.016746657646, 55.5152255367571, 0.000129652043540728, -7.84614316830425e-20 ], - [ 0, 0, 0, 0, 0, 0 ], - [ 5.15498080035973, 0.172047686718185, 0, 15.4649424010792, 4.98293311364154, 0 ], - [ 4.84406846366228, 4.82713108803621, 0, 14.5322053909869, 0.0169373756260739, 0 ], - [ 1.0, 0, 0, 0, 0, 0 ], - [ 0, 1.0, 2.0, 2.0, 0, 0 ] - ] -} diff --git a/Resources/files/TestRealLip/chemisystem.json b/Resources/files/TestRealLip/chemisystem.json deleted file mode 100644 index 9724c5c8..00000000 --- a/Resources/files/TestRealLip/chemisystem.json +++ /dev/null @@ -1,354 +0,0 @@ -{ - "label": "chemisystem", - "symbol": "TestRealLip", - "Nelements": 6, - "Nspecies": 27, - "Nphases": 6, - "Ntdbases": 2, - - "cselems": [ - "C", - "Ca", - "H", - "O", - "Sr", - "Zz" - ], - "cselclass": [ - "element", - "element", - "element", - "element", - "element", - "charge" - ], - "elamass": [ - 0.0120108003616333, - 0.0400779991149902, - 0.00100794994831085, - 0.015999400138855, - 0.087620002746582, - 0 - ], - "nElements": [ - 10.0010001413112, - 5, - 111.016746657646, - 85.5123733288231, - 5.00000014131116, - 0 - ], - - "csspecies": [ - "Ca(CO3)@", - "Ca(HCO3)+", - "Ca+2", - "CaOH+", - "Sr(CO3)@", - "Sr(HCO3)+", - "Sr+2", - "SrOH+", - "CO2@", - "CO3-2", - "HCO3-", - "CH4@", - "H2@", - "O2@", - "OH-", - "H+", - "H2O@", - "CO2", - "CH4", - "H2", - "O2", - "Arg", - "Str2", - "Cal", - "SrCO3-cal", - "Gr", - "Portlandite" - ], - "csspclass": [ - "aqsolute", - "aqsolute", - "aqsolute", - "aqsolute", - "aqsolute", - "aqsolute", - "aqsolute", - "aqsolute", - "aqsolute", - "aqsolute", - "aqsolute", - "aqsolute", - "aqsolute", - "aqsolute", - "aqsolute", - "aqsolute", - "aqsolvent", - "gasfluid", - "gasfluid", - "gasfluid", - "gasfluid", - "component", - "component", - "component", - "component", - "component", - "component" - ], - "spmolmass": [ - 0.100086999893188, - 0.101094949841499, - 0.0400779991149902, - 0.0570853492021561, - 0.14762900352478, - 0.148636953473091, - 0.087620002746582, - 0.104627352833748, - 0.0440096006393433, - 0.0600090007781982, - 0.0610169507265091, - 0.0160426001548767, - 0.0020158998966217, - 0.03199880027771, - 0.0170073500871658, - 0.00100794994831085, - 0.0180153000354767, - 0.0440096006393433, - 0.0160426001548767, - 0.0020158998966217, - 0.03199880027771, - 0.100086999893188, - 0.14762900352478, - 0.100086999893188, - 0.14762900352478, - 0.0120108003616333, - 0.0740926992893219 - ], - "matrixA": [ - [ 1, 1, 0, 3, 0, 0 ], - [ 1, 1, 1, 3, 0, 1 ], - [ 0, 1, 0, 0, 0, 2 ], - [ 0, 1, 1, 1, 0, 1 ], - [ 1, 0, 0, 3, 1, 0 ], - [ 1, 0, 1, 3, 1, 1 ], - [ 0, 0, 0, 0, 1, 2 ], - [ 0, 0, 1, 1, 1, 1 ], - [ 1, 0, 0, 2, 0, 0 ], - [ 1, 0, 0, 3, 0, -2 ], - [ 1, 0, 1, 3, 0, -1 ], - [ 1, 0, 4, 0, 0, 0 ], - [ 0, 0, 2, 0, 0, 0 ], - [ 0, 0, 0, 2, 0, 0 ], - [ 0, 0, 1, 1, 0, -1 ], - [ 0, 0, 1, 0, 0, 1 ], - [ 0, 0, 2, 1, 0, 0 ], - [ 1, 0, 0, 2, 0, 0 ], - [ 1, 0, 4, 0, 0, 0 ], - [ 0, 0, 2, 0, 0, 0 ], - [ 0, 0, 0, 2, 0, 0 ], - [ 1, 1, 0, 3, 0, 0 ], - [ 1, 0, 0, 3, 1, 0 ], - [ 1, 1, 0, 3, 0, 0 ], - [ 1, 0, 0, 3, 1, 0 ], - [ 1, 0, 0, 0, 0, 0 ], - [ 0, 1, 2, 2, 0, 0 ] - ], - "nSpecies": [ - 0.0, - 0.0, - 0.0, - 0.0, - 0.0, - 0.0, - 0.0, - 0.0, - 0.0, - 0.0, - 0.0, - 0.0, - 0.0, - 0.0, - 0.0, - 0.0, - 0.0, - 0.0, - 0.0, - 0.0, - 0.0, - 0.0, - 0.0, - 0.0, - 0.0, - 0.0, - 0.0 - ], - - "csphases": [ - "aq_gen", - "gas_gen", - "Str-Arag", - "Cal-Sr_cal", - "Graphite", - "Portlandite" - ], - "aggrstates": [ - "aqueous", - "gaseous", - "cryst", - "cryst", - "cryst", - "cryst", - ], - "ncinph": [ - 17, - 4, - 2, - 2, - 1, - 1 - ], - "ssaPhases": [ - 0, - 0, - 0, - 0, - 0, - 0 - ], - "nPhases": [ - 0, - 0, - 0, - 0, - 0, - 0 - ], - - "phasemodels": [ - { - "symbol": "aq_gen", - "aggrstate": "aqueous", - "mixmodel": "H", - "eosmodel": "N", - "ratemodel": "none", - "Ncomps": 17, - "NParams": 2, - "NPcoefs": 4, - "MaxOrder": 0, - "NPperDC": 0, - "NSublat": 0, - "NMoiet": 0, - "NDQFpDC": 0, - - "arIPx" : [ ], - "arIPc": [ - [ 0.0642049834132195, 3.72000002861023, 0, 0.5, 0, 0, 0, 0 ] - ] - }, - - - { - "symbol": "gas_gen", - "aggrstate": "gaseous", - "mixmodel": "I", - "eosmodel": "N", - "ratemodel": "none", - "Ncomps": 4, - "NParams": 0, - "NPcoefs": 0, - "MaxOrder": 0, - "NPperDC": 0, - "NSublat": 0, - "NMoiet": 0, - "NDQFpDC": 0 - }, - { - "symbol": "Str-Arag", - "aggrstate": "cryst", - "mixmodel": "K", - "eosmodel": "N", - "ratemodel": "none", - "Ncomps": 2, - "NParams": 1, - "NPcoefs": 16, - "MaxOrder": 2, - "NPperDC": 0, - "NSublat": 0, - "NMoiet": 0, - "NDQFpDC": 0, - - "arIPx": [ - [ 1, 0 ] - ], - "arIPc": [ - [ 6212.96, 3.15903, 0, 0, - 138.87, 0.51069, 0, 0, - 2429.75, -4.8891, 0, 0, - 0, 0, 0, 0 ] - ] - }, - { - "symbol": "Cal-Sr_cal", - "aggrstate": "cryst", - "mixmodel": "K", - "eosmodel": "N", - "ratemodel": "none", - "Ncomps": 2, - "NParams": 1, - "NPcoefs": 16, - "MaxOrder": 2, - "NPperDC": 0, - "NSublat": 0, - "NMoiet": 0, - "NDQFpDC": 0, - - "arIPx": [ - [ 0, 1 ] - ], - - "arIPc": [ - [ 2798.65, 3.74635, 0, 0, - -807.403, 0.25327, 0, 0, - 2991.92, -4.27231, 0, 0, - 0, 0, 0, 0 ] - ] - }, - { - "symbol": "Graphite", - "aggrstate": "cryst", - "mixmodel": "N", - "eosmodel": "N", - "ratemodel": "none", - "Ncomps": 1, - "NParams": 0, - "NPcoefs": 0, - "MaxOrder": 0, - "NPperDC": 0, - "NSublat": 0, - "NMoiet": 0, - "NDQFpDC": 0 - }, - { - "symbol": "Portlandite", - "aggrstate": "cryst", - "mixmodel": "N", - "eosmodel": "N", - "ratemodel": "none", - "Ncomps": 1, - "NParams": 0, - "NPcoefs": 0, - "MaxOrder": 0, - "NPperDC": 0, - "NSublat": 0, - "NMoiet": 0, - "NDQFpDC": 0 - } - ], - - "thermodatabases": [ - "PSI-Nagra", - "Cemdata-14" - ] -} diff --git a/Resources/files/TestRealLip/configfiles.json b/Resources/files/TestRealLip/configfiles.json deleted file mode 100644 index cea74c9b..00000000 --- a/Resources/files/TestRealLip/configfiles.json +++ /dev/null @@ -1,12 +0,0 @@ -{ - "cheminode_file_name" : "cheminode.0000001.json", - "chemsystem_file_name" : "chemisystem.json", - "host_name" : "localhost", - "io_file_format" : "-j", - "numsettings_file_name" : "numericsettings.json", - "pipe_name" : "pipe", - "port" : 9090, - "protocol" : "-b", - "thermodata_file_name" : "thermodata.json", - "transport" : "-s" -} diff --git a/Resources/files/TestRealLip/numsettings.json b/Resources/files/TestRealLip/numsettings.json deleted file mode 100644 index 20839a39..00000000 --- a/Resources/files/TestRealLip/numsettings.json +++ /dev/null @@ -1,57 +0,0 @@ -{ - "Type": "NumMethods", - "MeqsID": "IPM3-Karpov", - "MkmID": "KKMC", - "MethodEQS": { - # IPM text input file for the internal GEM IPM-3 kernel data - # # (1) Numerical controls and tolerances of GEM IPM-3 kernel - "pa_PE": 1, # PE: Flag for using electroneutrality condition in GEM IPM calculations (1 or 0) - "pa_DB": 1e-17, # DB: Minimum amount of IC in the bulk composition, moles (except charge Zz) { 1e-17 } - "pa_DHB": 1e-13, # DHB: Maximum allowed relative mass balance residual for ICs { 1e-13 } - "pa_EPS": 1e-10, # EPS: Tolerance of the SolveSimplex() balance residual for ICs { 1e-10 } - "pa_DK": 3e-06, # DK: Tolerance for the Dikin's criterion of IPM convergence { 1e-6 } - "pa_DS": 1e-20, # DS: Cutoff minimum amount of stable phase in GEM IPM primal solution, moles { 1e-20 } - "pa_DF": 0.01, # DF: Tolerance DF of the stability criterion for a lost phase to be inserted to mass balance { 0.01 } - "pa_DFM": 0.01, # DFM: Tolerance for stability criterion for a phase to be eliminated from mass balance { 0.01 } - "pa_DP": 130, # DP: Maximal number of iterations in MassBalanceRefinement MBR() procedure { 130 } - "pa_IIM": 7000, # IIM: Maximum allowed number of iterations in one main GEM IPM descent run { 7000 } - "pa_PD": 2, # PD: Mode of calculation of DC activity coefficients { 2 } - "pa_PRD": -5, # PRD: Disable (0) or activate (-4 or less- max.dec.exp.for DC amount correction) SpeciationCleanup() { -5 } - "pa_AG": 1, # AG: Smoothing parameter 1 for non-ideal primal chemical potential increments (-1 to +1) { 1.0 } - "pa_DGC": 0, # DGC: Smoothing parameter 2- exponent in smoothing function (-1 to +1) { 0 or 0.001 for adsorption } - "pa_PSM": 1, # PSM: Level of diagnostic messages { 0- disabled (no ipmlog file); 1- default; 2-including warnings } - "pa_GAR": 1, # GAR: Activity coefficient for major (M) species in solution phases at Simplex LP AIA { 1 } - "pa_GAH": 1000, # GAH: Activity coefficient for minor (J) species in solution phases at Simplex LP AIA { 1000 } - # X*Min: Cutoff amounts for elimination of unstable species ans phases from mass balance - "pa_XwMin": 1e-13, # XwMin: Cutoff mole amount of water-solvent for aqueous phase elimination { 1e-13 } - "pa_ScMin": 1e-13, # ScMin: Cutoff mole amount of solid sorbent for sorption phase elimination { 1e-13 } - "pa_DcMin": 1e-33, # DcMin: Cutoff mole amount for elimination of DC (species) in multi-component phase { 1e-33 } - "pa_PhMin": 1e-20, # PhMin: Cutoff mole amount for elimination of solution phases other than aqueous { 1e-20 } - "pa_ICmin": 1e-05, # ICmin: Cutoff effective molal ionic strength for calculation of aqueous activity coefficients { 1e-5 } - "pa_PC": 2, # PC: Mode of Phase Selection: 1 old (Select-2), 2 new (PSSC), default { 2 } - # DFY: Insertion mole amounts used after the LPP AIA and in PhaseSelection() algorithm - "pa_DFYw": 1e-05, # DFYw: Insertion mole amount for water-solvent at Simplex()->MBR() bridge { 1e-5 } - "pa_DFYaq": 1e-05, # DFYaq: Insertion mole amount for aqueous species at Simplex()->MBR() bridge { 1e-5 } - "pa_DFYid": 1e-05, # DFYid: Insertion mole amount for DCs of ideal solution phases at Simplex()->MBR() bridge { 1e-5 } - "pa_DFYr": 1e-05, # DFYr: Insertion mole amount for major DCs in solution phases at Simplex()->MBR()bridge { 1e-5 } - "pa_DFYh": 1e-05, # DFYh: Insertion mole amount for junior DCs in solution phases Simplex()->MBR() bridge{ 1e-5 } - "pa_DFYc": 1e-05, # DFYc: Insertion mole amount for single-component phase at Simplex()->MBR() bridge { 1e-5 } - "pa_DFYs": 1e-06, # DFYs: Insertion mole amount for single-component phase in PSSC() algorithm { 1e-6 } - # Tolerances and controls of the high-precision IPM-3 algorithm - 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(1997) with new V from the sum of a1 values of ions" - }, - { - "Name": "Be+2", - "Symbol": "Be(+2)", - "G0": -349364, - "H0": -382836, - "S0": -233.0488, - "V0": -2.54001908596943, - "Cp0": -5.44062104945868, - "HKF" : [ -0.141867869300787, - -141.867869300787, - 9.97861011754209, - -23871.3534754033, - 22.9153609105802, - -32994.7918445859, - 190070], - "Z": 2, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for cations" - }, - { - "Name": "BENZENE,AQ", - "Symbol": "C6H6(0)", - "G0": 133888, - "H0": 51170.32, - "S0": 149.3688, - "V0": 8.3, - "Cp0": 372.868746288537, - "HKF" : [ 1.75199163037399, - 1751.99163037399, - -5.55713754088126, - -32915.1521513649, - 66.9, - 98000, - -25000], - "Z": 0, - "Comments": "Plyasunov & Shock (2001) for c1, c2 & omega; a1 predicted with new correlation for complex species from Sverjensky et al. (2014)" - }, - { - "Name": "BO(OH),aq", - "Symbol": "BO(OH)(0)", - "G0": -731589.136, - "H0": -788704.92, - "S0": 100.416, - "V0": 2.04884587925363, - "Cp0": 15.722369347697, - "HKF" : [ 0.554, - 554, - 3.1, - -28400, - 25, - -100000, - 10000], - "Z": 0, - "Comments": "Revised May, 2013" - }, - { - "Name": "BO2-", - "Symbol": "BO2(-)", - "G0": -678812.16, - "H0": -772366.4, - "S0": -37.2376, - "V0": -1.60183193119584, - "Cp0": -37.656138307481, - "HKF" : [ -0.0855, - -85.5, - 3.7, - -26717, - 17.102, - -48679, - 175950], - "Z": -1, - "Comments": "revised a1 - a4 using delkappan for BO2- instead of B(OH)4- used by Shock and Helgeson (1988); Shock et al. 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(1997) with new V from the sum of a1 values of ions" - }, - { - "Name": "CaCl2,aq", - "Symbol": "CaCl(0)", - "G0": -811696, - "H0": -883075.04, - "S0": 25.104, - "V0": 3.33, - "Cp0": 124.558218201251, - "HKF" : [ 0.796936611816846, - 796.936611816846, - 2.06731648018082, - -29156.0765209374, - 23.2636471809872, - 30295.7520258005, - -3800], - "Z": 0, - "Comments": "Sverjensky et al. (1997) with new V from the sum of a1 values of ions" - }, - { - "Name": "CaCO3,aq", - "Symbol": "CaCO3(0)", - "G0": -1099346, - "H0": -1202439.76, - "S0": 0, - "V0": 2.15257093021584, - "Cp0": 58.6117830712104, - "HKF" : [ 0.666, - 666, - 3.12, - -28600, - 32.8, - -1800, - 200000], - "Z": 0, - "Comments": "Facq et al. (2014)" - }, - { - "Name": "CaSO4,aq", - "Symbol": "CaSO4(0)", - "G0": -1309299.12, - "H0": -1447245.6, - "S0": 20.92, - "V0": 0.47, - "Cp0": -104.6, - "HKF" : [ 0.241496011816846, - 241.496011816846, - 6.50154407319332, - -26969.8744875043, - -8.83502404150842, - -81271, - -3800], - "Z": 0, - "Comments": "Sverjensky et al. (1997) revised using exptl V and pred. a1 from new correlation" - }, - { - "Name": "Cd+2", - "Symbol": "Cd(+2)", - "G0": -77655.04, - "H0": -75897.76, - "S0": -72.8016, - "V0": -1.55999436407579, - "Cp0": -14.6441262223884, - "HKF" : [ 0.0541960607797426, - 54.1960607797426, - 8.55507242361216, - -24102.3702939566, - 15.6572108827406, - -37475.5614519611, - 125280], - "Z": 2, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for cations" - }, - { - "Name": "Ce+3", - "Symbol": "Ce(+3)", - "G0": -676134.4, - "H0": -700401.6, - "S0": -205.016, - "V0": -3.97998059487303, - "Cp0": -161.500575556487, - "HKF" : [ -0.768664331746466, - -768.664331746466, - 13.5863571312258, - -26731.8422726747, - 4.04436014311644, - -108973.311761129, - 222510], - "Z": 3, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for cations" - }, - { - "Name": "Ce+4", - "Symbol": "Ce(+4)", - "G0": -507519.2, - "H0": -576136.8, - "S0": -418.8184, - "V0": -5.33000709261696, - "Cp0": 0.417270788924628, - "HKF" : [ -1.5635482300041, - -1563.5482300041, - 17.6099912644607, - -32464.2892407186, - 40.2793758897062, - -30142.8497617018, - 369640], - "Z": 4, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for cations" - }, - { - "Name": "Cl-", - "Symbol": "Cl(-)", - "G0": -131289.736, - "H0": -167079.672, - "S0": 56.73504, - "V0": 1.7785995151106, - "Cp0": -123.115437438856, - "HKF" : [ 0.4032, - 403.2, - 5.563, - -28470, - -4.4, - -57140, - 145600], - "Z": -1, - "Comments": "Shock & Helgeson (1988)" - }, - { - "Name": "CN-", - "Symbol": "CN(-)", - "G0": 172380.8, - "H0": 150624, - "S0": 94.14, - "V0": 2.41998650625684, - "Cp0": -136.818752077839, - "HKF" : [ 0.50522444349362, - 505.22444349362, - 3.70835804037863, - -30632.3972631862, - -1.11332719480748, - -96956.8503782405, - 129000], - "Z": -1, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for cations" - }, - { - "Name": "CO,aq", - "Symbol": "CO(0)", - "G0": -120005.488, - "H0": -120959.44, - "S0": 102.63352, - "V0": 3.38, - "Cp0": 269.868, - "HKF" : [ 0.790650624735742, - 790.650624735742, - 2.1174991592366, - -29131.3350134947, - 40.5450119599561, - 101040.5, - -37150], - "Z": 0, - "Comments": "Shock & McKibben (1993) for c1, c2 and omega with revised a1 from correlation for complex species" - }, - { - "Name": "Co+2", - "Symbol": "Co(+2)", - "G0": -54392, - "H0": -58157.6, - "S0": -112.968, - "V0": -2.44002626148702, - "Cp0": -32.6370457008829, - "HKF" : [ -0.142985946929835, - -142.985946929835, - 9.98672800872703, - -23870.0360748154, - 15.2015013179926, - -46235.4985881211, - 147690], - "Z": 2, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for cations" - }, - { - "Name": "Co+3", - "Symbol": "Co(+3)", - "G0": 133888, - "H0": 92048, - "S0": -305.432, - "V0": -4.38998456233669, - "Cp0": -135.141695623859, - "HKF" : [ -0.875453432572538, - -875.453432572538, - 14.2438768696871, - -27055.6503458375, - 12.2498714875676, - -96140.3675874287, - 271500], - "Z": 3, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for cations" - }, - { - "Name": "CO2,aq", - "Symbol": "CO2(0)", - "G0": -385974, - "H0": -413797.6, - "S0": 117.5704, - "V0": 3.27830094365969, - "Cp0": 217.782237645397, - "HKF" : [ 0.779, - 779, - 2.21, - -29100, - 37, - 65000, - -20000], - "Z": 0, - "Comments": "Facq et al. (2014)" - }, - { - "Name": "CO3-2", - "Symbol": "CO3(-2)", - "G0": -527983.144, - "H0": -675234.84, - "S0": -54.1828, - "V0": -0.500919546000396, - "Cp0": -272.047868520606, - "HKF" : [ 0.58, - 580, - -2, - -108000, - 18, - -200000, - 460000], - "Z": -2, - "Comments": "Facq et al. (2014)" - }, - { - "Name": "Cr+2", - "Symbol": "Cr(+2)", - "G0": -164849.6, - "H0": -163176, - "S0": -101.2528, - "V0": -2.23, - "Cp0": -30.5432, - "HKF" : [ -0.0956149883524283, - -95.6149883524283, - 9.64278741187766, - -23925.8519922964, - 15.0507320204684, - -45216.1, - 142870], - "Z": 2, - "Comments": "Shock et al. (1997) revised with new predicted a1 for cations" - }, - { - "Name": "Cr+3", - "Symbol": "Cr(+3)", - "G0": -206271.2, - "H0": -251040, - "S0": -322.168, - "V0": -3.99999950688365, - "Cp0": -95.8138539816461, - "HKF" : [ -0.729045123518463, - -729.045123518463, - 13.3424145263101, - -26611.708107509, - 17.9916893000701, - -76993.4236521543, - 274030], - "Z": 3, - "Comments": "Shock et al. (1997) revised with new predicted a1 for cations" - }, - { - "Name": "Cr2O7-2", - "Symbol": "Cr2O7(-2)", - "G0": -1301224, - "H0": -1490340.8, - "S0": 261.9184, - "V0": 7.30002007783762, - "Cp0": -85.352530016151, - "HKF" : [ 1.67843789431994, - 1678.43789431994, - -4.96993882695934, - -32625.6462576151, - 15.0818535006395, - -71900.2790733506, - 226540], - "Z": -2, - "Comments": "Shock et al. (1997) revised with new predicted a1 for cations" - }, - { - "Name": "CrO4-2", - "Symbol": "CrO4(-2)", - "G0": -731363.2, - "H0": -882531.12, - "S0": 57.7392, - "V0": 1.97999374382431, - "Cp0": -261.919730952576, - "HKF" : [ 1.00392510999334, - 1003.92510999334, - 1.65948943687678, - -25221.4103098679, - -2.86042447225216, - -157862.847980497, - 300240], - "Z": -2, - "Comments": "Shock et al. (1997) revised with new predicted a1 for cations" - }, - { - "Name": "Cs+", - "Symbol": "Cs(+)", - "G0": -291666.64, - "H0": -258027.28, - "S0": 132.842, - "V0": 2.14201411429416, - "Cp0": -26.2899308678266, - "HKF" : [ 0.61475, - 614.75, - 4.2094, - -27736, - 6.27, - -57360, - 9740], - "Z": 1, - "Comments": "Shock & Helgeson (1988)" - }, - { - "Name": "Cu+", - "Symbol": "Cu(+)", - "G0": 49998.8, - "H0": 71680.288, - "S0": 40.5848, - "V0": -0.800003387748251, - "Cp0": 57.3218472063263, - "HKF" : [ 0.129575874487656, - 129.575874487656, - 7.8447460385269, - -24813.2813075198, - 17.2830167170429, - -2438.5901626944, - 33510], - "Z": 1, - "Comments": "Shock et al. (1997) revised with new predicted a1 for cations" - }, - { - "Name": "Cu+2", - "Symbol": "Cu(+2)", - "G0": 65584.2, - "H0": 65688.8, - "S0": -97.0688, - "V0": -2.46000867753005, - "Cp0": -9.31921670648105, - "HKF" : [ -0.147763742605723, - -147.763742605723, - 10.0214175726653, - -23864.4065275739, - 18.467678426493, - -34883.1043095368, - 147690], - "Z": 2, - "Comments": "Shock et al. (1997) revised with new predicted a1 for cations" - }, - { - "Name": "DIGLYCINE,AQ", - "Symbol": "C4H8O3N2", - "G0": -489611.68, - "H0": -734877.76, - "S0": 226.7728, - "V0": 7.62700141675233, - "Cp0": 158.992181866346, - "HKF" : [ 1.61021814308272, - 1610.21814308272, - -4.42532270900807, - -32357.1348112514, - 24.0074411994697, - 47060.0885424827, - -48080], - "Z": 0, - "Comments": "Shock & Helgeson (1990) revised with new predicted a1 for complex species" - }, - { - "Name": "DKP,AQ", - "Symbol": "C4H6O2N2", - "G0": -240328.96, - "H0": -415471.2, - "S0": 223.844, - "V0": 7.67300032759005, - "Cp0": 71.1285705975924, - "HKF" : [ 1.61966002562865, - 1619.66002562865, - -4.50069972702794, - -32394.2978541067, - 11.7978573326761, - 4283.27779811085, - -47020], - "Z": 0, - "Comments": "Shock & Helgeson (1990) revised with new predicted a1 for complex species" - }, - { - "Name": "Dy+3", - "Symbol": "Dy(+3)", - "G0": -664000.8, - "H0": -696636, - "S0": -230.9568, - "V0": -4.07001092365793, - "Cp0": -132.63300115158, - "HKF" : [ -0.78786765811433, - -787.86765811433, - 13.7045954723422, - -26790.0709876034, - 9.50759957967865, - -94918.9979315892, - 237920], - "Z": 3, - "Comments": "Shock et al. (1997) revised with new predicted a1 for cations" - }, - { - "Name": "Er+3", - "Symbol": "Er(+3)", - "G0": -669021.6, - "H0": -705004, - "S0": -243.9272, - "V0": -4.29999539941109, - "Cp0": -143.510872601213, - "HKF" : [ -0.869899283827142, - -869.899283827142, - 14.2096789749375, - -27038.8089435839, - 8.28148793022524, - -100214.940604367, - 241150], - "Z": 3, - "Comments": "Shock et al. (1997) revised with new predicted a1 for cations" - }, - { - "Name": "ETHANE,AQ", - "Symbol": "C2H6", - "G0": -16259.024, - "H0": -103135.6, - "S0": 112.17304, - "V0": 5.12000166666145, - "Cp0": 369.447382321756, - "HKF" : [ 1.12692153940967, - 1126.92153940967, - -0.567039508939056, - -30454.8899668859, - 54.1754616412644, - 149521.188764201, - -40600], - "Z": 0, - "Comments": "Shock & Helgeson (1990) revised with new predicted a1 for complex species" - }, - { - "Name": "ETHANOL,AQ", - "Symbol": "C2H5OH", - "G0": -181292.72, - "H0": -287231.6, - "S0": 150.2056, - "V0": 5.5080070558532, - "Cp0": 260.246438700027, - "HKF" : [ 0.92333, - 923.33, - 12.1445, - -31906, - 60.0175, - 1507, - -20370], - "Z": 0, - "Comments": "Plyasunov & Shock (2001)" - }, - { - "Name": "ETHYLENE,AQ", - "Symbol": "C2H4", - "G0": 81378.8, - "H0": 35856.88, - "S0": 119.6624, - "V0": 4.6, - "Cp0": 279.9096, - "HKF" : [ 1.03053670166374, - 1030.53670166374, - 0.202425861581267, - -30075.521357043, - 42.5181492402495, - 105929.3, - -31000], - "Z": 0, - "Comments": "Plyasunov & Shock (2001) for c1, c2 & omega; a1 predicted with new correlation for complex species from Sverjensky et al. (2014)" - }, - { - "Name": "Eu+2", - "Symbol": "Eu(+2)", - "G0": -540572.8, - "H0": -527811.6, - "S0": -10.0416, - "V0": -1.53000014248061, - "Cp0": -47.6982140005252, - "HKF" : [ 0.0519252174409929, - 51.9252174409929, - 8.57156006153919, - -24099.6946207548, - 9.55412331314926, - -53568.098929032, - 109290], - "Z": 2, - "Comments": "Shock et al. (1997) revised with new predicted a1 for cations" - }, - { - "Name": "Eu+3", - "Symbol": "Eu(+3)", - "G0": -574463.2, - "H0": -605424.8, - "S0": -221.752, - "V0": -4.12998099542058, - "Cp0": -153.133375780634, - "HKF" : [ -0.815784988569341, - -815.784988569341, - 13.8764875069911, - -26874.7224821151, - 6.05473931220669, - -104899.701354004, - 231610], - "Z": 3, - "Comments": "Shock et al. (1997) revised with new predicted a1 for cations" - }, - { - "Name": "F-", - "Symbol": "F(-)", - "G0": -281750.56, - "H0": -335347.6, - "S0": -13.1796, - "V0": -0.13198710849504, - "Cp0": -113.887166220321, - "HKF" : [ 0.0687, - 68.7, - 7.6033, - -28352, - 4.46, - -74880, - 178700], - "Z": -1, - "Comments": "Shock & Helgeson (1988)" - }, - { - "Name": "Fe(CH3COO)+", - "Symbol": "Fe(CH3COO)(+)", - "G0": -468189.6, - "H0": -581827.04, - "S0": -6.276, - "V0": 2.52, - "Cp0": 339.739969043908, - "HKF" : [ 0.669058129426936, - 669.058129426936, - 3.08820385349472, - -28652.7496157145, - 59.0576009255934, - 135057.995445134, - 57560], - "Z": 1, - "Comments": "Sverjensky et al. (1997) with revised volume increased in order that a1 of the complex is the sum of the a1 values of the ions" - }, - { - "Name": "Fe(CH3COO)2,aq", - "Symbol": "Fe(CH3COO)2(0)", - "G0": -844331.2, - "H0": -1084074.4, - "S0": 48.24152, - "V0": 6.69, - "Cp0": 770.693002442526, - "HKF" : [ 1.44948221181685, - 1449.48221181685, - -3.14212572699472, - -31724.4817070685, - 113.769098687703, - 344869.498560092, - -3800], - "Z": 0, - "Comments": "Sverjensky et al. (1997) with revised volume increased in order that a1 of the complex is the sum of the a1 values of the ions" - }, - { - "Name": "Fe+2", - "Symbol": "Fe(+2)", - "G0": -91504.08, - "H0": -92257.2, - "S0": -105.8552, - "V0": -2.22001111114365, - "Cp0": -33.0546143692942, - "HKF" : [ -0.0915318442049491, - -91.5318442049491, - 9.61314142038246, - -23930.6630504561, - 14.96336131819, - -46438.7938504427, - 145740], - "Z": 2, - "Comments": "Shock et al. (1997) revised with new predicted a1 for cations" - }, - { - "Name": "Fe+3", - "Symbol": "Fe(+3)", - "G0": -17238.08, - "H0": -49580.4, - "S0": -277.3992, - "V0": -3.69999885120989, - "Cp0": -77.8219147097519, - "HKF" : [ -0.632714052089309, - -632.714052089309, - 12.7492867595078, - -26319.6110827762, - 19.0460958402282, - -68233.9637341693, - 258120], - "Z": 3, - "Comments": "Shock et al. (1997) revised with new predicted a1 for cations" - }, - { - "Name": "FeCl+", - "Symbol": "FeCl(+)", - "G0": -221877.52, - "H0": -256311.84, - "S0": -42.09104, - "V0": 0.58, - "Cp0": 86.0650510969312, - "HKF" : [ 0.298272024596393, - 298.272024596393, - 6.04828631261857, - -27193.3436299992, - 24.6736647838752, - 11555.1732993426, - 70030], - "Z": 1, - "Comments": "Sverjensky et al. (1997) with revised volume increased in order that a1 of the complex is the sum of the a1 values of the ions" - }, - { - "Name": "FeCl++", - "Symbol": "FeCl(++)", - "G0": -157205.432, - "H0": -212861, - "S0": -120.0808, - "V0": -2.28, - "Cp0": 12.9687897542679, - "HKF" : [ -0.219168750064997, - -219.168750064997, - 10.1791513605702, - -25156.7080766279, - 21.733628544405, - -24032.0839556779, - 149253.28], - "Z": 2, - "Comments": "Sverjensky et al. (1997) with revised volume increased in order that a1 of the complex is the sum of the a1 values of the ions" - }, - { - "Name": "FeCl2,aq", - "Symbol": "FeCl2(0)", - "G0": -307440.32, - "H0": -328402.16, - "S0": 179.912, - "V0": 2.84, - "Cp0": 117.73806164904, - "HKF" : [ 0.701773711816846, - 701.773711816846, - 2.82702680206058, - -28781.5174312932, - 22.3083335789974, - 26975.3268592481, - -3800], - "Z": 0, - "Comments": "Sverjensky et al. (1997) with revised volume increased in order that a1 of the complex is the sum of the a1 values of the ions" - }, - { - "Name": "FORMATE,AQ", - "Symbol": "HCOO-", - "G0": -350878.608, - "H0": -425429.12, - "S0": 90.7928, - "V0": 2.6159971565219, - "Cp0": -84.4225118879878, - "HKF" : [ 0.526836690949239, - 526.836690949239, - 3.47058058408901, - -30966.4185596819, - 17, - -124000, - 130030], - "Z": -1, - "Comments": "Shock & Helgeson (1990) revised with new predicted a1 for ions" - }, - { - "Name": "FORMIC-ACID,AQ", - "Symbol": "HCOOH", - "G0": -372300.688, - "H0": -425429.12, - "S0": 162.7576, - "V0": 3.46900143097129, - "Cp0": 79.596938471357, - "HKF" : [ 0.809245050207837, - 809.245050207837, - 1.96905499706232, - -29204.5222648005, - 22.1924, - -31196, - -34420], - "Z": 0, - "Comments": "Shock & Helgeson (1990) revised with new predicted a1 for complex species" - }, - { - "Name": "Ga+3", - "Symbol": "Ga(+3)", - "G0": -158992, - "H0": -211710.4, - "S0": -330.536, - "V0": -4.49000212783272, - "Cp0": -128.866431090606, - "HKF" : [ -0.911260070398471, - -911.260070398471, - 14.4643447915664, - -27164.2239578556, - 13.2449426450721, - -93085.2256528594, - 272760], - "Z": 3, - "Comments": "Shock et al. (1997) revised with new predicted a1 for cations" - }, - { - "Name": "Gd+3", - "Symbol": "Gd(+3)", - "G0": -663582.4, - "H0": -687012.8, - "S0": -205.8528, - "V0": -4.04000916947148, - "Cp0": -150.205564495927, - "HKF" : [ -0.781591314174929, - -781.591314174929, - 13.6659508916349, - -26771.0397304639, - 6.5606574503928, - -103474.282714676, - 232650], - "Z": 3, - "Comments": "Shock et al. (1997) revised with new predicted a1 for cations" - }, - { - "Name": "GLUTAMATE", - "Symbol": "C5H8NO4-", - "G0": -699606.64, - "H0": -979683.6, - "S0": 183.51024, - "V0": 8.07594495626225, - "Cp0": 30.6922458731237, - "HKF" : [ 1.84757778799145, - 1847.57778799145, - -6.32022683903014, - -33291.377173719, - 34.8797444674277, - -15403.3363184625, - 265000], - "Z": -1, - "Comments": "Shock & Helgeson (1990) revised with new predicted a1 for complex species" - }, - { - "Name": "GLUTAMIC-ACID,AQ", - "Symbol": "C5H9NO4", - "G0": -724041.2, - "H0": -982486.88, - "S0": 256.0608, - "V0": 9.02505798297414, - "Cp0": 181.991844265697, - "HKF" : [ 1.91199133264902, - 1911.99133264902, - -6.8344570142898, - -33544.9074743686, - 33.040508365119, - 58257.5819238109, - 15000], - "Z": 0, - "Comments": "Shock & Helgeson (1990) revised with new predicted a1 for complex species" - }, - { - "Name": "GLUTAMINE,AQ", - "Symbol": "C5H10N2O3", - "G0": -528355.52, - "H0": -802742.24, - "S0": 261.12344, - "V0": 9.37168584488672, - "Cp0": 183.157831948135, - "HKF" : [ 1.98074889406618, - 1980.74889406618, - -7.38336661157929, - -33815.5357298186, - 33.4802157500622, - 58825.2484890894, - 18000], - "Z": 0, - "Comments": "Shock & Helgeson (1990) revised with new predicted a1 for complex species" - }, - { - "Name": "GLUTARATE-", - "Symbol": "C5H7O4-", - "G0": -714878.24, - "H0": -935416.88, - "S0": 221.3336, - "V0": 8.59090594824493, - "Cp0": 84.135200823759, - "HKF" : [ 1.86019046386216, - 1860.19046386216, - -6.42091712952679, - -33341.0203896373, - 25.5789043631804, - 10615.616653441, - 82790], - "Z": -1, - "Comments": "Shock & Helgeson (1990) revised with new predicted a1 for complex species" - }, - { - "Name": "GLUTARIC-ACID,AQ", - "Symbol": "C5H8O4", - "G0": -739647.52, - "H0": -934872.96, - "S0": 306.2688, - "V0": 9.90911049024688, - "Cp0": 268.216398490898, - "HKF" : [ 2.07169180046044, - 2071.69180046044, - -8.10938762070644, - -34173.4850170789, - 42.8149533824839, - 100236.410068346, - -10000], - "Z": 0, - "Comments": "Shock & Helgeson (1990) revised with new predicted a1 for complex species" - }, - { - "Name": "GLYCINE,AQ", - "Symbol": "C2H5NO2", - "G0": -380534.8, - "H0": -522079.52, - "S0": 164.4312, - "V0": 4.32907614662759, - "Cp0": 39.7238556715915, - "HKF" : [ 1.08, - 1080, - 7.6, - -35000, - 28, - -82000, - 20000], - "Z": 0, - "Comments": "Plyasunov & Shock (2001)" - }, - { - "Name": "GLYCOLATE,AQ", - "Symbol": "C2H3O3-", - "G0": -506975.28, - "H0": -647264.8, - "S0": 109.6208, - "V0": 3.98499610916751, - "Cp0": 27.1948596047795, - "HKF" : [ 0.673821478709146, - 673.821478709146, - 1.85188150744711, - -33244.1087899913, - 21.3389561922355, - -17106.0552067553, - 123340], - "Z": -1, - "Comments": "Shock & Helgeson (1990) revised with new predicted a1 for complex species" - }, - { - "Name": "GLYCOLIC-ACID,AQ", - "Symbol": "C2H4O3", - "G0": -528857.6, - "H0": -648059.76, - "S0": 180.3304, - "V0": 5.17501133308878, - "Cp0": 190.373969403058, - "HKF" : [ 1.1426077661345, - 1142.6077661345, - -0.692266759834068, - -30516.6306116329, - 30.0531726063325, - 62338.4588131042, - -30170], - "Z": 0, - "Comments": "Shock & Helgeson (1990) revised with new predicted a1 for complex species" - }, - { - "Name": "H+", - "Symbol": "H(+)", - "G0": 0, - "H0": 0, - "S0": 0, - "V0": 0, - "Cp0": 0, - "HKF" : [ 0, - 0, - 0, - 0, - 0, - 0, - 0], - "Z": 1, - "Comments": "Perfectly known, by convention!" - }, - { - "Name": "H2,aq", - "Symbol": "H2(0)", - "G0": 17723.424, - "H0": -4184, - "S0": 57.7392, - "V0": 2.51999807716819, - "Cp0": 166.941841205453, - "HKF" : [ 0.51427, - 514.27, - 3.8729, - -29764, - 27.6251, - 50930, - -20900], - "Z": 0, - "Comments": "Shock et al. 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(1997) revised with new predicted a1 for complex species" - }, - { - "Name": "H2P2O7-2", - "Symbol": "H2P2O7(-2)", - "G0": -2009993.6, - "H0": -2278606.4, - "S0": 163.176, - "V0": 5.24000274417688, - "Cp0": -84.9337099204506, - "HKF" : [ 1.29545682448853, - 1295.45682448853, - -1.91250077247097, - -31118.2411568144, - 18.4239729019815, - -71696.3745477911, - 262180], - "Z": -2, - "Comments": "Shock et al. (1997) revised with new predicted a1 for complex species" - }, - { - "Name": "H2PO4-", - "Symbol": "H2PO4(-)", - "G0": -1130265.76, - "H0": -1296286.88, - "S0": 90.3744, - "V0": 3.12997044192027, - "Cp0": -29.2885125292996, - "HKF" : [ 0.822281071224164, - 822.281071224164, - 1.86498503153642, - -29255.8317579376, - 14.0435507063909, - -44605.2495272904, - 130030], - "Z": -1, - "Comments": "Shock et al. (1997) revised with new predicted a1 for complex species" - }, - { - "Name": "H2S,aq", - "Symbol": "H2S(0)", - "G0": -27919.832, - "H0": -37660.184, - "S0": 125.52, - "V0": 3.4920046426392, - "Cp0": 179.213719934967, - "HKF" : [ 0.825425673796553, - 825.425673796553, - 1.83988084668652, - -29268.208844773, - 30.3481619258524, - 56905.0390792372, - -10000], - "Z": 0, - "Comments": "Shock et al. (1989) with revised prediction of a1 using new correlation" - }, - { - "Name": "H2VO4-", - "Symbol": "H2VO4(-)", - "G0": -1020896, - "H0": -1174030.4, - "S0": 121.336, - "V0": 2.90001359512636, - "Cp0": 2.50950751131463, - "HKF" : [ 0.77232096663362, - 772.32096663362, - 2.2638296142428, - -29059.1898807569, - 17.4795476551971, - -29124.2345122973, - 118980], - "Z": -1, - "Comments": "Shock et al. 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(2014)" - }, - { - "Name": "HCrO4-", - "Symbol": "HCrO4(-)", - "G0": -764835.2, - "H0": -878221.6, - "S0": 184.096, - "V0": 4.40002332549264, - "Cp0": 85.3552268049261, - "HKF" : [ 1.05272091346053, - 1052.72091346053, - 0.0253234962184035, - -30162.8379286805, - 26.9870796962219, - 11209.592017599, - 96220], - "Z": -1, - "Comments": "Shock et al. (1997) revised with new predicted a1 for complex species" - }, - { - "Name": "He,aq", - "Symbol": "He(0)", - "G0": 19489.072, - "H0": -627.6, - "S0": 58.65968, - "V0": 1.30001571838305, - "Cp0": 156.062618014204, - "HKF" : [ 0.34722, - 347.22, - 5.4762, - -28078, - 26.0707, - 45634, - -21230], - "Z": 0, - "Comments": "Shock et al. 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(1997) revised using published estimated V and pred. a1 from new correlation" - }, - { - "Name": "HSO4-", - "Symbol": "HSO4(-)", - "G0": -755755.92, - "H0": -889100, - "S0": 125.52, - "V0": 3.51999336118176, - "Cp0": 22.1756595878648, - "HKF" : [ 0.892007754821677, - 892.007754821677, - 1.30833867839381, - -29530.2744570586, - 20.0960342103181, - -19549.6762474951, - 117480], - "Z": -1, - "Comments": "Shock et al. (1997) revised with new predicted a1 for complex species" - }, - { - "Name": "HSO5-", - "Symbol": "HSO5(-)", - "G0": -637516.08, - "H0": -775629.92, - "S0": 212.1288, - "V0": 5.06998407736731, - "Cp0": 122.171720973258, - "HKF" : [ 1.17798468120535, - 1177.98468120535, - -0.974689926168759, - -30655.8733743415, - 31.2126254681266, - 29133.874670776, - 86110], - "Z": -1, - "Comments": "Shock et al. (1997) revised with new predicted a1 for complex species" - }, - { - "Name": "H-SUCCINATE,AQ", - "Symbol": "C4H504-", - "G0": -719899.04, - "H0": -909392.4, - "S0": 189.1168, - "V0": 6.99900771138804, - "Cp0": 38.9111259822668, - "HKF" : [ 1.5566254786236, - 1556.6254786236, - -3.99747845072436, - -32146.1952580073, - 20.3194113963877, - -11401.9360358801, - 94460], - "Z": -1, - "Comments": "Shock & Helgeson (1990) revised with new predicted a1 for complex species" - }, - { - "Name": "HVO4-2", - "Symbol": "HVO4(-2)", - "G0": -974872, - "H0": -1158968, - "S0": 16.736, - "V0": 1.73998621681699, - "Cp0": -202.085577192435, - "HKF" : [ 0.641183487247775, - 641.183487247775, - 3.31073441301123, - -28543.0356347536, - 6.90535977071533, - -128732.309928535, - 315270], - "Z": -2, - "Comments": "Shock et al. (1997) revised with new predicted a1 for complex species" - }, - { - "Name": "I-", - "Symbol": "I(-)", - "G0": -51923.44, - "H0": -56902.4, - "S0": 106.692, - "V0": 3.63099204325014, - "Cp0": -118.125086774593, - "HKF" : [ 0.77623, - 776.23, - 1.4609, - -31211, - -6.27, - -49440, - 129340], - "Z": -1, - "Comments": "Shock & Helgeson (1988)" - }, - { - "Name": "In+3", - "Symbol": "In(+3)", - "G0": -97905.6, - "H0": -104600, - "S0": -263.592, - "V0": -4.21998616214774, - "Cp0": -146.022620368412, - "HKF" : [ -0.832232147397517, - -832.232147397517, - 13.9777556278712, - -26924.5938900393, - 8.74776191170459, - -101437.796771141, - 250030], - "Z": 3, - "Comments": "Shock et al. (1997) revised with new predicted a1 for cations" - }, - { - "Name": "K+", - "Symbol": "K(+)", - "G0": -282461.84, - "H0": -252169.68, - "S0": 101.0436, - "V0": 0.906801954096976, - "Cp0": 8.30607332851692, - "HKF" : [ 0.3559, - 355.9, - 5.435, - -27120, - 7.4, - -17910, - 19270], - "Z": 1, - "Comments": "Shock & Helgeson (1988)" - }, - { - "Name": "KCl,aq", - "Symbol": "KCl(0)", - "G0": -413379.2, - "H0": -401714.208, - "S0": 184.096, - "V0": 3.4, - "Cp0": -71.128, - "HKF" : [ 0.831540191401624, - 831.540191401624, - 1.79106705330812, - -29292.2754521143, - -0.111309218863548, - -64975, - 40000], - "Z": 0, - "Comments": "Fitted to Ho & Palmer (1997) data with new a1 pred. from the volume" - }, - { - "Name": "KOH,aq", - "Symbol": "KOH(0)", - "G0": -430115.2, - "H0": -753120, - "S0": 151.8792, - "V0": 2.03, - "Cp0": -27.196, - "HKF" : [ 0.569309729681948, - 569.309729681948, - 3.88452141923995, - -28260.1420995297, - 6.77936476523284, - -43586.5, - 48000], - "Z": 0, - "Comments": "Fitted to Ho & Palmer (1997) data with a1 pred. from the sum of the ions and used to predict the volume" - }, - { - "Name": "Kr,aq", - "Symbol": "Kr(0)", - "G0": 14869.936, - "H0": -15271.6, - "S0": 63.01104, - "V0": 3.35003414046157, - "Cp0": 240.999455001835, - "HKF" : [ 0.62721, - 627.21, - 2.7891, - -30904, - 37.8226, - 86985, - -22810], - "Z": 0, - "Comments": "Shock et al. (1989)" - }, - { - "Name": "KSO4-", - "Symbol": "KSO4(-)", - "G0": -1031648.88, - "H0": -1158884.32, - "S0": 142.256, - "V0": 5.07, - "Cp0": -92.048, - "HKF" : [ 1.18942754016306, - 1189.42754016306, - -1.06604126226705, - -30700.9122165176, - 3.4036819642334, - -75160, - 109960], - "Z": -1, - "Comments": "Revised G, S and Cp to fit Noyes et al. (1906) & Sharygin et al. (2006) with a1 of the complex equal to the sum of the a1 values of the ions" - }, - { - "Name": "La+3", - "Symbol": "La(+3)", - "G0": -686176, - "H0": -709606.4, - "S0": -217.568, - "V0": -3.85999288691227, - "Cp0": -155.642951091605, - "HKF" : [ -0.730525301688857, - -730.525301688857, - 13.3515282500511, - -26616.1963337192, - 4.23929836467658, - -106121.499850287, - 215720], - "Z": 3, - "Comments": "Shock et al. (1997) revised with new predicted a1 for cations" - }, - { - "Name": "LACTATE,AQ", - "Symbol": "C3H5O3-", - "G0": -512665.52, - "H0": -686468.88, - "S0": 133.4696, - "V0": 5.62499039209265, - "Cp0": 111.711106558993, - "HKF" : [ 0.84976664002451, - 849.76664002451, - -0.0855076207025629, - -35969.649042259, - 32.3804135573831, - 24041.0755403129, - 114690], - "Z": -1, - "Comments": "Shock & Helgeson (1990) revised with new predicted a1 for ions" - }, - { - "Name": "LACTIC-ACID,AQ", - "Symbol": "C3H6O3", - "G0": -534715.2, - "H0": -686176, - "S0": 208.3632, - "V0": 6.93799220653643, - "Cp0": 279.071665343352, - "HKF" : [ 1.4871307453602, - 1487.1307453602, - -3.44268381776874, - -31872.6655103199, - 42.8872156672021, - 105521.347587096, - -25720], - "Z": 0, - "Comments": "Shock & Helgeson (1990) revised with new predicted a1 for complex species" - }, - { - "Name": "LEUCINE,AQ", - "Symbol": "C6H13NO2", - "G0": -343088, - "H0": -632076.88, - "S0": 215.476, - "V0": 10.7569952023521, - "Cp0": 397.898201077798, - "HKF" : [ 2.22005602425487, - 2220.05602425487, - -9.29381802598324, - -34757.4433516841, - 57.8483122618736, - 163372.603153794, - -43990], - "Z": 0, - "Comments": "Shock & Helgeson (1990) revised with new predicted a1 for complex species" - }, - { - "Name": "Li+", - "Symbol": "Li(+)", - "G0": -292599.672, - "H0": -278453.568, - "S0": 11.2968, - "V0": -0.0870117831345254, - "Cp0": 59.5509393709128, - "HKF" : [ -0.00237, - -2.37, - 11.58, - -27761, - 19.2, - -2400, - 48620], - "Z": 1, - "Comments": "Shock & Helgeson (1988)" - }, - { - "Name": "Lu+3", - "Symbol": "Lu(+3)", - "G0": -666929.6, - "H0": -702493.6, - "S0": -264.0104, - "V0": -4.50001614483955, - "Cp0": -137.235447969291, - "HKF" : [ -0.939800716704966, - -939.800716704966, - 14.6400746942418, - -27250.7654833094, - 9.56494324858524, - -97159.720725011, - 245540], - "Z": 3, - "Comments": "Shock et al. (1997) revised with new predicted a1 for ions" - }, - { - "Name": "METHANE,AQ", - "Symbol": "CH4", - "G0": -34451.056, - "H0": -87905.84, - "S0": 87.82216, - "V0": 3.60023793740113, - "Cp0": 241.384023070956, - "HKF" : [ 0.832, - 832, - 1.79, - -29300, - 40.9, - 64500, - -40000], - "Z": 0, - "Comments": "Plyasunov & Shock (2001) for c1, c2 & omega; a1 predicted with new correlation for complex species from Sverjensky et al. (2014)" - }, - { - "Name": "METHANOL,AQ", - "Symbol": "CH3OH", - "G0": -175937.2, - "H0": -246312.08, - "S0": 132.2144, - "V0": 3.86884518644431, - "Cp0": 157.873781372877, - "HKF" : [ 0.84, - 840, - -0.24, - -14300, - 34.4, - 9600, - -15000], - "Z": 0, - "Comments": "Plyasunov & Shock (2001)" - }, - { - "Name": "Mg(HCO3)+", - "Symbol": "Mg(HCO3)(+)", - "G0": -1046836.8, - "H0": -1153738, - "S0": -12.552, - "V0": 2.59, - "Cp0": 254.176828604145, - "HKF" : [ 0.683751238884679, - 683.751238884679, - 2.97090491750646, - -28710.5813726548, - 47.2835666929098, - 93401.1797004405, - 59850], - "Z": 1, - "Comments": "Sverjensky et al. (1997) revised V increased so that a1 of the complex is the sum of the a1 values of the ions" - }, - { - "Name": "Mg(HSiO3)+", - "Symbol": "Mg(HSiO3)(+)", - "G0": -1477056.6, - "H0": -1613768.8, - "S0": -99.49552, - "V0": 0.25, - "Cp0": 158.23888, - "HKF" : [ 0.244328589820438, - 244.328589820438, - 6.47893086209047, - -26981.0234524725, - 36.7319427076326, - 46693.34, - 91182.432], - "Z": 1, - "Comments": "Sverjensky et al. (1997) with new a1 from the sum of the ions and V predicted from a1 value" - }, - { - "Name": "Mg+2", - "Symbol": "Mg(+2)", - "G0": -453984.92, - "H0": -465959.528, - "S0": -138.072, - "V0": -2.15431049706471, - "Cp0": -22.3220224247161, - "HKF" : [ -0.08217, - -82.17, - 8.39, - -23900, - 20.8, - -58920, - 153720], - "Z": 2, - "Comments": "Shock & Helgeson (1988)" - }, - { - "Name": "MgCl+", - "Symbol": "MgCl(+)", - "G0": -584504.8, - "H0": -631503.672, - "S0": -79.496, - "V0": 0.12529488954192, - "Cp0": 104.592190148857, - "HKF" : [ 0.321, - 321, - 6.27, - -25800, - 28.6, - 20580, - 84490], - "Z": 1, - "Comments": "Sverjensky et al. (1997) revised V increased so that a1 of the complex is the sum of the a1 values of the ions" - }, - { - "Name": "MgCO3,aq", - "Symbol": "MgCO3(0)", - "G0": -998971.84, - "H0": -1132064.88, - "S0": -100.416, - "V0": 1.79, - "Cp0": -103.7632, - "HKF" : [ 0.497853211816846, - 497.853211816846, - 4.45497749180293, - -27978.8908106273, - -8.7178117141923, - -80863.6, - -3800], - "Z": 0, - "Comments": "Sverjensky et al. (1997) revised volume increased in order that a1 of the complex is the sum of the a1 values of the ions; and Cp revised using isocoulombic reln with CaCO3,aq" - }, - { - "Name": "MgOH+", - "Symbol": "MgOH(+)", - "G0": -624357.4, - "H0": -639963.72, - "S0": -79.9144, - "V0": -0.33, - "Cp0": 128.865752263745, - "HKF" : [ 0.128476732788079, - 128.476732788079, - 7.40380653944396, - -26525.0330811868, - 32.0010245137424, - 32392.8951628223, - 84490], - "Z": 1, - "Comments": "Shock et al. (1997) with revised a1 equal to the sum of the ions used to predict new values of V using new correlation in Sverjensky et al. (2014)" - }, - { - "Name": "MgSO4,aq", - "Symbol": "MgSO4", - "G0": -1211054.616, - "H0": -1370046.616, - "S0": -4.184, - "V0": 3.5, - "Cp0": 83.68, - "HKF" : [ 0.834173273925203, - 834.173273925203, - 1.77004646680304, - -29302.6392072436, - 18.348479084619, - 10394, - 5000], - "Z": 0, - "Comments": "S, Cp, V, omega from fit to Akilan et al. (2006a) and Frantz et al. (1994)" - }, - { - "Name": "Mn+2", - "Symbol": "Mn(+2)", - "G0": -228028, - "H0": -220597.216, - "S0": -73.6384, - "V0": -1.70999746995345, - "Cp0": -17.1540215863475, - "HKF" : [ -0.112878159446875, - -112.878159446875, - 9.33060577388377, - -25575.065512768, - 16.6673015992186, - -38697.5157675406, - 140060], - "Z": 2, - "Comments": "Shock et al. (1997) revised with new predicted a1 for cations" - }, - { - "Name": "MnCl+", - "Symbol": "MnCl(+)", - "G0": -361037.36, - "H0": -369363.52, - "S0": 50.208, - "V0": 0.63, - "Cp0": 103.050176577302, - "HKF" : [ 0.292072375376596, - 292.072375376596, - 6.09777973394466, - -27168.9419464873, - 23.9969094881211, - 19824.4612064924, - 36860], - "Z": 1, - "Comments": "Sverjensky et al. (1997) with revised a1 equal to the sum of the ions used to predict new values of V using new correlation in Sverjensky et al. (2014)" - }, - { - "Name": "MnO4-", - "Symbol": "MnO4(-)", - "G0": -447269.6, - "H0": -541409.6, - "S0": 191.2088, - "V0": 4.19999685425673, - "Cp0": -7.5297722898385, - "HKF" : [ 0.689229404983946, - 689.229404983946, - 1.68221984338678, - -33482.7906778704, - 13.742477467512, - -34011.9049126198, - 93680], - "Z": -1, - "Comments": "Shock et al. (1997) revised with new predicted a1 for ions" - }, - { - "Name": "MnO4-2", - "Symbol": "MnO4(-2)", - "G0": -500824.8, - "H0": -652704, - "S0": 58.576, - "V0": 2.73997969015227, - "Cp0": -248.113062033957, - "HKF" : [ 1.18563774976035, - 1185.63774976035, - 0.340150422986751, - -25435.5173917399, - -0.926495461216696, - -151141.006539955, - 300240], - "Z": -2, - "Comments": "Shock et al. (1997) revised with new predicted a1 for ions" - }, - { - "Name": "MnSO4,aq", - "Symbol": "MnSO4(0)", - "G0": -985917.76, - "H0": -1116082, - "S0": 20.92, - "V0": 2.92, - "Cp0": -89.8713094795125, - "HKF" : [ 0.717310511816846, - 717.310511816846, - 2.70299246379449, - -28842.6699357249, - -6.77194553502511, - -74100.2680233669, - -3800], - "Z": 0, - "Comments": "Sverjensky et al. (1997) with revised a1 equal to the sum of the ions used to predict new values of V using new correlation in Sverjensky et al. (2014)" - }, - { - "Name": "MoO4-2", - "Symbol": "MoO4(-2)", - "G0": -836381.6, - "H0": -997884, - "S0": 27.196, - "V0": 3.04001214628427, - "Cp0": -198.738116647828, - "HKF" : [ 1.26399527211691, - 1263.99527211691, - -0.228770574525159, - -25527.8439380714, - 7.02231527800825, - -127102.583081172, - 311450], - "Z": -2, - "Comments": "Shock et al. (1997) revised with new predicted a1 for ions" - }, - { - "Name": "N2,aq", - "Symbol": "N2(0)", - "G0": 18187.848, - "H0": -10439.08, - "S0": 95.8136, - "V0": 3.33002347170321, - "Cp0": 234.304229812389, - "HKF" : [ 0.782129430494273, - 782.129430494273, - 2.18552608170308, - -29097.7957796361, - 35.7910772638231, - 83726.111885238, - -34680], - "Z": 0, - "Comments": "Shock et al. (1989) + new a1 predicted for complex species" - }, - { - "Name": "Na+", - "Symbol": "Na(+)", - "G0": -261880.744, - "H0": -240299.672, - "S0": 58.40864, - "V0": -0.110680869183899, - "Cp0": 37.9762960742529, - "HKF" : [ 0.1839, - 183.9, - 3.256, - -27260, - 18.18, - -29810, - 33060], - "Z": 1, - "Comments": "Shock & Helgeson (1988)" - }, - { - "Name": "NaCl,aq", - "Symbol": "NaCl(0)", - "G0": -388735.44, - "H0": -402166.08, - "S0": 117.152, - "V0": 2.40000657937439, - "Cp0": 35.5989795988406, - "HKF" : [ 0.616322589597147, - 616.322589597147, - 3.50920546166967, - -28445.1836862342, - 10.8029404495594, - -13014.4700184421, - -3800], - "Z": 0, - "Comments": "Sverjensky et al. (1997) with new predicted a1 value" - }, - { - "Name": "NaCO3-", - "Symbol": "NaCO3(-)", - "G0": -797311.408, - "H0": 0, - "S0": 33.472, - "V0": 2.78, - "Cp0": -4.184, - "HKF" : [ 0.764273247379239, - 764.273247379239, - 2.32807666204339, - -29027.5142340749, - 19.4730190790062, - -32383, - 150794.8], - "Z": -1, - "Comments": "Fit to Stefansson et al. (2013; 80 to 200 C) & Garrels et al., (1961; at 25 C) to get G, S and Cp; with a1 pred. from the sum of the ions and used to predict the volume" - }, - { - "Name": "NaHCO3,aq", - "Symbol": "NaHCO3(0)", - "G0": -849720.192, - "H0": -627600, - "S0": 154.808, - "V0": 4.12, - "Cp0": 146.44, - "HKF" : [ 0.950362511816846, - 950.362511816846, - 0.842477389803241, - -29759.9575022003, - 26.3286741533281, - 40949, - -3800], - "Z": 0, - "Comments": "Fit to Stefansson et al. (2013; 80 to 200 C) & Nakayama (1971; at 25 C) to get G, S and Cp; with a1 pred. from the sum of the ions and used to predict the volume" - }, - { - "Name": "NaHSiO3,aq", - "Symbol": "NaHSiO3(0)", - "G0": -1285073.76, - "H0": -1393456.096, - "S0": 79.496, - "V0": 1.87, - "Cp0": 9.79092591302185, - "HKF" : [ 0.513390011816846, - 513.390011816846, - 4.33094315353685, - -28040.043315059, - 7.1879523568082, - -25579.2418535312, - -3800], - "Z": 0, - "Comments": "Sverjensky et al. (1997) with revised a1 equal to the sum of the ions used to predict new values of V using new correlation in Sverjensky et al. (2014)" - }, - { - "Name": "NaOH,aq", - "Symbol": "NaOH(0)", - "G0": -422165.6, - "H0": 0, - "S0": 27.196, - "V0": 1.2, - "Cp0": 175.728, - "HKF" : [ 0.394685095700812, - 394.685095700812, - 5.27859554781258, - -27572.8233657226, - 32.6237603393924, - 55208, - 20000], - "Z": 0, - "Comments": "Fitted to Ho & Palmer (1997) data with a1 pred. from the sum of the ions and used to predict the volume" - }, - { - "Name": "Nd+3", - "Symbol": "Nd(+3)", - "G0": -671950.4, - "H0": -696636, - "S0": -207.108, - "V0": -4.30999913556667, - "Cp0": -180.748814827277, - "HKF" : [ -0.887877564002377, - -887.877564002377, - 14.3203744858779, - -27093.3230486498, - 1.62368275083673, - -118344.407218729, - 225500], - "Z": 3, - "Comments": "Shock et al. (1997) revised with new predicted a1 for cations" - }, - { - "Name": "Ne,aq", - "Symbol": "Ne(0)", - "G0": 19099.96, - "H0": -3640.08, - "S0": 70.04016, - "V0": 2.04001221683175, - "Cp0": 166.104475397845, - "HKF" : [ 0.44709, - 447.09, - 4.5177, - -29086, - 27.0977, - 50523, - -25350], - "Z": 0, - "Comments": "Shock et al. (1989)" - }, - { - "Name": "NH3,aq", - "Symbol": "NH3(0)", - "G0": -26706.472, - "H0": -81336.96, - "S0": 107.82168, - "V0": 2.44300581474313, - "Cp0": 76.9148363648684, - "HKF" : [ 0.624097885356061, - 624.097885356061, - 3.44713324188954, - -28475.7870800061, - 16.4795849556178, - 7100.34839274313, - -5000], - "Z": 0, - "Comments": "Shock et al. (1989) + new a1" - }, - { - "Name": "NH4+", - "Symbol": "NH4(+)", - "G0": -79454.16, - "H0": -133260.4, - "S0": 111.16888, - "V0": 1.8130099154302, - "Cp0": 67.0425671946465, - "HKF" : [ 0.511349070547009, - 511.349070547009, - 4.34723652153052, - -28032.0102149323, - 16.9411651185393, - 2293.98790045293, - 15020], - "Z": 1, - "Comments": "Shock & Helgeson (1988) + new a1" - }, - { - "Name": "Ni+2", - "Symbol": "Ni(+2)", - "G0": -45605.6, - "H0": -53973.6, - "S0": -128.8672, - "V0": -2.90001861621336, - "Cp0": -48.9535626197456, - "HKF" : [ -0.251210360600186, - -251.210360600186, - 10.7724999362811, - -23742.5181793736, - 13.1905551277698, - -54179.2712849957, - 150670], - "Z": 2, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "NO2-", - "Symbol": "NO2(-)", - "G0": -32216.8, - "H0": -104600, - "S0": 123.0096, - "V0": 2.50000581404839, - "Cp0": -97.486337151247, - "HKF" : [ 0.511095611901146, - 511.095611901146, - 3.64370870443078, - -30723.3466573208, - 3.42593495620931, - -77807.6799180425, - 118470], - "Z": -1, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "NO3-", - "Symbol": "NO3(-)", - "G0": -110905.288, - "H0": -206810.936, - "S0": 146.94208, - "V0": 2.90001029667788, - "Cp0": -67.2736492286119, - "HKF" : [ 0.55224045870334, - 552.24045870334, - 3.19064947689639, - -31360.7153425089, - 6.85637273985144, - -63098.4912711956, - 109770], - "Z": -1, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "O2,aq", - "Symbol": "O2(0)", - "G0": 16543.536, - "H0": -12133.6, - "S0": 108.95136, - "V0": 3.03797300470105, - "Cp0": 234.302178240289, - "HKF" : [ 0.57889, - 578.89, - 3.2528, - -30417, - 35.353, - 83726, - -39430], - "Z": 0, - "Comments": "Shock et al. (1989)" - }, - { - "Name": "OH-", - "Symbol": "OH(-)", - "G0": -157297.48, - "H0": -230023.768, - "S0": -20.92, - "V0": -0.90995333789813, - "Cp0": -79.5271841480039, - "HKF" : [ 0.21, - 210, - 1, - -27000, - 12.12, - -75200, - 172000], - "Z": -1, - "Comments": "August 16th, 2013 fit to Bandura & Lvov (2005)" - }, - { - "Name": "Pb+2", - "Symbol": "Pb(+2)", - "G0": -23890.64, - "H0": 920.48, - "S0": 17.5728, - "V0": -1.55999413568919, - "Cp0": -53.1370030805364, - "HKF" : [ 0.0439210163272197, - 43.9210163272197, - 8.62967519771224, - -24090.2634873709, - 8.66239977051731, - -56215.9988707105, - 107880], - "Z": 2, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "PbCl+", - "Symbol": "PbCl(+)", - "G0": -163385.2, - "H0": -161627.92, - "S0": 117.152, - "V0": 1.38, - "Cp0": 20.500643793278, - "HKF" : [ 0.42619417779637, - 426.19417779637, - 5.02705030380518, - -27696.8424225739, - 10.218336847875, - -20365.165533722, - 12810], - "Z": 1, - "Comments": "Sverjensky et al. (1997) with revised a1 equal to the sum of the ions used to predict new values of V using new correlation in Sverjensky et al. (2014)" - }, - { - "Name": "PbCl2,aq", - "Symbol": "PbCl2(0)", - "G0": -297900.8, - "H0": -325096.8, - "S0": 196.648, - "V0": 3.49700035580091, - "Cp0": 8.36826385823792, - "HKF" : [ 0.829369750916941, - 829.369750916941, - 1.80839424740624, - -29283.732645915, - 6.98867710534362, - -26271.8715393808, - -3800], - "Z": 0, - "Comments": "Sverjensky et al. (1997) with revised a1 equal to the sum of the ions used to predict new values of V using new correlation in Sverjensky et al. (2014)" - }, - { - "Name": "PbCl3-", - "Symbol": "PbCl3(-)", - "G0": -427395.6, - "H0": -492456.8, - "S0": 246.856, - "V0": 5.38, - "Cp0": -50.2060049861204, - "HKF" : [ 1.23217320598759, - 1232.17320598759, - -1.40729109326751, - -30869.1582207637, - 5.91110583580892, - -54789.028718147, - 73560], - "Z": -1, - "Comments": "Sverjensky et al. (1997) with revised a1 equal to the sum of the ions used to predict new values of V using new correlation in Sverjensky et al. (2014)" - }, - { - "Name": "Pd+2", - "Symbol": "Pd(+2)", - "G0": 176564.8, - "H0": 176062.72, - "S0": -94.5584, - "V0": -2.08000131603529, - "Cp0": -26.3587509420284, - "HKF" : [ -0.0614096724623226, - -61.4096724623226, - 9.39443700656678, - -23966.1551895815, - 15.3779758940389, - -43178.8813740229, - 140060], - "Z": 2, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "PO4-3", - "Symbol": "PO4(-3)", - "G0": -1018804, - "H0": -1277375.2, - "S0": -221.752, - "V0": -3.0600095804682, - "Cp0": -480.741449024356, - "HKF" : [ -0.11970758608927, - -119.70758608927, - 9.59061349843539, - -24764.0624922318, - -9.47495397363052, - -264397.2264968, - 561140], - "Z": -3, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "Pr+3", - "Symbol": "Pr(+3)", - "G0": -680318.4, - "H0": -706259.2, - "S0": -209.2, - "V0": -4.20999937869876, - "Cp0": -199.57542381584, - "HKF" : [ -0.852752816736265, - -852.752816736265, - 14.1041050870603, - -26986.8170789901, - -1.19765647189277, - -127510.229998295, - 223500], - "Z": 3, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "PROPANE,AQ", - "Symbol": "C3H8", - "G0": -8213.192, - "H0": -127570.16, - "S0": 139.62008, - "V0": 6.6999936220909, - "Cp0": 462.74865642142, - "HKF" : [ 1.42900880505817, - 1429.00880505817, - -2.978681165736, - -31643.8988265821, - 66.3295318566212, - 194945.3511306, - -50530], - "Z": 0, - "Comments": "Shock & Helgeson (1990) with new a1-a4 based on revised correlation to predict a1 in Sverjensky et al. (2013)" - }, - { - "Name": "PROPANOATE,AQ", - "Symbol": "C2H5COO-", - "G0": -363045.68, - "H0": -513083.92, - "S0": 110.876, - "V0": 5.4950066467725, - "Cp0": 135.793862781649, - "HKF" : [ 0.837861896743715, - 837.861896743715, - 0.045978122076491, - -35783.7127967373, - 52.3, - -42000, - 122760], - "Z": -1, - "Comments": "Revised a1 from new delVn correlation for -1 ions; kept original regression c1 and c2 plus omega from Shock & Helgeson (1990)" - }, - { - "Name": "PROPANOIC-ACID,AQ", - "Symbol": "C3H6O2", - "G0": -390994.8, - "H0": -512414.48, - "S0": 206.6896, - "V0": 6.82706415128194, - "Cp0": 256.413167879237, - "HKF" : [ 1.46, - 1460, - 6.9, - -43000, - 63.3, - -14000, - -9000], - "Z": 0, - "Comments": "Plyasunov & Shock (2001)" - }, - { - "Name": "PROPANOL,AQ", - "Symbol": "C3H7OH", - "G0": -175351.44, - "H0": -315138.88, - "S0": 169.8704, - "V0": 7.08819997412168, - "Cp0": 346.63808388914, - "HKF" : [ 1.46, - 1460, - 12.2, - -55000, - 74.3, - 33000, - -20000], - "Z": 0, - "Comments": "Plyasunov & Shock (2001)" - }, - { - "Name": "Ra+2", - "Symbol": "Ra(+2)", - "G0": -561492.8, - "H0": -527602.4, - "S0": 54.392, - "V0": -1.05999928958129, - "Cp0": -60.2507773491743, - "HKF" : [ 0.154623750473273, - 154.623750473273, - 7.82590922804468, - -24220.7015207056, - 6.28587583748314, - -59679.3731979608, - 92900], - "Z": 2, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "Rb+", - "Symbol": "Rb(+)", - "G0": -283675.2, - "H0": -251123.68, - "S0": 120.4992, - "V0": 1.42602787650693, - "Cp0": -12.5515293429486, - "HKF" : [ 0.42913, - 429.13, - 7.407, - -27416, - 5.7923, - -36457, - 15020], - "Z": 1, - "Comments": "Shock & Helgeson (1988)" - }, - { - "Name": "ReO4-", - "Symbol": "ReO4(-)", - "G0": -694544, - "H0": -787428.8, - "S0": 201.2504, - "V0": 4.81000094358864, - "Cp0": -0.835744066223826, - "HKF" : [ 0.754559639003168, - 754.559639003168, - 0.962847487920568, - -34494.8115892628, - 14.3447768165446, - -30752.8859136945, - 90040], - "Z": -1, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "Rn,aq", - "Symbol": "Rn(0)", - "G0": 11673.36, - "H0": -20920, - "S0": 66.944, - "V0": 5.4100091845361, - "Cp0": 347.271788629771, - "HKF" : [ 0.90862, - 908.62, - 0.0884, - -33745, - 52.5774, - 138725, - -24230], - "Z": 0, - "Comments": "Shock et al. 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"G0": -1115036, - "H0": -1344737.6, - "S0": 244.3456, - "V0": 7.90001053289553, - "Cp0": -104.601108140733, - "HKF" : [ 2.37958216278903, - 2379.58216278903, - -8.32857755622526, - -26842.3097564245, - 12.9633096323999, - -81271.5395035069, - 232810], - "Z": -2, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "S3-2", - "Symbol": "S3(-2)", - "G0": 73638.4, - "H0": 25940.8, - "S0": 66.1072, - "V0": 2.91997637448247, - "Cp0": -242.255013035331, - "HKF" : [ 1.22705101891391, - 1227.05101891391, - 0.0394661020882161, - -25484.3135251328, - -0.359299240326539, - -148288.98794287, - 297490], - "Z": -2, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "S3O6-2", - "Symbol": "S3O6(-2)", - "G0": -958136, - "H0": -1167336, - "S0": 138.072, - "V0": 4.64000479976677, - "Cp0": -184.513521490717, - "HKF" : [ 1.62284992497499, - 1622.84992497499, - -2.83426320530023, - -25950.6726561955, - 5.31675212293586, - 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"V0": 4.69999530298551, - "Cp0": -182.421632506421, - "HKF" : [ 1.63672123594702, - 1636.72123594702, - -2.93497695731361, - -25967.0168462186, - 5.53606471102412, - -119158.826342156, - 270510], - "Z": -2, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "S5O6-2", - "Symbol": "S5O6(-2)", - "G0": -958136, - "H0": -1175704, - "S0": 167.36, - "V0": 5.33999198773356, - "Cp0": -161.083659153591, - "HKF" : [ 1.7839868446592, - 1783.9868446592, - -4.00421057379386, - -26140.5359243735, - 7.62666788372318, - -108770.334057329, - 260760], - "Z": -2, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "Sc+3", - "Symbol": "Sc(+3)", - "G0": -586596.8, - "H0": -614211.2, - "S0": -255.224, - "V0": -4.19000410187954, - "Cp0": -148.114916539588, - "HKF" : [ -0.821153776128418, - -821.153776128418, - 13.9095440995121, - -26891.0018284274, - 8.45468960809784, - -102456.440963466, - 250030], - "Z": 3, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - 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(1997) with revised a1 equal to the sum of the ions used to predict new values of V using new correlation in Sverjensky et al. (2014)" - }, - { - "Name": "ZnCl2,aq", - "Symbol": "ZnCl2(0)", - "G0": -411287.2, - "H0": -456390.72, - "S0": 113.09352, - "V0": 2.6, - "Cp0": 145.017864487691, - "HKF" : [ 0.655163311816846, - 655.163311816846, - 3.19912981685883, - -28598.0599179982, - 26.12947265577, - 40256.626663821, - -3800], - "Z": 0, - "Comments": "Sverjensky et al. (1997) with revised a1 equal to the sum of the ions used to predict new values of V using new correlation in Sverjensky et al. (2014)" - }, - { - "Name": "ZnCl3-", - "Symbol": "ZnCl3(-)", - "G0": -541033.04, - "H0": -632035.04, - "S0": 104.6, - "V0": 4.39, - "Cp0": 175.60248, - "HKF" : [ 1.06464110325213, - 1064.64110325213, - -0.0698384967792958, - -30209.7555345618, - 42.2916319257949, - 55146.89, - 125130], - "Z": -1, - "Comments": "Sverjensky et al. (1997) with revised a1 equal to the sum of the ions used to predict new values of V using new correlation in Sverjensky et al. (2014)" - } -] diff --git a/Resources/files/TestSubstance/DEW-11-0-1-AQv2-Sverjensky2014.json b/Resources/files/TestSubstance/DEW-11-0-1-AQv2-Sverjensky2014.json deleted file mode 100644 index 2d66550b..00000000 --- a/Resources/files/TestSubstance/DEW-11-0-1-AQv2-Sverjensky2014.json +++ /dev/null @@ -1,3710 +0,0 @@ -[ - { - "Name": "ACETATE,AQ", - "Symbol": "CH3COO-", - "G0": -88270, - "H0": -116180, - "S0": 20.6, - "V0": 40.4999259568755, - "Cp0": 6.311742607473, - "a1x10": 7.7525, - "a2x10-2": 8.6996, - "a3": 7.5825, - "a4x10-4": -3.1385, - "c1": 26.3, - "c2x10-4": -3.86, - "ωx10-5": 1.3182, - "Z": -1, - "Comments": "Shock & Helgeson (1990); Shock (1995)" - }, - { - "Name": "ACETIC-ACID,AQ", - "Symbol": "CH3COOH", - "G0": -94760, - "H0": -116100, - "S0": 42.7, - "V0": 51.5650511917523, - "Cp0": 40.2557577094207, - "a1x10": 11.5, - "a2x10-2": 5.5, - "a3": 1.67, - "a4x10-4": -2.87, - "c1": 44.9, - "c2x10-4": -2.63, - "ωx10-5": -0.076, - "Z": 0, - "Comments": "Plyasunov & Shock (2001)" - }, - { - "Name": "Ag+", - "Symbol": "Ag(+)", - "G0": 18427, - "H0": 25275, - "S0": 17.54, - "V0": -0.800077918318649, - "Cp0": 7.89967514506627, - "a1x10": 2.04641984513858, - "a2x10-2": -4.38771354121666, - "a3": 7.01816880065347, - "a4x10-4": -2.5976119222061, - "c1": 12.7862735069795, - "c2x10-4": -1.42543617295, - "ωx10-5": 0.216, - "Z": 1, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for cations" - }, - { - "Name": "AgCl,aq", - "Symbol": "AgCl(0)", - "G0": -17450, - "H0": -18270, - "S0": 34.1, - "V0": 27, - "Cp0": 6.70009369268357, - "a1x10": 6.74584311816846, - "a2x10-2": 2.13957558910928, - "a3": 3.04408689402622, - "a4x10-4": -2.86745005485378, - "c1": 9.74318474778434, - "c2x10-4": -1.66979091480036, - "ωx10-5": -0.038, - "Z": 0, - "Comments": "Sverjensky et al. (1997) with new V greater than the sum of a1 values of ions" - }, - { - "Name": "AgCl2-", - "Symbol": "AgCl2(-)", - "G0": -51560, - "H0": -61130, - "S0": 47, - "V0": 53, - "Cp0": 7.69989591460296, - "a1x10": 12.2533254724037, - "a2x10-2": 7.38324513254609, - "a3": -1.35268032521907, - "a4x10-4": -3.08422335377946, - "c1": 19.1264666157194, - "c2x10-4": -1.46613120219538, - "ωx10-5": 0.9169, - "Z": -1, - "Comments": "Sverjensky et al. (1997) with new V greater than the sum of a1 values of ions" - }, - { - "Name": "Al+3", - "Symbol": "Al(+3)", - "G0": -115609, - "H0": -126834, - "S0": -77.7, - "V0": -44.3999066394467, - "Cp0": -31.0416446674217, - "a1x10": -3.3802, - "a2x10-2": -17.0071, - "a3": 14.5185, - "a4x10-4": -2.0758, - "c1": 10.7, - "c2x10-4": -8.06, - "ωx10-5": 2.753, - "Z": 3, - "Comments": "Shock et al. (1997)" - }, - { - "Name": "AlO2-", - "Symbol": "AlO2(-)", - "G0": -198693, - "H0": -222125, - "S0": -7.22, - "V0": 10.0000247777584, - "Cp0": -9.54592362793974, - "a1x10": 4.298, - "a2x10-2": 2.4976, - "a3": -1.8258, - "a4x10-4": -2.8823, - "c1": 19.1, - "c2x10-4": -6.2, - "ωx10-5": 1.7418, - "Z": -1, - "Comments": "Sverjensky et al. (2014)" - }, - { - "Name": "Ar,aq", - "Symbol": "Ar(0)", - "G0": 3900, - "H0": -2870, - "S0": 14.3, - "V0": 31.7098370125479, - "Cp0": 53.3450331929289, - "a1x10": 6.0003, - "a2x10-2": 6.8698, - "a3": 3.0499, - "a4x10-4": -3.063, - "c1": 35.6471, - "c2x10-4": 7.316, - "ωx10-5": -0.3073, - "Z": 0, - "Comments": "Shock et al. (1989)" - }, - { - "Name": "Au+", - "Symbol": "Au(+)", - "G0": 39000, - "H0": 47580, - "S0": 24.5, - "V0": 11.1003248334715, - "Cp0": 0.600207473084757, - "a1x10": 3.33032890511487, - "a2x10-2": 0.423327522422944, - "a3": 5.60441497205432, - "a4x10-4": -2.79650035977696, - "c1": 8.17667347697076, - "c2x10-4": -2.91233773773264, - "ωx10-5": 0.18, - "Z": 1, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for cations" - }, - { - "Name": "Au+3", - "Symbol": "Au(+3)", - "G0": 103600, - "H0": 96930, - "S0": -57.9, - "V0": -41.3003434887161, - "Cp0": -36.1998871338686, - "a1x10": -8.0309244309481, - "a2x10-2": -2.30712170100828, - "a3": 13.7983372171556, - "a4x10-4": -2.68362358888032, - "c1": 7.57243456429844, - "c2x10-4": -10.408517009169, - "ωx10-5": 2.4554, - "Z": 3, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for cations" - }, - { - "Name": "Ba+2", - "Symbol": "Ba(+2)", - "G0": -134030, - "H0": -128500, - "S0": 2.3, - "V0": -12.5998411652121, - "Cp0": -12.2853805888778, - "a1x10": 1.10114306784965, - "a2x10-2": -8.76086780668558, - "a3": 8.14907356939055, - "a4x10-4": -2.41682572487162, - "c1": 8.04125682407346, - "c2x10-4": -5.5371320259544, - "ωx10-5": 0.985, - "Z": 2, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for cations" - }, - { - "Name": "BaCl+", - "Symbol": "BaCl(+)", - "G0": -164730, - "H0": -165770, - "S0": 22.5, - "V0": 16.8, - "Cp0": 6.17955806305758, - "a1x10": 4.88510260729963, - "a2x10-2": 0.367966037318573, - "a3": 4.52956471410829, - "a4x10-4": -2.79421171598275, - "c1": 11.7468552357872, - "c2x10-4": -1.77582402255517, - "ωx10-5": 0.2126, - "Z": 1, - "Comments": "Sverjensky et al. (1997) with new V from the sum of a1 values of ions" - }, - { - "Name": "Be+2", - "Symbol": "Be(+2)", - "G0": -83500, - "H0": -91500, - "S0": -55.7, - "V0": -25.4001908596943, - "Cp0": -1.30033963897196, - "a1x10": -1.41867869300787, - "a2x10-2": -9.4790675486132, - "a3": 9.97861011754209, - "a4x10-4": -2.38713534754033, - "c1": 22.9153609105802, - "c2x10-4": -3.29947918445859, - "ωx10-5": 1.9007, - "Z": 2, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for cations" - }, - { - "Name": "BENZENE,AQ", - "Symbol": "C6H6(0)", - "G0": 32000, - "H0": 12230, - "S0": 35.7, - "V0": 83, - "Cp0": 89.1177691894209, - "a1x10": 17.5199163037399, - "a2x10-2": 12.3975620497458, - "a3": -5.55713754088126, - "a4x10-4": -3.29151521513649, - "c1": 66.9, - "c2x10-4": 9.8, - "ωx10-5": -0.25, - "Z": 0, - "Comments": "Plyasunov & Shock (2001) for c1, c2 & omega; a1 predicted with new correlation for complex species from Sverjensky et al. (2014)" - }, - { - "Name": "BO(OH),aq", - "Symbol": "BO(OH)(0)", - "G0": -174854, - "H0": -188505, - "S0": 24, - "V0": 20.4884587925363, - "Cp0": 3.75773645977461, - "a1x10": 5.54, - "a2x10-2": 1.38, - "a3": 3.1, - "a4x10-4": -2.84, - "c1": 25, - "c2x10-4": -10, - "ωx10-5": 0.1, - "Z": 0, - "Comments": "Revised May, 2013" - }, - { - "Name": "BO2-", - "Symbol": "BO2(-)", - "G0": -162240, - "H0": -184600, - "S0": -8.9, - "V0": -16.0183193119584, - "Cp0": -9.00003305628132, - "a1x10": -0.855, - "a2x10-2": -2.596, - "a3": 3.7, - "a4x10-4": -2.6717, - "c1": 17.102, - "c2x10-4": -4.8679, - "ωx10-5": 1.7595, - "Z": -1, - "Comments": "revised a1 - a4 using delkappan for BO2- instead of B(OH)4- used by Shock and Helgeson (1988); Shock et al. (1997)" - }, - { - "Name": "Br-", - "Symbol": "Br(-)", - "G0": -24870, - "H0": -29040, - "S0": 19.8, - "V0": 24.8524639565706, - "Cp0": -30.4077662483975, - "a1x10": 5.269, - "a2x10-2": 6.594, - "a3": 4.745, - "a4x10-4": -3.143, - "c1": -3.8, - "c2x10-4": -6.811, - "ωx10-5": 1.3858, - "Z": -1, - "Comments": "Shock & Helgeson (1988)" - }, - { - "Name": "Ca(HCO3)+", - "Symbol": "Ca(HCO3)(+)", - "G0": -273830, - "H0": -294350, - "S0": 16, - "V0": 37.5087138674343, - "Cp0": 90.9485345623494, - "a1x10": 9.14, - "a2x10-2": 4.42, - "a3": 1.13, - "a4x10-4": -2.96, - "c1": 65.9, - "c2x10-4": 15.5, - "ωx10-5": 0.7, - "Z": 1, - "Comments": "Facq et al. (2014)" - }, - { - "Name": "Ca(OH)+", - "Symbol": "Ca(OH)(+)", - "G0": -171300, - "H0": -179600, - "S0": 6.7, - "V0": 1.9, - "Cp0": 1.4, - "a1x10": 2.10505179135425, - "a2x10-2": -2.27891812047981, - "a3": 6.74895199657232, - "a4x10-4": -2.68478952489936, - "c1": 11.1291815102197, - "c2x10-4": -2.74942, - "ωx10-5": 0.4496, - "Z": 1, - "Comments": "Shock et al. (1997) with new a1 prediction" - }, - { - "Name": "Ca+2", - "Symbol": "Ca(+2)", - "G0": -132120, - "H0": -129800, - "S0": -13.5, - "V0": -18.4493150776946, - "Cp0": -7.5134787311368, - "a1x10": -0.245, - "a2x10-2": -7.252, - "a3": 5, - "a4x10-4": -2.48, - "c1": 9, - "c2x10-4": -2.52, - "ωx10-5": 1.2366, - "Z": 2, - "Comments": "Facq et al. (2014)" - }, - { - "Name": "CaCl+", - "Symbol": "CaCl(+)", - "G0": -163100, - "H0": -168607, - "S0": 4.5, - "V0": 11.3, - "Cp0": 17.5, - "a1x10": 3.93921161200648, - "a2x10-2": -0.532616022579567, - "a3": 5.28469423674509, - "a4x10-4": -2.75698165362656, - "c1": 20.7296836056674, - "c2x10-4": 0.53015, - "ωx10-5": 0.4675, - "Z": 1, - "Comments": "Sverjensky et al. (1997) with new V from the sum of a1 values of ions" - }, - { - "Name": "CaCl2,aq", - "Symbol": "CaCl(0)", - "G0": -194000, - "H0": -211060, - "S0": 6, - "V0": 33.3, - "Cp0": 29.7701286331863, - "a1x10": 7.96936611816846, - "a2x10-2": 3.30449085858094, - "a3": 2.06731648018082, - "a4x10-4": -2.91560765209374, - "c1": 23.2636471809872, - "c2x10-4": 3.02957520258005, - "ωx10-5": -0.038, - "Z": 0, - "Comments": "Sverjensky et al. (1997) with new V from the sum of a1 values of ions" - }, - { - "Name": "CaCO3,aq", - "Symbol": "CaCO3(0)", - "G0": -262750, - "H0": -287390, - "S0": 0, - "V0": 21.5257093021584, - "Cp0": 14.0085523592759, - "a1x10": 6.66, - "a2x10-2": 2.05, - "a3": 3.12, - "a4x10-4": -2.86, - "c1": 32.8, - "c2x10-4": -0.18, - "ωx10-5": 2, - "Z": 0, - "Comments": "Facq et al. (2014)" - }, - { - "Name": "CaSO4,aq", - "Symbol": "CaSO4(0)", - "G0": -312930, - "H0": -345900, - "S0": 5, - "V0": 4.7, - "Cp0": -25, - "a1x10": 2.41496011816846, - "a2x10-2": -1.98385465044918, - "a3": 6.50154407319332, - "a4x10-4": -2.69698744875043, - "c1": -8.83502404150842, - "c2x10-4": -8.1271, - "ωx10-5": -0.038, - "Z": 0, - "Comments": "Sverjensky et al. (1997) revised using exptl V and pred. a1 from new correlation" - }, - { - "Name": "Cd+2", - "Symbol": "Cd(+2)", - "G0": -18560, - "H0": -18140, - "S0": -17.4, - "V0": -15.5999436407579, - "Cp0": -3.50003016787486, - "a1x10": 0.541960607797426, - "a2x10-2": -8.9202460233271, - "a3": 8.55507242361216, - "a4x10-4": -2.41023702939566, - "c1": 15.6572108827406, - "c2x10-4": -3.74755614519611, - "ωx10-5": 1.2528, - "Z": 2, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for cations" - }, - { - "Name": "Ce+3", - "Symbol": "Ce(+3)", - "G0": -161600, - "H0": -167400, - "S0": -49, - "V0": -39.7998059487303, - "Cp0": -38.5995639475352, - "a1x10": -7.68664331746466, - "a2x10-2": -2.55964617156575, - "a3": 13.5863571312258, - "a4x10-4": -2.67318422726747, - "c1": 4.04436014311644, - "c2x10-4": -10.8973311761129, - "ωx10-5": 2.2251, - "Z": 3, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for cations" - }, - { - "Name": "Ce+4", - "Symbol": "Ce(+4)", - "G0": -121300, - "H0": -137700, - "S0": -100.1, - "V0": -53.3000709261696, - "Cp0": 0.099730112075676, - "a1x10": -15.635482300041, - "a2x10-2": 11.3069405919656, - "a3": 17.6099912644607, - "a4x10-4": -3.24642892407186, - "c1": 40.2793758897062, - "c2x10-4": -3.01428497617018, - "ωx10-5": 3.6964, - "Z": 4, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for cations" - }, - { - "Name": "Cl-", - "Symbol": "Cl(-)", - "G0": -31379, - "H0": -39933, - "S0": 13.56, - "V0": 17.785995151106, - "Cp0": -29.4252957549848, - "a1x10": 4.032, - "a2x10-2": 4.801, - "a3": 5.563, - "a4x10-4": -2.847, - "c1": -4.4, - "c2x10-4": -5.714, - "ωx10-5": 1.456, - "Z": -1, - "Comments": "Shock & Helgeson (1988)" - }, - { - "Name": "CN-", - "Symbol": "CN(-)", - "G0": 41200, - "H0": 36000, - "S0": 22.5, - "V0": 24.1998650625684, - "Cp0": -32.7004665578009, - "a1x10": 5.0522444349362, - "a2x10-2": 6.87565859503193, - "a3": 3.70835804037863, - "a4x10-4": -3.06323972631862, - "c1": -1.11332719480748, - "c2x10-4": -9.69568503782405, - "ωx10-5": 1.29, - "Z": -1, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for cations" - }, - { - "Name": "CO,aq", - "Symbol": "CO(0)", - "G0": -28682, - "H0": -28910, - "S0": 24.53, - "V0": 33.8, - "Cp0": 64.5, - "a1x10": 7.90650624735742, - "a2x10-2": 3.24464202587016, - "a3": 2.1174991592366, - "a4x10-4": -2.91313350134947, - "c1": 40.5450119599561, - "c2x10-4": 10.10405, - "ωx10-5": -0.3715, - "Z": 0, - "Comments": "Shock & McKibben (1993) for c1, c2 and omega with revised a1 from correlation for complex species" - }, - { - "Name": "Co+2", - "Symbol": "Co(+2)", - "G0": -13000, - "H0": -13900, - "S0": -27, - "V0": -24.4002626148702, - "Cp0": -7.80044113309821, - "a1x10": -1.42985946929835, - "a2x10-2": -9.4822542941089, - "a3": 9.98672800872703, - "a4x10-4": -2.38700360748154, - "c1": 15.2015013179926, - "c2x10-4": -4.62354985881211, - "ωx10-5": 1.4769, - "Z": 2, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for cations" - }, - { - "Name": "Co+3", - "Symbol": "Co(+3)", - "G0": 32000, - "H0": 22000, - "S0": -73, - "V0": -43.8998456233669, - "Cp0": -32.2996404454731, - "a1x10": -8.75453432572538, - "a2x10-2": -1.77636587847733, - "a3": 14.2438768696871, - "a4x10-4": -2.70556503458375, - "c1": 12.2498714875676, - "c2x10-4": -9.61403675874287, - "ωx10-5": 2.715, - "Z": 3, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for cations" - }, - { - "Name": "CO2,aq", - "Symbol": "CO2(0)", - "G0": -92250, - "H0": -98900, - "S0": 28.1, - "V0": 32.7830094365969, - "Cp0": 52.0512040261465, - "a1x10": 7.79, - "a2x10-2": 3.14, - "a3": 2.21, - "a4x10-4": -2.91, - "c1": 37, - "c2x10-4": 6.5, - "ωx10-5": -0.2, - "Z": 0, - "Comments": "Facq et al. (2014)" - }, - { - "Name": "CO3-2", - "Symbol": "CO3(-2)", - "G0": -126191, - "H0": -161385, - "S0": -12.95, - "V0": -5.00919546000396, - "Cp0": -65.0210010804508, - "a1x10": 5.8, - "a2x10-2": 5, - "a3": -2, - "a4x10-4": -10.8, - "c1": 18, - "c2x10-4": -20, - "ωx10-5": 4.6, - "Z": -2, - "Comments": "Facq et al. (2014)" - }, - { - "Name": "Cr+2", - "Symbol": "Cr(+2)", - "G0": -39400, - "H0": -39000, - "S0": -24.2, - "V0": -22.3, - "Cp0": -7.3, - "a1x10": -0.956149883524283, - "a2x10-2": -9.34723756096671, - "a3": 9.64278741187766, - "a4x10-4": -2.39258519922964, - "c1": 15.0507320204684, - "c2x10-4": -4.52161, - "ωx10-5": 1.4287, - "Z": 2, - "Comments": "Shock et al. (1997) revised with new predicted a1 for cations" - }, - { - "Name": "Cr+3", - "Symbol": "Cr(+3)", - "G0": -49300, - "H0": -60000, - "S0": -77, - "V0": -39.9999950688365, - "Cp0": -22.9000607030703, - "a1x10": -7.29045123518463, - "a2x10-2": -2.85024647433733, - "a3": 13.3424145263101, - "a4x10-4": -2.6611708107509, - "c1": 17.9916893000701, - "c2x10-4": -7.69934236521543, - "ωx10-5": 2.7403, - "Z": 3, - "Comments": "Shock et al. (1997) revised with new predicted a1 for cations" - }, - { - "Name": "Cr2O7-2", - "Symbol": "Cr2O7(-2)", - "G0": -311000, - "H0": -356200, - "S0": 62.6, - "V0": 73.0002007783762, - "Cp0": -20.3997442677225, - "a1x10": 16.7843789431994, - "a2x10-2": 11.6972575172111, - "a3": -4.96993882695934, - "a4x10-4": -3.26256462576151, - "c1": 15.0818535006395, - "c2x10-4": -7.19002790733506, - "ωx10-5": 2.2654, - "Z": -2, - "Comments": "Shock et al. (1997) revised with new predicted a1 for cations" - }, - { - "Name": "CrO4-2", - "Symbol": "CrO4(-2)", - "G0": -174800, - "H0": -210930, - "S0": 13.8, - "V0": 19.7999374382431, - "Cp0": -62.6003181053002, - "a1x10": 10.0392510999334, - "a2x10-2": -6.21332774584448, - "a3": 1.65948943687678, - "a4x10-4": -2.52214103098679, - "c1": -2.86042447225216, - "c2x10-4": -15.7862847980497, - "ωx10-5": 3.0024, - "Z": -2, - "Comments": "Shock et al. (1997) revised with new predicted a1 for cations" - }, - { - "Name": "Cs+", - "Symbol": "Cs(+)", - "G0": -69710, - "H0": -61670, - "S0": 31.75, - "V0": 21.4201411429416, - "Cp0": -6.28344428007329, - "a1x10": 6.1475, - "a2x10-2": -0.1309, - "a3": 4.2094, - "a4x10-4": -2.7736, - "c1": 6.27, - "c2x10-4": -5.736, - "ωx10-5": 0.0974, - "Z": 1, - "Comments": "Shock & Helgeson (1988)" - }, - { - "Name": "Cu+", - "Symbol": "Cu(+)", - "G0": 11950, - "H0": 17132, - "S0": 9.7, - "V0": -8.00003387748251, - "Cp0": 13.7002502883189, - "a1x10": 1.29575874487656, - "a2x10-2": -7.20057738867962, - "a3": 7.8447460385269, - "a4x10-4": -2.48132813075198, - "c1": 17.2830167170429, - "c2x10-4": -0.24385901626944, - "ωx10-5": 0.3351, - "Z": 1, - "Comments": "Shock et al. (1997) revised with new predicted a1 for cations" - }, - { - "Name": "Cu+2", - "Symbol": "Cu(+2)", - "G0": 15675, - "H0": 15700, - "S0": -23.2, - "V0": -24.6000867753005, - "Cp0": -2.22734624915895, - "a1x10": -1.47763742605723, - "a2x10-2": -9.495871970068, - "a3": 10.0214175726653, - "a4x10-4": -2.38644065275739, - "c1": 18.467678426493, - "c2x10-4": -3.48831043095368, - "ωx10-5": 1.4769, - "Z": 2, - "Comments": "Shock et al. (1997) revised with new predicted a1 for cations" - }, - { - "Name": "DIGLYCINE,AQ", - "Symbol": "C4H8O3N2", - "G0": -117020, - "H0": -175640, - "S0": 54.2, - "V0": 76.2700141675233, - "Cp0": 38.0000434671, - "a1x10": 16.1021814308272, - "a2x10-2": 11.0477378114451, - "a3": -4.42532270900807, - "a4x10-4": -3.23571348112514, - "c1": 24.0074411994697, - "c2x10-4": 4.70600885424827, - "ωx10-5": -0.4808, - "Z": 0, - "Comments": "Shock & Helgeson (1990) revised with new predicted a1 for complex species" - }, - { - "Name": "DKP,AQ", - "Symbol": "C4H6O2N2", - "G0": -57440, - "H0": -99300, - "S0": 53.5, - "V0": 76.7300032759005, - "Cp0": 17.0001363760976, - "a1x10": 16.1966002562865, - "a2x10-2": 11.1376338996291, - "a3": -4.50069972702794, - "a4x10-4": -3.23942978541067, - "c1": 11.7978573326761, - "c2x10-4": 0.428327779811085, - "ωx10-5": -0.4702, - "Z": 0, - "Comments": "Shock & Helgeson (1990) revised with new predicted a1 for complex species" - }, - { - "Name": "Dy+3", - "Symbol": "Dy(+3)", - "G0": -158700, - "H0": -166500, - "S0": -55.2, - "V0": -40.7001092365793, - "Cp0": -31.7000480763815, - "a1x10": -7.8786765811433, - "a2x10-2": -2.41879296661002, - "a3": 13.7045954723422, - "a4x10-4": -2.67900709876034, - "c1": 9.50759957967865, - "c2x10-4": -9.49189979315892, - "ωx10-5": 2.3792, - "Z": 3, - "Comments": "Shock et al. (1997) revised with new predicted a1 for cations" - }, - { - "Name": "Er+3", - "Symbol": "Er(+3)", - "G0": -159900, - "H0": -168500, - "S0": -58.3, - "V0": -42.9999539941109, - "Cp0": -34.2999217498119, - "a1x10": -8.69899283827142, - "a2x10-2": -1.81710463574279, - "a3": 14.2096789749375, - "a4x10-4": -2.70388089435839, - "c1": 8.28148793022524, - "c2x10-4": -10.0214940604367, - "ωx10-5": 2.4115, - "Z": 3, - "Comments": "Shock et al. (1997) revised with new predicted a1 for cations" - }, - { - "Name": "ETHANE,AQ", - "Symbol": "C2H6", - "G0": -3886, - "H0": -24650, - "S0": 26.81, - "V0": 51.2000166666145, - "Cp0": 88.3000435759454, - "a1x10": 11.2692153940967, - "a2x10-2": 6.44627471428605, - "a3": -0.567039508939056, - "a4x10-4": -3.04548899668859, - "c1": 54.1754616412644, - "c2x10-4": 14.9521188764201, - "ωx10-5": -0.406, - "Z": 0, - "Comments": "Shock & Helgeson (1990) revised with new predicted a1 for complex species" - }, - { - "Name": "ETHANOL,AQ", - "Symbol": "C2H5OH", - "G0": -43330, - "H0": -68650, - "S0": 35.9, - "V0": 55.080070558532, - "Cp0": 62.2003916587062, - "a1x10": 9.2333, - "a2x10-2": 9.9581, - "a3": 12.1445, - "a4x10-4": -3.1906, - "c1": 60.0175, - "c2x10-4": 0.1507, - "ωx10-5": -0.2037, - "Z": 0, - "Comments": "Plyasunov & Shock (2001)" - }, - { - "Name": "ETHYLENE,AQ", - "Symbol": "C2H4", - "G0": 19450, - "H0": 8570, - "S0": 28.6, - "V0": 46, - "Cp0": 66.9, - "a1x10": 10.3053670166374, - "a2x10-2": 5.52859544519357, - "a3": 0.202425861581267, - "a4x10-4": -3.0075521357043, - "c1": 42.5181492402495, - "c2x10-4": 10.59293, - "ωx10-5": -0.31, - "Z": 0, - "Comments": "Plyasunov & Shock (2001) for c1, c2 & omega; a1 predicted with new correlation for complex species from Sverjensky et al. (2014)" - }, - { - "Name": "Eu+2", - "Symbol": "Eu(+2)", - "G0": -129200, - "H0": -126150, - "S0": -2.4, - "V0": -15.3000014248061, - "Cp0": -11.4001467496475, - "a1x10": 0.519252174409929, - "a2x10-2": -8.92671838230575, - "a3": 8.57156006153919, - "a4x10-4": -2.40996946207548, - "c1": 9.55412331314926, - "c2x10-4": -5.3568098929032, - "ωx10-5": 1.0929, - "Z": 2, - "Comments": "Shock et al. (1997) revised with new predicted a1 for cations" - }, - { - "Name": "Eu+3", - "Symbol": "Eu(+3)", - "G0": -137300, - "H0": -144700, - "S0": -53, - "V0": -41.2998099542058, - "Cp0": -36.5997552056964, - "a1x10": -8.15784988569341, - "a2x10-2": -2.21402399101332, - "a3": 13.8764875069911, - "a4x10-4": -2.68747224821151, - "c1": 6.05473931220669, - "c2x10-4": -10.4899701354004, - "ωx10-5": 2.3161, - "Z": 3, - "Comments": "Shock et al. (1997) revised with new predicted a1 for cations" - }, - { - "Name": "F-", - "Symbol": "F(-)", - "G0": -67340, - "H0": -80150, - "S0": -3.15, - "V0": -1.3198710849504, - "Cp0": -27.2196859991208, - "a1x10": 0.687, - "a2x10-2": 1.3588, - "a3": 7.6033, - "a4x10-4": -2.8352, - "c1": 4.46, - "c2x10-4": -7.488, - "ωx10-5": 1.787, - "Z": -1, - "Comments": "Shock & Helgeson (1988)" - }, - { - "Name": "Fe(CH3COO)+", - "Symbol": "Fe(CH3COO)(+)", - "G0": -111900, - "H0": -139060, - "S0": -1.5, - "V0": 25.2, - "Cp0": 81.1998013967276, - "a1x10": 6.69058129426936, - "a2x10-2": 2.08696085078485, - "a3": 3.08820385349472, - "a4x10-4": -2.86527496157145, - "c1": 59.0576009255934, - "c2x10-4": 13.5057995445134, - "ωx10-5": 0.5756, - "Z": 1, - "Comments": "Sverjensky et al. (1997) with revised volume increased in order that a1 of the complex is the sum of the a1 values of the ions" - }, - { - "Name": "Fe(CH3COO)2,aq", - "Symbol": "Fe(CH3COO)2(0)", - "G0": -201800, - "H0": -259100, - "S0": 11.53, - "V0": 66.9, - "Cp0": 184.200048384925, - "a1x10": 14.4948221181685, - "a2x10-2": 9.51737229576321, - "a3": -3.14212572699472, - "a4x10-4": -3.17244817070685, - "c1": 113.769098687703, - "c2x10-4": 34.4869498560092, - "ωx10-5": -0.038, - "Z": 0, - "Comments": "Sverjensky et al. (1997) with revised volume increased in order that a1 of the complex is the sum of the a1 values of the ions" - }, - { - "Name": "Fe+2", - "Symbol": "Fe(+2)", - "G0": -21870, - "H0": -22050, - "S0": -25.3, - "V0": -22.2001111114365, - "Cp0": -7.90024244007987, - "a1x10": -0.915318442049491, - "a2x10-2": -9.33559978118988, - "a3": 9.61314142038246, - "a4x10-4": -2.39306630504561, - "c1": 14.96336131819, - "c2x10-4": -4.64387938504427, - "ωx10-5": 1.4574, - "Z": 2, - "Comments": "Shock et al. (1997) revised with new predicted a1 for cations" - }, - { - "Name": "Fe+3", - "Symbol": "Fe(+3)", - "G0": -4120, - "H0": -11850, - "S0": -66.3, - "V0": -36.9999885120989, - "Cp0": -18.599884012847, - "a1x10": -6.32714052089309, - "a2x10-2": -3.55681886120892, - "a3": 12.7492867595078, - "a4x10-4": -2.63196110827762, - "c1": 19.0460958402282, - "c2x10-4": -6.82339637341693, - "ωx10-5": 2.5812, - "Z": 3, - "Comments": "Shock et al. (1997) revised with new predicted a1 for cations" - }, - { - "Name": "FeCl+", - "Symbol": "FeCl(+)", - "G0": -53030, - "H0": -61260, - "S0": -10.06, - "V0": 5.8, - "Cp0": 20.570040893148, - "a1x10": 2.98272024596393, - "a2x10-2": -1.44329068698783, - "a3": 6.04828631261857, - "a4x10-4": -2.71933436299992, - "c1": 24.6736647838752, - "c2x10-4": 1.15551732993426, - "ωx10-5": 0.7003, - "Z": 1, - "Comments": "Sverjensky et al. (1997) with revised volume increased in order that a1 of the complex is the sum of the a1 values of the ions" - }, - { - "Name": "FeCl++", - "Symbol": "FeCl(++)", - "G0": -37573, - "H0": -50875, - "S0": -28.7, - "V0": -22.8, - "Cp0": 3.09961514203344, - "a1x10": -2.19168750064997, - "a2x10-2": -6.36984016297073, - "a3": 10.1791513605702, - "a4x10-4": -2.51567080766279, - "c1": 21.733628544405, - "c2x10-4": -2.40320839556779, - "ωx10-5": 1.4925328, - "Z": 2, - "Comments": "Sverjensky et al. (1997) with revised volume increased in order that a1 of the complex is the sum of the a1 values of the ions" - }, - { - "Name": "FeCl2,aq", - "Symbol": "FeCl2(0)", - "G0": -73480, - "H0": -78490, - "S0": 43, - "V0": 28.4, - "Cp0": 28.1400720958508, - "a1x10": 7.01773711816846, - "a2x10-2": 2.39844564899187, - "a3": 2.82702680206058, - "a4x10-4": -2.87815174312932, - "c1": 22.3083335789974, - "c2x10-4": 2.69753268592481, - "ωx10-5": -0.038, - "Z": 0, - "Comments": "Sverjensky et al. (1997) with revised volume increased in order that a1 of the complex is the sum of the a1 values of the ions" - }, - { - "Name": "FORMATE,AQ", - "Symbol": "HCOO-", - "G0": -83862, - "H0": -101680, - "S0": 21.7, - "V0": 26.159971565219, - "Cp0": -20.1774646003795, - "a1x10": 5.26836690949239, - "a2x10-2": 7.68364431466351, - "a3": 3.47058058408901, - "a4x10-4": -3.09664185596819, - "c1": 17, - "c2x10-4": -12.4, - "ωx10-5": 1.3003, - "Z": -1, - "Comments": "Shock & Helgeson (1990) revised with new predicted a1 for ions" - }, - { - "Name": "FORMIC-ACID,AQ", - "Symbol": "HCOOH", - "G0": -88982, - "H0": -101680, - "S0": 38.9, - "V0": 34.6900143097129, - "Cp0": 19.0241248736513, - "a1x10": 8.09245050207837, - "a2x10-2": 3.42167940203307, - "a3": 1.96905499706232, - "a4x10-4": -2.92045222648005, - "c1": 22.1924, - "c2x10-4": -3.1196, - "ωx10-5": -0.3442, - "Z": 0, - "Comments": "Shock & Helgeson (1990) revised with new predicted a1 for complex species" - }, - { - "Name": "Ga+3", - "Symbol": "Ga(+3)", - "G0": -38000, - "H0": -50600, - "S0": -79, - "V0": -44.9000212783272, - "Cp0": -30.7998162262442, - "a1x10": -9.11260070398471, - "a2x10-2": -1.51373014548725, - "a3": 14.4643447915664, - "a4x10-4": -2.71642239578556, - "c1": 13.2449426450721, - "c2x10-4": -9.30852256528594, - "ωx10-5": 2.7276, - "Z": 3, - "Comments": "Shock et al. (1997) revised with new predicted a1 for cations" - }, - { - "Name": "Gd+3", - "Symbol": "Gd(+3)", - "G0": -158600, - "H0": -164200, - "S0": -49.2, - "V0": -40.4000916947148, - "Cp0": -35.8999915143228, - "a1x10": -7.81591314174929, - "a2x10-2": -2.46482890550592, - "a3": 13.6659508916349, - "a4x10-4": -2.67710397304639, - "c1": 6.5606574503928, - "c2x10-4": -10.3474282714676, - "ωx10-5": 2.3265, - "Z": 3, - "Comments": "Shock et al. (1997) revised with new predicted a1 for cations" - }, - { - "Name": "GLUTAMATE", - "Symbol": "C5H8NO4-", - "G0": -167210, - "H0": -234150, - "S0": 43.86, - "V0": 80.7594495626225, - "Cp0": 7.3356228186242, - "a1x10": 18.4757778799145, - "a2x10-2": 13.3076370917247, - "a3": -6.32022683903014, - "a4x10-4": -3.3291377173719, - "c1": 34.8797444674277, - "c2x10-4": -1.54033363184625, - "ωx10-5": 2.65, - "Z": -1, - "Comments": "Shock & Helgeson (1990) revised with new predicted a1 for complex species" - }, - { - "Name": "GLUTAMIC-ACID,AQ", - "Symbol": "C5H9NO4", - "G0": -173050, - "H0": -234820, - "S0": 61.2, - "V0": 90.2505798297414, - "Cp0": 43.4970947097746, - "a1x10": 19.1199133264902, - "a2x10-2": 13.9209179350958, - "a3": -6.8344570142898, - "a4x10-4": -3.35449074743686, - "c1": 33.040508365119, - "c2x10-4": 5.82575819238109, - "ωx10-5": 0.15, - "Z": 0, - "Comments": "Shock & Helgeson (1990) revised with new predicted a1 for complex species" - }, - { - "Name": "GLUTAMINE,AQ", - "Symbol": "C5H10N2O3", - "G0": -126280, - "H0": -191860, - "S0": 62.41, - "V0": 93.7168584488672, - "Cp0": 43.7757724541431, - "a1x10": 19.8074889406618, - "a2x10-2": 14.5755581272825, - "a3": -7.38336661157929, - "a4x10-4": -3.38155357298186, - "c1": 33.4802157500622, - "c2x10-4": 5.88252484890894, - "ωx10-5": 0.18, - "Z": 0, - "Comments": "Shock & Helgeson (1990) revised with new predicted a1 for complex species" - }, - { - "Name": "GLUTARATE-", - "Symbol": "C5H7O4-", - "G0": -170860, - "H0": -223570, - "S0": 52.9, - "V0": 85.9090594824493, - "Cp0": 20.108795607973, - "a1x10": 18.6019046386216, - "a2x10-2": 13.4277222777873, - "a3": -6.42091712952679, - "a4x10-4": -3.33410203896373, - "c1": 25.5789043631804, - "c2x10-4": 1.0615616653441, - "ωx10-5": 0.8279, - "Z": -1, - "Comments": "Shock & Helgeson (1990) revised with new predicted a1 for complex species" - }, - { - "Name": "GLUTARIC-ACID,AQ", - "Symbol": "C5H8O4", - "G0": -176780, - "H0": -223440, - "S0": 73.2, - "V0": 99.0911049024688, - "Cp0": 64.1052577655109, - "a1x10": 20.7169180046044, - "a2x10-2": 15.4414248115117, - "a3": -8.10938762070644, - "a4x10-4": -3.41734850170789, - "c1": 42.8149533824839, - "c2x10-4": 10.0236410068346, - "ωx10-5": -0.1, - "Z": 0, - "Comments": "Shock & Helgeson (1990) revised with new predicted a1 for complex species" - }, - { - "Name": "GLYCINE,AQ", - "Symbol": "C2H5NO2", - "G0": -90950, - "H0": -124780, - "S0": 39.3, - "V0": 43.2907614662759, - "Cp0": 9.49422936701518, - "a1x10": 10.8, - "a2x10-2": 1.3, - "a3": 7.6, - "a4x10-4": -3.5, - "c1": 28, - "c2x10-4": -8.2, - "ωx10-5": 0.2, - "Z": 0, - "Comments": "Plyasunov & Shock (2001)" - }, - { - "Name": "GLYCOLATE,AQ", - "Symbol": "C2H3O3-", - "G0": -121170, - "H0": -154700, - "S0": 26.2, - "V0": 39.8499610916751, - "Cp0": 6.49972743900083, - "a1x10": 6.73821478709146, - "a2x10-2": 13.1932965408594, - "a3": 1.85188150744711, - "a4x10-4": -3.32441087899913, - "c1": 21.3389561922355, - "c2x10-4": -1.71060552067553, - "ωx10-5": 1.2334, - "Z": -1, - "Comments": "Shock & Helgeson (1990) revised with new predicted a1 for complex species" - }, - { - "Name": "GLYCOLIC-ACID,AQ", - "Symbol": "C2H4O3", - "G0": -126400, - "H0": -154890, - "S0": 43.1, - "V0": 51.7501133308878, - "Cp0": 45.5004706986275, - "a1x10": 11.426077661345, - "a2x10-2": 6.59562315344203, - "a3": -0.692266759834068, - "a4x10-4": -3.05166306116329, - "c1": 30.0531726063325, - "c2x10-4": 6.23384588131042, - "ωx10-5": -0.3017, - "Z": 0, - "Comments": "Shock & Helgeson (1990) revised with new predicted a1 for complex species" - }, - { - "Name": "H+", - "Symbol": "H(+)", - "G0": 0, - "H0": 0, - "S0": 0, - "V0": 0, - "Cp0": 0, - "a1x10": 0, - "a2x10-2": 0, - "a3": 0, - "a4x10-4": 0, - "c1": 0, - "c2x10-4": 0, - "ωx10-5": 0, - "Z": 1, - "Comments": "Perfectly known, by convention!" - }, - { - "Name": "H2,aq", - "Symbol": "H2(0)", - "G0": 4236, - "H0": -1000, - "S0": 13.8, - "V0": 25.1999807716819, - "Cp0": 39.9000576494868, - "a1x10": 5.1427, - "a2x10-2": 4.7758, - "a3": 3.8729, - "a4x10-4": -2.9764, - "c1": 27.6251, - "c2x10-4": 5.093, - "ωx10-5": -0.209, - "Z": 0, - "Comments": "Shock et al. (1989)" - }, - { - "Name": "H2AsO3-", - "Symbol": "H2AsO3(-)", - "G0": -140330, - "H0": -170840, - "S0": 26.4, - "V0": 26.3998817113441, - "Cp0": -2.90015836148291, - "a1x10": 7.23773624015259, - "a2x10-2": 2.60790663703188, - "a3": 2.65139574859769, - "a4x10-4": -2.8868108603749, - "c1": 15.8033265148332, - "c2x10-4": -3.62536225823407, - "ωx10-5": 1.2305, - "Z": -1, - "Comments": "Shock et al. (1997) revised with new predicted a1 for complex species" - }, - { - "Name": "H2AsO4-", - "Symbol": "H2AsO4(-)", - "G0": -180010, - "H0": -217390, - "S0": 28, - "V0": 35.1001008349097, - "Cp0": -0.700254370880408, - "a1x10": 8.91541442651424, - "a2x10-2": 4.20522269611064, - "a3": 1.31206137041937, - "a4x10-4": -2.95284390625721, - "c1": 16.8622849728859, - "c2x10-4": -3.17724181534834, - "ωx10-5": 1.2055, - "Z": -1, - "Comments": "Shock et al. (1997) revised with new predicted a1 for complex species" - }, - { - "Name": "H2P2O7-2", - "Symbol": "H2P2O7(-2)", - "G0": -480400, - "H0": -544600, - "S0": 39, - "V0": 52.4000274417688, - "Cp0": -20.2996438624404, - "a1x10": 12.9545682448853, - "a2x10-2": 8.05089781522593, - "a3": -1.91250077247097, - "a4x10-4": -3.11182411568144, - "c1": 18.4239729019815, - "c2x10-4": -7.16963745477911, - "ωx10-5": 2.6218, - "Z": -2, - "Comments": "Shock et al. (1997) revised with new predicted a1 for complex species" - }, - { - "Name": "H2PO4-", - "Symbol": "H2PO4(-)", - "G0": -270140, - "H0": -309820, - "S0": 21.6, - "V0": 31.2997044192027, - "Cp0": -7.00012249744254, - "a1x10": 8.22281071224164, - "a2x10-2": 3.54579525384029, - "a3": 1.86498503153642, - "a4x10-4": -2.92558317579376, - "c1": 14.0435507063909, - "c2x10-4": -4.46052495272904, - "ωx10-5": 1.3003, - "Z": -1, - "Comments": "Shock et al. (1997) revised with new predicted a1 for complex species" - }, - { - "Name": "H2S,aq", - "Symbol": "H2S(0)", - "G0": -6673, - "H0": -9001, - "S0": 30, - "V0": 34.920046426392, - "Cp0": 42.8331070590266, - "a1x10": 8.25425673796553, - "a2x10-2": 3.57573498977493, - "a3": 1.83988084668652, - "a4x10-4": -2.9268208844773, - "c1": 30.3481619258524, - "c2x10-4": 5.69050390792372, - "ωx10-5": -0.1, - "Z": 0, - "Comments": "Shock et al. (1989) with revised prediction of a1 using new correlation" - }, - { - "Name": "H2VO4-", - "Symbol": "H2VO4(-)", - "G0": -244000, - "H0": -280600, - "S0": 29, - "V0": 29.0001359512636, - "Cp0": 0.599786690084759, - "a1x10": 7.7232096663362, - "a2x10-2": 3.07012549771861, - "a3": 2.2638296142428, - "a4x10-4": -2.90591898807569, - "c1": 17.4795476551971, - "c2x10-4": -2.91242345122973, - "ωx10-5": 1.1898, - "Z": -1, - "Comments": "Shock et al. (1997) revised with new predicted a1 for complex species" - }, - { - "Name": "H3P2O7-", - "Symbol": "H3P2O7(-)", - "G0": -483600, - "H0": -544100, - "S0": 51, - "V0": 50.9998581572065, - "Cp0": 29.5995732842471, - "a1x10": 11.8360506725338, - "a2x10-2": 6.98595812941322, - "a3": -1.01955893808034, - "a4x10-4": -3.06779950906994, - "c1": 31.4073359920603, - "c2x10-4": 2.99483307800113, - "ωx10-5": 0.8568, - "Z": -1, - "Comments": "Shock et al. (1997) revised with new predicted a1 for complex species" - }, - { - "Name": "H3PO4,aq", - "Symbol": "H3PO4(0)", - "G0": -273100, - "H0": -307920, - "S0": 38, - "V0": 48.1001467315767, - "Cp0": 23.5999238317308, - "a1x10": 10.7564054440306, - "a2x10-2": 5.9580287710802, - "a3": -0.157649912543956, - "a4x10-4": -3.02530490939646, - "c1": 17.9707908870086, - "c2x10-4": 1.77270448452355, - "ωx10-5": -0.22, - "Z": 0, - "Comments": "Shock et al. (1989) with revised prediction of a1 using new correlation" - }, - { - "Name": "HAlO2,aq", - "Symbol": "HAlO2(0)", - "G0": -207500, - "H0": -230730, - "S0": -6.5, - "V0": 13, - "Cp0": 47.5, - "a1x10": 4.2849573925203, - "a2x10-2": -0.203431741551792, - "a3": 5.00867633669925, - "a4x10-4": -2.77059013180425, - "c1": 38.6109498405857, - "c2x10-4": 6.64115, - "ωx10-5": 0.5, - "Z": 0, - "Comments": "Sverjensky et al. (2014)" - }, - { - "Name": "HAsO4-2", - "Symbol": "HAsO4(-2)", - "G0": -170790, - "H0": -216620, - "S0": -0.4, - "V0": 13.0000480679283, - "Cp0": -51.8002579615514, - "a1x10": 5.58948384666755, - "a2x10-2": 1.03860685181006, - "a3": 3.9672387466501, - "a4x10-4": -2.82193600725383, - "c1": 5.47102549626226, - "c2x10-4": -13.586312546768, - "ωx10-5": 3.2197, - "Z": -2, - "Comments": "Shock et al. (1997) revised with new predicted a1 for complex species" - }, - { - "Name": "HCl,aq", - "Symbol": "HCl(0)", - "G0": -30410, - "H0": -42054, - "S0": 3.2, - "V0": 15, - "Cp0": 39, - "a1x10": 4.33761904299188, - "a2x10-2": -0.153292626267539, - "a3": 4.96663516368908, - "a4x10-4": -2.7726628828301, - "c1": 27.1804414296505, - "c2x10-4": 4.9097, - "ωx10-5": -0.2, - "Z": 0, - "Comments": "Regression of Sverjensky et al. (1991) & Tagirov et al. 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(2014)" - }, - { - "Name": "HCrO4-", - "Symbol": "HCrO4(-)", - "G0": -182800, - "H0": -209900, - "S0": 44, - "V0": 44.0002332549264, - "Cp0": 20.4003888157089, - "a1x10": 10.5272091346053, - "a2x10-2": 5.73981114823531, - "a3": 0.0253234962184035, - "a4x10-4": -3.01628379286805, - "c1": 26.9870796962219, - "c2x10-4": 1.1209592017599, - "ωx10-5": 0.9622, - "Z": -1, - "Comments": "Shock et al. (1997) revised with new predicted a1 for complex species" - }, - { - "Name": "He,aq", - "Symbol": "He(0)", - "G0": 4658, - "H0": -150, - "S0": 14.02, - "V0": 13.0001571838305, - "Cp0": 37.2998609020564, - "a1x10": 3.4722, - "a2x10-2": 0.6967, - "a3": 5.4762, - "a4x10-4": -2.8078, - "c1": 26.0707, - "c2x10-4": 4.5634, - "ωx10-5": -0.2123, - "Z": 0, - "Comments": "Shock et al. 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(1997) revised with new predicted a1 for complex species" - }, - { - "Name": "HSeO3-", - "Symbol": "HSeO3(-)", - "G0": -98340, - "H0": -122980, - "S0": 32.3, - "V0": 32.3002509991193, - "Cp0": 4.9003579478081, - "a1x10": 8.34033413244225, - "a2x10-2": 3.6576892081936, - "a3": 1.7711630112018, - "a4x10-4": -2.93020887186672, - "c1": 19.54299086873, - "c2x10-4": -2.03639708603149, - "ωx10-5": 1.1402, - "Z": -1, - "Comments": "Shock et al. (1997) revised with new predicted a1 for complex species" - }, - { - "Name": "HSeO4-", - "Symbol": "HSeO4(-)", - "G0": -108100, - "H0": -139000, - "S0": 35.7, - "V0": 30.9999457073159, - "Cp0": -41.9003319648392, - "a1x10": 8.06300368933449, - "a2x10-2": 3.39364311517731, - "a3": 1.9925631578981, - "a4x10-4": -2.91929320638143, - "c1": -8.36140162407764, - "c2x10-4": -11.5696976212377, - "ωx10-5": 1.0885, - "Z": -1, - "Comments": "Shock et al. (1997) revised with new predicted a1 for complex species" - }, - { - "Name": "HSiO3-", - "Symbol": "HSiO3(-)", - "G0": -242801, - "H0": -273872, - "S0": 5, - "V0": 5, - "Cp0": -21, - "a1x10": 3.23544253707646, - "a2x10-2": -1.20267399579946, - "a3": 5.84653149732048, - "a4x10-4": -2.72928145701365, - "c1": 8.14933860331401, - "c2x10-4": -7.3123, - "ωx10-5": 1.5511, - "Z": -1, - "Comments": "Sverjensky et al. (1997), revised to predict a1 using new correlation for complex species in Sverjensky et al. (2014)" - }, - { - "Name": "HSO3-", - "Symbol": "HSO3(-)", - "G0": -126130, - "H0": -149670, - "S0": 33.4, - "V0": 33.299883324899, - "Cp0": -1.40003650925402, - "a1x10": 6.7014, - "a2x10-2": 8.5816, - "a3": 2.3771, - "a4x10-4": -3.1338, - "c1": 15.6949, - "c2x10-4": -3.3198, - "ωx10-5": 1.1233, - "Z": -1, - "Comments": "Sverjensky et al. (1997) revised using published estimated V and pred. a1 from new correlation" - }, - { - "Name": "HSO4-", - "Symbol": "HSO4(-)", - "G0": -180630, - "H0": -212500, - "S0": 30, - "V0": 35.1999336118176, - "Cp0": 5.30010984413594, - "a1x10": 8.92007754821677, - "a2x10-2": 4.20966245055308, - "a3": 1.30833867839381, - "a4x10-4": -2.95302744570586, - "c1": 20.0960342103181, - "c2x10-4": -1.95496762474951, - "ωx10-5": 1.1748, - "Z": -1, - "Comments": "Shock et al. (1997) revised with new predicted a1 for complex species" - }, - { - "Name": "HSO5-", - "Symbol": "HSO5(-)", - "G0": -152370, - "H0": -185380, - "S0": 50.7, - "V0": 50.6998407736731, - "Cp0": 29.1997421064193, - "a1x10": 11.7798468120535, - "a2x10-2": 6.93244647881342, - "a3": -0.974689926168759, - "a4x10-4": -3.06558733743415, - "c1": 31.2126254681266, - "c2x10-4": 2.9133874670776, - "ωx10-5": 0.8611, - "Z": -1, - "Comments": "Shock et al. (1997) revised with new predicted a1 for complex species" - }, - { - "Name": "H-SUCCINATE,AQ", - "Symbol": "C4H504-", - "G0": -172060, - "H0": -217350, - "S0": 45.2, - "V0": 69.9900771138804, - "Cp0": 9.2999823093372, - "a1x10": 15.566254786236, - "a2x10-2": 10.5374824818755, - "a3": -3.99747845072436, - "a4x10-4": -3.21461952580073, - "c1": 20.3194113963877, - "c2x10-4": -1.14019360358801, - "ωx10-5": 0.9446, - "Z": -1, - "Comments": "Shock & Helgeson (1990) revised with new predicted a1 for complex species" - }, - { - "Name": "HVO4-2", - "Symbol": "HVO4(-2)", - "G0": -233000, - "H0": -277000, - "S0": 4, - "V0": 17.3998621681699, - "Cp0": -48.2996121396833, - "a1x10": 6.41183487247775, - "a2x10-2": 1.82156660559647, - "a3": 3.31073441301123, - "a4x10-4": -2.85430356347536, - "c1": 6.90535977071533, - "c2x10-4": -12.8732309928535, - "ωx10-5": 3.1527, - "Z": -2, - "Comments": "Shock et al. (1997) revised with new predicted a1 for complex species" - }, - { - "Name": "I-", - "Symbol": "I(-)", - "G0": -12410, - "H0": -13600, - "S0": 25.5, - "V0": 36.3099204325014, - "Cp0": -28.2325733208874, - "a1x10": 7.7623, - "a2x10-2": 8.2762, - "a3": 1.4609, - "a4x10-4": -3.1211, - "c1": -6.27, - "c2x10-4": -4.944, - "ωx10-5": 1.2934, - "Z": -1, - "Comments": "Shock & Helgeson (1988)" - }, - { - "Name": "In+3", - "Symbol": "In(+3)", - "G0": -23400, - "H0": -25000, - "S0": -63, - "V0": -42.1998616214774, - "Cp0": -34.9002438739034, - "a1x10": -8.32232147397517, - "a2x10-2": -2.09338681654747, - "a3": 13.9777556278712, - "a4x10-4": -2.69245938900393, - "c1": 8.74776191170459, - "c2x10-4": -10.1437796771141, - "ωx10-5": 2.5003, - "Z": 3, - "Comments": "Shock et al. (1997) revised with new predicted a1 for cations" - }, - { - "Name": "K+", - "Symbol": "K(+)", - "G0": -67510, - "H0": -60270, - "S0": 24.15, - "V0": 9.06801954096976, - "Cp0": 1.98519917029563, - "a1x10": 3.559, - "a2x10-2": -1.473, - "a3": 5.435, - "a4x10-4": -2.712, - "c1": 7.4, - "c2x10-4": -1.791, - "ωx10-5": 0.1927, - "Z": 1, - "Comments": "Shock & Helgeson (1988)" - }, - { - "Name": "KCl,aq", - "Symbol": "KCl(0)", - "G0": -98800, - "H0": -96012, - "S0": 44, - "V0": 34, - "Cp0": -17, - "a1x10": 8.31540191401624, - "a2x10-2": 3.63395126297617, - "a3": 1.79106705330812, - "a4x10-4": -2.92922754521143, - "c1": -0.111309218863548, - "c2x10-4": -6.4975, - "ωx10-5": 0.4, - "Z": 0, - "Comments": "Fitted to Ho & Palmer (1997) data with new a1 pred. from the volume" - }, - { - "Name": "KOH,aq", - "Symbol": "KOH(0)", - "G0": -102800, - "H0": -180000, - "S0": 36.3, - "V0": 20.3, - "Cp0": -6.5, - "a1x10": 5.69309729681948, - "a2x10-2": 1.13725713480812, - "a3": 3.88452141923995, - "a4x10-4": -2.82601420995297, - "c1": 6.77936476523284, - "c2x10-4": -4.35865, - "ωx10-5": 0.48, - "Z": 0, - "Comments": "Fitted to Ho & Palmer (1997) data with a1 pred. from the sum of the ions and used to predict the volume" - }, - { - "Name": "Kr,aq", - "Symbol": "Kr(0)", - "G0": 3554, - "H0": -3650, - "S0": 15.06, - "V0": 33.5003414046157, - "Cp0": 57.6002521514901, - "a1x10": 6.2721, - "a2x10-2": 7.5333, - "a3": 2.7891, - "a4x10-4": -3.0904, - "c1": 37.8226, - "c2x10-4": 8.6985, - "ωx10-5": -0.2281, - "Z": 0, - "Comments": "Shock et al. (1989)" - }, - { - "Name": "KSO4-", - "Symbol": "KSO4(-)", - "G0": -246570, - "H0": -276980, - "S0": 34, - "V0": 50.7, - "Cp0": -22, - "a1x10": 11.8942754016306, - "a2x10-2": 7.04139384740601, - "a3": -1.06604126226705, - "a4x10-4": -3.07009122165176, - "c1": 3.4036819642334, - "c2x10-4": -7.516, - "ωx10-5": 1.0996, - "Z": -1, - "Comments": "Revised G, S and Cp to fit Noyes et al. (1906) & Sharygin et al. (2006) with a1 of the complex equal to the sum of the a1 values of the ions" - }, - { - "Name": "La+3", - "Symbol": "La(+3)", - "G0": -164000, - "H0": -169600, - "S0": -52, - "V0": -38.5999288691227, - "Cp0": -37.199558100288, - "a1x10": -7.30525301688857, - "a2x10-2": -2.83938961364498, - "a3": 13.3515282500511, - "a4x10-4": -2.66161963337192, - "c1": 4.23929836467658, - "c2x10-4": -10.6121499850287, - "ωx10-5": 2.1572, - "Z": 3, - "Comments": "Shock et al. (1997) revised with new predicted a1 for cations" - }, - { - "Name": "LACTATE,AQ", - "Symbol": "C3H5O3-", - "G0": -122530, - "H0": -164070, - "S0": 31.9, - "V0": 56.2499039209265, - "Cp0": 26.6995952578856, - "a1x10": 8.4976664002451, - "a2x10-2": 19.7862821535051, - "a3": -0.0855076207025629, - "a4x10-4": -3.5969649042259, - "c1": 32.3804135573831, - "c2x10-4": 2.40410755403129, - "ωx10-5": 1.1469, - "Z": -1, - "Comments": "Shock & Helgeson (1990) revised with new predicted a1 for ions" - }, - { - "Name": "LACTIC-ACID,AQ", - "Symbol": "C3H6O3", - "G0": -127800, - "H0": -164000, - "S0": 49.8, - "V0": 69.3799220653643, - "Cp0": 66.6997288105527, - "a1x10": 14.871307453602, - "a2x10-2": 9.87582368243811, - "a3": -3.44268381776874, - "a4x10-4": -3.18726655103199, - "c1": 42.8872156672021, - "c2x10-4": 10.5521347587096, - "ωx10-5": -0.2572, - "Z": 0, - "Comments": "Shock & Helgeson (1990) revised with new predicted a1 for complex species" - }, - { - "Name": "LEUCINE,AQ", - "Symbol": "C6H13NO2", - "G0": -82000, - "H0": -151070, - "S0": 51.5, - "V0": 107.569952023521, - "Cp0": 95.0999524564527, - "a1x10": 22.2005602425487, - "a2x10-2": 16.8539993993326, - "a3": -9.29381802598324, - "a4x10-4": -3.47574433516841, - "c1": 57.8483122618736, - "c2x10-4": 16.3372603153794, - "ωx10-5": -0.4399, - "Z": 0, - "Comments": "Shock & Helgeson (1990) revised with new predicted a1 for complex species" - }, - { - "Name": "Li+", - "Symbol": "Li(+)", - "G0": -69933, - "H0": -66552, - "S0": 2.7, - "V0": -0.870117831345254, - "Cp0": 14.2330161020346, - "a1x10": -0.0237, - "a2x10-2": -0.069, - "a3": 11.58, - "a4x10-4": -2.7761, - "c1": 19.2, - "c2x10-4": -0.24, - "ωx10-5": 0.4862, - "Z": 1, - "Comments": "Shock & Helgeson (1988)" - }, - { - "Name": "Lu+3", - "Symbol": "Lu(+3)", - "G0": -159400, - "H0": -167900, - "S0": -63.1, - "V0": -45.0001614483955, - "Cp0": -32.800059266083, - "a1x10": -9.39800716704966, - "a2x10-2": -1.3043892517916, - "a3": 14.6400746942418, - "a4x10-4": -2.72507654833094, - "c1": 9.56494324858524, - "c2x10-4": -9.7159720725011, - "ωx10-5": 2.4554, - "Z": 3, - "Comments": "Shock et al. (1997) revised with new predicted a1 for ions" - }, - { - "Name": "METHANE,AQ", - "Symbol": "CH4", - "G0": -8234, - "H0": -21010, - "S0": 20.99, - "V0": 36.0023793740113, - "Cp0": 57.6921661259454, - "a1x10": 8.32, - "a2x10-2": 3.64, - "a3": 1.79, - "a4x10-4": -2.93, - "c1": 40.9, - "c2x10-4": 6.45, - "ωx10-5": -0.4, - "Z": 0, - "Comments": "Plyasunov & Shock (2001) for c1, c2 & omega; a1 predicted with new correlation for complex species from Sverjensky et al. (2014)" - }, - { - "Name": "METHANOL,AQ", - "Symbol": "CH3OH", - "G0": -42050, - "H0": -58870, - "S0": 31.6, - "V0": 38.6884518644431, - "Cp0": 37.7327393338616, - "a1x10": 8.4, - "a2x10-2": 4.1, - "a3": -0.24, - "a4x10-4": -1.43, - "c1": 34.4, - "c2x10-4": 0.96, - "ωx10-5": -0.15, - "Z": 0, - "Comments": "Plyasunov & Shock (2001)" - }, - { - "Name": "Mg(HCO3)+", - "Symbol": "Mg(HCO3)(+)", - "G0": -250200, - "H0": -275750, - "S0": -3, - "V0": 25.9, - "Cp0": 60.7497200296713, - "a1x10": 6.83751238884679, - "a2x10-2": 2.22685382838596, - "a3": 2.97090491750646, - "a4x10-4": -2.87105813726548, - "c1": 47.2835666929098, - "c2x10-4": 9.34011797004405, - "ωx10-5": 0.5985, - "Z": 1, - "Comments": "Sverjensky et al. (1997) revised V increased so that a1 of the complex is the sum of the a1 values of the ions" - }, - { - "Name": "Mg(HSiO3)+", - "Symbol": "Mg(HSiO3)(+)", - "G0": -353025, - "H0": -385700, - "S0": -23.78, - "V0": 2.5, - "Cp0": 37.82, - "a1x10": 2.44328589820438, - "a2x10-2": -1.95688569793783, - "a3": 6.47893086209047, - "a4x10-4": -2.69810234524725, - "c1": 36.7319427076326, - "c2x10-4": 4.669334, - "ωx10-5": 0.91182432, - "Z": 1, - "Comments": "Sverjensky et al. (1997) with new a1 from the sum of the ions and V predicted from a1 value" - }, - { - "Name": "Mg+2", - "Symbol": "Mg(+2)", - "G0": -108505, - "H0": -111367, - "S0": -33, - "V0": -21.5431049706471, - "Cp0": -5.3350914017008, - "a1x10": -0.8217, - "a2x10-2": -8.599, - "a3": 8.39, - "a4x10-4": -2.39, - "c1": 20.8, - "c2x10-4": -5.892, - "ωx10-5": 1.5372, - "Z": 2, - "Comments": "Shock & Helgeson (1988)" - }, - { - "Name": "MgCl+", - "Symbol": "MgCl(+)", - "G0": -139700, - "H0": -150933, - "S0": -19, - "V0": 1.2529488954192, - "Cp0": 24.9981334007784, - "a1x10": 3.21, - "a2x10-2": -4.92, - "a3": 6.27, - "a4x10-4": -2.58, - "c1": 28.6, - "c2x10-4": 2.058, - "ωx10-5": 0.8449, - "Z": 1, - "Comments": "Sverjensky et al. (1997) revised V increased so that a1 of the complex is the sum of the a1 values of the ions" - }, - { - "Name": "MgCO3,aq", - "Symbol": "MgCO3(0)", - "G0": -238760, - "H0": -270570, - "S0": -24, - "V0": 17.9, - "Cp0": -24.8, - "a1x10": 4.97853211816846, - "a2x10-2": 0.456920199872419, - "a3": 4.45497749180293, - "a4x10-4": -2.79788908106273, - "c1": -8.7178117141923, - "c2x10-4": -8.08636, - "ωx10-5": -0.038, - "Z": 0, - "Comments": "Sverjensky et al. (1997) revised volume increased in order that a1 of the complex is the sum of the a1 values of the ions; and Cp revised using isocoulombic reln with CaCO3,aq" - }, - { - "Name": "MgOH+", - "Symbol": "MgOH(+)", - "G0": -149225, - "H0": -152955, - "S0": -19.1, - "V0": -3.3, - "Cp0": 30.7996539827306, - "a1x10": 1.28476732788079, - "a2x10-2": -3.05991030191866, - "a3": 7.40380653944396, - "a4x10-4": -2.65250330811868, - "c1": 32.0010245137424, - "c2x10-4": 3.23928951628223, - "ωx10-5": 0.8449, - "Z": 1, - "Comments": "Shock et al. (1997) with revised a1 equal to the sum of the ions used to predict new values of V using new correlation in Sverjensky et al. (2014)" - }, - { - "Name": "MgSO4,aq", - "Symbol": "MgSO4", - "G0": -289449, - "H0": -327449, - "S0": -1, - "V0": 35, - "Cp0": 20, - "a1x10": 8.34173273925203, - "a2x10-2": 3.6590208206183, - "a3": 1.77004646680304, - "a4x10-4": -2.93026392072436, - "c1": 18.348479084619, - "c2x10-4": 1.0394, - "ωx10-5": 0.05, - "Z": 0, - "Comments": "S, Cp, V, omega from fit to Akilan et al. (2006a) and Frantz et al. (1994)" - }, - { - "Name": "Mn+2", - "Symbol": "Mn(+2)", - "G0": -54500, - "H0": -52724, - "S0": -17.6, - "V0": -17.0999746995345, - "Cp0": -4.09990955696642, - "a1x10": -1.12878159446875, - "a2x10-2": -5.35784830002894, - "a3": 9.33060577388377, - "a4x10-4": -2.5575065512768, - "c1": 16.6673015992186, - "c2x10-4": -3.86975157675406, - "ωx10-5": 1.4006, - "Z": 2, - "Comments": "Shock et al. (1997) revised with new predicted a1 for cations" - }, - { - "Name": "MnCl+", - "Symbol": "MnCl(+)", - "G0": -86290, - "H0": -88280, - "S0": 12, - "V0": 6.3, - "Cp0": 24.6295833119747, - "a1x10": 2.92072375376596, - "a2x10-2": -1.50231749761181, - "a3": 6.09777973394466, - "a4x10-4": -2.71689419464873, - "c1": 23.9969094881211, - "c2x10-4": 1.98244612064924, - "ωx10-5": 0.3686, - "Z": 1, - "Comments": "Sverjensky et al. (1997) with revised a1 equal to the sum of the ions used to predict new values of V using new correlation in Sverjensky et al. (2014)" - }, - { - "Name": "MnO4-", - "Symbol": "MnO4(-)", - "G0": -106900, - "H0": -129400, - "S0": 45.7, - "V0": 41.9999685425673, - "Cp0": -1.79965876908186, - "a1x10": 6.89229404983946, - "a2x10-2": 13.7706595981383, - "a3": 1.68221984338678, - "a4x10-4": -3.34827906778704, - "c1": 13.742477467512, - "c2x10-4": -3.40119049126198, - "ωx10-5": 0.9368, - "Z": -1, - "Comments": "Shock et al. (1997) revised with new predicted a1 for ions" - }, - { - "Name": "MnO4-2", - "Symbol": "MnO4(-2)", - "G0": -119700, - "H0": -156000, - "S0": 14, - "V0": 27.3997969015227, - "Cp0": -59.3004450367967, - "a1x10": 11.8563774976035, - "a2x10-2": -5.69541027639123, - "a3": 0.340150422986751, - "a4x10-4": -2.54355173917399, - "c1": -0.926495461216696, - "c2x10-4": -15.1141006539955, - "ωx10-5": 3.0024, - "Z": -2, - "Comments": "Shock et al. (1997) revised with new predicted a1 for ions" - }, - { - "Name": "MnSO4,aq", - "Symbol": "MnSO4(0)", - "G0": -235640, - "H0": -266750, - "S0": 5, - "V0": 29.2, - "Cp0": -21.479758479807, - "a1x10": 7.17310511816846, - "a2x10-2": 2.54637139749621, - "a3": 2.70299246379449, - "a4x10-4": -2.88426699357249, - "c1": -6.77194553502511, - "c2x10-4": -7.41002680233669, - "ωx10-5": -0.038, - "Z": 0, - "Comments": "Sverjensky et al. (1997) with revised a1 equal to the sum of the ions used to predict new values of V using new correlation in Sverjensky et al. (2014)" - }, - { - "Name": "MoO4-2", - "Symbol": "MoO4(-2)", - "G0": -199900, - "H0": -238500, - "S0": 6.5, - "V0": 30.4001214628427, - "Cp0": -47.4995498680277, - "a1x10": 12.6399527211691, - "a2x10-2": -5.47207562150113, - "a3": -0.228770574525159, - "a4x10-4": -2.55278439380714, - "c1": 7.02231527800825, - "c2x10-4": -12.7102583081172, - "ωx10-5": 3.1145, - "Z": -2, - "Comments": "Shock et al. (1997) revised with new predicted a1 for ions" - }, - { - "Name": "N2,aq", - "Symbol": "N2(0)", - "G0": 4347, - "H0": -2495, - "S0": 22.9, - "V0": 33.3002347170321, - "Cp0": 56.0000549264791, - "a1x10": 7.82129430494273, - "a2x10-2": 3.16351180366738, - "a3": 2.18552608170308, - "a4x10-4": -2.90977957796361, - "c1": 35.7910772638231, - "c2x10-4": 8.3726111885238, - "ωx10-5": -0.3468, - "Z": 0, - "Comments": "Shock et al. (1989) + new a1 predicted for complex species" - }, - { - "Name": "Na+", - "Symbol": "Na(+)", - "G0": -62591, - "H0": -57433, - "S0": 13.96, - "V0": -1.10680869183899, - "Cp0": 9.07655259900881, - "a1x10": 1.839, - "a2x10-2": -2.285, - "a3": 3.256, - "a4x10-4": -2.726, - "c1": 18.18, - "c2x10-4": -2.981, - "ωx10-5": 0.3306, - "Z": 1, - "Comments": "Shock & Helgeson (1988)" - }, - { - "Name": "NaCl,aq", - "Symbol": "NaCl(0)", - "G0": -92910, - "H0": -96120, - "S0": 28, - "V0": 24.0000657937439, - "Cp0": 8.5083603247707, - "a1x10": 6.16322589597147, - "a2x10-2": 1.58486619795403, - "a3": 3.50920546166967, - "a4x10-4": -2.84451836862342, - "c1": 10.8029404495594, - "c2x10-4": -1.30144700184421, - "ωx10-5": -0.038, - "Z": 0, - "Comments": "Sverjensky et al. (1997) with new predicted a1 value" - }, - { - "Name": "NaCO3-", - "Symbol": "NaCO3(-)", - "G0": -190562, - "H0": "", - "S0": 8, - "V0": 27.8, - "Cp0": -1, - "a1x10": 7.64273247379239, - "a2x10-2": 2.99350322708006, - "a3": 2.32807666204339, - "a4x10-4": -2.90275142340749, - "c1": 19.4730190790062, - "c2x10-4": -3.2383, - "ωx10-5": 1.507948, - "Z": -1, - "Comments": "Fit to Stefansson et al. (2013; 80 to 200 C) & Garrels et al., (1961; at 25 C) to get G, S and Cp; with a1 pred. from the sum of the ions and used to predict the volume" - }, - { - "Name": "NaHCO3,aq", - "Symbol": "NaHCO3(0)", - "G0": -203088, - "H0": -150000, - "S0": 37, - "V0": 41.2, - "Cp0": 35, - "a1x10": 9.50362511816846, - "a2x10-2": 4.76525762506129, - "a3": 0.842477389803241, - "a4x10-4": -2.97599575022003, - "c1": 26.3286741533281, - "c2x10-4": 4.0949, - "ωx10-5": -0.038, - "Z": 0, - "Comments": "Fit to Stefansson et al. (2013; 80 to 200 C) & Nakayama (1971; at 25 C) to get G, S and Cp; with a1 pred. from the sum of the ions and used to predict the volume" - }, - { - "Name": "NaHSiO3,aq", - "Symbol": "NaHSiO3(0)", - "G0": -307140, - "H0": -333044, - "S0": 19, - "V0": 18.7, - "Cp0": 2.34008745531115, - "a1x10": 5.13390011816846, - "a2x10-2": 0.604845948376757, - "a3": 4.33094315353685, - "a4x10-4": -2.8040043315059, - "c1": 7.1879523568082, - "c2x10-4": -2.55792418535312, - "ωx10-5": -0.038, - "Z": 0, - "Comments": "Sverjensky et al. (1997) with revised a1 equal to the sum of the ions used to predict new values of V using new correlation in Sverjensky et al. (2014)" - }, - { - "Name": "NaOH,aq", - "Symbol": "NaOH(0)", - "G0": -100900, - "H0": "", - "S0": 6.5, - "V0": 12, - "Cp0": 42, - "a1x10": 3.94685095700812, - "a2x10-2": -0.525342608315042, - "a3": 5.27859554781258, - "a4x10-4": -2.75728233657226, - "c1": 32.6237603393924, - "c2x10-4": 5.5208, - "ωx10-5": 0.2, - "Z": 0, - "Comments": "Fitted to Ho & Palmer (1997) data with a1 pred. from the sum of the ions and used to predict the volume" - }, - { - "Name": "Nd+3", - "Symbol": "Nd(+3)", - "G0": -160600, - "H0": -166500, - "S0": -49.5, - "V0": -43.0999913556667, - "Cp0": -43.2000035438043, - "a1x10": -8.87877564002377, - "a2x10-2": -1.68523694085679, - "a3": 14.3203744858779, - "a4x10-4": -2.70933230486498, - "c1": 1.62368275083673, - "c2x10-4": -11.8344407218729, - "ωx10-5": 2.255, - "Z": 3, - "Comments": "Shock et al. (1997) revised with new predicted a1 for cations" - }, - { - "Name": "Ne,aq", - "Symbol": "Ne(0)", - "G0": 4565, - "H0": -870, - "S0": 16.74, - "V0": 20.4001221683175, - "Cp0": 39.6999224182231, - "a1x10": 4.4709, - "a2x10-2": 3.1352, - "a3": 4.5177, - "a4x10-4": -2.9086, - "c1": 27.0977, - "c2x10-4": 5.0523, - "ωx10-5": -0.2535, - "Z": 0, - "Comments": "Shock et al. (1989)" - }, - { - "Name": "NH3,aq", - "Symbol": "NH3(0)", - "G0": -6383, - "H0": -19440, - "S0": 25.77, - "V0": 24.4300581474313, - "Cp0": 18.3830870852936, - "a1x10": 6.24097885356061, - "a2x10-2": 1.65889472667166, - "a3": 3.44713324188954, - "a4x10-4": -2.84757870800061, - "c1": 16.4795849556178, - "c2x10-4": 0.710034839274313, - "ωx10-5": -0.05, - "Z": 0, - "Comments": "Shock et al. (1989) + new a1" - }, - { - "Name": "NH4+", - "Symbol": "NH4(+)", - "G0": -18990, - "H0": -31850, - "S0": 26.57, - "V0": 18.130099154302, - "Cp0": 16.0235581249155, - "a1x10": 5.11349070547009, - "a2x10-2": 0.585414162874339, - "a3": 4.34723652153052, - "a4x10-4": -2.80320102149323, - "c1": 16.9411651185393, - "c2x10-4": 0.229398790045293, - "ωx10-5": 0.1502, - "Z": 1, - "Comments": "Shock & Helgeson (1988) + new a1" - }, - { - "Name": "Ni+2", - "Symbol": "Ni(+2)", - "G0": -10900, - "H0": -12900, - "S0": -30.8, - "V0": -29.0001861621336, - "Cp0": -11.7001822704937, - "a1x10": -2.51210360600186, - "a2x10-2": -9.79071557964785, - "a3": 10.7724999362811, - "a4x10-4": -2.37425181793736, - "c1": 13.1905551277698, - "c2x10-4": -5.41792712849957, - "ωx10-5": 1.5067, - "Z": 2, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "NO2-", - "Symbol": "NO2(-)", - "G0": -7700, - "H0": -25000, - "S0": 29.4, - "V0": 25.0000581404839, - "Cp0": -23.2997937741986, - "a1x10": 5.11095611901146, - "a2x10-2": 7.09566196739438, - "a3": 3.64370870443078, - "a4x10-4": -3.07233466573208, - "c1": 3.42593495620931, - "c2x10-4": -7.78076799180425, - "ωx10-5": 1.1847, - "Z": -1, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "NO3-", - "Symbol": "NO3(-)", - "G0": -26507, - "H0": -49429, - "S0": 35.12, - "V0": 29.0001029667788, - "Cp0": -16.0787880565516, - "a1x10": 5.5224045870334, - "a2x10-2": 8.63743430698806, - "a3": 3.19064947689639, - "a4x10-4": -3.13607153425089, - "c1": 6.85637273985144, - "c2x10-4": -6.30984912711956, - "ωx10-5": 1.0977, - "Z": -1, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "O2,aq", - "Symbol": "O2(0)", - "G0": 3954, - "H0": -2900, - "S0": 26.04, - "V0": 30.3797300470105, - "Cp0": 55.9995645889791, - "a1x10": 5.7889, - "a2x10-2": 6.3536, - "a3": 3.2528, - "a4x10-4": -3.0417, - "c1": 35.353, - "c2x10-4": 8.3726, - "ωx10-5": -0.3943, - "Z": 0, - "Comments": "Shock et al. (1989)" - }, - { - "Name": "OH-", - "Symbol": "OH(-)", - "G0": -37595, - "H0": -54977, - "S0": -5, - "V0": -9.0995333789813, - "Cp0": -19.0074531902495, - "a1x10": 2.1, - "a2x10-2": -5, - "a3": 1, - "a4x10-4": -2.7, - "c1": 12.12, - "c2x10-4": -7.52, - "ωx10-5": 1.72, - "Z": -1, - "Comments": "August 16th, 2013 fit to Bandura & Lvov (2005)" - }, - { - "Name": "Pb+2", - "Symbol": "Pb(+2)", - "G0": -5710, - "H0": 220, - "S0": 4.2, - "V0": -15.5999413568919, - "Cp0": -12.7000485374131, - "a1x10": 0.439210163272197, - "a2x10-2": -8.94953196088319, - "a3": 8.62967519771224, - "a4x10-4": -2.40902634873709, - "c1": 8.66239977051731, - "c2x10-4": -5.62159988707105, - "ωx10-5": 1.0788, - "Z": 2, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "PbCl+", - "Symbol": "PbCl(+)", - "G0": -39050, - "H0": -38630, - "S0": 28, - "V0": 13.8, - "Cp0": 4.8997714611085, - "a1x10": 4.2619417779637, - "a2x10-2": -0.225344889758445, - "a3": 5.02705030380518, - "a4x10-4": -2.76968424225739, - "c1": 10.218336847875, - "c2x10-4": -2.0365165533722, - "ωx10-5": 0.1281, - "Z": 1, - "Comments": "Sverjensky et al. (1997) with revised a1 equal to the sum of the ions used to predict new values of V using new correlation in Sverjensky et al. (2014)" - }, - { - "Name": "PbCl2,aq", - "Symbol": "PbCl2(0)", - "G0": -71200, - "H0": -77700, - "S0": 47, - "V0": 34.9700035580091, - "Cp0": 2.00006306363239, - "a1x10": 8.29369750916941, - "a2x10-2": 3.61328651648521, - "a3": 1.80839424740624, - "a4x10-4": -2.9283732645915, - "c1": 6.98867710534362, - "c2x10-4": -2.62718715393808, - "ωx10-5": -0.038, - "Z": 0, - "Comments": "Sverjensky et al. (1997) with revised a1 equal to the sum of the ions used to predict new values of V using new correlation in Sverjensky et al. (2014)" - }, - { - "Name": "PbCl3-", - "Symbol": "PbCl3(-)", - "G0": -102150, - "H0": -117700, - "S0": 59, - "V0": 53.8, - "Cp0": -11.9995231802391, - "a1x10": 12.3217320598759, - "a2x10-2": 7.44837498975249, - "a3": -1.40729109326751, - "a4x10-4": -3.08691582207637, - "c1": 5.91110583580892, - "c2x10-4": -5.4789028718147, - "ωx10-5": 0.7356, - "Z": -1, - "Comments": "Sverjensky et al. (1997) with revised a1 equal to the sum of the ions used to predict new values of V using new correlation in Sverjensky et al. (2014)" - }, - { - "Name": "Pd+2", - "Symbol": "Pd(+2)", - "G0": 42200, - "H0": 42080, - "S0": -22.6, - "V0": -20.8000131603529, - "Cp0": -6.29989267256892, - "a1x10": -0.614096724623226, - "a2x10-2": -9.24974555011724, - "a3": 9.39443700656678, - "a4x10-4": -2.39661551895815, - "c1": 15.3779758940389, - "c2x10-4": -4.31788813740229, - "ωx10-5": 1.4006, - "Z": 2, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "PO4-3", - "Symbol": "PO4(-3)", - "G0": -243500, - "H0": -305300, - "S0": -53, - "V0": -30.600095804682, - "Cp0": -114.899963915955, - "a1x10": -1.1970758608927, - "a2x10-2": -7.3196359646062, - "a3": 9.59061349843539, - "a4x10-4": -2.47640624922318, - "c1": -9.47495397363052, - "c2x10-4": -26.43972264968, - "ωx10-5": 5.6114, - "Z": -3, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "Pr+3", - "Symbol": "Pr(+3)", - "G0": -162600, - "H0": -168800, - "S0": -50, - "V0": -42.0999937869876, - "Cp0": -47.6996710840918, - "a1x10": -8.52752816736265, - "a2x10-2": -1.94287112000459, - "a3": 14.1041050870603, - "a4x10-4": -2.69868170789901, - "c1": -1.19765647189277, - "c2x10-4": -12.7510229998295, - "ωx10-5": 2.235, - "Z": 3, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "PROPANE,AQ", - "Symbol": "C3H8", - "G0": -1963, - "H0": -30490, - "S0": 33.37, - "V0": 66.999936220909, - "Cp0": 110.599583274718, - "a1x10": 14.2900880505817, - "a2x10-2": 9.32244515380278, - "a3": -2.978681165736, - "a4x10-4": -3.16438988265821, - "c1": 66.3295318566212, - "c2x10-4": 19.49453511306, - "ωx10-5": -0.5053, - "Z": 0, - "Comments": "Shock & Helgeson (1990) with new a1-a4 based on revised correlation to predict a1 in Sverjensky et al. (2013)" - }, - { - "Name": "PROPANOATE,AQ", - "Symbol": "C2H5COO-", - "G0": -86770, - "H0": -122630, - "S0": 26.5, - "V0": 54.950066467725, - "Cp0": 32.4555121371053, - "a1x10": 8.37861896743715, - "a2x10-2": 19.3365089422771, - "a3": 0.045978122076491, - "a4x10-4": -3.57837127967373, - "c1": 52.3, - "c2x10-4": -4.2, - "ωx10-5": 1.2276, - "Z": -1, - "Comments": "Revised a1 from new delVn correlation for -1 ions; kept original regression c1 and c2 plus omega from Shock & Helgeson (1990)" - }, - { - "Name": "PROPANOIC-ACID,AQ", - "Symbol": "C3H6O2", - "G0": -93450, - "H0": -122470, - "S0": 49.4, - "V0": 68.2706415128194, - "Cp0": 61.2842179443684, - "a1x10": 14.6, - "a2x10-2": 7.9, - "a3": 6.9, - "a4x10-4": -4.3, - "c1": 63.3, - "c2x10-4": -1.4, - "ωx10-5": -0.09, - "Z": 0, - "Comments": "Plyasunov & Shock (2001)" - }, - { - "Name": "PROPANOL,AQ", - "Symbol": "C3H7OH", - "G0": -41910, - "H0": -75320, - "S0": 40.6, - "V0": 70.8819997412168, - "Cp0": 82.8484904132744, - "a1x10": 14.6, - "a2x10-2": 9.1, - "a3": 12.2, - "a4x10-4": -5.5, - "c1": 74.3, - "c2x10-4": 3.3, - "ωx10-5": -0.2, - "Z": 0, - "Comments": "Plyasunov & Shock (2001)" - }, - { - "Name": "Ra+2", - "Symbol": "Ra(+2)", - "G0": -134200, - "H0": -126100, - "S0": 13, - "V0": -10.5999928958129, - "Cp0": -14.4002813932061, - "a1x10": 1.54623750473273, - "a2x10-2": -8.63400696491157, - "a3": 7.82590922804468, - "a4x10-4": -2.42207015207056, - "c1": 6.28587583748314, - "c2x10-4": -5.96793731979608, - "ωx10-5": 0.929, - "Z": 2, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "Rb+", - "Symbol": "Rb(+)", - "G0": -67800, - "H0": -60020, - "S0": 28.8, - "V0": 14.2602787650693, - "Cp0": -2.99988751026497, - "a1x10": 4.2913, - "a2x10-2": -0.9041, - "a3": 7.407, - "a4x10-4": -2.7416, - "c1": 5.7923, - "c2x10-4": -3.6457, - "ωx10-5": 0.1502, - "Z": 1, - "Comments": "Shock & Helgeson (1988)" - }, - { - "Name": "ReO4-", - "Symbol": "ReO4(-)", - "G0": -166000, - "H0": -188200, - "S0": 48.1, - "V0": 48.1000094358864, - "Cp0": -0.199747625770513, - "a1x10": 7.54559639003168, - "a2x10-2": 16.218702441371, - "a3": 0.962847487920568, - "a4x10-4": -3.44948115892628, - "c1": 14.3447768165446, - "c2x10-4": -3.07528859136945, - "ωx10-5": 0.9004, - "Z": -1, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "Rn,aq", - "Symbol": "Rn(0)", - "G0": 2790, - "H0": -5000, - "S0": 16, - "V0": 54.100091845361, - "Cp0": 82.9999494813027, - "a1x10": 9.0862, - "a2x10-2": 14.4045, - "a3": 0.0884, - "a4x10-4": -3.3745, - "c1": 52.5774, - "c2x10-4": 13.8725, - "ωx10-5": -0.2423, - "Z": 0, - "Comments": "Shock et al. (1989)" - }, - { - "Name": "S2-2", - "Symbol": "S2(-2)", - "G0": 19000, - "H0": 7200, - "S0": 6.8, - "V0": 20.2002102526536, - "Cp0": -65.0999080550493, - "a1x10": 10.1974927086192, - "a2x10-2": -6.16822571351594, - "a3": 1.54459686351063, - "a4x10-4": -2.52400554900325, - "c1": -3.34969902248253, - "c2x10-4": -16.2954512708135, - "ωx10-5": 3.1083, - "Z": -2, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "S2O3-2", - "Symbol": "S2O3(-2)", - "G0": -124900, - "H0": -155000, - "S0": 16, - "V0": 28.5001855325617, - "Cp0": -57.2995447549579, - "a1x10": 12.0999931624475, - "a2x10-2": -5.62597492570955, - "a3": 0.163271339927078, - "a4x10-4": -2.54642219657117, - "c1": -0.0578681224076476, - "c2x10-4": -14.7065172665849, - "ωx10-5": 2.9694, - "Z": -2, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "S2O4-2", - "Symbol": "S2O4(-2)", - "G0": -143500, - "H0": -180100, - "S0": 22, - "V0": 35.3998478034818, - "Cp0": -52.9003519269525, - "a1x10": 13.6952561968664, - "a2x10-2": -5.17129296469797, - "a3": -0.994982021767589, - "a4x10-4": -2.56521874883939, - "c1": 1.67090663900688, - "c2x10-4": -13.8104016875202, - "ωx10-5": 2.8772, - "Z": -2, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "S2O5-2", - "Symbol": "S2O5(-2)", - "G0": -189000, - "H0": -232000, - "S0": 25, - "V0": 38.3997746614282, - "Cp0": -50.5001318010863, - "a1x10": 14.3872052747127, - "a2x10-2": -4.97407359908414, - "a3": -1.49737713043935, - "a4x10-4": -2.57337179741386, - "c1": 2.68235295262574, - "c2x10-4": -13.3214768478813, - "ωx10-5": 2.8343, - "Z": -2, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "S2O6-2", - "Symbol": "S2O6(-2)", - "G0": -231000, - "H0": -280400, - "S0": 30, - "V0": 43.299857952622, - "Cp0": -46.4999848116083, - "a1x10": 15.5141716557913, - "a2x10-2": -4.65286557690392, - "a3": -2.31561999775217, - "a4x10-4": -2.58665053705079, - "c1": 4.33019531784219, - "c2x10-4": -12.5066469061246, - "ωx10-5": 2.7587, - "Z": -2, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "S2O8-2", - "Symbol": "S2O8(-2)", - "G0": -266500, - "H0": -321400, - "S0": 58.4, - "V0": 79.0001053289553, - "Cp0": -25.0002648519916, - "a1x10": 23.7958216278903, - "a2x10-2": -2.29242922974248, - "a3": -8.32857755622526, - "a4x10-4": -2.68423097564245, - "c1": 12.9633096323999, - "c2x10-4": -8.12715395035069, - "ωx10-5": 2.3281, - "Z": -2, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "S3-2", - "Symbol": "S3(-2)", - "G0": 17600, - "H0": 6200, - "S0": 15.8, - "V0": 29.1997637448247, - "Cp0": -57.9003377235494, - "a1x10": 12.2705101891391, - "a2x10-2": -5.5773741530412, - "a3": 0.0394661020882161, - "a4x10-4": -2.54843135251328, - "c1": -0.359299240326539, - "c2x10-4": -14.828898794287, - "ωx10-5": 2.9749, - "Z": -2, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "S3O6-2", - "Symbol": "S3O6(-2)", - "G0": -229000, - "H0": -279000, - "S0": 33, - "V0": 46.4000479976677, - "Cp0": -44.0997900312421, - "a1x10": 16.2284992497499, - "a2x10-2": -4.44926788535199, - "a3": -2.83426320530023, - "a4x10-4": -2.59506726561955, - "c1": 5.31675212293586, - "c2x10-4": -12.017727229364, - "ωx10-5": 2.7131, - "Z": -2, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "S4-2", - "Symbol": "S4(-2)", - "G0": 16500, - "H0": 5500, - "S0": 24.7, - "V0": 38.0999694446451, - "Cp0": -50.70043851435, - "a1x10": 14.3182973051719, - "a2x10-2": -4.99371375249091, - "a3": -1.44734595335684, - "a4x10-4": -2.57255987347203, - "c1": 2.60826119693232, - "c2x10-4": -13.3622793253731, - "ωx10-5": 2.839, - "Z": -2, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "S4O6-2", - "Symbol": "S4O6(-2)", - "G0": -248700, - "H0": -292600, - "S0": 61.5, - "V0": 74.8997008394251, - "Cp0": -21.3000416403598, - "a1x10": 22.7873060227629, - "a2x10-2": -2.57987640500856, - "a3": -7.5963368130015, - "a4x10-4": -2.67234790941695, - "c1": 14.6933375575224, - "c2x10-4": -7.37341848214129, - "ωx10-5": 2.2805, - "Z": -2, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "S5-2", - "Symbol": "S5(-2)", - "G0": 15700, - "H0": 5100, - "S0": 33.6, - "V0": 46.9999530298551, - "Cp0": -43.5998165646322, - "a1x10": 16.3672123594702, - "a2x10-2": -4.40973186691188, - "a3": -2.93497695731361, - "a4x10-4": -2.59670168462186, - "c1": 5.53606471102412, - "c2x10-4": -11.9158826342156, - "ωx10-5": 2.7051, - "Z": -2, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "S5O6-2", - "Symbol": "S5O6(-2)", - "G0": -229000, - "H0": -281000, - "S0": 40, - "V0": 53.3999198773356, - "Cp0": -38.4999185357532, - "a1x10": 17.839868446592, - "a2x10-2": -3.98999534500838, - "a3": -4.00421057379386, - "a4x10-4": -2.61405359243735, - "c1": 7.62666788372318, - "c2x10-4": -10.8770334057329, - "ωx10-5": 2.6076, - "Z": -2, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "Sc+3", - "Symbol": "Sc(+3)", - "G0": -140200, - "H0": -146800, - "S0": -61, - "V0": -41.9000410187954, - "Cp0": -35.4003146605133, - "a1x10": -8.21153776128418, - "a2x10-2": -2.1746448272197, - "a3": 13.9095440995121, - "a4x10-4": -2.68910018284274, - "c1": 8.45468960809784, - "c2x10-4": -10.2456440963466, - "ωx10-5": 2.5003, - "Z": 3, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "SeO3-2", - "Symbol": "SeO3(-2)", - "G0": -88400, - "H0": -121700, - "S0": 3, - "V0": 16.4000330622271, - "Cp0": -68.1001611578075, - "a1x10": 9.32282541112014, - "a2x10-2": -6.41752343651145, - "a3": 2.17965598281231, - "a4x10-4": -2.51369958113462, - "c1": -4.57829425354105, - "c2x10-4": -16.9066028278454, - "ωx10-5": 3.1658, - "Z": -2, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "SeO4-2", - "Symbol": "SeO4(-2)", - "G0": -105500, - "H0": -143200, - "S0": 12.9, - "V0": 20.7001837561158, - "Cp0": -60.199604228934, - "a1x10": 10.2644207798358, - "a2x10-2": -6.14914987084239, - "a3": 1.4960032072885, - "a4x10-4": -2.52479414433938, - "c1": -1.29868254090719, - "c2x10-4": -15.2972593814339, - "ωx10-5": 3.0192, - "Z": -2, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "Si2O4,aq", - "Symbol": "Si2O4(0)", - "G0": -400751, - "H0": -427304, - "S0": 18, - "V0": 40.0001740252365, - "Cp0": 48.9999917045434, - "a1x10": 10.0724, - "a2x10-2": 2.6931, - "a3": 0.6715, - "a4x10-4": -2.8903, - "c1": 35.8049, - "c2x10-4": 6.9467, - "ωx10-5": 0.1, - "Z": 0, - "Comments": "Fit to Raman speciation and quartz solubility data (Sverjensky et al., 2014)." - }, - { - "Name": "SiO2,aq", - "Symbol": "SiO2(0)", - "G0": -199557, - "H0": -213937, - "S0": 5.3, - "V0": 18.0001256613464, - "Cp0": 27.6999877846904, - "a1x10": 4.8998, - "a2x10-2": 1.409, - "a3": 4.4066, - "a4x10-4": -2.8372, - "c1": 25.7171, - "c2x10-4": 2.6079, - "ωx10-5": 0.36, - "Z": 0, - "Comments": "Fit to Raman speciation and quartz solubility data (Sverjensky et al., 2014)." - }, - { - "Name": "Sm+2", - "Symbol": "Sm(+2)", - "G0": -123000, - "H0": -120500, - "S0": -6.2, - "V0": -5.70007655287458, - "Cp0": 3.700319865125, - "a1x10": 2.89466912120273, - "a2x10-2": -8.24967690871497, - "a3": 6.84686977242248, - "a4x10-4": -2.43795835659372, - "c1": 19.6531879165337, - "c2x10-4": -2.28084484347404, - "ωx10-5": 1.2285, - "Z": 2, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "Sm+3", - "Symbol": "Sm(+3)", - "G0": -159100, - "H0": -165200, - "S0": -50.7, - "V0": -42.0002084361898, - "Cp0": -43.2996781605864, - "a1x10": -8.4354463026213, - "a2x10-2": -2.01041163626027, - "a3": 14.0474086235135, - "a4x10-4": -2.695889582957, - "c1": 1.93838709929989, - "c2x10-4": -11.8547444413114, - "ωx10-5": 2.2955, - "Z": 3, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "Sn+2", - "Symbol": "Sn(+2)", - "G0": -6630, - "H0": -2100, - "S0": -3.8, - "V0": -15.4999031726034, - "Cp0": -11.2001387993838, - "a1x10": 0.58548564515754, - "a2x10-2": -8.90784051469748, - "a3": 8.52347072548931, - "a4x10-4": -2.41074987312241, - "c1": 11.4503387383099, - "c2x10-4": -5.31606827343448, - "ωx10-5": 1.286, - "Z": 2, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "SO2,aq", - "Symbol": "SO2(0)", - "G0": -71980, - "H0": -77194, - "S0": 38.7, - "V0": 38.5000255673879, - "Cp0": 46.6002611838768, - "a1x10": 8.87944692284391, - "a2x10-2": 4.17097806464042, - "a3": 1.34077516937947, - "a4x10-4": -2.95142823319224, - "c1": 31.2099512440134, - "c2x10-4": 6.45787320315569, - "ωx10-5": -0.2461, - "Z": 0, - "Comments": "Shock et al. (1989) with revised a1 predicted as a complex from delVn" - }, - { - "Name": "SO3-2", - "Symbol": "SO3(-2)", - "G0": -116300, - "H0": -151900, - "S0": -7, - "V0": 5.60009580604624, - "Cp0": -76.1000000571626, - "a1x10": 6.83220957259687, - "a2x10-2": -7.12739890479041, - "a3": 3.98798733972253, - "a4x10-4": -2.48435332927596, - "c1": -7.83686093927834, - "c2x10-4": -18.536170011644, - "ωx10-5": 3.321, - "Z": -2, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "SO4-2", - "Symbol": "SO4(-2)", - "G0": -177930, - "H0": -217400, - "S0": 4.5, - "V0": 13.8799132723265, - "Cp0": -63.9200426368977, - "a1x10": 8.3014, - "a2x10-2": -1.9846, - "a3": -6.2122, - "a4x10-4": -2.697, - "c1": 1.64, - "c2x10-4": -17.998, - "ωx10-5": 3.1463, - "Z": -2, - "Comments": "Shock & Helgeson (1988)" - }, - { - "Name": "Sr+2", - "Symbol": "Sr(+2)", - "G0": -134760, - "H0": -131670, - "S0": -7.53, - "V0": -17.4100372056418, - "Cp0": -10.0500600473417, - "a1x10": 0.0403713145680473, - "a2x10-2": -9.06320903227754, - "a3": 8.91925530288547, - "a4x10-4": -2.40432693860565, - "c1": 10.7451943744283, - "c2x10-4": -5.08179723164351, - "ωx10-5": 1.1363, - "Z": 2, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "SrCl+", - "Symbol": "SrCl(+)", - "G0": -165800, - "H0": -169790, - "S0": 11, - "V0": 11.1, - "Cp0": 11.2497896033117, - "a1x10": 3.86017454102007, - "a2x10-2": -0.607867154635422, - "a3": 5.34779159783803, - "a4x10-4": -2.75387077182737, - "c1": 16.2946394986111, - "c2x10-4": -0.743017857805416, - "ωx10-5": 0.3837, - "Z": 1, - "Comments": "Sverjensky et al. (1997) with revised a1 equal to the sum of the ions used to predict new values of V using new correlation in Sverjensky et al. (2014)" - }, - { - "Name": "Tb+3", - "Symbol": "Tb(+3)", - "G0": -159500, - "H0": -166900, - "S0": -54, - "V0": -40.199927595867, - "Cp0": -40.4994064140919, - "a1x10": -7.70362408639681, - "a2x10-2": -2.54719105998306, - "a3": 13.5968124966712, - "a4x10-4": -2.6736991215803, - "c1": 4.25205589692087, - "c2x10-4": -11.2843290865505, - "ωx10-5": 2.3685, - "Z": 3, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "Tl+", - "Symbol": "Tl(+)", - "G0": -7740, - "H0": 1280, - "S0": 30, - "V0": 18.2002094244711, - "Cp0": -4.19983226244808, - "a1x10": 4.09408612042124, - "a2x10-2": 3.28526489792355, - "a3": 4.76341717795857, - "a4x10-4": -2.91481285088016, - "c1": 5.08901185091244, - "c2x10-4": -3.89010583186067, - "ωx10-5": 0.1502, - "Z": 1, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "Tl+3", - "Symbol": "Tl(+3)", - "G0": 51300, - "H0": 47000, - "S0": -46, - "V0": -39.3000380548206, - "Cp0": -39.2998708434088, - "a1x10": -7.39037036953911, - "a2x10-2": -2.77695745117213, - "a3": 13.4039365379947, - "a4x10-4": -2.66420057896854, - "c1": 4.76066685811207, - "c2x10-4": -11.0399836908024, - "ωx10-5": 2.3474, - "Z": 3, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "Tm+3", - "Symbol": "Tm(+3)", - "G0": -159900, - "H0": -168500, - "S0": -58.1, - "V0": -42.9996595789696, - "Cp0": -34.2996615528119, - "a1x10": -8.67898977630398, - "a2x10-2": -1.83177654899923, - "a3": 14.1973627292051, - "a4x10-4": -2.70327435746437, - "c1": 8.48248022470489, - "c2x10-4": -10.0214410583078, - "ωx10-5": 2.4333, - "Z": 3, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "TOLUENE,AQ", - "Symbol": "C6H5CH3", - "G0": 30260, - "H0": 3280, - "S0": 44, - "V0": 97.5, - "Cp0": 109, - "a1x10": 20.3167751123382, - "a2x10-2": 15.0604490839026, - "a3": -7.78994308351661, - "a4x10-4": -3.40159896512853, - "c1": 67.3756008402932, - "c2x10-4": 19.1687, - "ωx10-5": -0.29, - "Z": 0, - "Comments": "Plyasunov & Shock (2001) with new a1 to a4 predicted with revised a1 consistent with Sverjensky et al. (2013)" - }, - { - "Name": "U+4", - "Symbol": "U(+4)", - "G0": -126650, - "H0": -141300, - "S0": -99.6, - "V0": -53.2999593762937, - "Cp0": 0.200127273057333, - "a1x10": -15.6513533917693, - "a2x10-2": 11.3263133089266, - "a3": 17.618925783281, - "a4x10-4": -3.24722979219102, - "c1": 40.2193692426792, - "c2x10-4": -2.99383407447822, - "ωx10-5": 3.6835, - "Z": 4, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "UO2+2", - "Symbol": "UO2(+2)", - "G0": -227680, - "H0": -243550, - "S0": -23.5, - "V0": 5.72998183074506, - "Cp0": 8.95462607522969, - "a1x10": 5.73471694103885, - "a2x10-2": -7.44020631720207, - "a3": 4.78483055774406, - "a4x10-4": -2.47142187084687, - "c1": 24.4037434821233, - "c2x10-4": -1.21054266847571, - "ωx10-5": 1.4099, - "Z": 2, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "UREA,AQ", - "Symbol": "CH4N2O", - "G0": -48720, - "H0": -76100, - "S0": 42.3, - "V0": 21, - "Cp0": 21.0002224290034, - "a1x10": 5.4546257716168, - "a2x10-2": 0.910208586441794, - "a3": 4.0748994753636, - "a4x10-4": -2.8166280229635, - "c1": 23.584, - "c2x10-4": -2.6343, - "ωx10-5": -0.3006, - "Z": 0, - "Comments": "Shock & McKibben (1993) for c1, c2 and omega with revised a1 from correlation for complex species" - }, - { - "Name": "VO+2", - "Symbol": "VO(+2)", - "G0": -106700, - "H0": -116300, - "S0": -32, - "V0": -29.3999918557769, - "Cp0": -11.9997271265395, - "a1x10": -2.58360381162563, - "a2x10-2": -9.81109457233077, - "a3": 10.8244132269039, - "a4x10-4": -2.37340935037985, - "c1": 13.3908870472063, - "c2x10-4": -5.4789444156761, - "ωx10-5": 1.5475, - "Z": 2, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "VO2+", - "Symbol": "VO2(+)", - "G0": -140300, - "H0": -155300, - "S0": -10.1, - "V0": -33.5000254370902, - "Cp0": 31.1000911117764, - "a1x10": -1.3780471312324, - "a2x10-2": -17.2198149399737, - "a3": 10.788960245061, - "a4x10-4": -2.06713285038149, - "c1": 30.8449232482805, - "c2x10-4": 3.30048855946885, - "ωx10-5": 0.7003, - "Z": 1, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "WO4-2", - "Symbol": "WO4(-2)", - "G0": -219150, - "H0": -257100, - "S0": 9.7, - "V0": 32.2003622026895, - "Cp0": -44.4994484297695, - "a1x10": 13.0415727628644, - "a2x10-2": -5.3576058543219, - "a3": -0.52036998689851, - "a4x10-4": -2.55751657398233, - "c1": 8.33097328882169, - "c2x10-4": -12.099137645144, - "ωx10-5": 3.0657, - "Z": -2, - "Comments": "Shock & Helgeson (1988) revised with new predicted a1 for ions" - }, - { - "Name": "Xe,aq", - "Symbol": "Xe(0)", - "G0": 3225, - "H0": -4510, - "S0": 14.62, - "V0": 42.6002586140237, - "Cp0": 64.8000042994899, - "a1x10": 7.5196, - "a2x10-2": 10.5793, - "a3": 1.5919, - "a4x10-4": -3.2163, - "c1": 42.1036, - "c2x10-4": 10.1652, - "ωx10-5": -0.2214, - "Z": 0, - "Comments": "Shock et al. 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(2014)" - }, - { - "Name": "ZnCl3-", - "Symbol": "ZnCl3(-)", - "G0": -129310, - "H0": -151060, - "S0": 25, - "V0": 43.9, - "Cp0": 41.97, - "a1x10": 10.6464110325213, - "a2x10-2": 5.85330317987863, - "a3": -0.0698384967792958, - "a4x10-4": -3.02097555345618, - "c1": 42.2916319257949, - "c2x10-4": 5.514689, - "ωx10-5": 1.2513, - "Z": -1, - "Comments": "Sverjensky et al. (1997) with revised a1 equal to the sum of the ions used to predict new values of V using new correlation in Sverjensky et al. 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"mtime": "Wed, 03 Aug 2016 15:45:13 +0100" -} -] \ No newline at end of file diff --git a/Resources/files/TestSubstance/README.md b/Resources/files/TestSubstance/README.md deleted file mode 100644 index 3f8e5340..00000000 --- a/Resources/files/TestSubstance/README.md +++ /dev/null @@ -1,2 +0,0 @@ -This folder is for Substance files. - diff --git a/Resources/files/TestSubstance/Substance2.DEW-11-0-1.FormatStructDataFile.json b/Resources/files/TestSubstance/Substance2.DEW-11-0-1.FormatStructDataFile.json deleted file mode 100644 index 4ef53b6f..00000000 --- a/Resources/files/TestSubstance/Substance2.DEW-11-0-1.FormatStructDataFile.json +++ /dev/null @@ -1,56 +0,0 @@ -{ - "block" : { - "defaults" : { - "properties.aggregate_state" : "4", - "properties.method_genEoS" : "101", - "properties.method_corrT" : "205", - "properties.method_corrP" : "319", - "properties.class_" : "2", - "properties.Tst" : "298.15", - "properties.Pst" : "1.0e5", - "properties.eos_hkf_coeffs.list_size" : "7", - "properties.sourcetdb" : "18", - "properties.standard_cscale" : "2", - "properties.datasources" : "[\"DEW_Model_11.0.1\"]" - }, - "pairs" : { - - }, - "matches" : { - "Name" : { - "field" : "properties.name" - }, - "Symbol" : { - "field" : "properties.symbol" - }, - "Comments" : { - "field" : "properties.comment" - }, - "Z" : { - "field" : "properties.formula_charge" - }, - "G0" : { - "field" : "properties.sm_gibbs_energy.values" - }, - "H0" : { - "field" : "properties.sm_enthalpy.values", - "script" : "field = field * 4.184" - }, - "S0" : { - "field" : "properties.sm_entropy_abs.values" - }, - "Cp0" : { - "field" : "properties.sm_heat_capacity_p.values" - }, - "V0" : { - "field" : "properties.sm_volume.values" - }, - "HKF" : { - "field" : "properties.eos_hkf_coeffs.values" - } - } - }, - "renderer" : "JSON", - "label" : "VertexSubstance", - "comment" : "Second test" -} diff --git a/Resources/files/TestSubstance/Substance2.DEW-11-0-1v2.FormatStructDataFile.json b/Resources/files/TestSubstance/Substance2.DEW-11-0-1v2.FormatStructDataFile.json deleted file mode 100644 index 24375dc0..00000000 --- a/Resources/files/TestSubstance/Substance2.DEW-11-0-1v2.FormatStructDataFile.json +++ /dev/null @@ -1,85 +0,0 @@ -{ - "block" : { - "defaults" : { - "properties.aggregate_state" : "4", - "properties.method_genEoS" : "101", - "properties.method_corrT" : "205", - "properties.method_corrP" : "319", - "properties.class_" : "2", - "properties.Tst" : "298.15", - "properties.Pst" : "1.0e5", - "properties.eos_hkf_coeffs.list_size" : "7", - "properties.sourcetdb" : "18", - "properties.standard_cscale" : "2", - "properties.eos_hkf_coeffs.values" : "[ 0, 0, 0, 0, 0, 0, 0 ]", - "properties.datasources" : "[\"DEW_Model_11.0.1\"]" - }, - "pairs" : { - - }, - "matches" : { - "Name" : { - "field" : "properties.name" - }, - "Symbol" : { - "field" : "properties.symbol" - }, - "Comments" : { - "field" : "properties.comment" - }, - "Z" : { - "field" : "properties.formula_charge" - }, - "G0" : { - "field" : "properties.sm_gibbs_energy.values", - "script" : "field[1] = field[1] * 4.184;" - }, - "H0" : { - "field" : "properties.sm_enthalpy.values", - "script" : "field[1] = field[1] * 4.184;" - }, - "S0" : { - "field" : "properties.sm_entropy_abs.values", - "script" : "field[1] = field[1] * 4.184;" - }, - "Cp0" : { - "field" : "properties.sm_heat_capacity_p.values", - "script" : "field[1] = field[1] * 4.184;" - }, - "V0" : { - "field" : "properties.sm_volume.values", - "script" : "field[1] = field[1] / 10;" - }, - "a1x10" : { - "field" : "properties.eos_hkf_coeffs.values.0", - "script" : "field = field / 10;" - }, - "a2x10-2" : { - "field" : "properties.eos_hkf_coeffs.values.1", - "script" : "field = field / 1e-02;" - }, - "a3" : { - "field" : "properties.eos_hkf_coeffs.values.2" - }, - "a4x10-4" : { - "field" : "properties.eos_hkf_coeffs.values.3", - "script" : "field = field / 1e-04;" - }, - "c1" : { - "field" : "properties.eos_hkf_coeffs.values.4" - }, - "c2x10-4" : { - "field" : "properties.eos_hkf_coeffs.values.5", - "script" : "field = field / 1e-04;" - }, - "ωx10-5" : { - "field" : "properties.eos_hkf_coeffs.values.6", - "script" : "field = field / 1e-05;" - } - }, - "script" : "rintable.properties.formula = rintable.properties.symbol;rintable.properties.eos_hkf_coeffs.values[1] = rintable.properties.eos_hkf_coeffs.values[1] * 1;" - }, - "renderer" : "JSON", - "label" : "VertexSubstance", - "comment" : "Second test" -} diff --git a/Resources/files/TestSubstance/Substance2.FormatStructDataFile.json b/Resources/files/TestSubstance/Substance2.FormatStructDataFile.json deleted file mode 100644 index 03993bfe..00000000 --- a/Resources/files/TestSubstance/Substance2.FormatStructDataFile.json +++ /dev/null @@ -1,226 +0,0 @@ -{ - "block" : { - "defaults" : { - - }, - "pairs" : { - - }, - "matches" : { - "key.0.fv" : { - "field" : "properties.aggregate_state", - "convert" : { - "a" : "4", - "g" : "0", - "s" : "3", - "c" : "5", - "l" : "1" - } - }, - "dod.14.val" : { - "field" : "properties.name" - }, - "dod.0.val.0" : { - "field" : "properties.method_genEoS", - "convert" : { - "C" : "100", - "H" : "101", - "K" : "102", - "S" : "103", - "I" : "104", - "X" : "105", - "N" : "106" - } - }, - "dod.0.val.1" : { - "field" : "properties.method_corrT", - "convert" : { - "S" : "200", - "H" : "201", - "B" : "202", - "F" : "203", - "X" : "204", - "K" : "205", - "W" : "206", - "V" : "207", - "L" : "208", - "0" : "209", - "1" : "210", - "2" : "211", - "3" : "212", - "Z" : "213", - "R" : "214", - "E" : "215", - "Y" : "216", - "C" : "217", - "G" : "218" - } - }, - "dod.0.val.2" : { - "field" : "4.25", - "convert" : { - "N" : "300", - "0" : "301", - "1" : "302", - "2" : "303", - "3" : "304", - "C" : "305", - "K" : "306", - "V" : "307", - "B" : "308", - "E" : "309", - "H" : "310", - "G" : "311", - "R" : "312", - "S" : "313", - "T" : "314", - "6" : "315", - "7" : "316", - "8" : "317", - "9" : "318", - "F" : "319", - "A" : "320", - "P" : "321", - "Z" : "322" - } - }, - "key.2.fv" : { - "field" : "properties.symbol" - }, - "dod.1.val.0" : { - "field" : "properties.class_", - "convert" : { - "d" : "---", - "r" : "---", - "n" : "---", - "i" : "---", - "f" : "---", - "T" : "---", - "E" : "---", - "S" : "2", - "K" : "4", - "W" : "3", - "L" : "---", - "G" : "1", - "V" : "---", - "C" : "---", - "H" : "---", - "N" : "---", - "I" : "---", - "J" : "---", - "M" : "---", - "F" : "---", - "D" : "---", - "Q" : "---", - "P" : "---", - "R" : "---", - "0" : "---", - "2" : "---", - "4" : "---", - "6" : "---", - "8" : "---", - "1" : "---", - "3" : "---", - "5" : "---", - "7" : "---", - "9" : "---", - "A" : "---", - "B" : "---", - "X" : "5", - "Y" : "---", - "Z" : "---", - "O" : "0" - } - }, - "dod.3.val" : { - "field" : "properties.formula_charge" - }, - "dod.4.val" : { - "field" : "properties.mass_per_mole" - }, - "dod.5.val.0" : { - "field" : "properties.sm_volume.values" - }, - "dod.6.val.0" : { - "field" : "properties.sm_gibbs_energy.values" - }, - "dod.7.val.0" : { - "field" : "properties.sm_enthalpy.values" - }, - "dod.8.val.0" : { - "field" : "properties.sm_entropy_f.values" - }, - "dod.9.val.0" : { - "field" : "properties.sm_heat_capacity_p.values" - }, - "dod.12.val.0" : { - "field" : "properties.m_compressibility.values" - }, - "dod.12.val.1" : { - "field" : "properties.m_expansivity.values" - }, - "dod.13.val" : { - "field" : "properties.aq_edh_props.values" - }, - "dod.18.val" : { - "field" : "properties.m_heat_capacity_p_t_coeffs.values" - }, - "dod.19.val" : { - "field" : "properties.eos_ad_coeffs.values" - }, - "dod.20.val" : { - "field" : "properties.eos_hkf_coeffs.values" - }, - "dod.21.val" : { - "field" : "properties.m_volume_pt_coeffs.values" - }, - "dod.22.val" : { - "field" : "properties.eos_gas_crit_props.values" - }, - "dod.25.val" : { - "field" : "properties.m_phase_trans_props.values" - }, - "dod.26.val" : { - "field" : "properties.eos_cg_coeffs.values" - }, - "dod.11.val" : { - "field" : "properties.m_lambda_trans_props.values" - }, - "dod.29.val" : { - "field" : "properties.comment" - }, - "dod.28.val" : { - "field" : "properties.datasources" - }, - "dod.17.val.0" : { - "field" : "properties.limitsTP.lowerT", - "script" : "field = field+273.15" - }, - "dod.17.val.1" : { - "field" : "properties.limitsTP.upperT", - "script" : "field = field + 273.15" - }, - "dod.6.val.1" : { - "field" : "properties.sm_gibbs_energy.errors" - }, - "dod.5.val.1" : { - "field" : "properties.sm_volume.errors" - }, - "dod.7.val.1" : { - "field" : "properties.sm_enthalpy.errors" - }, - "dod.8.val.1" : { - "field" : "properties.sm_entropy_f.errors" - }, - "dod.9.val.1" : { - "field" : "properties.sm_heat_capacity_p.errors" - }, - "35" : { - "field" : "properties.sm_heat_capacity_p.errors" - } - } - }, - "renderer" : "JSON", - "label" : "VertexSubstance", - "comment" : "first test" -} diff --git a/Resources/files/TestSubstance/Substance2.Mines.FormatStructDataFile.json b/Resources/files/TestSubstance/Substance2.Mines.FormatStructDataFile.json deleted file mode 100644 index 945669d1..00000000 --- a/Resources/files/TestSubstance/Substance2.Mines.FormatStructDataFile.json +++ /dev/null @@ -1,226 +0,0 @@ -{ - "block" : { - "defaults" : { - "properties.sourcetdb" : "19" - }, - "pairs" : { - - }, - "matches" : { - "key.0.fv" : { - "field" : "properties.aggregate_state", - "convert" : { - "a" : "4", - "g" : "0", - "s" : "3", - "c" : "5", - "l" : "1" - } - }, - "dod.14.val" : { - "field" : "properties.name" - }, - "dod.15.val" : { - "field" : "properties.formula" - }, - "dod.0.val.0" : { - "field" : "4.23", - "convert" : { - "C" : "100", - "H" : "101", - "K" : "102", - "S" : "103", - "I" : "104", - "X" : "105", - "N" : "106" - } - }, - "dod.0.val.1" : { - "field" : "properties.method_corrT", - "convert" : { - "S" : "200", - "H" : "201", - "B" : "202", - "F" : "203", - "X" : "204", - "K" : "205", - "W" : "206", - "V" : "207", - "L" : "208", - "0" : "209", - "1" : "210", - "2" : "211", - "3" : "212", - "Z" : "213", - "R" : "214", - "E" : "215", - "Y" : "216", - "C" : "217", - "G" : "218" - } - }, - "dod.0.val.2" : { - "field" : "4.25", - "convert" : { - "N" : "300", - "0" : "301", - "1" : "302", - "2" : "303", - "3" : "304", - "C" : "305", - "K" : "306", - "V" : "307", - "B" : "308", - "E" : "309", - "H" : "310", - "G" : "311", - "R" : "312", - "S" : "313", - "T" : "314", - "6" : "315", - "7" : "316", - "8" : "317", - "9" : "318", - "F" : "319", - "A" : "320", - "P" : "321", - "Z" : "322" - } - }, - "key.2.fv" : { - "field" : "properties.symbol" - }, - "dod.1.val.0" : { - "field" : "properties.class_", - "convert" : { - "d" : "---", - "r" : "---", - "n" : "---", - "i" : "---", - "f" : "---", - "T" : "---", - "E" : "---", - "S" : "2", - "K" : "4", - "W" : "3", - "L" : "---", - "G" : "1", - "V" : "---", - "C" : "---", - "H" : "---", - "N" : "---", - "I" : "---", - "J" : "---", - "M" : "---", - "F" : "---", - "D" : "---", - "Q" : "---", - "P" : "---", - "R" : "---", - "0" : "---", - "2" : "---", - "4" : "---", - "6" : "---", - "8" : "---", - "1" : "---", - "3" : "---", - "5" : "---", - "7" : "---", - "9" : "---", - "A" : "---", - "B" : "---", - "X" : "5", - "Y" : "---", - "Z" : "---", - "O" : "0" - } - }, - "dod.3.val" : { - "field" : "properties.formula_charge" - }, - "dod.4.val" : { - "field" : "properties.mass_per_mole" - }, - "dod.5.val.0" : { - "field" : "properties.sm_volume.values" - }, - "dod.6.val.0" : { - "field" : "properties.sm_gibbs_energy.values" - }, - "dod.7.val.0" : { - "field" : "properties.sm_enthalpy.values" - }, - "dod.8.val.0" : { - "field" : "properties.sm_entropy_abs.values" - }, - "dod.9.val.0" : { - "field" : "properties.sm_heat_capacity_p.values" - }, - "dod.12.val.0" : { - "field" : "properties.m_compressibility.values" - }, - "dod.12.val.1" : { - "field" : "properties.m_expansivity.values" - }, - "dod.13.val" : { - "field" : "properties.aq_edh_props.values" - }, - "dod.18.val" : { - "field" : "properties.m_heat_capacity_p_t_coeffs.values" - }, - "dod.19.val" : { - "field" : "properties.eos_ad_coeffs.values" - }, - "dod.20.val" : { - "field" : "properties.eos_hkf_coeffs.values" - }, - "dod.21.val" : { - "field" : "properties.m_volume_pt_coeffs.values" - }, - "dod.22.val" : { - "field" : "properties.eos_gas_crit_props.values" - }, - "dod.25.val" : { - "field" : "properties.m_phase_trans_props.values" - }, - "dod.26.val" : { - "field" : "properties.eos_cg_coeffs.values" - }, - "dod.11.val" : { - "field" : "properties.m_lambda_trans_props.values" - }, - "dod.29.val" : { - "field" : "properties.comment" - }, - "dod.28.val" : { - "field" : "properties.datasources" - }, - "dod.17.val.0" : { - "field" : "properties.limitsTP.lowerT", - "script" : "field = field+273.15" - }, - "dod.17.val.1" : { - "field" : "properties.limitsTP.upperT", - "script" : "field = field + 273.15" - }, - "dod.6.val.1" : { - "field" : "properties.sm_gibbs_energy.errors" - }, - "dod.5.val.1" : { - "field" : "properties.sm_volume.errors" - }, - "dod.7.val.1" : { - "field" : "properties.sm_enthalpy.errors" - }, - "dod.8.val.1" : { - "field" : "properties.sm_entropy_f.errors" - }, - "dod.9.val.1" : { - "field" : "properties.sm_heat_capacity_p.errors" - } - } - }, - "renderer" : "JSON", - "label" : "VertexSubstance", - "comment" : "Second test" -} diff --git a/Resources/files/TestSubstance/Substance2.PSI-Nagra-12-07.FormatStructDataFile.json b/Resources/files/TestSubstance/Substance2.PSI-Nagra-12-07.FormatStructDataFile.json deleted file mode 100644 index f1b62ed3..00000000 --- a/Resources/files/TestSubstance/Substance2.PSI-Nagra-12-07.FormatStructDataFile.json +++ /dev/null @@ -1,226 +0,0 @@ -{ - "block" : { - "defaults" : { - "properties.sourcetdb" : "15" - }, - "pairs" : { - - }, - "matches" : { - "key.0.fv" : { - "field" : "properties.aggregate_state", - "convert" : { - "a" : "4", - "g" : "0", - "s" : "3", - "c" : "5", - "l" : "1" - } - }, - "dod.14.val" : { - "field" : "properties.name" - }, - "dod.15.val" : { - "field" : "properties.formula" - }, - "dod.0.val.0" : { - "field" : "4.23", - "convert" : { - "C" : "100", - "H" : "101", - "K" : "102", - "S" : "103", - "I" : "104", - "X" : "105", - "N" : "106" - } - }, - "dod.0.val.1" : { - "field" : "properties.method_corrT", - "convert" : { - "S" : "200", - "H" : "201", - "B" : "202", - "F" : "203", - "X" : "204", - "K" : "205", - "W" : "206", - "V" : "207", - "L" : "208", - "0" : "209", - "1" : "210", - "2" : "211", - "3" : "212", - "Z" : "213", - "R" : "214", - "E" : "215", - "Y" : "216", - "C" : "217", - "G" : "218" - } - }, - "dod.0.val.2" : { - "field" : "4.25", - "convert" : { - "N" : "300", - "0" : "301", - "1" : "302", - 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0 - ] - }, - { - "id": 516, - "label": "G0d", - "dot": -6, - "dN": 1, - "dM": 2, - "dyn": false, - "val": [ - -1154900, - 1200 - ] - }, - { - "id": 517, - "label": "H0d", - "dot": -6, - "dN": 1, - "dM": 2, - "dyn": false, - "val": [ - -1293100, - 1200 - ] - }, - { - "id": 518, - "label": "S0d", - "dot": -5, - "dN": 1, - "dM": 2, - "dyn": false, - "val": [ - 68.4000015258789, - 0.100000001490116 - ] - }, - { - "id": 519, - "label": "Cp0d", - "dot": -5, - "dN": 1, - "dM": 2, - "dyn": false, - "val": [ - 91.7202835083008, - 0 - ] - }, - { - "id": 520, - "label": "PrTr", - "dot": -5, - "dN": 1, - "dM": 2, - "dyn": false, - "val": [ - 1, - 25 - ] - }, - { - "id": 521, - "label": "LamST", - "dot": -5, - "dN": 1, - "dM": 2, - "dyn": false, - "val": [ - null, - null - ] - }, - { - "id": 522, - "label": "BetAlp", - "dot": -5, - "dN": 1, - "dM": 2, - "dyn": false, - "val": [ - null, - null - ] - }, - { - "id": 523, - "label": "ab", - "dot": -5, - "dN": 1, - "dM": 2, - "dyn": false, - "val": [ - null, - null - ] - }, - { - "id": 525, - "label": "DCname", - "dot": 0, - "dN": 1, - "dM": 72, - "dyn": false, - "val": "Gibbsite (gbs)" - }, - { - "id": 526, - "label": "DCform", - "dot": 0, - "dN": 1, - "dM": 72, - "dyn": false, - "val": "Al(OH)3" - }, - { - "id": 527, - "label": "DC_cnt", - "dot": -1, - "dN": 1, - "dM": 4, - "dyn": false, - "val": [ - 1, - 0, - 1, - 0 - ] - }, - { - "id": 531, - "label": "TCint", - "dot": -5, - "dN": 2, - "dM": 1, - "dyn": true, - "val": [ - 0, - 310 - ] - }, - { - "id": 532, - "label": "aiCpT", - "dot": -5, - "dN": 12, - "dM": 1, - "dyn": true, - "val": [ - 54.6974296569824, - 0.170271992683411, - -1221728, - 0, - 0, - 0, - 0, - 0, - 0, - 0, - 0, - 0 - ] - }, - { - "id": 533, - "label": "aiNEs", - "dot": -5, - "dN": 7, - "dM": 0, - "dyn": true, - "val": null - }, - { - "id": 534, - "label": "aiHKF", - "dot": -5, - "dN": 8, - "dM": 0, - "dyn": true, - "val": null - }, - { - "id": 535, - "label": "aiVTP", - "dot": -5, - "dN": 5, - "dM": 0, - "dyn": true, - "val": null - }, - { - "id": 536, - "label": "CritPg", - "dot": -5, - "dN": 7, - "dM": 0, - "dyn": true, - "val": null - }, - { - "id": 537, - "label": "aiODc", - "dot": -5, - "dN": 12, - "dM": 0, - "dyn": true, - "val": null - }, - { - "id": 538, - "label": "FT_p", - "dot": -5, - "dN": 5, - "dM": 0, - "dyn": true, - "val": null - }, - { - "id": 539, - "label": "FT_pb", - "dot": -5, - "dN": 3, - "dM": 0, - "dyn": true, - "val": null - }, - { - "id": 540, - "label": "Cemp_s", - "dot": -5, - "dN": 20, - "dM": 0, - "dyn": true, - "val": null - }, - { - "id": 541, - "label": "FT_typ", - "dot": 4, - "dN": 1, - "dM": 0, - "dyn": true, - "val": null - }, - { - "id": 542, - "label": "dSDref", - "dot": 32, - "dN": 1, - "dM": 1, - "dyn": true, - "val": [ - "Robie and Hemingway 1991" - ] - }, - { - "id": 543, - "label": "dSDval", - "dot": 24, - "dN": 1, - "dM": 1, - "dyn": true, - "val": [ - "Cp(T) Pokrovskii et al. " - ] - } - ], - "mtime": "Thu, 19 May 2016 10:15:21 +0100" -}, -{ - "key": [ - { - "fx": 0, - "fl": 4, - "fv": "s" - }, - { - "fx": 1, - "fl": 8, - "fv": "sht" - }, - { - "fx": 2, - "fl": 16, - "fv": "Talc-Mg" - }, - { - "fx": 3, - "fl": 4, - "fv": "hp0_" - } - ], - "dod": [ - { - "id": 510, - "label": "TPcMod", - "dot": -9, - "dN": 1, - "dM": 6, - "dyn": false, - "val": [ - "C", - "S", - "E", - " ", - " ", - " " - ] - }, - { - "id": 511, - "label": "DCset", - "dot": -9, - "dN": 1, - "dM": 9, - "dyn": false, - "val": [ - "O", - "j", - "j", - "b", - "C", - "+", - "-", - "-", - "-" - ] - }, - { - "id": 512, - "label": "Cdate", - "dot": 9, - "dN": 1, - "dM": 1, - "dyn": false, - "val": [ - "12.Jul.04" - ] - }, - { - "id": 513, - "label": "Zz", - "dot": -5, - "dN": 1, - "dM": 1, - "dyn": false, - "val": [ - 0 - ] - }, - { - "id": 514, - "label": "M0", - "dot": -5, - "dN": 1, - "dM": 1, - "dyn": false, - "val": [ - 379.265716552734 - ] - }, - { - "id": 515, - "label": "V0d", - "dot": -5, - 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"dM": 2, - "dyn": false, - "val": [ - null, - null - ] - }, - { - "id": 525, - "label": "DCname", - "dot": 0, - "dN": 1, - "dM": 72, - "dyn": false, - "val": "Talc-Mg (ta)" - }, - { - "id": 526, - "label": "DCform", - "dot": 0, - "dN": 1, - "dM": 72, - "dyn": false, - "val": "Mg3Si4O10(OH)2" - }, - { - "id": 527, - "label": "DC_cnt", - "dot": -1, - "dN": 1, - "dM": 4, - "dyn": false, - "val": [ - 1, - 0, - 1, - 0 - ] - }, - { - "id": 531, - "label": "TCint", - "dot": -5, - "dN": 2, - "dM": 1, - "dyn": true, - "val": [ - 0, - 2000 - ] - }, - { - "id": 532, - "label": "aiCpT", - "dot": -5, - "dN": 12, - "dM": 1, - "dyn": true, - "val": [ - 622.200012207031, - 0, - -6385500, - -3916.30004882812, - 0, - 0, - 0, - 0, - 0, - 0, - 0, - 0 - ] - }, - { - "id": 533, - "label": "aiNEs", - "dot": -5, - "dN": 7, - "dM": 0, - "dyn": true, - "val": null - }, - { - "id": 534, - "label": "aiHKF", - "dot": -5, - "dN": 8, - "dM": 0, - "dyn": true, - "val": null - }, - { - "id": 535, - "label": "aiVTP", - "dot": -5, - "dN": 5, - "dM": 0, - "dyn": true, - "val": null - }, - { - "id": 536, - "label": "CritPg", - "dot": -5, - "dN": 7, - "dM": 0, - "dyn": true, - "val": null - }, - { - "id": 537, - "label": "aiODc", - "dot": -5, - "dN": 12, - "dM": 0, - "dyn": true, - "val": null - }, - { - "id": 538, - "label": "FT_p", - "dot": -5, - "dN": 5, - "dM": 0, - "dyn": true, - "val": null - }, - { - "id": 539, - "label": "FT_pb", - "dot": -5, - "dN": 3, - "dM": 0, - "dyn": true, - "val": null - }, - { - "id": 540, - "label": "Cemp_s", - "dot": -5, - "dN": 20, - "dM": 0, - "dyn": true, - "val": null - }, - { - "id": 541, - "label": "FT_typ", - "dot": 4, - "dN": 1, - "dM": 0, - "dyn": true, - "val": null - }, - { - "id": 542, - "label": "dSDref", - "dot": 32, - "dN": 1, - "dM": 1, - "dyn": true, - "val": [ - "Holland and Powell (2002)" - ] - }, - { - "id": 543, - "label": "dSDval", - "dot": 24, - "dN": 1, - "dM": 1, - "dyn": true, - "val": [ - "" - ] - } - ], - "mtime": "Thu, 19 May 2016 10:15:21 +0100" -} -] \ No newline at end of file diff --git a/Resources/files/TestThereda/Element-Thereda.FormatStructDataFile.json b/Resources/files/TestThereda/Element-Thereda.FormatStructDataFile.json deleted file mode 100644 index 279681ab..00000000 --- a/Resources/files/TestThereda/Element-Thereda.FormatStructDataFile.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "block": { - "defaults": { - "properties.radioactivity.half_life_lambda.values": "[ 0 ]", - "properties.datasources": "[\"THEREDA\"]", - "properties.sourcetdb": "{\"12\" : \"THEREDA\"}", - "properties.class_": "{\"0\" : \"ELEMENT\"}", - "properties.atomic_mass.status":"[{\"4\" : \"IMPORTED\"}]", - "properties.entropy.status":"[{\"4\" : \"IMPORTED\"}]", - "properties.heat_capacity.status":"[{\"4\" : \"IMPORTED\"}]", - "properties.temp_import": "[\"\",\"\"]" - }, - "pairs": {}, - "matches": { - "symbol": { - "field": "properties.symbol" - }, - "name": { - "field": "properties.name" - }, - "molarmass": { - "field": "properties.atomic_mass.values" - }, - "molarmass_referenceid": { - "field": "properties.atomic_mass.datasources" - }, - "s298": { - "field": "properties.entropy.values" - }, - "s298_positiveunc": { - "field": "properties.entropy.errors" - }, - "s298_unctype": { - "field": "properties.entropy.errortypes", - "convert" : { - "Gauss2s" : "{\"0\" : \"NORMAL\"}" - } - }, - "s298_referenceid": { - "field": "properties.entropy.datasources" - }, - "cp298": { - "field": "properties.heat_capacity.values" - }, - "cp298_positiveunc": { - "field": "properties.heat_capacity.errors" - }, - "cp298_unctype": { - "field": "properties.heat_capacity.errortypes", - "convert" : { - "Gauss2s" : "{\"0\" : \"NORMAL\"}" - } - }, - "cp298_referenceid": { - "field": "properties.heat_capacity.datasources" - }, - "description": { - "field": "properties.comment" - }, - "atomicnumber": { - "field": "properties.number" - }, - "referencestate": { - "field": "properties.temp_import.0" - }, - "stoichiometriccoefficient": { - "field": "properties.temp_import.1" - } - }, - "script": "s1 = \"referencestate: \" .. rintable.properties.temp_import[1] if rintable.properties.comment == nil then rintable.properties.comment = s1 else rintable.properties.comment = rintable.properties.comment .. \"; \" .. s1 end; -if rintable.properties.symbol == \"EA\" then rintable.properties.class_ = {} rintable.properties.class_['4'] = 'CHARGE' rintable.properties.symbol = \"Zz\" end; -if rintable.properties.temp_import[2] ~=\"1\" then tmp = tonumber(rintable.properties.temp_import[2]) rintable.properties.entropy.values[1] = rintable.properties.entropy.values[1] / tmp rintable.properties.entropy.errors[1] = rintable.properties.entropy.errors[1] / tmp rintable.properties.heat_capacity.values[1] = rintable.properties.heat_capacity.values[1] / tmp rintable.properties.heat_capacity.errors[1] = rintable.properties.heat_capacity.errors[1] / tmp end; -rintable.properties.temp_import[1] = nil; rintable.properties.temp_import[2] = nil; " - }, - "renderer": "JSON", - "label": "VertexElement", - "comment": "Second test" -} \ No newline at end of file diff --git a/Resources/files/TestThereda/Phase-Thereda.FormatStructDataFile.json b/Resources/files/TestThereda/Phase-Thereda.FormatStructDataFile.json deleted file mode 100644 index 9f6a4907..00000000 --- a/Resources/files/TestThereda/Phase-Thereda.FormatStructDataFile.json +++ /dev/null @@ -1,33 +0,0 @@ -{ - "block": { - "defaults": { - "properties.sourcetdb": "{\"12\" : \"THEREDA\"}", - "properties.aggregate_state": "{\"3\" : \"AS_CRYSTAL\"}", - "properties.mixmod": "{\"0\" : \"M_PURE\"}", - "properties.temp_import": "[\"\", \"\"]" - }, - "pairs": {}, - "matches": { - "symbol": { - "field": "properties.symbol" - }, - "description": { - "field": "properties.comment" - }, - "modification": { - "field": "properties.temp_import.0" - }, - "phase": { - "field": "properties.temp_import.1" - } - }, - "script": "if rintable.properties.symbol == 'g' then rintable.properties.mixmod = {} rintable.properties.mixmod['1'] = 'M_IDEAL' rintable.properties.aggregate_state = {} rintable.properties.aggregate_state['0'] = 'AS_GAS' end; -if rintable.properties.temp_import[2] == 'aq' then rintable.properties.symbol = 'aq' end; -if rintable.properties.symbol == 'aq' then rintable.properties.mixmod = {} rintable.properties.mixmod['32'] = 'M_AQPITZERHMW' rintable.properties.aggregate_state = {} rintable.properties.aggregate_state['4'] = 'AS_AQUEOUS' end; -rintable.properties.name = rintable.properties.symbol; -rintable.properties.temp_import[1] = nil; rintable.properties.temp_import[2] = nil;" - }, - "renderer": "JSON", - "label": "VertexPhase", - "comment": "Second test" -} \ No newline at end of file diff --git a/Resources/files/TestThereda/Reaction2.Thereda_aq_Reac.FormatStructDataFile.json b/Resources/files/TestThereda/Reaction2.Thereda_aq_Reac.FormatStructDataFile.json deleted file mode 100644 index 3167c731..00000000 --- a/Resources/files/TestThereda/Reaction2.Thereda_aq_Reac.FormatStructDataFile.json +++ /dev/null @@ -1,208 +0,0 @@ -{ - "block": { - "defaults": { - "properties.sourcetdb": "{\"12\" : \"THEREDA\"}", - "properties.TPMethods": "[{\"method\" :{\"10\" : \"dr_heat_capacity_ft\"}, \"dr_heat_capacity_ft_coeffs\" :{\"values\" : [0,0,0,0,0,0]}},{\"method\" :{\"2\" : \"logk_nordstrom_munoz88\"}, \"logk_ft_coeffs\" :{\"values\" : [0,0,0,0,0,0]}}]", - "properties.reactyp": "{\"12\" : \"FE_FORMATION\"}", - "properties.drsm_gibbs_energy": "{\"units\": [\"J/mol\"]}", - "properties.drsm_enthalpy": "{\"units\": [\"J/mol\"]}", - "properties.drsm_entropy_abs": "{\"units\": [\"J/(mol*K)\"]}", - "properties.drsm_heat_capacity_p": "{\"units\": [\"J/(mol*K)\"]}", - "properties.drsm_gibbs_energy.datasources": "[\"\",\"\"]", - "properties.drsm_enthalpy.datasources": "[\"\",\"\"]", - "properties.drsm_entropy_abs.datasources": "[\"\",\"\"]", - "properties.drsm_heat_capacity_p.datasources": "[\"\",\"\"]", - "properties.drsm_gibbs_energy.status": "[{\"4\" : \"IMPORTED\"}]", - "properties.drsm_enthalpy.status": "[{\"4\" : \"IMPORTED\"}]", - "properties.drsm_entropy_abs.status": "[{\"4\" : \"IMPORTED\"}]", - "properties.drsm_heat_capacity_p.status": "[{\"4\" : \"IMPORTED\"}]", - "properties.Tst": "298.15", - "properties.Pst": "1.0e5" - }, - "pairs": {}, - "matches": { - "symbol": { - "field": "properties.symbol" - }, - "DataStandard.4.datatype": { - "field": "properties.drsm_gibbs_energy.name" - }, - "DataStandard.4.value": { - "field": "properties.drsm_gibbs_energy.values" - }, - "DataStandard.4.positiveunc": { - "field": "properties.drsm_gibbs_energy.errors" - }, - "DataStandard.4.reference_1": { - "field": "properties.drsm_gibbs_energy.datasources.0" - }, - "DataStandard.4.reference_2": { - "field": "properties.drsm_gibbs_energy.datasources.1" - }, - "DataStandard.4.unctype": { - "field": "properties.drsm_gibbs_energy.errortypes", - "convert": { - "Gauss2s": "{\"0\" : \"NORMAL\"}" - } - }, - "DataStandard.5.datatype": { - "field": "properties.drsm_enthalpy.name" - }, - "DataStandard.5.value": { - "field": "properties.drsm_enthalpy.values" - }, - "DataStandard.5.positiveunc": { - "field": "properties.drsm_enthalpy.errors" - }, - "DataStandard.5.reference_1": { - "field": "properties.drsm_enthalpy.datasources.0" - }, - "DataStandard.5.reference_2": { - "field": "properties.drsm_enthalpy.datasources.1" - }, - "DataStandard.5.unctype": { - "field": "properties.drsm_enthalpy.errortypes", - "convert": { - "Gauss2s": "{\"0\" : \"NORMAL\"}" - } - }, - "DataStandard.6.datatype": { - "field": "properties.drsm_entropy.name" - }, - "DataStandard.6.value": { - "field": "properties.drsm_entropy.values" - }, - "DataStandard.6.positiveunc": { - "field": "properties.drsm_entropy_abs.errors" - }, - "DataStandard.6.reference_1": { - "field": "properties.drsm_entropy_abs.datasources.0" - }, - "DataStandard.6.reference_2": { - "field": "properties.drsm_entropy_abs.datasources.1" - }, - "DataStandard.6.unctype": { - "field": "properties.drsm_entropy_abs.errortypes", - "convert": { - "Gauss2s": "{\"0\" : \"NORMAL\"}" - } - }, - "DataStandard.7.datatype": { - "field": "properties.drsm_heat_capacity_p.name" - }, - "DataStandard.7.value": { - "field": "properties.drsm_heat_capacity_p.values" - }, - "DataStandard.7.positiveunc": { - "field": "properties.drsm_heat_capacity_p.errors" - }, - "DataStandard.7.reference_1": { - "field": "properties.drsm_heat_capacity_p.datasources.0" - }, - "DataStandard.7.reference_2": { - "field": "properties.drsm_heat_capacity_p.datasources.1" - }, - "DataStandard.7.unctype": { - "field": "properties.drsm_heat_capacity_p.errortypes", - "convert": { - "Gauss2s": "{\"0\" : \"NORMAL\"}" - } - }, - "DataStandard.8.datatype": { - "field": "properties.logKr.name" - }, - "DataStandard.8.value": { - "field": "properties.logKr.values" - }, - "DataStandard.8.positiveunc": { - "field": "properties.logKr.errors" - }, - "DataStandard.8.reference_1": { - "field": "properties.logKr.datasources.0" - }, - "DataStandard.8.reference_2": { - "field": "properties.logKr.datasources.1" - }, - "DataStandard.8.unctype": { - "field": "properties.logKr.errortypes", - "convert": { - "Gauss2s": "{\"0\" : \"NORMAL\"}" - } - }, - "DataVariable.1.mintk": { - "field": "properties.TPMethods.0.limitsTP.lowerT" - }, - "DataVariable.1.maxtk": { - "field": "properties.TPMethods.0.limitsTP.upperT" - }, - "DataVariable.1.minpbar": { - "field": "properties.TPMethods.0.limitsTP.lowerP", - "script": "field = field*1e05;" - }, - "DataVariable.1.maxpbar": { - "field": "properties.TPMethods.0.limitsTP.upperP", - "script": "field = field*1e05;" - }, - "DataVariable.1.a": { - "field": "properties.TPMethods.0.dr_heat_capacity_ft_coeffs.values.0" - }, - "DataVariable.1.b": { - "field": "properties.TPMethods.0.dr_heat_capacity_ft_coeffs.values.1" - }, - "DataVariable.1.c": { - "field": "properties.TPMethods.0.dr_heat_capacity_ft_coeffs.values.2" - }, - "DataVariable.1.d": { - "field": "properties.TPMethods.0.dr_heat_capacity_ft_coeffs.values.3" - }, - "DataVariable.1.e": { - "field": "properties.TPMethods.0.dr_heat_capacity_ft_coeffs.values.4" - }, - "DataVariable.1.f": { - "field": "properties.TPMethods.0.dr_heat_capacity_ft_coeffs.values.5" - }, - "DataVariable.2.mintk": { - "field": "properties.TPMethods.1.limitsTP.lowerT" - }, - "DataVariable.2.maxtk": { - "field": "properties.TPMethods.1.limitsTP.upperT" - }, - "DataVariable.2.minpbar": { - "field": "properties.TPMethods.1.limitsTP.lowerP", - "script": "field = field * 1e05;" - }, - "DataVariable.2.maxpbar": { - "field": "properties.TPMethods.1.limitsTP.upperP", - "script": "field = field * 1e05;" - }, - "DataVariable.2.tpfunc": { - "field": "properties.TPMethods.1.logk_ft_coeffs.comment" - }, - "DataVariable.2.a": { - "field": "properties.TPMethods.1.logk_ft_coeffs.values.0" - }, - "DataVariable.2.b": { - "field": "properties.TPMethods.1.logk_ft_coeffs.values.1" - }, - "DataVariable.2.c": { - "field": "properties.TPMethods.1.logk_ft_coeffs.values.2" - }, - "DataVariable.2.d": { - "field": "properties.TPMethods.1.logk_ft_coeffs.values.3" - }, - "DataVariable.2.e": { - "field": "properties.TPMethods.1.logk_ft_coeffs.values.4" - }, - "DataVariable.2.f": { - "field": "properties.TPMethods.1.logk_ft_coeffs.values.5" - } - }, - "script": "rintable.properties.name = rintable.properties.symbol;" - }, - "renderer": "JSON", - "label": "VertexReaction", - "comment": "", - "fname": "", - "Nblocks": 0, - "Nlines": 0 -} \ No newline at end of file diff --git a/Resources/files/TestThereda/ReactionDependentSubstance2.Thereda_aq_Reac.FormatStructDataFile.json b/Resources/files/TestThereda/ReactionDependentSubstance2.Thereda_aq_Reac.FormatStructDataFile.json deleted file mode 100644 index 67a5355d..00000000 --- a/Resources/files/TestThereda/ReactionDependentSubstance2.Thereda_aq_Reac.FormatStructDataFile.json +++ /dev/null @@ -1,196 +0,0 @@ -{ - "block": { - "defaults": { - "properties.sourcetdb": "{\"12\" : \"THEREDA\"}", - "properties.TPMethods": "[{\"method\" :{\"0\" : \"cp_ft_equation\"}, \"m_heat_capacity_ft_coeffs\" :{\"values\" : [0,0,0,0,0,0]}}]", - "properties.aggregate_state": "{\"4\" : \"AS_AQUEOUS\"}", - "properties.class_": "{\"2\" : \"SC_AQSOLUTE\"}", - "properties.sm_gibbs_energy": "{\"units\": [\"J/mol\"]}", - "properties.sm_enthalpy": "{\"units\": [\"J/mol\"]}", - "properties.sm_entropy_abs": "{\"units\": [\"J/(mol*K)\"]}", - "properties.sm_heat_capacity_p": "{\"units\": [\"J/(mol*K)\"]}", - "properties.sm_gibbs_energy.datasources": "[\"\",\"\"]", - "properties.sm_enthalpy.datasources": "[\"\",\"\"]", - "properties.sm_entropy_abs.datasources": "[\"\",\"\"]", - "properties.sm_heat_capacity_p.datasources": "[\"\",\"\"]", - "properties.sm_gibbs_energy.status": "[{\"4\" : \"IMPORTED\"}]", - "properties.sm_enthalpy.status": "[{\"4\" : \"IMPORTED\"}]", - "properties.sm_entropy_abs.status": "[{\"4\" : \"IMPORTED\"}]", - "properties.sm_heat_capacity_p.status": "[{\"4\" : \"IMPORTED\"}]", - "properties.Tst": "298.15", - "properties.Pst": "1.0e5" - }, - "pairs": {}, - "matches": { - "symbol": { - "field": "properties.symbol" - }, - "Declaration.charge": { - "field": "properties.formula_charge" - }, - "Declaration.molarmass": { - "field": "properties.mass_per_mole" - }, - "DataStandard.0.datatype": { - "field": "properties.sm_gibbs_energy.name" - }, - "DataStandard.0.value": { - "field": "properties.sm_gibbs_energy.values" - }, - "DataStandard.0.positiveunc": { - "field": "properties.sm_gibbs_energy.errors" - }, - "DataStandard.0.reference_1": { - "field": "properties.sm_gibbs_energy.datasources.0" - }, - "DataStandard.0.reference_2": { - "field": "properties.sm_gibbs_energy.datasources.1" - }, - "DataStandard.0.unctype": { - "field": "properties.sm_gibbs_energy.errortypes", - "convert": { - "Gauss2s": "{\"0\" : \"NORMAL\"}" - } - }, - "DataStandard.1.datatype": { - "field": "properties.sm_enthalpy.name" - }, - "DataStandard.1.value": { - "field": "properties.sm_enthalpy.values" - }, - "DataStandard.1.positiveunc": { - "field": "properties.sm_enthalpy.errors" - }, - "DataStandard.1.reference_1": { - "field": "properties.sm_enthalpy.datasources.0" - }, - "DataStandard.1.reference_2": { - "field": "properties.sm_enthalpy.datasources.1" - }, - "DataStandard.1.unctype": { - "field": "properties.sm_enthalpy.errortypes", - "convert": { - "Gauss2s": "{\"0\" : \"NORMAL\"}" - } - }, - "DataStandard.2.datatype": { - "field": "properties.sm_entropy_abs.name" - }, - "DataStandard.2.value": { - "field": "properties.sm_entropy_abs.values" - }, - "DataStandard.2.positiveunc": { - "field": "properties.sm_entropy_abs.errors" - }, - "DataStandard.2.reference_1": { - "field": "properties.sm_entropy_abs.datasources.0" - }, - "DataStandard.2.reference_2": { - "field": "properties.sm_entropy_abs.datasources.1" - }, - "DataStandard.2.unctype": { - "field": "properties.sm_entropy_abs.errortypes", - "convert": { - "Gauss2s": "{\"0\" : \"NORMAL\"}" - } - }, - "DataStandard.3.datatype": { - "field": "properties.sm_heat_capacity_p.name" - }, - "DataStandard.3.value": { - "field": "properties.sm_heat_capacity_p.values" - }, - "DataStandard.3.positiveunc": { - "field": "properties.sm_heat_capacity_p.errors" - }, - "DataStandard.3.reference_1": { - "field": "properties.sm_heat_capacity_p.datasources.0" - }, - "DataStandard.3.reference_2": { - "field": "properties.sm_heat_capacity_p.datasources.1" - }, - "DataStandard.3.unctype": { - "field": "properties.sm_heat_capacity_p.errortypes", - "convert": { - "Gauss2s": "{\"0\" : \"NORMAL\"}" - } - }, - "DataStandard.4.datatype": { - "field": "properties.sm_volume.name" - }, - "DataStandard.4.value": { - "field": "properties.sm_volume.values" - }, - "DataStandard.4.positiveunc": { - "field": "properties.sm_volume.errors" - }, - "DataStandard.4.reference_1": { - "field": "properties.sm_volume.datasources.0" - }, - "DataStandard.4.reference_2": { - "field": "properties.sm_volume.datasources.1" - }, - "DataStandard.4.unctype": { - "field": "properties.sm_volume.errortypes", - "convert": { - "Gauss2s": "{\"0\" : \"NORMAL\"}" - } - }, - "DataVariable.0.mintk": { - "field": "properties.TPMethods.0.limitsTP.lowerT" - }, - "DataVariable.0.maxtk": { - "field": "properties.TPMethods.0.limitsTP.upperT" - }, - "DataVariable.0.minpbar": { - "field": "properties.TPMethods.0.limitsTP.lowerP", - "script": "field = field*1e05;" - }, - "DataVariable.0.maxpbar": { - "field": "properties.TPMethods.0.limitsTP.upperP", - "script": "field = field*1e05;" - }, - "DataVariable.0.a": { - "field": "properties.TPMethods.0.m_heat_capacity_ft_coeffs.values.0" - }, - "DataVariable.0.b": { - "field": "properties.TPMethods.0.m_heat_capacity_ft_coeffs.values.1" - }, - "DataVariable.0.c": { - "field": "properties.TPMethods.0.m_heat_capacity_ft_coeffs.values.2" - }, - "DataVariable.0.d": { - "field": "properties.TPMethods.0.m_heat_capacity_ft_coeffs.values.3" - }, - "DataVariable.0.e": { - "field": "properties.TPMethods.0.m_heat_capacity_ft_coeffs.values.4" - }, - "DataVariable.0.f": { - "field": "properties.TPMethods.0.m_heat_capacity_ft_coeffs.values.5" - } - }, - "script": "formula = rintable.properties.symbol; -if (formula == 'H2O(l)') then rintable.properties.class_ = {} rintable.properties.class_['3'] = 'SC_AQSOLVENT' rintable.properties.aggregate_state = {} rintable.properties.aggregate_state['4'] = 'AS_AQUEOUS' end; -if string.match(formula, '(g)') then rintable.properties.class_ = {} rintable.properties.class_['1'] = 'SC_GASFLUID' rintable.properties.aggregate_state = {} rintable.properties.aggregate_state['0'] = 'AS_GAS' end; -if string.match(formula, '(cr)') then rintable.properties.class_ = {} rintable.properties.class_['0'] = 'SC_COMPONENT' rintable.properties.aggregate_state = {} rintable.properties.aggregate_state['3'] = 'AS_CRYSTAL' end; -formula = string.gsub(formula, '<(%d*)->', '-%1' ); -formula = string.gsub(formula, '<(%d*)+>', '+%1' ); -formula = string.gsub(formula, '<0>', '@' ); -formula = string.gsub(formula, '%(l%)', '@' ); -formula = string.gsub(formula, '%(g%)', '' ); -formula = string.gsub(formula, '%(cr%)', '' ); -formula = string.gsub(formula, '%(am%)', '' ); -formula = string.gsub(formula, '%(s%)', '' ); -formula = string.gsub(formula, '^O2(@?)$', 'O|0|2%1' ); -formula = string.gsub(formula, '^H2(@?)$', 'H|0|2%1' ); -rintable.properties.formula = formula; -rintable.properties.name = rintable.properties.symbol; -print(rintable.properties.TPMethods[1]);" - }, - "renderer": "JSON", - "label": "VertexSubstance", - "comment": "", - "fname": "", - "Nblocks": 0, - "Nlines": 0 -} \ No newline at end of file diff --git a/Resources/files/TestThereda/ReactionEdges2.Thereda_aq_Reac.FormatStructDataFile.json b/Resources/files/TestThereda/ReactionEdges2.Thereda_aq_Reac.FormatStructDataFile.json deleted file mode 100644 index e732632a..00000000 --- a/Resources/files/TestThereda/ReactionEdges2.Thereda_aq_Reac.FormatStructDataFile.json +++ /dev/null @@ -1,26 +0,0 @@ -{ - "block" : { - "defaults" : { - "properties.rct" : "1", - "properties.level" : "11" - }, - "pairs" : { - - }, - "matches" : { - "FormingReaction.%.coefficient" : { - "field" : "properties.stoi_coeff" - }, - "FormingReaction.%.pcon_reactant" : { - "field" : "@key" - } - }, - "script" : "" - }, - "renderer" : "JSON", - "label" : "EdgeTakes", - "comment" : "", - "fname" : "", - "Nblocks" : 0, - "Nlines" : 0 -} diff --git a/Resources/files/TestThereda/Substance2.Thereda_aq_Master.FormatStructDataFile.json b/Resources/files/TestThereda/Substance2.Thereda_aq_Master.FormatStructDataFile.json deleted file mode 100644 index af83b19e..00000000 --- a/Resources/files/TestThereda/Substance2.Thereda_aq_Master.FormatStructDataFile.json +++ /dev/null @@ -1,197 +0,0 @@ -{ - "block": { - "defaults": { - "properties.sourcetdb": "{\"12\" : \"THEREDA\"}", - "properties.TPMethods": "[{\"method\" :{\"0\" : \"cp_ft_equation\"}, \"limitsTP\" : {\"range\" : \"false\", \"lowerP\" : \"1.0e5\", \"lowerT\" : \"298.15\", \"upperP\" : \"1.0e5\", \"upperT\" : \"298.15\"}, \"m_heat_capacity_ft_coeffs\" :{\"values\" : [0,0,0,0,0,0]}}]", - "properties.aggregate_state": "{\"4\" : \"AS_AQUEOUS\"}", - "properties.class_": "{\"2\" : \"SC_AQSOLUTE\"}", - "properties.sm_gibbs_energy": "{\"units\": [\"J/mol\"]}", - "properties.sm_enthalpy": "{\"units\": [\"J/mol\"]}", - "properties.sm_entropy_abs": "{\"units\": [\"J/(mol*K)\"]}", - "properties.sm_heat_capacity_p": "{\"units\": [\"J/(mol*K)\"]}", - "properties.sm_gibbs_energy.datasources": "[\"\",\"\"]", - "properties.sm_enthalpy.datasources": "[\"\",\"\"]", - "properties.sm_entropy_abs.datasources": "[\"\",\"\"]", - "properties.sm_heat_capacity_p.datasources": "[\"\",\"\"]", - "properties.sm_gibbs_energy.status": "[{\"4\" : \"IMPORTED\"}]", - "properties.sm_enthalpy.status": "[{\"4\" : \"IMPORTED\"}]", - "properties.sm_entropy_abs.status": "[{\"4\" : \"IMPORTED\"}]", - "properties.sm_heat_capacity_p.status": "[{\"4\" : \"IMPORTED\"}]", - "properties.Tst": "298.15", - "properties.Pst": "1.0e5", - "properties.limitsTP": "{\"range\": false, \"lowerT\": 273.15, \"upperT\": 298.15, \"lowerP\": 0.1, \"upperP\": 1e6 }" - }, - "pairs": {}, - "matches": { - "symbol": { - "field": "properties.symbol" - }, - "Declaration.charge": { - "field": "properties.formula_charge" - }, - "Declaration.molarmass": { - "field": "properties.mass_per_mole" - }, - "DataStandard.0.datatype": { - "field": "properties.sm_gibbs_energy.name" - }, - "DataStandard.0.value": { - "field": "properties.sm_gibbs_energy.values" - }, - "DataStandard.0.positiveunc": { - "field": "properties.sm_gibbs_energy.errors" - }, - "DataStandard.0.reference_1": { - "field": "properties.sm_gibbs_energy.datasources.0" - }, - "DataStandard.0.reference_2": { - "field": "properties.sm_gibbs_energy.datasources.1" - }, - "DataStandard.0.unctype": { - "field": "properties.sm_gibbs_energy.errortypes", - "convert": { - "Gauss2s": "{\"0\" : \"NORMAL\"}" - } - }, - "DataStandard.1.datatype": { - "field": "properties.sm_enthalpy.name" - }, - "DataStandard.1.value": { - "field": "properties.sm_enthalpy.values" - }, - "DataStandard.1.positiveunc": { - "field": "properties.sm_enthalpy.errors" - }, - "DataStandard.1.reference_1": { - "field": "properties.sm_enthalpy.datasources.0" - }, - "DataStandard.1.reference_2": { - "field": "properties.sm_enthalpy.datasources.1" - }, - "DataStandard.1.unctype": { - "field": "properties.sm_enthalpy.errortypes", - "convert": { - "Gauss2s": "{\"0\" : \"NORMAL\"}" - } - }, - "DataStandard.2.datatype": { - "field": "properties.sm_entropy_abs.name" - }, - "DataStandard.2.value": { - "field": "properties.sm_entropy_abs.values" - }, - "DataStandard.2.positiveunc": { - "field": "properties.sm_entropy_abs.errors" - }, - "DataStandard.2.reference_1": { - "field": "properties.sm_entropy_abs.datasources.0" - }, - "DataStandard.2.reference_2": { - "field": "properties.sm_entropy_abs.datasources.1" - }, - "DataStandard.2.unctype": { - "field": "properties.sm_entropy_abs.errortypes", - "convert": { - "Gauss2s": "{\"0\" : \"NORMAL\"}" - } - }, - "DataStandard.3.datatype": { - "field": "properties.sm_heat_capacity_p.name" - }, - "DataStandard.3.value": { - "field": "properties.sm_heat_capacity_p.values" - }, - "DataStandard.3.positiveunc": { - "field": "properties.sm_heat_capacity_p.errors" - }, - "DataStandard.3.reference_1": { - "field": "properties.sm_heat_capacity_p.datasources.0" - }, - "DataStandard.3.reference_2": { - "field": "properties.sm_heat_capacity_p.datasources.1" - }, - "DataStandard.3.unctype": { - "field": "properties.sm_heat_capacity_p.errortypes", - "convert": { - "Gauss2s": "{\"0\" : \"NORMAL\"}" - } - }, - "DataStandard.4.datatype": { - "field": "properties.sm_volume.name" - }, - "DataStandard.4.value": { - "field": "properties.sm_volume.values" - }, - "DataStandard.4.positiveunc": { - "field": "properties.sm_volume.errors" - }, - "DataStandard.4.reference_1": { - "field": "properties.sm_volume.datasources.0" - }, - "DataStandard.4.reference_2": { - "field": "properties.sm_volume.datasources.1" - }, - "DataStandard.4.unctype": { - "field": "properties.sm_volume.errortypes", - "convert": { - "Gauss2s": "{\"0\" : \"NORMAL\"}" - } - }, - "DataVariable.0.mintk": { - "field": "properties.TPMethods.0.limitsTP.lowerT" - }, - "DataVariable.0.maxtk": { - "field": "properties.TPMethods.0.limitsTP.upperT" - }, - "DataVariable.0.minpbar": { - "field": "properties.TPMethods.0.limitsTP.lowerP", - "script": "field = field*1e05;" - }, - "DataVariable.0.maxpbar": { - "field": "properties.TPMethods.0.limitsTP.upperP", - "script": "field = field*1e05;" - }, - "DataVariable.0.a": { - "field": "properties.TPMethods.0.m_heat_capacity_ft_coeffs.values.0" - }, - "DataVariable.0.b": { - "field": "properties.TPMethods.0.m_heat_capacity_ft_coeffs.values.1" - }, - "DataVariable.0.c": { - "field": "properties.TPMethods.0.m_heat_capacity_ft_coeffs.values.2" - }, - "DataVariable.0.d": { - "field": "properties.TPMethods.0.m_heat_capacity_ft_coeffs.values.3" - }, - "DataVariable.0.e": { - "field": "properties.TPMethods.0.m_heat_capacity_ft_coeffs.values.4" - }, - "DataVariable.0.f": { - "field": "properties.TPMethods.0.m_heat_capacity_ft_coeffs.values.5" - } - }, - "script": "formula = rintable.properties.symbol; -if (formula == 'H2O(l)') then rintable.properties.class_ = {} rintable.properties.class_['3'] = 'SC_AQSOLVENT' rintable.properties.aggregate_state = {} rintable.properties.aggregate_state['4'] = 'AS_AQUEOUS' end; -if string.match(formula, '(g)') then rintable.properties.class_ = {} rintable.properties.class_['1'] = 'SC_GASFLUID' rintable.properties.aggregate_state = {} rintable.properties.aggregate_state['0'] = 'AS_GAS' end; -if string.match(formula, '(cr)') then rintable.properties.class_ = {} rintable.properties.class_['0'] = 'SC_COMPONENT' rintable.properties.aggregate_state = {} rintable.properties.aggregate_state['3'] = 'AS_CRYSTAL' end; -formula = string.gsub(formula, '<(%d*)->', '-%1' ); -formula = string.gsub(formula, '<(%d*)+>', '+%1' ); -formula = string.gsub(formula, '<0>', '@' ); -formula = string.gsub(formula, '%(l%)', '@' ); -formula = string.gsub(formula, '%(g%)', '' ); -formula = string.gsub(formula, '%(cr%)', '' ); -formula = string.gsub(formula, '%(am%)', '' ); -formula = string.gsub(formula, '%(s%)', '' ); -formula = string.gsub(formula, '^O2(@?)$', 'O|0|2%1' ); -formula = string.gsub(formula, '^H2(@?)$', 'H|0|2%1' ); -rintable.properties.formula = formula; -rintable.properties.name = rintable.properties.symbol; -print(rintable.properties.TPMethods[1]);" - }, - "renderer": "JSON", - "label": "VertexSubstance", - "comment": "", - "fname": "", - "Nblocks": 0, - "Nlines": 0 -} \ No newline at end of file diff --git a/Resources/files/TestThereda/THEREDA_PIT_JSON_r01.dat b/Resources/files/TestThereda/THEREDA_PIT_JSON_r01.dat deleted file mode 100644 index 25b828fb..00000000 --- a/Resources/files/TestThereda/THEREDA_PIT_JSON_r01.dat +++ /dev/null @@ -1,23541 +0,0 @@ -{ - "Elements": [ - { - "symbol": "EA", - "name": "Electron", - "atomicnumber": 0, - "molarmass": 0.00054858, - "molarmass_referenceid": "Definition\/Convention", - "s298": 65.34, - "s298_unctype": "Gauss2s", - "s298_negativeunc": 0.0015, - "s298_positiveunc": 0.0015, - "s298_referenceid": "Definition\/Convention", - "cp298": 14.418, - "cp298_unctype": "Gauss2s", - "cp298_negativeunc": 0.001, - "cp298_positiveunc": 0.001, - "cp298_referenceid": "Definition\/Convention", - "referencestate": "aqueous", - "stoichiometriccoefficient": 1, - "description": "equal to value for 0.5H2(g), since reaction value for H2(g) = H<+> + e<-> is equal to zero (convention). Exact value for molar mass is 0.00054857990943. It was rounded to eight digits. " - }, - { - "symbol": "H", - "name": "Hydrogen", - "atomicnumber": 1, - "molarmass": 1.00794, - "molarmass_referenceid": "WIE2006", - "s298": 130.68, - "s298_unctype": "Gauss2s", - "s298_negativeunc": 0.003, - "s298_positiveunc": 0.003, - "s298_referenceid": "COX\/WAG1989", - "cp298": 28.836, - "cp298_unctype": "Gauss2s", - "cp298_negativeunc": 0.002, - "cp298_positiveunc": 0.002, - "cp298_referenceid": "COX\/WAG1989", - "referencestate": "gaseous", - "stoichiometriccoefficient": 2, - "description": null - }, - { - "symbol": "O", - "name": "Oxygen", - "atomicnumber": 8, - "molarmass": 15.9994, - "molarmass_referenceid": "WIE2006", - "s298": 205.152, - "s298_unctype": "Gauss2s", - "s298_negativeunc": 0.005, - "s298_positiveunc": 0.005, - "s298_referenceid": "COX\/WAG1989", - "cp298": 29.378, - "cp298_unctype": "Gauss2s", - "cp298_negativeunc": 0.003, - "cp298_positiveunc": 0.003, - "cp298_referenceid": "COX\/WAG1989", - "referencestate": "gaseous", - "stoichiometriccoefficient": 2, - "description": null - 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C., Richter, A., Scharge, T., Voigt, W., Wilhelm, S., Wilms, T., Wollmann, G.", - "year": 2011, - "volume": null, - "page": null, - "editors": null, - "language": "German", - "publisher": "GRS", - "ISBN_ISSN": "978-3-939355-41-0", - "citedinid": null, - "citationmetainfo": null, - "doi": null, - "puburl": null, - "cascit": null, - "chapter": null, - "edition": null, - "location": null, - "thesisdeg": null, - "thesisumipubnum": null - }, - { - "ID": "VOI\/SUK2011", - "type": "Report", - "pubname": null, - "origin": null, - "title": "Thermodynamic standard functions for pure water", - "author": "Voigt, W., Sukhanov, D.", - "year": 2011, - "volume": null, - "page": null, - "editors": null, - "language": "English", - "publisher": null, - "ISBN_ISSN": null, - "citedinid": null, - "citationmetainfo": null, - "doi": null, - "puburl": null, - "cascit": null, - "chapter": null, - "edition": null, - "location": null, - "thesisdeg": null, - "thesisumipubnum": null - } - ] -} diff --git a/Resources/files/TestThereda/THEREDA_Release_notes_r01.pdf b/Resources/files/TestThereda/THEREDA_Release_notes_r01.pdf deleted file mode 100644 index 24822f3d..00000000 Binary files a/Resources/files/TestThereda/THEREDA_Release_notes_r01.pdf and /dev/null differ diff --git a/Resources/files/TestThereda/THEREDA_TP_JSON-Format_Rev_1-0.pdf b/Resources/files/TestThereda/THEREDA_TP_JSON-Format_Rev_1-0.pdf deleted file mode 100644 index 95990e64..00000000 Binary files a/Resources/files/TestThereda/THEREDA_TP_JSON-Format_Rev_1-0.pdf and /dev/null differ diff --git a/Resources/files/TestThereda/issues.txt b/Resources/files/TestThereda/issues.txt deleted file mode 100644 index ea756428..00000000 --- a/Resources/files/TestThereda/issues.txt +++ /dev/null @@ -1 +0,0 @@ -- take agregate state gaseous, aqueous, and for crystal search with lua script is string contains crystal diff --git a/Resources/files/TestThereda/other/Thereda_Elements.json b/Resources/files/TestThereda/other/Thereda_Elements.json deleted file mode 100644 index d4ea0f9b..00000000 --- a/Resources/files/TestThereda/other/Thereda_Elements.json +++ /dev/null @@ -1,182 +0,0 @@ -[ - { - "symbol": "EA", - "name": "Electron", - "atomicnumber": 0, - "molarmass": 0.00054858, - "molarmass_referenceid": "Definition\/Convention", - "s298": 65.34, - "s298_unctype": "Gauss2s", - "s298_negativeunc": 0.0015, - "s298_positiveunc": 0.0015, - "s298_referenceid": "Definition\/Convention", - "cp298": 14.418, - "cp298_unctype": "Gauss2s", - "cp298_negativeunc": 0.001, - "cp298_positiveunc": 0.001, - "cp298_referenceid": "Definition\/Convention", - "referencestate": "aqueous", - "stoichiometriccoefficient": 1, - "description": "equal to value for 0.5H2(g), since reaction value for H2(g) = H<+> + e<-> is equal to zero (convention). 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"description": null - }, - { - "symbol": "Mg", - "name": "Magnesium", - "atomicnumber": 12, - "molarmass": 24.305, - "molarmass_referenceid": "WIE2006", - "s298": 32.67, - "s298_unctype": "Gauss2s", - "s298_negativeunc": 0.1, - "s298_positiveunc": 0.1, - "s298_referenceid": "COX\/WAG1989", - "cp298": 24.869, - "cp298_unctype": "Gauss2s", - "cp298_negativeunc": 0.02, - "cp298_positiveunc": 0.02, - "cp298_referenceid": "COX\/WAG1989", - "referencestate": "crystalline, hexagonal", - "stoichiometriccoefficient": 1, - "description": null - }, - { - "symbol": "Ca", - "name": "Calcium", - "atomicnumber": 20, - "molarmass": 40.078, - "molarmass_referenceid": "WIE2006", - "s298": 41.59, - "s298_unctype": "Gauss2s", - "s298_negativeunc": 0.4, - "s298_positiveunc": 0.4, - "s298_referenceid": "COX\/WAG1989", - "cp298": 25.929, - "cp298_unctype": "Gauss2s", - "cp298_negativeunc": 0.3, - "cp298_positiveunc": 0.3, - "cp298_referenceid": "COX\/WAG1989", - "referencestate": "crystalline, cubic, fcc, alpha", - 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"dataquality": -1, - "datasource": -1, - "reference_1": "InternallyCalculated", - "reference_2": null, - "description": null - }, - "IPT": { - "tpfunc": "Pitzer-function", - "ip_1_a": 0, - "ip_1_b": -0.33575218581995, - "ip_1_c": 0.14531158458115, - "ip_1_d": -0.0022722938962054, - "ip_1_e": 1.9538423356786e-6, - "ip_1_f": 0, - "ip_2_a": 0, - "ip_2_b": 0, - "ip_2_c": 0, - "ip_2_d": 0, - "ip_2_e": 0, - "ip_2_f": 0, - "ip_3_a": 0, - "ip_3_b": 0, - "ip_3_c": 0, - "ip_3_d": 0, - "ip_3_e": 0, - "ip_3_f": 0, - "ip_4_a": 0, - "ip_4_b": 0, - "ip_4_c": 0, - "ip_4_d": 0, - "ip_4_e": 0, - "ip_4_f": 0, - "ip_5_a": 0, - "ip_5_b": 0, - "ip_5_c": 0, - "ip_5_d": 0, - "ip_5_e": 0, - "ip_5_f": 0, - "ip_6_a": 0, - "ip_6_b": 0, - "ip_6_c": 0, - "ip_6_d": 0, - "ip_6_e": 0, - "ip_6_f": 0, - "mintk": 273.15, - "maxtk": 393.15, - "minpbar": 1.01325, - "maxpbar": 1.01325, - "calcmode": "Entered", - "ipclass": 1, - "dataquality": 1, - "datasource": 4, - "reference_1": "ALT\/BRE2011", - "reference_2": null, - "description": null - } - }, - { - "Declaration": { - "interactiontype": "Pitzer_theta", - "pcon_1": "SO4<2->", - "pcon_2": "HSO4<->", - "pcon_3": null, - "description": null - }, - "IP298": { - "ip298_1": -0.11850909385801, - "ip298_1_unctype": null, - "ip298_1_negativeunc": 0, - "ip298_1_positiveunc": 0, - "ip298_2": 0, - "ip298_2_unctype": null, - "ip298_2_negativeunc": 0, - "ip298_2_positiveunc": 0, - "ip298_3": 0, - "ip298_3_unctype": null, - "ip298_3_negativeunc": 0, - "ip298_3_positiveunc": 0, - "ip298_4": 0, - "ip298_4_unctype": null, - "ip298_4_negativeunc": 0, - "ip298_4_positiveunc": 0, - "ip298_5": 0, - "ip298_5_unctype": null, - "ip298_5_negativeunc": 0, - "ip298_5_positiveunc": 0, - "ip298_6": 0, - "ip298_6_unctype": null, - "ip298_6_negativeunc": 0, - "ip298_6_positiveunc": 0, - "calcmode": "CTPFUNC", - "ipclass": 1, - "dataquality": -1, - "datasource": -1, - "reference_1": "InternallyCalculated", - "reference_2": null, - "description": null - }, - "IPT": { - "tpfunc": "Pitzer-function", - "ip_1_a": 121059.80972999, - "ip_1_b": -2844.522811955, - "ip_1_c": 478.64841878646, - "ip_1_d": -0.83397701136569, - "ip_1_e": 0.00027042821215948, - "ip_1_f": -5704023.4169222, - "ip_2_a": 0, - "ip_2_b": 0, - "ip_2_c": 0, - "ip_2_d": 0, - "ip_2_e": 0, - "ip_2_f": 0, - "ip_3_a": 0, - "ip_3_b": 0, - "ip_3_c": 0, - "ip_3_d": 0, - "ip_3_e": 0, - "ip_3_f": 0, - "ip_4_a": 0, - "ip_4_b": 0, - "ip_4_c": 0, - "ip_4_d": 0, - "ip_4_e": 0, - "ip_4_f": 0, - "ip_5_a": 0, - "ip_5_b": 0, - "ip_5_c": 0, - "ip_5_d": 0, - "ip_5_e": 0, - "ip_5_f": 0, - "ip_6_a": 0, - "ip_6_b": 0, - "ip_6_c": 0, - "ip_6_d": 0, - "ip_6_e": 0, - "ip_6_f": 0, - "mintk": 273.15, - "maxtk": 393.15, - "minpbar": 1.01325, - "maxpbar": 1.01325, - "calcmode": "Entered", - "ipclass": 1, - "dataquality": 1, - "datasource": 4, - "reference_1": "ALT\/BRE2011", - "reference_2": null, - "description": null - } - } - ] - }] diff --git a/Resources/files/my.TimeStamp.yaml b/Resources/files/my.TimeStamp.yaml deleted file mode 100644 index 0df29941..00000000 --- a/Resources/files/my.TimeStamp.yaml +++ /dev/null @@ -1,6 +0,0 @@ -year: 16 -month: 3 -day: 16 -hour: 14 -minute: 26 -second: 32 \ No newline at end of file diff --git a/Resources/help/HowToISOCReactions.html b/Resources/help/HowToISOCReactions.html deleted file mode 100644 index 25004688..00000000 --- a/Resources/help/HowToISOCReactions.html +++ /dev/null @@ -1,491 +0,0 @@ - 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Isocoulombic Reactions Generator

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Given a list of selected non isocoulombic reactions and a list of selected model reactions, the isocoulombic reactions generator will generate all possible isocoulombic reactions, by combining the non isocoulombic reactions with the model reactions. The logK values for the non isocoulombic reactions can be then calculated by using the isocoulombic reactions using one-, two- or three-term extrapolation methods.

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Isocoulombic Reactions Generator Window
-Empty Isocoulombic Reactions Generator Window

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How to generate isocoulombic reactions

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Note
-Follow the messages written in the status bar for the work flow, success, and error messages.

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1. To start using the Isocoulombic Reactions Generator Application first click the Select Database source and Elements Source Database Elements. Chose the desired source database (Step 1), in the next step the desired elements (Step 2), and in the last step if present the desired reaction sets (Step 3). This will filter the data available for generating reactions.

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Note
-The available elements are based on the available substances in the selected source database. If a substance contains an element, the element will be selectable.

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Select Source Database Select Elements Select Reaction Sets
Step 1 Step 2 Step 3
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2. Select one or more non-isocoulombic reactions to be investigated, by clicking Select Investigated Reactions Select.Investigate.Reactions.

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Select Investigated Reactions
-Select Investigated reaction/s

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3. Select the model reactions which will be used for generating isocoulombic reactions, by clicking Select Model Reaction Select Model Reactions.

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Select Model Reactions
-Select Model Reactions

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4. Generate isocoulombic reactions, by clicking Generate Isocoulombic Reaction Generate Isocoulombic Reactions. If the reactions were successfully generated, they will be displayed in the window, together with their properties at 25 C 1 bar.

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You can now calculate the logK values for the investigated reactions (or the isocoulombic reactions) using the one-, two-, and three-term extrapolation methods. Or you can now save a selection from the generated isocoulombic reactions as reaction sets.

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Successfully generated isocoulombic reactions
-Successfully generated isocoulombic reactions

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5. Calculated logK values for the investigated reactions at different temperature and pressure points, by clicking Calculate Properties of Invesitgated Reactions Calculate Properties of Invesitgated Reactions. Step 1 , the user will be asked to define the temperature and pressure points at which the logK values will be calculated. Step 2, the user will be asked to select the isocoulombic reactions which will be used in the calculations. Step 3, the user will be asked to select one or more extrapolation method to be used when doing the calculations using the previously selected isocoulombic reactions.

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Note
-The selected extrapolation method/s if possible (depending on the thermodynamic data available) will be automatically set for all the selected isocoulombic reactions.

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Based on the selected isocoulombic reactions and the selected extrapolation methods in the results file a collumn with the name: \extrapolation type_\number of the investigated reaction_\reaction equation. For example: 1T_0_CeCl+2+Cm+3+NO3-=Ce+3+Cl-+Cam(NO3)+2, this means that the values in found in this column were calculated using the one-term extrapolation method and the isocoulombic reaction with the given equation (index 0, first investigated reaction in the investigated reactions list).

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1T - one-term; 2T - two-term; 3T -three-term;

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Select temperature and pressure points Select Isocoulombic Reactions Select extrapolation methods
Step 1 Step 2 Step 3
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If calculation was successful, view and plot the result by clicking Show and Plot Results Show and Plot Results.

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Note
-The result are written in a result_.csv file found in the application folder.

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Calculated logK values using isocoulombic reactions
-Plot of calculated logK values for an investigated reaction using several isocoulombic reactions and extrapolation methods.

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Calculated logK values from the CSV results file
-Calculated logK values for an investigated reaction using several isocoulombic reactions and extrapolation methods as present in the results_.csv file. The column names are related to the extrapolation method type (1T, 2T, 3T), the index of the investigated reaction (0, 1, 2, …)

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5b. Calculated logK values for the generated isocoulombic reactions at different temperature and pressure points, by clicking Tools/Calculate Properties of Generated Isocoulombic Reactions Calculate Properties of Generated Isocoulombic Reactions. If calculation was successful, view and plot the result by clicking Show and Plot Results Show and Plot Results.

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6. Save the generated isocoulombic reactions, by clicking Save Reactions Set Save.Reactions.Set. Step 1, the user is asked to select the isocoulombic reactions he wants to save. Step 2, the user must select one extrapolation method which will be set in the saved reactions record. Step 3, the user is asked to choose which substance participating in the investigated reaction/s is the reaction defined substance.

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Note
-The substance selected as reaction defined will have a defines edge (link) created between its record and the saved isocoulombic reaction/s. For example, if three isocoulombic reactions are saved for one investigated reaction, three defines edges with different level values will be created between the reaction defined substance and the saved isocoulombic reactions.

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Select Isocoulombic Reactions Select extrapolation method Select Substance defined by the reaction
Step 1 Step 2 Step 3
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Note
-When the Set Extrapolation Methods individually is activated in the preferences, when doing logK values calculations or saving generated isocoulombic reactions, you will be asked to select the desired extrapolation method for each reaction individually.

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Application Menu

- - - - - diff --git a/Resources/help/HowToISOCReactions.md b/Resources/help/HowToISOCReactions.md deleted file mode 100644 index 90d85999..00000000 --- a/Resources/help/HowToISOCReactions.md +++ /dev/null @@ -1,95 +0,0 @@ -# Isocoulombic Reactions Generator -* [How to use the isocoulombic reactions generator](#How.to.generate.isocoulombic.reactions) -* [Application Menu](#Application.Menu) - -Given a list of selected non isocoulombic reactions and a list of selected model reactions, the isocoulombic reactions generator will generate all possible isocoulombic reactions, by combining the non isocoulombic reactions with the model reactions. The logK values for the non isocoulombic reactions can be then calculated by using the isocoulombic reactions using one-, two- or three-term extrapolation methods. - -![Isocoulombic Reactions Generator Window](images/IsocGenWidgetEmpty.png =840x "Isocoulombic Reactions Generator Window") -_Empty Isocoulombic Reactions Generator Window_ - -## How to generate isocoulombic reactions -> __Note__ -Follow the messages written in the status bar for the work flow, success, and error messages. - -__1.__ To start using the Isocoulombic Reactions Generator Application first click the [Select Database source and Elements](#Source.Database.Elements) ![Source Database Elements](images/SourceElementFilter.png "Source Database Elements"). Chose the desired source database (_Step 1_), in the next step the desired elements (_Step 2_), and in the last step if present the desired reaction sets (_Step 3_). This will filter the data available for generating reactions. - -> __Note__ -The available elements are based on the available substances in the selected source database. If a substance contains an element, the element will be selectable. - -| ![Select Source Database](images/SelectSource.png =x250 "Select Source Database") | ![Select Elements](images/SelectElements.png =x250 "Select Elements") | ![Select Reaction Sets](images/SelectReactionSets.png =x250 "Select Reaction Sets") | -|::|::|::| -| _Step 1_ | _Step 2_ | _Step 3_ | - -__2.__ Select one or more non-isocoulombic reactions to be investigated, by clicking [Select Investigated Reactions](#) ![Select.Investigate.Reactions](images/SelectData.png "Select Investigated Reactions"). - -![Select Investigated Reactions](images/SelectInvReact.png =420x"Select Investigated Reactions") -_Select Investigated reaction/s_ - -__3.__ Select the model reactions which will be used for generating isocoulombic reactions, by clicking [Select Model Reaction](#) ![Select Model Reactions](images/SelectMaster.png "Select Model Reactions"). - -![Select Model Reactions](images/SelectModelReact.png =420x"Select Model Reactions") -_Select Model Reactions_ - -__4.__ Generate isocoulombic reactions, by clicking [Generate Isocoulombic Reaction](#) ![Generate Isocoulombic Reactions](images/ReacDCModuleIcon24.png "Generate Isocoulombic Reactions"). If the reactions were successfully generated, they will be displayed in the window, together with their properties at 25 C 1 bar. - -You can now calculate the logK values for the investigated reactions (or the isocoulombic reactions) using the one-, two-, and three-term extrapolation methods. Or you can now save a selection from the generated isocoulombic reactions as reaction sets. - -![Successfully generated isocoulombic reactions](images/IsocGen.png =840x"Successfully generated isocoulombic reactions") -_Successfully generated isocoulombic reactions_ - -__5.__ Calculated logK values for the investigated reactions at different temperature and pressure points, by clicking [Calculate Properties of Invesitgated Reactions](#) ![Calculate Properties of Invesitgated Reactions](images/CalculateRecrod.png "Calculate Properties of Invesitgated Reactions"). _Step 1_ , define the temperature and pressure points at which the logK values will be calculated. _Step 2_, select the isocoulombic reactions which will be used in the calculations. _Step 3_, select one or more extrapolation method to be used when doing the calculations using the previously selected isocoulombic reactions. - -> __Note__ -The selected extrapolation method/s if possible (depending on the thermodynamic data available) will be automatically set for all the selected isocoulombic reactions. - -> Based on the selected isocoulombic reactions and the selected extrapolation methods in the results file a collumn with the name: \extrapolation type\_\number of the investigated reaction\_\reaction equation. For example: __1T_0_CeCl+2+Cm+3+NO3-=Ce+3+Cl-+Cam(NO3)+2__, this means that the values in found in this column were calculated using the one-term extrapolation method and the isocoulombic reaction with the given equation (index 0, first investigated reaction in the investigated reactions list). - -> 1T - one-term; 2T - two-term; 3T -three-term; - -| ![Select temperature and pressure points](images/SelectTP.png =x250 "Select temperature and pressure points") | ![Select Isocoulombic Reactions](images/SelectIsocReact.png =x250"Select Isocoulombic Reactions") | ![Select extrapolation methods](images/SelectIsocExtrapolationMethod.png =x250 "Select extrapolation methods") | -|::|::|::| -| _Step 1_ | _Step 2_ | _Step 3_ | - -If calculation was successful, view and plot the result by clicking [Show and Plot Results](#) ![Show and Plot Results](images/ShowResults.png "Show and Plot Results"). - -> __Note__ -The result are written in a result_.csv file found in the application folder. - -![Calculated logK values using isocoulombic reactions](images/ResultsPlotInvReact.png =520x"Calculated logK values using isocoulombic reactions") -_Plot of calculated logK values for an investigated reaction using several isocoulombic reactions and extrapolation methods._ - -![Calculated logK values from the CSV results file](images/ResultsCsvInvReact.png =520x"Calculated logK values from the CSV results file") -_Calculated logK values for an investigated reaction using several isocoulombic reactions and extrapolation methods as present in the results\_.csv file. The column names are related to the extrapolation method type (1T, 2T, 3T), the index of the investigated reaction (0, 1, 2, ...)_ - -__5b.__ Calculated logK values for the generated isocoulombic reactions at different temperature and pressure points, by clicking Tools/[Calculate Properties of Generated Isocoulombic Reactions](#) ![Calculate Properties of Generated Isocoulombic Reactions](images/CalculateRecrod.png "Calculate Properties of Generated Isocoulombic Reactions"). If calculation was successful, view and plot the result by clicking [Show and Plot Results](#) ![Show and Plot Results](images/ShowResults.png "Show and Plot Results"). - -__6.__ Save the generated isocoulombic reactions, by clicking [Save Reactions Set](#) ![Save.Reactions.Set](images/SaveCurrentRecordIcon.png "Save Reactions Set"). _Step 1_, select the isocoulombic reactions you want to save. _Step 2_, select __one__ extrapolation method which will be set in the saved reactions record. _Step 3_, choose which substance participating in the investigated reaction/s is the reaction defined substance. - -> __Note__ -The substance selected as reaction defined will have a defines edge (link) created between its record and the saved isocoulombic reaction/s. For example, if three isocoulombic reactions are saved for one investigated reaction, three defines edges with different level values will be created between the reaction defined substance and the saved isocoulombic reactions. - -| ![Select Isocoulombic Reactions](images/SelectIsocReact.png =x250"Select Isocoulombic Reactions") | ![Select extrapolation method](images/SelectOneExrapMeth.png =x250 "Select extrapolation methods") | ![Select Substance defined by the reaction](images/SelectDefinedSubst.png =x250"Select Substance defined by the reaction") | -|::|::|::| -| _Step 1_ | _Step 2_ | _Step 3_ | - -> __Note__ -When the __Set Extrapolation Methods individually__ is activated in the preferences, when doing logK values calculations or saving generated isocoulombic reactions, you will be asked to select the desired extrapolation method for each reaction individually. - -## Application Menu -* __File__ - * ![New.Reset](images/NewCreateRecordIcon24.png "New/Reset") __New/Reset__: Resets the Isocoulombic Reactions Generator window. - * ![Save.Reactions.Set](images/SaveCurrentRecordIcon.png "Save Reactions Set") __Save Reaction Set__: Save generated isocoulombic reactions in the database as a Reactions Set, for each isocoulombic reaction. Set the Reaction Set __Symbol__, __Comment__ and __Reaction Level__ in the respective fields. -> __Note__ -The symbol of the saved reaction set will be the value entered in the __Symbol__ field _ the symbol of the isocoulombic reaction -* __Data__ - * ![Source.Database.Elements](images/SourceElementFilter.png "Source Database Elements") __Select Data Source and Elements__: Opens a wizard for selecting the source database and elements for filtering the data to be used for generating reactions. Select the source database from the available list of source databases. Next, select the elements which the substances and reactions should contain. - * ![Select.Investigate.Reactions](images/SelectData.png "Select Investigated Reactions") __Select Investigated Reactions__: Select one or more reactions which are not isocoulombic, but which will be combined into isocoulombic reactions. - * ![Select.Model.Reactions](images/SelectMaster.png "Select Model Reactions") __Select Model Reactions__: Select the model reactions, which will be used to generate isocoulombic reactions, by combining them with the selected investigated reactions. -* __Tools__ - * ![Generate.Isocoulombic.Reactions](images/ReacDCModuleIcon24.png "Generate Isocoulombic Reactions") __Generate Isocoulombic Reactions__: Generate isocoulombic reactions form the selecte reactions to ivestigate and model reactions. - * ![Calculate Properties of Invesitgated Reactions](images/CalculateRecrod.png "Calculate Properties of Invesitgated Reactions") __Calculate Properties of Reactions to Investigate at TP__: Calculates the logK values of the reactions to investigate at different temperature and pressure points, using the properties of the generated isocoulombic reactions and the one-, two-, or three-term extrapolation method. - * ![Calculate Properties of Isocoulombic Reactions](images/CalculateRecrod.png "Calculate Properties of Isocoulombic Reactions") __Calculate Properties of Generated Isocoulombic Reactions at TP__: Calculates the logK values of the generated isocoulombic reactions at different temperature and pressure points, using the one-, two-, or three-term extrapolation method. -* __Results__ - * ![Show and Plot Results](images/ShowResults.png "Show and Plot Results") __Show table with Results__: Opens the output CSV (Comma Separated Value) file with result and automatically plots the logK values against temperature. -* __Preferences__ - * __Set extrapolation methods individually__: If set, you will be asked to choose the extrapolation method for each generated isocoulombic reaction when calculating logK values or when saving the reactions. \ No newline at end of file diff --git a/Resources/help/HowToReactionsGenerator.html b/Resources/help/HowToReactionsGenerator.html deleted file mode 100644 index 32835909..00000000 --- a/Resources/help/HowToReactionsGenerator.html +++ /dev/null @@ -1,432 +0,0 @@ - - - - - - - -

Reactions Generator

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Given a list of substances and selected master substances, the reactions generator will generate a set of independent reactions. One reaction for each reaction dependent substance.

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Reactions Generator window -Empty Reactions Generator Window

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How to generate reactions using the Reactions Generator

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Note
-Follow the messages written in the status bar for the work flow, success, and error messages.

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1. To start using the Reactions Generator Application first click the Select Database source and Elements Source Database Elements. Chose the desired source database (Step 1), in the next step the desired elements (Step 2), and in the last step if present the desired reaction sets (Step 3). This will filter the data available for generating reactions.

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Note
-The available elements are based on the available substances in the selected source database. If a substance contains an element, the element will be selectable.

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Select Source Database Select Elements Select Reaction Sets
Step 1 Step 2 Step 3
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2. Select the substances to use for generating reactions (default - all substances are selected) by clicking the Select Substances Select Substances. Clear all to deselect all. Highlighted means selected. After selecting, the SUBSTANCES list on the left should contain only the selected substances.

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Select Substances
-Select Substances

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3. Select the master substances by clicking the Select Master Substances Select Master Substances. After clicking OK, the “Type” in the SUBSTANCES list on the left side, should be set to “M” for the master substances, and to “D” for the reaction dependent substances.

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Note
-The number of master substances is given by the rank (R) of the elements stoichiometry matrix which results from the selected substances. The reactions generator algorithm will always try to have as master species the first R substances in the list.

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If the user selects more master substances than possible, the algorithm will eliminate master species from the bottom of the selected list.

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If a selected master substance can not be set as master it will be automatically switched with a different substance during the process of generating reactions.

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Select Master Substances
-Select Master Substances

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4. Generate reactions by clicking Generate Reactions Generate Reactions. If the reactions are generated succesfuly they are displayed in the window, together with their calculated properties for 1 bar and 25 C.

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Reactions Generated
-Reactions were generated successfully

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5. Save the generated reactions in a Reactions Set (with Symbol, Name, Comment, Set Type, and Reaction Level) by clicking Save Reactions Set Save Reactions Set. Before saving set the desired Reactions Set Symbol, Name, Comment, Set Type, and Reaction Level. If the reactions are saved successfully they should be visible when browsing the reaction data inside the database.

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Note
-When saving the generated reactions, the symbol of the saved reactions is set the same as the symbol of the reaction defined substance. For example: Ca+2 + CO3-2 = CaCO3@ will have the symbol CaCO3@.

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When saving the reactions, if a reaction with the same symbol is already exists in the database the symbol of the saved reaction will be the symbol of the defined substance underscore _ and the level number. For example: CaCO3@_1.

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When saving the reactions, if a reaction dependent substance is already dependent on one or many reactions (already in the database). The level of the reaction to be saved is calculated as the maximum existing level for this substance plus 1. For example: the substance with the symbol CaCO3@ has already 3 reactions which is dependent on stored in the database with levels 0, 1, 2. The symbol for the new reaction will be CaCO3@_3 and the level will be 3.

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Save Reactions
-All set for saving the generated reactions

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Saved Reactions Set
-A data entry in the database for a saved Reactions set

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Saved Reactions
-Entries in the database for saved generated reactions

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Application Menu

- - - - - diff --git a/Resources/help/HowToReactionsGenerator.md b/Resources/help/HowToReactionsGenerator.md deleted file mode 100644 index 685f8d3c..00000000 --- a/Resources/help/HowToReactionsGenerator.md +++ /dev/null @@ -1,71 +0,0 @@ -# Reactions Generator -* [How to use the Reactions Generator](#How.to.generate.reactions.using.the.Reactions.Generator) -* [Application Menu](#Application.Menu) - -Given a list of substances and selected master substances, the reactions generator will generate a set of independent reactions. One reaction for each reaction dependent substance. - -![Reactions Generator window](images/ReacGenEmpty.png =840x "Reactions Generator window") -_Empty Reactions Generator Window_ - -## How to generate reactions using the Reactions Generator -> __Note__ -Follow the messages written in the status bar for the work flow, success, and error messages. - -__1.__ To start using the Reactions Generator Application first click the [Select Database source and Elements](#Source.Database.Elements) ![Source Database Elements](images/SourceElementFilter.png "Source Database Elements"). Chose the desired source database (_Step 1_), in the next step the desired elements (_Step 2_), and in the last step if present the desired reaction sets (_Step 3_). This will filter the data available for generating reactions. - -> __Note__ -The available elements are based on the available substances in the selected source database. If a substance contains an element, the element will be selectable. - -| ![Select Source Database](images/SelectSource.png =x250 "Select Source Database") | ![Select Elements](images/SelectElements.png =x250 "Select Elements") | ![Select Reaction Sets](images/SelectReactionSets.png =x250 "Select Reaction Sets") | -|::|::|::| -| _Step 1_ | _Step 2_ | _Step 3_ | - -__2.__ Select the substances to use for generating reactions (default - all substances are selected) by clicking the [Select Substances](#Select.Substances) ![Select Substances](images/SelectData.png "Select Substances"). Clear all to deselect all. Highlighted means selected. After selecting, the SUBSTANCES list on the left should contain only the selected substances. - -![Select Substances](images/SelectSubstances.png =420x "Select Substances") -_Select Substances_ - -__3.__ Select the master substances by clicking the [Select Master Substances](#Select.Master.Substances) ![Select Master Substances](images/SelectMaster.png "Select Master Substances"). After clicking OK, the "Type" in the SUBSTANCES list on the left side, should be set to "__M__" for the master substances, and to "__D__" for the reaction dependent substances. - -> __Note__ -The number of master substances is given by the rank (__R__) of the elements stoichiometry matrix which results from the selected substances. The reactions generator algorithm will always try to have as master species the first R substances in the list. - -> If the user selects more master substances than possible, the algorithm will eliminate master species from the bottom of the selected list. - -> If a selected master substance can not be set as master it will be automatically switched with a different substance during the process of generating reactions. - -![Select Master Substances](images/SelectMasterSubst.png =420x "Select Master Substances") -_Select Master Substances_ - -__4.__ Generate reactions by clicking [Generate Reactions](#Generate.Reactions) ![Generate Reactions](images/ReacDCModuleIcon24.png "Generate Reactions"). If the reactions are generated succesfuly they are displayed in the window, together with their calculated properties for 1 bar and 25 C. - -![Reactions Generated](images/ReactGenerated.png =840x "Reactions Generated") -_Reactions were generated successfully_ - -__5.__ Save the generated reactions in a Reactions Set (with __Symbol__, __Name__, __Comment__, __Set Type__, and __Reaction Level__) by clicking [Save Reactions Set](#Save.Reactions.Set) ![Save Reactions Set](images/SaveCurrentRecordIcon.png "Save Reactions Set"). Before saving set the desired Reactions Set __Symbol__, __Name__, __Comment__, __Set Type__, and __Reaction Level__. If the reactions are saved successfully they should be visible when browsing the reaction data inside the database. - -> __Note__ -When saving the generated reactions, the symbol of the saved reactions is set the same as the symbol of the reaction defined substance. For example: Ca+2 + CO3-2 = CaCO3@ will have the symbol CaCO3@. - -> When saving the reactions, if a reaction with the same symbol is already exists in the database the symbol of the saved reaction will be the symbol of the defined substance underscore _ and the level number. For example: CaCO3@_1. - -![Save Reactions](images/SaveReactions.png =840x "Save Reactions") -_All set for saving the generated reactions_ - -![Saved Reactions Set](images/SavedGenReacSet.png =840x "Saved Reactions Set") -_A data entry in the database for a saved Reactions set_ - -![Saved Reactions in the database](images/SavedGenReact.png =840x "Saved Reactions in the database") -_Entries in the database for saved generated reactions_ - -## Application Menu -* __File__ - * ![New.Reset](images/NewCreateRecordIcon24.png "New/Reset") __New/Reset__: Resets the Reactions Generator window. - * ![Load.Reactions](images/ReactionDatabaseIcon24.png "Load Reactions") __Load Reactions__: Load reactions from the database which will be decomposed in a list of substances which participate in these reactions. The resulted list of substances can be further used to generate reactions. - * ![Save.Reactions.Set](images/SaveCurrentRecordIcon.png "Save Reactions Set") __Save Reaction Set__: Save generated reactions in the database as a Reactions Set. Set the Reaction Set __Symbol__, __Name__, __Comment__, __Set Type__, and __Reaction Level__ in the respective fields. -* __Data__ - * ![Source.Database.Elements](images/SourceElementFilter.png "Source Database Elements") __Select Data Source and Elements__: Opens a wizard for selecting the source database and elements for filtering the data to be used for generating reactions. Select the source database from the available list of source databases. Next, select the elements which the substances and reactions should contain. - * ![Select.Substances](images/SelectData.png "Select Substances") __Select Substances__: Select the list of substances to be used for generating reactions. - * ![Select.Master.Substances](images/SelectMaster.png "Select Master Substances") __Select Master Substances__: Select the list of desired master substances which will be used for generating reaction. -* __Tools__ - * ![Generate.Reactions](images/ReacDCModuleIcon24.png "Generate Reactions") __Generate Reactions__: Generate reactions form the selected substances. \ No newline at end of file diff --git a/Resources/help/images/CalculateRecrod.png b/Resources/help/images/CalculateRecrod.png deleted file mode 100644 index e1fe0543..00000000 Binary files a/Resources/help/images/CalculateRecrod.png and /dev/null differ diff --git a/Resources/help/images/IsocGen.png b/Resources/help/images/IsocGen.png deleted file mode 100644 index e835de4d..00000000 Binary 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coding: utf-8 -*- --- --- Simple JSON encoding and decoding in pure Lua. --- --- Copyright 2010-2017 Jeffrey Friedl --- http://regex.info/blog/ --- Latest version: http://regex.info/blog/lua/json --- --- This code is released under a Creative Commons CC-BY "Attribution" License: --- http://creativecommons.org/licenses/by/3.0/deed.en_US --- --- It can be used for any purpose so long as: --- 1) the copyright notice above is maintained --- 2) the web-page links above are maintained --- 3) the 'AUTHOR_NOTE' string below is maintained --- -local VERSION = '20170927.26' -- version history at end of file -local AUTHOR_NOTE = "-[ JSON.lua package by Jeffrey Friedl (http://regex.info/blog/lua/json) version 20170927.26 ]-" - --- --- The 'AUTHOR_NOTE' variable exists so that information about the source --- of the package is maintained even in compiled versions. It's also --- included in OBJDEF below mostly to quiet warnings about unused variables. --- -local OBJDEF = { - VERSION = VERSION, - AUTHOR_NOTE = AUTHOR_NOTE, -} - - --- --- Simple JSON encoding and decoding in pure Lua. --- JSON definition: http://www.json.org/ --- --- --- JSON = assert(loadfile "JSON.lua")() -- one-time load of the routines --- --- local lua_value = JSON:decode(raw_json_text) --- --- local raw_json_text = JSON:encode(lua_table_or_value) --- local pretty_json_text = JSON:encode_pretty(lua_table_or_value) -- "pretty printed" version for human readability --- --- --- --- DECODING (from a JSON string to a Lua table) --- --- --- JSON = assert(loadfile "JSON.lua")() -- one-time load of the routines --- --- local lua_value = JSON:decode(raw_json_text) --- --- If the JSON text is for an object or an array, e.g. --- { "what": "books", "count": 3 } --- or --- [ "Larry", "Curly", "Moe" ] --- --- the result is a Lua table, e.g. --- { what = "books", count = 3 } --- or --- { "Larry", "Curly", "Moe" } --- --- --- The encode and decode routines accept an optional second argument, --- "etc", which is not used during encoding or decoding, but upon error --- is passed along to error handlers. It can be of any type (including nil). --- --- --- --- ERROR HANDLING DURING DECODE --- --- With most errors during decoding, this code calls --- --- JSON:onDecodeError(message, text, location, etc) --- --- with a message about the error, and if known, the JSON text being --- parsed and the byte count where the problem was discovered. You can --- replace the default JSON:onDecodeError() with your own function. --- --- The default onDecodeError() merely augments the message with data --- about the text and the location (and, an 'etc' argument had been --- provided to decode(), its value is tacked onto the message as well), --- and then calls JSON.assert(), which itself defaults to Lua's built-in --- assert(), and can also be overridden. --- --- For example, in an Adobe Lightroom plugin, you might use something like --- --- function JSON:onDecodeError(message, text, location, etc) --- LrErrors.throwUserError("Internal Error: invalid JSON data") --- end --- --- or even just --- --- function JSON.assert(message) --- LrErrors.throwUserError("Internal Error: " .. message) --- end --- --- If JSON:decode() is passed a nil, this is called instead: --- --- JSON:onDecodeOfNilError(message, nil, nil, etc) --- --- and if JSON:decode() is passed HTML instead of JSON, this is called: --- --- JSON:onDecodeOfHTMLError(message, text, nil, etc) --- --- The use of the 'etc' argument allows stronger coordination between --- decoding and error reporting, especially when you provide your own --- error-handling routines. Continuing with the the Adobe Lightroom --- plugin example: --- --- function JSON:onDecodeError(message, text, location, etc) --- local note = "Internal Error: invalid JSON data" --- if type(etc) = 'table' and etc.photo then --- note = note .. " while processing for " .. etc.photo:getFormattedMetadata('fileName') --- end --- LrErrors.throwUserError(note) --- end --- --- : --- : --- --- for i, photo in ipairs(photosToProcess) do --- : --- : --- local data = JSON:decode(someJsonText, { photo = photo }) --- : --- : --- end --- --- --- --- If the JSON text passed to decode() has trailing garbage (e.g. as with the JSON "[123]xyzzy"), --- the method --- --- JSON:onTrailingGarbage(json_text, location, parsed_value, etc) --- --- is invoked, where: --- --- 'json_text' is the original JSON text being parsed, --- 'location' is the count of bytes into 'json_text' where the garbage starts (6 in the example), --- 'parsed_value' is the Lua result of what was successfully parsed ({123} in the example), --- 'etc' is as above. --- --- If JSON:onTrailingGarbage() does not abort, it should return the value decode() should return, --- or nil + an error message. --- --- local new_value, error_message = JSON:onTrailingGarbage() --- --- The default JSON:onTrailingGarbage() simply invokes JSON:onDecodeError("trailing garbage"...), --- but you can have this package ignore trailing garbage via --- --- function JSON:onTrailingGarbage(json_text, location, parsed_value, etc) --- return parsed_value --- end --- --- --- DECODING AND STRICT TYPES --- --- Because both JSON objects and JSON arrays are converted to Lua tables, --- it's not normally possible to tell which original JSON type a --- particular Lua table was derived from, or guarantee decode-encode --- round-trip equivalency. --- --- However, if you enable strictTypes, e.g. --- --- JSON = assert(loadfile "JSON.lua")() --load the routines --- JSON.strictTypes = true --- --- then the Lua table resulting from the decoding of a JSON object or --- JSON array is marked via Lua metatable, so that when re-encoded with --- JSON:encode() it ends up as the appropriate JSON type. --- --- (This is not the default because other routines may not work well with --- tables that have a metatable set, for example, Lightroom API calls.) --- --- --- ENCODING (from a lua table to a JSON string) --- --- JSON = assert(loadfile "JSON.lua")() -- one-time load of the routines --- --- local raw_json_text = JSON:encode(lua_table_or_value) --- local pretty_json_text = JSON:encode_pretty(lua_table_or_value) -- "pretty printed" version for human readability --- local custom_pretty = JSON:encode(lua_table_or_value, etc, { pretty = true, indent = "| ", align_keys = false }) --- --- On error during encoding, this code calls: --- --- JSON:onEncodeError(message, etc) --- --- which you can override in your local JSON object. Also see "HANDLING UNSUPPORTED VALUE TYPES" below. --- --- The 'etc' in the error call is the second argument to encode() and encode_pretty(), or nil if it wasn't provided. --- --- --- --- --- ENCODING OPTIONS --- --- An optional third argument, a table of options, can be provided to encode(). --- --- encode_options = { --- -- options for making "pretty" human-readable JSON (see "PRETTY-PRINTING" below) --- pretty = true, -- turn pretty formatting on --- indent = " ", -- use this indent for each level of an array/object --- align_keys = false, -- if true, align the keys in a way that sounds like it should be nice, but is actually ugly --- array_newline = false, -- if true, array elements become one to a line rather than inline --- --- -- other output-related options --- null = "\0", -- see "ENCODING JSON NULL VALUES" below --- stringsAreUtf8 = false, -- see "HANDLING UNICODE LINE AND PARAGRAPH SEPARATORS FOR JAVA" below --- } --- --- json_string = JSON:encode(mytable, etc, encode_options) --- --- --- --- For reference, the defaults are: --- --- pretty = false --- null = nil, --- stringsAreUtf8 = false, --- --- --- --- PRETTY-PRINTING --- --- Enabling the 'pretty' encode option helps generate human-readable JSON. --- --- pretty = JSON:encode(val, etc, { --- pretty = true, --- indent = " ", --- align_keys = false, --- }) --- --- encode_pretty() is also provided: it's identical to encode() except --- that encode_pretty() provides a default options table if none given in the call: --- --- { pretty = true, indent = " ", align_keys = false, array_newline = false } --- --- For example, if --- --- JSON:encode(data) --- --- produces: --- --- {"city":"Kyoto","climate":{"avg_temp":16,"humidity":"high","snowfall":"minimal"},"country":"Japan","wards":11} --- --- then --- --- JSON:encode_pretty(data) --- --- produces: --- --- { --- "city": "Kyoto", --- "climate": { --- "avg_temp": 16, --- "humidity": "high", --- "snowfall": "minimal" --- }, --- "country": "Japan", --- "wards": 11 --- } --- --- The following lines all return identical strings: --- JSON:encode_pretty(data) --- JSON:encode_pretty(data, nil, { pretty = true, indent = " ", align_keys = false, array_newline = false}) --- JSON:encode_pretty(data, nil, { pretty = true, indent = " " }) --- JSON:encode (data, nil, { pretty = true, indent = " " }) --- --- An example of setting your own indent string: --- --- JSON:encode_pretty(data, nil, { pretty = true, indent = "| " }) --- --- produces: --- --- { --- | "city": "Kyoto", --- | "climate": { --- | | "avg_temp": 16, --- | | "humidity": "high", --- | | "snowfall": "minimal" --- | }, --- | "country": "Japan", --- | "wards": 11 --- } --- --- An example of setting align_keys to true: --- --- JSON:encode_pretty(data, nil, { pretty = true, indent = " ", align_keys = true }) --- --- produces: --- --- { --- "city": "Kyoto", --- "climate": { --- "avg_temp": 16, --- "humidity": "high", --- "snowfall": "minimal" --- }, --- "country": "Japan", --- "wards": 11 --- } --- --- which I must admit is kinda ugly, sorry. This was the default for --- encode_pretty() prior to version 20141223.14. --- --- --- HANDLING UNICODE LINE AND PARAGRAPH SEPARATORS FOR JAVA --- --- If the 'stringsAreUtf8' encode option is set to true, consider Lua strings not as a sequence of bytes, --- but as a sequence of UTF-8 characters. --- --- Currently, the only practical effect of setting this option is that Unicode LINE and PARAGRAPH --- separators, if found in a string, are encoded with a JSON escape instead of being dumped as is. --- The JSON is valid either way, but encoding this way, apparently, allows the resulting JSON --- to also be valid Java. --- --- AMBIGUOUS SITUATIONS DURING THE ENCODING --- --- During the encode, if a Lua table being encoded contains both string --- and numeric keys, it fits neither JSON's idea of an object, nor its --- idea of an array. To get around this, when any string key exists (or --- when non-positive numeric keys exist), numeric keys are converted to --- strings. --- --- For example, --- JSON:encode({ "one", "two", "three", SOMESTRING = "some string" })) --- produces the JSON object --- {"1":"one","2":"two","3":"three","SOMESTRING":"some string"} --- --- To prohibit this conversion and instead make it an error condition, set --- JSON.noKeyConversion = true --- --- --- ENCODING JSON NULL VALUES --- --- Lua tables completely omit keys whose value is nil, so without special handling there's --- no way to represent JSON object's null value in a Lua table. For example --- JSON:encode({ username = "admin", password = nil }) --- --- produces: --- --- {"username":"admin"} --- --- In order to actually produce --- --- {"username":"admin", "password":null} --- - --- one can include a string value for a "null" field in the options table passed to encode().... --- any Lua table entry with that value becomes null in the JSON output: --- --- JSON:encode({ username = "admin", password = "xyzzy" }, -- First arg is the Lua table to encode as JSON. --- nil, -- Second arg is the 'etc' value, ignored here --- { null = "xyzzy" }) -- Third arg is th options table --- --- produces: --- --- {"username":"admin", "password":null} --- --- Just be sure to use a string that is otherwise unlikely to appear in your data. --- The string "\0" (a string with one null byte) may well be appropriate for many applications. --- --- The "null" options also applies to Lua tables that become JSON arrays. --- JSON:encode({ "one", "two", nil, nil }) --- --- produces --- --- ["one","two"] --- --- while --- --- NullPlaceholder = "\0" --- encode_options = { null = NullPlaceholder } --- JSON:encode({ "one", "two", NullPlaceholder, NullPlaceholder}, nil, encode_options) --- produces --- --- ["one","two",null,null] --- --- --- --- HANDLING LARGE AND/OR PRECISE NUMBERS --- --- --- Without special handling, numbers in JSON can lose precision in Lua. --- For example: --- --- T = JSON:decode('{ "small":12345, "big":12345678901234567890123456789, "precise":9876.67890123456789012345 }') --- --- print("small: ", type(T.small), T.small) --- print("big: ", type(T.big), T.big) --- print("precise: ", type(T.precise), T.precise) --- --- produces --- --- small: number 12345 --- big: number 1.2345678901235e+28 --- precise: number 9876.6789012346 --- --- Precision is lost with both 'big' and 'precise'. --- --- This package offers ways to try to handle this better (for some definitions of "better")... --- --- The most precise method is by setting the global: --- --- JSON.decodeNumbersAsObjects = true --- --- When this is set, numeric JSON data is encoded into Lua in a form that preserves the exact --- JSON numeric presentation when re-encoded back out to JSON, or accessed in Lua as a string. --- --- This is done by encoding the numeric data with a Lua table/metatable that returns --- the possibly-imprecise numeric form when accessed numerically, but the original precise --- representation when accessed as a string. --- --- Consider the example above, with this option turned on: --- --- JSON.decodeNumbersAsObjects = true --- --- T = JSON:decode('{ "small":12345, "big":12345678901234567890123456789, "precise":9876.67890123456789012345 }') --- --- print("small: ", type(T.small), T.small) --- print("big: ", type(T.big), T.big) --- print("precise: ", type(T.precise), T.precise) --- --- This now produces: --- --- small: table 12345 --- big: table 12345678901234567890123456789 --- precise: table 9876.67890123456789012345 --- --- However, within Lua you can still use the values (e.g. T.precise in the example above) in numeric --- contexts. In such cases you'll get the possibly-imprecise numeric version, but in string contexts --- and when the data finds its way to this package's encode() function, the original full-precision --- representation is used. --- --- You can force access to the string or numeric version via --- JSON:forceString() --- JSON:forceNumber() --- For example, --- local probably_okay = JSON:forceNumber(T.small) -- 'probably_okay' is a number --- --- Code the inspects the JSON-turned-Lua data using type() can run into troubles because what used to --- be a number can now be a table (e.g. as the small/big/precise example above shows). Update these --- situations to use JSON:isNumber(item), which returns nil if the item is neither a number nor one --- of these number objects. If it is either, it returns the number itself. For completeness there's --- also JSON:isString(item). --- --- If you want to try to avoid the hassles of this "number as an object" kludge for all but really --- big numbers, you can set JSON.decodeNumbersAsObjects and then also set one or both of --- JSON:decodeIntegerObjectificationLength --- JSON:decodeDecimalObjectificationLength --- They refer to the length of the part of the number before and after a decimal point. If they are --- set and their part is at least that number of digits, objectification occurs. If both are set, --- objectification occurs when either length is met. --- --- ----------------------- --- --- Even without using the JSON.decodeNumbersAsObjects option, you can encode numbers in your Lua --- table that retain high precision upon encoding to JSON, by using the JSON:asNumber() function: --- --- T = { --- imprecise = 123456789123456789.123456789123456789, --- precise = JSON:asNumber("123456789123456789.123456789123456789") --- } --- --- print(JSON:encode_pretty(T)) --- --- This produces: --- --- { --- "precise": 123456789123456789.123456789123456789, --- "imprecise": 1.2345678912346e+17 --- } --- --- --- ----------------------- --- --- A different way to handle big/precise JSON numbers is to have decode() merely return the exact --- string representation of the number instead of the number itself. This approach might be useful --- when the numbers are merely some kind of opaque object identifier and you want to work with them --- in Lua as strings anyway. --- --- This approach is enabled by setting --- --- JSON.decodeIntegerStringificationLength = 10 --- --- The value is the number of digits (of the integer part of the number) at which to stringify numbers. --- NOTE: this setting is ignored if JSON.decodeNumbersAsObjects is true, as that takes precedence. --- --- Consider our previous example with this option set to 10: --- --- JSON.decodeIntegerStringificationLength = 10 --- --- T = JSON:decode('{ "small":12345, "big":12345678901234567890123456789, "precise":9876.67890123456789012345 }') --- --- print("small: ", type(T.small), T.small) --- print("big: ", type(T.big), T.big) --- print("precise: ", type(T.precise), T.precise) --- --- This produces: --- --- small: number 12345 --- big: string 12345678901234567890123456789 --- precise: number 9876.6789012346 --- --- The long integer of the 'big' field is at least JSON.decodeIntegerStringificationLength digits --- in length, so it's converted not to a Lua integer but to a Lua string. Using a value of 0 or 1 ensures --- that all JSON numeric data becomes strings in Lua. --- --- Note that unlike --- JSON.decodeNumbersAsObjects = true --- this stringification is simple and unintelligent: the JSON number simply becomes a Lua string, and that's the end of it. --- If the string is then converted back to JSON, it's still a string. After running the code above, adding --- print(JSON:encode(T)) --- produces --- {"big":"12345678901234567890123456789","precise":9876.6789012346,"small":12345} --- which is unlikely to be desired. --- --- There's a comparable option for the length of the decimal part of a number: --- --- JSON.decodeDecimalStringificationLength --- --- This can be used alone or in conjunction with --- --- JSON.decodeIntegerStringificationLength --- --- to trip stringification on precise numbers with at least JSON.decodeIntegerStringificationLength digits after --- the decimal point. (Both are ignored if JSON.decodeNumbersAsObjects is true.) --- --- This example: --- --- JSON.decodeIntegerStringificationLength = 10 --- JSON.decodeDecimalStringificationLength = 5 --- --- T = JSON:decode('{ "small":12345, "big":12345678901234567890123456789, "precise":9876.67890123456789012345 }') --- --- print("small: ", type(T.small), T.small) --- print("big: ", type(T.big), T.big) --- print("precise: ", type(T.precise), T.precise) --- --- produces: --- --- small: number 12345 --- big: string 12345678901234567890123456789 --- precise: string 9876.67890123456789012345 --- --- --- HANDLING UNSUPPORTED VALUE TYPES --- --- Among the encoding errors that might be raised is an attempt to convert a table value that has a type --- that this package hasn't accounted for: a function, userdata, or a thread. You can handle these types as table --- values (but not as table keys) if you supply a JSON:unsupportedTypeEncoder() method along the lines of the --- following example: --- --- function JSON:unsupportedTypeEncoder(value_of_unsupported_type) --- if type(value_of_unsupported_type) == 'function' then --- return "a function value" --- else --- return nil --- end --- end --- --- Your unsupportedTypeEncoder() method is actually called with a bunch of arguments: --- --- self:unsupportedTypeEncoder(value, parents, etc, options, indent, for_key) --- --- The 'value' is the function, thread, or userdata to be converted to JSON. --- --- The 'etc' and 'options' arguments are those passed to the original encode(). The other arguments are --- probably of little interest; see the source code. (Note that 'for_key' is never true, as this function --- is invoked only on table values; table keys of these types still trigger the onEncodeError method.) --- --- If your unsupportedTypeEncoder() method returns a string, it's inserted into the JSON as is. --- If it returns nil plus an error message, that error message is passed through to an onEncodeError invocation. --- If it returns only nil, processing falls through to a default onEncodeError invocation. --- --- If you want to handle everything in a simple way: --- --- function JSON:unsupportedTypeEncoder(value) --- return tostring(value) --- end --- --- --- SUMMARY OF METHODS YOU CAN OVERRIDE IN YOUR LOCAL LUA JSON OBJECT --- --- assert --- onDecodeError --- onDecodeOfNilError --- onDecodeOfHTMLError --- onTrailingGarbage --- onEncodeError --- unsupportedTypeEncoder --- --- If you want to create a separate Lua JSON object with its own error handlers, --- you can reload JSON.lua or use the :new() method. --- ---------------------------------------------------------------------------- - -local default_pretty_indent = " " -local default_pretty_options = { pretty = true, indent = default_pretty_indent, align_keys = false, array_newline = false } - -local isArray = { __tostring = function() return "JSON array" end } isArray.__index = isArray -local isObject = { __tostring = function() return "JSON object" end } isObject.__index = isObject - -function OBJDEF:newArray(tbl) - return setmetatable(tbl or {}, isArray) -end - -function OBJDEF:newObject(tbl) - return setmetatable(tbl or {}, isObject) -end - - - - -local function getnum(op) - return type(op) == 'number' and op or op.N -end - -local isNumber = { - __tostring = function(T) return T.S end, - __unm = function(op) return getnum(op) end, - - __concat = function(op1, op2) return tostring(op1) .. tostring(op2) end, - __add = function(op1, op2) return getnum(op1) + getnum(op2) end, - __sub = function(op1, op2) return getnum(op1) - getnum(op2) end, - __mul = function(op1, op2) return getnum(op1) * getnum(op2) end, - __div = function(op1, op2) return getnum(op1) / getnum(op2) end, - __mod = function(op1, op2) return getnum(op1) % getnum(op2) end, - __pow = function(op1, op2) return getnum(op1) ^ getnum(op2) end, - __lt = function(op1, op2) return getnum(op1) < getnum(op2) end, - __eq = function(op1, op2) return getnum(op1) == getnum(op2) end, - __le = function(op1, op2) return getnum(op1) <= getnum(op2) end, -} -isNumber.__index = isNumber - -function OBJDEF:asNumber(item) - - if getmetatable(item) == isNumber then - -- it's already a JSON number object. - return item - elseif type(item) == 'table' and type(item.S) == 'string' and type(item.N) == 'number' then - -- it's a number-object table that lost its metatable, so give it one - return setmetatable(item, isNumber) - else - -- the normal situation... given a number or a string representation of a number.... - local holder = { - S = tostring(item), -- S is the representation of the number as a string, which remains precise - N = tonumber(item), -- N is the number as a Lua number. - } - return setmetatable(holder, isNumber) - end -end - --- --- Given an item that might be a normal string or number, or might be an 'isNumber' object defined above, --- return the string version. This shouldn't be needed often because the 'isNumber' object should autoconvert --- to a string in most cases, but it's here to allow it to be forced when needed. --- -function OBJDEF:forceString(item) - if type(item) == 'table' and type(item.S) == 'string' then - return item.S - else - return tostring(item) - end -end - --- --- Given an item that might be a normal string or number, or might be an 'isNumber' object defined above, --- return the numeric version. --- -function OBJDEF:forceNumber(item) - if type(item) == 'table' and type(item.N) == 'number' then - return item.N - else - return tonumber(item) - end -end - --- --- If the given item is a number, return it. Otherwise, return nil. --- This, this can be used both in a conditional and to access the number when you're not sure its form. --- -function OBJDEF:isNumber(item) - if type(item) == 'number' then - return item - elseif type(item) == 'table' and type(item.N) == 'number' then - return item.N - else - return nil - end -end - -function OBJDEF:isString(item) - if type(item) == 'string' then - return item - elseif type(item) == 'table' and type(item.S) == 'string' then - return item.S - else - return nil - end -end - - -local function unicode_codepoint_as_utf8(codepoint) - -- - -- codepoint is a number - -- - if codepoint <= 127 then - return string.char(codepoint) - - elseif codepoint <= 2047 then - -- - -- 110yyyxx 10xxxxxx <-- useful notation from http://en.wikipedia.org/wiki/Utf8 - -- - local highpart = math.floor(codepoint / 0x40) - local lowpart = codepoint - (0x40 * highpart) - return string.char(0xC0 + highpart, - 0x80 + lowpart) - - elseif codepoint <= 65535 then - -- - -- 1110yyyy 10yyyyxx 10xxxxxx - -- - local highpart = math.floor(codepoint / 0x1000) - local remainder = codepoint - 0x1000 * highpart - local midpart = math.floor(remainder / 0x40) - local lowpart = remainder - 0x40 * midpart - - highpart = 0xE0 + highpart - midpart = 0x80 + midpart - lowpart = 0x80 + lowpart - - -- - -- Check for an invalid character (thanks Andy R. at Adobe). - -- See table 3.7, page 93, in http://www.unicode.org/versions/Unicode5.2.0/ch03.pdf#G28070 - -- - if ( highpart == 0xE0 and midpart < 0xA0 ) or - ( highpart == 0xED and midpart > 0x9F ) or - ( highpart == 0xF0 and midpart < 0x90 ) or - ( highpart == 0xF4 and midpart > 0x8F ) - then - return "?" - else - return string.char(highpart, - midpart, - lowpart) - end - - else - -- - -- 11110zzz 10zzyyyy 10yyyyxx 10xxxxxx - -- - local highpart = math.floor(codepoint / 0x40000) - local remainder = codepoint - 0x40000 * highpart - local midA = math.floor(remainder / 0x1000) - remainder = remainder - 0x1000 * midA - local midB = math.floor(remainder / 0x40) - local lowpart = remainder - 0x40 * midB - - return string.char(0xF0 + highpart, - 0x80 + midA, - 0x80 + midB, - 0x80 + lowpart) - end -end - -function OBJDEF:onDecodeError(message, text, location, etc) - if text then - if location then - message = string.format("%s at byte %d of: %s", message, location, text) - else - message = string.format("%s: %s", message, text) - end - end - - if etc ~= nil then - message = message .. " (" .. OBJDEF:encode(etc) .. ")" - end - - if self.assert then - self.assert(false, message) - else - assert(false, message) - end -end - -function OBJDEF:onTrailingGarbage(json_text, location, parsed_value, etc) - return self:onDecodeError("trailing garbage", json_text, location, etc) -end - -OBJDEF.onDecodeOfNilError = OBJDEF.onDecodeError -OBJDEF.onDecodeOfHTMLError = OBJDEF.onDecodeError - -function OBJDEF:onEncodeError(message, etc) - if etc ~= nil then - message = message .. " (" .. OBJDEF:encode(etc) .. ")" - end - - if self.assert then - self.assert(false, message) - else - assert(false, message) - end -end - -local function grok_number(self, text, start, options) - -- - -- Grab the integer part - -- - local integer_part = text:match('^-?[1-9]%d*', start) - or text:match("^-?0", start) - - if not integer_part then - self:onDecodeError("expected number", text, start, options.etc) - return nil, start -- in case the error method doesn't abort, return something sensible - end - - local i = start + integer_part:len() - - -- - -- Grab an optional decimal part - -- - local decimal_part = text:match('^%.%d*', i) or "" - - i = i + decimal_part:len() - - -- - -- Grab an optional exponential part - -- - local exponent_part = text:match('^[eE][-+]?%d+', i) or "" - - i = i + exponent_part:len() - - local full_number_text = integer_part .. decimal_part .. exponent_part - - if options.decodeNumbersAsObjects then - - local objectify = false - - if not options.decodeIntegerObjectificationLength and not options.decodeDecimalObjectificationLength then - -- no options, so objectify - objectify = true - - elseif (options.decodeIntegerObjectificationLength - and - (integer_part:len() >= options.decodeIntegerObjectificationLength or exponent_part:len() > 0)) - - or - (options.decodeDecimalObjectificationLength - and - (decimal_part:len() >= options.decodeDecimalObjectificationLength or exponent_part:len() > 0)) - then - -- have options and they are triggered, so objectify - objectify = true - end - - if objectify then - return OBJDEF:asNumber(full_number_text), i - end - -- else, fall through to try to return as a straight-up number - - else - - -- Not always decoding numbers as objects, so perhaps encode as strings? - - -- - -- If we're told to stringify only under certain conditions, so do. - -- We punt a bit when there's an exponent by just stringifying no matter what. - -- I suppose we should really look to see whether the exponent is actually big enough one - -- way or the other to trip stringification, but I'll be lazy about it until someone asks. - -- - if (options.decodeIntegerStringificationLength - and - (integer_part:len() >= options.decodeIntegerStringificationLength or exponent_part:len() > 0)) - - or - - (options.decodeDecimalStringificationLength - and - (decimal_part:len() >= options.decodeDecimalStringificationLength or exponent_part:len() > 0)) - then - return full_number_text, i -- this returns the exact string representation seen in the original JSON - end - - end - - - local as_number = tonumber(full_number_text) - - if not as_number then - self:onDecodeError("bad number", text, start, options.etc) - return nil, start -- in case the error method doesn't abort, return something sensible - end - - return as_number, i -end - - -local function grok_string(self, text, start, options) - - if text:sub(start,start) ~= '"' then - self:onDecodeError("expected string's opening quote", text, start, options.etc) - return nil, start -- in case the error method doesn't abort, return something sensible - end - - local i = start + 1 -- +1 to bypass the initial quote - local text_len = text:len() - local VALUE = "" - while i <= text_len do - local c = text:sub(i,i) - if c == '"' then - return VALUE, i + 1 - end - if c ~= '\\' then - VALUE = VALUE .. c - i = i + 1 - elseif text:match('^\\b', i) then - VALUE = VALUE .. "\b" - i = i + 2 - elseif text:match('^\\f', i) then - VALUE = VALUE .. "\f" - i = i + 2 - elseif text:match('^\\n', i) then - VALUE = VALUE .. "\n" - i = i + 2 - elseif text:match('^\\r', i) then - VALUE = VALUE .. "\r" - i = i + 2 - elseif text:match('^\\t', i) then - VALUE = VALUE .. "\t" - i = i + 2 - else - local hex = text:match('^\\u([0123456789aAbBcCdDeEfF][0123456789aAbBcCdDeEfF][0123456789aAbBcCdDeEfF][0123456789aAbBcCdDeEfF])', i) - if hex then - i = i + 6 -- bypass what we just read - - -- We have a Unicode codepoint. It could be standalone, or if in the proper range and - -- followed by another in a specific range, it'll be a two-code surrogate pair. - local codepoint = tonumber(hex, 16) - if codepoint >= 0xD800 and codepoint <= 0xDBFF then - -- it's a hi surrogate... see whether we have a following low - local lo_surrogate = text:match('^\\u([dD][cdefCDEF][0123456789aAbBcCdDeEfF][0123456789aAbBcCdDeEfF])', i) - if lo_surrogate then - i = i + 6 -- bypass the low surrogate we just read - codepoint = 0x2400 + (codepoint - 0xD800) * 0x400 + tonumber(lo_surrogate, 16) - else - -- not a proper low, so we'll just leave the first codepoint as is and spit it out. - end - end - VALUE = VALUE .. unicode_codepoint_as_utf8(codepoint) - - else - - -- just pass through what's escaped - VALUE = VALUE .. text:match('^\\(.)', i) - i = i + 2 - end - end - end - - self:onDecodeError("unclosed string", text, start, options.etc) - return nil, start -- in case the error method doesn't abort, return something sensible -end - -local function skip_whitespace(text, start) - - local _, match_end = text:find("^[ \n\r\t]+", start) -- [http://www.ietf.org/rfc/rfc4627.txt] Section 2 - if match_end then - return match_end + 1 - else - return start - end -end - -local grok_one -- assigned later - -local function grok_object(self, text, start, options) - - if text:sub(start,start) ~= '{' then - self:onDecodeError("expected '{'", text, start, options.etc) - return nil, start -- in case the error method doesn't abort, return something sensible - end - - local i = skip_whitespace(text, start + 1) -- +1 to skip the '{' - - local VALUE = self.strictTypes and self:newObject { } or { } - - if text:sub(i,i) == '}' then - return VALUE, i + 1 - end - local text_len = text:len() - while i <= text_len do - local key, new_i = grok_string(self, text, i, options) - - i = skip_whitespace(text, new_i) - - if text:sub(i, i) ~= ':' then - self:onDecodeError("expected colon", text, i, options.etc) - return nil, i -- in case the error method doesn't abort, return something sensible - end - - i = skip_whitespace(text, i + 1) - - local new_val, new_i = grok_one(self, text, i, options) - - VALUE[key] = new_val - - -- - -- Expect now either '}' to end things, or a ',' to allow us to continue. - -- - i = skip_whitespace(text, new_i) - - local c = text:sub(i,i) - - if c == '}' then - return VALUE, i + 1 - end - - if text:sub(i, i) ~= ',' then - self:onDecodeError("expected comma or '}'", text, i, options.etc) - return nil, i -- in case the error method doesn't abort, return something sensible - end - - i = skip_whitespace(text, i + 1) - end - - self:onDecodeError("unclosed '{'", text, start, options.etc) - return nil, start -- in case the error method doesn't abort, return something sensible -end - -local function grok_array(self, text, start, options) - if text:sub(start,start) ~= '[' then - self:onDecodeError("expected '['", text, start, options.etc) - return nil, start -- in case the error method doesn't abort, return something sensible - end - - local i = skip_whitespace(text, start + 1) -- +1 to skip the '[' - local VALUE = self.strictTypes and self:newArray { } or { } - if text:sub(i,i) == ']' then - return VALUE, i + 1 - end - - local VALUE_INDEX = 1 - - local text_len = text:len() - while i <= text_len do - local val, new_i = grok_one(self, text, i, options) - - -- can't table.insert(VALUE, val) here because it's a no-op if val is nil - VALUE[VALUE_INDEX] = val - VALUE_INDEX = VALUE_INDEX + 1 - - i = skip_whitespace(text, new_i) - - -- - -- Expect now either ']' to end things, or a ',' to allow us to continue. - -- - local c = text:sub(i,i) - if c == ']' then - return VALUE, i + 1 - end - if text:sub(i, i) ~= ',' then - self:onDecodeError("expected comma or ']'", text, i, options.etc) - return nil, i -- in case the error method doesn't abort, return something sensible - end - i = skip_whitespace(text, i + 1) - end - self:onDecodeError("unclosed '['", text, start, options.etc) - return nil, i -- in case the error method doesn't abort, return something sensible -end - - -grok_one = function(self, text, start, options) - -- Skip any whitespace - start = skip_whitespace(text, start) - - if start > text:len() then - self:onDecodeError("unexpected end of string", text, nil, options.etc) - return nil, start -- in case the error method doesn't abort, return something sensible - end - - if text:find('^"', start) then - return grok_string(self, text, start, options.etc) - - elseif text:find('^[-0123456789 ]', start) then - return grok_number(self, text, start, options) - - elseif text:find('^%{', start) then - return grok_object(self, text, start, options) - - elseif text:find('^%[', start) then - return grok_array(self, text, start, options) - - elseif text:find('^true', start) then - return true, start + 4 - - elseif text:find('^false', start) then - return false, start + 5 - - elseif text:find('^null', start) then - return options.null, start + 4 - - else - self:onDecodeError("can't parse JSON", text, start, options.etc) - return nil, 1 -- in case the error method doesn't abort, return something sensible - end -end - -function OBJDEF:decode(text, etc, options) - -- - -- If the user didn't pass in a table of decode options, make an empty one. - -- - if type(options) ~= 'table' then - options = {} - end - - -- - -- If they passed in an 'etc' argument, stuff it into the options. - -- (If not, any 'etc' field in the options they passed in remains to be used) - -- - if etc ~= nil then - options.etc = etc - end - - - if type(self) ~= 'table' or self.__index ~= OBJDEF then - local error_message = "JSON:decode must be called in method format" - OBJDEF:onDecodeError(error_message, nil, nil, options.etc) - return nil, error_message -- in case the error method doesn't abort, return something sensible - end - - if text == nil then - local error_message = "nil passed to JSON:decode()" - self:onDecodeOfNilError(error_message, nil, nil, options.etc) - return nil, error_message -- in case the error method doesn't abort, return something sensible - - elseif type(text) ~= 'string' then - local error_message = "expected string argument to JSON:decode()" - self:onDecodeError(string.format("%s, got %s", error_message, type(text)), nil, nil, options.etc) - return nil, error_message -- in case the error method doesn't abort, return something sensible - end - - if text:match('^%s*$') then - -- an empty string is nothing, but not an error - return nil - end - - if text:match('^%s*<') then - -- Can't be JSON... we'll assume it's HTML - local error_message = "HTML passed to JSON:decode()" - self:onDecodeOfHTMLError(error_message, text, nil, options.etc) - return nil, error_message -- in case the error method doesn't abort, return something sensible - end - - -- - -- Ensure that it's not UTF-32 or UTF-16. - -- Those are perfectly valid encodings for JSON (as per RFC 4627 section 3), - -- but this package can't handle them. - -- - if text:sub(1,1):byte() == 0 or (text:len() >= 2 and text:sub(2,2):byte() == 0) then - local error_message = "JSON package groks only UTF-8, sorry" - self:onDecodeError(error_message, text, nil, options.etc) - return nil, error_message -- in case the error method doesn't abort, return something sensible - end - - -- - -- apply global options - -- - if options.decodeNumbersAsObjects == nil then - options.decodeNumbersAsObjects = self.decodeNumbersAsObjects - end - if options.decodeIntegerObjectificationLength == nil then - options.decodeIntegerObjectificationLength = self.decodeIntegerObjectificationLength - end - if options.decodeDecimalObjectificationLength == nil then - options.decodeDecimalObjectificationLength = self.decodeDecimalObjectificationLength - end - if options.decodeIntegerStringificationLength == nil then - options.decodeIntegerStringificationLength = self.decodeIntegerStringificationLength - end - if options.decodeDecimalStringificationLength == nil then - options.decodeDecimalStringificationLength = self.decodeDecimalStringificationLength - end - - - -- - -- Finally, go parse it - -- - local success, value, next_i = pcall(grok_one, self, text, 1, options) - - if success then - - local error_message = nil - if next_i ~= #text + 1 then - -- something's left over after we parsed the first thing.... whitespace is allowed. - next_i = skip_whitespace(text, next_i) - - -- if we have something left over now, it's trailing garbage - if next_i ~= #text + 1 then - value, error_message = self:onTrailingGarbage(text, next_i, value, options.etc) - end - end - return value, error_message - - else - - -- If JSON:onDecodeError() didn't abort out of the pcall, we'll have received - -- the error message here as "value", so pass it along as an assert. - local error_message = value - if self.assert then - self.assert(false, error_message) - else - assert(false, error_message) - end - -- ...and if we're still here (because the assert didn't throw an error), - -- return a nil and throw the error message on as a second arg - return nil, error_message - - end -end - -local function backslash_replacement_function(c) - if c == "\n" then - return "\\n" - elseif c == "\r" then - return "\\r" - elseif c == "\t" then - return "\\t" - elseif c == "\b" then - return "\\b" - elseif c == "\f" then - return "\\f" - elseif c == '"' then - return '\\"' - elseif c == '\\' then - return '\\\\' - else - return string.format("\\u%04x", c:byte()) - end -end - -local chars_to_be_escaped_in_JSON_string - = '[' - .. '"' -- class sub-pattern to match a double quote - .. '%\\' -- class sub-pattern to match a backslash - .. '%z' -- class sub-pattern to match a null - .. '\001' .. '-' .. '\031' -- class sub-pattern to match control characters - .. ']' - - -local LINE_SEPARATOR_as_utf8 = unicode_codepoint_as_utf8(0x2028) -local PARAGRAPH_SEPARATOR_as_utf8 = unicode_codepoint_as_utf8(0x2029) -local function json_string_literal(value, options) - local newval = value:gsub(chars_to_be_escaped_in_JSON_string, backslash_replacement_function) - if options.stringsAreUtf8 then - -- - -- This feels really ugly to just look into a string for the sequence of bytes that we know to be a particular utf8 character, - -- but utf8 was designed purposefully to make this kind of thing possible. Still, feels dirty. - -- I'd rather decode the byte stream into a character stream, but it's not technically needed so - -- not technically worth it. - -- - newval = newval:gsub(LINE_SEPARATOR_as_utf8, '\\u2028'):gsub(PARAGRAPH_SEPARATOR_as_utf8,'\\u2029') - end - return '"' .. newval .. '"' -end - -local function object_or_array(self, T, etc) - -- - -- We need to inspect all the keys... if there are any strings, we'll convert to a JSON - -- object. If there are only numbers, it's a JSON array. - -- - -- If we'll be converting to a JSON object, we'll want to sort the keys so that the - -- end result is deterministic. - -- - local string_keys = { } - local number_keys = { } - local number_keys_must_be_strings = false - local maximum_number_key - - for key in pairs(T) do - if type(key) == 'string' then - table.insert(string_keys, key) - elseif type(key) == 'number' then - table.insert(number_keys, key) - if key <= 0 or key >= math.huge then - number_keys_must_be_strings = true - elseif not maximum_number_key or key > maximum_number_key then - maximum_number_key = key - end - elseif type(key) == 'boolean' then - table.insert(string_keys, tostring(key)) - else - self:onEncodeError("can't encode table with a key of type " .. type(key), etc) - end - end - - if #string_keys == 0 and not number_keys_must_be_strings then - -- - -- An empty table, or a numeric-only array - -- - if #number_keys > 0 then - return nil, maximum_number_key -- an array - elseif tostring(T) == "JSON array" then - return nil - elseif tostring(T) == "JSON object" then - return { } - else - -- have to guess, so we'll pick array, since empty arrays are likely more common than empty objects - return nil - end - end - - table.sort(string_keys) - - local map - if #number_keys > 0 then - -- - -- If we're here then we have either mixed string/number keys, or numbers inappropriate for a JSON array - -- It's not ideal, but we'll turn the numbers into strings so that we can at least create a JSON object. - -- - - if self.noKeyConversion then - self:onEncodeError("a table with both numeric and string keys could be an object or array; aborting", etc) - end - - -- - -- Have to make a shallow copy of the source table so we can remap the numeric keys to be strings - -- - map = { } - for key, val in pairs(T) do - map[key] = val - end - - table.sort(number_keys) - - -- - -- Throw numeric keys in there as strings - -- - for _, number_key in ipairs(number_keys) do - local string_key = tostring(number_key) - if map[string_key] == nil then - table.insert(string_keys , string_key) - map[string_key] = T[number_key] - else - self:onEncodeError("conflict converting table with mixed-type keys into a JSON object: key " .. number_key .. " exists both as a string and a number.", etc) - end - end - end - - return string_keys, nil, map -end - --- --- Encode --- --- 'options' is nil, or a table with possible keys: --- --- pretty -- If true, return a pretty-printed version. --- --- indent -- A string (usually of spaces) used to indent each nested level. --- --- align_keys -- If true, align all the keys when formatting a table. The result is uglier than one might at first imagine. --- Results are undefined if 'align_keys' is true but 'pretty' is not. --- --- array_newline -- If true, array elements are formatted each to their own line. The default is to all fall inline. --- Results are undefined if 'array_newline' is true but 'pretty' is not. --- --- null -- If this exists with a string value, table elements with this value are output as JSON null. --- --- stringsAreUtf8 -- If true, consider Lua strings not as a sequence of bytes, but as a sequence of UTF-8 characters. --- (Currently, the only practical effect of setting this option is that Unicode LINE and PARAGRAPH --- separators, if found in a string, are encoded with a JSON escape instead of as raw UTF-8. --- The JSON is valid either way, but encoding this way, apparently, allows the resulting JSON --- to also be valid Java.) --- --- -local function encode_value(self, value, parents, etc, options, indent, for_key) - - -- - -- keys in a JSON object can never be null, so we don't even consider options.null when converting a key value - -- - if value == nil or (not for_key and options and options.null and value == options.null) then - return 'null' - - elseif type(value) == 'string' then - return json_string_literal(value, options) - - elseif type(value) == 'number' then - if value ~= value then - -- - -- NaN (Not a Number). - -- JSON has no NaN, so we have to fudge the best we can. This should really be a package option. - -- - return "null" - elseif value >= math.huge then - -- - -- Positive infinity. JSON has no INF, so we have to fudge the best we can. This should - -- really be a package option. Note: at least with some implementations, positive infinity - -- is both ">= math.huge" and "<= -math.huge", which makes no sense but that's how it is. - -- Negative infinity is properly "<= -math.huge". So, we must be sure to check the ">=" - -- case first. - -- - return "1e+9999" - elseif value <= -math.huge then - -- - -- Negative infinity. - -- JSON has no INF, so we have to fudge the best we can. This should really be a package option. - -- - return "-1e+9999" - else - return tostring(value) - end - - elseif type(value) == 'boolean' then - return tostring(value) - - elseif type(value) ~= 'table' then - - if self.unsupportedTypeEncoder then - local user_value, user_error = self:unsupportedTypeEncoder(value, parents, etc, options, indent, for_key) - -- If the user's handler returns a string, use that. If it returns nil plus an error message, bail with that. - -- If only nil returned, fall through to the default error handler. - if type(user_value) == 'string' then - return user_value - elseif user_value ~= nil then - self:onEncodeError("unsupportedTypeEncoder method returned a " .. type(user_value), etc) - elseif user_error then - self:onEncodeError(tostring(user_error), etc) - end - end - - self:onEncodeError("can't convert " .. type(value) .. " to JSON", etc) - - elseif getmetatable(value) == isNumber then - return tostring(value) - else - -- - -- A table to be converted to either a JSON object or array. - -- - local T = value - - if type(options) ~= 'table' then - options = {} - end - if type(indent) ~= 'string' then - indent = "" - end - - if parents[T] then - self:onEncodeError("table " .. tostring(T) .. " is a child of itself", etc) - else - parents[T] = true - end - - local result_value - - local object_keys, maximum_number_key, map = object_or_array(self, T, etc) - if maximum_number_key then - -- - -- An array... - -- - local key_indent - if options.array_newline then - key_indent = indent .. tostring(options.indent or "") - else - key_indent = indent - end - - local ITEMS = { } - for i = 1, maximum_number_key do - table.insert(ITEMS, encode_value(self, T[i], parents, etc, options, key_indent)) - end - - if options.array_newline then - result_value = "[\n" .. key_indent .. table.concat(ITEMS, ",\n" .. key_indent) .. "\n" .. indent .. "]" - elseif options.pretty then - result_value = "[ " .. table.concat(ITEMS, ", ") .. " ]" - else - result_value = "[" .. table.concat(ITEMS, ",") .. "]" - end - - elseif object_keys then - -- - -- An object - -- - local TT = map or T - - if options.pretty then - - local KEYS = { } - local max_key_length = 0 - for _, key in ipairs(object_keys) do - local encoded = encode_value(self, tostring(key), parents, etc, options, indent, true) - if options.align_keys then - max_key_length = math.max(max_key_length, #encoded) - end - table.insert(KEYS, encoded) - end - local key_indent = indent .. tostring(options.indent or "") - local subtable_indent = key_indent .. string.rep(" ", max_key_length) .. (options.align_keys and " " or "") - local FORMAT = "%s%" .. string.format("%d", max_key_length) .. "s: %s" - - local COMBINED_PARTS = { } - for i, key in ipairs(object_keys) do - local encoded_val = encode_value(self, TT[key], parents, etc, options, subtable_indent) - table.insert(COMBINED_PARTS, string.format(FORMAT, key_indent, KEYS[i], encoded_val)) - end - result_value = "{\n" .. table.concat(COMBINED_PARTS, ",\n") .. "\n" .. indent .. "}" - - else - - local PARTS = { } - for _, key in ipairs(object_keys) do - local encoded_val = encode_value(self, TT[key], parents, etc, options, indent) - local encoded_key = encode_value(self, tostring(key), parents, etc, options, indent, true) - table.insert(PARTS, string.format("%s:%s", encoded_key, encoded_val)) - end - result_value = "{" .. table.concat(PARTS, ",") .. "}" - - end - else - -- - -- An empty array/object... we'll treat it as an array, though it should really be an option - -- - result_value = "[]" - end - - parents[T] = false - return result_value - end -end - -local function top_level_encode(self, value, etc, options) - local val = encode_value(self, value, {}, etc, options) - if val == nil then - --PRIVATE("may need to revert to the previous public verison if I can't figure out what the guy wanted") - return val - else - return val - end -end - -function OBJDEF:encode(value, etc, options) - if type(self) ~= 'table' or self.__index ~= OBJDEF then - OBJDEF:onEncodeError("JSON:encode must be called in method format", etc) - end - - -- - -- If the user didn't pass in a table of decode options, make an empty one. - -- - if type(options) ~= 'table' then - options = {} - end - - return top_level_encode(self, value, etc, options) -end - -function OBJDEF:encode_pretty(value, etc, options) - if type(self) ~= 'table' or self.__index ~= OBJDEF then - OBJDEF:onEncodeError("JSON:encode_pretty must be called in method format", etc) - end - - -- - -- If the user didn't pass in a table of decode options, use the default pretty ones - -- - if type(options) ~= 'table' then - options = default_pretty_options - end - - return top_level_encode(self, value, etc, options) -end - -function OBJDEF.__tostring() - return "JSON encode/decode package" -end - -OBJDEF.__index = OBJDEF - -function OBJDEF:new(args) - local new = { } - - if args then - for key, val in pairs(args) do - new[key] = val - end - end - - return setmetatable(new, OBJDEF) -end - -return OBJDEF:new() - --- --- Version history: --- --- 20170927.26 Use option.null in decoding as well. Thanks to Max Sindwani for the bump, and sorry to Oliver Hitz --- whose first mention of it four years ago was completely missed by me. --- --- 20170823.25 Added support for JSON:unsupportedTypeEncoder(). --- Thanks to Chronos Phaenon Eosphoros (https://github.com/cpeosphoros) for the idea. --- --- 20170819.24 Added support for boolean keys in tables. --- --- 20170416.23 Added the "array_newline" formatting option suggested by yurenchen (http://www.yurenchen.com/) --- --- 20161128.22 Added: --- JSON:isString() --- JSON:isNumber() --- JSON:decodeIntegerObjectificationLength --- JSON:decodeDecimalObjectificationLength --- --- 20161109.21 Oops, had a small boo-boo in the previous update. --- --- 20161103.20 Used to silently ignore trailing garbage when decoding. Now fails via JSON:onTrailingGarbage() --- http://seriot.ch/parsing_json.php --- --- Built-in error message about "expected comma or ']'" had mistakenly referred to '[' --- --- Updated the built-in error reporting to refer to bytes rather than characters. --- --- The decode() method no longer assumes that error handlers abort. --- --- Made the VERSION string a string instead of a number --- - --- 20160916.19 Fixed the isNumber.__index assignment (thanks to Jack Taylor) --- --- 20160730.18 Added JSON:forceString() and JSON:forceNumber() --- --- 20160728.17 Added concatenation to the metatable for JSON:asNumber() --- --- 20160709.16 Could crash if not passed an options table (thanks jarno heikkinen ). --- --- Made JSON:asNumber() a bit more resilient to being passed the results of itself. --- --- 20160526.15 Added the ability to easily encode null values in JSON, via the new "null" encoding option. --- (Thanks to Adam B for bringing up the issue.) --- --- Added some support for very large numbers and precise floats via --- JSON.decodeNumbersAsObjects --- JSON.decodeIntegerStringificationLength --- JSON.decodeDecimalStringificationLength --- --- Added the "stringsAreUtf8" encoding option. (Hat tip to http://lua-users.org/wiki/JsonModules ) --- --- 20141223.14 The encode_pretty() routine produced fine results for small datasets, but isn't really --- appropriate for anything large, so with help from Alex Aulbach I've made the encode routines --- more flexible, and changed the default encode_pretty() to be more generally useful. --- --- Added a third 'options' argument to the encode() and encode_pretty() routines, to control --- how the encoding takes place. --- --- Updated docs to add assert() call to the loadfile() line, just as good practice so that --- if there is a problem loading JSON.lua, the appropriate error message will percolate up. --- --- 20140920.13 Put back (in a way that doesn't cause warnings about unused variables) the author string, --- so that the source of the package, and its version number, are visible in compiled copies. --- --- 20140911.12 Minor lua cleanup. --- Fixed internal reference to 'JSON.noKeyConversion' to reference 'self' instead of 'JSON'. --- (Thanks to SmugMug's David Parry for these.) --- --- 20140418.11 JSON nulls embedded within an array were being ignored, such that --- ["1",null,null,null,null,null,"seven"], --- would return --- {1,"seven"} --- It's now fixed to properly return --- {1, nil, nil, nil, nil, nil, "seven"} --- Thanks to "haddock" for catching the error. --- --- 20140116.10 The user's JSON.assert() wasn't always being used. Thanks to "blue" for the heads up. --- --- 20131118.9 Update for Lua 5.3... it seems that tostring(2/1) produces "2.0" instead of "2", --- and this caused some problems. --- --- 20131031.8 Unified the code for encode() and encode_pretty(); they had been stupidly separate, --- and had of course diverged (encode_pretty didn't get the fixes that encode got, so --- sometimes produced incorrect results; thanks to Mattie for the heads up). --- --- Handle encoding tables with non-positive numeric keys (unlikely, but possible). --- --- If a table has both numeric and string keys, or its numeric keys are inappropriate --- (such as being non-positive or infinite), the numeric keys are turned into --- string keys appropriate for a JSON object. So, as before, --- JSON:encode({ "one", "two", "three" }) --- produces the array --- ["one","two","three"] --- but now something with mixed key types like --- JSON:encode({ "one", "two", "three", SOMESTRING = "some string" })) --- instead of throwing an error produces an object: --- {"1":"one","2":"two","3":"three","SOMESTRING":"some string"} --- --- To maintain the prior throw-an-error semantics, set --- JSON.noKeyConversion = true --- --- 20131004.7 Release under a Creative Commons CC-BY license, which I should have done from day one, sorry. --- --- 20130120.6 Comment update: added a link to the specific page on my blog where this code can --- be found, so that folks who come across the code outside of my blog can find updates --- more easily. --- --- 20111207.5 Added support for the 'etc' arguments, for better error reporting. --- --- 20110731.4 More feedback from David Kolf on how to make the tests for Nan/Infinity system independent. --- --- 20110730.3 Incorporated feedback from David Kolf at http://lua-users.org/wiki/JsonModules: --- --- * When encoding lua for JSON, Sparse numeric arrays are now handled by --- spitting out full arrays, such that --- JSON:encode({"one", "two", [10] = "ten"}) --- returns --- ["one","two",null,null,null,null,null,null,null,"ten"] --- --- In 20100810.2 and earlier, only up to the first non-null value would have been retained. --- --- * When encoding lua for JSON, numeric value NaN gets spit out as null, and infinity as "1+e9999". --- Version 20100810.2 and earlier created invalid JSON in both cases. --- --- * Unicode surrogate pairs are now detected when decoding JSON. --- --- 20100810.2 added some checking to ensure that an invalid Unicode character couldn't leak in to the UTF-8 encoding --- --- 20100731.1 initial public release --- diff --git a/Resources/lua/gems-script.lua b/Resources/lua/gems-script.lua deleted file mode 100644 index 138878f7..00000000 --- a/Resources/lua/gems-script.lua +++ /dev/null @@ -1,17 +0,0 @@ -print(lib_path..'\n') -print(ijsdata..'\n') - - --- load JSON4Lua module - dofile(lib_path..'json.lua') - json = require('json') - --- Now JSON decode the json string - rintable = json.decode(ijsdata) - --- Make changes into structure - print( rintable.properties.element_symbol) - rintable.properties.isotope_mass = 55 - --- Encodes a table - ojsdata = json.encode(rintable) diff --git a/Resources/lua/json-old.lua b/Resources/lua/json-old.lua deleted file mode 100644 index f14adf27..00000000 --- a/Resources/lua/json-old.lua +++ /dev/null @@ -1,377 +0,0 @@ ------------------------------------------------------------------------------ --- JSON4Lua: JSON encoding / decoding support for the Lua language. --- json Module. --- Author: Craig Mason-Jones --- Homepage: http://json.luaforge.net/ --- Version: 0.9.20 --- This module is released under the The GNU General Public License (GPL). --- Please see LICENCE.txt for details. --- --- USAGE: --- This module exposes two functions: --- encode(o) --- Returns the table / string / boolean / number / nil / json.null value as a JSON-encoded string. --- decode(json_string) --- Returns a Lua object populated with the data encoded in the JSON string json_string. --- --- REQUIREMENTS: --- compat-5.1 if using Lua 5.0 --- --- CHANGELOG --- 0.9.20 Introduction of local Lua functions for private functions (removed _ function prefix). --- Fixed Lua 5.1 compatibility issues. --- Introduced json.null to have null values in associative arrays. --- encode() performance improvement (more than 50%) through table.concat rather than .. --- Introduced decode ability to ignore /**/ comments in the JSON string. --- 0.9.10 Fix to array encoding / decoding to correctly manage nil/null values in arrays. ------------------------------------------------------------------------------ - ------------------------------------------------------------------------------ --- Imports and dependencies ------------------------------------------------------------------------------ -local math = require('math') -local string = require("string") -local table = require("table") - -local base = _G - ------------------------------------------------------------------------------ --- Module declaration ------------------------------------------------------------------------------ ---module("json") - --- Public functions - --- Private functions -local decode_scanArray -local decode_scanComment -local decode_scanConstant -local decode_scanNumber -local decode_scanObject -local decode_scanString -local decode_scanWhitespace -local encodeString -local isArray -local isEncodable - ------------------------------------------------------------------------------ --- PUBLIC FUNCTIONS ------------------------------------------------------------------------------ ---- Encodes an arbitrary Lua object / variable. --- @param v The Lua object / variable to be JSON encoded. --- @return String containing the JSON encoding in internal Lua string format (i.e. not unicode) -function encode (v) - -- Handle nil values - if v==nil then - return "null" - end - - local vtype = base.type(v) - - -- Handle strings - if vtype=='string' then - return '"' .. encodeString(v) .. '"' -- Need to handle encoding in string - end - - -- Handle booleans - if vtype=='number' or vtype=='boolean' then - return base.tostring(v) - end - - -- Handle tables - if vtype=='table' then - local rval = {} - -- Consider arrays separately - local bArray, maxCount = isArray(v) - if bArray then - for i = 1,maxCount do - table.insert(rval, encode(v[i])) - end - else -- An object, not an array - for i,j in base.pairs(v) do - if isEncodable(i) and isEncodable(j) then - table.insert(rval, '"' .. encodeString(i) .. '":' .. encode(j)) - end - end - end - if bArray then - return '[' .. table.concat(rval,',') ..']' - else - return '{' .. table.concat(rval,',') .. '}' - end - end - - -- Handle null values - if vtype=='function' and v==null then - return 'null' - end - - base.assert(false,'encode attempt to encode unsupported type ' .. vtype .. ':' .. base.tostring(v)) -end - - ---- Decodes a JSON string and returns the decoded value as a Lua data structure / value. --- @param s The string to scan. --- @param [startPos] Optional starting position where the JSON string is located. Defaults to 1. --- @param Lua object, number The object that was scanned, as a Lua table / string / number / boolean or nil, --- and the position of the first character after --- the scanned JSON object. -function decode(s, startPos) - startPos = startPos and startPos or 1 - startPos = decode_scanWhitespace(s,startPos) - base.assert(startPos<=string.len(s), 'Unterminated JSON encoded object found at position in [' .. s .. ']') - local curChar = string.sub(s,startPos,startPos) - -- Object - if curChar=='{' then - return decode_scanObject(s,startPos) - end - -- Array - if curChar=='[' then - return decode_scanArray(s,startPos) - end - -- Number - if string.find("+-0123456789.e", curChar, 1, true) then - return decode_scanNumber(s,startPos) - end - -- String - if curChar==[["]] or curChar==[[']] then - return decode_scanString(s,startPos) - end - if string.sub(s,startPos,startPos+1)=='/*' then - return decode(s, decode_scanComment(s,startPos)) - end - -- Otherwise, it must be a constant - return decode_scanConstant(s,startPos) -end - ---- The null function allows one to specify a null value in an associative array (which is otherwise --- discarded if you set the value with 'nil' in Lua. Simply set t = { first=json.null } -function null() - return null -- so json.null() will also return null ;-) -end ------------------------------------------------------------------------------ --- Internal, PRIVATE functions. --- Following a Python-like convention, I have prefixed all these 'PRIVATE' --- functions with an underscore. ------------------------------------------------------------------------------ - ---- Scans an array from JSON into a Lua object --- startPos begins at the start of the array. --- Returns the array and the next starting position --- @param s The string being scanned. --- @param startPos The starting position for the scan. --- @return table, int The scanned array as a table, and the position of the next character to scan. -function decode_scanArray(s,startPos) - local array = {} -- The return value - local stringLen = string.len(s) - base.assert(string.sub(s,startPos,startPos)=='[','decode_scanArray called but array does not start at position ' .. startPos .. ' in string:\n'..s ) - startPos = startPos + 1 - -- Infinite loop for array elements - repeat - startPos = decode_scanWhitespace(s,startPos) - base.assert(startPos<=stringLen,'JSON String ended unexpectedly scanning array.') - local curChar = string.sub(s,startPos,startPos) - if (curChar==']') then - return array, startPos+1 - end - if (curChar==',') then - startPos = decode_scanWhitespace(s,startPos+1) - end - base.assert(startPos<=stringLen, 'JSON String ended unexpectedly scanning array.') - object, startPos = decode(s,startPos) - table.insert(array,object) - until false -end - ---- Scans a comment and discards the comment. --- Returns the position of the next character following the comment. --- @param string s The JSON string to scan. --- @param int startPos The starting position of the comment -function decode_scanComment(s, startPos) - base.assert( string.sub(s,startPos,startPos+1)=='/*', "decode_scanComment called but comment does not start at position " .. startPos) - local endPos = string.find(s,'*/',startPos+2) - base.assert(endPos~=nil, "Unterminated comment in string at " .. startPos) - return endPos+2 -end - ---- Scans for given constants: true, false or null --- Returns the appropriate Lua type, and the position of the next character to read. --- @param s The string being scanned. --- @param startPos The position in the string at which to start scanning. --- @return object, int The object (true, false or nil) and the position at which the next character should be --- scanned. -function decode_scanConstant(s, startPos) - local consts = { ["true"] = true, ["false"] = false, ["null"] = nil } - local constNames = {"true","false","null"} - - for i,k in base.pairs(constNames) do - --print ("[" .. string.sub(s,startPos, startPos + string.len(k) -1) .."]", k) - if string.sub(s,startPos, startPos + string.len(k) -1 )==k then - return consts[k], startPos + string.len(k) - end - end - base.assert(nil, 'Failed to scan constant from string ' .. s .. ' at starting position ' .. startPos) -end - ---- Scans a number from the JSON encoded string. --- (in fact, also is able to scan numeric +- eqns, which is not --- in the JSON spec.) --- Returns the number, and the position of the next character --- after the number. --- @param s The string being scanned. --- @param startPos The position at which to start scanning. --- @return number, int The extracted number and the position of the next character to scan. -function decode_scanNumber(s,startPos) - local endPos = startPos+1 - local stringLen = string.len(s) - local acceptableChars = "+-0123456789.e" - while (string.find(acceptableChars, string.sub(s,endPos,endPos), 1, true) - and endPos<=stringLen - ) do - endPos = endPos + 1 - end - local stringValue = 'return ' .. string.sub(s,startPos, endPos-1) - local stringEval = base.loadstring(stringValue) - base.assert(stringEval, 'Failed to scan number [ ' .. stringValue .. '] in JSON string at position ' .. startPos .. ' : ' .. endPos) - return stringEval(), endPos -end - ---- Scans a JSON object into a Lua object. --- startPos begins at the start of the object. --- Returns the object and the next starting position. --- @param s The string being scanned. --- @param startPos The starting position of the scan. --- @return table, int The scanned object as a table and the position of the next character to scan. -function decode_scanObject(s,startPos) - local object = {} - local stringLen = string.len(s) - local key, value - base.assert(string.sub(s,startPos,startPos)=='{','decode_scanObject called but object does not start at position ' .. startPos .. ' in string:\n' .. s) - startPos = startPos + 1 - repeat - startPos = decode_scanWhitespace(s,startPos) - base.assert(startPos<=stringLen, 'JSON string ended unexpectedly while scanning object.') - local curChar = string.sub(s,startPos,startPos) - if (curChar=='}') then - return object,startPos+1 - end - if (curChar==',') then - startPos = decode_scanWhitespace(s,startPos+1) - end - base.assert(startPos<=stringLen, 'JSON string ended unexpectedly scanning object.') - -- Scan the key - key, startPos = decode(s,startPos) - base.assert(startPos<=stringLen, 'JSON string ended unexpectedly searching for value of key ' .. key) - startPos = decode_scanWhitespace(s,startPos) - base.assert(startPos<=stringLen, 'JSON string ended unexpectedly searching for value of key ' .. key) - base.assert(string.sub(s,startPos,startPos)==':','JSON object key-value assignment mal-formed at ' .. startPos) - startPos = decode_scanWhitespace(s,startPos+1) - base.assert(startPos<=stringLen, 'JSON string ended unexpectedly searching for value of key ' .. key) - value, startPos = decode(s,startPos) - object[key]=value - until false -- infinite loop while key-value pairs are found -end - ---- Scans a JSON string from the opening inverted comma or single quote to the --- end of the string. --- Returns the string extracted as a Lua string, --- and the position of the next non-string character --- (after the closing inverted comma or single quote). --- @param s The string being scanned. --- @param startPos The starting position of the scan. --- @return string, int The extracted string as a Lua string, and the next character to parse. -function decode_scanString(s,startPos) - base.assert(startPos, 'decode_scanString(..) called without start position') - local startChar = string.sub(s,startPos,startPos) - base.assert(startChar==[[']] or startChar==[["]],'decode_scanString called for a non-string') - local escaped = false - local endPos = startPos + 1 - local bEnded = false - local stringLen = string.len(s) - repeat - local curChar = string.sub(s,endPos,endPos) - if not escaped then - if curChar==[[\]] then - escaped = true - else - bEnded = curChar==startChar - end - else - -- If we're escaped, we accept the current character come what may - escaped = false - end - endPos = endPos + 1 - base.assert(endPos <= stringLen+1, "String decoding failed: unterminated string at position " .. endPos) - until bEnded - local stringValue = 'return ' .. string.sub(s, startPos, endPos-1) - local stringEval = base.loadstring(stringValue) - base.assert(stringEval, 'Failed to load string [ ' .. stringValue .. '] in JSON4Lua.decode_scanString at position ' .. startPos .. ' : ' .. endPos) - return stringEval(), endPos -end - ---- Scans a JSON string skipping all whitespace from the current start position. --- Returns the position of the first non-whitespace character, or nil if the whole end of string is reached. --- @param s The string being scanned --- @param startPos The starting position where we should begin removing whitespace. --- @return int The first position where non-whitespace was encountered, or string.len(s)+1 if the end of string --- was reached. -function decode_scanWhitespace(s,startPos) - local whitespace=" \n\r\t" - local stringLen = string.len(s) - while ( string.find(whitespace, string.sub(s,startPos,startPos), 1, true) and startPos <= stringLen) do - startPos = startPos + 1 - end - return startPos -end - ---- Encodes a string to be JSON-compatible. --- This just involves back-quoting inverted commas, back-quotes and newlines, I think ;-) --- @param s The string to return as a JSON encoded (i.e. backquoted string) --- @return The string appropriately escaped. -function encodeString(s) - s = string.gsub(s,'\\','\\\\') - s = string.gsub(s,'"','\\"') - s = string.gsub(s,"'","\\'") - s = string.gsub(s,'\n','\\n') - s = string.gsub(s,'\t','\\t') - return s -end - --- Determines whether the given Lua type is an array or a table / dictionary. --- We consider any table an array if it has indexes 1..n for its n items, and no --- other data in the table. --- I think this method is currently a little 'flaky', but can't think of a good way around it yet... --- @param t The table to evaluate as an array --- @return boolean, number True if the table can be represented as an array, false otherwise. If true, --- the second returned value is the maximum --- number of indexed elements in the array. -function isArray(t) - -- Next we count all the elements, ensuring that any non-indexed elements are not-encodable - -- (with the possible exception of 'n') - local maxIndex = 0 - for k,v in base.pairs(t) do - if (base.type(k)=='number' and math.floor(k)==k and 1<=k) then -- k,v is an indexed pair - if (not isEncodable(v)) then return false end -- All array elements must be encodable - maxIndex = math.max(maxIndex,k) - else - if (k=='n') then - if v ~= table.getn(t) then return false end -- False if n does not hold the number of elements - else -- Else of (k=='n') - if isEncodable(v) then return false end - end -- End of (k~='n') - end -- End of k,v not an indexed pair - end -- End of loop across all pairs - return true, maxIndex -end - ---- Determines whether the given Lua object / table / variable can be JSON encoded. The only --- types that are JSON encodable are: string, boolean, number, nil, table and json.null. --- In this implementation, all other types are ignored. --- @param o The object to examine. --- @return boolean True if the object should be JSON encoded, false if it should be ignored. -function isEncodable(o) - local t = base.type(o) - return (t=='string' or t=='boolean' or t=='number' or t=='nil' or t=='table') or (t=='function' and o==null) -end - ---print('@@@ json.lua\n ') \ No newline at end of file diff --git a/ThermoFun/Batch/OutputBatch.cpp b/ThermoFun/Batch/OutputBatch.cpp index c7ff614d..93c1e2f4 100644 --- a/ThermoFun/Batch/OutputBatch.cpp +++ b/ThermoFun/Batch/OutputBatch.cpp @@ -2,7 +2,9 @@ #include "ThermoBatch.h" #include #include +#include #include +#include #include "../GlobalVariables.h" #include "../Common/Units.hpp" @@ -62,6 +64,20 @@ auto Output::toCSVTransposed(std::string filename) -> void pimpl->fProperties.close(); } +auto Output::toCSVPropertyGrid(std::string filename) -> void +{ + auto properties = pimpl->api.properties(); + for (size_t i = 0; ifProperties.open(std::string(properties[i]+"_"+filename), std::ios::trunc ); + + pimpl->fProperties << CSVHeaderPropertyGrid() << std::endl; + + foutPropertyGrid(properties[i], i); + + pimpl->fProperties.close(); + } +} auto Output::toDouble() -> double { @@ -120,9 +136,45 @@ auto Output::CSVHeaderTransposed( ) -> std::string return header; } +auto Output::CSVHeaderPropertyGrid() -> std::string +{ + auto symbols = pimpl->api.symbols(); + auto units = pimpl->api.units(); + auto s = pimpl->api.outputSettings().separator; + auto digits = pimpl->api.digits(); + auto temperatures = pimpl->api.Temperatures(); + auto pressures = pimpl->api.Pressures(); + std::string header = ""; + std::vector columns; + std::string ColData = ""; + + if (pimpl->api.outputSettings().loopTemperatureThenPressure) + { + columns = pressures; ColData = "pressure"; + header = header + "Symbol" + s + "T" + "(" + units.at("temperature") + ")" + "_" + "P" + "(" + units.at("pressure") + ")"; + } + else + { + columns = temperatures; ColData = "temperature"; + header = header + "Symbol" + s + "P" + "(" + units.at("pressure") + ")" + "_" + "T" + "(" + units.at("temperature") + ")"; + } + + for (auto col : columns) + { + std::ostringstream out; + out.precision(digits.at(ColData)); + if (pimpl->api.outputSettings().isFixed) out << std::fixed; + if (pimpl->api.outputSettings().isScientific) out << std::scientific; + out << col; + header = header + s + out.str(); + } + + return header; +} + auto Output::foutResults()-> void { - unsigned j_size, i_size; + size_t j_size, i_size; auto outSettings = pimpl->api.outputSettings(); auto s = outSettings.separator; auto symbols = pimpl->api.symbols(); @@ -178,7 +230,7 @@ auto Output::foutResults()-> void auto Output::foutResultsTransposed()-> void { - unsigned j_size, i_size; + size_t j_size, i_size; auto outSettings = pimpl->api.outputSettings(); auto s = outSettings.separator; auto properties = pimpl->api.properties(); @@ -236,4 +288,62 @@ auto Output::foutResultsTransposed()-> void } } +auto Output::foutPropertyGrid(const std::string &property, const size_t &index_property)-> void +{ + auto outSettings = pimpl->api.outputSettings(); + auto s = outSettings.separator; + auto properties = pimpl->api.properties(); + auto digits = pimpl->api.digits(); + auto fromUnits = defaultPropertyUnits; + auto toUnits = pimpl->api.units(); + auto tpPairs = pimpl->api.TPpairs(); + auto results = pimpl->api.results(); + auto symbols = pimpl->api.symbols(); + auto temperatures = pimpl->api.Temperatures(); + auto pressures = pimpl->api.Pressures(); + auto columns = temperatures; + auto rows = pressures; + auto rowData = "pressure"; + auto colData = "temperature"; + + if (!outSettings.loopOverTPpairsFirst) + { + pimpl->fProperties << "Only a loop over T-P pairs is possible when generating property grids"; + return; + } + + if (pimpl->api.outputSettings().isFixed) pimpl->fProperties << std::fixed; + if (pimpl->api.outputSettings().isScientific) pimpl->fProperties << std::scientific; + + size_t count = 0; + + if (outSettings.loopTemperatureThenPressure) + { + columns = pressures; + rows = temperatures; + rowData = "temperature"; + colData = "pressure"; + } + + for (unsigned i=0; ifProperties << find_and_replace(symbols[i], s, "_"); + pimpl->fProperties << std::setprecision(digits.at(rowData)); + pimpl->fProperties << s << r; + + for(auto c : columns) + { + pimpl->fProperties << std::setprecision(digits.at(property)); + pimpl->fProperties << s << units::convert(results[count][index_property].val, + fromUnits.at(property), + toUnits.at(property)); + count++; + } + pimpl->fProperties << std::endl; + } +} + } diff --git a/ThermoFun/Batch/OutputBatch.h b/ThermoFun/Batch/OutputBatch.h index dd66bd43..660ac3c6 100644 --- a/ThermoFun/Batch/OutputBatch.h +++ b/ThermoFun/Batch/OutputBatch.h @@ -17,14 +17,49 @@ class Output public: /// /// \brief Output constructor - /// \param interface + /// \param batch object of ThermoBatch calculation used for output /// Output(const ThermoBatch& batch); + /** + * @brief toCSV write results to CSV file + * with substances/reactions on rows and proeprties on columns + * @param filename + */ auto toCSV (std::string filename) -> void; + + /** + * @brief toCSVTransposed write results to CSV file in a special transposed format. + * with substances/reactions on columns and proeprties on rows + * @param filename + */ auto toCSVTransposed (std::string filename) -> void; + + /** + * @brief toCSVPropertyGrid write results to CSV file in a property grid format + * one file will be created for each property + * if loopTemperatureThenPressure in BatchPreferences is True the grid will have T in horizontal and P in vertical + * if loopTemperatureThenPressure in BatchPreferences is False the grid will have P in horizontal and T in vertical + * @param filename will be modified to include the property name + */ + auto toCSVPropertyGrid (std::string filename) -> void; + + /** + * @brief toDouble + * @return property value + */ auto toDouble () -> double; + + /** + * @brief toThermoScalar + * @return property in ThermoScalar type + */ auto toThermoScalar () -> Reaktoro_::ThermoScalar; + + /** + * @brief to2DVectorDouble + * @return vector of calculated properties + */ auto to2DVectorDouble () -> std::vector>; private: @@ -33,8 +68,10 @@ class Output auto CSVHeader () -> std::string; auto CSVHeaderTransposed () -> std::string; + auto CSVHeaderPropertyGrid() -> std::string; auto foutResults () -> void; auto foutResultsTransposed() -> void; + auto foutPropertyGrid (const std::string &property, const size_t &index_property) -> void; }; } diff --git a/ThermoFun/Batch/ThermoBatch.cpp b/ThermoFun/Batch/ThermoBatch.cpp index 959c60a1..1f8f19c8 100644 --- a/ThermoFun/Batch/ThermoBatch.cpp +++ b/ThermoFun/Batch/ThermoBatch.cpp @@ -32,6 +32,14 @@ struct ThermoBatch::Impl vvd tpPairs; + std::vector Ts; + + std::vector Ps; + + std::map Tincrement = defaultTemperatureIncrement; + + std::map Pincrement = defaultPressureIncrement; + vstr properties; std::map givenPropertyUnits = defaultPropertyUnits; @@ -42,6 +50,7 @@ struct ThermoBatch::Impl vvThScalar results; + Impl(const Database& database) : thermo(ThermoEngine(database)) {} @@ -50,6 +59,10 @@ struct ThermoBatch::Impl : thermo(filename) {} + Impl(const ThermoEngine& engine) + : thermo(engine) + {} + // clear functions auto clearSymbols () -> void { @@ -61,9 +74,21 @@ struct ThermoBatch::Impl properties.clear(); } + auto clearTemperatures () -> void + { + Ts.clear(); + } + + auto clearPressures () -> void + { + Ps.clear(); + } + auto clearTPpairs () -> void { tpPairs.clear(); + clearTemperatures(); + clearPressures(); } auto clearAll() -> void @@ -71,6 +96,8 @@ struct ThermoBatch::Impl clearProperties(); clearSymbols(); clearTPpairs(); + clearTemperatures(); + clearPressures(); } // Add functions @@ -84,37 +111,68 @@ struct ThermoBatch::Impl properties = names; } + auto addSymbolsProperties(const vstr &symbols_, const vstr &properties) -> void + { + clearAll(); + addSymbols(symbols_); + addProperties(properties); + } + auto addTPpair (const double &T, const double &P) -> void { std::vector one_pair = {T, P}; + if ( std::find(Ts.begin(), Ts.end(), T) == Ts.end() ) + Ts.push_back(T); + if ( std::find(Ps.begin(), Ps.end(), P) == Ps.end() ) + Ps.push_back(P); + tpPairs.push_back(one_pair); } - auto addSymbolsProperties(const vstr &symbols_, const vstr &properties) -> void + auto addTPpairs (const std::vector &temperatures, const std::vector &pressures) -> void { - clearAll(); - addSymbols(symbols_); - addProperties(properties); + clearTPpairs(); + std::vector rows, columns; + if (outSettings.loopTemperatureThenPressure) + { rows = temperatures; columns = pressures; } + else + { rows = pressures; columns = temperatures; } + + for (auto r : rows) + for (auto c : columns) + if (outSettings.loopTemperatureThenPressure) + addTPpair(r,c); + else + addTPpair(c,r); } auto addTPpairs (const double &Tmin, const double &Tmax, const double &Tstep, const double &Pmin, const double &Pmax, const double &Pstep) -> void { + clearTPpairs(); double t = Tmin-Tstep; double p = Pmin-Pstep; + std::vector temperatures; + std::vector pressures; do - { t = t + Tstep; - do - { - p = p + Pstep; - addTPpair(t,p); - } while (p < Pmax); + { + p = p + Pstep; + pressures.push_back(p); + } while (p < Pmax); + + do + { + t = t + Tstep; + temperatures.push_back(t); } while (t < Tmax); + + addTPpairs(temperatures, pressures); } auto addTPpairs (const vvd &tpPairs) -> void { + clearTPpairs(); for (unsigned i=0; i void @@ -249,20 +320,20 @@ struct ThermoBatch::Impl } // Calculate functions - auto calculateSubstProp( double T, double P, string symbol, unsigned index ) -> void + auto calculateSubstProp( double T, double &P, string symbol, unsigned index ) -> void { - results[index] = selectResultsSubst(thermo.thermoPropertiesSubstance(T, P, symbol)); + results[index] = selectResultsSubst(thermo.thermoPropertiesSubstance(T, P, symbol)); } - auto calculateReactProp( double T, double P, string symbol, unsigned index ) -> void + auto calculateReactProp( double T, double &P, string symbol, unsigned index ) -> void { - if (outSettings.calcReactFromSubst) + if (outSettings.reactionPropertiesFromReactants) results[index] = selectResultsReact(thermo.thermoPropertiesReactionFromReactants(T, P, symbol)); else results[index] = selectResultsReact(thermo.thermoPropertiesReaction(T, P, symbol)); } - auto calculateSolventProp( double T, double P, string symbol, unsigned index ) -> void + auto calculateSolventProp( double T, double &P, string symbol, unsigned index ) -> void { results[index] = selectResultsSolvent(thermo.propertiesSolvent(T, P, symbol), thermo.electroPropertiesSolvent(T, P, symbol)); @@ -273,6 +344,10 @@ ThermoBatch::ThermoBatch(const Database& database) : pimpl(new Impl(database)) {} +ThermoBatch::ThermoBatch(const ThermoEngine& engine) + : pimpl(new Impl(engine)) +{} + ThermoBatch::ThermoBatch(std::string filename) : pimpl(new Impl(filename)) {} @@ -299,17 +374,43 @@ auto ThermoBatch::thermoPropertiesSubstance(double T, double P, vstr symbols, vs return Output (*this); } -auto ThermoBatch::thermoPropertiesSubstance(std::array aT, std::array aP, vstr symbols, vstr properties) -> Output +auto ThermoBatch::thermoPropertiesSubstance(vstr symbols, vstr properties) -> Output +{ + pimpl->addSymbolsProperties(symbols, properties); + + pimpl->addTPpairs(pimpl->Tincrement["Tmin"], pimpl->Tincrement["Tmax"], pimpl->Tincrement["Tstep"], + pimpl->Pincrement["Pmin"], pimpl->Pincrement["Pmax"], pimpl->Pincrement["Pstep"]); + + pimpl->calculate(forSUBSTANCE); + + return Output (*this); +} + +auto ThermoBatch::thermoPropertiesSubstance(std::vector temperatures, std::vector pressures, vstr symbols, vstr properties) -> Output { pimpl->addSymbolsProperties(symbols, properties); - pimpl->addTPpairs(aT[0], aT[1], aT[2], aP[0], aP[1], aP[2]); + pimpl->addTPpairs(temperatures, pressures); pimpl->calculate(forSUBSTANCE); return Output (*this); } +auto ThermoBatch::thermoPropertiesSubstance(std::vector temperatures, std::vector pressures, vstr symbols, vstr properties, vtps vTps) -> Output +{ + pimpl->addSymbolsProperties(symbols, properties); + + pimpl->addTPpairs(temperatures, pressures); + + if (vTps.empty()) + pimpl->calculate(forSUBSTANCE); + else + pimpl->selectProvidedSubstancesProperties(vTps); + + return Output (*this); +} + auto ThermoBatch::thermoPropertiesSubstance(vvd tpPairs, vstr symbols, vstr properties) -> Output { return thermoPropertiesSubstance(tpPairs,symbols,properties,{}); @@ -352,17 +453,43 @@ auto ThermoBatch::thermoPropertiesReaction(double T, double P, vstr symbols, vst return Output (*this); } -auto ThermoBatch::thermoPropertiesReaction(std::array aT, std::array aP, vstr symbols, vstr properties) -> Output +auto ThermoBatch::thermoPropertiesReaction(vstr symbols, vstr properties) -> Output { pimpl->addSymbolsProperties(symbols, properties); - pimpl->addTPpairs(aT[0], aT[1], aT[2], aP[0], aP[1], aP[2]); + pimpl->addTPpairs(pimpl->Tincrement["Tmin"], pimpl->Tincrement["Tmax"], pimpl->Tincrement["Tstep"], + pimpl->Pincrement["Pmin"], pimpl->Pincrement["Pmax"], pimpl->Pincrement["Pstep"]); pimpl->calculate(forREACTION); return Output (*this); } +auto ThermoBatch::thermoPropertiesReaction(std::vector temperatures, std::vector pressures, vstr symbols, vstr properties) -> Output +{ + pimpl->addSymbolsProperties(symbols, properties); + + pimpl->addTPpairs(temperatures, pressures); + + pimpl->calculate(forREACTION); + + return Output (*this); +} + +auto ThermoBatch::thermoPropertiesReaction(std::vector temperatures, std::vector pressures, vstr symbols, vstr properties, vtpr vTpr) -> Output +{ + pimpl->addSymbolsProperties(symbols, properties); + + pimpl->addTPpairs(temperatures, pressures); + + if (vTpr.empty()) + pimpl->calculate(forREACTION); + else + pimpl->selectProvidedReactionsProperties(vTpr); + + return Output (*this); +} + auto ThermoBatch::thermoPropertiesReaction(vvd tpPairs, vstr symbols, vstr properties) -> Output { return thermoPropertiesReaction(tpPairs, symbols, properties, {}); @@ -431,6 +558,19 @@ auto ThermoBatch::setSolventSymbol(const std::string solventSymbol) -> void pimpl->thermo.setSolventSymbol(solventSymbol); } +auto ThermoBatch::setTemperatureIncrement (const double& Tmin, const double& Tmax, const double& Tstep) -> void +{ + pimpl->Tincrement["Tmin"] = Tmin; + pimpl->Tincrement["Tmax"] = Tmax; + pimpl->Tincrement["Tstep"] = Tstep; +} +auto ThermoBatch::setPressureIncrement (const double& Pmin, const double& Pmax, const double& Pstep) -> void +{ + pimpl->Pincrement["Pmin"] = Pmin; + pimpl->Pincrement["Pmax"] = Pmax; + pimpl->Pincrement["Pstep"] = Pstep; +} + // Private // get functions auto ThermoBatch::symbols() -> const vstr @@ -448,6 +588,16 @@ auto ThermoBatch::TPpairs() -> const vvd return pimpl->tpPairs; } +auto ThermoBatch::Temperatures() -> const std::vector +{ + return pimpl->Ts; +} + +auto ThermoBatch::Pressures() -> const std::vector +{ + return pimpl->Ps; +} + auto ThermoBatch::properties() -> const vstr { return pimpl->properties; diff --git a/ThermoFun/Batch/ThermoBatch.h b/ThermoFun/Batch/ThermoBatch.h index b418e262..e917d34b 100644 --- a/ThermoFun/Batch/ThermoBatch.h +++ b/ThermoFun/Batch/ThermoBatch.h @@ -14,6 +14,7 @@ namespace ThermoFun { class Database; +class ThermoEngine; struct ThermoPropertiesSubstance; struct ThermoPropertiesReaction; struct PropertiesSolvent; @@ -48,20 +49,20 @@ struct BatchPreferences std::string solventFileName = "tpSolventResults.csv"; /// write solvent properties - bool outSolventProp = false; + bool outputSolventProperties = false; - bool calcSubstFromReact = false; + bool substancePropertiesFromReaction = false; - bool calcReactFromSubst = false; + bool reactionPropertiesFromReactants = false; bool loopOverTPpairsFirst = true; -}; - -struct BatchCalculationSettings -{ - bool dependentSubstancesFromReactions = false; - bool reactionsFromSubstances = false; + /** + * @brief loopTemperatureThenPressure + * @value True generate T-P pairs by first incrementing temperature + * @value False generate T-P pairs by first incrementing pressure + */ + bool loopTemperatureThenPressure = true; }; /// @@ -97,6 +98,12 @@ class ThermoBatch /// ThermoBatch(std::string filename); + /// + /// \brief ThermoBatch + /// \param engine + /// + ThermoBatch(const ThermoEngine &engine); + auto setUnits (const std::map &units)-> void; auto setDigits (const std::map &digits)-> void; auto setPropertiesUnits (const vstr &properties, const vstr &units)-> void; @@ -104,22 +111,28 @@ class ThermoBatch auto setPropertyUnit (const std::string &property, const std::string &unit)-> void; auto setPropertyDigit (const std::string &property, const int &digit)-> void; auto setPropertyUnitDigit (const std::string &property, const std::string &unit, const int &digit)-> void; + auto setTemperatureIncrement (const double& Tmin, const double& Tmax, const double& Tstep) -> void; + auto setPressureIncrement (const double& Pmin, const double& Pmax, const double& Pstep) -> void; // claculate functions substances auto thermoPropertiesSubstance (double T, double P, std::string symbol, std::string property) -> Output; auto thermoPropertiesSubstance (double T, double P, vstr symbols, vstr properties) -> Output; - auto thermoPropertiesSubstance (std::array aT, std::array aP, vstr symbols, vstr properties) -> Output; + auto thermoPropertiesSubstance (vstr symbols, vstr properties) -> Output; auto thermoPropertiesSubstance (vvd tpPairs, vstr symbols, vstr properties) -> Output; auto thermoPropertiesSubstance (vvd tpPairs, vstr symbols, vstr properties, vtps vTps) -> Output; + auto thermoPropertiesSubstance (std::vector temperatures, std::vector pressures, vstr symbols, vstr properties) -> Output; + auto thermoPropertiesSubstance (std::vector temperatures, std::vector pressures, vstr symbols, vstr properties, vtps vTps) -> Output; // claculate functions reactions auto thermoPropertiesReaction (double T, double P, std::string symbol, std::string property) -> Output; auto thermoPropertiesReaction (double T, double P, vstr symbols, vstr properties) -> Output; - auto thermoPropertiesReaction (std::array aT, std::array aP, vstr symbols, vstr properties) -> Output; + auto thermoPropertiesReaction (vstr symbols, vstr properties) -> Output; auto thermoPropertiesReaction (vvd tpPairs, vstr symbols, vstr properties) -> Output; auto thermoPropertiesReaction (vvd tpPairs, vstr symbols, vstr properties, vtpr vTpr) -> Output; + auto thermoPropertiesReaction (std::vector temperatures, std::vector pressures, vstr symbols, vstr properties) -> Output; + auto thermoPropertiesReaction (std::vector temperatures, std::vector pressures, vstr symbols, vstr properties, vtpr vTpr) -> Output; - auto setBatchPreferences (const BatchPreferences &value) -> void; + auto setBatchPreferences (const BatchPreferences &value) -> void; auto setSolventSymbol (const std::string solventSymbol) ->void; private: @@ -131,6 +144,8 @@ class ThermoBatch auto results () -> const vvThScalar; auto TPpairs () -> const vvd; + auto Temperatures () -> const std::vector ; + auto Pressures () -> const std::vector ; auto properties () -> const vstr; auto units () -> const std::map; auto digits () -> const std::map; @@ -289,6 +304,20 @@ const std::map defaultPropertyDigits = {"lnK0", 0 } }; +const std::map defaultTemperatureIncrement = +{ + {"Tmin", 25.}, + {"Tmax", 300.}, + {"Tstep", 25.} +}; + +const std::map defaultPressureIncrement = +{ + {"Pmin", 0.}, + {"Pmax", 0.}, + {"Pstep", 0.} +}; + } diff --git a/ThermoFun/Common/ParseJsonToData.cpp b/ThermoFun/Common/ParseJsonToData.cpp index a7fe11c9..f1d64efd 100644 --- a/ThermoFun/Common/ParseJsonToData.cpp +++ b/ThermoFun/Common/ParseJsonToData.cpp @@ -433,11 +433,11 @@ auto parseElement(const std::string &data) -> Element if (!j["isotope_mass"].is_null()) e.setIsotopeMass(j["isotope_mass"].get()); } - catch (json::exception &e) + catch (json::exception &ex) { // output exception information - std::cout << "message: " << e.what() << '\n' - << "exception id: " << e.id << std::endl; + std::cout << "message: " << ex.what() << '\n' + << "exception id: " << ex.id << std::endl; } return e; diff --git a/ThermoFun/Common/ThermoOmp.cpp b/ThermoFun/Common/ThermoOmp.cpp new file mode 100644 index 00000000..e69de29b diff --git a/ThermoFun/Common/ThermoOmp.h b/ThermoFun/Common/ThermoOmp.h new file mode 100644 index 00000000..f5822d81 --- /dev/null +++ b/ThermoFun/Common/ThermoOmp.h @@ -0,0 +1,4 @@ +#ifndef THERMOOMP_H +#define THERMOOMP_H + +#endif // THERMOOMP_H diff --git a/ThermoFun/Database.cpp b/ThermoFun/Database.cpp index 65111f16..bbdee496 100644 --- a/ThermoFun/Database.cpp +++ b/ThermoFun/Database.cpp @@ -18,13 +18,13 @@ using json = nlohmann::json; namespace ThermoFun { -auto errorNonExistent(std::string type, std::string name, int line) -> void +[[ noreturn ]] auto errorNonExistent(std::string type, std::string name, int line) -> void { Exception exception; exception.error << "Cannot get an instance of the " << type << " `" << name << "` in the database."; exception.reason << "There is no such " << type << " in the database."; exception.line = line; - RaiseError(exception); + RaiseError(exception) } @@ -63,45 +63,58 @@ struct Database::Impl Impl(vector jsons) { - string _label; - flog.open(parsinglogfile, ios::trunc); flog.close(); + try { + string _label; + flog.open(parsinglogfile, ios::trunc); flog.close(); - for (int i=0; i(); + if (j.contains("properties")) + if (!j["properties"].is_null()) + properties = j["properties"]; + if (j.contains("_label")) + if (!j["_label"].is_null()) + _label = j["_label"].get(); - if (_label == "substance") - { - Substance substance = parseSubstance(properties.dump()); - substances_map[substance.symbol()] = substance; - } else - if (_label == "reaction") - { - Reaction reaction = parseReaction(properties.dump()); - reactions_map[reaction.symbol()] = reaction; - } else - if (_label == "element") - { - Element element = parseElement(properties.dump()); - elements_map[element.symbol()] = element; - } else - { - Exception exception; - exception.error << "Unknown JSON type " << _label << " "; - exception.reason << "The JSON object needs to be a substance or reaction."; - exception.line = __LINE__; - RaiseError(exception); + auto props = properties.dump(); + + if (_label == "substance") + { + Substance substance = parseSubstance(props); + substance.setJsonString(props); + substances_map[substance.symbol()] = substance; + } else + if (_label == "reaction") + { + Reaction reaction = parseReaction(props); + reaction.setJsonString(props); + reactions_map[reaction.symbol()] = reaction; + } else + if (_label == "element") + { + Element element = parseElement(props); + element.setJsonString(props); + elements_map[element.symbol()] = element; + } else + { + Exception exception; + exception.error << "Unknown JSON type " << _label << " "; + exception.reason << "The JSON object needs to be a substance or reaction."; + exception.line = __LINE__; + RaiseError(exception) + } + if (elements_map.size()>0) + ChemicalFormula::setDBElements( elements_map ); } - if (elements_map.size()>0) - ChemicalFormula::setDBElements( elements_map ); + } catch (json::exception &ex) + { + // output exception information + std::cout << "message: " << ex.what() << '\n' + << "exception id: " << ex.id << std::endl; } + } template @@ -180,17 +193,17 @@ struct Database::Impl // reaction.second.calcParameters(); // } - auto numberOfElements() -> int + auto numberOfElements() -> size_t { return collectValues(elements_map).size(); } - auto numberOfSubstances() -> int + auto numberOfSubstances() -> size_t { return collectValues(substances_map).size(); } - auto numberOfReactions() -> int + auto numberOfReactions() -> size_t { return collectValues(reactions_map).size(); } @@ -253,47 +266,60 @@ struct Database::Impl /// @param filename name of the file (in the working directory) auto parseJson(std::string filename) -> void { - std::ifstream ifs(filename); - if (!ifs.good()) - funError("File reading error", "Database file not found!", __LINE__, __FILE__); - json j = json::parse(ifs); - std::string _label; - - for(auto it = j.begin(); it != j.end(); ++it) - { - auto properties = it.value(); - if (it.value().contains("properties")) - if (!it.value()["properties"].is_null()) - properties = it.value()["properties"]; - if (it.value().contains("_label")) - if (!it.value()["_label"].is_null()) - _label = it.value()["_label"].get(); - - if (_label == "substance") + try { + std::ifstream ifs(filename); + if (!ifs.good()) + funError("File reading error", std::string("Database file "+ filename +" not found!"), __LINE__, __FILE__); + json j = json::parse(ifs); + std::string _label; + + for(auto it = j.begin(); it != j.end(); ++it) { - Substance substance = parseSubstance(properties.dump()); - substances_map[substance.symbol()] = substance; - } else - if (_label == "reaction") + auto properties = it.value(); + if (it.value().contains("properties")) + if (!it.value()["properties"].is_null()) + properties = it.value()["properties"]; + if (it.value().contains("_label")) + if (!it.value()["_label"].is_null()) + _label = it.value()["_label"].get(); + + auto props = properties.dump(); + + if (_label == "substance") { - Reaction reaction = parseReaction(properties.dump()); - reactions_map[reaction.symbol()] = reaction; + Substance substance = parseSubstance(props); + substance.setJsonString(props); + substances_map[substance.symbol()] = substance; } else - if (_label == "element") - { - Element element = parseElement(properties.dump()); - elements_map[element.symbol()] = element; - } - else + if (_label == "reaction") { - Exception exception; - exception.error << "Unknown JSON type " << _label << " "; - exception.reason << "The JSON object needs to be an element, a substance or a reaction file " << filename << "."; - exception.line = __LINE__; - RaiseError(exception); - } + Reaction reaction = parseReaction(props); + reaction.setJsonString(props); + reactions_map[reaction.symbol()] = reaction; + } else + if (_label == "element") + { + Element element = parseElement(props); + element.setJsonString(props); + elements_map[element.symbol()] = element; + } + else + { + Exception exception; + exception.error << "Unknown JSON type " << _label << " "; + exception.reason << "The JSON object needs to be an element, a substance or a reaction file " << filename << "."; + exception.line = __LINE__; + RaiseError(exception) + } + } + } catch (json::exception &ex) + { + // output exception information + std::cout << "message: " << ex.what() << '\n' + << "exception id: " << ex.id << std::endl; } + } }; @@ -418,17 +444,17 @@ auto Database::getReactions() -> std::vector return pimpl->getReactions(); } -auto Database::numberOfElements() -> int +auto Database::numberOfElements() -> size_t { return pimpl->numberOfElements(); } -auto Database::numberOfSubstances() -> int +auto Database::numberOfSubstances() -> size_t { return pimpl->numberOfSubstances(); } -auto Database::numberOfReactions() -> int +auto Database::numberOfReactions() -> size_t { return pimpl->numberOfReactions(); } diff --git a/ThermoFun/Database.h b/ThermoFun/Database.h index 383dd716..be3b85dc 100644 --- a/ThermoFun/Database.h +++ b/ThermoFun/Database.h @@ -103,13 +103,13 @@ class Database auto mapReactions() const -> const ReactionsMap&; /// Returns the number of elements in the databse - auto numberOfElements() -> int; + auto numberOfElements() -> size_t; /// Returns the number of substances in the databse - auto numberOfSubstances() -> int; + auto numberOfSubstances() -> size_t; /// Returns the number of reactions in the database - auto numberOfReactions() -> int; + auto numberOfReactions() -> size_t; /// Return a element in the database auto getElement(std::string symbol) const -> const Element&; diff --git a/ThermoFun/Element.cpp b/ThermoFun/Element.cpp index b2abe716..1120645e 100644 --- a/ThermoFun/Element.cpp +++ b/ThermoFun/Element.cpp @@ -33,6 +33,8 @@ struct Element::Impl /// Element Mendeleev table number int number; + + std::string jString; }; Element::Element() @@ -89,6 +91,11 @@ auto Element::setNumber(int value) -> void pimpl->number = value; } +auto Element::setJsonString(const std::string &jString) ->void +{ + pimpl->jString = jString; +} + auto Element::name() const -> std::string { return pimpl->name; @@ -139,6 +146,11 @@ auto Element::number() const -> int return pimpl->number; } +auto Element::jsonString() const -> std::string +{ + return pimpl->jString; +} + auto operator<(const Element& lhs, const Element& rhs) -> bool { if (lhs.symbol() < rhs.symbol()) diff --git a/ThermoFun/Element.h b/ThermoFun/Element.h index 7e17700b..ad69a989 100644 --- a/ThermoFun/Element.h +++ b/ThermoFun/Element.h @@ -44,6 +44,12 @@ class Element /// Set the element Mendeleev table number auto setNumber(int value) -> void; + /** + * @brief setJsonString stores the json object of the record + * @param jString + */ + auto setJsonString(const std::string &jString) ->void; + /// Return the name of the element auto name() const -> std::string; @@ -74,6 +80,12 @@ class Element /// Return the Mendeleev table number of the element auto number() const -> int; + /** + * @brief jonString + * @return record in json string + */ + auto jsonString() const -> std::string; + private: struct Impl; diff --git a/ThermoFun/Reaction.cpp b/ThermoFun/Reaction.cpp index ed8abbff..7632179e 100644 --- a/ThermoFun/Reaction.cpp +++ b/ThermoFun/Reaction.cpp @@ -61,6 +61,7 @@ struct Reaction::Impl /// Upper pressure limit (in Pa) double upper_P; + std::string jString; }; Reaction::Reaction() @@ -155,6 +156,11 @@ auto Reaction::setEquation(std::string equation) -> void pimpl->equation = equation; } +auto Reaction::setJsonString(const std::string &jString) ->void +{ + pimpl->jString = jString; +} + auto Reaction::name() const -> std::string { return pimpl->name; @@ -230,6 +236,11 @@ auto Reaction::equation() const -> std::string return pimpl->equation; } +auto Reaction::jsonString() const -> std::string +{ + return pimpl->jString; +} + auto Reaction::checkCalcMethodBounds(string modelName, double T, double P, ThermoPropertiesReaction &tpr) -> void { if (pimpl->upper_P<(P) || pimpl->upper_T<(T) || diff --git a/ThermoFun/Reaction.h b/ThermoFun/Reaction.h index db28a751..42f4e88c 100644 --- a/ThermoFun/Reaction.h +++ b/ThermoFun/Reaction.h @@ -77,6 +77,12 @@ class Reaction /// Set the parameters used for calculating the proeprties of reaction at T and P auto setThermoParameters(ThermoParametersReaction param) -> void; + /** + * @brief setJsonString stores the json object of the record + * @param jString + */ + auto setJsonString(const std::string &jString) ->void; + // /// Set the formula of the Reaction. // auto setFormula(std::string formula) -> void; @@ -129,6 +135,12 @@ class Reaction /// Return the pressure correction method code auto method_P() const -> MethodCorrP_Thrift::type; + /** + * @brief jonString + * @return record in json string + */ + auto jsonString() const -> std::string; + /// Checks if the method of clauclation is out of provided T and P bounds. If out of bounds sets the corresponding message /// inside the property status /// @param modelName Given model name diff --git a/ThermoFun/Substance.cpp b/ThermoFun/Substance.cpp index bd653bd4..cae85db4 100644 --- a/ThermoFun/Substance.cpp +++ b/ThermoFun/Substance.cpp @@ -74,6 +74,8 @@ struct Substance::Impl int charge; + std::string jString; + // /// Concentration scale used in defining the properties of the substance // ConcentrationScales::type StdConcentration_scale; }; @@ -195,6 +197,11 @@ auto Substance::setMolarMass(double molar_mass) -> void pimpl->molar_mass = molar_mass; } +auto Substance::setJsonString(const std::string &jString) ->void +{ + pimpl->jString = jString; +} + auto Substance::name() const -> std::string { return pimpl->name; @@ -300,6 +307,11 @@ auto Substance::charge() const -> int return pimpl->charge; } +auto Substance::jsonString() const -> std::string +{ + return pimpl->jString; +} + auto Substance::checkCalcMethodBounds(string modelName, double T, double P, ThermoPropertiesSubstance &tps) -> void { if (pimpl->upper_P<(P) || pimpl->upper_T<(T) || diff --git a/ThermoFun/Substance.h b/ThermoFun/Substance.h index 12dbdbdd..db6e38da 100644 --- a/ThermoFun/Substance.h +++ b/ThermoFun/Substance.h @@ -98,6 +98,12 @@ class Substance * @param P pressure in Pa */ auto setReferenceP(double P) -> void; + + /** + * @brief setJsonString stores the json object of the record + * @param jString + */ + auto setJsonString(const std::string &jString) ->void; // Get functions /// Return the name of the chemical Substance @@ -169,6 +175,12 @@ class Substance */ auto charge() const -> int; + /** + * @brief jonString + * @return record in json string + */ + auto jsonString() const -> std::string; + /// Checks if the method of clauclation is out of provided T and P bounds. If out of bounds sets the corresponding message /// inside the property status /// @param modelName Given model name diff --git a/ThermoFun/Substances/Gases/GasCORK.cpp b/ThermoFun/Substances/Gases/GasCORK.cpp index e04565b2..d12075bd 100644 --- a/ThermoFun/Substances/Gases/GasCORK.cpp +++ b/ThermoFun/Substances/Gases/GasCORK.cpp @@ -9,7 +9,7 @@ namespace ThermoFun { auto thermoPropertiesGasCORK(Reaktoro_::Temperature TK, Reaktoro_::Pressure Pbar, Substance subst, ThermoPropertiesSubstance tps) -> ThermoPropertiesSubstance { double FugProps[6]; - char Eos_Code; + char Eos_Code = 'G'; if (Pbar.val == 0.0) Pbar += 1e-5; diff --git a/ThermoFun/Substances/Solute/SoluteHKFgems.cpp b/ThermoFun/Substances/Solute/SoluteHKFgems.cpp index 06d0526a..4dabbbe8 100644 --- a/ThermoFun/Substances/Solute/SoluteHKFgems.cpp +++ b/ThermoFun/Substances/Solute/SoluteHKFgems.cpp @@ -175,12 +175,14 @@ auto gShok2(Reaktoro_::Temperature TC, Reaktoro_::Pressure Pbar, const Propertie if (D.val >= 1.4) { - Exception exception; - exception.error << "Error in gShock2"; - exception.reason << "water density higher than 1.4 g*cm-3, Dw = " - << D.val << "g*cm-3."; - exception.line = __LINE__; - RaiseError(exception); + std::cout << "water density higher than 1.4 g*cm-3, Dw = " + << ps.density / 1000 << "g*cm-3." << std::endl << __FILE__ << std::endl << __LINE__; +// Exception exception; +// exception.error << "Error in gShock2"; +// exception.reason << "water density higher than 1.4 g*cm-3, Dw = " +// << D.val << "g*cm-3."; +// exception.line = __LINE__; +// RaiseError(exception); } // Check if the point (T,P) is inside region III or the shaded region in Fig. 6 of diff --git a/ThermoFun/Substances/Solute/SoluteHKFreaktoro.cpp b/ThermoFun/Substances/Solute/SoluteHKFreaktoro.cpp index e5b349f5..b94eb2f1 100644 --- a/ThermoFun/Substances/Solute/SoluteHKFreaktoro.cpp +++ b/ThermoFun/Substances/Solute/SoluteHKFreaktoro.cpp @@ -213,7 +213,8 @@ auto functionG(Reaktoro_::Temperature T, Reaktoro_::Pressure P, const Properties // Check if the point (T,P) is inside region III or the shaded region in Fig. 6 of // Shock and others (1992), on page 809. In this case, we assume the g function to be zero. - if(ps.density > 1000.0 || ps.density < 350.0) + //if(ps.density > 1000.0 || ps.density < 350.0) + if(ps.density > 1000.0) return funcG; // Auxiliary references diff --git a/ThermoFun/Substances/Solvent/WaterHGK-JNgems.cpp b/ThermoFun/Substances/Solvent/WaterHGK-JNgems.cpp index 9f564c8d..e898b67c 100644 --- a/ThermoFun/Substances/Solvent/WaterHGK-JNgems.cpp +++ b/ThermoFun/Substances/Solvent/WaterHGK-JNgems.cpp @@ -143,7 +143,7 @@ auto WaterHGKgems::propertiesWaterHGKgems(int state) -> PropertiesSolvent wp.densityTT = rho * ( pow(alp,2.) - dal ); wp.densityP = bet * rho; // wp.densityPP = -// wp.pressure = P; + wp.pressure = aSta.Pres*1e5; return wp; } diff --git a/ThermoFun/ThermoEngine.cpp b/ThermoFun/ThermoEngine.cpp index 30b25d6c..b3574665 100644 --- a/ThermoFun/ThermoEngine.cpp +++ b/ThermoFun/ThermoEngine.cpp @@ -170,7 +170,8 @@ struct ThermoEngine::Impl preferences.solventState = 0; // liquid // check if the substance is reaction dependent - if (preferences.workSubstance.thermoCalculationType() == SubstanceThermoCalculationType::type::REACDC) + if ((preferences.workSubstance.thermoCalculationType() == SubstanceThermoCalculationType::type::REACDC) || + (!preferences.method_genEOS && !preferences.method_P && !preferences.method_T)) preferences.isReacDC = true; else preferences.isReacDC = false; @@ -620,6 +621,10 @@ ThermoEngine::ThermoEngine(const Database& database) : pimpl(new Impl(database)) {} +ThermoEngine::ThermoEngine(const ThermoEngine& other) +: pimpl(new Impl(*other.pimpl)) +{} + auto ThermoEngine::thermoPropertiesSubstance(double T, double &P, std::string substance) -> ThermoPropertiesSubstance { return pimpl->thermo_properties_substance_fn(T, P, P, substance); diff --git a/ThermoFun/ThermoEngine.h b/ThermoFun/ThermoEngine.h index e87fcb71..c753b222 100644 --- a/ThermoFun/ThermoEngine.h +++ b/ThermoFun/ThermoEngine.h @@ -36,6 +36,9 @@ class ThermoEngine /// Construct a Thermo instance with given Database instance ThermoEngine(const Database& database); + /// Construct a copy of an ThermoEngine instance + ThermoEngine(const ThermoEngine& other); + /// Sets the symbol of the solvent which is used to calculate properties using the thermo instance auto setSolventSymbol(const std::string solvent_symbol) -> void; diff --git a/ThermoFunGui/CMakeLists.txt b/ThermoFunGui/CMakeLists.txt deleted file mode 100644 index c6012448..00000000 --- a/ThermoFunGui/CMakeLists.txt +++ /dev/null @@ -1,83 +0,0 @@ -# Require a certain version of cmake -cmake_minimum_required(VERSION 3.0) - -# Set the name of the project -project(ThermoFunGui VERSION 0.1.5 LANGUAGES CXX) - -# Set the cmake module path of the project -#set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake/modules") - -#set(CMAKE_MACOSX_RPATH ON) - -find_package(Qt5Widgets REQUIRED) -if ( NOT Qt5Widgets_FOUND ) - message(FATAL_ERROR "Package Qt5 required, but not found!") -endif( NOT Qt5Widgets_FOUND ) - -find_package(Qt5Core REQUIRED) -find_package(Qt5Gui REQUIRED) -find_package(Qt5PrintSupport REQUIRED) -find_package (Qt5WebEngineWidgets REQUIRED ) -find_package (Qt5Charts REQUIRED ) -find_package (Qt5Concurrent REQUIRED ) -# Add the include directories for the Qt 5 Widgets module to -# the compile lines. -include_directories(${Qt5Widgets_INCLUDE_DIRS}) -include_directories(${Qt5Core_INCLUDE_DIRS}) -include_directories(${Qt5Gui_INCLUDE_DIRS}) -include_directories(${Qt5PrintSupport_INCLUDE_DIRS}) -include_directories(${Qt5WebEngineWidgets_INCLUDE_DIRS}) -include_directories(${Qt5Concurrent_INCLUDE_DIRS}) - -find_library(JSONUI_LIB jsonui) -if(NOT JSONUI_LIB) - message(FATAL_ERROR "jsonui library not found") -endif() - -find_library(THRIFT_LIB thrift) -if(NOT THRIFT_LIB) - message(FATAL_ERROR "thrift library not found") -endif() - -# Set the default build type to Release -if(NOT CMAKE_BUILD_TYPE) - message(STATUS "Setting build type to 'Release' as none was specified.") - set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build." FORCE) - set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release" "MinSizeRel" "RelWithDebInfo") -endif() - -# Define variables with the GNU standard installation directories -include(GNUInstallDirs) - -# Define which types of libraries to build -option(TFUN_BUILD_SHARED_LIBS "Build shared libraries." ON) -option(TFUN_BUILD_STATIC_LIBS "Build static libraries." ON) - -# Set the thermofun source directory path -set(THERMOFUNGUI_SOURCE_DIR ${CMAKE_SOURCE_DIR}/ThermoFunGui/src) - -# Set the directory where the third-party libraries are temporarily installed before installed to CMAKE_INSTALL_PREFIX -#set(THIRDPARTY_DIR ${CMAKE_BINARY_DIR}/thirdparty) - -# Set the include and library directories where the third party libraries were installed -#set(THIRDPARTY_INCLUDE_DIR ${THIRDPARTY_DIR}/include) -#set(THIRDPARTY_LIBRARY_DIR ${THIRDPARTY_DIR}/lib) - -# Install the third-party libraries first -#include(InstallThirdPartyLibs) - -# Set the include directories -include_directories(${THERMOFUNGUI_SOURCE_DIR}) -#include_directories(${THIRDPARTY_INCLUDE_DIR}) - -# Set the lib directory of the third party libraries installed automatically -#link_directories(${THIRDPARTY_LIBRARY_DIR}) - -# Build thermofun library -add_subdirectory(src) - -if(TFUN_BUILD_GUIDEMO) - add_subdirectory(demo) -#else() -# add_subdirectory(demo EXCLUDE_FROM_ALL) -endif() diff --git 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mode 100644 index 670a9932..00000000 --- a/ThermoFunGui/ThermoFunDemoGUI.pro.user +++ /dev/null @@ -1,214 +0,0 @@ - - - - - - EnvironmentId - {70dfe32a-3b07-4c3c-b4aa-de333d567f37} - - - ProjectExplorer.Project.ActiveTarget - 0 - - - ProjectExplorer.Project.EditorSettings - - true - false - true - - Cpp - - CppGlobal - - - - QmlJS - - QmlJSGlobal - - - 2 - UTF-8 - false - 4 - false - 80 - true - true - 1 - true - false - 0 - true - true - 0 - 8 - true - 1 - true - true - true - false - - - - ProjectExplorer.Project.PluginSettings - - - true - - - - ProjectExplorer.Project.Target.0 - - Desktop Qt 5.11.2 GCC 64bit - Desktop Qt 5.11.2 GCC 64bit - qt.qt5.5112.gcc_64_kit - 0 - 0 - 0 - - /home/dmiron/gitTHERMOFUN/build-demogui/debug - - - true - qmake - - QtProjectManager.QMakeBuildStep - true - - false - false - false - - - true - Make - - Qt4ProjectManager.MakeStep - - false - - - false - - 2 - Build - - ProjectExplorer.BuildSteps.Build - - - - true - Make - - Qt4ProjectManager.MakeStep - - true - clean - - false - - 1 - Clean - - ProjectExplorer.BuildSteps.Clean - - 2 - false - - Debug - Debug - Qt4ProjectManager.Qt4BuildConfiguration - 2 - true - - 1 - - - 0 - Deploy - - ProjectExplorer.BuildSteps.Deploy - - 1 - Deploy Configuration - - ProjectExplorer.DefaultDeployConfiguration - - 1 - - - false - false - 1000 - - true - - false - false - false - false - true - 0.01 - 10 - true - 1 - 25 - - 1 - true - false - true - valgrind - - 0 - 1 - 2 - 3 - 4 - 5 - 6 - 7 - 8 - 9 - 10 - 11 - 12 - 13 - 14 - - 2 - - ThermoFunDemoGUI - ThermoFunDemoGUI2 - Qt4ProjectManager.Qt4RunConfiguration:/home/dmiron/gitTHERMOFUN/thermofun/ThermoFunGui/ThermoFunDemoGUI.pro - ThermoFunDemoGUI.pro - - 3768 - false - true - true - false - false - true - - /home/dmiron/gitTHERMOFUN/build-demogui/debug - - 1 - - - - ProjectExplorer.Project.TargetCount - 1 - - - ProjectExplorer.Project.Updater.FileVersion - 20 - - - Version - 20 - - diff --git a/ThermoFunGui/ThermoFunGuiDemo.pro b/ThermoFunGui/ThermoFunGuiDemo.pro deleted file mode 100644 index 81f3be27..00000000 --- a/ThermoFunGui/ThermoFunGuiDemo.pro +++ /dev/null @@ -1,144 +0,0 @@ -#------------------------------------------------- -# -# Project created by QtCreator 2016-02-08T16:01:53 -# -#------------------------------------------------- - - -TARGET = ThermoFunDemoGui -TEMPLATE = app - -CONFIG += thread -CONFIG += c++11 -CONFIG += warn_on - -#QMAKE_CXXFLAGS_RELEASE = -Wpedantic -#QMAKE_CFLAGS_RELEASE = -Wno-unknown-pragmas -Wpedantic - -DEFINES += FROM_SRC - -win32:DEFINES += NO_QWEBENGINE - -!win32 { - DEFINES += __unix -} else -{ - DEFINES += IMPEX_OFF -} - -QT += core gui widgets -QT += svg printsupport concurrent -QT += charts - -!contains(DEFINES, NO_QWEBENGINE) { - QT += webenginewidgets -} - - -# Define the directory where source code is located -#THRIFT_DIR = ./thrift -FUN_DIR = ../ThermoFun -FUN_CPP = $$FUN_DIR -FUN_H = $$FUN_DIR -GUI_DIR = ./src -GUI_CPP = $$GUI_DIR -GUI_H = $$GUI_DIR -CLIENT_DIR = ../ThermoHubClient -CLIENT_CPP = $$CLIENT_DIR -CLIENT_H = $$CLIENT_DIR -#GUI_CPP = ./GUI -#GUI_H = $$GUI_CPP - -DEPENDPATH += $$GUI_H -DEPENDPATH += $$GUI_DIR - -INCLUDEPATH += $$GUI_H -INCLUDEPATH += $$GUI_DIR - -DEPENDPATH += $$FUN_H -DEPENDPATH += $$FUN_DIR - -INCLUDEPATH += $$FUN_H -INCLUDEPATH += $$FUN_DIR - -DEPENDPATH += $$CLIENT_H -DEPENDPATH += $$CLIENT_DIR - -INCLUDEPATH += $$CLIENT_H -INCLUDEPATH += $$CLIENT_DIR - -macx-clang { - DEFINES += __APPLE__ - CONFIG -= warn_on - CONFIG += warn_off - INCLUDEPATH += "/usr/local/include" - DEPENDPATH += "/usr/local/include" - LIBPATH += "/usr/local/lib/" -} - -!win32 { - - INCLUDEPATH += "/usr/local/include" - DEPENDPATH += "/usr/local/include" - LIBPATH += "/usr/local/lib" - - ## Markdown editor - contains(DEFINES, USE_MARKDOWN) { - LIBS += -lmarkdown - } - else - { - contains(DEFINES, NO_QWEBENGINE) { - LIBS += -lmarkdown - } - } - - LIBS += -ljsonui -ljsonio -ljsonimpex - LIBS += -lyaml-cpp -lpugixml - LIBS += -lboost_regex -lboost_system -lboost_filesystem - LIBS += -lcurl -lvelocypack -lthrift - - !macx-clang:LIBS += -llua5.3 -} - -MOC_DIR = tmp -UI_DIR = $$MOC_DIR -UI_SOURSEDIR = $$MOC_DIR -UI_HEADERDIR = $$MOC_DIR -OBJECTS_DIR = obj - -#include($$THRIFT_DIR/thrift.pri) -#include($$GEN_DIR/generator.pri) -include($$GUI_DIR/ThermoFunGui.pri) -include($$CLIENT_DIR/ThermoHubClient.pri) -include($$FUN_DIR/ThermoFun.pri) - -RESOURCES += \ - ThermoFunGuiDemo.qrc - -#thrift -r -v --gen cpp - -SOURCES += \ - demo/main.cpp \ - demo/ThermoFunMainWindow.cpp - -HEADERS += \ - demo/ThermoFunMainWindow.h - -FORMS += \ - demo/ThermoFunMainWindow.ui - -win32 { - QT += webenginewidgets - QMAKE_CXXFLAGS_WARN_ON = -wd4068 -wd4138 -} - -win32:DEFINES += IMPEX_OFF -win32:CONFIG(release, debug|release): LIBS += -L$$PWD/../../dependencies/lib-dll-release-x64/ -llibcurl -win32:CONFIG(release, debug|release): LIBS += -L$$PWD/../../dependencies/lib-static-release-x64/ -lvelocypack -llibboost_regex* -llibboost_filesystem-vc-mt* -llibboost_system* -llibjsonio -llibjsonui - -win32:CONFIG(debug, debug|release): LIBS += -L$$PWD/../../dependencies/lib-dll-debug-x64/ -llibcurl_debug -win32:CONFIG(debug, debug|release): LIBS += -L$$PWD/../../dependencies/lib-static-debug-x64/ -lvelocypack -llibboost_regex* -llibboost_filesystem* -llibboost_system* -llibjsonio -llibjsonui -win32:INCLUDEPATH += $$PWD/../../dependencies/include -win32:DEPENDPATH += $$PWD/../../dependencies/include - diff --git a/ThermoFunGui/ThermoFunGuiDemo.qrc b/ThermoFunGui/ThermoFunGuiDemo.qrc deleted file mode 100644 index 2442177d..00000000 --- a/ThermoFunGui/ThermoFunGuiDemo.qrc +++ /dev/null @@ -1,295 +0,0 @@ - - - Icons/outgoing24.png - Icons/outgoing200.png - Icons/outgoing.png - Icons/icons_files_gems3mdi_2012_GG.doc - Icons/icons_files_gems3mdi.odt - Icons/icons_files_gems3mdi.doc - Icons/gems512.png - Icons/gems50.png - Icons/gems24.png - Icons/gems1024.png - Icons/gems1.png - Icons/WarningMessageIcon24.png - 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-set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/modules") - -# Set the default build type to Release -if(NOT CMAKE_BUILD_TYPE) - message(STATUS "Setting build type to 'Release' as none was specified.") - set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build." FORCE) - set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release" "MinSizeRel" "RelWithDebInfo") -endif() - -# Set the directory where the third-party libraries are temporarily installed before installed to CMAKE_INSTALL_PREFIX -set(THIRDPARTY_DIR ${CMAKE_INSTALL_PREFIX}) - -# Install the third-party libraries first -include(InstallThirdPartyLibs) diff --git a/ThermoFunGui/ThirdParty/InstallThirdParty.cmake b/ThermoFunGui/ThirdParty/InstallThirdParty.cmake deleted file mode 100644 index 0c4c0640..00000000 --- a/ThermoFunGui/ThirdParty/InstallThirdParty.cmake +++ /dev/null @@ -1,56 +0,0 @@ -# Include the ExternalProject module -include(ExternalProject) - -# Ignore all warning from the third-party libraries -if(CMAKE_COMPILER_IS_GNUCXX) - add_definitions("-w") -endif() - -# Set the list of compiler flags for the external projects -if(NOT ${CMAKE_SYSTEM_NAME} MATCHES "Windows") - set(CXXFLAGS "-fPIC") -endif() - -option(BUILD_THIRDPARTY "Build thirdparty libaries." OFF) -set(BUILD_THIRDPARTY OFF) - -if (REFRESH_THIRDPARTY) - set(BUILD_THIRDPARTY ON) -else () - find_library(JSONUI_LIB jsonui PATHS /usr/local/lib NO_DEFAULT_PATH) - if(NOT JSONUI_LIB) - set(BUILD_THIRDPARTY ON) - endif() -endif() - -if (BUILD_THIRDPARTY) -# Download and install the bsonui library -ExternalProject_Add(JSONUI - PREFIX thirdparty - GIT_REPOSITORY https://bitbucket.org/gems4/jsonui.git -# GIT_TAG impex-move - UPDATE_COMMAND "" - CMAKE_ARGS -DCMAKE_PREFIX_PATH:PATH=${CMAKE_PREFIX_PATH} - CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${THIRDPARTY_DIR} - -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} - -DCMAKE_CXX_FLAGS=${CXXFLAGS} - -DCMAKE_INSTALL_INCLUDEDIR=include - -DCMAKE_INSTALL_LIBDIR=lib - -DCMAKE_INSTALL_BINDIR=bin - -DBUILD_SHARED_LIBS=ON -) - - -# Create the install target for the third-party libraries -install(DIRECTORY ${THIRDPARTY_DIR}/lib - DESTINATION /usr/local) -install(DIRECTORY ${THIRDPARTY_DIR}/include - DESTINATION /usr/local) -#install(DIRECTORY ${THIRDPARTY_DIR}/lib -# DESTINATION .) -#install(DIRECTORY ${THIRDPARTY_DIR}/include -# DESTINATION .) - -else () - message(STATUS "JSONUI already present at /usr/local/lib. CMake will Stop. \n Use -DREFRESH_THIRDPARTY=ON to reinstall ThirdParty") -endif() diff --git a/ThermoFunGui/ThirdParty/modules/InstallThirdParty.cmake b/ThermoFunGui/ThirdParty/modules/InstallThirdParty.cmake deleted file mode 100644 index 92b3c1a0..00000000 --- a/ThermoFunGui/ThirdParty/modules/InstallThirdParty.cmake +++ /dev/null @@ -1,57 +0,0 @@ -# Include the ExternalProject module -include(ExternalProject) - -# Ignore all warning from the third-party libraries -if(CMAKE_COMPILER_IS_GNUCXX) - add_definitions("-w") -endif() - -# Set the list of compiler flags for the external projects -if(NOT ${CMAKE_SYSTEM_NAME} MATCHES "Windows") - set(CXXFLAGS "-fPIC") -endif() - -option(BUILD_THIRDPARTY "Build thirdparty libaries." OFF) -set(BUILD_THIRDPARTY OFF) - -if (REFRESH_THIRDPARTY) - set(BUILD_THIRDPARTY ON) -else () - find_library(JSONUI_LIB jsonui PATHS /usr/local/lib NO_DEFAULT_PATH) - if(NOT JSONUI_LIB) - set(BUILD_THIRDPARTY ON) - endif() -endif() - -if (BUILD_THIRDPARTY) -# Download and install the bsonui library -ExternalProject_Add(JSONUI - PREFIX thirdparty - GIT_REPOSITORY https://bitbucket.org/gems4/jsonui.git -# GIT_TAG impex-move - UPDATE_COMMAND "" - CMAKE_ARGS -DCMAKE_PREFIX_PATH:PATH=${CMAKE_PREFIX_PATH} - CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${THIRDPARTY_DIR} - -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} - -DCMAKE_CXX_FLAGS=${CXXFLAGS} - -DCMAKE_INSTALL_INCLUDEDIR=include - -DCMAKE_INSTALL_LIBDIR=lib - -DCMAKE_INSTALL_BINDIR=bin - -DREFRESH_THIRDPARTY=ON - -DBUILD_SHARED_LIBS=ON -) - - -# Create the install target for the third-party libraries -install(DIRECTORY ${THIRDPARTY_DIR}/lib - DESTINATION /usr/local) -install(DIRECTORY ${THIRDPARTY_DIR}/include - DESTINATION /usr/local) -#install(DIRECTORY ${THIRDPARTY_DIR}/lib -# DESTINATION .) -#install(DIRECTORY ${THIRDPARTY_DIR}/include -# DESTINATION .) - -else () - message(STATUS "JSONUI already present at /usr/local/lib. CMake will Stop. \n Use -DREFRESH_THIRDPARTY=ON to reinstall ThirdParty") -endif() diff --git a/ThermoFunGui/ThirdParty/modules/InstallThirdPartyLibs.cmake b/ThermoFunGui/ThirdParty/modules/InstallThirdPartyLibs.cmake deleted file mode 100644 index 0c4c0640..00000000 --- a/ThermoFunGui/ThirdParty/modules/InstallThirdPartyLibs.cmake +++ /dev/null @@ -1,56 +0,0 @@ -# Include the ExternalProject module -include(ExternalProject) - -# Ignore all warning from the third-party libraries -if(CMAKE_COMPILER_IS_GNUCXX) - add_definitions("-w") -endif() - -# Set the list of compiler flags for the external projects -if(NOT ${CMAKE_SYSTEM_NAME} MATCHES "Windows") - set(CXXFLAGS "-fPIC") -endif() - -option(BUILD_THIRDPARTY "Build thirdparty libaries." OFF) -set(BUILD_THIRDPARTY OFF) - -if (REFRESH_THIRDPARTY) - set(BUILD_THIRDPARTY ON) -else () - find_library(JSONUI_LIB jsonui PATHS /usr/local/lib NO_DEFAULT_PATH) - if(NOT JSONUI_LIB) - set(BUILD_THIRDPARTY ON) - endif() -endif() - -if (BUILD_THIRDPARTY) -# Download and install the bsonui library -ExternalProject_Add(JSONUI - PREFIX thirdparty - GIT_REPOSITORY https://bitbucket.org/gems4/jsonui.git -# GIT_TAG impex-move - UPDATE_COMMAND "" - CMAKE_ARGS -DCMAKE_PREFIX_PATH:PATH=${CMAKE_PREFIX_PATH} - CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${THIRDPARTY_DIR} - -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} - -DCMAKE_CXX_FLAGS=${CXXFLAGS} - -DCMAKE_INSTALL_INCLUDEDIR=include - -DCMAKE_INSTALL_LIBDIR=lib - -DCMAKE_INSTALL_BINDIR=bin - -DBUILD_SHARED_LIBS=ON -) - - -# Create the install target for the third-party libraries -install(DIRECTORY ${THIRDPARTY_DIR}/lib - DESTINATION /usr/local) -install(DIRECTORY ${THIRDPARTY_DIR}/include - DESTINATION /usr/local) -#install(DIRECTORY ${THIRDPARTY_DIR}/lib -# DESTINATION .) -#install(DIRECTORY ${THIRDPARTY_DIR}/include -# DESTINATION .) - -else () - message(STATUS "JSONUI already present at /usr/local/lib. CMake will Stop. \n Use -DREFRESH_THIRDPARTY=ON to reinstall ThirdParty") -endif() diff --git a/ThermoFunGui/demo/CMakeLists.txt b/ThermoFunGui/demo/CMakeLists.txt deleted file mode 100644 index e4121008..00000000 --- a/ThermoFunGui/demo/CMakeLists.txt +++ /dev/null @@ -1,81 +0,0 @@ -# Require a certain version of cmake -cmake_minimum_required(VERSION 3.0) - -# Set the name of the project -project(ThermoFunGuiDemo VERSION 0.1.5 LANGUAGES CXX) - -set(CMAKE_AUTORCC ON) - -add_definitions(-DFROM_SRC) - -find_package(Qt5Widgets REQUIRED) -if ( NOT Qt5Widgets_FOUND ) - message(FATAL_ERROR "Package Qt5 required, but not found!") -endif( NOT Qt5Widgets_FOUND ) - -find_package(Qt5Core REQUIRED) -find_package(Qt5Gui REQUIRED) -find_package(Qt5PrintSupport REQUIRED) -find_package (Qt5WebEngineWidgets REQUIRED ) -find_package (Qt5Charts REQUIRED ) -# Add the include directories for the Qt 5 Widgets module to -# the compile lines. -include_directories(${Qt5Widgets_INCLUDE_DIRS}) -include_directories(${Qt5Core_INCLUDE_DIRS}) -include_directories(${Qt5Gui_INCLUDE_DIRS}) -include_directories(${Qt5PrintSupport_INCLUDE_DIRS}) -include_directories(${Qt5WebEngineWidgets_INCLUDE_DIRS}) - -file(GLOB_RECURSE ThermoFunGuiDemo_SOURCES "*.cpp") -file(GLOB_RECURSE ThermoFunGuiDemo_HEADERS "*.h") - -# Recursively collect all source files from the current directory -file(GLOB_RECURSE UI_FILES *.ui) -file(GLOB QRC_FILES ../*.qrc) - -set (ThermoFunGuiDemo_INCLUDE_DIRS "") -foreach (_headerFile ${ThermoFunGuiDemo_HEADERS}) - get_filename_component(_dir ${_headerFile} PATH) - list (APPEND Foo_INCLUDE_DIRS ${_dir}) -endforeach() -list(REMOVE_DUPLICATES ThermoFunGuiDemo_INCLUDE_DIRS) - -# Set the list of compiler flags for gnu and clang compilers -if(${CMAKE_CXX_COMPILER_ID} MATCHES "GNU" OR ${CMAKE_CXX_COMPILER_ID} MATCHES "Clang") - add_definitions("-std=c++11") -# add_definitions("-std=c++11 -stdlib=libc++ -Wall -pedantic -Wno-variadic-macros -Wno-deprecated") - if(NOT ${CMAKE_SYSTEM_NAME} MATCHES "Windows") - add_definitions("-fPIC") - endif() -endif() - -set(ThermoFunGuiDemo_FORMS ${UI_FILES}) -set(RESOURCE ${QRC_FILES}) - -qt5_wrap_cpp(ThermoFunGuiDemo_HEADERS_MOC ${ThermoFunGuiDemo_HEADERS}) -qt5_wrap_ui(ThermoFunGuiDemo_FORMS_HEADERS ${ThermoFunGuiDemo_FORMS}) -qt5_add_resources(ThermoFunGuiDemo_SRCS ${RESOURCE}) -#qt5_add_binary_resources(target inputfile ... OPTIONS ... DESTINATION ...) - -include_directories(${CMAKE_BINARY_DIR}/ThermoFunGui/demo) -include_directories(${CMAKE_SOURCE_DIR}/../src/) -include_directories(${CMAKE_BINARY_DIR}/../../ThermoHubClient/) -#include_directories(${CMAKE_BINARY_DIR}/../) - -add_executable(ThermoFunGuiDemo ${ThermoFunGuiDemo_SOURCES} ${ThermoFunGuiDemo_HEADERS_MOC} ${ThermoFunGuiDemo_FORMS_HEADERS} ${ThermoFunGuiDemo_SRCS}) - -target_link_libraries (ThermoFunGuiDemo jsonio jsonui jsonimpex yaml-cpp pugixml lua5.3 Qt5::Widgets Qt5::Core Qt5::WebEngineWidgets Qt5::Gui Qt5::PrintSupport Qt5::Charts boost_regex boost_system boost_filesystem curl velocypack thrift) -target_link_libraries (ThermoFunGuiDemo THERMOFUNGUI_STATIC) -target_link_libraries (ThermoFunGuiDemo THERMOHUBCLIENT_STATIC) -target_link_libraries (ThermoFunGuiDemo ThermoFun::ThermoFun) - -file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/ThermoFunGuiDemo.sh - DESTINATION ${CMAKE_BINARY_DIR}) - -# Copy the binary file -add_custom_command(TARGET ThermoFunGuiDemo POST_BUILD - COMMAND ${CMAKE_COMMAND} -E copy $ - $/../../$ - COMMENT "Copying ThermoFunGuiDemo to build directory.") - - diff --git a/ThermoFunGui/demo/ThermoFunGuiDemo.sh b/ThermoFunGui/demo/ThermoFunGuiDemo.sh deleted file mode 100755 index 54a7483b..00000000 --- a/ThermoFunGui/demo/ThermoFunGuiDemo.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash -appname=ThermoFunGuiDemo -dirname=`dirname $0` -if [ "${dirname:0:1}" != "/" ]; then - dirname=$PWD/$dirname -fi -export LD_LIBRARY_PATH=/usr/local/lib -cd $dirname -./$appname $* diff --git a/ThermoFunGui/demo/ThermoFunMainWindow.cpp b/ThermoFunGui/demo/ThermoFunMainWindow.cpp deleted file mode 100644 index 6aa6e187..00000000 --- a/ThermoFunGui/demo/ThermoFunMainWindow.cpp +++ /dev/null @@ -1,384 +0,0 @@ -#include -#include -#include -#include - -#include "jsonui/VertexWidget.h" -#include "jsonui/EdgesWidget.h" -#include "jsonui/HelpMainWindow.h" -#include "jsonui/helpBrowser.h" -#include "ThermoFunMainWindow.h" -#include "ui_ThermoFunMainWindow.h" -#include "ThermoFunWidgetNew.h" -#ifdef FROM_SRC -#include "../ThermoFun/Database.h" -#include "../ThermoFun/Element.h" -#include "../ThermoFun/Common/formuladata.h" -#include "../ThermoHubClient/ElementData.h" -#else -#include "ThermoFun/Database.h" -#include "ThermoFun/Element.h" -#include "ThermoFun/Common/formuladata.h" -#include "ThermoHubClient/ElementData.h" -#endif - -TThermoFunMainWin::TThermoFunMainWin(QWidget *parent) : - QMainWindow(parent), - ui(new Ui::TThermoFunMainWindow) -{ - ui->setupUi(this); - //setWindowIcon(QIcon(":/main/GUI/Icons/thermomatch-logo-icon.png")); - - ui->centralWidget_->setStyleSheet( - "border-image: url(:/main/GUI/Icons/BackgroundAqueosReactions900.png) stretch;"); - - onCloseEvent = [&](QMainWindow* win) - { - auto it = bsonuiWindows.begin(); - while( it != bsonuiWindows.end() ) - if( *it == win ) // pointer - { bsonuiWindows.erase(it); - break; - } else - it++; - return true; - }; - - showWidget = [=]( bool isVertex, const std::string& testschema, - const std::string& recordkey, const jsonio::DBQueryData& query ) - { - OpenNewWidget( isVertex, testschema, recordkey, query ); - }; - - - //set up main parameters - setActions(); - - setAllElements(); - new HelpMainWindow(0); -} - -TThermoFunMainWin::~TThermoFunMainWin() -{ - delete ui; -} - -// Connect all actions -void TThermoFunMainWin::setActions() -{ - // File - connect( ui->actionNew_Element_Window , SIGNAL( triggered()), this, SLOT(CmNewElement())); - connect( ui->actionNew_Substance_Window , SIGNAL( triggered()), this, SLOT(CmNewSubstance())); - connect( ui->actionNew_Reaction_Window , SIGNAL( triggered()), this, SLOT(CmNewReaction())); - connect( ui->actionNew_Reaction_Se_t_Window , SIGNAL( triggered()), this, SLOT(CmNewReactionSet())); - connect( ui->actionNew_Data_Source_Window , SIGNAL( triggered()), this, SLOT(CmNewDataSource())); - connect( ui->actionNew_ThermoDataSet_Window , SIGNAL( triggered()), this, SLOT(CmNewThermoDataSet())); - connect( ui->actionNew_Edge_Editor_Window , SIGNAL( triggered()), this, SLOT(CmNewEdge())); - connect( ui->actionE_xit, SIGNAL( triggered()), qApp, SLOT(quit())); - - // Help - connect( ui->action_Help_About, SIGNAL( triggered()), this, SLOT(CmHelpAbout())); - connect( ui->actionContents, SIGNAL( triggered()), this, SLOT(CmHelpContens())); - connect( ui->actionAuthors, SIGNAL( triggered()), this, SLOT(CmHelpAuthors())); - connect( ui->actionLicense, SIGNAL( triggered()), this, SLOT(CmHelpLicense())); - connect( ui->actionPreferences, SIGNAL( triggered()), &jsonui::uiSettings(), SLOT(CmSettingth())); - - // View - connect( ui->action_Show_comments, SIGNAL( toggled(bool)), &jsonui::uiSettings(), SLOT(CmShowComments(bool))); - connect( ui->action_Display_enums, SIGNAL( toggled(bool)), &jsonui::uiSettings(), SLOT(CmDisplayEnums(bool))); - connect( ui->action_Edit_id, SIGNAL(toggled(bool)), &jsonui::uiSettings(), SLOT(CmEditID(bool))); - connect( ui->action_Keep_Data_Fields_Expanded, SIGNAL(toggled(bool)), &jsonui::uiSettings(), SLOT(CmEditExpanded(bool))); - - //Data -// connect( ui->actionGenerate_a_ThermoDataSet_record, SIGNAL( triggered()), this, SLOT(CmGenerateThermoDataSet())); -// connect( ui->actionExport_ThermoDataSet, SIGNAL( triggered()), this, SLOT(CmExportThermoDataSet())); - - //Tools - connect( ui->actionThermo_Fun_Properties_at_TP, SIGNAL( triggered()), this, SLOT(CmThermoFun())); -// connect( ui->actionRecord_Calculator, SIGNAL( triggered()), this, SLOT(CmSelectElementsTest())); - - connect( &jsonui::uiSettings(), SIGNAL(dbChanged()), this, SLOT(setAllElements())); - connect( &jsonui::uiSettings(), SIGNAL(schemaChanged()), this, SLOT(setAllElements())); - - connect( &jsonui::uiSettings(), SIGNAL(dbChanged()), this, SLOT(updateDB())); - connect( &jsonui::uiSettings(), SIGNAL(schemaChanged()), this, SLOT(closeAll())); - connect( &jsonui::uiSettings(), SIGNAL(viewMenuChanged()), this, SLOT(updateViewMenu())); - connect( &jsonui::uiSettings(), SIGNAL(modelChanged()), this, SLOT(updateModel())); - connect( &jsonui::uiSettings(), SIGNAL(tableChanged()), this, SLOT(updateTable())); - connect( &jsonui::uiSettings(), SIGNAL(errorSettings(std::string)), this, SLOT(closeAll())); - -} - - -/// Open new EdgesWidget or JSONUIWidget window -void TThermoFunMainWin::OpenNewWidget( bool isVertex, const std::string& testschema, - const std::string& recordkey, const jsonio::DBQueryData& query ) -{ - jsonui::JSONUIBase* testWidget; - if( isVertex ) - { - testWidget = new jsonui::VertexWidget( testschema/*, this*/ ); - connect( (jsonui::VertexWidget*)testWidget, SIGNAL(vertexDeleted()), this, SLOT(onDeleteVertex())); - connect( (jsonui::VertexWidget*)testWidget, SIGNAL(graphLoaded()), this, SLOT(onLoadGraph())); - } - else - { - testWidget = new jsonui::EdgesWidget( testschema, query/*, this*/ ); - connect( (jsonui::EdgesWidget*)testWidget, SIGNAL(edgeDeleted()), this, SLOT(onDeleteEdge())); - connect( (jsonui::EdgesWidget*)testWidget, SIGNAL(graphLoaded()), this, SLOT(onLoadGraph())); - } - - testWidget->setOnCloseEventFunction(onCloseEvent); - testWidget->setShowWidgetFunction(showWidget); - bsonuiWindows.push_back(testWidget); - - if( !recordkey.empty() ) - { testWidget->openRecordKey( recordkey ); - if( isVertex ) - testWidget->changeKeyList(); - } - testWidget->show(); -} - - -// Open new JSONUIWidget window -void TThermoFunMainWin::newSchemaWin(const char* testschema ) -{ - try{ - OpenNewWidget( true, testschema, "" ); - } - catch(jsonio::jsonio_exception& e) - { - QMessageBox::critical( this, e.title(), e.what() ); - } - catch(std::exception& e) - { - QMessageBox::critical( this, "std::exception", e.what() ); - } -} - -void TThermoFunMainWin::closeEvent(QCloseEvent *e) -{ - if( HelpMainWindow::pDia ) - delete HelpMainWindow::pDia; - closeAll(); - QWidget::closeEvent(e); -} - -void TThermoFunMainWin::CmHelpContens() -{ - helpWin( "ThermoFun", "" ); -} - -void TThermoFunMainWin::CmHelpAbout() -{ - helpWin( "AboutThermoFun", "" ); -} - -void TThermoFunMainWin::CmHelpAuthors() -{ - helpWin( "AuthorsThermoFun", "" ); -} - -void TThermoFunMainWin::CmHelpLicense() -{ - helpWin( "LicenseThermoFun", "" ); -} - - -/// Open new EdgesWidget window -void TThermoFunMainWin::CmNewEdge() -{ - try{ - OpenNewWidget( false, "", "" ); - } - catch(jsonio::jsonio_exception& e) - { - QMessageBox::critical( this, e.title(), e.what() ); - } - catch(std::exception& e) - { - QMessageBox::critical( this, "std::exception", e.what() ); - } -} - - -/// Update menu for all windows -void TThermoFunMainWin::updateViewMenu() -{ - ui->action_Show_comments->setChecked( jsonui::TJsonSchemaModel::showComments ); - ui->action_Display_enums->setChecked(jsonui::TJsonSchemaModel::useEnumNames); - ui->action_Edit_id->setChecked(jsonui::TJsonSchemaModel::editID ); - - auto it = bsonuiWindows.begin(); - while( it != bsonuiWindows.end() ) - { (*it)->updateViewMenu(); it++; } -} - - -/// Update model for all windows -void TThermoFunMainWin::updateModel() -{ - auto it = bsonuiWindows.begin(); - while( it != bsonuiWindows.end() ) - { (*it)->updateModel(); it++; } -} - - -/// Update table for all windows -void TThermoFunMainWin::updateTable() -{ - auto it = bsonuiWindows.begin(); - while( it != bsonuiWindows.end() ) - { (*it)->updateTable(); it++; } -} - - -/// Update DB for all windows -void TThermoFunMainWin::updateDB() -{ - HelpMainWindow::pDia->resetDBClient(); - auto it = bsonuiWindows.begin(); - while( it != bsonuiWindows.end() ) - { (*it)->updateDB(); it++; } -} - -/// close all bson windows -void TThermoFunMainWin::closeAll() -{ - auto it = bsonuiWindows.begin(); - while( it != bsonuiWindows.end() ) - { (*it)->close(); it = bsonuiWindows.begin(); } - - // bsonuiWindows.clear(); -} - -void TThermoFunMainWin::onLoadGraph() -{ - auto it = bsonuiWindows.begin(); - while( it != bsonuiWindows.end() ) - { - jsonui::EdgesWidget* edgWin = dynamic_cast(*it); - if( edgWin ) - edgWin->updateQuery(); - else - { - jsonui::VertexWidget* verWin = dynamic_cast(*it); - if( verWin ) - verWin->updateQuery(); - } - it++; - } -} - - -void TThermoFunMainWin::onDeleteEdge() -{ - auto it = bsonuiWindows.begin(); - while( it != bsonuiWindows.end() ) - { - jsonui::EdgesWidget* edgWin = dynamic_cast(*it); - if( edgWin ) - edgWin->changeKeyList(); - it++; - } -} - -void TThermoFunMainWin::onDeleteVertex() -{ - auto it = bsonuiWindows.begin(); - while( it != bsonuiWindows.end() ) - { - jsonui::EdgesWidget* edgWin = dynamic_cast(*it); - if( edgWin ) - edgWin->changeKeyList(); - else - { - jsonui::VertexWidget* verWin = dynamic_cast(*it); - if( verWin ) - verWin->changeKeyList(); - } - it++; - } -} - -// ---------------------------------------- - -void TThermoFunMainWin::CmThermoFun() -{ - try{ - ThermoFunWidgetNew* testWidget = new ThermoFunWidgetNew( this ); - - testWidget->setOnCloseEventFunction(onCloseEvent); - //testWidget->setShowWidgetFunction(showWidget); - bsonuiWindows.push_back(testWidget); - testWidget->show(); - testWidget->CmSelectThermoDataSet(); - - } - catch(jsonio::jsonio_exception& e) - { - QMessageBox::critical( this, e.title(), e.what() ); - } - catch(std::exception& e) - { - QMessageBox::critical( this, "std::exception", e.what() ); - } -} - -/// Set up all elements to formula parser -void TThermoFunMainWin::setAllElements() -{ - try{ - if( jsonio::ioSettings().Schema()->getStruct("VertexElement") == nullptr ) - return; - - // Connect to DataBase - std::unique_ptr elementDB( jsonio::TDBVertexDocument::newVertexDocumentQuery( - jsonui::uiSettings().database(), "VertexElement" )); - - if(elementDB.get() == nullptr ) - return; - - // <<<<<<<<<< from ThermoMatch - auto resultData = elementDB->runQuery( jsonio::DBQueryData("{\"_label\": \"element\" }",jsonio::DBQueryData::qTemplate ) ); - - ThermoFun::Database fundb(resultData); - - ThermoFun::ChemicalFormula::setDBElements(fundb.mapElements()); - /* >>>>>>> test old - ThermoFun::setDBElements(elementDB.get()); - >>>>>>>>>> */ - // test - const ThermoFun::DBElementsData& elements = ThermoFun::ChemicalFormula::getDBElements(); - - // save data to file - std::fstream outFile("elementsDB_All.csv", std::ios::out ); - jsonio::jsonioErrIf( !outFile.good() , "elementsDB_All.csv", "Fileopen error..."); - - outFile << "symbol,class_,isotope,atomic_mass,"; - outFile << "entropy,heat_capacity,volume,valence,number" << std::endl; - - auto itr = elements.begin(); - while( itr != elements.end() ) - { - outFile << itr->first.Symbol() << ","<< itr->first.Class() << ","; - outFile << itr->first.Isotope() << ","<< itr->second.atomic_mass << ","; - outFile << itr->second.entropy << ","<< itr->second.heat_capacity << ","; - outFile << itr->second.volume << ","<< itr->second.valence << ","; - outFile << itr->second.number; - outFile << "\n"; - itr++; - } - - } - catch(jsonio::jsonio_exception& e) - { - QMessageBox::critical( this, e.title(), e.what() ); - } - catch(std::exception& e) - { - QMessageBox::critical( this, "std::exception", e.what() ); - } -} - diff --git a/ThermoFunGui/demo/ThermoFunMainWindow.h b/ThermoFunGui/demo/ThermoFunMainWindow.h deleted file mode 100644 index 71706971..00000000 --- a/ThermoFunGui/demo/ThermoFunMainWindow.h +++ /dev/null @@ -1,83 +0,0 @@ -#ifndef TMAINWINDOW_H -#define TMAINWINDOW_H - -#include -#include "jsonui/JSONUIBase.h" - -namespace Ui { -class TThermoFunMainWindow; -} - -class TThermoFunMainWin : public QMainWindow -{ - Q_OBJECT - - // Internal data - std::list bsonuiWindows; - jsonui::onEventfunction onCloseEvent; - jsonui::ShowWidgetFunction showWidget; - - // Work functions - void setActions(); - - /// Open new JSONUIWidget window - void newSchemaWin(const char* testschema ); - - void closeEvent(QCloseEvent* e); - - -public slots: - - // update after change preferences - void updateViewMenu(); - void updateModel(); - void updateTable(); - void updateDB(); - /// Close All JSONUIWidget windows - void closeAll(); - - // File - void CmNewElement() - { newSchemaWin( "VertexElement" ); } - void CmNewSubstance() - { newSchemaWin( "VertexSubstance" ); } - void CmNewReaction() - { newSchemaWin( "VertexReaction" ); } - void CmNewReactionSet() - { newSchemaWin( "VertexReactionSet" ); } - void CmNewDataSource() - { newSchemaWin( "VertexDataSource" ); } - void CmNewThermoDataSet() - { newSchemaWin( "VertexThermoDataSet" ); } - void CmNewEdge(); - - // Tools - void CmThermoFun(); - - // Help - void CmHelpAbout(); - void CmHelpAuthors(); - void CmHelpLicense(); - void CmHelpContens(); - - /// Load all elements properties - void setAllElements(); - - void onDeleteVertex(); - void onDeleteEdge(); - void onLoadGraph(); - -public: - explicit TThermoFunMainWin(QWidget *parent = 0); - ~TThermoFunMainWin(); - - /// Open new EdgesWidget or JSONUIWidget window - void OpenNewWidget( bool isVertex, const std::string& testschema, const std::string& recordkey, - const jsonio::DBQueryData& query = jsonio::emptyQuery ); - -private: - - Ui::TThermoFunMainWindow *ui; -}; - -#endif // TMAINWINDOW_H diff --git a/ThermoFunGui/demo/ThermoFunMainWindow.ui b/ThermoFunGui/demo/ThermoFunMainWindow.ui deleted file mode 100644 index bd333a0a..00000000 --- a/ThermoFunGui/demo/ThermoFunMainWindow.ui +++ /dev/null @@ -1,363 +0,0 @@ - - - TThermoFunMainWindow - - - - 0 - 0 - 470 - 255 - - - - Welcome to Thermo Start Window - - - - - 4 - - - 4 - - - 4 - - - 4 - - - 0 - - - - - - - 0 - 0 - 470 - 22 - - - - - &Module - - - - - - - - - - - - - - - &Help - - - - - - - - - - - - - - &View - - - - - - - - - - - - - - 0 - 0 - - - - - - - ThermoFun Thermodynamic data at T and P - - - - 50 - 50 - - - - true - - - TopToolBarArea - - - true - - - - - - - toolBar - - - Click desired icon to view data in the database - - - - 50 - 50 - - - - TopToolBarArea - - - true - - - - - - - - - - - - - 0 - 0 - - - - - 0 - 0 - - - - toolBar - - - Click to set database connection and preferences - - - - 50 - 50 - - - - TopToolBarArea - - - true - - - - - - - E&xit - - - - - - :/Icons/SetKeyTemplateIcon24.png:/Icons/SetKeyTemplateIcon24.png - - - &Preferences ... - - - Preferences ... - - - Preferences ... - - - - - - :/Icons/ShowHelpWindowIcon24.png:/Icons/ShowHelpWindowIcon24.png - - - Help &About - - - Open Help Viewer ... - - - - - Au&thors ... - - - - - &License ... - - - - - Help &Contents ... - - - - - true - - - &Display Comments to Data Fields - - - - - true - - - &Show Enum Names Instead of Values - - - - - &Version ... - - - - - true - - - - :/Icons/CancelIcon24.png:/Icons/CancelIcon24.png - - - &Edit _id of DB Documents (Records) - - - - - - :/Icons/ICompModuleIcon.png:/Icons/ICompModuleIcon.png - - - &Element Data (Vertex) ... - - - - - - :/Icons/DCompModuleIcon.png:/Icons/DCompModuleIcon.png - - - &Substance Data (Vertex) ... - - - - - - :/Icons/ReacDCModuleIcon.png:/Icons/ReacDCModuleIcon.png - - - &Reaction Data (Vertex) ... - - - - - - :/Icons/ReactionEquilibriumIcon.png:/Icons/ReactionEquilibriumIcon.png - - - ReactionSe&t Data (Vertex) ... - - - - - - :/Icons/SDrefModuleIcon.png:/Icons/SDrefModuleIcon.png - - - &DataSource (Vertex) ... - - - - - true - - - &Keep Data Fields Expanded - - - - - - :/Icons/DualThModuleIcon.png - :/main/GUI/Icons/DualThModuleIcon24.png:/Icons/DualThModuleIcon.png - - - &Graph Link Data (Edge) ... - - - - - - :/Icons/thermofun-logo-icon.png:/Icons/thermofun-logo-icon.png - - - Thermo&Fun Properties at TP - - - - - Record &Calculator - - - - - Generate a ThermoDataSet record - - - - - - :/Icons/ThermoDatabasesIcon.png:/Icons/ThermoDatabasesIcon.png - - - &ThermoDataSet (Vertex) ... - - - ThermoDataSet (Vertex) - - - - - Export ThermoDataSet - - - - - - - - - diff --git a/ThermoFunGui/demo/main.cpp b/ThermoFunGui/demo/main.cpp deleted file mode 100644 index 6d6bad60..00000000 --- a/ThermoFunGui/demo/main.cpp +++ /dev/null @@ -1,20 +0,0 @@ - -#include -#include -#include -#include "ThermoFunMainWindow.h" - -int main(int argc, char *argv[]) -{ -#ifdef _WIN32 - jsonio::JsonioSettings::settingsFileName = "Resources/fun-hubclient-config-win.json"; -#else - jsonio::JsonioSettings::settingsFileName = "Resources/fun-hubclient-config.json"; -#endif - QApplication a(argc, argv); - a.setWindowIcon(QIcon(":/Icons/thermofun-logo-icon.png")); - - TThermoFunMainWin w; - w.show(); - return a.exec(); -} diff --git a/ThermoFunGui/install-thirdparty.sh b/ThermoFunGui/install-thirdparty.sh deleted file mode 100755 index 2bd73648..00000000 --- a/ThermoFunGui/install-thirdparty.sh +++ /dev/null @@ -1,32 +0,0 @@ -#!/bin/bash - -J=8 - -while [[ $# > 2 ]] -do -key="$2" - -case $key in - -j) - J="$3" - shift - ;; - *) - - ;; -esac -shift -done - -CMAKE_FILE_DIR=$(pwd)/ThirdParty - -mkdir -p ../../build-DemoGUI/release/thirdparty - -cd ../../build-DemoGUI/release/thirdparty - -cmake $CMAKE_FILE_DIR -DCMAKE_BUILD_TYPE=Release -DREFRESH_THIRDPARTY=OFF -DCMAKE_INSTALL_PREFIX=. -DCMAKE_PREFIX_PATH=$1 - -make -j$J -sudo make install -sudo ldconfig - diff --git a/ThermoFunGui/src/CMakeLists.txt b/ThermoFunGui/src/CMakeLists.txt deleted file mode 100644 index 4e1daf56..00000000 --- a/ThermoFunGui/src/CMakeLists.txt +++ /dev/null @@ -1,70 +0,0 @@ -set(CMAKE_AUTORCC ON) - -# Recursively collect all header files from the current directory -file(GLOB_RECURSE HEADER_FILES *.h) - -# Recursively collect all source files from the current directory -file(GLOB_RECURSE SOURCE_FILES *.cpp) - -# Recursively collect all source files from the current directory -file(GLOB_RECURSE UI_FILES *.ui) -file(GLOB QRC_FILES ../*.qrc) - -# Set the list of compiler flags for gnu and clang compilers -if(${CMAKE_CXX_COMPILER_ID} MATCHES "GNU" OR ${CMAKE_CXX_COMPILER_ID} MATCHES "Clang") - add_definitions("-std=c++11") -# add_definitions("-std=c++11 -stdlib=libc++ -Wall -pedantic -Wno-variadic-macros -Wno-deprecated") - if(NOT ${CMAKE_SYSTEM_NAME} MATCHES "Windows") - add_definitions("-fPIC") - endif() -endif() - - -# Set some necessary definitions to compile JSONUI -add_definitions(-DFROM_SRC) - -set(ThermoFunGui_SOURCES ${SOURCE_FILES} ) -set(ThermoFunGui_HEADERS ${HEADER_FILES} ) -set(ThermoFunGui_FORMS ${UI_FILES}) - -qt5_wrap_cpp(ThermoFunGui_HEADERS_MOC ${ThermoFunGui_HEADERS}) -qt5_wrap_ui(ThermoFunGui_FORMS_HEADERS ${ThermoFunGui_FORMS}) - -set(RESOURCE ${QRC_FILES}) -qt5_add_resources(ThermoFunGui_SRCS ${RESOURCE}) -#qt5_add_binary_resources(target inputfile ... OPTIONS ... DESTINATION ...) - -include_directories(${CMAKE_BINARY_DIR}/ThermoFunGui/src) -include_directories(${CMAKE_BINARY_DIR}/../ThermoHubClient) -# access to thirdpary includes -include_directories(${CMAKE_BINARY_DIR}/../../../include) - -# Create the shared library using the collected source files -add_library(THERMOFUNGUI_OBJECTS OBJECT ${ThermoFunGui_HEADERS} ${ThermoFunGui_SOURCES} ${ThermoFunGui_HEADERS_MOC} ${ThermoFunGui_FORMS_HEADERS} ${ThermoFunGui_SRCS} ) -#target_link_libraries(BSONUI_OBJECTS Qt5::Widgets Qt5::Core Qt5::Gui) - -# Specify the dependencies of BSONIO to ensure proper build sequence -#add_dependencies(ThermoFunGui_OBJECTS ${THIRDPARTY_TARGETS}) - -# Check if a shared library is to be built -if(TFUN_BUILD_SHARED_LIBS) - add_library(THERMOFUNGUI_SHARED SHARED $) - target_link_libraries(THERMOFUNGUI_SHARED ${THIRDPARTY_LIBS} ) -if( ${CMAKE_CXX_COMPILER_ID} MATCHES "Clang") - target_link_libraries(THERMOFUNGUI_SHARED Qt5::Widgets Qt5::Core Qt5::WebEngineWidgets Qt5::Gui Qt5::PrintSupport Qt5::Charts thrift jsonio jsonui ThermoFun::ThermoFun ThermoHubClient ) -endif() - set_target_properties(THERMOFUNGUI_SHARED PROPERTIES OUTPUT_NAME ThermoFunGui) - install(TARGETS THERMOFUNGUI_SHARED DESTINATION lib) -endif() - -# Check if a static library is to be built -if(TFUN_BUILD_STATIC_LIBS) - add_library(THERMOFUNGUI_STATIC STATIC $) - target_link_libraries(THERMOFUNGUI_STATIC ${THIRDPARTY_LIBS} ) - set_target_properties(THERMOFUNGUI_STATIC PROPERTIES OUTPUT_NAME ThermoFunGui) - install(TARGETS THERMOFUNGUI_STATIC DESTINATION lib) -endif() - -# Install the header files preserving the directory hierarchy -install(FILES ${HEADER_FILES} - DESTINATION include/ThermoFunGui ) diff --git a/ThermoFunGui/src/ElementsWidget.cpp b/ThermoFunGui/src/ElementsWidget.cpp deleted file mode 100644 index cea811ad..00000000 --- a/ThermoFunGui/src/ElementsWidget.cpp +++ /dev/null @@ -1,279 +0,0 @@ -#include "ElementsWidget.h" -#include "ui_ElementsWidget.h" -#include "jsonio/ar2base.h" - -ElementsWidget::ElementsWidget(QWidget *parent) : - QWidget(parent), - ui(new Ui::ElementsWidget) -{ - ui->setupUi(this); - setUpButtonGroups(); - - connect( ui->pbE_REE, SIGNAL( clicked() ), this, SLOT( CmResetREE() ) ); - connect( ui->pbE_ACT, SIGNAL( clicked() ), this, SLOT( CmResetACT() ) ); - connect( ui->cbIsotopes, SIGNAL( clicked() ),this, SLOT( SetIsotopes() ) ); -} - -ElementsWidget::~ElementsWidget() -{ - delete ui; -} - -void ElementsWidget::SetIsotopes() -{ -} - -void ElementsWidget::CmSelectAll() -{ - int ii; - for( ii=0; iibuttons().count(); ii++ ) - if( bgOther->button(ii)->isEnabled() ) - bgOther->button(ii)->setChecked ( true ); - for( ii=0; ii<99/*bgElem->buttons()->count()-1*/; ii++ ) - if( bgElem->button(ii)->isEnabled() ) - bgElem->button(ii)->setChecked ( true ); -} - -void ElementsWidget::CmResetREE() -{ - for(int ii=57; ii<=71; ii++ ) - if( bgElem->button(ii)->isEnabled() ) - bgElem->button(ii)->setChecked ( true ); -} - -void ElementsWidget::CmResetACT() -{ - for(int ii=89; ii<=98; ii++ ) - if( bgElem->button(ii)->isEnabled() ) - bgElem->button(ii)->setChecked ( true ); -} - -void ElementsWidget::allSelected( std::vector& elementKeys ) const -{ - std::size_t ii; - elementKeys.clear(); - for( ii=0; iibutton( aBtmId1[ii] )->isChecked() ) - elementKeys.push_back( aICkey1[ii] ); - } - - for( ii=0; iibutton( aBtmId2[ii] )->isChecked() ) - elementKeys.push_back( aICkey2[ii] ); - } -} - -void ElementsWidget::setElementList(const std::vector &elements ) -{ - ResetData(); - EmptyData(); - - QAbstractButton* bb; - int nmbOther=0; - aBtmId1.clear(); - aICkey1.clear(); - aBtmId2.clear(); - aICkey2.clear(); - - //const DBElementsData& allElements = ChemicalFormula::getDBElements(); - - for(auto const &elkey : elements) - { - auto eldata = ThermoFun::ChemicalFormula::getDBElements().find(elkey); - if( eldata == ThermoFun::ChemicalFormula::getDBElements().end() ) - continue; - - std::string name =elkey.Symbol(); - int aIndMT = eldata->second.number; - if( aIndMT == -1 || aIndMT > 101 ) // additional - { - jsonio::jsonioErrIf( nmbOther>12, name, "More than 11 additional Elements!"); - bb = bgOther->button(nmbOther); - bb->setText( tr( name.c_str() ) ); - bb->setEnabled( true ); - aBtmId2.push_back( nmbOther ); - aICkey2.push_back( elkey ); - nmbOther ++; - } - else //elements - { - bb = bgElem->button( aIndMT ); - jsonio::jsonioErrIf( !bb, name, "E01EDrem: Invalid Element "); - aBtmId1.push_back( aIndMT ); - aICkey1.push_back( elkey ); - bb->setEnabled( true ); - } - } -} - -void ElementsWidget::selectElementList( const std::vector& elements ) -{ - for(auto const &elkey : elements) - { - auto eldata = ThermoFun::ChemicalFormula::getDBElements().find(elkey); - if( eldata == ThermoFun::ChemicalFormula::getDBElements().end() ) - continue; - - std::string name =elkey.Symbol(); - int aIndMT = eldata->second.number; - if( aIndMT == -1 || aIndMT > 101 ) // additional - { - for(int ii=0; iibuttons().count(); ii++ ) - if( name == bgOther->button(ii)->text().toStdString() ) - bgOther->button(ii)->setChecked ( true ); - } - else //elements - { - QAbstractButton* bb = bgElem->button( aIndMT ); - if( bb->isEnabled() ) - bb->setChecked( true); - } - } -} - - -void ElementsWidget::setUpButtonGroups() -{ - bgElem = new QButtonGroup( ui->bgElemBox); - bgElem->setExclusive(false); - bgElem->addButton(ui->pbE_0, 0); - bgElem->addButton(ui->pbE_1, 1); - bgElem->addButton(ui->pbE_2, 2); - bgElem->addButton(ui->pbE_3, 3); - bgElem->addButton(ui->pbE_4, 4); - bgElem->addButton(ui->pbE_5, 5); - bgElem->addButton(ui->pbE_6, 6); - bgElem->addButton(ui->pbE_7, 7); - bgElem->addButton(ui->pbE_8, 8); - bgElem->addButton(ui->pbE_9, 9); - bgElem->addButton(ui->pbE_10, 10); - bgElem->addButton(ui->pbE_11, 11); - bgElem->addButton(ui->pbE_12, 12); - bgElem->addButton(ui->pbE_13, 13); - bgElem->addButton(ui->pbE_14, 14); - bgElem->addButton(ui->pbE_15, 15); - bgElem->addButton(ui->pbE_16, 16); - bgElem->addButton(ui->pbE_17, 17); - bgElem->addButton(ui->pbE_18, 18); - bgElem->addButton(ui->pbE_19, 19); - bgElem->addButton(ui->pbE_20, 20); - bgElem->addButton(ui->pbE_21, 21); - bgElem->addButton(ui->pbE_22, 22); - bgElem->addButton(ui->pbE_23, 23); - bgElem->addButton(ui->pbE_24, 24); - bgElem->addButton(ui->pbE_25, 25); - bgElem->addButton(ui->pbE_26, 26); - bgElem->addButton(ui->pbE_27, 27); - bgElem->addButton(ui->pbE_28, 28); - bgElem->addButton(ui->pbE_29, 29); - bgElem->addButton(ui->pbE_30, 30); - bgElem->addButton(ui->pbE_31, 31); - bgElem->addButton(ui->pbE_32, 32); - bgElem->addButton(ui->pbE_33, 33); - bgElem->addButton(ui->pbE_34, 34); - bgElem->addButton(ui->pbE_35, 35); - bgElem->addButton(ui->pbE_36, 36); - bgElem->addButton(ui->pbE_37, 37); - bgElem->addButton(ui->pbE_38, 38); - bgElem->addButton(ui->pbE_39, 39); - bgElem->addButton(ui->pbE_40, 40); - bgElem->addButton(ui->pbE_41, 41); - bgElem->addButton(ui->pbE_42, 42); - bgElem->addButton(ui->pbE_43, 43); - bgElem->addButton(ui->pbE_44, 44); - bgElem->addButton(ui->pbE_45, 45); - bgElem->addButton(ui->pbE_46, 46); - bgElem->addButton(ui->pbE_47, 47); - bgElem->addButton(ui->pbE_48, 48); - bgElem->addButton(ui->pbE_49, 49); - bgElem->addButton(ui->pbE_50, 50); - bgElem->addButton(ui->pbE_51, 51); - bgElem->addButton(ui->pbE_52, 52); - bgElem->addButton(ui->pbE_53, 53); - bgElem->addButton(ui->pbE_54, 54); - bgElem->addButton(ui->pbE_55, 55); - bgElem->addButton(ui->pbE_56, 56); - bgElem->addButton(ui->pbE_57, 57); - bgElem->addButton(ui->pbE_58, 58); - bgElem->addButton(ui->pbE_59, 59); - bgElem->addButton(ui->pbE_60, 60); - bgElem->addButton(ui->pbE_61, 61); - bgElem->addButton(ui->pbE_62, 62); - bgElem->addButton(ui->pbE_63, 63); - bgElem->addButton(ui->pbE_64, 64); - bgElem->addButton(ui->pbE_65, 65); - bgElem->addButton(ui->pbE_66, 66); - bgElem->addButton(ui->pbE_67, 67); - bgElem->addButton(ui->pbE_68, 68); - bgElem->addButton(ui->pbE_69, 69); - bgElem->addButton(ui->pbE_70, 70); - bgElem->addButton(ui->pbE_71, 71); - bgElem->addButton(ui->pbE_72, 72); - bgElem->addButton(ui->pbE_73, 73); - bgElem->addButton(ui->pbE_74, 74); - bgElem->addButton(ui->pbE_75, 75); - bgElem->addButton(ui->pbE_76, 76); - bgElem->addButton(ui->pbE_77, 77); - bgElem->addButton(ui->pbE_78, 78); - bgElem->addButton(ui->pbE_79, 79); - bgElem->addButton(ui->pbE_80, 80); - bgElem->addButton(ui->pbE_81, 81); - bgElem->addButton(ui->pbE_82, 82); - bgElem->addButton(ui->pbE_83, 83); - bgElem->addButton(ui->pbE_84, 84); - bgElem->addButton(ui->pbE_85, 85); - bgElem->addButton(ui->pbE_86, 86); - bgElem->addButton(ui->pbE_87, 87); - bgElem->addButton(ui->pbE_88, 88); - bgElem->addButton(ui->pbE_89, 89); - bgElem->addButton(ui->pbE_90, 90); - bgElem->addButton(ui->pbE_91, 91); - bgElem->addButton(ui->pbE_92, 92); - bgElem->addButton(ui->pbE_93, 93); - bgElem->addButton(ui->pbE_94, 94); - bgElem->addButton(ui->pbE_95, 95); - bgElem->addButton(ui->pbE_96, 96); - bgElem->addButton(ui->pbE_97, 97); - bgElem->addButton(ui->pbE_98, 98); - -// bgElem->addButton(ui->pbE_100, 100); -// bgElem->addButton(ui->pbE_101, 101); - - bgOther = new QButtonGroup( ui->bgOtherBox); - bgOther->setExclusive(false); - bgOther->addButton(ui->pbA_0, 0); - bgOther->addButton(ui->pbA_1, 1); - bgOther->addButton(ui->pbA_2, 2); - bgOther->addButton(ui->pbA_3, 3); - bgOther->addButton(ui->pbA_4, 4); - bgOther->addButton(ui->pbA_5, 5); - bgOther->addButton(ui->pbA_6, 6); - bgOther->addButton(ui->pbA_7, 7); - bgOther->addButton(ui->pbA_8, 8); - bgOther->addButton(ui->pbA_9, 9); - bgOther->addButton(ui->pbA_10, 10); - bgOther->addButton(ui->pbA_11, 11); -} - -void ElementsWidget::EmptyData() -{ - int ii; - for( ii=0; iibuttons().count(); ii++ ) - { bgOther->button(ii)->setEnabled( false ); - bgOther->button(ii)->setText( tr( "...") ); - } - for( ii=0; ii<99/*bgElem->buttons()->count()-1*/; ii++ ) // we have not 99 - bgElem->button(ii)->setEnabled( false ); -} - -void ElementsWidget::ResetData() -{ - int ii; - for( ii=0; iibuttons().count(); ii++ ) - bgOther->button(ii)->setChecked ( false ); - for( ii=1; ii<99/*bgElem->buttons()->count()-1*/; ii++ ) // 0 always - bgElem->button(ii)->setChecked ( false ); -} - diff --git a/ThermoFunGui/src/ElementsWidget.h b/ThermoFunGui/src/ElementsWidget.h deleted file mode 100644 index 98cdee3a..00000000 --- a/ThermoFunGui/src/ElementsWidget.h +++ /dev/null @@ -1,55 +0,0 @@ -#ifndef ELEMENTSWIDGET_H -#define ELEMENTSWIDGET_H - -#include -#include -#ifdef FROM_SRC -#include "../../ThermoFun/Common/formuladata.h" -#endif -#ifndef FROM_SRC -#include "ThermoFun/Common/formuladata.h" -#endif - -namespace Ui { -class ElementsWidget; -} - -class ElementsWidget : public QWidget -{ - Q_OBJECT - - void setUpButtonGroups(); - void EmptyData(); - void ResetData(); - -public slots: - void CmSelectAll(); - void CmReset() - { - ResetData(); - } - void CmResetREE(); - void CmResetACT(); - void SetIsotopes(); - -public: - explicit ElementsWidget(QWidget *parent = nullptr); - ~ElementsWidget(); - - void setElementList( const std::vector& elements ); - void selectElementList( const std::vector& elements ); - void allSelected( std::vector& elementKeys ) const; - -private: - Ui::ElementsWidget *ui; - - std::vector aBtmId1; // lists correspondanse betvin bgElem - std::vector aICkey1; // buttons and IComp records - std::vector aBtmId2; // lists correspondanse betvin bgOther - std::vector aICkey2; // buttons and IComp records - QButtonGroup* bgElem; - QButtonGroup* bgOther; - -}; - -#endif // ELEMENTSWIDGET_H diff --git a/ThermoFunGui/src/ElementsWidget.ui b/ThermoFunGui/src/ElementsWidget.ui deleted file mode 100644 index aa8228cf..00000000 --- a/ThermoFunGui/src/ElementsWidget.ui +++ /dev/null @@ -1,2617 +0,0 @@ - - - ElementsWidget - - - - 0 - 0 - 674 - 462 - - - - Form - - - - - - - 0 - 0 - - - - - - - - - 85 - 0 - 127 - - - - - - - - - 85 - 0 - 127 - - - - - - - - - 128 - 128 - 128 - - - - - - - - - 75 - true - - - - Step 2: Select Elements (not available if shown in light gray color) - - - - false - - - - 330 - 210 - 50 - 30 - - - - Tc - - - true - - - - - false - - - - 180 - 120 - 50 - 30 - - - - Si - - - true - - - - - false - - - - 30 - 240 - 50 - 30 - - - - Ag - - - true - - - - - false - - - - 330 - 150 - 50 - 30 - - - - Mn - - - true - - - - - false - - - - 370 - 370 - 40 - 30 - - - - Dy - - - true - - - - - - 10 - 210 - 20 - 31 - - - - 5 - - - Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter - - - false - - - - - false - - - - 230 - 180 - 50 - 30 - - - - As - - - true - - - - - - 10 - 120 - 20 - 31 - - - - 3 - - - Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter - - - false - - - - - - 380 - 30 - 50 - 31 - - - - VIII - - - Qt::AlignCenter - - - false - - - - - - 10 - 240 - 20 - 31 - - - - 5a - - - Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter - - - false - - - - - false - - - - 130 - 180 - 50 - 30 - - - - Ga - - - true - - - - - false - - - - 30 - 60 - 50 - 30 - - - - H - - - true - - - - - false - - - - 30 - 330 - 50 - 30 - - - - Fr - - - true - - - - - false - - - - 370 - 400 - 40 - 30 - - - - Cf - - - true - - - - - false - - - - 30 - 270 - 50 - 30 - - - - Cs - - - true - - - - - - 330 - 30 - 50 - 31 - - - - VII - - - Qt::AlignCenter - - - false - - - - - - 10 - 60 - 20 - 31 - - - - 1 - - - Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter - - - false - - - - - false - - - - 210 - 400 - 40 - 30 - - - - Pu - - - true - - - - - - 30 - 30 - 50 - 31 - - - - I - - - Qt::AlignCenter - - - false - - - - - false - - - - 330 - 120 - 50 - 30 - - - - Cl - - - true - - - - - false - - - - 380 - 240 - 50 - 30 - - - - Xe - - - true - - - - - false - - - - 280 - 240 - 50 - 30 - - - - Te - - - true - - - - - false - - - - 330 - 180 - 50 - 30 - - - - Br - - - true - - - - - false - - - - 180 - 180 - 50 - 30 - - - - Ge - - - true - - - - - false - - - - 480 - 210 - 50 - 30 - - - - Pd - - - true - - - - - - 180 - 30 - 50 - 31 - - - - IV - - - Qt::AlignCenter - - - false - - - - - false - - - - 170 - 370 - 40 - 30 - - - - Pm - - - true - - - - - false - - - - 130 - 370 - 40 - 30 - - - - Nd - - - true - - - - - false - - - - 280 - 300 - 50 - 30 - - - - Po - - - true - - - - - - 130 - 30 - 50 - 31 - - - - III - - - Qt::AlignCenter - - - false - - - - - false - - - - 50 - 370 - 40 - 30 - - - - Ce - - - true - - - - - false - - - - 330 - 370 - 40 - 30 - - - - Tb - - - true - - - - - false - - - - 380 - 300 - 50 - 30 - - - - Rn - - - true - - - - - false - - - - 90 - 400 - 40 - 30 - - - - Pa - - - true - - - - - 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-// ThermoFun includes -#ifdef FROM_SRC -#include "../ThermoHubClient/DatabaseClient.h" -#else -#include "ThermoHubClient/DatabaseClient.h" -#endif - -using namespace std; -using namespace jsonui; - - -struct SelectElementsDialogPrivate -{ - SelectElementsDialog* window; - - /// Selected SourceTDB - int sourceTDB = -1; - /// Define ELEMENTS table data - vector elementsRow; - /// Connect to ReactionSet record - ThermoFun::DatabaseClient ThermoHubClient; -// ReactionSetData rcSetData; - std::shared_ptr rcsetData; - std::shared_ptr rcsetModel; - - /// Current id of ReactionSet - string idReactopnSet = ""; - -// --------------------------------------------- - - SelectElementsDialogPrivate(SelectElementsDialog* awindow, ThermoFun::DatabaseClient ThermoHubClient_): - window(awindow), ThermoHubClient( ThermoHubClient_ ) - { - rcsetData.reset( new jsonui::StringTable( "records", ThermoHubClient.reactSetData().getDataHeaders()) ); - rcsetModel.reset( new jsonui::TMatrixModel( rcsetData.get() ) ); - } - - virtual ~SelectElementsDialogPrivate() - { } - - void clearAll() - { - elementsRow.clear(); - } - - vector getSourcetdbList() - { - return ThermoHubClient.sourcetdbListAll(); - } - - bool makeAvailableElementsList( int sourcendx ) - { - if( sourceTDB == sourcendx ) // Source did not chaged - return false; - elementsRow = ThermoHubClient.availableElementsKey(sourcendx); - sourceTDB = sourcendx; - return true; - } - - const vector& allAvailableElementsList() const - { - return elementsRow; - } - - int loadReacSetRecords( const vector& elements ) - { - jsonio::ValuesTable matr = ThermoHubClient.reactSetData().loadRecordsValues( jsonio::emptyQuery, sourceTDB, elements ); - -// here - /// auto jsonT = ThermoHubClient.substData().getJsonBsonRecordVertex("59a7dcedf3830548000000e7:").first; -// here - matr.insert( matr.begin(), {"All","", "", "",""}); - rcsetData->updateValues( matr ); - rcsetModel->resetMatrixData(); - if( !idReactopnSet.empty() ) - { - for( std::size_t ii=1; iigetValues(); - if( ndx< (int)matr.size() && ndx > 0 ) - return matr[ndx][4]; - else - return ""; - } -}; - - -//=========================================================================== - - -SelectElementsDialog::SelectElementsDialog(ThermoFun::DatabaseClient ThermoHubClient, QWidget *parent) : - QDialog(parent), - ui(new Ui::SelectElements), data(0), pTable(0), - pdata(new SelectElementsDialogPrivate(this, ThermoHubClient)) -{ - ui->setupUi(this); - - ui->stackedWidget->setCurrentIndex(0); - resetNextButton(); - resetBackButton(); - - // init elems - elmsWidget = new ElementsWidget( ui->page_2 ); - ui->gridLayout_2->addWidget(elmsWidget); - - defineSource(); - defineReactionSets(); - - // signals and slots connections - connect( ui->bBack, SIGNAL(clicked()), this, SLOT(CmBack())); - connect( ui->bHelp, SIGNAL( clicked() ), this, SLOT( CmHelp() ) ); - connect( ui->bReset, SIGNAL( clicked() ), this, SLOT( CmReset() ) ); - connect( ui->bSelectAll, SIGNAL( clicked() ), this, SLOT( CmSelectAll() ) ); - connect( ui->pCancelButton, SIGNAL( clicked() ),this, SLOT( reject() ) ); -} - -SelectElementsDialog::~SelectElementsDialog() -{ - delete pTable; - delete data; - delete elmsWidget; - delete ui; -} - - -//------------------- Actions - -void SelectElementsDialog::CmBack() -{ - ui->stackedWidget->setCurrentIndex( ui->stackedWidget->currentIndex()-1 ); - resetNextButton(); - resetBackButton(); -} - -void SelectElementsDialog::CmNext() -{ - try - { - if(ui->stackedWidget->currentIndex()==0) - { - int ndx = pTable->currentIndex().sibling(pTable->currentIndex().row(),0).data().toInt(); - defineElements( ndx ); - } - if(ui->stackedWidget->currentIndex()==1) - { - // select - updateReactionSets(); - } - ui->stackedWidget->setCurrentIndex ( ui->stackedWidget->currentIndex()+1 ); - resetNextButton(); - resetBackButton(); - } - catch(jsonio::jsonio_exception& e) - { - QMessageBox::critical( this, e.title(), e.what() ); - } - catch(std::exception& e) - { - QMessageBox::critical( this, "std::exception", e.what() ); - } -} - -void SelectElementsDialog::CmOk() -{ - accept(); -} - - -void SelectElementsDialog::CmSelectAll() -{ - switch( ui->stackedWidget->currentIndex() ) - { - case 1: elmsWidget->CmSelectAll(); - break; - default: - break; - } -} - - -void SelectElementsDialog::CmReset() -{ - switch( ui->stackedWidget->currentIndex() ) - { - case 1: elmsWidget->CmReset(); - break; - default: - break; - } -} - -//-------------------------------------------------------------------- - -void SelectElementsDialog::defineSource() -{ - vector _list = pdata->getSourcetdbList(); - - data = new SelectTable("select", _list, '-'); - TMatrixModel* model = new TMatrixModel( data, this ); - pTable = new TMatrixTable(this, TMatrixTable::tbNoMenu ); - pTable->setModel(model); - ui->gridLayout->addWidget(pTable, 2, 0, 1, 1); - pTable->horizontalHeader()->hide(); - pTable->setSelectionBehavior(QAbstractItemView::SelectRows); - pTable->setSelectionMode(QAbstractItemView::SingleSelection); - pTable->setCurrentIndex( pTable->model()->index(0,0) ); - pTable->SelectRow(); -} - -void SelectElementsDialog::defineElements( int sourcetdb ) -{ - if( pdata->makeAvailableElementsList(sourcetdb)) - { - const vector& elements = pdata->allAvailableElementsList(); - //foreach ( ElementKey elm, elements) - // cout << elm.symbol << endl; - elmsWidget->setElementList( elements ); - } -} - -void SelectElementsDialog::defineReactionSets() -{ - rcsetTable = new TMatrixTable( this ); - rcsetTable->setModel(pdata->rcsetModel.get()); - rcsetTable->horizontalHeader()->setSectionResizeMode( QHeaderView::Interactive ); - rcsetTable->setSelectionBehavior(QAbstractItemView::SelectRows); - rcsetTable->setSelectionMode(QAbstractItemView::SingleSelection); - QObject::disconnect( rcsetTable, SIGNAL(customContextMenuRequested(QPoint)), - rcsetTable, SLOT(slotPopupContextMenu(QPoint))); - ui->verticalLayout->addWidget(rcsetTable); -} - -void SelectElementsDialog::updateReactionSets() -{ - vector elementKeys; - allSelected( elementKeys ); - int curndx = pdata->loadReacSetRecords( elementKeys ); - rcsetTable->setCurrentIndex(rcsetTable->model()->index( curndx,0 )); - rcsetTable->SelectRow(); -} - -// -- Returns selection array -void SelectElementsDialog::allSelected( vector& elementKeys ) const -{ - elementKeys.clear(); - string idrc = idReactionSet(); - if( !idrc.empty() ) - { - auto ellst = pdata->ThermoHubClient.reactSetData().getElementsList(idrc); - elementKeys.insert( elementKeys.end(), ellst.begin(), ellst.end() ); - return; - } - elmsWidget->allSelected( elementKeys ); -} - -int SelectElementsDialog::sourceTDB() const -{ - return pdata->sourceTDB; -} - -string SelectElementsDialog::idReactionSet() const -{ - int ndx = rcsetTable->currentIndex().row(); - return pdata->getReactionSetId( ndx ); -} - - -void SelectElementsDialog::setData( int sourcetdb, - const vector& elementKeys, const string& idRcSet ) -{ - if( elementKeys.empty() ) - return; - - pdata->idReactopnSet = idRcSet; - auto index = pTable->currentIndex(); - for( int ii =0; ii< pTable->model()->rowCount(); ii++ ) - { - index = index.sibling( ii,0 ); - if( index.data().toInt() == sourcetdb ) - { - pTable->setCurrentIndex(index); - CmNext(); - elmsWidget->selectElementList(elementKeys); - } - } -} - - -// ------------------------ OK old - -void SelectElementsDialog::resetNextButton() -{ - - ui->bReset->setVisible(ui->stackedWidget->currentIndex() == 1 ); - ui->bSelectAll->setVisible(ui->stackedWidget->currentIndex() == 1 ); - - if( ui->stackedWidget->currentIndex() == ui->stackedWidget->count() - 1 ) - { - ui->bNext->disconnect(); - connect( ui->bNext, SIGNAL(clicked()), this, SLOT(CmOk()) ); - ui->bNext->setText("&Finish"); - } - else - { - ui->bNext->disconnect(); - connect( ui->bNext, SIGNAL(clicked()), this, SLOT(CmNext()) ); - ui->bNext->setText("&Next>"); - } -} - -void SelectElementsDialog::resetBackButton() -{ - ui->bBack->setEnabled( ui->stackedWidget->currentIndex() > 0 ); -} - - diff --git a/ThermoFunGui/src/SelectElementsDialog.h b/ThermoFunGui/src/SelectElementsDialog.h deleted file mode 100644 index 0a0534e5..00000000 --- a/ThermoFunGui/src/SelectElementsDialog.h +++ /dev/null @@ -1,81 +0,0 @@ -#ifndef SELECTELEMENTSDIALOG_H -#define SELECTELEMENTSDIALOG_H - -#include -#include -#include "jsonui/SelectDialog.h" - -// ThermoFun includes -#ifdef FROM_SRC -#include "../ThermoFun/Common/formuladata.h" -#include "../ThermoHubClient/DatabaseClient.h" -#include "../ThermoHubClient/ReactionSetData.h" -#include "../ThermoHubClient/SubstanceData.h" -#endif -#ifndef FROM_SRC -#include "ThermoFun/Common/formuladata.h" -#include "ThermoHubClient/DatabaseClient.h" -#include "ThermoHubClient/ReactionSetData.h" -#include "ThermoHubClient/SubstanceData.h" -#endif - -namespace Ui { -class SelectElements; -} - -class SelectElementsDialogPrivate; -class ElementsWidget; - -class SelectElementsDialog : public QDialog -{ - Q_OBJECT - - void resetNextButton(); - void resetBackButton(); - - void defineSource(); - void defineElements( int sourcetdb ); - void defineReactionSets(); - void updateReactionSets(); - -protected slots: - - void objectChanged(){} - - void CmHelp() {} - void CmOk(); - void CmNext(); - void CmBack(); - void CmReset(); - void CmSelectAll(); - -public: - - explicit SelectElementsDialog(ThermoFun::DatabaseClient ThermoHubClient, QWidget *parent = 0); - ~SelectElementsDialog(); - - void setData( int sourcetdb, const std::vector& elementKeys, const std::string& idRcSet ); - void allSelected( std::vector& elementKeys ) const; - int sourceTDB() const; - std::string idReactionSet() const; - -private: - - Ui::SelectElements *ui; - - // Step1 - jsonui::SelectTable *data; - jsonui::TMatrixTable *pTable; - // Step2 - /// Widget to selection of elements - ElementsWidget* elmsWidget; - // Step3 - /// ReactionSet selection table - jsonui::TMatrixTable* rcsetTable = 0; - - /// Internal Data - std::unique_ptr pdata; - -}; - -#endif // SELECTELEMENTSDIALOG_H diff --git a/ThermoFunGui/src/SelectElementsDialog.ui b/ThermoFunGui/src/SelectElementsDialog.ui deleted file mode 100644 index c07f2531..00000000 --- a/ThermoFunGui/src/SelectElementsDialog.ui +++ /dev/null @@ -1,233 +0,0 @@ - - - SelectElements - - - Qt::WindowModal - - - - 0 - 0 - 724 - 529 - - - - - 0 - 0 - - - - - 10 - - - - Selection of Independent Components into Modelling Project - - - true - - - true - - - - - - - 0 - 0 - - - - 1 - - - - - - - Qt::Horizontal - - - - - - - - 0 - 0 - - - - - 75 - true - - - - Step 1 - Selection of databases - - - - - - - - - - - - - - - 0 - 0 - - - - - 75 - true - - - - Step 3 - Selection of ReactionSet - - - - - - - Qt::Horizontal - - - - - - - - - - - - - - 75 - true - - - - &Learn more - - - F1 - - - - - - - - 75 - true - - - - Clear Selection - - - - - - - - 75 - true - - - - Select All - - - - - - - Qt::Horizontal - - - - 40 - 20 - - - - - - - - - 75 - true - - - - < &Back - - - - - - - - 75 - true - - - - &Next > - - - - - - - - 75 - true - - - - &Cancel - - - - - - - - - - - - pCancelButton - clicked() - SelectElements - reject() - - - 651 - 524 - - - 351 - 276 - - - - - diff --git a/ThermoFunGui/src/SelectThermoDataDialog.cpp b/ThermoFunGui/src/SelectThermoDataDialog.cpp deleted file mode 100644 index e096a2b3..00000000 --- a/ThermoFunGui/src/SelectThermoDataDialog.cpp +++ /dev/null @@ -1,605 +0,0 @@ -#include -#include -#include -#include "SelectThermoDataDialog.h" -#include "ui_SelectThermoDataDialog.h" -#include "ElementsWidget.h" -#include "thermomodel.h" -#include "jsonui/TCSVPage.h" - -// ThermoFun includes -#ifdef FROM_SRC -#include "../ThermoHubClient/ThermoSetData.h" -#include "../ThermoHubClient/SubstanceData.h" -#include "../ThermoHubClient/ReactionData.h" -#include "../ThermoHubClient/ReactionSetData.h" -#else -#include "ThermoHubClient/ThermoSetData.h" -#include "ThermoHubClient/SubstanceData.h" -#include "ThermoHubClient/ReactionData.h" -#include "tThermoHubClient/ReactionSetData.h" -#endif - -using namespace std; -using namespace jsonui; - -struct SelectThermoDataDialogPrivate -{ - // Window data --------------------------- - - /// Link to top level widget - SelectThermoDataDialog* _window; - /// Connect to DatabaseClient for requests - ThermoFun::DatabaseClient& _ThermoHubClient; - - // Thermodata selection containers - std::shared_ptr thermoModel; - std::shared_ptr substModel; - std::shared_ptr reactModel; - std::shared_ptr rcsetModel; - - // Selected data --------------------------- - - /// Selected ThermoDataSet - string idThermoDataSet; - /// Selected SourceTDBs - vector sourceTDBs; - - /// Define ELEMENTS table data - vector elementsAll; - /// Selected elements - vector elementsSelected; - - /// Solvent substances Values ( for selected elements ) - jsonio::ValuesTable solventValues; - - // --------------------------------------------- - - SelectThermoDataDialogPrivate(SelectThermoDataDialog* awindow, ThermoFun::DatabaseClient& aThermoHubClient): - _window(awindow), _ThermoHubClient( aThermoHubClient ), idThermoDataSet("") - { - sourceTDBs.clear(); - thermoModel.reset(new ThermoViewModel( &_ThermoHubClient.thermoDataSet() , _window )); - substModel.reset(new ThermoViewModel( &_ThermoHubClient.substData(), _window )); - reactModel.reset(new ThermoViewModel( &_ThermoHubClient.reactData(), _window )); - rcsetModel.reset(new ThermoViewModel( &_ThermoHubClient.reactSetData(), _window )); - } - - ~SelectThermoDataDialogPrivate() - { } - - vector getSourcetdbList() - { - return _ThermoHubClient.sourcetdbListAll(); - } - - bool makeAvailableElementsListA( size_t selrow ) - { - auto matr = thermoModel->getValues(); - string idThermo = matr[selrow][_ThermoHubClient.thermoDataSet().getDataName_DataIndex().at("_id")]; - auto elmnts = _ThermoHubClient.thermoDataSet().getElementsList(idThermo); - elementsAll.clear(); - if( !elmnts.empty() ) - { - idThermoDataSet = idThermo; - sourceTDBs = _ThermoHubClient.thermoDataSet().sourceTDBs(idThermoDataSet); - elementsAll.insert( elementsAll.begin(), elmnts.begin(), elmnts.end() ); - } - return true; - } - - bool makeAvailableElementsListB( const vector& sourcetdbs ) - { - sourceTDBs = sourcetdbs; - auto elmnts = _ThermoHubClient.thermoDataSet().selectElementsFromSubstancesGiven( sourceTDBs ); - elementsAll.clear(); - if( !elmnts.empty() ) - for(auto s : elmnts) { - elementsAll.push_back(s); - } - return true; - } - - const vector& allAvailableElementsList() const - { - return elementsAll; - } - - void loadSubstanceRecords( bool typeA, const vector& elements, bool unique ) - { - elementsSelected = elements; - vector substanceSymbols; - - // search for solvent in all ThermoDataSet - substanceSymbols = _ThermoHubClient.substData().selectGiven( {idThermoDataSet}, false ); - const jsonio::ValuesTable& subData = _ThermoHubClient.substData().getValuesTable(); - substModel->loadModeRecords( subData ); - - // build solvents table - solventValues.clear(); - std::map name_datindex = _ThermoHubClient.substData().getDataName_DataIndex(); - for( auto subRecord: subData ) - { - size_t x = name_datindex["class_"]; - if( subRecord[x] == "{\"3\":\"SC_AQSOLVENT\"}" ) - solventValues.push_back(subRecord); - } - - if( typeA ) - substanceSymbols = _ThermoHubClient.substData().selectGiven( idThermoDataSet, elements, false ); - else - substanceSymbols = _ThermoHubClient.substData().selectGiven( sourceTDBs, elements, unique ); - - const jsonio::ValuesTable& subData2 = _ThermoHubClient.substData().getValuesTable(); - - substModel->loadModeRecords( subData2 ); - } - - void loadReactionRecords( bool typeA, const std::set& substSelectedRows, bool unique ) - { - vector reactSymbols; - auto substanceSymbols = substModel->getColumn( _ThermoHubClient.substData().getDataName_DataIndex().at("symbol"), substSelectedRows ); - if( typeA ) - reactSymbols = _ThermoHubClient.reactData().selectGiven( idThermoDataSet, substanceSymbols ); - else - reactSymbols = _ThermoHubClient.reactData().selectGiven( sourceTDBs, substanceSymbols, unique ); - - reactModel->loadModeRecords( _ThermoHubClient.reactData().getValuesTable() ); - } - - void loadReacSetRecords( bool typeA, const std::set& reactSelectedRows, bool unique ) - { - vector scsetSymbols; - auto reactSymbols = reactModel->getColumn( _ThermoHubClient.reactData().getDataName_DataIndex().at("symbol"), reactSelectedRows ); - if( typeA ) - scsetSymbols = _ThermoHubClient.reactSetData().selectGiven( idThermoDataSet, reactSymbols ); - else - scsetSymbols = _ThermoHubClient.reactSetData().selectGiven( sourceTDBs, reactSymbols, unique ); - - rcsetModel->loadModeRecords( _ThermoHubClient.reactSetData().getValuesTable() ); - } - -}; - -//=========================================================================== - -SelectThermoDataDialog::SelectThermoDataDialog( char acase, ThermoFun::DatabaseClient& ThermoHubClient, QWidget *parent) : - QDialog(parent), useCase(acase), - ui(new Ui::SelectThermoData), pdata(new SelectThermoDataDialogPrivate( this, ThermoHubClient)) -{ - updateFrom = 0; - ui->setupUi(this); - ui->checkUnique->hide(); - - if( useCase=='A') - { - defineTermodata(); - ui->stackedWidget->setCurrentIndex(0); - } - else - { - defineSourceTDB(); - ui->stackedWidget->setCurrentIndex(1); - } - resetButtons(); - - // init elems - elmsWidget = new ElementsWidget( ui->page_2 ); - ui->gridLayout_2->addWidget(elmsWidget); - - defineSubstance(); - defineReaction(); - defineReactionSets(); - - // signals and slots connections - connect( ui->bBack, SIGNAL(clicked()), this, SLOT(CmBack())); - connect( ui->bNext, SIGNAL(clicked()), this, SLOT(CmNext())); - connect( ui->bFinish, SIGNAL(clicked()), this, SLOT(CmFinish())); - - connect( ui->bHelp, SIGNAL( clicked() ), this, SLOT( CmHelp() ) ); - connect( ui->bReset, SIGNAL( clicked() ), this, SLOT( CmClearSelection() ) ); - connect( ui->bSelectAll, SIGNAL( clicked() ), this, SLOT( CmSelectAll() ) ); - connect( ui->pCancelButton, SIGNAL( clicked() ),this, SLOT( reject() ) ); -} - -SelectThermoDataDialog::SelectThermoDataDialog( const std::string& aThermoDataSet, - const std::vector& elementKeys, - ThermoFun::DatabaseClient& ThermoHubClient, QWidget *parent ): - SelectThermoDataDialog('A', ThermoHubClient, parent ) -{ - // set old selection - selectA( aThermoDataSet, elementKeys ); -} - -SelectThermoDataDialog::SelectThermoDataDialog( const std::vector& sourcetdbs, - const std::vector& elementKeys, - ThermoFun::DatabaseClient& ThermoHubClient, QWidget *parent ): - SelectThermoDataDialog('B', ThermoHubClient, parent ) -{ - // set old selection - selectB( sourcetdbs, elementKeys ); -} - -SelectThermoDataDialog::~SelectThermoDataDialog() -{ - if( thermoTable ) - delete thermoTable; - if( data ) - delete data; - if( sourceDBTable ) - delete sourceDBTable; - if( substTable ) - delete substTable; - if( reactTable ) - delete reactTable; - if( rcsetTable ) - delete rcsetTable; - - delete elmsWidget; - delete ui; -} - -// -- Returns selection elements array -void SelectThermoDataDialog::allSelected( vector& elementKeys ) const -{ - elementKeys.clear(); - elmsWidget->allSelected( elementKeys ); -} - -// Selection of data starting from ThermoDataSet -std::string SelectThermoDataDialog::idThermoDataSet() const -{ - return pdata->idThermoDataSet; -} - -// Selection of data starting from sourceTDBs -const std::vector& SelectThermoDataDialog::sourceTDBs() const -{ - return pdata->sourceTDBs; -} - -// Get the selected substances container -const jsonio::ValuesTable& SelectThermoDataDialog::getSubstanceValues() const -{ - return pdata->substModel->getValues(); -} - -// Get the selected reactions container -const jsonio::ValuesTable& SelectThermoDataDialog::getReactionValues() const -{ - return pdata->reactModel->getValues(); -} - -// Get Solvent substances container -const jsonio::ValuesTable& SelectThermoDataDialog::getSolventValues() const -{ - return pdata->solventValues; -} - -const jsonio::ValuesTable &SelectThermoDataDialog::getReactionSetValues() const -{ - return pdata->rcsetModel->getValues(); -} - -//------------------- Actions - -void SelectThermoDataDialog::CmBack() -{ - ui->stackedWidget->setCurrentIndex( ui->stackedWidget->currentIndex()-1 ); - if( useCase=='A' && ui->stackedWidget->currentIndex()==1 ) - ui->stackedWidget->setCurrentIndex( ui->stackedWidget->currentIndex()-1 ); - resetButtons(); -} - -void SelectThermoDataDialog::CmNext() -{ - try - { - auto current = ui->stackedWidget->currentIndex(); - switch( current ) - { - case 0: - updateElementsThermo(); - current++; - break; - case 1: - updateElementsSourceTDBs(); - ui->checkUnique->show(); - break; - case 2: - updateSubstance(); - break; - case 3: - updateReaction(); - break; - case 4: - updateReactionSets(); - break; - } - ui->stackedWidget->setCurrentIndex ( current+1 ); - resetButtons(); - } - catch(jsonio::jsonio_exception& e) - { - QMessageBox::critical( this, e.title(), e.what() ); - } - catch(std::exception& e) - { - QMessageBox::critical( this, "std::exception", e.what() ); - } -} - -void SelectThermoDataDialog::CmFinish() -{ - try - { - auto current = ui->stackedWidget->currentIndex(); - switch( current ) - { - // The container for substances, reactions, and reactionsSets belonging to the ThermoDataset - // and containing the selected elements will be field - case 2: updateSubstance(); - // The selected substances will be loaded in the substance container (SubstanceData::ValuesTable), - // followed by the reactions container (ReactionData::ValuesTable) containing the selected substances - // and reactionSets container (ReactionSetData::ValuesTable) containing the reactions - case 3: updateReaction(); - // The selected reactions will be loaded in the reactions container (ReactionData::ValuesTable), - // followed by the reactionSets container (ReactionSetData::ValuesTable) containing the selected reactions - case 4: updateReactionSets(); - break; - } - // left only selected in mode - leftOnlySelected(); - accept(); - } - catch(jsonio::jsonio_exception& e) - { - QMessageBox::critical( this, e.title(), e.what() ); - } - catch(std::exception& e) - { - QMessageBox::critical( this, "std::exception", e.what() ); - } - -} - - -void SelectThermoDataDialog::CmSelectAll() -{ - switch( ui->stackedWidget->currentIndex() ) - { - case 2: elmsWidget->CmSelectAll(); - break; - case 1: sourceDBTable->SelectAll(); - break; - case 3: substTable->SelectAll(); - break; - case 4: reactTable->SelectAll(); - break; - case 5: rcsetTable->SelectAll(); - break; - default: - break; - } -} - - -void SelectThermoDataDialog::CmClearSelection() -{ - switch( ui->stackedWidget->currentIndex() ) - { - case 2: elmsWidget->CmReset(); - break; - case 1: sourceDBTable->clearSelection(); - break; - case 3: substTable->clearSelection(); - break; - case 4: reactTable->clearSelection(); - break; - case 5: rcsetTable->clearSelection(); - break; - default: - break; - } -} - -void SelectThermoDataDialog::resetButtons() -{ - auto current = ui->stackedWidget->currentIndex(); - ui->bReset->setVisible( current != 0 ); - ui->bSelectAll->setVisible(current != 0 ); - ui->bBack->setEnabled( current > 1 ); - ui->bNext->setEnabled( current < ui->stackedWidget->count() - 1 ); - ui->bFinish->setEnabled( current > 1 ); -} - - -//-------------------------------------------------------------------- - -void SelectThermoDataDialog::defineSourceTDB() -{ - vector _list = pdata->getSourcetdbList(); - - data = new SelectTable("select", _list, '-'); - TMatrixModel* model = new TMatrixModel( data, this ); - sourceDBTable = new TMatrixTable(this, TMatrixTable::tbNoMenu ); - sourceDBTable->setModel(model); - ui->verticalLayout_2->addWidget(sourceDBTable); - sourceDBTable->horizontalHeader()->hide(); - sourceDBTable->setSelectionBehavior(QAbstractItemView::SelectRows); - sourceDBTable->setSelectionMode(QAbstractItemView::MultiSelection); - sourceDBTable->setCurrentIndex( sourceDBTable->model()->index(0,0) ); - sourceDBTable->SelectRow(); - connect( sourceDBTable->selectionModel(), SIGNAL(selectionChanged(const QItemSelection &, const QItemSelection &)), - this, SLOT(updateAllFrom1(const QItemSelection &, const QItemSelection &)) ); -} - - -void SelectThermoDataDialog::setModel( TMatrixTable* table, TMatrixModel* model ) -{ - table->setModel(model); - table->horizontalHeader()->setSectionResizeMode( QHeaderView::Interactive ); - table->setSelectionBehavior(QAbstractItemView::SelectRows); - table->setSelectionMode(QAbstractItemView::MultiSelection); - QObject::disconnect( table, SIGNAL(customContextMenuRequested(QPoint)), - table, SLOT(slotPopupContextMenu(QPoint))); -} - -void SelectThermoDataDialog::defineTermodata() -{ - thermoTable = new TMatrixTableProxy( this, TMatrixTable::tbSort ); - setModel( thermoTable, pdata->thermoModel->getModel() ); - thermoTable->setSelectionMode(QAbstractItemView::SingleSelection); - ui->verticalLayout_3->addWidget(thermoTable); - pdata->thermoModel->loadModeRecords( jsonio::emptyQuery, -1, {} ); - connect( thermoTable->selectionModel(), SIGNAL(selectionChanged(const QItemSelection &, const QItemSelection &)), - this, SLOT(updateAllFrom0(const QItemSelection &, const QItemSelection &)) ); -} - -void SelectThermoDataDialog::defineSubstance() -{ - substTable = new TMatrixTableProxy( this, TMatrixTable::tbSort ); - setModel( substTable, pdata->substModel->getModel() ); - ui->verticalLayout->addWidget(substTable); - connect( substTable->selectionModel(), SIGNAL(selectionChanged(const QItemSelection &, const QItemSelection &)), - this, SLOT(updateAllFrom3(const QItemSelection &, const QItemSelection &)) ); -} - -void SelectThermoDataDialog::defineReaction() -{ - reactTable = new TMatrixTableProxy( this, TMatrixTable::tbSort ); - setModel( reactTable, pdata->reactModel->getModel() ); - ui->verticalLayout_5->addWidget(reactTable); - connect( reactTable->selectionModel(), SIGNAL(selectionChanged(const QItemSelection &, const QItemSelection &)), - this, SLOT(updateAllFrom4(const QItemSelection &, const QItemSelection &)) ); -} - -void SelectThermoDataDialog::defineReactionSets() -{ - rcsetTable = new TMatrixTableProxy( this, TMatrixTable::tbSort ); - setModel( rcsetTable, pdata->rcsetModel->getModel() ); - ui->verticalLayout_6->addWidget(rcsetTable); -} - -void SelectThermoDataDialog::updateElementsThermo() -{ - if( updateFrom > 1) // nothing change on page 0 - return; - - auto ndxthermo = thermoTable->getCurrentRow(); - if( pdata->makeAvailableElementsListA(ndxthermo)) - { - const vector& elements = pdata->allAvailableElementsList(); - //foreach ( ElementKey elm, elements) - // cout << elm.symbol << endl; - elmsWidget->setElementList( elements ); - elmsWidget->selectElementList( pdata->elementsSelected ); - updateFrom = 2; - } -} - -void SelectThermoDataDialog::updateElementsSourceTDBs() -{ - if( updateFrom > 1) // nothing change on page 0 - return; - std::vector sourcetdbs; - QModelIndexList indexList = sourceDBTable->selectionModel()->selectedIndexes(); - foreach (QModelIndex index, indexList) - { - if(index.column() == 0 ) - sourcetdbs.push_back( index.data().toInt() ); - } - if( pdata->makeAvailableElementsListB(sourcetdbs) ) - { - const vector& elements = pdata->allAvailableElementsList(); - elmsWidget->setElementList( elements ); - elmsWidget->selectElementList( pdata->elementsSelected ); - updateFrom = 2; - } -} - - -void SelectThermoDataDialog::updateSubstance() -{ - vector elementKeys; - allSelected( elementKeys ); - - // test change element selected - if( elementKeys != pdata->elementsSelected ) - updateFrom = min( 2, updateFrom); - - if( updateFrom > 2 ) // nothing change on pages 0-2 - return; - - pdata->loadSubstanceRecords( (useCase=='A'), elementKeys, ui->checkUnique->isChecked() ); - substTable->selectAll(); - - updateFrom = 3; -} - -void SelectThermoDataDialog::updateReaction() -{ - if( updateFrom > 3 ) // nothing change on pages 0-3 - return; - - auto substsel = substTable->allSelectedRows(); - pdata->loadReactionRecords( (useCase=='A'), substsel, ui->checkUnique->isChecked() ); - reactTable->selectAll(); - - updateFrom = 4; -} - - -void SelectThermoDataDialog::updateReactionSets() -{ - if( updateFrom > 4 ) // nothing change on pages 0-4 - return; - - auto reactsel = reactTable->allSelectedRows(); - pdata->loadReacSetRecords( (useCase=='A'), reactsel, ui->checkUnique->isChecked() ); - rcsetTable->selectAll(); - updateFrom = 5; -} - - - -void SelectThermoDataDialog::leftOnlySelected() -{ - pdata->substModel->leftOnlySelected( substTable->allSelectedRows()); - pdata->reactModel->leftOnlySelected(reactTable->allSelectedRows()); - pdata->rcsetModel->leftOnlySelected(rcsetTable->allSelectedRows()); -} - -void SelectThermoDataDialog::selectRows( jsonui::TMatrixTable *dataTable, const std::vector& rows ) -{ - for(auto row: rows) - { - QModelIndex index = dataTable->model()->index(row,0); - dataTable->selectionModel()->select(index, QItemSelectionModel::Rows|QItemSelectionModel::Select); - } -} - -void SelectThermoDataDialog::selectA( const std::string& aThermoDataSet, const std::vector& elementKeys ) -{ - auto row = pdata->thermoModel->findRow( pdata->_ThermoHubClient.thermoDataSet().getDataName_DataIndex().at("_id"), aThermoDataSet, true ); - thermoTable->setCurrentRow( row ); - pdata->elementsSelected = elementKeys; -} - -void SelectThermoDataDialog::selectB( const std::vector& sourcetdbs, const std::vector& elementKeys ) -{ - vector rows; - for( auto sourcetdb: sourcetdbs ) - for( int ii=0; iirowCount(); ii++ ) - { - if( data->data( ii, 0 ).toInt() == sourcetdb ) - rows.push_back(ii); - } - - if( rows.size() > 0) - sourceDBTable->clearSelection(); - selectRows( sourceDBTable, rows ); - pdata->elementsSelected = elementKeys; -} - -//-------------------------------------------------------------------------------------------------- diff --git a/ThermoFunGui/src/SelectThermoDataDialog.h b/ThermoFunGui/src/SelectThermoDataDialog.h deleted file mode 100644 index 781d3424..00000000 --- a/ThermoFunGui/src/SelectThermoDataDialog.h +++ /dev/null @@ -1,145 +0,0 @@ -#ifndef SELECTTHERMODIALOG_H -#define SELECTTHERMODIALOG_H - -#include -#include -#include "jsonui/SelectDialog.h" -// ThermoFun includes -#ifdef FROM_SRC -#include "../ThermoHubClient/DatabaseClient.h" -#else -#include "ThermoHubClient/DatabaseClient.h" -#endif - -namespace Ui { -class SelectThermoData; -} - -struct SelectThermoDataDialogPrivate; -class ElementsWidget; - -class SelectThermoDataDialog : public QDialog -{ - Q_OBJECT - -protected slots: - - void objectChanged(){} - - void CmHelp() {} - void CmFinish(); - void CmNext(); - void CmBack(); - void CmClearSelection(); - void CmSelectAll(); - - void updateAllFrom0(const QItemSelection &, const QItemSelection &) - { - updateFrom = 0; - } - void updateAllFrom1(const QItemSelection &, const QItemSelection &) - { - updateFrom = 1; - } - void updateAllFrom3(const QItemSelection &, const QItemSelection &) - { - updateFrom = std::min(3,updateFrom ); - } - void updateAllFrom4(const QItemSelection &, const QItemSelection &) - { - updateFrom = std::min(4,updateFrom ); - } - -public: - - explicit SelectThermoDataDialog( char acase, ThermoFun::DatabaseClient& ThermoHubClient, QWidget *parent = nullptr); - - SelectThermoDataDialog( const std::string& aThermoDataSet, const std::vector& elementKeys, - ThermoFun::DatabaseClient& ThermoHubClient, QWidget *parent = nullptr); - SelectThermoDataDialog( const std::vector& sourcetdbs, const std::vector& elementKeys, - ThermoFun::DatabaseClient& ThermoHubClient, QWidget *parent = nullptr); - - ~SelectThermoDataDialog(); - - /// Return all selected elements - void allSelected( std::vector& elementKeys ) const; - - /// Selection of data starting from ThermoDataSet - std::string idThermoDataSet() const; - - /// Selection of data starting from sourceTDBs - const std::vector& sourceTDBs() const; - - /// Get the selected substances container - const jsonio::ValuesTable& getSubstanceValues() const; - - /// Get the selected reactions container - const jsonio::ValuesTable& getReactionValues() const; - - /// Get Solvent substances container - const jsonio::ValuesTable& getSolventValues() const; - - /// Get the selected reactions container - const jsonio::ValuesTable& getReactionSetValues() const; - - -private: - - /// There are two cases for selecting data in the widgets that I foresee: - /// A. Selection of data starting from ThermoDataSet list – select one ThermoDataSet - /// B. Selection of data starting from sourcetdb list – select one or more sourceDB - char useCase; - /// Flag for reset old selection - int updateFrom = 0; - - Ui::SelectThermoData *ui; - - // StepA - /// ThermoDataSet selection table - jsonui::TMatrixTableProxy *thermoTable = nullptr; - // StepB - /// Selection of data starting from sourcetdb list - jsonui::SelectTable *data = nullptr; - jsonui::TMatrixTable *sourceDBTable = nullptr; - // Step2 - /// Widget to selection of elements - ElementsWidget* elmsWidget; - // Step3 - /// SubstanceData::ValuesTable selection table - jsonui::TMatrixTableProxy* substTable = nullptr; - // Step4 - /// ReactionData::ValuesTable selection table - jsonui::TMatrixTableProxy* reactTable = nullptr; - // Step5 - /// ReactionSetData::ValuesTable selection table - jsonui::TMatrixTableProxy* rcsetTable = nullptr; - - /// Internal Data - std::unique_ptr pdata; - - void resetButtons(); - void setModel( jsonui::TMatrixTable* table, jsonui::TMatrixModel* model ); - void selectRows( jsonui::TMatrixTable *dataTable, const std::vector& rows ); - - // define windows - void defineTermodata(); - void defineSourceTDB(); - void defineSubstance(); - void defineReaction(); - void defineReactionSets(); - void selectA( const std::string& aThermoDataSet, const std::vector& elementKeys ); - void selectB( const std::vector& sourcetdbs, const std::vector& elementKeys ); - - // updateData - void updateElementsThermo(); - void updateElementsSourceTDBs(); - void updateSubstance(); - void updateReaction(); - void updateReactionSets(); - - /// Update all table containers - left only selected values - void leftOnlySelected(); - -}; - -#endif // SELECTTHERMODIALOG_H diff --git a/ThermoFunGui/src/SelectThermoDataDialog.ui b/ThermoFunGui/src/SelectThermoDataDialog.ui deleted file mode 100644 index 3e652863..00000000 --- a/ThermoFunGui/src/SelectThermoDataDialog.ui +++ /dev/null @@ -1,346 +0,0 @@ - - - SelectThermoData - - - Qt::WindowModal - - - - 0 - 0 - 724 - 551 - - - - - 0 - 0 - - - - - 10 - - - - Selection of Independent Components into Modelling Project - - - true - - - true - - - - - - - 0 - 0 - - - - 5 - - - - - - - - 0 - 0 - - - - - 75 - true - - - - Step 1 - Selection of data starting from ThermoDataSet list – select one ThermoDataSet - - - - - - - Qt::Horizontal - - - - - - - - - - - - 0 - 0 - - - - - 75 - true - - - - Step 1 - Selection of data starting from sourcetdb list – select one or more sourceDB - - - - - - - Qt::Horizontal - - - - - - - - - - - - - - - 0 - 0 - - - - - 75 - true - - - - Step 3 - Select the list of substances linked to - - - - - - - Qt::Horizontal - - - - - - - - - - - - 0 - 0 - - - - - 75 - true - - - - Step 4 - Select list of reactions connected to - - - - - - - Qt::Horizontal - - - - - - - - - - - - 0 - 0 - - - - - 75 - true - - - - Step 5 - Select the list of reactionSets connected to - - - - - - - Qt::Horizontal - - - - - - - - - - - Unique symbols can be selected in the following page - - - false - - - - - - - - - - 75 - true - - - - &Learn more - - - F1 - - - - - - - - 75 - true - - - - Select All - - - - - - - - 75 - true - - - - Clear Selection - - - - - - - Qt::Horizontal - - - - 40 - 20 - - - - - - - - - 75 - true - - - - < &Back - - - - - - - - 75 - true - - - - &Next > - - - - - - - - 75 - true - - - - &Finish - - - - - - - - 75 - true - - - - &Cancel - - - - - - - - - - - - pCancelButton - clicked() - SelectThermoData - reject() - - - 651 - 524 - - - 351 - 276 - - - - - diff --git a/ThermoFunGui/src/TPSetDialog.cpp b/ThermoFunGui/src/TPSetDialog.cpp deleted file mode 100644 index 9f4ae1af..00000000 --- a/ThermoFunGui/src/TPSetDialog.cpp +++ /dev/null @@ -1,166 +0,0 @@ -#include -#include -#include "TPSetDialog.h" -#include "ui_TPSetDialog.h" - -TPSetDialog::TPSetDialog(QWidget *parent) : - QDialog(parent), - ui(new Ui::TPSetDialog) -{ - ui->setupUi(this); - PairwiseChecked(); - - QObject::connect( ui->pTfrom, SIGNAL(valueChanged( double )), this, SLOT(TChange())); - QObject::connect( ui->pTuntil, SIGNAL(valueChanged( double )), this, SLOT(TChange())); - QObject::connect( ui->pTstep, SIGNAL(valueChanged( double )), this, SLOT(TChange())); - QObject::connect( ui->pPfrom, SIGNAL(valueChanged( double )), this, SLOT(PChange())); - QObject::connect( ui->pPuntil, SIGNAL(valueChanged( double )), this, SLOT(PChange())); - QObject::connect( ui->pPstep, SIGNAL(valueChanged( double )), this, SLOT(PChange())); - QObject::connect( ui->pMode, SIGNAL(currentIndexChanged( int ) ), this, SLOT(PairwiseChecked())); -} - -TPSetDialog::~TPSetDialog() -{ - delete ui; -} - -QString TPSetDialog::getTUnits() -{ - return ui->pTun->currentText(); -} - -QString TPSetDialog::getPUnits() -{ - return ui->pPun->currentText(); -} - -std::vector> TPSetDialog::getTPpairs() -{ - std::vector> tppairs; - - long int j, i; - long int mode = ui->pMode->currentIndex(); - long int NT = ui->pNT->value(); - long int NP = ui->pNP->value(); - - long int NV = calcSize( mode, NT, NP ); - double Ti0 = ui->pTfrom->value(); - double Ti2 = ui->pTstep->value(); - double Pi0 = ui->pPfrom->value(); - double Pi2 = ui->pPstep->value(); - double Tij, Pij; - - // insert values to arrays rp->T, rp->P - switch( mode ) - { - default: - case 0: // the user must enter all P and T values in xP and xT vectors - for( i=0; ipTfrom->value(); - Tai[1] = ui->pTuntil->value(); - Tai[2] = ui->pTstep->value(); - nT = calcNpoints( Tai ); - ui->pNT->setValue(nT); -} - -void TPSetDialog::PChange() -{ - double Pai[4]; - long int nP; - Pai[0] = ui->pPfrom->value(); - Pai[1] = ui->pPuntil->value(); - Pai[2] = ui->pPstep->value(); - nP = calcNpoints( Pai ); - ui->pNP->setValue(nP); -} - -void TPSetDialog::PairwiseChecked() -{ - bool modeNoPair = ( ui->pMode->currentIndex() != 0); - - ui->pTfrom->setEnabled ( modeNoPair ); - ui->pTuntil->setEnabled ( modeNoPair ); - ui->pTstep->setEnabled ( modeNoPair ); - ui->pPfrom->setEnabled ( modeNoPair ); - ui->pPuntil->setEnabled ( modeNoPair ); - ui->pPstep->setEnabled ( modeNoPair ); - - ui->pNP->setEnabled ( !modeNoPair ); - ui->pNT->setEnabled ( !modeNoPair ); -} - - -long int TPSetDialog::calcSize( long int mode, long int NT, long int NP) -{ - long int NV; - switch( mode ) - { - default: - case 3: // parallel increments of T and P in one cycle - case 0: // the user must enter all P and T values in xP and xT vectors - NV = std::max( NP, NT ); - break; - case 1: // increments in cycle on P nested into cycle on T - case 2: // increments in cycle on T nested into cycle on P (default) - NV = NP * NT; - break; - } - return NV; -} - -/// Calculate number of points from iterators -long int TPSetDialog::calcNpoints( double Tai[4] ) -{ - long int nPoints = 0; - - if( fabs(Tai[2]) <= 1e-30 ) - nPoints = 1; - else - nPoints = (long int)( (Tai[1]-Tai[0]) / Tai[2] )+1; - - if( nPoints < 1 ) - nPoints = 1; - - return nPoints; -} diff --git a/ThermoFunGui/src/TPSetDialog.h b/ThermoFunGui/src/TPSetDialog.h deleted file mode 100644 index 34c9cef4..00000000 --- a/ThermoFunGui/src/TPSetDialog.h +++ /dev/null @@ -1,39 +0,0 @@ -#ifndef TPSETDIALOG_H -#define TPSETDIALOG_H - -#include -#include -#include - -namespace Ui { -class TPSetDialog; -} - -class TPSetDialog : public QDialog -{ - Q_OBJECT - - long int calcSize( long int mode, long int NT, long int NP); - /// Calculate number of points from iterators - long int calcNpoints( double Tai[4] ); - -protected slots: - - void PChange(); - void TChange(); - void PairwiseChecked(); - -public: - explicit TPSetDialog(QWidget *parent = 0); - ~TPSetDialog(); - - QString getTUnits(); - QString getPUnits(); - std::vector> getTPpairs(); - -private: - - Ui::TPSetDialog *ui; -}; - -#endif // TPSETDIALOG_H diff --git a/ThermoFunGui/src/TPSetDialog.ui b/ThermoFunGui/src/TPSetDialog.ui deleted file mode 100644 index d248fb4f..00000000 --- a/ThermoFunGui/src/TPSetDialog.ui +++ /dev/null @@ -1,499 +0,0 @@ - - - TPSetDialog - - - - 0 - 0 - 700 - 340 - - - - Define Temperature and Pressure points for ThermoFun calculations - - - - - - - - - - - - Temperature T - - - - - - Units - - - - - - - - 0 - 0 - - - - - 140 - 0 - - - - - C Celsius - - - - - K Kelvin - - - - - - - - Minimal - - - - - - - - 140 - 0 - - - - Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter - - - 2 - - - 5000.000000000000000 - - - 0.000000000000000 - - - - - - - Maximal - - - - - - - - 140 - 0 - - - - Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter - - - 2 - - - 5000.000000000000000 - - - 350.000000000000000 - - - - - - - Step - - - - - - - - 140 - 0 - - - - Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter - - - 2 - - - 200.000000000000000 - - - 5.000000000000000 - - - - - - - Number of points - - - Qt::AlignVCenter - - - true - - - - - - - - 0 - 0 - - - - - 0 - 0 - - - - 0 - - - 999 - - - 71 - - - - - - - - - - Pressure P - - - - - - Units - - - - - - - - 0 - 0 - - - - - 140 - 0 - - - - - b bar - - - - - B kbar - - - - - p Pa - - - - - P MPa - - - - - A atm - - - - - - - - Minimal - - - - - - - - 0 - 0 - - - - - 140 - 0 - - - - Qt::LeftToRight - - - Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter - - - 2 - - - 10000.000000000000000 - - - 0.000000000000000 - - - - - - - - 0 - 0 - - - - - 140 - 0 - - - - Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter - - - 2 - - - 100000.000000000000000 - - - 0.000000000000000 - - - - - - - Maximal - - - - - - - Step - - - - - - - - 0 - 0 - - - - - 140 - 0 - - - - Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter - - - 2 - - - 10000.000000000000000 - - - - - - - Number of points - - - Qt::AlignVCenter - - - true - - - - - - - - 0 - 0 - - - - - 0 - 0 - - - - 0 - - - 999 - - - 1 - - - - - - - - - - - - - 0 - 0 - - - - - 100 - 0 - - - - 2 - - - 4 - - - - 0 Pairwise given T and P - - - - - 1 P then T increments - - - - - 2 T then P increments - - - - - 3 P and T increments - - - - - - - - Select mode for iterating Pressure and Temperature. Default mode: 2. - - - Qt::AlignVCenter - - - true - - - - - - - - - - - - Qt::Horizontal - - - QDialogButtonBox::Cancel|QDialogButtonBox::Ok - - - - - - - - - buttonBox - accepted() - TPSetDialog - accept() - - - 248 - 254 - - - 157 - 274 - - - - - buttonBox - rejected() - TPSetDialog - reject() - - - 316 - 260 - - - 286 - 274 - - - - - diff --git a/ThermoFunGui/src/ThermoFunGui.pri b/ThermoFunGui/src/ThermoFunGui.pri deleted file mode 100644 index 5db13346..00000000 --- a/ThermoFunGui/src/ThermoFunGui.pri +++ /dev/null @@ -1,29 +0,0 @@ -HEADERS += \ - $$PWD/SelectElementsDialog.h \ - $$PWD/thermomodel.h \ - $$PWD/ThermoFunPrivateNew.h \ - $$PWD/ThermoFunWidgetNew.h \ - $$PWD/ElementsWidget.h \ - $$PWD/TPSetDialog.h \ - $$PWD/containers.h \ - $$PWD/model_reactions.h \ - $$PWD/SelectThermoDataDialog.h - -SOURCES += \ -# $$PWD/main.cpp \ - $$PWD/SelectElementsDialog.cpp \ - $$PWD/ThermoFunPrivateNew.cpp \ - $$PWD/ThermoFunWidgetNew.cpp \ - $$PWD/ElementsWidget.cpp \ - $$PWD/TPSetDialog.cpp \ - $$PWD/model_reactions.cpp \ - $$PWD/SelectThermoDataDialog.cpp - -FORMS += \ - $$PWD/ThermoFunWidget.ui \ - $$PWD/SelectElementsDialog.ui \ - $$PWD/ElementsWidget.ui \ - $$PWD/TPSetDialog.ui \ - $$PWD/SelectThermoDataDialog.ui - - diff --git a/ThermoFunGui/src/ThermoFunPrivateNew.cpp b/ThermoFunGui/src/ThermoFunPrivateNew.cpp deleted file mode 100644 index 2c110b71..00000000 --- a/ThermoFunGui/src/ThermoFunPrivateNew.cpp +++ /dev/null @@ -1,719 +0,0 @@ -#ifdef _WIN32 -#else -#include -#endif -#include -#include -#include "ThermoFunPrivateNew.h" -#include "ui_ThermoFunWidget.h" - -// ThermoFun includes -#ifdef FROM_SRC -#include "../ThermoFun/Database.h" -#include "../ThermoHubClient/TraversalData.h" -#include "../ThermoHubClient/ReactionData.h" -#include "../ThermoHubClient/ReactionSetData.h" -#include "../ThermoFun/Batch/OutputBatch.h" -//#include "../ThermoFun/Common/ParseBsonTraversalData.h" -#include "../ThermoFun/Common/ParseJsonToData.h" -#else -#include "ThermoFun/Database.h" -#include "ThermoHubClient/TraversalData.h" -#include "ThermoHubClient/ReactionData.h" -#include "ThermoHubClient/ReactionSetData.h" -#include "ThermoFun/Interfaces/Output.h" -//#include "ThermoFun/Common/ParseBsonTraversalData.h" -#include "ThermoFun/Common/ParseJsonToData.h" -#endif - -ThermoFunData::ThermoFunData() -{ - name = "ThermoFunTask1"; - comment = "write comment here..."; - calcStatus = "Select a thermodynamic dataset."; // status - schemaName = "VertexSubstance"; - idThermoDataSet = ""; - sourceTDBs.clear(); - - tPrecision = 0; - unitsT = "C Celsius"; - pPrecision = 0; - tppairs.push_back({25.,1.}); - unitsP = "b bar"; - properties.push_back("gibbs_energy"); - propertyUnits.push_back("J/mol"); - propertyPrecision.push_back(0); - - propertiesS.push_back("gibbs_energy"); - propertyUnitsS.push_back("J/mol"); - propertyPrecisionS.push_back(0); - - propertiesR.push_back("reaction_gibbs_energy"); - propertyUnitsR.push_back("J/mol"); - propertyPrecisionR.push_back(0); - - // old - _query = jsonio::emptyQuery; - _idReactionSet = ""; - _sourcetdb = -1;//defSourcetdb; -} - -void ThermoFunData::resetSchemaName( const string& newSchemaName ) -{ - schemaName = newSchemaName; - - if (schemaName == "VertexSubstance") - { - properties = propertiesS; - propertyUnits = propertyUnitsS; - propertyPrecision = propertyPrecisionS; - } - if (schemaName == "VertexReaction") - { - properties = propertiesR; - propertyUnits = propertyUnitsR; - propertyPrecision = propertyPrecisionR; - } - // old - _query = jsonio::emptyQuery; -} - - -void ThermoFunData::toJsonNode( jsonio::JsonDom *object ) const -{ - std::size_t ii; - object->appendString( "Name", name ); - object->appendString( "Description", comment ); - object->appendString( "SchemaName", schemaName ); - - object->appendString( "ThermoDataSetId", idThermoDataSet ); - auto arr = object->appendArray("SourceTDBs"); - for( ii=0; iiappendInt(to_string(ii), sourceTDBs[ii] ); - - arr = object->appendArray("ElementsList"); - for( ii=0; iiappendArray( to_string(ii) ); - arr2->appendString( "0", elements[ii].Symbol() ); - arr2->appendInt( "1", elements[ii].Class() ); - arr2->appendInt( "2", elements[ii].Isotope() ); - } - - object->appendDouble("TemperaturePrecision", tPrecision ); - object->appendString("TemperatureUnits", unitsT ); - object->appendDouble("PressurePrecision", pPrecision ); - object->appendString("PressureUnits", unitsP ); - - arr = object->appendArray( "TemperaturePressurePoints"); - for( ii=0; iiappendObject( to_string(ii) ); - obj->appendDouble( "T", tppairs[ii][0] ); - obj->appendDouble( "P", tppairs[ii][1] ); - } - - arr = object->appendArray("PropertiesList"); - for( ii=0; iiappendString( to_string(ii), properties[ii] ); - - arr = object->appendArray( "PropertyUnits"); - for( ii=0; iiappendString( to_string(ii), propertyUnits[ii] ); - - arr = object->appendArray( "PropertyPrecision"); - for( ii=0; iiappendInt( to_string(ii), propertyPrecision[ii] ); - - // old - object->appendInt("SourceTDB", _sourcetdb ); - object->appendString( "ReactionSetId", _idReactionSet ); - if(!_query.empty()) - _query.toJsonNode(object); - -} - -void ThermoFunData::fromJsonNode( const jsonio::JsonDom *object ) -{ - ThermoFunData deflt; - - if(!object->findValue( "Name", name ) ) - name=deflt.name; - if(!object->findValue( "Description", comment ) ) - comment=deflt.comment; - if(!object->findValue( "SchemaName", schemaName ) ) - schemaName=deflt.schemaName; - - if(!object->findValue( "ThermoDataSetId", idThermoDataSet ) ) - idThermoDataSet=""; - object->findArray( "SourceTDBs", sourceTDBs ); - - elements.clear(); - auto arr = object->field( "ElementsList" ); - if( arr!=nullptr && arr->getType() == jsonio::JSON_ARRAY ) - { - string symbol; - int class_, isotope; - for( int ii=0; iigetChildrenCount(); ii++ ) - { - auto obj = arr->getChild( ii); - if(!obj->findValue( "0", symbol ) ) - continue; - if(!obj->findValue( "1", class_ ) ) - continue; - if(!obj->findValue( "2", isotope ) ) - continue; - elements.push_back( ThermoFun::ElementKey(symbol,class_, isotope ) ); - } - } - - if(!object->findValue( "TemperaturePrecision", tPrecision ) ) - tPrecision=deflt.tPrecision; - if(!object->findValue( "TemperatureUnits", unitsT ) ) - unitsT=deflt.unitsT; - - if(!object->findValue( "PressurePrecision", pPrecision ) ) - pPrecision=deflt.pPrecision; - if(!object->findValue( "PressureUnits", unitsP ) ) - unitsP=deflt.unitsP; - - // read tp pairs - tppairs.clear(); - arr = object->field( "TemperaturePressurePoints" ); - if( arr==nullptr && arr->getType() != jsonio::JSON_ARRAY ) - tppairs =deflt.tppairs; - else - { - double Ti, Pi; - for( int ii=0; iigetChildrenCount(); ii++ ) - { - auto obj = arr->getChild( ii); - if(!obj->findValue( "T", Ti ) ) - Ti=100.; - if(!obj->findValue( "P", Pi ) ) - Pi = 5.; - tppairs.push_back({Ti, Pi}); - } - } - - object->findArray( "PropertiesList", properties ); - if( properties.empty() ) - properties =deflt.properties; - object->findArray( "PropertyUnits", propertyUnits ); - if( properties.empty() ) - properties =deflt.properties; - object->findArray( "PropertyPrecision", propertyPrecision ); - if( properties.empty() ) - properties =deflt.properties; - - // old - if(!object->findValue( "SourceTDB", _sourcetdb ) ) - _sourcetdb=deflt._sourcetdb; - if(!object->findValue( "ReactionSetId", _idReactionSet ) ) - _idReactionSet=""; - _query.fromJsonNode(object); - -} - - std::string ThermoFunData::selection_to_string() const - { - std::string output; - output += " idThermoDataSet: " + idThermoDataSet; - output += "\n sourceTDBs: "; - - jsonio::ThriftEnumDef* enumdef = jsonio::ioSettings().Schema()->getEnum( "SourceTDB" ); - if(enumdef != nullptr ) - { - for( std::size_t ii=0; iigetNamebyId(sourceTDBs[ii]) + " "; - } - output += "\n"; - return output; - } - -// ThermoFunPrivateNew ------------------------------------------------------------------ - -ThermoFunPrivateNew::ThermoFunPrivateNew( ThermoFunWidgetNew* awindow ): - QObject(awindow), window(awindow), ThermoHubClient( jsonui::uiSettings().dbclient() ) -{ - initWindow(); -} - -void ThermoFunPrivateNew::freeInternal() -{ - delete _TPlistTable; - delete _TPContainer; - delete _PropertyTable; - delete _PropertyContainer; - delete elementContainer; - delete elementTable; -} - -void ThermoFunPrivateNew::initWindow() -{ - // define all keys tables - valuesTable = new jsonui::TMatrixTable( window ); - valuesTable->horizontalHeader()->setSectionResizeMode( QHeaderView::Interactive ); - valuesTable->setEditTriggers( QAbstractItemView::AnyKeyPressed ); - //valuesTable->setSortingEnabled(true); - QObject::disconnect( valuesTable, SIGNAL(customContextMenuRequested(QPoint)), - valuesTable, SLOT(slotPopupContextMenu(QPoint))); - window->ui->keySplitter->insertWidget(0, valuesTable); - window->ui->keySplitter->setStretchFactor(0, 4); - substModel.reset(new ThermoViewModel( &ThermoHubClient.substData(), window )); - reactModel.reset(new ThermoViewModel( &ThermoHubClient.reactData(), window )); - substModel->updateModel(valuesTable); - - // Elements list - elementContainer = new ElementsDataContainer( _data.elements ); - elementModel = new jsonui::TMatrixModel( elementContainer, window ); - elementTable = new jsonui::TMatrixTable( window, jsonui::TMatrixTable::tbShow ); - elementTable->setModel(elementModel); - elementTable->horizontalHeader()->hide(); - elementTable->verticalHeader()->hide(); - elementTable->verticalHeader()->setStretchLastSection(true); - //elementTable->setHorizontalScrollBarPolicy(Qt::ScrollBarAlwaysOn); - int iHeight = 1.5*elementTable->verticalHeader()->sectionSize(0); - //iHeight += elementTable->horizontalScrollBar()->height(); - elementTable->setMaximumHeight(iHeight); - window->ui->verticalLayout_2->insertWidget(0, elementTable); - - // define ThermoFun data - _TPContainer = new TPContainer( "T", { "T", "P" }, _data.tppairs ); - _TPlistTable = new jsonui::TMatrixTable( window->ui->outWidget ); - jsonui::TMatrixDelegate* deleg = new jsonui::TMatrixDelegate(); - _TPlistTable->setItemDelegate(deleg); - _TPlistModel = new jsonui::TMatrixModel( _TPContainer, window ); - _TPlistTable->setModel(_TPlistModel); - _TPlistTable->horizontalHeader()->setSectionResizeMode( QHeaderView::Stretch/*Interactive*/ ); - window->ui->gridLayout_3->addWidget(_TPlistTable, 1, 0, 1, 1); - - _PropertyContainer = new TPropertyContainer( "Property", _data.properties, _data.propertyUnits, _data.propertyPrecision ); - _PropertyTable = new jsonui::TMatrixTable( window->ui->inWidget ); - deleg = new jsonui::TMatrixDelegate(); - _PropertyTable->setItemDelegate(deleg); - _PropertyModel = new jsonui::TMatrixModel( _PropertyContainer, window ); - _PropertyTable->setModel(_PropertyModel); - _PropertyTable->horizontalHeader()->setSectionResizeMode( QHeaderView::Stretch/*Interactive*/ ); - window->ui->gridLayout->addWidget(_PropertyTable, 7, 0, 1, 8); -} - - -// Edit part -------------------------------------------------------------------- - - -// Reset internal data -void ThermoFunPrivateNew::updateData( const std::string& aThermoDataSet, - const std::vector& sourcetdbs, - const std::vector& elementKeys, - const jsonio::ValuesTable& substanceValues, - const jsonio::ValuesTable& reactionValues ) -{ - _data.idThermoDataSet = aThermoDataSet; - _data.sourceTDBs = move(sourcetdbs); - _data.elements = elementKeys; - substValues = substanceValues; - reactValues = reactionValues; -// substModel->loadModeRecords( substanceValues ); -// reactModel->loadModeRecords( reactionValues ); - updateElementsModel(); - -} - -void ThermoFunPrivateNew::updateElementsModel() -{ - if( elementModel) - { - elementModel->resetMatrixData(); - if( elementTable->horizontalScrollBar()->isVisible() ) - { - int iHeight = elementTable->verticalHeader()->sectionSize(0); - iHeight += elementTable->horizontalScrollBar()->height(); - elementTable->setMaximumHeight(iHeight); - } - } - updateSelectMessage(); -} - -void ThermoFunPrivateNew::updateSelectMessage() -{ - window->ui->taskQuery->setText( _data.selection_to_string().c_str() ); -} - -void ThermoFunPrivateNew::reallocTP( int newsize ) -{ - _data.tppairs.clear(); - for (unsigned int i = 0; iresetMatrixData(); -} - -void ThermoFunPrivateNew::updateTP( const string& unitsT, const string& unitsP, - const std::vector>& tppairs) -{ - _data.unitsT = unitsT; - _data.unitsP = unitsP; - window->ui->pTunit->setCurrentText(unitsT.c_str()); - window->ui->pPunit->setCurrentText(unitsP.c_str()); - _data.tppairs = tppairs; - _TPlistModel->resetMatrixData(); -} - - -void ThermoFunPrivateNew::updateProperty( const vector& properties ) -{ - // store previous settings - for (unsigned i = 0; i<_data.properties.size(); i++) - { - _data.mapUnits[_data.properties[i]] = _data.propertyUnits[i]; - _data.mapPrecision[_data.properties[i]] = _data.propertyPrecision[i]; - } - _data.properties = properties; - _data.propertyUnits.resize(_data.properties.size()); - _data.propertyPrecision.resize(_data.properties.size()); - for (unsigned i = 0; i<_data.properties.size(); i++) - { - _data.propertyUnits[i] = _data.mapUnits[_data.properties[i]]; - _data.propertyPrecision[i] = _data.mapPrecision[_data.properties[i]]; - } - _PropertyModel->resetMatrixData(); -} - - -void ThermoFunPrivateNew::linkChange() -{ - if( _data.schemaName == "VertexReaction") - { - reactModel->updateModel(valuesTable); - } - else - { - substModel->updateModel(valuesTable); - } -} - -void ThermoFunPrivateNew::typeChanged(const string& newSchemaName) -{ - if( newSchemaName != _curSchemaName ) - { - if (_curSchemaName == "VertexSubstance") - { - _data.propertiesS = _data.properties; - _data.propertyUnitsS = _data.propertyUnits; - _data.propertyPrecisionS = _data.propertyPrecision; - - _data.properties = _data.propertiesR; - _data.propertyUnits = _data.propertyUnitsR; - _data.propertyPrecision = _data.propertyPrecisionR; - } - else - { - _data.propertiesR = _data.properties; - _data.propertyUnitsR = _data.propertyUnits; - _data.propertyPrecisionR = _data.propertyPrecision; - - _data.properties = _data.propertiesS; - _data.propertyUnits = _data.propertyUnitsS; - _data.propertyPrecision = _data.propertyPrecisionS; - } - _curSchemaName = newSchemaName; - _data.resetSchemaName( _curSchemaName ); - _PropertyModel->resetMatrixData(); - //isDefaultQuery = !_data.query.empty(); - //window->ui->edgeQuery->setText(_data.query.getQueryString().c_str()); - linkChange(); - } -} - -// Reset ThermoFun data -void ThermoFunPrivateNew::newThermoFunData( const ThermoFunData& newdata ) -{ - _data = newdata; - - _curSchemaName = _data.schemaName; - // update models - updateElementsModel(); - _TPlistModel->resetMatrixData(); - _PropertyModel->resetMatrixData(); - linkChange(); - //isDefaultQuery = !_data.query.empty(); - // clear selection lists - jsonio::ValuesTable emptytable; - substModel->loadModeRecords( emptytable ); - reactModel->loadModeRecords( emptytable ); -} - - -// Calc part ------------------------------ - -// extract init for calculation data -void ThermoFunPrivateNew::loadSubstData( const vector& selNdx, - vector& aKeyList, vector& substancesSymbols, - vector& substancesClass ) -{ - //if(_data.schemaName != "VertexSubstance") - // return; - - const jsonio::ValuesTable& values= substModel->getValues(); - aKeyList.resize(selNdx.size()); - substancesSymbols.resize(selNdx.size()); - substancesClass.resize(selNdx.size()); - auto name_ndx = ThermoHubClient.substData().getDataName_DataIndex(); - - for( std::size_t ii=0; ii& selNdx, - vector& aKeyList, vector& reactionsSymbols ) -{ - //if (_data.schemaName != "VertexReaction") - // return; - const jsonio::ValuesTable& values= reactModel->getValues(); - auto name_ndx = ThermoHubClient.reactData().getDataName_DataIndex(); - aKeyList.resize(selNdx.size()); - reactionsSymbols.resize(selNdx.size()); - for( std::size_t ii=0; ii &linkedSubstSymbols, vector &linkedReactSymbols, - vector &linkedSubstClasses, vector &linkedSubstIds) -{ - string valDB; - for (auto idType : mapOfConnectedIds) - { - if (idType.second == "reaction") - { - string symbol; - string jsonrecord = ThermoHubClient.reactData().getJsonRecordVertex(idType.first); - auto domdata = jsonio::unpackJson( jsonrecord ); - domdata->findValue("properties.symbol", symbol); - // record = ThermoHubClient.reactData().getJsonRecordVertex(idType.first).second; - // jsonio::bson_to_key( record.data, "properties.symbol", symbol); - linkedReactSymbols.push_back(symbol); - } - if (idType.second == "substance") - { - string symbol, class_; - string jsonrecord = ThermoHubClient.substData().getJsonRecordVertex(idType.first); - auto domdata = jsonio::unpackJson( jsonrecord ); - domdata->findValue("properties.symbol", symbol); - domdata->findValue("properties.class_", class_); - // record = ThermoHubClient.substData().getJsonBsonRecordVertex(idType.first).second; - // jsonio::bson_to_key( record.data, "properties.symbol", symbol); - // jsonio::bson_to_key( record.data, "properties.class_", class_); - /// !!!! class now struct - linkedSubstClasses.push_back(class_); - linkedSubstSymbols.push_back(symbol); - linkedSubstIds.push_back(idType.first); - } - } -} - -void ThermoFunPrivateNew::retrieveConnectedDataSymbols( const vector& substKeys, const vector& reactKeys, vector &linkedSubstSymbols, - vector &linkedReactSymbols, vector &linkedSubstClasses, vector &linkedSubstIds) -{ - linkedReactSymbols.clear(); linkedSubstSymbols.clear(); linkedSubstClasses.clear(); - - retrieveConnectedData(ThermoHubClient.getTraversal().getMapOfConnectedIds(substKeys), linkedSubstSymbols, linkedReactSymbols, linkedSubstClasses, linkedSubstIds); - retrieveConnectedData(ThermoHubClient.getTraversal().getMapOfConnectedIds(reactKeys), linkedSubstSymbols, linkedReactSymbols, linkedSubstClasses, linkedSubstIds); -// react.getLinkedDataSymbols(reactKeys, linkedSubstSymbols, linkedReactSymbols, linkedSubstClasses); -// subst.getLinkedDataSymbols(substKeys, linkedSubstSymbols, linkedReactSymbols, linkedSubstClasses); -} - -void ThermoFunPrivateNew::setSubstanceLevel(string substSymbol, string level) -{ - ThermoHubClient.substData().setSubstanceLevel(substSymbol, level); -} - -//void ThermoFunWidgetPrivate::setReactionLevel(string reactSymbol, string level) -//{ -// react.setReactionLevel(reactSymbol, level); -//} - -MapSymbolMapLevelReaction ThermoFunPrivateNew::recordsMapLevelDefinesReaction_(ThermoFun::MapSubstSymbol_MapLevel_IdReaction mapSymbol_Level_idReact) -{ - MapSymbolMapLevelReaction recordsLevelReact; - - for (auto symbol_Level_idReact : mapSymbol_Level_idReact) - { - MapLevelReaction levelReact; - for (auto level_idReact : symbol_Level_idReact.second) - { - levelReact[level_idReact.first] = ThermoFun::parseReaction( - ThermoHubClient.reactData().getJsonRecordVertex(level_idReact.second) ); - } - recordsLevelReact[symbol_Level_idReact.first] = levelReact; - } - return recordsLevelReact; -} - -MapSymbolMapLevelReaction ThermoFunPrivateNew::recordsMapLevelDefinesReaction() -{ - return recordsMapLevelDefinesReaction_(ThermoHubClient.substData().recordsMapLevelDefinesReaction()); -} - -MapSymbolMapLevelReaction ThermoFunPrivateNew::recordsMapLevelDefinesReaction(vector connectedSubstIds , vector connectedSubstSymbols) -{ - return recordsMapLevelDefinesReaction_(ThermoHubClient.substData().recordsMapLevelDefinesReaction(connectedSubstIds, connectedSubstSymbols)); -} - -ThermoFun::Database setSubstanceCalcType_ (ThermoFun::Database tdb, ThermoFun::SubstanceThermoCalculationType::type type_) -{ - auto substances = tdb.getSubstances(); - for (auto substance : substances) - { - substance.setThermoCalculationType(type_); - tdb.setSubstance(substance); - } - return tdb; -} - -//MapSymbolMapLevelSubstances ThermoFunWidgetPrivate::recordsMapLevelTakesSubstances() -//{ -// return react.recordsMapLevelTakesSubstances(); -//} - -ThermoLoadData ThermoFunPrivateNew::loadData( vector selNdx ) -{ - ThermoLoadData data; - - try{ - - if( isSubstances() ) - loadSubstData( selNdx, data.substKeys, data.substancesSymbols, data.substancesClass ); - else - loadReactData( selNdx, data.reactKeys, data.reactionsSymbols ); - -// retrieveConnectedDataSymbols( data.substKeys, data.reactKeys, data.linkedSubstSymbols, -// data.linkedReactSymbols, data.linkedSubstClasses, data.linkedSubstIds); - } - catch(std::exception& e) - { - data.errorMessage = e.what(); - } - return data; -} - -string ThermoFunPrivateNew::calcData( ThermoLoadData loadedData, string solventSymbol, - bool FormatBox, bool calcSubstFromReact, bool calcReactFromSubst ) -{ - string returnMessage; - QTime time; - time.start(); - - try{ - - vector keys; - - keys.insert(keys.end(), loadedData.substKeys.begin(), loadedData.substKeys.end()); - keys.insert(keys.end(), loadedData.reactKeys.begin(), loadedData.reactKeys.end()); - - auto tr = ThermoHubClient.getTraversal(); - -// ThermoFun::VertexId_VertexType resultTraversal = tr.getMapOfConnectedIds(keys, ThermoHubClient.substData().getSubstSymbol_DefinesLevel()); - ThermoFun::Database tdb_ = tr.getDatabase(keys);// tr.getDatabaseFromMapOfIds(resultTraversal, ThermoHubClient.substData().getSubstSymbol_DefinesLevel()); - - // ThermoFun::Traversal tr(subst.getDB()); - // ThermoFun::MapIdType resultTraversal = tr.getMapOfConnectedIds(keys, subst.mapSymbolLevel()); - // ThermoFun::Database tdb_ = tr.getDatabaseFromMapOfIds(resultTraversal, subst.mapSymbolLevel()); - - if (!calcSubstFromReact) // make all reactions to be calculated using the method in the record - tdb_ = setSubstanceCalcType_(tdb_, ThermoFun::SubstanceThermoCalculationType::type::DCOMP); - - - ThermoFun::ThermoBatch batchCalc (tdb_); - batchCalc.setSolventSymbol(solventSymbol); - - ThermoFun::BatchPreferences op; - if( FormatBox ) - { - op.isFixed = true; - } else - op.isFixed = false; - - op.outSolventProp = true; - op.calcReactFromSubst = calcReactFromSubst; - op.calcSubstFromReact = calcSubstFromReact; - batchCalc.setBatchPreferences(op); - - batchCalc.setPropertiesUnits({"temperature", "pressure"},{"degC","bar"}); - - if (_data.unitsP == "B kbar") - batchCalc.setPropertyUnit("pressure","kbar"); - if (_data.unitsP == "p Pa") - batchCalc.setPropertyUnit("pressure","Pa"); - if (_data.unitsP == "P MPa") - batchCalc.setPropertyUnit("pressure","MPa"); - if (_data.unitsP == "A Atm") - batchCalc.setPropertyUnit("pressure","atm"); - - /// check !!! - vector solventPropNames = {"density", "alpha", "beta", "alphaT", "epsilon", "bornZ", "bornY", "bornQ", "bornX"}; - // tpCalc.addSolventProperties(solventPropNames); - - std::map precision = ThermoFun::defaultPropertyDigits; - for (std::size_t jj = 0; jj <_data.properties.size(); jj++) - { - precision.at(_data.properties[jj]) = _data.propertyPrecision[jj]; - } - - precision.at("temperature") = _data.tPrecision; - precision.at("pressure") = _data.pPrecision; - - batchCalc.setDigits(precision); - - if (_data.schemaName == "VertexReaction") - { - batchCalc.thermoPropertiesReaction(_data.tppairs, loadedData.reactionsSymbols, - _data.properties/*, calcReactFromSubst*/).toCSV(op.fileName); - - vector reactionsEquations; - for (auto symb : loadedData.reactionsSymbols) - { - reactionsEquations.push_back(tdb_.getReaction(symb).equation()); - } - - /// check !!! - // tpCalc.clearReactions(); - // tpCalc.addReactions(reactionsEquations); - - // ThermoFun::Output (tpCalc).toCSV("equations.csv"); - } - - if (_data.schemaName == "VertexSubstance") - batchCalc.thermoPropertiesSubstance( _data.tppairs, loadedData.substancesSymbols, - _data.properties/*, calcSubstFromReact*/).toCSV(op.fileName); - - double delta_calc = time.elapsed()+ loadedData.time; - returnMessage = "Calculation finished ("+ to_string(delta_calc/1000) + "s). Click view results."; - } - catch(std::exception& e) - { - returnMessage = string("Calculation finished with error: \n") + e.what(); - } - return returnMessage; -} - -//----------------------------------------------------------------------- - -// temporaly functions -void ThermoFunPrivateNew::resetElementsintoRecord( bool isreact, const string& aKey ) -{ - if(isreact) - ThermoHubClient.reactData().resetRecordElements( aKey ); - else - ThermoHubClient.reactSetData().resetRecordElements( aKey ); -} - diff --git a/ThermoFunGui/src/ThermoFunPrivateNew.h b/ThermoFunGui/src/ThermoFunPrivateNew.h deleted file mode 100644 index 57cdf998..00000000 --- a/ThermoFunGui/src/ThermoFunPrivateNew.h +++ /dev/null @@ -1,256 +0,0 @@ -#ifndef THERMOFUNWIDGETPRIVATE_H -#define THERMOFUNWIDGETPRIVATE_H - -#include -#include -#include "ThermoFunWidgetNew.h" -#include "thermomodel.h" -#include "containers.h" -// ThermoFun includes -#ifdef FROM_SRC -#include "../ThermoFun/Batch/ThermoBatch.h" -#include "../ThermoHubClient/DatabaseClient.h" -#include "../ThermoHubClient/SubstanceData.h" -#include "../ThermoFun/Reaction.h" -#include "../ThermoFun/Substance.h" -#else -#include "ThermoFun/Batch/ThermoBatch.h" -#include "ThermoHubClient/DatabaseClient.h" -#include "ThermoHubClient/SubstanceData.h" -#include "ThermoFun/Reaction.h" -#include "ThermoFun/Substance.h" -#endif - -using MapLevelReaction = map; -using MapLevelSubstances = map>; -using MapSymbolMapLevelReaction = map; -using MapSymbolMapLevelSubstances = map; - -extern const int defSourcetdb; - -/// ThermoFun data to calculation -struct ThermoFunData -{ - string name; ///< Task (file) name - string comment; ///< Task description - string calcStatus; ///< ThermoFun colaculation status - - string schemaName; ///< Selected schema ( "VertexSubstance" or "VertexReaction" ) - - // selection data - /// Selected ThermoDataSet - string idThermoDataSet; - /// Selected SourceTDBs - vector sourceTDBs; - /// Define ELEMENTS table data - vector elements; - - // old selection data - jsonio::DBQueryData _query; ///< Current schema - string _idReactionSet; ///< Id of reaction set, - ///< if not empty we load records only from ReactionSet - int _sourcetdb; ///< Current sourcetdb - - // TP data - string unitsT; ///< Current units of T - string unitsP; ///< Current units of P - std::vector> tppairs; - - // Properties data - vector properties, propertiesS, propertiesR; ///< Properties names list - vector propertyUnits, propertyUnitsS, propertyUnitsR; ///< Units of property - vector propertyPrecision, propertyPrecisionS, propertyPrecisionR; ///< Units of property - int pPrecision, tPrecision; - - // work data - map mapUnits = ThermoFun::defaultPropertyUnits; - map mapPrecision = ThermoFun::defaultPropertyDigits; - - - /// Default values to task - ThermoFunData(); - - /// Write current task to configuration file fileName - void toJsonNode( jsonio::JsonDom *object ) const; - /// Read current task from configuration file fileName - void fromJsonNode( const jsonio::JsonDom *object ); - - /// Clear properies and query if schema changed - void resetSchemaName( const string& newSchemaName ); - - /// Get string definition of selection - std::string selection_to_string() const; -}; - - -class ThermoFunPrivateNew: public QObject -{ - - Q_OBJECT - - friend class ThermoFunWidgetNew; - - ThermoFunWidgetNew* window; - - // Internal data - string _curSchemaName = ""; - bool isDefaultQuery = false; - - /// Current project description - ThermoFunData _data; - /// Selected substances - std::shared_ptr substModel; - /// Selected reactions - std::shared_ptr reactModel; - - /// Selected substances all - jsonio::ValuesTable substValues; - /// Selected reactions all - jsonio::ValuesTable reactValues; - - // Window data ------------------------------------ - - // keys list data - /// Selected data view - jsonui::TMatrixTable* valuesTable = nullptr; - - // define ELEMENTS table model - ElementsDataContainer *elementContainer = nullptr; - jsonui::TMatrixTable *elementTable = nullptr; - jsonui::TMatrixModel* elementModel = nullptr; - - //ThermoFun data to edit; - TPContainer* _TPContainer = nullptr; - jsonui::TMatrixTable* _TPlistTable = nullptr; - jsonui::TMatrixModel* _TPlistModel = nullptr; - - TPropertyContainer* _PropertyContainer = nullptr; - jsonui::TMatrixTable* _PropertyTable = nullptr; - jsonui::TMatrixModel* _PropertyModel = nullptr; - - // internal functions - void initWindow(); - void freeInternal(); - void updateElementsModel(); - void updateSelectMessage(); - void linkChange(); - - MapSymbolMapLevelReaction recordsMapLevelDefinesReaction_(ThermoFun::MapSubstSymbol_MapLevel_IdReaction mapSymbol_Level_idReact); - -public slots: - - void pPChanged(int val) - { - _data.pPrecision = val; - } - void tPChanged(int val) - { - _data.tPrecision = val; - } - void TUnitsChanged(const QString& text) - { - _data.unitsT = text.toStdString(); - } - void PUnitsChanged(const QString& text) - { - _data.unitsP = text.toStdString(); - } - void nameChanged(const QString& text) - { - _data.name = text.toStdString(); - } - void commentChanged(const QString& text) - { - _data.comment = text.toStdString(); - } - - void retrieveConnectedData(map mapOfConnectedIds, vector &linkedSubstSymbols, - vector &linkedReactSymbols, vector &linkedSubstClasses, vector &linkedSubstIds); - - -public: - - ThermoFun::DatabaseClient ThermoHubClient; - - ThermoFunPrivateNew( ThermoFunWidgetNew* awindow ); - - ~ThermoFunPrivateNew() - { - freeInternal(); - } - - const ThermoFunData& data() const - { - return _data; - } - - bool isSubstances() const - { - return _data.schemaName != "VertexReaction"; - } - - const jsonio::ValuesTable& getValues( bool isSubst ) const - { - if( isSubst ) - return substModel->getValues(); - else - return reactModel->getValues(); - } - - string getThermoPropertiesName() const - { - std::size_t pos = std::string("Vertex").length(); - std::string schemaName = "ThermoProperties" + _data.schemaName.substr (pos); - return schemaName; - } - - void newThermoFunData( const ThermoFunData& newdata ); - - /// Reset internal data (after select dialog ) - void updateData( const std::string& aThermoDataSet, - const std::vector& sourcetdbs, - const std::vector& elementKeys, - const jsonio::ValuesTable& substanceValues, - const jsonio::ValuesTable& reactionValues ); - - void reallocTP( int newsize ); - void updateTP( const string& unitsT, const string& unitsP, - const std::vector>& tppairs); - void updateProperty( const vector& properties ); - - void typeChanged(const string& newSchemaName); - - // calc functions - void loadSubstData( const vector& selNdx, - vector& aKeyList, vector& substancesSymbols, - vector& substancesClass ); - void loadReactData( const vector& selNdx, - vector& aKeyList, vector& reactionsSymbols ); - - std::map getSubstDataIndex() - { - return ThermoHubClient.substData().getDataName_DataIndex(); - } - - void retrieveConnectedDataSymbols(const vector& substKeys, const vector& reactKeys, - vector &linkedSubstSymbols, vector &linkedReactSymbols, - vector &linkedSubstClasses, vector &linkedSubstIds); - - MapSymbolMapLevelReaction recordsMapLevelDefinesReaction(); - MapSymbolMapLevelReaction recordsMapLevelDefinesReaction(vector connectedSubstIds , vector connectedSubstSymbols); - - void setSubstanceLevel(string substSymbol, string level); - - ThermoLoadData loadData( std::vector selNdx ); - - std::string calcData( ThermoLoadData loadedData, string solventSymbol, - bool FormatBox, bool calcSubstFromReact, bool calcReactFromSubst ); - - // temporaly functions - void resetElementsintoRecord( bool isreact, const string& aKey ); - -}; - - - -#endif // THERMOFUNWIDGETPRIVATE_H diff --git a/ThermoFunGui/src/ThermoFunWidget.ui b/ThermoFunGui/src/ThermoFunWidget.ui deleted file mode 100644 index a57e173b..00000000 --- a/ThermoFunGui/src/ThermoFunWidget.ui +++ /dev/null @@ -1,773 +0,0 @@ - - - ThermoFunWidget - - - - 0 - 0 - 872 - 631 - - - - ThermoFun Tabulation of Thermodynamic Properties - - - - - - - Qt::Horizontal - - - true - - - - - 0 - - - 0 - - - 0 - - - 0 - - - 0 - - - - - Qt::Vertical - - - - - 1 - - - 1 - - - 1 - - - 1 - - - 1 - - - - - true - - - - - - - - - - - - - 0 - - - 0 - - - 0 - - - 0 - - - 0 - - - - - Qt::Vertical - - - - - - - Units - - - Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter - - - - - - - Number of digits after decimal point for pressure - - - 5 - - - 2 - - - - - - - Data type - - - - - - - Calculation task name - - - - - - - true - - - Symbol of the solvent used for calculating properties of disolved solute species - - - - - - - true - - - - 120 - 16777215 - - - - Pressure - - - Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter - - - - - - - Number of digits after decimal point - - - Precision of temperature values - - - Precision - - - Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter - - - - - - - - b bar - - - - - B kbar - - - - - p Pa - - - - - P MPa - - - - - A atm - - - - - - - - Units - - - Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter - - - - - - - C Celsius - - - - C Celsius - - - - - K Kelvin - - - - - - - - - 16777215 - 16777215 - - - - Properties table - - - - - - - Number of digits after decimal point - - - Precision of pressure values - - - Precision - - - Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter - - - - - - - Task Name - - - Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter - - - - - - - Type of data to calculate properties for - - - - - - - Symbol of the solvent used for calculating properties of disolved solute species - - - Solvent Symbol - - - Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter - - - - - - - Calculation task comment - - - - - - - Temperature - - - Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter - - - - - - - Number of digits after decimal point for temperature - - - 5 - - - 2 - - - - - - - - - 2 - - - 2 - - - 2 - - - 2 - - - 2 - - - - - Temperature T points - - - - - - - - - - - - - - - - 125 - 0 - - - - Status bar, what to do next and error messages - - - true - - - - - - - - - 0 - 0 - 872 - 22 - - - - - &File - - - - - - - - - - - - &Help - - - - - - - - - - - - &Calculate - - - - - - - &Preferences - - - - - - - - - - Se&lect - - - - - - - - - &Set - - - - - - - - - &View - - - - - - - - - - - - - - - - - - true - - - TopToolBarArea - - - false - - - - - - - - true - - - toolBar - - - TopToolBarArea - - - false - - - - - - - - - - - - - - toolBar - - - TopToolBarArea - - - false - - - - - - E&xit - - - - - - :/Icons/ShowFilesIcon24.png:/Icons/ShowFilesIcon24.png - - - &Open Task Definition from File ... - - - Read Task Definition from File ... - - - Read calculation setup from file ... - - - - - - :/Icons/SaveCurrentRecordIcon24.png:/Icons/SaveCurrentRecordIcon24.png - - - &Save Task Definition to File ... - - - Save Task Definition to File ... - - - Save calculation setup to file... - - - - - - :/Icons/QuestionMessageIcon24.png:/Icons/QuestionMessageIcon24.png - - - Help &About - - - Show Help VIewer ... - - - - - Au&thors ... - - - - - &License ... - - - - - Help &Contents ... - - - - - &Version ... - - - - - false - - - - :/Icons/CalculateRecordDataIcon24.png:/Icons/CalculateRecordDataIcon24.png - - - &Properties ... - - - - - false - - - - :/Icons/RTparmModuleIcon24.png:/Icons/RTparmModuleIcon24.png - - - &Tabulate the temperature and pressure points - - - - - false - - - - :/Icons/ShowGEMResultsIcon24.png:/Icons/ShowGEMResultsIcon24.png - - - Table with &Results ... - - - - - false - - - - :/Icons/DocumentsPileIcon24.png:/Icons/DocumentsPileIcon24.png - - - &Properties to Calculate ... - - - Set properties to calculate - - - - - &Size of Temperature and Pressure points list ... - - - Realloc TP pairs list - - - - - false - - - - :/Icons/SelectTP24.png:/Icons/SelectTP24.png - - - &Temperature and Pressure points ... - - - Set temperature and pressure points - - - - - - :/Icons/NewCreateRecordIcon24.png:/Icons/NewCreateRecordIcon24.png - - - &New/Reset Task Definition - - - Reset window - - - - - true - - - - :/Icons/ThermoDatabasesIcon24.png:/Icons/ThermoDatabasesIcon24.png - - - Select &ThermoDataSet ... - - - Select thermodynamic dataset - - - - - &Set Elemets to reactions - - - - - true - - - true - - - Calculate &Substances Records from Dependent Reactions - - - - - true - - - Calculate &Reactions Records from Reactants - - - - - &Set Elemets to reactionsets - - - Set Elemets to ReactionSets - - - - - false - - - Select &Elements ... - - - - - false - - - - :/Icons/DCompModuleIcon24.png:/Icons/DCompModuleIcon24.png - - - Select &Substances ... - - - - - Select ReactionSets ... - - - - - false - - - - :/Icons/ReacDCModuleIcon24.png:/Icons/ReacDCModuleIcon24.png - - - Select Reactions ... - - - - - true - - - true - - - Fixed output number format - - - Output values that have a fixed number of digits after the decima point - - - - - - - - - diff --git a/ThermoFunGui/src/ThermoFunWidgetNew.cpp b/ThermoFunGui/src/ThermoFunWidgetNew.cpp deleted file mode 100644 index 16829396..00000000 --- a/ThermoFunGui/src/ThermoFunWidgetNew.cpp +++ /dev/null @@ -1,831 +0,0 @@ -// This is ThermoFun library+API (https://bitbucket.org/gems4/ThermoFun) -// -/// \file ThermoFunWidget.cpp -/// ThermoFunWidget - Widget to work with ThermoFun data -// -// JSONUI is a C++ Qt5-based widget library and API aimed at implementing -// the GUI for editing/viewing the structured data kept in a NoSQL database, -// with rendering documents to/from JSON/YAML/XML files, and importing/ -// exporting data from/to arbitrary foreign formats (csv etc.). Graphical -// presentation of tabular data (csv format fields) is also possible. -// -// Copyright (c) 2015-2016 Svetlana Dmytriieva (svd@ciklum.com) and -// Dmitrii Kulik (dmitrii.kulik@psi.ch) -// -// This program is free software: you can redistribute it and/or modify -// it under the terms of the GNU (Lesser) General Public License as published -// by the Free Software Foundation, either version 3 of the License, or -// (at your option) any later version. -// -// This program is distributed in the hope that it will be useful, -// but WITHOUT ANY WARRANTY; without even the implied warranty of -// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. -// See the GNU General Public License for more details. -// -// You should have received a copy of the GNU General Public License -// along with this program. If not, see . -// -// JSONUI depends on the following open-source software products: -// jsonio (https://bitbucket.org/gems4/jsonio); Qt5 (https://qt.io); -// Qwtplot (http://qwt.sourceforge.net). - -#include -#include -#include -#include -#ifdef _WIN32 -#include -#else -#include -#endif -#include -#include "ThermoFunPrivateNew.h" -#include "ui_ThermoFunWidget.h" -#include "TPSetDialog.h" -#include "SelectThermoDataDialog.h" -#include "jsonui/TableEditWindow.h" -#include "jsonui/SchemaSelectDialog.h" -#include "jsonui/waitingspinnerwidget.h" -// ThermoFun includes -#ifdef FROM_SRC -#include "../ThermoHubClient/ReactionData.h" -#include "../ThermoHubClient/ReactionSetData.h" -#else -#include "ThermoHubClient/ReactionData.h" -#include "ThermoHubClient/ReactionSetData.h" -#endif - -ThermoFunWidgetNew::ThermoFunWidgetNew( QWidget *parent) : - JSONUIBase( "", parent), - ui(new Ui::ThermoFunWidget), _csvWin(nullptr) -{ - // set up widget data - ui->setupUi(this); - ui->keySplitter->setStretchFactor(0, 1); - ui->mainSplitter->setCollapsible(0, false); - ui->mainSplitter->setCollapsible(1, false); - - //define schema checkbox - ui->typeBox->addItem("Substances"); - ui->typeBox->addItem("Reactions"); - - setAttribute(Qt::WA_DeleteOnClose); // automatically delete itself when window is closed - QString title = qApp->applicationName()+" application for tabulating standard state thermodynamic properties"; - setWindowTitle(title); - - // init internal data - pdata.reset( new ThermoFunPrivateNew(this) ); - resetThermoFunData( pdata->data() ); - - // define menu - setActions(); - waitDialog = new WaitingSpinnerWidget(this, Qt::ApplicationModal, true); - - //show(); -// CmSelectThermoDataSet(); -} - -ThermoFunWidgetNew::~ThermoFunWidgetNew() -{ - // Cancel and wait - if (loadingWatcher.isRunning()) - { - loadingWatcher.cancel(); - loadingWatcher.waitForFinished(); - } - - if (calcWatcher.isRunning()) - { - calcWatcher.cancel(); - calcWatcher.waitForFinished(); - } - - if( _csvWin ) - { - _csvWin->close(); - delete _csvWin; - } - if( waitDialog ) - delete waitDialog; - - delete ui; - cout << "~ThermoFunWidget" << endl; -} - -void ThermoFunWidgetNew::closeEvent(QCloseEvent* e) -{ - if( _csvWin ) - _csvWin->close(); - - - if( !onCloseEvent(this) ) - e->ignore(); - else - QWidget::closeEvent(e); -} - -void ThermoFunWidgetNew::updtDB() -{ - // clear internal data - resetThermoFunData( pdata->data() ); -} - -// Connect all actions -void ThermoFunWidgetNew::setActions() -{ - connect( ui->typeBox, SIGNAL(currentIndexChanged(const QString&)), - this, SLOT(typeChanged(const QString&))); - - // File - connect( ui->actionNew_Reset_Task_Definition, SIGNAL( triggered()), this, SLOT(CmResetThermoFunData())); - connect( ui->actionE_xit, SIGNAL( triggered()), this, SLOT(close())); - connect( ui->actionExport_CfgFile, SIGNAL( triggered()), this, SLOT(CmExportCFG())); - connect( ui->actionImport_CfgFile, SIGNAL( triggered()), this, SLOT(CmImportCFG())); - - // Edit - connect(ui->actionRealloc_TP, SIGNAL(triggered()), this, SLOT(CmReallocTP())); - connect(ui->actionReset_TP, SIGNAL(triggered()), this, SLOT(CmResetTP())); - connect(ui->actionChange_Property_list, SIGNAL(triggered()), this, SLOT(CmResetProperty())); - connect(ui->actionSelect_ThermoDataSet, SIGNAL(triggered()), this, SLOT(CmSelectThermoDataSet())); - connect(ui->actionSelect_Elements, SIGNAL(triggered()), this, SLOT(CmSelectSourceTDBs())); - connect(ui->actionSelect_Substances, SIGNAL(triggered()), this, SLOT(CmSelectSubstances())); - connect(ui->actionSelect_Reactions, SIGNAL(triggered()), this, SLOT(CmSelectReactions())); - - - connect(ui->action_Set_Elemets_to_reactions, SIGNAL(triggered()), this, SLOT(CmSetElementsReactions())); - connect(ui->action_Set_Elemets_to_reactionsets, SIGNAL(triggered()), this, SLOT(CmSetElementsReactionSets())); - - // Help - connect( ui->action_Help_About, SIGNAL( triggered()), this, SLOT(CmHelpAbout())); - connect( ui->actionContents, SIGNAL( triggered()), this, SLOT(CmHelpContens())); - connect( ui->actionAuthors, SIGNAL( triggered()), this, SLOT(CmHelpAuthors())); - connect( ui->actionLicense, SIGNAL( triggered()), this, SLOT(CmHelpLicense())); - - //TCorpt data - connect( ui->pName, SIGNAL( textEdited(const QString&)), pdata.get(), SLOT(nameChanged(const QString&))); - connect( ui->pComment, SIGNAL( textEdited(const QString&)), pdata.get(), SLOT(commentChanged(const QString&))); - connect( ui->pTunit, SIGNAL( currentIndexChanged(const QString&)), pdata.get(), SLOT(TUnitsChanged(const QString&))); - connect( ui->pPunit, SIGNAL( currentIndexChanged(const QString&)), pdata.get(), SLOT(PUnitsChanged(const QString&))); - connect( ui->pPrecision, SIGNAL( valueChanged(int)), pdata.get(), SLOT(pPChanged(int))); - connect( ui->tPrecision, SIGNAL( valueChanged(int)), pdata.get(), SLOT(tPChanged(int))); - - //Calc - connect( ui->actionCalculate_Properties, SIGNAL( triggered()), this, SLOT(CmCalcMTPARM_load())); - connect(&loadingWatcher, &QFutureWatcher::finished, this, &ThermoFunWidgetNew::CmCalcMTPARM_calculate ); - connect(&calcWatcher, &QFutureWatcher::finished, this, &ThermoFunWidgetNew::CmCalcMTPARM_finish ); - connect( ui->actionCalculate_TP, SIGNAL( triggered()), this, SLOT(CmCalcRTParm())); - connect( ui->actionShow_Results, SIGNAL( triggered()), this, SLOT(CmShowResult())); - - ui->actionCalculate_Reactions_Records_from_Reactants->setChecked(false); - ui->actionCalculate_Reactions_Records_from_Reactants->setEnabled(false); - - ui->actionReset_TP->setEnabled(false); - ui->actionRealloc_TP->setEnabled(false); - ui->actionChange_Property_list->setEnabled(false); - ui->actionCalculate_Properties->setEnabled(false); - ui->actionShow_Results->setEnabled(false); - ui->actionSelect_Substances->setEnabled(false); - ui->actionSelect_Reactions->setEnabled(false); - ui->actionSelect_ReactionSets->setEnabled(false); - - ui->nameToolBar->setSizePolicy( QSizePolicy::Expanding, QSizePolicy::Fixed ); -} - - -//----------------------------------------------------- - -void ThermoFunWidgetNew::resetTypeBox( const QString& text ) -{ - disconnect( ui->typeBox, SIGNAL(currentIndexChanged(const QString&)), - this, SLOT(typeChanged(const QString&))); - ui->typeBox->setCurrentText(text); - connect( ui->typeBox, SIGNAL(currentIndexChanged(const QString&)), - this, SLOT(typeChanged(const QString&))); -} - -// Reset ThermoFun data -void ThermoFunWidgetNew::resetThermoFunData( const ThermoFunData& newdata ) -{ - pdata->newThermoFunData(newdata); - - // update view - ui->pName->setText(newdata.name.c_str()); - ui->pComment->setText(newdata.comment.c_str()); - ui->pTunit->setCurrentText( newdata.unitsT.c_str()); - ui->pPunit->setCurrentText(newdata.unitsP.c_str()); - ui->pPrecision->setValue(newdata.pPrecision); - ui->tPrecision->setValue(newdata.tPrecision); - ui->calcStatus->setText(newdata.calcStatus.c_str()); - ui->actionShow_Results->setEnabled(false); - ui->actionCalculate_Properties->setEnabled(false); - ui->actionChange_Property_list->setEnabled(false); - ui->typeBox->setEnabled(false); - ui->actionReset_TP->setEnabled(false); - ui->actionSelect_Substances->setEnabled(false); - ui->actionSelect_Reactions->setEnabled(false); - ui->pSolventSymbol->clear(); - resetTypeBox( newdata.schemaName.c_str() ); -} - -void ThermoFunWidgetNew::resetSolvents( const jsonio::ValuesTable& solventValues ) -{ - string sSymbol, sId; - auto substDataNdx = pdata->getSubstDataIndex(); - ui->pSolventSymbol->clear(); - - if (solventValues.size() == 0) - ui->pSolventSymbol->addItem("No solvent!", 0); - - for( auto solvent: solventValues ) - { - sSymbol = solvent[substDataNdx["symbol"]]; - sId = solvent[substDataNdx["_id"]]; - ui->pSolventSymbol->addItem(sSymbol.c_str(), sId.c_str()); - } -} - -bool ThermoFunWidgetNew::calcSubstFromReact() const -{ - return ui->actionCalculate_Substances_Records_from_Dependent_Reactions->isChecked(); -} - -bool ThermoFunWidgetNew::calcReactFromSubst() const -{ - return ui->actionCalculate_Reactions_Records_from_Reactants->isChecked(); -} - -// Menu commands ----------------------------------------------------------- - -void ThermoFunWidgetNew::CmResetThermoFunData() -{ - ThermoFunData dt; - dt.resetSchemaName( pdata->data().schemaName ); - resetThermoFunData(dt); -} - -// Change current Vertex -void ThermoFunWidgetNew::typeChanged(const QString& text) -{ - try { - string newname = text.toStdString(); - if (newname == "Substances") - { - pdata->typeChanged( "VertexSubstance" ); - ui->actionCalculate_Substances_Records_from_Dependent_Reactions->setEnabled(true); -// ui->actionCalculate_Reactions_Records_from_Reactants->setChecked(false); - ui->actionCalculate_Reactions_Records_from_Reactants->setEnabled(false); - - ui->actionSelect_Substances->setEnabled(true); - ui->actionSelect_Reactions->setEnabled(false); - } - if (newname == "Reactions") - { - pdata->typeChanged( "VertexReaction" ); -// ui->actionCalculate_Substances_Records_from_Dependent_Reactions->setChecked(false); -// ui->actionCalculate_Substances_Records_from_Dependent_Reactions->setEnabled(false); - ui->actionCalculate_Reactions_Records_from_Reactants->setEnabled(true); - ui->actionSelect_Substances->setEnabled(false); - ui->actionSelect_Reactions->setEnabled(true); - } - } - catch(jsonio::jsonio_exception& e) - { - QMessageBox::critical( this, e.title(), e.what() ); - } - catch(std::exception& e) - { - QMessageBox::critical( this, "std::exception", e.what() ); - } -} - -void ThermoFunWidgetNew::CmSelectThermoDataSet() -{ - try { - SelectThermoDataDialog dlg( pdata->data().idThermoDataSet, pdata->data().elements, pdata->ThermoHubClient, this); - - if( dlg.exec() ) - { - vector elKeys; - dlg.allSelected( elKeys ); - // Reset internal data - pdata->updateData( dlg.idThermoDataSet(), dlg.sourceTDBs(), elKeys, - dlg.getSubstanceValues(), dlg.getReactionValues() ); - resetSolvents( dlg.getSolventValues() ); - -// ui->actionReset_TP->setEnabled(true); -// ui->actionRealloc_TP->setEnabled(true); -// ui->actionChange_Property_list->setEnabled(true); -// ui->actionCalculate_Properties->setEnabled(true); - ui->typeBox->setEnabled(true); -// ui->actionSelect_Substances->setEnabled(true); -// ui->actionSelect_ThermoDataSet->setEnabled(true); - ui->calcStatus->setText("Select substances or reactions, set temperature and pressure points, properties to calculate, and click calculate."); // status - typeChanged(ui->typeBox->currentText()); - } -// else { -// ui->actionRealloc_TP->setEnabled(false); -// ui->actionChange_Property_list->setEnabled(false); -// ui->actionCalculate_Properties->setEnabled(false); -// ui->typeBox->setEnabled(false); -// pdata-> -// ui->actionSelect_Substances->setEnabled(false); -// ui->actionSelect_Reactions->setEnabled(false); -// ui->actionSelect_ThermoDataSet->setEnabled(true); -// } - } - catch(jsonio::jsonio_exception& e) - { - QMessageBox::critical( this, e.title(), e.what() ); - } - catch(std::exception& e) - { - QMessageBox::critical( this, "std::exception", e.what() ); - } -} - -void ThermoFunWidgetNew::CmSelectSourceTDBs() -{ - try { - SelectThermoDataDialog dlg( pdata->data().sourceTDBs, pdata->data().elements, pdata->ThermoHubClient, this); - - if( dlg.exec() ) - { - vector elKeys; - dlg.allSelected( elKeys ); - // Reset internal data - pdata->updateData( "", dlg.sourceTDBs() ,elKeys, - dlg.getSubstanceValues(), dlg.getReactionValues() ); - resetSolvents( dlg.getSolventValues() ); - - ui->actionReset_TP->setEnabled(true); - ui->actionRealloc_TP->setEnabled(true); - ui->actionChange_Property_list->setEnabled(true); - ui->actionCalculate_Properties->setEnabled(true); - ui->typeBox->setEnabled(true); - ui->calcStatus->setText("Set temperature and pressure points, set properties to calculate, and click calculate."); // status - } - } - catch(jsonio::jsonio_exception& e) - { - QMessageBox::critical( this, e.title(), e.what() ); - } - catch(std::exception& e) - { - QMessageBox::critical( this, "std::exception", e.what() ); - } -} - -void ThermoFunWidgetNew::CmReallocTP() -{ - try{ - bool ok = 0; - auto size = QInputDialog::getInt( this, "Please, select new TP pairs array size", - "Array size ", pdata->data().tppairs.size(), 0, 999, 1, &ok ); - if(ok) - pdata->reallocTP( size ); - } - catch(jsonio::jsonio_exception& e) - { - QMessageBox::critical( this, e.title(), e.what() ); - } - catch(std::exception& e) - { - QMessageBox::critical( this, "std::exception", e.what() ); - } -} - -void ThermoFunWidgetNew::CmResetTP() -{ - try{ - TPSetDialog dlg( this); - if( dlg.exec() ) - pdata->updateTP( dlg.getTUnits().toStdString(), - dlg.getPUnits().toStdString(), dlg.getTPpairs() ); - } - catch(jsonio::jsonio_exception& e) - { - QMessageBox::critical( this, e.title(), e.what() ); - } - catch(std::exception& e) - { - QMessageBox::critical( this, "std::exception", e.what() ); - } -} - -void ThermoFunWidgetNew::CmResetProperty() -{ - try - { - std::string schemaName = pdata->getThermoPropertiesName(); - jsonui::SchemaSelectDialog dlg(this, "Please, mark property fields", - schemaName, pdata->data().properties); - if( dlg.exec() ) - pdata->updateProperty( dlg.allSelected() ); - } - catch(jsonio::jsonio_exception& e) - { - QMessageBox::critical( this, e.title(), e.what() ); - } - catch(std::exception& e) - { - QMessageBox::critical( this, "std::exception", e.what() ); - } - -} - -/// Read bson record from json file fileName -void ThermoFunWidgetNew::CmImportCFG() -{ - try{ - string fileName; - if( ChooseFileOpen( this, fileName, - "Please, select Structured Data file", "*.json" )) - { //_data.readfromCFG(fileName); - // read data to dom - shared_ptr domdata(jsonio::JsonDomFree::newObject()); - jsonio::FJson file( fileName); - file.LoadJson( domdata.get() ); - ThermoFunData thdata; - thdata.fromJsonNode(domdata.get()); - resetThermoFunData(thdata); - } - } - catch(jsonio::jsonio_exception& e) - { - QMessageBox::critical( this, e.title(), e.what() ); - } - catch(std::exception& e) - { - QMessageBox::critical( this, "std::exception", e.what() ); - } -} - -/// Write current task to configuration file file -void ThermoFunWidgetNew::CmExportCFG() -{ - try { - string fileName = pdata->data().name+".json"; - if( ChooseFileSave( this, fileName, - "Please, select file to write the data", "*.json", fileName )) - { - //_data.savetoCFG(fileName); - jsonio::FJson file( fileName); - shared_ptr domdata(jsonio::JsonDomFree::newObject()); - pdata->data().toJsonNode(domdata.get()); - file.SaveJson( domdata.get() ); - } - } - catch(jsonio::jsonio_exception& e) - { - QMessageBox::critical( this, e.title(), e.what() ); - } - catch(std::exception& e) - { - QMessageBox::critical( this, "std::exception", e.what() ); - } -} - - -void ThermoFunWidgetNew::CmCalcMTPARM_load() -{ - try { - // MapSymbolMapLevelReaction levelDefinesReaction = pdata->recordsMapLevelDefinesReaction(/*3, 0*/); - // Now we use all into window - // select components - const jsonio::ValuesTable& values= pdata->getValues( pdata->isSubstances() ); - vector selNdx; - for(size_t ii=0; ii< values.size(); ii++) - selNdx.push_back(ii); - // Run into other thread - loadingWatcher.setFuture(QtConcurrent::run( pdata.get(), &ThermoFunPrivateNew::loadData, selNdx)); - waitDialog->start(); - } - catch(jsonio::jsonio_exception& e) - { - QMessageBox::critical( this, e.title(), e.what() ); - } - catch(std::exception& e) - { - QMessageBox::critical( this, "std::exception", e.what() ); - } -} - - -void ThermoFunWidgetNew::CmCalcMTPARM_calculate() -{ - try { - waitDialog->stop(); - cout<< "Load Finished" << endl; - - auto loadData = loadingWatcher.result(); - - // test error when loading - if( !loadData.errorMessage.empty() ) - { - ui->calcStatus->setText("Data loading error."); - QMessageBox::critical( this, "Data loading error", loadData.errorMessage.c_str() ); - return; - } - - if (calcReactFromSubst() && calcSubstFromReact()) // check - reaction with substance dependent on another reaction - { - MapSymbolMapLevelReaction levelDefinesReaction = - pdata->recordsMapLevelDefinesReaction(loadData.linkedSubstIds, loadData.linkedSubstSymbols); - for (auto substSymbol : loadData.linkedSubstSymbols) - { - MapLevelReaction levelReaction = levelDefinesReaction[substSymbol]; - if (levelReaction.size() == 0) - continue; - if (levelReaction.size() == 1) - { - pdata->setSubstanceLevel(substSymbol, levelReaction.begin()->first); - } - if (levelReaction.size() > 1) - { - jsonio::ValuesTable values_; - vector levels; - for (auto react : levelReaction) - { - vector symbolEq; - symbolEq.push_back(react.second.symbol()); - symbolEq.push_back(react.second.equation()); - levels.push_back(react.first); - values_.push_back(symbolEq); - } - - jsonui::SelectDialog selDlg_lvl( false, this, ("Please, select the reaction which defines substance: "+substSymbol).c_str(), values_ ); - if( !selDlg_lvl.exec() ) - return; - auto solvNdx = selDlg_lvl.getSelectedIndex(); - - pdata->setSubstanceLevel(substSymbol, levels[solvNdx]); - } - } - } - - // check for solvent - string solventSymbol = ui->pSolventSymbol->currentText().toStdString(); - if (solventSymbol != "No solvent!") - { - auto sId = ui->pSolventSymbol->currentData().toString().toStdString(); - if (std::find(loadData.substKeys.begin(), loadData.substKeys.end(), sId) == loadData.substKeys.end()) - loadData.substKeys.push_back(sId); - } - - // run in other thread - bool calcSubstFromReact_= calcSubstFromReact(); - bool calcReactFromSubst_= calcReactFromSubst(); - bool output_number_format= ui->actionFixed_Outputnumber_format->isChecked(); - - calcWatcher.setFuture(QtConcurrent::run( pdata.get(), &ThermoFunPrivateNew::calcData, std::move(loadData), std::move(solventSymbol), - output_number_format, calcSubstFromReact_, calcReactFromSubst() )); - - waitDialog->start(); - } - catch(jsonio::jsonio_exception& e) - { - QMessageBox::critical( this, e.title(), e.what() ); - } - catch(std::exception& e) - { - QMessageBox::critical( this, "std::exception", e.what() ); - } -} - -void ThermoFunWidgetNew::CmCalcMTPARM_finish() -{ - try { - waitDialog->stop(); - - auto retMessage = calcWatcher.result(); - if( retMessage.find("Click view results") == string::npos ) - { - ui->calcStatus->setText("Calculation finished with error."); - jsonio::jsonioErr("Calculation finished with error.", retMessage ); - } - ui->calcStatus->setText(retMessage.c_str()); - ui->actionShow_Results->setEnabled(true); - CmShowResult(); - } - catch(jsonio::jsonio_exception& e) - { - QMessageBox::critical( this, e.title(), e.what() ); - } - catch(std::exception& e) - { - QMessageBox::critical( this, "std::exception", e.what() ); - } -} - -void ThermoFunWidgetNew::CmCalcRTParm() -{ - try { - cout << "CmCalcRTParm" << endl; - - } - catch(jsonio::jsonio_exception& e) - { - QMessageBox::critical( this, e.title(), e.what() ); - } - catch(std::exception& e) - { - QMessageBox::critical( this, "std::exception", e.what() ); - } -} - - -//Result -void ThermoFunWidgetNew::CmShowResult() -{ - try { - // define new dialog - ThermoFun::BatchPreferences op; - string fileName = op.fileName; - if(!_csvWin) - { - _csvWin = new jsonui::TableEditWidget("CSV editor ", fileName, - jsonui::TMatrixTable::tbEdit|jsonui::TMatrixTable::tbGraph/*|TMatrixTable::tbSort*/ ); - } - else - { - _csvWin->openNewCSV(fileName); - _csvWin->raise(); - } - _csvWin->show(); - } - catch(jsonio::jsonio_exception& e) - { - QMessageBox::critical( this, e.title(), e.what() ); - } - catch(std::exception& e) - { - QMessageBox::critical( this, "std::exception", e.what() ); - } -} - -/// temporary function to reset old reactions -void ThermoFunWidgetNew::CmSetElementsReactions() -{ - try { - - //auto graphdb = pdata->ThermoHubClient.reactData().getDB(); - std::unique_ptr graphdb( jsonio::TDBVertexDocument::newVertexDocumentQuery( - jsonui::uiSettings().database(), "VertexReaction" )); - - // Select keys to delete - vector aKeyList; - vector> aValList; - graphdb->lastQueryData()->getKeyValueList( aKeyList, aValList ); - if( aKeyList.empty() ) - return; - - jsonui::SelectDialog selDlg( true, this, "Please, select a record to update", aValList ); - if( !selDlg.exec() ) - return; - - vector selNdx; - selDlg.getSelection(selNdx); - for( size_t ii=0; iiresetElementsintoRecord( true, aKeyList[selNdx[ii]]); - - } - catch(jsonio::jsonio_exception& e) - { - QMessageBox::critical( this, e.title(), e.what() ); - } - catch(std::exception& e) - { - QMessageBox::critical( this, "std::exception", e.what() ); - } -} - -/// temporary function to reset old reactionSets -void ThermoFunWidgetNew::CmSetElementsReactionSets() -{ - try { - - //auto graphdb = pdata->ThermoHubClient.reactSetData().getDB(); - std::unique_ptr graphdb( jsonio::TDBVertexDocument::newVertexDocumentQuery( - jsonui::uiSettings().database(), "VertexReactionSet" )); - - // Select keys to delete - vector aKeyList; - vector> aValList; - graphdb->lastQueryData()->getKeyValueList( aKeyList, aValList ); - if( aKeyList.empty() ) - return; - - jsonui::SelectDialog selDlg( true, this, "Please, select a record to update", aValList ); - if( !selDlg.exec() ) - return; - - vector selNdx; - selDlg.getSelection(selNdx); - for( size_t ii=0; iiresetElementsintoRecord(false, aKeyList[selNdx[ii]]); - - } - catch(jsonio::jsonio_exception& e) - { - QMessageBox::critical( this, e.title(), e.what() ); - } - catch(std::exception& e) - { - QMessageBox::critical( this, "std::exception", e.what() ); - } -} - - -void ThermoFunWidgetNew::CmSelectSubstances() -{ - try{ - std::size_t colId = pdata->ThermoHubClient.substData().getDataName_DataIndex().at("_id"); - vector oldids = pdata->substModel->getColumn( colId ); - // read full list - pdata->substModel->loadModeRecords( pdata->substValues ); - - // select components - const jsonio::ValuesTable& values= pdata->getValues( pdata->isSubstances() ); - vector selNdx = pdata->substModel->recordToValues( colId, oldids ); - jsonui::SelectDialog selDlg( true, this, "Please, select records for calculating their properties", values, pdata->ThermoHubClient.substData().getDataHeaders(), - jsonui::TMatrixTable::tbNoMenu|jsonui::TMatrixTable::tbSort ); - selDlg.setSelection(selNdx); - std::set selNdx2; - if( selDlg.exec() ) - { - selNdx2 = selDlg.allSelected(); - } - else - { - selNdx2.insert(selNdx.begin(), selNdx.end()); - } - pdata->substModel->leftOnlySelected( selNdx2 ); - - ui->actionReset_TP->setEnabled(true); - ui->actionRealloc_TP->setEnabled(true); - ui->actionChange_Property_list->setEnabled(true); - ui->actionCalculate_Properties->setEnabled(true); - - ui->calcStatus->setText("Set temperature and pressure points, set properties to calculate, and click calculate. (see preferences)"); // status - } - catch(jsonio::jsonio_exception& e) - { - QMessageBox::critical( this, e.title(), e.what() ); - ui->calcStatus->setText(e.what()); - } - catch(std::exception& e) - { - QMessageBox::critical( this, "std::exception", e.what() ); - ui->calcStatus->setText(e.what()); - } -} - - -void ThermoFunWidgetNew::CmSelectReactions() -{ - try{ - std::size_t colId = pdata->ThermoHubClient.reactData().getDataName_DataIndex().at("_id"); - vector oldids = pdata->reactModel->getColumn( colId ); - // read full list - pdata->reactModel->loadModeRecords( pdata->reactValues ); - - // select components - jsonio::ValuesTable values= pdata->reactModel->getValues(); - vector selNdx = pdata->reactModel->recordToValues( colId, oldids ); - - jsonui::SelectDialog selDlg( true, this, "Please, select records for calculating their properties", values, pdata->ThermoHubClient.reactData().getDataHeaders(), - jsonui::TMatrixTable::tbNoMenu|jsonui::TMatrixTable::tbSort ); - selDlg.setSelection(selNdx); - std::set selNdx2; - if( selDlg.exec() ) - { - selNdx2 = selDlg.allSelected(); - } - else - { - selNdx2.insert(selNdx.begin(), selNdx.end()); - } - pdata->reactModel->leftOnlySelected( selNdx2 ); - - ui->actionReset_TP->setEnabled(true); - ui->actionRealloc_TP->setEnabled(true); - ui->actionChange_Property_list->setEnabled(true); - ui->actionCalculate_Properties->setEnabled(true); - - ui->calcStatus->setText("Set temperature and pressure points, set properties to calculate, and click calculate. (see preferences)"); // status - } - catch(jsonio::jsonio_exception& e) - { - QMessageBox::critical( this, e.title(), e.what() ); - ui->calcStatus->setText(e.what()); - } - catch(std::exception& e) - { - QMessageBox::critical( this, "std::exception", e.what() ); - ui->calcStatus->setText(e.what()); - } -} - -// end of ThermoFunMenu.cpp - - diff --git a/ThermoFunGui/src/ThermoFunWidgetNew.h b/ThermoFunGui/src/ThermoFunWidgetNew.h deleted file mode 100644 index 94f15e20..00000000 --- a/ThermoFunGui/src/ThermoFunWidgetNew.h +++ /dev/null @@ -1,159 +0,0 @@ -// This is ThermoFun library+API (https://bitbucket.org/gems4/ThermoFun) -// -/// \file ThermoFunWidget.h -/// ThermoFunWidget - Widget to work with ThermoFun data -// -// JSONUI is a C++ Qt5-based widget library and API aimed at implementing -// the GUI for editing/viewing the structured data kept in a NoSQL database, -// with rendering documents to/from JSON/YAML/XML files, and importing/ -// exporting data from/to arbitrary foreign formats (csv etc.). Graphical -// presentation of tabular data (csv format fields) is also possible. -// -// Copyright (c) 2015-2016 Svetlana Dmytriieva (svd@ciklum.com) and -// Dmitrii Kulik (dmitrii.kulik@psi.ch) -// -// This program is free software: you can redistribute it and/or modify -// it under the terms of the GNU (Lesser) General Public License as published -// by the Free Software Foundation, either version 3 of the License, or -// (at your option) any later version. -// -// This program is distributed in the hope that it will be useful, -// but WITHOUT ANY WARRANTY; without even the implied warranty of -// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. -// See the GNU General Public License for more details. -// -// You should have received a copy of the GNU General Public License -// along with this program. If not, see . -// -// JSONUI depends on the following open-source software products: -// jsonio (https://bitbucket.org/gems4/jsonio); Qt5 (https://qt.io); -// Qwtplot (http://qwt.sourceforge.net). -// - -#ifndef ThermoFunWIDGETNEW_H -#define ThermoFunWIDGETNEW_H - -#include -#include "jsonui/JSONUIBase.h" - -namespace jsonui { -class TableEditWidget; -} - - -namespace Ui { -class ThermoFunWidget; -} - -struct ThermoFunData; -class ThermoFunPrivateNew; -class WaitingSpinnerWidget; - -struct ThermoLoadData -{ - std::vector substKeys; - std::vector reactKeys; - std::vector substancesSymbols; - std::vector substancesClass; - std::vector reactionsSymbols; - std::vector linkedSubstSymbols; - std::vector linkedReactSymbols; - std::vector linkedSubstClasses; - std::vector linkedSubstIds; - double time = 0.; - std::string errorMessage; -}; - -/// Widget to work with CorrPT data -class ThermoFunWidgetNew : public jsonui::JSONUIBase -{ - Q_OBJECT - - friend class ThermoFunPrivateNew; - -protected slots: - - void typeChanged(const QString& text); - -public slots: - - // internal slots - void openRecordKey( const std::string& , bool = false ) {} - void openRecordKey( const QModelIndex& ) {} - void changeKeyList() {} - void objectChanged() {} - - // File - void CmResetThermoFunData(); - void CmExportCFG(); - void CmImportCFG(); - - //Edit - void CmSelectThermoDataSet(); - void CmSelectSourceTDBs(); - void CmSelectSubstances(); - void CmSelectReactions(); - void CmResetTP(); - void CmReallocTP(); - void CmResetProperty(); - //temporaly - void CmSetElementsReactions(); - void CmSetElementsReactionSets(); - - // Calc - //void CmCalcMTPARM(); - void CmCalcMTPARM_load(); - void CmCalcMTPARM_calculate(); - void CmCalcMTPARM_finish(); - - void CmCalcRTParm(); - - //Result - void CmShowResult(); - -public: - - explicit ThermoFunWidgetNew( QWidget *parent = nullptr); - ~ThermoFunWidgetNew(); - - void setQuery( jsonui::QueryWidget* ) {} - -private: - - Ui::ThermoFunWidget *ui; - std::unique_ptr pdata; - // The future watcher that provides monitoring for the currently loading - QFutureWatcher loadingWatcher; - // The future watcher that provides monitoring for the currently calculating - QFutureWatcher calcWatcher; - - - // Extern windows - jsonui::TableEditWidget* _csvWin = nullptr; - WaitingSpinnerWidget *waitDialog; - - bool calcSubstFromReact() const; - bool calcReactFromSubst() const; - - // Internal functions ------------------------ - - /// Reset new ThermoFun data and update editors - void resetThermoFunData( const ThermoFunData& newdata ); - /// Set up menu commands - void setActions(); - - void resetTypeBox( const QString& text ); - /// Reset Solvewnts Checkbox - void resetSolvents( const jsonio::ValuesTable& solventValues ); - - void closeEvent(QCloseEvent* e); - // update after change preferences - virtual void updtViewMenu() {} - virtual void updtModel() {} - virtual void updtTable() {} - virtual void updtDB(); - -}; - - -#endif // ThermoFunWINDOW_H diff --git a/ThermoFunGui/src/containers.h b/ThermoFunGui/src/containers.h deleted file mode 100644 index f55ef1a5..00000000 --- a/ThermoFunGui/src/containers.h +++ /dev/null @@ -1,391 +0,0 @@ -#ifndef CONTAINERS_H -#define CONTAINERS_H - -#include "jsonui/SelectDialog.h" -#include "model_reactions.h" - -#ifdef FROM_SRC -#include "../ThermoFun/Common/formuladata.h" -#endif -#ifndef FROM_SRC -#include "ThermoFun/Common/formuladata.h" -#endif - -/// Class Elements table data container -class ElementsDataContainer : public jsonui::TAbstractDataContainer -{ - const std::vector& elements_; - -public: - - ElementsDataContainer( const std::vector& elements ): - TAbstractDataContainer("ElementsDataContainer"), - elements_( elements ) - { resetData(); } - - virtual ~ElementsDataContainer() {} - - int rowCount() const - { return 1; } - - int columnCount() const - { return elements_.size(); } - - QVariant data( int /*line*/, int column ) const - { - std::string key_ = elements_[column].formulaKey(); - return key_.c_str(); - } - - std::vector symbolsList( ) const - { - std::vector lst; - for (std::size_t i = 0; i < elements_.size(); i++) - { - lst.push_back(elements_[i].Symbol()); - } - return lst; - } - - bool setData( int /*line*/, int /*column*/, const QVariant & /*value*/ ) - { return true; } - - virtual QString headerData ( int ) const - { - return ""; - } - - virtual bool IsEditable( int /*line*/, int /*column*/ ) const - { return false; } - - virtual int getType( int /*line*/, int /*column*/ ) const - { return jsonui::ftString; } - - virtual QString getToolTip( int /*line*/, int column ) const - { - return QString::number(column); - } - - void resetData() - { } - -}; - -/// Class for double T P std::vector container -class TPContainer : public jsonui::TAbstractDataContainer -{ - std::vector _keys; - std::vector>& _fields; - - public: - - TPContainer( const char * aname, const std::vector& akeys, std::vector>& afields ): - TAbstractDataContainer(aname), - _keys(akeys),_fields( afields ) {} - - virtual ~TPContainer() {} - - int rowCount() const - { return _fields.size(); } - - int columnCount() const - { - if(_fields.size()>0 ) - return _fields[0].size(); - else - return 2; - } - - QVariant data( int line, int column ) const - { - return _fields[line][column]; - } - - bool setData( int line, int column, const QVariant &value ) - { - _fields[line][column] = value.toDouble(); - return true; - } - - virtual QString headerData ( int section ) const - { - return _keys[section].c_str(); - } - - virtual bool IsEditable( int /*line*/, int /*column*/ ) const - { return true; } - - virtual int getType( int /*line*/, int /*column*/ ) const - { return jsonui::ftDouble; } - - virtual QString getToolTip( int line, int column ) const - { - return (_keys[column]+" "+std::to_string(line)).c_str(); - } - - void resetData() - { } -}; - - -/// Class for double T P std::vector container -class TPropertyContainer : public jsonui::TAbstractDataContainer -{ - std::vector& _properties; ///< Properties names list - std::vector& _propertyUnits; ///< Units of property - std::vector& _propertyPrecision; ///< Output formats of property - - public: - - TPropertyContainer( const char * aname, std::vector& aProperties, std::vector& aPUnits, std::vector& aPPrecision ): - TAbstractDataContainer(aname), - _properties(aProperties),_propertyUnits( aPUnits ), _propertyPrecision( aPPrecision ) {} - - virtual ~TPropertyContainer() {} - - int rowCount() const - { return _properties.size(); } - - int columnCount() const - { return 3; } - - QVariant data( int line, int column ) const - { - if(column == 0) - return _properties[line].c_str(); - else - if(column == 1) - return _propertyUnits[line].c_str(); - else - return _propertyPrecision[line]; - } - - bool setData( int line, int column, const QVariant &value ) - { - std::string val = value.toString().toUtf8().data(); - int vali= value.toInt(); - if(column == 0) - _properties[line] = val; - else - if(column == 1) - _propertyUnits[line] = val; - else - _propertyPrecision[line] = vali; - return true; - } - - virtual QString headerData ( int section ) const - { - if(section == 0) - return "Property"; - else - if(section == 1) - return "Unit"; - else - return "Precision"; - } - - virtual bool IsEditable( int /*line*/, int /*column*/ ) const - { return true; } - - virtual int getType( int /*line*/, int /*column*/ ) const - { return jsonui::ftString; } - - virtual QString getToolTip( int /*line*/, int column ) const - { - if(column == 0) - return "Property"; - else - if(column == 1) - return "Unit"; - else - return "Output precision / digits after decimal point (in Fixed Format)"; - } - - void resetData() - { } -}; - -//---------------------------------------------------------------------------- -struct ReactData -{ - std::vector symbols; - std::vector coeffs; - - void clear() - { - symbols.clear(); - coeffs.clear(); - } - - void add( const std::string& name, double acoef ) - { - symbols.push_back(name); - coeffs.push_back(std::fabs(acoef)); - } - - std::string reaction() - { - std::string reactR; - for( std::size_t jj = 0; jj 0 ) - reactR += " + "; - if( coeffs[jj] != 1) - { - long intPart = coeffs[jj]; - double fractionalPart = fabs(coeffs[jj] - intPart); - if (fractionalPart == 0) - reactR += std::to_string( intPart ); - else - { - auto str = std::to_string( coeffs[jj] ); - str.erase ( str.find_last_not_of('0') + 1, std::string::npos ); - reactR += str; - } - } - reactR += symbols[jj]; - } - return reactR; - } - - std::string reaction_rev() - { - std::string reactR; - for(size_t jj = symbols.size(); jj --> 0 ;) - { - if( jj < symbols.size()-1 ) - reactR += " + "; - if( coeffs[jj] != 1) - { - long intPart = (long) coeffs[jj]; - double fractionalPart = fabs(coeffs[jj] - intPart); - if (fractionalPart == 0) - reactR += std::to_string( intPart ); - else - { - auto str = std::to_string( coeffs[jj] ); - str.erase ( str.find_last_not_of('0') + 1, std::string::npos ); - reactR += str; - } - } - reactR += symbols[jj]; - } - return reactR; - } - - void buildList( ReactionTree* parent, std::size_t first, std::vector vTps ) - { - ReactionTree* newChild; - std::vector values(8); - std::vector errors(8); - std::vector status(8); - - for( std::size_t jj = 0; jj children.push_back( unique_ptr(newChild) ); - } - } - -}; - -struct ISOCReactData -{ - std::vector symbols; - std::vector coeffs; - - void clear() - { - symbols.clear(); - coeffs.clear(); - } - - void add( const std::string& name, double acoef ) - { - symbols.push_back(name); - coeffs.push_back(acoef); - } - - void buildList( ReactionTree* parent, int first ) - { - ReactionTree* newChild; - std::vector values(1); - std::vector errors(1); - std::vector status(1); - - for( std::size_t jj = 0; jj children.push_back( unique_ptr(newChild) ); - } - } - - void buildList( ReactionTree* parent, int first, std::vector vTpr ) - { - ReactionTree* newChild; - std::vector values(8); - std::vector errors(8); - std::vector status(8); - - for( std::size_t jj = 0; jj children.push_back( unique_ptr(newChild) ); - } - } -}; - -#endif // CONTAINERS_H diff --git a/ThermoFunGui/src/model_reactions.cpp b/ThermoFunGui/src/model_reactions.cpp deleted file mode 100644 index e58effb2..00000000 --- a/ThermoFunGui/src/model_reactions.cpp +++ /dev/null @@ -1,401 +0,0 @@ -#include -#include -#include -#include -#include -#include -#include -#include "model_reactions.h" -#include "jsonui/model_view.h" - -using namespace jsonio; - -int numDigits = 3; - -double toPrecision(double num, int n) { - if(num == 0) - { - return 0.0; - } - std::ostringstream oss; - oss.precision(n); - oss<(index.internalPointer()); - } else { - return rootNode; - } -} - - -QModelIndex TReactionModel::index(int row, int column, const QModelIndex &parent) const -{ - if (!rootNode) - return QModelIndex(); - ReactionTree *parentItem = lineFromIndex( parent ); - if(parentItem->children.size() > 0 ) - return createIndex(row, column, parentItem->children[row].get()); - else - return QModelIndex(); -} - -QModelIndex TReactionModel::parent(const QModelIndex& child) const -{ - if (!child.isValid()) - return QModelIndex(); - - ReactionTree *childItem = lineFromIndex(child); - ReactionTree *parentItem = childItem->parent; - if (parentItem == rootNode ) - return QModelIndex(); - return createIndex(parentItem->ndx, 0, parentItem); -} - - -int TReactionModel::rowCount( const QModelIndex& parent ) const -{ - if (!rootNode) - return 0; - if (parent.column() > 0) - return 0; - ReactionTree *parentItem = lineFromIndex( parent ); - return parentItem->children.size(); -} - -int TReactionModel::columnCount( const QModelIndex& ) const -{ - return hdData.size(); -} - -Qt::ItemFlags TReactionModel::flags( const QModelIndex& index ) const -{ - Qt::ItemFlags flags = QAbstractItemModel::flags(index); - return (flags & ~Qt::ItemIsEditable); -} - -QVariant TReactionModel::headerData( int section, Qt::Orientation orientation, int role ) const -{ - if( role == Qt::DisplayRole && orientation == Qt::Horizontal ) - return hdData[section]; - return QVariant(); -} - -QVariant TReactionModel::data( const QModelIndex& index, int role ) const -{ - if(!index.isValid()) - return QVariant(); - - auto ret = QVariant(); - - ret = "--"; - - switch( role ) - { case Qt::DisplayRole: - case Qt::EditRole: - { ReactionTree *item = lineFromIndex( index ); - if( index.column() == 0 ) - { - ret = item->rsnames.c_str(); - return ret; - } - else - if ( index.column() == 2 ) // ISOC - { - if (item->values[index.column()-1] == 1) - { - ret = "+"; - return ret; - } else return ret; - } - else - if( index.column() < item->values.size()+1 ) - { - if ((item->values[index.column()-1] != 0) && (index.column()<4)) - { - ret = toPrecision(item->values[index.column()-1], numDigits); - return ret; - } else - if (((item->status[index.column()-1] == Reaktoro_::Status::calculated) || (item->status[index.column()-1] == Reaktoro_::Status::read) - || (item->status[index.column()-1] == Reaktoro_::Status::assigned)) - && (index.column()>3)) - { - ret = toPrecision(item->values[index.column()-1], numDigits); - return ret; - } else return ret; - - } - } - default: break; - } - return QVariant(); -} - -//------------------------------------------------------------------------------------- -// class TReactionView implements a tree view that displays items from a model to reactions. -//------------------------------------------------------------------------------------- - -TReactionView::TReactionView( QWidget * parent ): - QTreeView( parent ) -{ - setSizePolicy(QSizePolicy::Preferred, QSizePolicy::Preferred); - header()->setSectionsClickable(true); - header()->setSectionResizeMode( /*QHeaderView::ResizeToContents*/QHeaderView::Interactive ); - - //setEditTriggers( QAbstractItemView::DoubleClicked|QAbstractItemView::AnyKeyPressed ); - setFocusPolicy(Qt::StrongFocus); - //setTabKeyNavigation( false ); - setContextMenuPolicy(Qt::CustomContextMenu); - setSelectionMode( QAbstractItemView::ContiguousSelection ); - //setSelectionBehavior( QAbstractItemView::SelectRows ); - setIndentation( 30 ); - - connect( this, SIGNAL(customContextMenuRequested(QPoint)), - this, SLOT(slotPopupContextMenu(QPoint))); - connect( header(), SIGNAL(sectionClicked(int)), - this, SLOT(changeCurrent(int))); -} - -void TReactionView::changeCurrent( int section ) -{ - if( !currentIndex().isValid() ) - { QModelIndex index = model()->index( 0, section, rootIndex()); - setCurrentIndex(index); - } -} - -void TReactionView::slotPopupContextMenu(const QPoint &pos) -{ - QModelIndex index = indexAt( pos ); - QMenu *menu = contextMenu( index); - if( menu) - { menu->exec( viewport()->mapToGlobal(pos) ); - delete menu; - } -} - -QMenu* TReactionView::contextMenu(const QModelIndex& /*index*/) -{ - const TReactionModel* model_ =dynamic_cast(model()); - if( !model_ ) - return nullptr; - QMenu *menu = new QMenu(this); - QAction* act; - - act = new QAction(tr("&Help"), this); - act->setIcon(QIcon(":/menu/ShowHelpWindowIcon.png")); - act->setShortcut(tr("F1")); - act->setStatusTip(tr("Help for specified cell")); - connect(act, SIGNAL(triggered()), this, SLOT(CmHelp())); - menu->addAction(act); - - menu->addSeparator(); - - act = new QAction(tr("Select &row"), this); - act->setShortcut(tr("Ctrl+R")); - act->setStatusTip(tr("Select current row")); - connect(act, SIGNAL(triggered()), this, SLOT(CmSelectRow())); - menu->addAction(act); - - act = new QAction(tr("Select co&lumn"), this); - act->setShortcut(tr("Ctrl+L")); - act->setStatusTip(tr("Select current column")); - connect(act, SIGNAL(triggered()), this, SLOT(CmSelectColumn())); - menu->addAction(act); - - act = new QAction(tr("Select &group"), this); - act->setShortcut(tr("Ctrl+G")); - act->setStatusTip(tr("Select current item with children")); - connect(act, SIGNAL(triggered()), this, SLOT(CmSelectGroup())); - menu->addAction(act); - - act = new QAction(tr("Select &all"), this); - act->setShortcut(tr("Ctrl+A")); - act->setStatusTip(tr("Select all")); - connect(act, SIGNAL(triggered()), this, SLOT(CmSelectAll())); - menu->addAction(act); - - menu->addSeparator(); - - act = new QAction(tr("&Copy"), this); - act->setShortcut(tr("Ctrl+C")); - act->setStatusTip(tr("Copy selected data")); - connect(act, SIGNAL(triggered()), this, SLOT(CmCopyData())); - menu->addAction(act); - - act = new QAction(tr("Copy with &header"), this); - act->setShortcut(tr("Ctrl+H")); - act->setStatusTip(tr("Copy selected header&cells")); - connect(act, SIGNAL(triggered()), this, SLOT(CmCopyDataHeader())); - menu->addAction(act); - - return menu; - } - -void TReactionView::keyPressEvent(QKeyEvent* e) -{ - if ( e->modifiers() & Qt::ControlModifier ) - { - switch ( e->key() ) - { - case Qt::Key_R: - CmSelectRow(); - return; - case Qt::Key_L: - CmSelectColumn(); - return; - case Qt::Key_G: - CmSelectGroup(); - return; - case Qt::Key_A: - CmSelectAll(); - return; - case Qt::Key_C: - CmCopyData(); - return; - case Qt::Key_H: - CmCopyDataHeader(); - return; - } - } - - switch( e->key() ) - { - case Qt::Key_F1: - CmHelp(); - return; - } - QTreeView::keyPressEvent(e); -} - -void TReactionView::CmSelectRow() -{ - selectionModel()->select( currentIndex(), - QItemSelectionModel::Rows|QItemSelectionModel::ClearAndSelect ); -} - -void TReactionView::CmSelectColumn() -{ - selectionModel()->select( currentIndex(), - QItemSelectionModel::Columns|QItemSelectionModel::ClearAndSelect ); -} - -void TReactionView::CmSelectAll() -{ - selectWithChildren(rootIndex()); -} - -void TReactionView::selectWithChildren(const QModelIndex& parIndex) -{ - selectionModel()->select( parIndex, - QItemSelectionModel::Rows|QItemSelectionModel::Select ); - - for(int row = 0; row < model()->rowCount( parIndex ); row++ ) - { - QModelIndex childIndex = model()->index( row, 0, parIndex); - selectWithChildren(childIndex); - } -} - -void TReactionView::CmSelectGroup() -{ - if( !currentIndex().isValid() ) - return; - selectWithChildren(currentIndex()); -} - - -void TReactionView::copyWithChildren( const QModelIndex& parIndex, - const QModelIndexList& selIndexes, QString& clipText ) -{ - QModelIndex index; - QString cText; - bool frst = true; - int row = parIndex.row(), col; - - for (col = 0; col < model()->columnCount( parIndex ); col++ ) - { - index = parIndex.sibling( row, col); - if( selIndexes.contains( index ) ) - { - if( !frst ) - clipText += jsonui::splitCol; - frst = false; - cText = model()->data(index).toString(); - if( cText == emptiness.c_str() ) - cText = " ";//"\r"; - clipText += cText; - } - } - if( !frst ) - clipText += jsonui::splitRow; - - for(int rw = 0; rw < model()->rowCount( parIndex ); rw++ ) - { - index = model()->index( rw, 0, parIndex); - copyWithChildren( index, selIndexes, clipText ); - } -} - -QString TReactionView::createString() -{ - QString clipText; - QModelIndexList selIndexes = selectedIndexes(); - copyWithChildren( rootIndex(),selIndexes, clipText ); - return clipText; -} - -QString TReactionView::createHeader() -{ - QString cText; - QString clipText; - int col; - bool frst = true; - for( col = 0; col < model()->columnCount( rootIndex() ); col++ ) - { - if( selectionModel()->columnIntersectsSelection( col, rootIndex() ) ) - { - if( !frst ) - clipText += jsonui::splitCol; - frst = false; - cText = model()->headerData( col, Qt::Horizontal, Qt::DisplayRole ).toString(); - if( cText == emptiness.c_str() ) - cText = " ";//"\r"; - clipText += cText; - } - } - if( !frst ) - clipText += jsonui::splitRow; - return clipText; -} - -void TReactionView::CmCopyData() -{ - QString clipText = createString(); - QApplication::clipboard()->setText(clipText/*, QClipboard::Clipboard*/); -} - -void TReactionView::CmCopyDataHeader() -{ - QString clipText = createHeader(); - clipText += createString(); - QApplication::clipboard()->setText(clipText/*, QClipboard::Clipboard*/); -} - - - -//---------------------- End of file model_reactions.cpp --------------------------- diff --git a/ThermoFunGui/src/model_reactions.h b/ThermoFunGui/src/model_reactions.h deleted file mode 100644 index 71d8d2b4..00000000 --- a/ThermoFunGui/src/model_reactions.h +++ /dev/null @@ -1,153 +0,0 @@ -#ifndef _model_reaction_h -#define _model_reaction_h - -#include -#include -#include -#include -#include "jsonio/ar2base.h" - -// ThermoFun includes -#ifdef FROM_SRC -#include "../ThermoFun/ThermoProperties.h" -#endif -#ifndef FROM_SRC -#include "ThermoFun/ThermoProperties.h" -#endif - - -/// Definition of tree reaction line structure -class ReactionTree -{ - -public: - - ReactionTree( std::size_t andx, const string& aname, vector& avalues, vector& aerrors, vector& astatus, ReactionTree* aparent ): - ndx(andx), rsnames(aname), values(avalues), errors(aerrors), status(astatus), parent(aparent) - {} - - ReactionTree( std::size_t andx, const string& aname, ReactionTree* aparent = nullptr ): - ndx(andx), rsnames(aname), parent(aparent) - {} - - ~ReactionTree(){} - - std::size_t ndx; - string rsnames; // name of field - vector values; // values of field - vector errors; // errors of field - vector status; // status of value - - ReactionTree *parent; - vector> children; - -/* /// Get Value from string - /// If field is not type T, the false will be returned. - template - bool getValue( int ndx, T& val ) - { - if(ndx >= values.size() ) - return false; - string valstr = values[ndx].toUtf8().data(); - return jsonio::TArray2Base::string2value( valstr, val ); - } - - /// Set Value to Node - template - void setValue( int ndx, const T& value ) - { - if(ndx < values.size() ) - { - string valstr = jsonio::TArray2Base::value2string( value ); - values[ndx] = valstr.c_str(); - } - } -*/ -}; - - -//=========================================== -// TReactionModel class -//=========================================== - - -/*! - \ class TReactionModel - \ class for represents the data set and is responsible for fetching the data - \ is needed for viewing and for writing back any changes. - \ Reading/writing data from/to ReactionLine object -*/ -class TReactionModel: public QAbstractItemModel -{ - Q_OBJECT - - QStringList hdData; - ReactionTree* rootNode; - - public: - - TReactionModel( ReactionTree* newRoot, QObject* parent = nullptr ); - ~TReactionModel(){} - - QModelIndex index(int row, int column, const QModelIndex& parent) const; - QModelIndex parent(const QModelIndex& child) const; - int rowCount ( const QModelIndex& parent ) const; //ok - int columnCount ( const QModelIndex& parent ) const; // ok - QVariant data ( const QModelIndex& index, int role ) const; - //bool setData ( const QModelIndex& index, const QVariant& value, int role ); - QVariant headerData ( int section, Qt::Orientation orientation, int role ) const; - Qt::ItemFlags flags ( const QModelIndex& index ) const; - - ReactionTree* lineFromIndex(const QModelIndex& index) const; - - void setModelData(ReactionTree* newRoot ) - { - beginResetModel(); - rootNode = newRoot; - endResetModel(); - } - -}; - - -/*! - \ class TReactionView implements a tree view of reactions structure - \ that displays items from a model. This class is used to - \ provide standard tree views that were previously provided by - \ the QTree class, but using the more flexible approach - \ provided by Qt's model/view architecture. -*/ -class TReactionView: public QTreeView -{ - Q_OBJECT - - void keyPressEvent(QKeyEvent* e); - QMenu* contextMenu(const QModelIndex &index); - - QString createString(); - QString createHeader(); - void selectWithChildren(const QModelIndex& parIndex); - void copyWithChildren( const QModelIndex& parIndex, - const QModelIndexList& selIndexes, QString& clipText ); - - protected slots: - - void slotPopupContextMenu(const QPoint& pos); - void changeCurrent( int section ); - - public slots: - void CmHelp(){} - void CmSelectRow(); - void CmSelectColumn(); - void CmSelectAll(); - void CmSelectGroup(); - void CmCopyData(); - void CmCopyDataHeader(); - - public: - - TReactionView( QWidget * parent = nullptr ); - -}; - -#endif // _model_reaction_h diff --git a/ThermoFunGui/src/thermomodel.h b/ThermoFunGui/src/thermomodel.h deleted file mode 100644 index b7820eeb..00000000 --- a/ThermoFunGui/src/thermomodel.h +++ /dev/null @@ -1,222 +0,0 @@ -#ifndef THERMOMODEL_H -#define THERMOMODEL_H - -#include -#include "jsonui/model_table.h" -// ThermoFun includes -#ifdef FROM_SRC -#include "../ThermoHubClient/AbstractData.h" -#else -#include "ThermoHubClient/AbstractData.h" -#endif - -class ThermoViewModel: public QObject -{ - Q_OBJECT - - //QSortFilterProxyModel *proxyModel; - ///std::shared_ptr data__; - ThermoFun::AbstractData* data_; - - /// loaded data - std::shared_ptr thermoData; - /// data model - std::shared_ptr thermoModel; - -public: - - ThermoViewModel( ThermoFun::AbstractData *data, QObject* parent = nullptr ): - QObject(parent), data_(data) - { - defineModels(); - } - virtual ~ThermoViewModel() - { } - - void linkData( ThermoFun::AbstractData *data ) - { - data_ = data; - thermoData->updateHeads( data_->getDataHeaders() ); - thermoData->updateValues( {} ); - thermoModel->resetMatrixData(); - } - - void loadModeRecords( const std::string& idReactionSet ) - { - auto matr = data_->loadRecordsValues( idReactionSet ); - thermoData->updateValues( matr ); - thermoModel->resetMatrixData(); - } - - void loadModeRecords( const jsonio::DBQueryData& query, int sourcetdb, - const std::vector& elements ) - { - auto matr = data_->loadRecordsValues( query, sourcetdb, elements ); - thermoData->updateValues( matr ); - thermoModel->resetMatrixData(); - } - - void loadModeRecords( const std::vector& ids ) - { - auto matr = data_->loadRecords( ids ); - thermoData->updateValues( matr ); - thermoModel->resetMatrixData(); - } - - void loadModeRecords(const jsonio::ValuesTable& matr ) - { - thermoData->updateValues( matr ); - thermoModel->resetMatrixData(); - } - - /// Resize model to selected - void leftOnlySelected( const std::set selrows ) - { - jsonio::ValuesTable newmatr; - const jsonio::ValuesTable& oldmatr = getValues(); - - for( auto rowndx: selrows) - newmatr.push_back( oldmatr[rowndx] ); - loadModeRecords(newmatr ); - } - - std::vector getColumn( size_t column, const std::set& selrows ) const - { - std::vector keys; - const jsonio::ValuesTable& matrix = getValues(); - for( auto rowndx: selrows) - { - auto row = matrix[rowndx]; - if( column >= row.size()) - keys.push_back( "" ); - else - keys.push_back( row[column]); - } - return keys; - } - - std::vector getColumn( size_t column ) const - { - return thermoData->getColumn(column); - } - - template< class T > - void fillColumn( size_t column, const T& ndxs, const std::string& value ) - { - for( size_t ii=0; iirowCount() ) - thermoData->setData( ndxs[ii], column, value.c_str() ); - } - - void fillColumn( size_t column, const std::string& value ) - { - for( int ii=0; ii< thermoData->rowCount(); ii++) - thermoData->setData( ii, column, value.c_str() ); - } - - size_t findRow( size_t column, const std::string& value, bool first = false ) const - { - const jsonio::ValuesTable& matrix = getValues(); - for( size_t ii=0; ii= matrix[ii].size()) - continue; - else - if( matrix[ii][column] == value ) - return ii; - } - jsonio::jsonioErrIf( !first, "ThermoViewModel", "Value " + value + " not exists" ); - return 0; - } - - /// Move record with values up - void moveUpByOrder( size_t column, const std::set& values ) - { - jsonio::ValuesTable newmatr; - const jsonio::ValuesTable& matrix = getValues(); - - // copy lines from values - for( auto val: values) - for( auto row: matrix ) - if( row[column] == val ) - newmatr.push_back( row ); - - // copy other record - for( auto row: matrix ) - if( values.find( row[column]) == values.end() ) - newmatr.push_back( row ); - - loadModeRecords(std::move( newmatr ) ); - } - - /// Gen indexes of record with value into column - std::vector recordToValue( size_t column, const std::string& value ) const - { - std::vector rowndxs; - const jsonio::ValuesTable& matrix = getValues(); - for(size_t ii=0; ii recordToValues( size_t column, const std::vector& values ) const - { - std::vector rowndxs; - const jsonio::ValuesTable& matrix = getValues(); - for( size_t ii=0; iigetDB()->getQuery(); - }*/ - - const jsonio::ValuesTable& getValues() const - { - return thermoData->getValues(); - } - void updateModel( jsonui::TMatrixTable *tableView ) - { - if( tableView ) - tableView->setModel(thermoModel.get()); - } - - jsonui::TMatrixModel* getModel() const - { - return thermoModel.get(); - } - -protected: - - // initialization - void defineModels() - { - thermoData.reset( new jsonui::StringTable( "records", data_->getDataHeaders() ) ); - thermoModel.reset( new jsonui::TMatrixModel( thermoData.get() ) ); - } - - void setHeader( std::vector heads) - { - data_->setDataHeaders(heads); - } - - void setFields( std::vector fields) - { - return data_->setDataFieldPaths(fields); - } -}; - - -#endif // THERMOMODEL_H diff --git a/ThermoFunGui/tmp/ThermoFunWidgetPrivate.cpp b/ThermoFunGui/tmp/ThermoFunWidgetPrivate.cpp deleted file mode 100644 index b7dd1ef0..00000000 --- a/ThermoFunGui/tmp/ThermoFunWidgetPrivate.cpp +++ /dev/null @@ -1,651 +0,0 @@ -#include -#include -#include -#include "jsonio/jsondomfree.h" -#include "ThermoFunWidgetPrivate.h" -#include "ui_ThermoFunWidget.h" -#include "containers.h" - -// ThermoFun includes -#ifdef FROM_SRC -#include "../src/Batch/ThermoBatch.h" -#include "../src/Database.h" -#include "../src/Substance.h" -#include "../src/DBClient/TraversalData.h" -#include "../src/Common/ParseBsonTraversalData.h" -#endif -#ifndef FROM_SRC -#include "thermofun/Batch/ThermoBatch.h" -#include "thermofun/Database.h" -#include "thermofun/Substance.h" -#include "thermofun/DBClient/TraversalData.h" -#include "thermofun/Common/ParseBsonTraversalData.h" -#endif - -using namespace jsonio; -using namespace jsonui; - -/* -bool operator !=( const DBQueryData& iEl, const DBQueryData& iEr) -{ - return (iEl.getType() != iEr.getType()) || - (iEl.getQueryString() != iEr.getQueryString()); -}*/ - -ThermoFunData::ThermoFunData() -{ - name = "ThermoFunTask1"; - comment = "write comment here..."; - calcStatus = "Select a thermodynamic dataset."; // status - schemaName = "VertexSubstance"; - query = emptyQuery; - idReactionSet = ""; - sourcetdb = -1;//defSourcetdb; - tPrecision = 0; - unitsT = "C Celsius"; - pPrecision = 0; - tppairs.push_back({25.,1.}); - unitsP = "b bar"; - properties.push_back("gibbs_energy"); - propertyUnits.push_back("J/mol"); - propertyPrecision.push_back(0); -} - - -void ThermoFunData::resetSchemaName( const string& newSchemaName ) -{ - schemaName = newSchemaName; - query = emptyQuery; - - properties.resize(1); - propertyUnits.resize(1); - propertyPrecision.resize(1); - - if (schemaName == "VertexSubstance") - properties[0] = "gibbs_energy"; - if (schemaName == "VertexReaction") - properties[0] = "reaction_gibbs_energy"; - - propertyUnits[0] = mapUnits[ properties[0]]; - propertyPrecision[0] = mapPrecision[ properties[0]]; -} - - -void ThermoFunData::toJsonNode( jsonio::JsonDom *object ) const -{ - std::size_t ii; - object->appendString( "Name", name ); - object->appendString( "Description", comment ); - object->appendString( "SchemaName", schemaName ); - object->appendInt("SourceTDB", sourcetdb ); - object->appendString( "ReactionSetId", idReactionSet ); - if(!query.empty()) - query.toJsonNode(object); - - auto arr = object->appendArray("ElementsList"); - for( ii=0; iiappendArray( to_string(ii) ); - arr2->appendString( "0", elements[ii].symbol ); - arr2->appendInt( "1", elements[ii].class_ ); - arr2->appendInt( "2", elements[ii].isotope ); - } - - object->appendDouble("TemperaturePrecision", tPrecision ); - object->appendString("TemperatureUnits", unitsT ); - object->appendDouble("PressurePrecision", pPrecision ); - object->appendString("PressureUnits", unitsP ); - - arr = object->appendArray( "TemperaturePressurePoints"); - for( ii=0; iiappendObject( to_string(ii) ); - obj->appendDouble( "T", tppairs[ii][0] ); - obj->appendDouble( "P", tppairs[ii][1] ); - } - - arr = object->appendArray("PropertiesList"); - for( ii=0; iiappendString( to_string(ii), properties[ii] ); - - arr = object->appendArray( "PropertyUnits"); - for( ii=0; iiappendString( to_string(ii), propertyUnits[ii] ); - - arr = object->appendArray( "PropertyPrecision"); - for( ii=0; iiappendInt( to_string(ii), propertyPrecision[ii] ); -} - -void ThermoFunData::fromJsonNode( const jsonio::JsonDom *object ) -{ - ThermoFunData deflt; - - if(!object->findValue( "Name", name ) ) - name=deflt.name; - if(!object->findValue( "Description", comment ) ) - comment=deflt.comment; - if(!object->findValue( "SchemaName", schemaName ) ) - schemaName=deflt.schemaName; - if(!object->findValue( "SourceTDB", sourcetdb ) ) - sourcetdb=deflt.sourcetdb; - if(!object->findValue( "ReactionSetId", idReactionSet ) ) - idReactionSet=""; - query.fromJsonNode(object); - - elements.clear(); - auto arr = object->field( "ElementsList" ); - if( arr!=nullptr && arr->getType() == JSON_ARRAY ) - { - string symbol; - int class_, isotope; - for( int ii=0; iigetChildrenCount(); ii++ ) - { - auto obj = arr->getChild( ii); - if(!obj->findValue( "0", symbol ) ) - continue; - if(!obj->findValue( "1", class_ ) ) - continue; - if(!obj->findValue( "2", isotope ) ) - continue; - elements.push_back( ThermoFun::ElementKey(symbol,class_, isotope ) ); - } - } - - if(!object->findValue( "TemperaturePrecision", tPrecision ) ) - tPrecision=deflt.tPrecision; - if(!object->findValue( "TemperatureUnits", unitsT ) ) - unitsT=deflt.unitsT; - - if(!object->findValue( "PressurePrecision", pPrecision ) ) - pPrecision=deflt.pPrecision; - if(!object->findValue( "PressureUnits", unitsP ) ) - unitsP=deflt.unitsP; - - // read tp pairs - tppairs.clear(); - arr = object->field( "TemperaturePressurePoints" ); - if( arr==nullptr && arr->getType() != JSON_ARRAY ) - tppairs =deflt.tppairs; - else - { - double Ti, Pi; - for( int ii=0; iigetChildrenCount(); ii++ ) - { - auto obj = arr->getChild( ii); - if(!obj->findValue( "T", Ti ) ) - Ti=100.; - if(!obj->findValue( "P", Pi ) ) - Pi = 5.; - tppairs.push_back({Ti, Pi}); - } - } - - object->findArray( "PropertiesList", properties ); - if( properties.empty() ) - properties =deflt.properties; - object->findArray( "PropertyUnits", propertyUnits ); - if( properties.empty() ) - properties =deflt.properties; - object->findArray( "PropertyPrecision", propertyPrecision ); - if( properties.empty() ) - properties =deflt.properties; - } - - -ThermoFunWidgetPrivate::ThermoFunWidgetPrivate( ThermoFunWidgetNew* awindow ): - QObject(awindow), window(awindow), dbclient( uiSettings().dbclient() ) -{ - initWindow(); -} - -void ThermoFunWidgetPrivate::updateDBClient() -{ - /** dbclient.substData().updateDBClient(); - dbclient.reactData().updateDBClient(); - dbclient.reactSetData().updateDBClient(); - */ -} - -// Edit part ---------------------------------------------------- - -void ThermoFunWidgetPrivate::loadModel() -{ - if( !_data.idReactionSet.empty() && dbclient.reactSetData().recordExists(_data.idReactionSet) ) - tableModel->loadModeRecords( _data.idReactionSet ); - else - tableModel->loadModeRecords( _data.query, _data.sourcetdb, _data.elements ); -} - -/// Reset internal query data -void ThermoFunWidgetPrivate::updateQuery( const DBQueryData& newquery ) -{ - // reset internal query data - if( newquery != _data.query ) - { - isDefaultQuery = true; - _data.query = newquery; - } - loadModel(); -} - -/// Reset internal elements list -void ThermoFunWidgetPrivate::updateElements( int sourcetdb, - const vector& elKeys, const string& idrcset ) -{ - _data.idReactionSet = idrcset; - _data.sourcetdb = sourcetdb; - _data.elements = elKeys; - updateElementsModel(); - loadModel(); -} - -void ThermoFunWidgetPrivate::updataSourceTDB() -{ - jsonio::ThriftEnumDef* enumdef = ioSettings().Schema()->getEnum("SourceTDB" ); - if(enumdef != nullptr ) - { - string curText = enumdef->getNamebyId(_data.sourcetdb); - window->ui->pSourceTDB->setCurrentText(curText.c_str()); - } -} - -void ThermoFunWidgetPrivate::updateElementsModel() -{ - if( elementModel) - { - elementModel->resetMatrixData(); - if( elementTable->horizontalScrollBar()->isVisible() ) - { - int iHeight = elementTable->verticalHeader()->sectionSize(0); - iHeight += elementTable->horizontalScrollBar()->height(); - elementTable->setMaximumHeight(iHeight); - } - } - updataSourceTDB(); -} - -void ThermoFunWidgetPrivate::reallocTP( int newsize ) -{ - _data.tppairs.clear(); - for (std::size_t i = 0; iresetMatrixData(); -} - -void ThermoFunWidgetPrivate::updateTP( const string& unitsT, const string& unitsP, - const std::vector>& tppairs) -{ - _data.unitsT = unitsT; - _data.unitsP = unitsP; - window->ui->pTunit->setCurrentText(unitsT.c_str()); - window->ui->pPunit->setCurrentText(unitsP.c_str()); - _data.tppairs = tppairs; - _TPlistModel->resetMatrixData(); -} - - -void ThermoFunWidgetPrivate::updateProperty( const vector& properties ) -{ - // store previous settings - for (unsigned i = 0; i<_data.properties.size(); i++) - { - _data.mapUnits[_data.properties[i]] = _data.propertyUnits[i]; - _data.mapPrecision[_data.properties[i]] = _data.propertyPrecision[i]; - } - _data.properties = properties; - _data.propertyUnits.resize(_data.properties.size()); - _data.propertyPrecision.resize(_data.properties.size()); - for (unsigned i = 0; i<_data.properties.size(); i++) - { - _data.propertyUnits[i] = _data.mapUnits[_data.properties[i]]; - _data.propertyPrecision[i] = _data.mapPrecision[_data.properties[i]]; - } - _PropertyModel->resetMatrixData(); -} - - -void ThermoFunWidgetPrivate::linkChange() -{ - if( _data.schemaName == "VertexReaction") - { - tableModel->linkData(new ThermoFun::SubstanceData_(dbclient.substData())); - loadModel(); - tableModel->linkData(new ThermoFun::ReactionData_(dbclient.reactData())); - loadModel(); - } - else - { - tableModel->linkData(new ThermoFun::ReactionData_(dbclient.reactData())); - loadModel(); - tableModel->linkData(new ThermoFun::SubstanceData_(dbclient.substData())); - loadModel(); - } -} - -void ThermoFunWidgetPrivate::typeChanged(const string& newSchemaName) -{ - if( newSchemaName != _curSchemaName ) - { - _curSchemaName = newSchemaName; - _data.resetSchemaName( _curSchemaName ); - _PropertyModel->resetMatrixData(); - isDefaultQuery = !_data.query.empty(); - window->ui->edgeQuery->setText(_data.query.getQueryString().c_str()); - } - linkChange(); -} - -// Reset ThermoFun data -void ThermoFunWidgetPrivate::newThermoFunData( const ThermoFunData& newdata ) -{ - _data = newdata; - - tableModel->linkData(new ThermoFun::SubstanceData_(dbclient.substData())); - - _curSchemaName = _data.schemaName; - // update models - updateElementsModel(); - _TPlistModel->resetMatrixData(); - _PropertyModel->resetMatrixData(); -// linkChange(); - isDefaultQuery = !_data.query.empty(); - // update view must be up -} - - -// Calc part ------------------------------ - -// extract init for calculation data -void ThermoFunWidgetPrivate::loadSubstData( const vector& selNdx, - vector& aKeyList, vector& substancesSymbols, - vector& substancesClass ) -{ - if(_data.schemaName != "VertexSubstance") - return; - - const jsonio::ValuesTable& values= tableModel->getValues(); - aKeyList.resize(selNdx.size()); - substancesSymbols.resize(selNdx.size()); - substancesClass.resize(selNdx.size()); - - for( std::size_t ii=0; ii& selNdx, - vector& aKeyList, vector& reactionsSymbols ) -{ - if (_data.schemaName != "VertexReaction") - return; - const jsonio::ValuesTable& values= tableModel->getValues(); - aKeyList.resize(selNdx.size()); - reactionsSymbols.resize(selNdx.size()); - for( std::size_t ii=0; ii &linkedSubstSymbols, vector &linkedReactSymbols, - vector &linkedSubstClasses, vector &linkedSubstIds) -{ - string valDB; - for (auto idType : mapOfConnectedIds) - { - if (idType.second == "reaction") - { - string symbol; - string jsonrecord = dbclient.reactData().getJsonRecordVertex(idType.first+":"); - auto domdata = jsonio::unpackJson( jsonrecord ); - domdata->findKey("properties.symbol", symbol); - // record = dbclient.reactData().getJsonRecordVertex(idType.first+":").second; - // jsonio::bson_to_key( record.data, "properties.symbol", symbol); - linkedReactSymbols.push_back(symbol); - } - if (idType.second == "substance") - { - string symbol, class_; - string jsonrecord = dbclient.substData().getJsonRecordVertex(idType.first+":"); - auto domdata = jsonio::unpackJson( jsonrecord ); - domdata->findKey("properties.symbol", symbol); - domdata->findKey("properties.class_", class_); - // record = dbclient.substData().getJsonBsonRecordVertex(idType.first+":").second; - // jsonio::bson_to_key( record.data, "properties.symbol", symbol); - // jsonio::bson_to_key( record.data, "properties.class_", class_); - linkedSubstClasses.push_back(class_); - linkedSubstSymbols.push_back(symbol); - linkedSubstIds.push_back(idType.first); - } - } -} - -void ThermoFunWidgetPrivate::retrieveConnectedDataSymbols( const vector& substKeys, const vector& reactKeys, vector &linkedSubstSymbols, - vector &linkedReactSymbols, vector &linkedSubstClasses, vector &linkedSubstIds) -{ - linkedReactSymbols.clear(); linkedSubstSymbols.clear(); linkedSubstClasses.clear(); - - retrieveConnectedData(dbclient.getTraversal().getMapOfConnectedIds(substKeys), linkedSubstSymbols, linkedReactSymbols, linkedSubstClasses, linkedSubstIds); - retrieveConnectedData(dbclient.getTraversal().getMapOfConnectedIds(reactKeys), linkedSubstSymbols, linkedReactSymbols, linkedSubstClasses, linkedSubstIds); -// react.getLinkedDataSymbols(reactKeys, linkedSubstSymbols, linkedReactSymbols, linkedSubstClasses); -// subst.getLinkedDataSymbols(substKeys, linkedSubstSymbols, linkedReactSymbols, linkedSubstClasses); -} - -void ThermoFunWidgetPrivate::setSubstanceLevel(string substSymbol, string level) -{ - dbclient.substData().setSubstanceLevel(substSymbol, level); -} - -//void ThermoFunWidgetPrivate::setReactionLevel(string reactSymbol, string level) -//{ -// react.setReactionLevel(reactSymbol, level); -//} - -MapSymbolMapLevelReaction ThermoFunWidgetPrivate::recordsMapLevelDefinesReaction_(ThermoFun::MapSubstSymbol_MapLevel_IdReaction mapSymbol_Level_idReact) -{ - MapSymbolMapLevelReaction recordsLevelReact; - - for (auto symbol_Level_idReact : mapSymbol_Level_idReact) - { - MapLevelReaction levelReact; - for (auto level_idReact : symbol_Level_idReact.second) - { - levelReact[level_idReact.first] = ThermoFun::parseReaction( - dbclient.reactData().getJsonRecordVertex(level_idReact.second+":") ); - } - recordsLevelReact[symbol_Level_idReact.first] = levelReact; - } - return recordsLevelReact; -} - -MapSymbolMapLevelReaction ThermoFunWidgetPrivate::recordsMapLevelDefinesReaction() -{ - return recordsMapLevelDefinesReaction_(dbclient.substData().recordsMapLevelDefinesReaction()); -} - -MapSymbolMapLevelReaction ThermoFunWidgetPrivate::recordsMapLevelDefinesReaction(vector connectedSubstIds , vector connectedSubstSymbols) -{ - return recordsMapLevelDefinesReaction_(dbclient.substData().recordsMapLevelDefinesReaction(connectedSubstIds, connectedSubstSymbols)); -} - -ThermoFun::Database setSubstanceCalcType_ (ThermoFun::Database tdb, ThermoFun::SubstanceThermoCalculationType::type type_) -{ - auto substances = tdb.getSubstances(); - for (auto substance : substances) - { - substance.setThermoCalculationType(type_); - tdb.setSubstance(substance); - } - return tdb; -} - -//MapSymbolMapLevelSubstances ThermoFunWidgetPrivate::recordsMapLevelTakesSubstances() -//{ -// return react.recordsMapLevelTakesSubstances(); -//} - -double ThermoFunWidgetPrivate::calcData(const vector& substKeys, const vector& reactKeys, - const vector& substancesSymbols, const vector& reactionsSymbols, - const string& solventSymbol, bool FormatBox , bool calcSubstFromReact, bool calcReactFromSubst, struct timeval start) -{ - vector keys; keys.insert(keys.end(), substKeys.begin(), substKeys.end()); - keys.insert(keys.end(), reactKeys.begin(), reactKeys.end()); - - auto tr = dbclient.getTraversal(); - - ThermoFun::VertexId_VertexType resultTraversal = tr.getMapOfConnectedIds(keys, dbclient.substData().getSubstSymbol_DefinesLevel()); - ThermoFun::Database tdb_ = tr.getDatabaseFromMapOfIds(resultTraversal, dbclient.substData().getSubstSymbol_DefinesLevel()); - -// ThermoFun::Traversal tr(subst.getDB()); -// ThermoFun::MapIdType resultTraversal = tr.getMapOfConnectedIds(keys, subst.mapSymbolLevel()); -// ThermoFun::Database tdb_ = tr.getDatabaseFromMapOfIds(resultTraversal, subst.mapSymbolLevel()); - - if (!calcSubstFromReact) // make all reactions to be calculated using the method in the record - tdb_ = setSubstanceCalcType_(tdb_, ThermoFun::SubstanceThermoCalculationType::type::DCOMP); - - - ThermoFun::ThermoBatch tpCalc (tdb_); - tpCalc.setSolventSymbol(solventSymbol); - - ThermoFun::OutputSettings op; - if( FormatBox ) - { - op.isFixed = true; - } else - op.isFixed = false; - - op.outSolventProp = true; - op.calcReactFromSubst = calcReactFromSubst; - op.calcSubstFromReact = calcSubstFromReact; - tpCalc.setOutputSettings(op); - - tpCalc.setPropertiesUnits({"temperature", "pressure"},{"degC","bar"}); - - if (_data.unitsP == "B kbar") - tpCalc.setPropertyUnit("pressure","kbar"); - if (_data.unitsP == "p Pa") - tpCalc.setPropertyUnit("pressure","Pa"); - if (_data.unitsP == "P MPa") - tpCalc.setPropertyUnit("pressure","MPa"); - if (_data.unitsP == "A Atm") - tpCalc.setPropertyUnit("pressure","atm"); - - /// check !!! - vector solventPropNames = {"density", "alpha", "beta", "alphaT", "epsilon", "bornZ", "bornY", "bornQ", "bornX"}; -// tpCalc.addSolventProperties(solventPropNames); - - std::map precision = ThermoFun::defaultPropertyDigits; - for (std::size_t jj = 0; jj <_data.properties.size(); jj++) - { - precision.at(_data.properties[jj]) = _data.propertyPrecision[jj]; - } - - precision.at("temperature") = _data.tPrecision; - precision.at("pressure") = _data.pPrecision; - - tpCalc.setDigits(precision); - - if (_data.schemaName == "VertexReaction") - { - tpCalc.thermoPropertiesReaction(_data.tppairs, reactionsSymbols, _data.properties/*, calcReactFromSubst*/).toCSV(op.fileName); - - vector reactionsEquations; - for (auto symb : reactionsSymbols) - { - reactionsEquations.push_back(tdb_.getReaction(symb).equation()); - } - - /// check !!! -// tpCalc.clearReactions(); -// tpCalc.addReactions(reactionsEquations); - -// ThermoFun::Output (tpCalc).toCSV("equations.csv"); - } - - - if (_data.schemaName == "VertexSubstance") - tpCalc.thermoPropertiesSubstance( _data.tppairs, substancesSymbols, _data.properties/*, calcSubstFromReact*/).toCSV(op.fileName); - - struct timeval end; - gettimeofday(&end, NULL); - double delta_calc = ((end.tv_sec - start.tv_sec) * 1000000u + - end.tv_usec - start.tv_usec) / 1.e6; - - return delta_calc; - -} - - -//----------------------------------------------------------------------- - -void ThermoFunWidgetPrivate::initWindow() -{ - // define all keys tables - valuesTable = new TMatrixTable( window ); - valuesTable->horizontalHeader()->setSectionResizeMode( QHeaderView::Interactive ); - valuesTable->setEditTriggers( QAbstractItemView::AnyKeyPressed ); - valuesTable->setSortingEnabled(true); - QObject::disconnect( valuesTable, SIGNAL(customContextMenuRequested(QPoint)), - valuesTable, SLOT(slotPopupContextMenu(QPoint))); - //TMatrixDelegate* deleg = new TMatrixDelegate(); - //pTable->setItemDelegate(deleg); - window->ui->keySplitter->insertWidget(0, valuesTable); - window->ui->keySplitter->setStretchFactor(0, 4); - //tableModel = new ThermoViewModel( new ThermoFun::SubstanceData_(dbclient.substData()), window ); - tableModel = new ThermoViewModel( &dbclient.substData(), window ); - tableModel->updateModel(valuesTable); - - // Elements list - elementContainer = new ElementsDataContainer( _data.elements ); - elementModel = new TMatrixModel( elementContainer, window ); - elementTable = new TMatrixTable( window, TMatrixTable::tbShow ); - elementTable->setModel(elementModel); - elementTable->horizontalHeader()->hide(); - elementTable->verticalHeader()->hide(); - elementTable->verticalHeader()->setStretchLastSection(true); - //elementTable->setHorizontalScrollBarPolicy(Qt::ScrollBarAlwaysOn); - int iHeight = 1.5*elementTable->verticalHeader()->sectionSize(0); - //iHeight += elementTable->horizontalScrollBar()->height(); - elementTable->setMaximumHeight(iHeight); - window->ui->verticalLayout_2->insertWidget(0, elementTable); - - // define ThermoFun data - _TPContainer = new TPContainer( "T", { "T", "P" }, _data.tppairs ); - _TPlistTable = new TMatrixTable( window->ui->outWidget ); - TMatrixDelegate* deleg = new TMatrixDelegate(); - _TPlistTable->setItemDelegate(deleg); - _TPlistModel = new TMatrixModel( _TPContainer, window ); - _TPlistTable->setModel(_TPlistModel); - _TPlistTable->horizontalHeader()->setSectionResizeMode( QHeaderView::Stretch/*Interactive*/ ); - window->ui->gridLayout_3->addWidget(_TPlistTable, 1, 0, 1, 1); - - _PropertyContainer = new TPropertyContainer( "Property", _data.properties, _data.propertyUnits, _data.propertyPrecision ); - _PropertyTable = new TMatrixTable( window->ui->inWidget ); - deleg = new TMatrixDelegate(); - _PropertyTable->setItemDelegate(deleg); - _PropertyModel = new TMatrixModel( _PropertyContainer, window ); - _PropertyTable->setModel(_PropertyModel); - _PropertyTable->horizontalHeader()->setSectionResizeMode( QHeaderView::Stretch/*Interactive*/ ); - window->ui->gridLayout->addWidget(_PropertyTable, 7, 0, 1, 8); -} - -void ThermoFunWidgetPrivate::freeInternal() -{ - delete tableModel; - delete valuesTable; - delete _TPlistTable; - delete _TPContainer; - delete _PropertyTable; - delete _PropertyContainer; - delete elementContainer; - delete elementTable; -} - diff --git a/ThermoFunGui/tmp/ThermoFunWidgetPrivate.h b/ThermoFunGui/tmp/ThermoFunWidgetPrivate.h deleted file mode 100644 index 5cac0417..00000000 --- a/ThermoFunGui/tmp/ThermoFunWidgetPrivate.h +++ /dev/null @@ -1,247 +0,0 @@ -#ifndef THERMOFUNWIDGETPRIVATE_H -#define THERMOFUNWIDGETPRIVATE_H - -#include -#include -#include "ThermoFunWidgetNew.h" -#include "thermomodel.h" - -// ThermoFun includes -#ifdef FROM_SRC -#include "../src/Batch/ThermoBatch.h" -#include "../src/DBClient/ReactionData.h" -#include "../src/DBClient/ReactionSetData.h" -#include "../src/DBClient/SubstanceData.h" -#include "../src/Reaction.h" -#include "../src/Substance.h" -#endif -#ifndef FROM_SRC -#include "thermofun/Batch/ThermoBatch.h" -#include "thermofun/DBClient/ReactionData.h" -#include "thermofun/DBClient/ReactionSetData.h" -#include "thermofun/DBClient/SubstanceData.h" -#endif - -class TPContainer; -class TPropertyContainer; -class ElementsDataContainer; - -using MapLevelReaction = map; -using MapLevelSubstances = map>; -using MapSymbolMapLevelReaction = map; -using MapSymbolMapLevelSubstances = map; - -extern const int defSourcetdb; - -/// ThermoFun data to calculation -struct ThermoFunData -{ - string name; ///< Task (file) name - string comment; ///< Task description - string calcStatus; ///< ThermoFun colaculation status - - string schemaName; ///< Selected schema - jsonio::DBQueryData query; ///< Current schema - int sourcetdb; ///< Current sourcetdb - vector elements; - string idReactionSet; ///< Id of reaction set, - ///< if not empty we load records only from ReactionSet - - string unitsT; ///< Current units of T - string unitsP; ///< Current units of P - - std::vector> tppairs; - - vector properties; ///< Properties names list - vector propertyUnits; ///< Units of property - vector propertyPrecision; ///< Units of property - int pPrecision, tPrecision; - - - // work data - map mapUnits = ThermoFun::defaultPropertyUnits; - map mapPrecision = ThermoFun::defaultPropertyDigits; - - - /// Default values to task - ThermoFunData(); - - /// Write current task to configuration file fileName - void toJsonNode( jsonio::JsonDom *object ) const; - /// Read current task from configuration file fileName - void fromJsonNode( const jsonio::JsonDom *object ); - - /// Clear properies and query if schema changed - void resetSchemaName( const string& newSchemaName ); -}; - - -class ThermoFunWidgetPrivate: public QObject -{ - - Q_OBJECT - - ThermoFunWidgetNew* window; - - // Internal data -// vector _shemaNames; - string _curSchemaName = ""; - bool isDefaultQuery = false; - - ThermoFunData _data; ///< Current project data -// ThermoFun::SubstanceData_ subst; ///< Working with SubstanceVerte -// ThermoFun::ReactionData_ react; ///< Working with ReactionVertex -// ThermoFun::ReactionSetData_ rcset; ///< working with ReactionSetVertex - - - // Window data ------------------------------------ - - // keys list data - jsonui::TMatrixTable* valuesTable = 0; - ThermoViewModel* tableModel = 0; - - // define ELEMENTS table model - ElementsDataContainer *elementContainer = 0; - jsonui::TMatrixTable *elementTable = 0; - jsonui::TMatrixModel* elementModel = 0; - - //ThermoFun data to edit; - TPContainer* _TPContainer = 0; - jsonui::TMatrixTable* _TPlistTable = 0; - jsonui::TMatrixModel* _TPlistModel = 0; - - TPropertyContainer* _PropertyContainer = 0; - jsonui::TMatrixTable* _PropertyTable = 0; - jsonui::TMatrixModel* _PropertyModel = 0; - - void initWindow(); - void freeInternal(); - void updateElementsModel(); - void updataSourceTDB(); - void linkChange(); - void loadModel(); - - MapSymbolMapLevelReaction recordsMapLevelDefinesReaction_(ThermoFun::MapSubstSymbol_MapLevel_IdReaction mapSymbol_Level_idReact); - -public slots: - - void pPChanged(int val) - { - _data.pPrecision = val; - } - void tPChanged(int val) - { - _data.tPrecision = val; - } - void TUnitsChanged(const QString& text) - { - _data.unitsT = text.toStdString(); - } - void PUnitsChanged(const QString& text) - { - _data.unitsP = text.toStdString(); - } - void nameChanged(const QString& text) - { - _data.name = text.toStdString(); - } - void commentChanged(const QString& text) - { - _data.comment = text.toStdString(); - } - - void retrieveConnectedData(map mapOfConnectedIds, vector &linkedSubstSymbols, - vector &linkedReactSymbols, vector &linkedSubstClasses, vector &linkedSubstIds); - - -public: - - ThermoFunWidgetPrivate( ThermoFunWidgetNew* awindow ); - - ~ThermoFunWidgetPrivate() - { - freeInternal(); - } - - const ThermoFunData& data() const - { - return _data; - } - const jsonio::DBQueryDef& getQuery( ) const - { - return tableModel->getQuery(); - } - const jsonio::ValuesTable& getValues() const - { - return tableModel->getValues(); - } - string getThermoPropertiesName() const - { - std::size_t pos = std::string("Vertex").length(); - std::string schemaName = "ThermoProperties" + _data.schemaName.substr (pos); - return schemaName; - } - void updateQuery( const jsonio::DBQueryData& newquery ); - void updateElements( int sourcetdb, const vector& elKeys, const string& idrcset ); - void reallocTP( int newsize ); - void updateTP( const string& unitsT, const string& unitsP, - const std::vector>& tppairs); - void updateProperty( const vector& properties ); - void typeChanged(const string& newSchemaName); - void newThermoFunData( const ThermoFunData& newdata ); - void updateDBClient(); - - // calc functions - void loadSubstData( const vector& selNdx, - vector& aKeyList, vector& substancesSymbols, - vector& substancesClass ); - void loadReactData( const vector& selNdx, - vector& aKeyList, vector& reactionsSymbols ); - jsonio::ValuesTable querySolvents() - { - return dbclient.substData().querySolvents(_data.sourcetdb); - } - - std::map getSubstDataIndex() - { - return dbclient.substData().getDataName_DataIndex(); - } - - void retrieveConnectedDataSymbols(const vector& substKeys, const vector& reactKeys, - vector &linkedSubstSymbols, vector &linkedReactSymbols, vector &linkedSubstClasses, vector &linkedSubstIds); - - MapSymbolMapLevelReaction recordsMapLevelDefinesReaction(); - MapSymbolMapLevelReaction recordsMapLevelDefinesReaction(vector connectedSubstIds , vector connectedSubstSymbols); -// MapSymbolMapLevelSubstances recordsMapLevelTakesSubstances(); - - void setSubstanceLevel(string substSymbol, string level); -// void setReactionLevel(string reactSymbol, string level); - - double calcData(const vector& substKeys, const vector& reactKeys, - const vector& substancesSymbols, const vector& reactionsSymbols, - const string& solventSymbol, bool FormatBox, bool calcSubstFromReact, bool calcReactFromSubst , struct timeval start); - - // temporaly functions - void resetElementsintoRecord( bool isreact, const string& aKey ) - { - if(isreact) - dbclient.reactData().resetRecordElements( aKey ); - else - dbclient.reactSetData().resetRecordElements( aKey ); - } - - ThermoFun::DatabaseClient dbclient; - -// const std::shared_ptr& getReactDB( bool isreact ) const -// { -// if(isreact) -// return *new std::shared_ptr(dbclient.reactData().getDB()); -// else -// return *new std::shared_ptr(dbclient.reactSetData().getDB()); -// } - -}; - - - -#endif // THERMOFUNWIDGETPRIVATE_H diff --git a/ThermoHubClient/AQLqueries.h b/ThermoHubClient/AQLqueries.h deleted file mode 100644 index 8962e7db..00000000 --- a/ThermoHubClient/AQLqueries.h +++ /dev/null @@ -1,145 +0,0 @@ -#ifndef AQLQUERIES_H -#define AQLQUERIES_H - -#include - -namespace ThermoFun { - -const std::string aql_fun_substances_reactions_ids = "/* Get substances */ \n" - "LET substances_ = ( \n" - "/* Get substances that are defined through a reaction */ \n" - "LET reacdcs_ = ( \n" - " FOR s IN substances \n" - " FILTER s._id IN @ids \n" - " FOR r IN 1..1 INBOUND s defines \n" - " RETURN { \n" - " name: s.properties.name, \n" - " symbol: s.properties.symbol, \n" - " reaction : r.properties.symbol, \n" - " formula: s.properties.formula, \n" - " formula_charge: s.properties.formula_charge, \n" - " mass_per_mole: s.properties.mass_per_mole, \n" - " aggregate_state: s.properties.aggregate_state, \n" - " class_: s.properties.class_, \n" - " limitsTP: s.properties.limitsTP, \n" - " Tst: s.properties.Tst, \n" - " Pst: s.properties.Pst, \n" - " TPMethods: s.properties.TPMethods, \n" - " sm_heat_capacity_p: s.properties.sm_heat_capacity_p, \n" - " sm_gibbs_energy: s.properties.sm_gibbs_energy, \n" - " sm_enthalpy: s.properties.sm_enthalpy, \n" - " sm_entropy_abs: s.properties.sm_entropy_abs, \n" - " sm_volume: s.properties.sm_volume, \n" - " m_compressibility: s.properties.m_compressibility, \n" - " m_expansivity: s.properties.m_expansivity, \n" - " id: s._id \n" - " } \n" - ") \n" - "/* Get substances from list of records ids */ \n" - "LET selected_substances_ = ( \n" - " FOR s IN substances \n" - " FILTER s._id IN @ids \n" - " FILTER s.properties.symbol NOT IN reacdcs_[*].symbol \n" - " RETURN { \n" - " name: s.properties.name, \n" - " symbol: s.properties.symbol, \n" - " formula: s.properties.formula, \n" - " formula_charge: s.properties.formula_charge, \n" - " mass_per_mole: s.properties.mass_per_mole, \n" - " aggregate_state: s.properties.aggregate_state, \n" - " class_: s.properties.class_, \n" - " limitsTP: s.properties.limitsTP, \n" - " Tst: s.properties.Tst, \n" - " Pst: s.properties.Pst, \n" - " TPMethods: s.properties.TPMethods, \n" - " sm_heat_capacity_p: s.properties.sm_heat_capacity_p, \n" - " sm_gibbs_energy: s.properties.sm_gibbs_energy, \n" - " sm_enthalpy: s.properties.sm_enthalpy, \n" - " sm_entropy_abs: s.properties.sm_entropy_abs, \n" - " sm_volume: s.properties.sm_volume, \n" - " m_compressibility: s.properties.m_compressibility, \n" - " m_expansivity: s.properties.m_expansivity, \n" - " id: s._id \n" - " }) \n" - "RETURN APPEND(reacdcs_, selected_substances_, true) \n" - ") \n" - "/* Get reactions */ \n" - "LET reactions_ = ( \n" - "LET reactions_defines_ = ( \n" - " FOR s IN substances \n" - " FILTER s._id IN @ids \n" - " FOR r IN 1..1 INBOUND s defines \n" - " LET reactants_ = ( \n" - " FOR ss, t IN 1..1 INBOUND r takes \n" - "/* LET ids_2 = PUSH(ids_, ss._id, true) /* add substance id to idlist */ \n" - " RETURN { \n" - " symbol: ss.properties.symbol, \n" - " coefficient: t.properties.stoi_coeff, \n" - " id: ss._id \n" - " } \n" - " ) \n" - " RETURN { \n" - " name: r.properties.name, \n" - " symbol: r.properties.symbol, \n" - " substance : s.properties.symbol, \n" - " equation: r.properties.equation, \n" - " reactants: reactants_, \n" - " limitsTP: r.properties.limitsTP, \n" - " Tst: r.properties.Tst, \n" - " Pst: r.properties.Pst, \n" - " TPMethods: r.properties.TPMethods, \n" - " logKr : r.properties.logKr, \n" - " drsm_heat_capacity_p : r.properties.drsm_heat_capacity_p, \n" - " drsm_gibbs_energy : r.properties.drsm_gibbs_energy, \n" - " drsm_enthalpy : r.properties.drsm_enthalpy, \n" - " drsm_entropy : r.properties.drsm_entropy, \n" - " drsm_volume : r.properties.drsm_volume, \n" - " id: r._id \n" - " } \n" - ") \n" - "LET selected_reactions_ = ( \n" - " FOR r IN reactions \n" - " FILTER r._id IN @ids \n" - " FILTER r.properties.symbol NOT IN reactions_defines_[*].symbol \n" - " LET reactants_ = ( \n" - " FOR ss, t IN 1..1 INBOUND r takes \n" - " RETURN { \n" - " symbol: ss.properties.symbol, \n" - " coefficient: t.properties.stoi_coeff, \n" - " id: ss._id \n" - " } \n" - " ) \n" - " RETURN { \n" - " name: r.properties.name, \n" - " symbol: r.properties.symbol, \n" - " equation: r.properties.equation, \n" - " reactants: reactants_, \n" - " limitsTP: r.properties.limitsTP, \n" - " Tst: r.properties.Tst, \n" - " Pst: r.properties.Pst, \n" - " TPMethods: r.properties.TPMethods, \n" - " logKr : r.properties.logKr, \n" - " drsm_heat_capacity_p : r.properties.drsm_heat_capacity_p, \n" - " drsm_gibbs_energy : r.properties.drsm_gibbs_energy, \n" - " drsm_enthalpy : r.properties.drsm_enthalpy, \n" - " drsm_entropy : r.properties.drsm_entropy, \n" - " drsm_volume : r.properties.drsm_volume, \n" - " id: r._id \n" - " }) \n" - "RETURN APPEND(reactions_defines_, selected_reactions_, true) \n" - ") \n" - "/* get ids of all traversed data */ \n" - "LET ids_substances_ = (substances_[*][*].id) \n" - "LET ids_reactions_ = (reactions_[*][*].id) \n" - "LET ids_reactants_ = ( \n" - " FOR r IN reactions_ \n" - " RETURN r[*].reactants[*].id \n" - ") \n" - "LET ids_ = (APPEND(FLATTEN(ids_substances_,1), FLATTEN(ids_reactions_,1), true)) \n" - "LET ids_all = SORTED_UNIQUE((FLATTEN(APPEND(ids_, FLATTEN(ids_reactants_,1), true),1))) \n" - "RETURN {\"substances\": SORTED_UNIQUE(FLATTEN(substances_,1)) , \"reactions\": SORTED_UNIQUE(FLATTEN(reactions_,1)), \"ids\": ids_all} \n"; - -} - - -#endif // AQLQUERIES_H diff --git a/ThermoHubClient/AbstractData.cpp b/ThermoHubClient/AbstractData.cpp deleted file mode 100644 index 384f524d..00000000 --- a/ThermoHubClient/AbstractData.cpp +++ /dev/null @@ -1,631 +0,0 @@ -#include "AbstractData.h" -#include "ElementData.h" - -// C++ includes -#include -#include "jsonio/jsondomfree.h" -// ThermoFun includes -#ifdef FROM_SRC -#include "../ThermoFun/OptimizationUtils.h" -#else -#include "ThermoFun/OptimizationUtils.h" -#endif -#include "sourcetdb.h" - -using namespace std; -using namespace jsonio; - -namespace ThermoFun { - -using QueryRecord = std::function)>; -using LoadRecord = std::function)>; -using LoadRecords = std::function)>; - -using QueryInEdgesDefines = std::function(string, string)>; -using DefinesReactionSymbol = std::function; - -using QueryInEdgesTakes = std::function(string)>; -using ReactantsCoeff = std::function(string)>; - -using GetJsonRecord = std::function; -//using GetJsonBsonRecord = std::function(std::string)>; - -// static std::shared_ptr dbc = std::shared_ptr(); -//const string ThermoDataSetQueryEdges = " basis, pulls, involves, master, prodreac, takes, defines, product "; -const string ThermoDataSetQueryEdges = " basis, pulls, involves, master, prodreac, takes, defines, product "; - -struct AbstractData::Impl -{ - /// Vertex name - const string name; - /// Default query to vertex - const DBQueryData query; - /// Paths to fields to be extracted - vector fieldPaths; - /// Columns headers names ( for extracted data ) - vector dataHeaders; - /// Data names which will be used throughout the code - vector dataNames; - - std::map dataIndex; - std::map dataPath; - - std::map substSymbolLevel; - - /// Data base connection - const jsonio::TDataBase* dbconnect; - std::shared_ptr dbvertex; - - /// Data base connection access to all data types - std::shared_ptr dbedge_all; - - QueryRecord query_record_fn; - LoadRecord load_record_fn; - LoadRecords load_records_fn; - - QueryInEdgesDefines query_in_edges_defines_fn; - DefinesReactionSymbol defines_reaction_symbol_fn; - - QueryInEdgesTakes query_in_edges_takes_fn; - ReactantsCoeff reactans_coeff_fn; - - // function for retrieving the full JSON record from the database using the record id - GetJsonRecord get_json_record_fn_; - GetJsonRecord get_json_bson_record_v_fn; - GetJsonRecord get_json_bson_record_e_fn; - - /// Reconect to other data base - void changeDataBase( const jsonio::TDataBase* adbconnect ) - { - dbconnect = adbconnect; -// auto v = jsonio::TDBVertexDocument::newDBVertexDocument( dbconnect, name, query ); - dbvertex.reset( jsonio::TDBVertexDocument::newVertexDocument( dbconnect, name ) ); - dbedge_all.reset( jsonio::documentAllEdges( dbconnect ) ); - // clear old data - dataIndex.clear(); - dataPath.clear(); - substSymbolLevel.clear(); - } - - /// Internl functiond for using internal selection part API - void loadQuery() - { - dbvertex->SetQuery( query, fieldPaths ); - } - - Impl( const jsonio::TDataBase* adbconnect, - const string &aname, const DBQueryData& aquery, const vector &apaths, - const vector &headers, const vector &names) : - name(aname), query(aquery), fieldPaths(apaths), - dataHeaders(headers), dataNames(names), dbconnect(adbconnect) - { - // init connections to data base - changeDataBase( adbconnect ); - - get_json_bson_record_v_fn = [=](string idRecord) { - return getJsonRecordVertex(idRecord); - }; - get_json_bson_record_v_fn = memoize(get_json_bson_record_v_fn); - - get_json_bson_record_e_fn = [=](string idRecord) { - return getJsonRecordEdge(idRecord); - }; - get_json_bson_record_e_fn = memoize(get_json_bson_record_e_fn); - - load_record_fn = [=](const string idRecord, const vector queryFields) { - return loadRecord(idRecord, queryFields); - }; - load_record_fn = memoize(load_record_fn); - - load_records_fn = [=](const vector idRecords) { - return loadRecords(idRecords); - }; - load_records_fn = memoize(load_records_fn); - - query_in_edges_defines_fn = [=](string idSubst, string level) { - return queryInEdgesDefines(idSubst, level); - }; - query_in_edges_defines_fn = memoize(query_in_edges_defines_fn); - - defines_reaction_symbol_fn = [=](string idSubst, string level) { - return definesReactionSymbol(idSubst, level); - }; - defines_reaction_symbol_fn = memoize(defines_reaction_symbol_fn); - - query_in_edges_takes_fn = [=](string idReact) { - return queryInEdgesTakes(idReact); - }; - query_in_edges_takes_fn = memoize(query_in_edges_takes_fn); - - reactans_coeff_fn = [=](string idReact) { - return reactantsCoeff(idReact); - }; - reactans_coeff_fn = memoize(reactans_coeff_fn); - } - - auto getJsonRecordVertex(string idRecord) -> std::string // id: "12234444" format - { - std::string json_str; - dbvertex->resetMode(true); - dbvertex->Read(idRecord); - json_str = dbvertex->GetJson(); - dbvertex->resetMode(false); - return json_str; - } - - auto getJsonRecordEdge(string idRecord) -> std::string // id: "12234444" format - { - std::string json_str; - dbedge_all->Read(idRecord); - json_str = dbedge_all->GetJson(); - return json_str; - } - - auto loadRecord(string idRecord, vector queryFields) -> jsonio::FieldSetMap - { - return dbvertex->loadRecordFields(idRecord, queryFields); - } - - auto loadRecords( vector idRecords) -> jsonio::ValuesTable - { - dbvertex->resetSchema(name, false); - return dbvertex->downloadDocuments(idRecords, fieldPaths); - } - - // return all record, no only fields - auto queryInEdgesDefines(string idSubst, string level) -> vector - { - string qrJson = "FOR e IN defines"; - qrJson += "\n FILTER e._to == '" + idSubst + "'"; - if (level != "-1") - qrJson += " && e.properties.level ==" + level; - qrJson += "\n RETURN e._from"; - - vector resultsEdgeIds = dbedge_all->runQuery( DBQueryData( qrJson, DBQueryData::qAQL ) ); - - for( std::size_t ii=0; ii std::string - { - string qrJson = "FOR v,e IN 1..1 INBOUND '"; - qrJson += idSubst + "' \n defines\n"; - if (level != "-1") - qrJson += "FILTER e.properties.level ==" + level +"\n"; - qrJson += "RETURN v.properties.symbol"; - - vector symbols = dbedge_all->runQuery( DBQueryData( qrJson, DBQueryData::qAQL ) ); - if( symbols.empty() ) - return ""; //"undefined"; - jsonio::strip_all( symbols[0] , "\""); - return symbols[0]; - } - - // return all record, no only fields - auto queryInEdgesTakes(string idReact) -> vector - { - auto queryin = dbedge_all->inEdgesQuery( "takes", idReact ); - vector resultEdge = dbedge_all->runQuery( queryin ); - return resultEdge; - //"FOR v,e IN 1..1 INBOUND 'reactions/OH-_1_15_1' takes RETURN e" - } - - auto reactantsCoeff(string idReact) -> std::map - { - std::map reactantsCoeff; - string coeff, symbol; - double stoi_coeff; - - string qrJson = "FOR v,e IN 1..1 INBOUND '"; - qrJson += idReact + "' \n takes\n"; - qrJson += "RETURN { 'stoi_coeff': e.properties.stoi_coeff, 'symbol': v.properties.symbol }"; - - vector resultsQuery = dbedge_all->runQuery( DBQueryData( qrJson, DBQueryData::qAQL ) ); - - for( auto result: resultsQuery ) - { - auto domdata = jsonio::unpackJson( result ); - domdata->findValue("stoi_coeff", coeff); - stoi_coeff = atof(coeff.c_str()); - domdata->findValue("symbol", symbol); - reactantsCoeff.insert(std::pair(symbol, stoi_coeff)); - } - return reactantsCoeff; - } -}; - - -AbstractData::AbstractData( const jsonio::TDataBase* dbconnect, const string &name, const DBQueryData& query, - const vector &paths, const vector &headers, const vector &names) - : pimpl(new Impl( dbconnect, name, query, paths, headers, names)) -{ - resetDataPathIndex(); -} - -AbstractData::AbstractData(const AbstractData& other) - : pimpl(new Impl(*other.pimpl)) -{ - resetDataPathIndex(); -} - -AbstractData::~AbstractData() -{ } - -auto AbstractData::getJsonRecordVertex(string idRecord) -> std::string -{ - return pimpl->get_json_bson_record_v_fn(idRecord); -} - -auto AbstractData::getJsonRecordEdge(string idRecord) -> std::string -{ - return pimpl->get_json_bson_record_e_fn(idRecord); -} - -auto AbstractData::queryRecord(string idRecord, vector queryFields) -> string -{ - return pimpl->query_record_fn(idRecord, queryFields); -} -auto AbstractData::queryInEdgesDefines_(string idSubst, string level) -> vector -{ - return pimpl->query_in_edges_defines_fn(idSubst, level); -} - -auto AbstractData::definesReactionSymbol_(string idSubst, string level) -> std::string -{ - return pimpl->defines_reaction_symbol_fn(idSubst, level); -} - -auto AbstractData::queryInEdgesTakes_(string idReact) -> vector -{ - return pimpl->query_in_edges_takes_fn(idReact); -} - -auto AbstractData::reactantsCoeff_(string idReact) -> std::map -{ - return pimpl->reactans_coeff_fn(idReact); -} - -/// Extract values from record into database -auto AbstractData::loadRecord( const string id, const vector queryFields ) -> jsonio::FieldSetMap -{ - return pimpl->load_record_fn( id, queryFields ); -} -/// Build table of fields values by ids list -auto AbstractData::loadRecords(const vector ids ) -> jsonio::ValuesTable -{ - //return pimpl->loadRecords(ids); - return pimpl->load_records_fn(ids); -} - -auto AbstractData::getName() const -> const string& -{ - return pimpl->name; -} - -auto AbstractData::getQuery() const -> const DBQueryData& -{ - return pimpl->query; -} - -// Execute query before load impex to compare data -auto AbstractData::loadQueryData() -> void -{ - pimpl->loadQuery(); -} - -auto AbstractData::getDataFieldPaths() const -> const vector& -{ - return pimpl->fieldPaths; -} - - -auto AbstractData::setDataFieldPaths(const vector &value) -> void -{ - pimpl->fieldPaths = value; -} - -auto AbstractData::getDataHeaders() const -> const vector& -{ - return pimpl->dataHeaders; -} - -auto AbstractData::setDataHeaders(const vector &value) -> void -{ - pimpl->dataHeaders = value; -} - -auto AbstractData::getDataNames() const -> const vector& -{ - return pimpl->dataNames; -} - -/*auto AbstractData::setDataNames(const vector &value) -> void -{ - pimpl->dataNames = value; -}*/ - -auto AbstractData::getDB() const -> const std::shared_ptr& -{ - return pimpl->dbvertex; -} - - -/* -auto AbstractData::setDB(const std::shared_ptr &value) -> void -{ - pimpl->graphdb = value; - pimpl->graphdb_all = value; - pimpl->graphdb_all->resetMode(true); -}*/ - -auto AbstractData::setDataNamesHeadersFieldpaths(const vector &names, const vector &headers, const vector &fieldpaths) -> void -{ - pimpl->dataNames = names; - pimpl->dataHeaders = headers; - pimpl->fieldPaths = fieldpaths; - resetDataPathIndex(); -} - -auto AbstractData::makeQueryFields() const -> jsonio::QueryFields -{ - jsonio::QueryFields fldsMap; - for(std::size_t ii=0; iifieldPaths.size() ; ii++ ) - { - auto fieldpath = replace(pimpl->fieldPaths[ii], "values.0", "values[0]"); - fldsMap[pimpl->dataNames[ii]] = fieldpath; - } - return fldsMap; -} - -bool AbstractData::recordExists(const string& id ) -{ - return getDB()->Find( id ); -} - -auto AbstractData::CreateRecord( const jsonio::FieldSetMap& fldvalues, bool testValues ) -> string -{ - return getDB()->CreateVertex( getName(), fldvalues, testValues ); -} - -auto AbstractData::resetDataPathIndex() -> void -{ - pimpl->dataIndex.clear(); pimpl->dataPath.clear(); - for (std::size_t i = 0; idataIndex[getDataNames()[i]] = i; - pimpl->dataPath[getDataNames()[i]] = getDataFieldPaths()[i]; - } -} - -auto AbstractData::testElementsFormula( const string& aformula, - const vector& elements ) -> bool -{ - FormulaToken parser(aformula); - - for( auto formelm: parser.getElements() ) - { - auto itr = elements.begin(); - while( itr != elements.end() ) - { - if( formelm == *itr ) - break; - itr++; - } - if( itr == elements.end() ) - return false; - } - return true; -} - -auto AbstractData::getInVertexIds( const string& edgeCollections, const string& idVertex ) -> vector -{ - vector vertexIds_; - string vertexId_; - - vector _queryFields = { "_from"}; - auto queryin = pimpl->dbedge_all->inEdgesQuery( edgeCollections, idVertex ); - queryin.setQueryFields(_queryFields); - - vector _resultData = pimpl->dbedge_all->runQuery( queryin ); - - for( auto rec: _resultData) - { - vertexId_ = jsonio::extractStringField( "_from", rec ); - vertexIds_.push_back(vertexId_); - } - return vertexIds_; -} - -auto AbstractData::getInVertexIds(const string& edgeCollections, const string& idVertex, vector &edgeIds_) -> vector -{ - vector vertexIds_; - string vertexId_, edgeId_; - edgeIds_.clear(); - - vector _queryFields = { "_from", "_id"}; - auto queryin = pimpl->dbedge_all->inEdgesQuery( edgeCollections, idVertex ); - queryin.setQueryFields(_queryFields); - - vector _resultData = pimpl->dbedge_all->runQuery( queryin ); - - for( auto rec: _resultData) - { - vertexId_ = jsonio::extractStringField( "_from", rec ); - vertexIds_.push_back(vertexId_); - edgeId_ = jsonio::extractStringField( "_id", rec ); - edgeIds_.push_back(edgeId_); - } - return vertexIds_; -} - -auto AbstractData::getOutVertexIds( const string &edgeCollections, const string& idVertex ) -> vector -{ - vector vertexIds_; - string vertexId_; - - // select all EdgeTakes for reaction - auto queryout = pimpl->dbedge_all->outEdgesQuery( edgeCollections, idVertex ); - vector _queryFields = { "_to"}; - queryout.setQueryFields(_queryFields); - - vector _resultData = pimpl->dbedge_all->runQuery( queryout ); - - for( auto rec: _resultData) - { - vertexId_ = jsonio::extractStringField( "_to", rec ); - vertexIds_.push_back(vertexId_); - } - return vertexIds_; -} - -auto AbstractData::getOutVertexIds(const string &edgeCollections, const string& idVertex, vector &edgeIds_) -> vector -{ - vector vertexIds_; - string vertexId_, edgeId_; - edgeIds_.clear(); - - vector _queryFields = { "_to", "_id"}; - auto queryout = pimpl->dbedge_all->outEdgesQuery( edgeCollections, idVertex ); - queryout.setQueryFields(_queryFields); - - vector _resultData = pimpl->dbedge_all->runQuery( queryout ); - - for( auto rec: _resultData) - { - vertexId_ = jsonio::extractStringField( "_to", rec ); - vertexIds_.push_back(vertexId_); - edgeId_ = jsonio::extractStringField( "_id", rec ); - edgeIds_.push_back(edgeId_); - } - return vertexIds_; -} - -// Connect to new Data Base -auto AbstractData::updateThermoHubClient( const jsonio::TDataBase* newdbconnect ) -> void -{ - try{ - pimpl->changeDataBase(newdbconnect); - } - catch(std::exception& e) - { - cout << "Internal comment " << e.what() << endl; - // throw; - } -} - -auto AbstractData::setDefaultLevelForReactionDefinedSubst(jsonio::ValuesTable avaluesTable) -> void -{ - for( const auto& subitem : avaluesTable ) - { - pimpl->substSymbolLevel[subitem[getDataName_DataIndex().at("symbol")]] = "0"; - } -} - -auto AbstractData::getDataName_DataIndex() const -> const std::map& -{ - return pimpl->dataIndex; -} - -auto AbstractData::getDataName_DataFieldPath() const -> const std::map& -{ - return pimpl->dataPath; -} - -auto AbstractData::getSubstSymbol_DefinesLevel() const -> const std::map& -{ - return pimpl->substSymbolLevel; -} - -auto AbstractData::setSubstSymbol_DefinesLevel(const std::map &value) -> void -{ - pimpl->substSymbolLevel = value; -} - -auto AbstractData::getSubstanceLevel_(const string& substSymbol) const -> const string& -{ - return pimpl->substSymbolLevel[substSymbol]; -} - -auto AbstractData::setSubstanceLevel_(const string &substSymbol, const string &level) -> void -{ - pimpl->substSymbolLevel[substSymbol] = level; -} - -auto AbstractData::getDB_edgeAccessMode() const -> std::shared_ptr -{ - return pimpl->dbedge_all; -} - -// delete not unique -void AbstractData::deleteNotUnique(jsonio::ValuesTable& dataMatr, std::size_t fldtestNdx ) -{ - ValuesTable newMatr; - for (const auto& subitem : dataMatr) - { - auto symbol = subitem[fldtestNdx]; - if ( newMatr.empty() || newMatr.back()[fldtestNdx] != symbol ) - newMatr.push_back(subitem); - } - dataMatr = move(newMatr); -} - -// addition functions to work with elemens - -auto AbstractData::selectElementsGiven( const vector& sourcetdbs, bool unique ) -> vector -{ - jsonio::QueryFields qwFields = { {"symbol", "properties.symbol"}, - {"class_","properties.class_"}, - {"isotope_mass", "properties.isotope_mass"} }; - string AQLreq = "FOR u IN elements \n" - " FILTER u.properties.sourcetdb IN @sourcetdbs\n" - " SORT u.properties.symbol "; - AQLreq += DBQueryData::generateReturn( unique, qwFields ); - - // generate bind values - shared_ptr domdata(JsonDomFree::newObject()); - auto arr = domdata->appendArray( "sourcetdbs"); - sourceTDB_from_indexes( sourcetdbs, arr ); - // make query - DBQueryData query( AQLreq, DBQueryData::qAQL ); - query.setBindVars( domdata.get() ); - - pimpl->dbvertex->resetMode(true); - vector resultsQuery = pimpl->dbvertex->runQuery( query ); - pimpl->dbvertex->resetMode(false); - - vector elements; - ElementKey elkey("",0,0); - for( auto result: resultsQuery ) - { - auto domdata = jsonio::unpackJson( result ); - elkey = fromElementNode(domdata.get()); - elements.push_back(elkey); - } - return elements; -} - -auto AbstractData::selectElementsFromSubstancesGiven( const vector& sourcetdbs ) -> set -{ - // Select all substances formulas - string AQLreq = "FOR u IN substances \n" - " FILTER u.properties.sourcetdb IN @sourcetdbs\n" - " SORT u.properties.symbol "; - AQLreq += "RETURN DISTINCT u.properties.formula"; - - // generate bind values - shared_ptr domdata(JsonDomFree::newObject()); - auto arr = domdata->appendArray( "sourcetdbs"); - sourceTDB_from_indexes( sourcetdbs, arr ); - // make query - DBQueryData query( AQLreq, DBQueryData::qAQL ); - query.setBindVars( domdata.get() ); - - vector formulas = getDB()->runQuery( query ); - return ChemicalFormula::extractElements(formulas); -} - - -} diff --git a/ThermoHubClient/AbstractData.h b/ThermoHubClient/AbstractData.h deleted file mode 100644 index c8bdd6f3..00000000 --- a/ThermoHubClient/AbstractData.h +++ /dev/null @@ -1,155 +0,0 @@ -#ifndef ABSTRACTDATA_H -#define ABSTRACTDATA_H - -// C++ includes -#include - -// ThermoFun includes -#ifdef FROM_SRC -#include "../ThermoFun/Common/formuladata.h" -#else -#include "ThermoFun/Common/formuladata.h" -#endif -#include "jsonio/dbconnect.h" -#include "jsonio/dbedgedoc.h" - -namespace ThermoFun { - -extern const std::string ThermoDataSetQueryEdges; - -class AbstractData -{ -public: - - AbstractData( const jsonio::TDataBase* dbconnect, - const std::string &name, const jsonio::DBQueryData& query, const std::vector &paths, - const std::vector &headers, const std::vector &names ); - - /// Construct a copy of an ThermoDataAbstract instance - AbstractData(const AbstractData& other); - - /// Destroy this instance - virtual ~AbstractData(); - - // load values function - /// Extract data connected to ReactionSet - virtual jsonio::ValuesTable loadRecordsValues( const std::string& idReactionSet ) = 0; - /// Extract data by condition - virtual jsonio::ValuesTable loadRecordsValues( const jsonio::DBQueryData& query, int sourcetdb, - const std::vector& elements = {} ) = 0; - /// Extract data connected to ThermoDataSet - virtual std::vector selectGiven( const std::vector& idThermoDataSets, bool unique = true ) = 0 ; - - /// Get Elements list from record - virtual std::set getElementsList( const std::string& idrec ) = 0; - - /// Link to table of fields values loaded before - virtual const jsonio::ValuesTable& getValuesTable() = 0; - - auto updateThermoHubClient( const jsonio::TDataBase* newdbconnect ) -> void; - - auto getDB() const -> const std::shared_ptr&; - auto getName() const -> const std::string&; - auto getQuery() const -> const jsonio::DBQueryData&; - auto getDataNames() const -> const std::vector&; - auto getDataHeaders() const -> const std::vector&; - auto getDataFieldPaths() const -> const std::vector&; - auto getDataName_DataIndex() const -> const std::map&; - auto getDataName_DataFieldPath() const -> const std::map&; - auto getSubstSymbol_DefinesLevel() const -> const std::map&; - - auto makeQueryFields() const -> jsonio::QueryFields; - -/// auto setDB(const std::shared_ptr &value) -> void; -/// auto setDataNames(const vector &value) -> void; - auto setDataHeaders(const std::vector &value) -> void; - auto setDataFieldPaths(const std::vector &value) -> void; - auto setSubstSymbol_DefinesLevel(const std::map &value) -> void; - auto setDataNamesHeadersFieldpaths(const std::vector &names, const std::vector &headers, const std::vector &fieldpaths) -> void; - /// Execute query before load impex to compare data - auto loadQueryData() -> void; - - /** - * @brief queryRecord returns a record queried by id - * @param idRecord record id in the database - * @param queryFields schema field paths which are copied and returned in the query result - * @return string representing the result in JSON format containing the queryFields as keys - */ - auto queryRecord(std::string idRecord, std::vector queryFields) -> std::string; - - /// Test record existence - auto recordExists(const std::string& id ) -> bool; - - /// Add new Vertex record to database - /// \return oid of new record - auto CreateRecord( const jsonio::FieldSetMap& fldvalues, bool testValues ) -> std::string; - - /// Extract values from record into database - auto loadRecord( const std::string id, const std::vector queryFields ) -> jsonio::FieldSetMap; - - /// Build table of fields values by ids list - auto loadRecords( const std::vector ids ) -> jsonio::ValuesTable; - - - /// Build ids list connected to idVertex by incoming edge, - /// edgeCollections ( "coll1, coll2") list of collections to search into - auto getInVertexIds(const std::string& edgeCollections, const std::string& idVertex) -> std::vector; - - /// Build ids list connected to idVertex by incoming edge, save edgesIds - /// edgeCollections ( "coll1, coll2") list of collections to search into - auto getInVertexIds(const std::string& edgeCollections, const std::string& idVertex, std::vector &edgesIds) -> std::vector; - - /// Build ids list connected to idVertex by outgoing edge, - /// edgeCollections ( "coll1, coll2") list of collections to search into - auto getOutVertexIds(const std::string& edgeCollections, const std::string& idVertex) -> std::vector; - - /// Build ids list connected to idVertex by outgoing edge, save edgesIds - /// edgeCollections ( "coll1, coll2") list of collections to search into - auto getOutVertexIds(const std::string& edgeCollections, const std::string& idVertex, std::vector &edgesIds) -> std::vector; - - /// Returns the record with idRecord as a pair of Json and Bson formats - auto getJsonRecordVertex(std::string idRecord) -> std::string; - /// Returns the record with idRecord as a pair of Json and Bson formats - auto getJsonRecordEdge(std::string idRecord) -> std::string; - - auto selectElementsGiven( const std::vector& sourcetdbs, bool unique = true ) -> std::vector; - auto selectElementsFromSubstancesGiven( const std::vector& sourcetdbs ) -> std::set; - -protected: - - // Returns a record from a database in JSON format using the record id - auto getJsonRecord(std::string idRecord) -> std::string; - // Test all elements from formula exist into list - static auto testElementsFormula( const std::string& aformula, const std::vector& elements) -> bool; - // Resets the data index and data names maps which connect the names to headers to paths - auto resetDataPathIndex() -> void; - // sets the level = 0 for substances in ValuesTable - auto setDefaultLevelForReactionDefinedSubst(jsonio::ValuesTable avaluesTable) -> void; - // returns the full access mode database connection (allows queryies on all types of records) - auto getDB_edgeAccessMode() const -> std::shared_ptr; - // query the ids of incoming edges of type defines - auto queryInEdgesDefines_(std::string idSubst, std::string level) -> std::vector; - // returns the reaction symbol which defines a substance - auto definesReactionSymbol_(std::string idSubst, std::string level) -> std::string; - // returns data of the incoming edges of type takes - auto queryInEdgesTakes_(std::string idReact ) -> std::vector; - // returns the map of reactants symbols and coefficients - auto reactantsCoeff_(std::string idReact) -> std::map; - // returns the level which is set for the substance - auto getSubstanceLevel_(const std::string &substSymbol) const -> const std::string&; - // sets the level - auto setSubstanceLevel_(const std::string &substSymbol, const std::string &level) -> void; - - void deleteNotUnique(jsonio::ValuesTable& dataMatr, std::size_t fldtestNdx ); - -private: - struct Impl; - - std::shared_ptr pimpl; - -}; - - -} - -#endif // ABSTRACTDATA_H diff --git a/ThermoHubClient/CMakeLists.txt b/ThermoHubClient/CMakeLists.txt deleted file mode 100644 index 510e9720..00000000 --- a/ThermoHubClient/CMakeLists.txt +++ /dev/null @@ -1,95 +0,0 @@ -# Require a certain version of cmake -cmake_minimum_required(VERSION 3.0) - -# Set the name of the project -project(ThermoHubClient VERSION 0.1.5 LANGUAGES CXX) - -find_library(BOOSTRE_LIB boost_regex) -if(NOT BOOSTRE_LIB) - message(FATAL_ERROR "boost_regex library not found") -endif() - -find_library(BOOSTFILE_LIB boost_filesystem) -if(NOT BOOSTFILE_LIB) - message(FATAL_ERROR "boost_filesystem library not found") -endif() - -find_library(CURL_LIB curl) -if(NOT CURL_LIB) - message(FATAL_ERROR "curl library not found") -endif() - -find_library(VELOCYPACK_LIB velocypack) -if(NOT VELOCYPACK_LIB) - message(FATAL_ERROR "velocypack library not found") -endif() - -find_library(JSONIO_LIB jsonio) -if(NOT JSONIO_LIB) - message(FATAL_ERROR "jsonio library not found") -endif() - - -# Set the default build type to Release -if(NOT CMAKE_BUILD_TYPE) - message(STATUS "Setting build type to 'Release' as none was specified.") - set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build." FORCE) - set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release" "MinSizeRel" "RelWithDebInfo") -endif() - -# Define variables with the GNU standard installation directories -include(GNUInstallDirs) - -# Define which types of libraries to build -option(THERMOHUBCLIENT_BUILD_SHARED_LIBS "Build shared libraries." ON) -option(THERMOHUBCLIENT_BUILD_STATIC_LIBS "Build static libraries." ON) - -# Set the ThermoHubClient source directory path -set(THERMOHUBCLIENT_SOURCE_DIR ${CMAKE_SOURCE_DIR}/ThermoHubClient) - -# Set the include directories -include_directories(${THERMOHUBCLIENT_SOURCE_DIR}) - -# Build ThermoHubClient library -# Recursively collect all header files from the current directory -file(GLOB_RECURSE HEADER_FILES RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} *.hpp *.h) - -# Recursively collect all source files from the current directory -file(GLOB_RECURSE SOURCE_FILES RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} *.cpp) - -add_definitions(-DFROM_SRC) - -# Set the list of names of the third-party targets and libraries -#set(THIRDPARTY_TARGETS JSONIO) -set(THIRDPARTY_LIBS jsonio boost_regex boost_filesystem curl velocypack) -set(THERMOHUBCLIENT_SOURCE_DIR ${CMAKE_SOURCE_DIR}/) - -# Create the shared library using the collected source files -add_library(THERMOHUBCLIENT_OBJECTS OBJECT ${HEADER_FILES} ${SOURCE_FILES}) - -# Specify the dependencies of THERMOFUN to ensure proper build sequence -#add_dependencies(THERMOFUN_OBJECTS ${THIRDPARTY_TARGETS}) - -# Check if a shared library is to be built -if(THERMOHUBCLIENT_BUILD_SHARED_LIBS) - add_library(THERMOHUBCLIENT_SHARED SHARED $) - target_link_libraries(THERMOHUBCLIENT_SHARED ${THIRDPARTY_LIBS} ) - if( ${CMAKE_CXX_COMPILER_ID} MATCHES "Clang") - #target_link_libraries(THERMOHUBCLIENT_SHARED jsonio boost_regex boost_filesystem curl ThermoFun ) - target_link_libraries(THERMOHUBCLIENT_SHARED jsonio ThermoFun::ThermoFun ) - endif() - set_target_properties(THERMOHUBCLIENT_SHARED PROPERTIES OUTPUT_NAME ThermoHubClient) - install(TARGETS THERMOHUBCLIENT_SHARED DESTINATION lib) -endif() - -# Check if a static library is to be built -if(THERMOHUBCLIENT_BUILD_STATIC_LIBS) - add_library(THERMOHUBCLIENT_STATIC STATIC $) - target_link_libraries(THERMOHUBCLIENT_STATIC ${THIRDPARTY_LIBS} ) - set_target_properties(THERMOHUBCLIENT_STATIC PROPERTIES OUTPUT_NAME ThermoHubClient) - install(TARGETS THERMOHUBCLIENT_STATIC DESTINATION lib) -endif() - -# Install the header files preserving the directory hierarchy -install(FILES ${HEADER_FILES} - DESTINATION include/ThermoHubClient ) diff --git a/ThermoHubClient/DatabaseClient.cpp b/ThermoHubClient/DatabaseClient.cpp deleted file mode 100644 index 6820251f..00000000 --- a/ThermoHubClient/DatabaseClient.cpp +++ /dev/null @@ -1,485 +0,0 @@ -#include "DatabaseClient.h" - -// C++ includes -//#include -#include - -// bonio includes -#include "jsonio/traversal.h" -#include "jsonio/io_settings.h" - -// ThermoFun includes -#ifdef FROM_SRC -#include "../ThermoFun/OptimizationUtils.h" -#include "../ThermoFun/Database.h" -#include "../ThermoFun/Element.h" -#else -#include "ThermoFun/OptimizationUtils.h" -#include "ThermoFun/Database.h" -#include "ThermoFun/Element.h" -#endif - -#include "ElementData.h" -#include "SubstanceData.h" -#include "ReactionData.h" -#include "ReactionSetData.h" -#include "ThermoSetData.h" -#include "TraversalData.h" -#include "sourcetdb.h" - -using namespace std; -using namespace jsonio; - -namespace ThermoFun -{ - -using QuerySubstancesFunction = std::function(int)>; -using QueryReactionsFunction = std::function(int)>; -using AvailableElementsSet = std::function(int)>; -using AvailableElementsKey = std::function(int)>; - -//std::vector queryFieldsSubstance = {"_id", "properties.formula", "properties.symbol", "properties.sourcetdb"}; -//std::vector queryFieldsReaction = {"_id", "properties.equation", "properties.symbol", "properties.sourcetdb"}; - -auto setDatabaseConnectionFilePath(const std::string &filePath) -> void -{ - jsonio::JsonioSettings::settingsFileName = filePath; -} - -struct DatabaseClient::Impl -{ - std::shared_ptr _dbconnect; - - /// access to substance records - SubstanceData_ substData; - - /// access to reaction records - ReactionData_ reactData; - - /// access to reactionSet records - ReactionSetData_ reactSetData; - - /// acccess to ThermoDataSet records - ThermoSetData thermoDataSet; - - /// for traversal operations - TraversalData traversal; - - QuerySubstancesFunction query_substances_fn; - - QueryReactionsFunction query_reactions_fn; - - AvailableElementsSet available_elements_set_fn; - - AvailableElementsKey available_elements_key_fn; - - Impl(const std::shared_ptr& otherdb) : - _dbconnect( otherdb), substData(_dbconnect.get()), - reactData(_dbconnect.get()), reactSetData(_dbconnect.get()), - thermoDataSet(_dbconnect.get()), traversal (&substData, &reactData) - { - setFunctions(); - } - - // read from default config - Impl() : _dbconnect( new TDataBase() ), substData(_dbconnect.get()), - reactData(_dbconnect.get()), reactSetData(_dbconnect.get()), - thermoDataSet(_dbconnect.get()), traversal (&substData, &reactData) - { - setFunctions(); - } - - auto setFunctions() -> void - { - query_substances_fn = [=](int sourcetdb) { - return querySubstances(sourcetdb); - }; - query_substances_fn = memoize(query_substances_fn); - - query_reactions_fn = [=](int sourcetdb) { - return queryReactions(sourcetdb); - }; - query_reactions_fn = memoize(query_reactions_fn); - - available_elements_key_fn = [=](int sourcetdb) { - return availableElementsKey(sourcetdb); - }; - available_elements_key_fn = memoize(available_elements_key_fn); - - available_elements_set_fn = [=](int sourcetdb) { - return availableElementsSet(sourcetdb); - }; - available_elements_set_fn = memoize(available_elements_set_fn); - - auto elementVertex = unique_ptr ( - TDBVertexDocument::newVertexDocument( _dbconnect.get(), "VertexElement" )); - // load all elements into system - setDBElements( elementVertex.get(), jsonio::DBQueryData("{\"_label\": \"element\" }",jsonio::DBQueryData::qTemplate ) ); - } - - auto availableElementsSet(int sourcetdb) -> set - { - std::set els_; - std::set set; - - auto _resultData = query_substances_fn(sourcetdb); - - - FormulaToken parser(""); - for (string subitem: _resultData) - { - string formula = extractStringField("formula", subitem); - //string symbol = bsonio::extractStringField("symbol", subitem); - // cout << formula << " " << symbol << endl; - // test elements - // addiditon test and parser parser.exeptionCheckElements(symbol, formula); - // parser.exeptionCheckElements(symbol, formula); - parser.setFormula(formula); - els_.insert(parser.getElements().begin(), parser.getElements().end()); - } - - for (auto el : els_) - { - auto itrdb = ChemicalFormula::getDBElements().find(el); - if (itrdb == ChemicalFormula::getDBElements().end()) - jsonioErr("E37FPrun: Invalid symbol ", el.Symbol()); - Element e = elementKeyToElement(el); - set.insert(e); - } - return set; - } - - auto availableElementsKey(int sourcetdb) -> std::vector - { - std::set elements; - std::vector set; - - auto _resultData = query_substances_fn(sourcetdb); - - FormulaToken parser(""); - for (string subitem: _resultData) - { - string formula = extractStringField("formula", subitem); - string symbol = extractStringField("symbol", subitem); - // cout << subitem << " " << formula << " " << symbol << endl; - // test elements - parser.exeptionCheckElements(symbol, formula); - parser.setFormula(formula); - elements.insert(parser.getElements().begin(), parser.getElements().end()); - } - - for (auto element : elements) - { - auto itrdb = ChemicalFormula::getDBElements().find(element); - if (itrdb == ChemicalFormula::getDBElements().end()) - jsonioErr("E37FPrun: Invalid symbol ", element.Symbol()); - set.push_back(element); - } - return set; - } - - auto querySubstances(int sourcetdb) -> std::vector - { - string query = "{ \"_label\" : \"substance\", \"_type\" : \"vertex\", \"properties.sourcetdb\" : "; - query += sourceTDB_from_index(sourcetdb); - query += " }"; - vector _resultData = substData.getDB()->runQuery(DBQueryData( query, DBQueryData::qTemplate ) ); - return _resultData; - } - - auto queryReactions(int sourcetdb) -> std::vector - { - string query = "{ \"_label\" : \"substance\", \"_type\" : \"vertex\", \"properties.sourcetdb\" : "; - query += sourceTDB_from_index(sourcetdb); - query += " }"; - vector _resultData = reactData.getDB()->runQuery(DBQueryData( query, DBQueryData::qTemplate ) ); - return _resultData; - } - - auto executeIncomingTraversal( const vector& ids, GraphElementFunction afunc ) -> void - { - GraphTraversal travel( _dbconnect.get() ); - travel.Traversal( true, ids, afunc, GraphTraversal::trIn ); - } - - // Collect record and all incoming _ids - auto TraverseAllIncomingEdges( const string& id ) -> std::vector - { - std::vector list; - GraphElementFunction afunc = [&list]( bool vert, const string& jsondata ) - { - if( vert) - { - string id = extractStringField( "_id", jsondata ); - list.push_back(id); - } - }; - executeIncomingTraversal( {id}, afunc ); - return list; - } -}; - -DatabaseClient::DatabaseClient(const std::shared_ptr& otherdb) - : pimpl(new Impl( otherdb )) -{ -} - -DatabaseClient::DatabaseClient() - : pimpl(new Impl()) -{ -} - -auto DatabaseClient::operator=(DatabaseClient other) -> DatabaseClient & -{ - pimpl = std::move(other.pimpl); - return *this; -} - -DatabaseClient::~DatabaseClient() -{ -} - -auto DatabaseClient::availableSubstances(int sourcetdb) -> std::vector -{ - return extractFieldValuesFromQueryResult(pimpl->query_substances_fn(sourcetdb), "symbol"); -} - -auto DatabaseClient::availableReactions(int sourcetdb) -> std::vector -{ - return extractFieldValuesFromQueryResult(pimpl->query_reactions_fn(sourcetdb), "symbol"); -} - -auto DatabaseClient::extractFieldValuesFromQueryResult(std::vector resultQuery, std::string fieldName) -> std::vector -{ - std::vector values; - for (auto result : resultQuery) - { - values.push_back(extractStringField(fieldName, result)); - } - return values; -} - -auto DatabaseClient::thermoFunDatabase(int sourcetdbIndex) -> Database -{ - // get substances ids - auto substKeyList = extractFieldValuesFromQueryResult(pimpl->query_substances_fn(sourcetdbIndex), "_id"); - - // get all ids conected to the keyList (by incoming edges, e.g. defines reactions and thier reactants) - auto resultTraversal = pimpl->traversal.getMapOfConnectedIds(substKeyList, "0"); - - return pimpl->traversal.getDatabaseFromMapOfIds(resultTraversal, "0"); -} - -auto DatabaseClient::parseSubstanceFormula(std::string formula_) -> std::map -{ - //std::set elements; - std::map map; - FormulaToken formula(""); - - formula.setFormula(formula_); - // elements.insert(formula.getElements().begin(), formula.getElements().end()); - - for (auto element : formula.getElements_map()) - { - Element e = elementKeyToElement(element.first); - map[e] = element.second; - } - - return map; - -} - -auto DatabaseClient::sourcetdbIndexes() -> std::set -{ - set _sourcetdb; -// vector _resultData = pimpl->substData.getDB()->fieldValues("properties.sourcetdb"); - - string qrJson1 = "FOR e IN elements "; - string qrJson2 = "COLLECT s = e.properties.sourcetdb RETURN s"; - std::vector resultsQuery = pimpl->substData.getDB()->runQuery( DBQueryData(qrJson1+qrJson2, DBQueryData::qAQL ) ); - qrJson1 = "FOR e IN substances "; - std::vector resultsQuery2 = pimpl->substData.getDB()->runQuery( DBQueryData(qrJson1+qrJson2, DBQueryData::qAQL ) ); - resultsQuery.insert( resultsQuery.end(), resultsQuery2.begin(), resultsQuery2.end() ); - qrJson1 = "FOR e IN reactions "; - resultsQuery2 = pimpl->substData.getDB()->runQuery( DBQueryData(qrJson1+qrJson2, DBQueryData::qAQL ) ); - resultsQuery.insert( resultsQuery.end(), resultsQuery2.begin(), resultsQuery2.end() ); - - // make unique - std::sort(resultsQuery.begin(), resultsQuery.end()); - auto last = std::unique(resultsQuery.begin(), resultsQuery.end()); - resultsQuery.erase(last, resultsQuery.end()); - - for (std::size_t ii = 0; ii < resultsQuery.size(); ii++) - { - auto first = resultsQuery[ii].find("\""); - auto second = resultsQuery[ii].find("\"", first+1); - string strNew = resultsQuery[ii].substr (first+1,second-(first+1)); - int asourcetdb = stoi(strNew); - _sourcetdb.insert(asourcetdb); - } - return _sourcetdb; -} - -auto DatabaseClient::sourcetdbNamesIndexes(const std::set &sourcetdbIndexes) -> std::map -{ - // set lists - std::map namesIndexes; - ThriftEnumDef *enumdef = ioSettings().Schema()->getEnum("SourceTDB"); - if (enumdef != nullptr) - { - for (int idx: sourcetdbIndexes) - { - string name = enumdef->getNamebyId(idx); - namesIndexes[name] = idx; - } - } - return namesIndexes; -} - -auto DatabaseClient::sourcetdbNamesComments(const std::set &sourcetdbIndexes) -> std::map -{ - // set lists - std::map namesComments; - ThriftEnumDef *enumdef = ioSettings().Schema()->getEnum("SourceTDB"); - if (enumdef != nullptr) - { - for (int idx: sourcetdbIndexes) - { - string name = enumdef->getNamebyId(idx); - namesComments[name] = enumdef->getDoc(name); - } - } - return namesComments; -} - -auto DatabaseClient::sourcetdbListAll() -> std::vector -{ - string name, comment; - vector _sourcetdbList; - auto indexes = sourcetdbIndexes(); - ThriftEnumDef *enumdef = ioSettings().Schema()->getEnum("SourceTDB"); - if (enumdef != nullptr) - { - for (int idx: indexes) - { - name = enumdef->getNamebyId(idx); - comment = enumdef->getDoc(name); - _sourcetdbList.push_back(std::to_string(idx)+"-"+ name + " - "+ comment ); - } - } - return _sourcetdbList; -} - -auto DatabaseClient::availableElementsSet(int sourcetdb) -> set -{ - return pimpl->available_elements_set_fn(sourcetdb); -} - -auto DatabaseClient::availableElements(int sourcetdb) -> std::set -{ - std::set set; - - auto elements = availableElementsSet(sourcetdb); - - for (auto element : elements) - { - set.insert(element.symbol()); - } - return set; -} - -auto DatabaseClient::availableElementsKey(int sourcetdb) -> std::vector -{ - return pimpl->available_elements_key_fn(sourcetdb); -} - -auto DatabaseClient::elementIds( const std::vector& elements) -> std::vector -{ - std::vector elmIds; - for (auto element : elements) - { - auto itrdb = ChemicalFormula::getDBElements().find(element); - if (itrdb == ChemicalFormula::getDBElements().end()) - jsonioErr("E37FPrun: Invalid symbol ", element.Symbol()); - elmIds.push_back(itrdb->second.recid); - } - return elmIds; -} - -auto DatabaseClient::substData() const -> SubstanceData_& -{ - return pimpl->substData; -} - -auto DatabaseClient::reactData() const -> ReactionData_& -{ - return pimpl->reactData; -} - -auto DatabaseClient::reactSetData() const -> ReactionSetData_& -{ - return pimpl->reactSetData; -} - -auto DatabaseClient::thermoDataSet() const -> ThermoSetData& -{ - return pimpl->thermoDataSet; -} - -auto DatabaseClient::getTraversal() const -> TraversalData& -{ - return pimpl->traversal; -} - -/// Output record and all incoming to json file -auto DatabaseClient::BackupAllIncoming( const vector& ids, const string fileName ) -> void -{ - FJsonArray file( fileName); - file.Open( OpenModeTypes::WriteOnly ); - - GraphElementFunction afunc = [&file]( bool , const string& data ) - { - file.SaveNext(data); - }; - - pimpl->executeIncomingTraversal( ids, afunc ); - - file.Close(); - -} - -// Collect record and all incoming _ids -auto DatabaseClient::TraverseAllIncomingEdges( const string& id ) -> List_VertexId_VertexType -{ - List_VertexId_VertexType list; - - GraphElementFunction afunc = [&list]( bool vert, const string& jsondata ) - { - if( vert) - { - string label = extractStringField( "_label", jsondata ); - string id = extractStringField( "_id", jsondata ); - - //string type, id; - //data->findKey( "_id", id ); - //data->findKey( "_label", type); - list.push_back(pair(id, label)); - } - }; - pimpl->executeIncomingTraversal( {id}, afunc ); - return list; -} - -auto DatabaseClient::recordsFromThermoDataSet( const string& ThermoDataSetSymbol ) -> List_VertexId_VertexType -{ - auto idThermoDataSet = thermoDataSet().idRecordFromSymbol(ThermoDataSetSymbol); - return TraverseAllIncomingEdges(idThermoDataSet); -} - -auto DatabaseClient::databaseFromThermoDataSet( const string& ThermoDataSetSymbol ) -> Database -{ - auto idThermoDataSet = thermoDataSet().idRecordFromSymbol(ThermoDataSetSymbol); - return getTraversal().getDatabase(pimpl->TraverseAllIncomingEdges(idThermoDataSet)); -} - -} diff --git a/ThermoHubClient/DatabaseClient.h b/ThermoHubClient/DatabaseClient.h deleted file mode 100644 index 93573dba..00000000 --- a/ThermoHubClient/DatabaseClient.h +++ /dev/null @@ -1,190 +0,0 @@ -#ifndef DATABASECLIENT_H -#define DATABASECLIENT_H - -#include -#include -#include -#include -#include -#include "jsonio/dbconnect.h" - -namespace ThermoFun -{ - -class Database; -//class Reaction; -//class Substance; -class Element; -class SubstanceData_; -class ReactionData_; -class ReactionSetData_; -class ThermoSetData; -class ElementKey; -class TraversalData; -class Database; - -using List_VertexId_VertexType = std::vector< std::pair >; - -auto setDatabaseConnectionFilePath(const std::string &filePath) -> void; - -class DatabaseClient -{ - public: - /// - /// \brief ThermoHubClient creates a ThermoHubClient instance - /// \param settingsFile path to the ThermoFun.ini file - /// - explicit DatabaseClient( const std::shared_ptr& otherdb ); - - DatabaseClient(); - - /// Assign a DatabaseClient instance to this instance - auto operator=(DatabaseClient other) -> DatabaseClient &; - - /// Destroy this instance - virtual ~DatabaseClient(); - - /// - /// \brief getDatabase reads from the EJDB database substances and reactions with the same sourceTDB - /// \param sourceTDB data set index - /// \return returns a ThermoFun Database structure containing the substances and reactions maps - /// - auto thermoFunDatabase(int sourcetdbIndex) -> Database; - - /** - * @brief parseSubstanceFormula parses a substance formula in GEMS format - * @param formula in GEMS format - * @return map of element object and coefficient - */ - auto parseSubstanceFormula(std::string formula) -> std::map; - - /** - * @brief getSourcetdbIndexes returns the indexes of all available thermodynamic data sets - * @return a set of indexes - */ - auto sourcetdbIndexes() -> std::set; - - /** - * @brief sourcetdbNamesIndexes returns a map with all available thermodynamic data sets names and their indexes - * @param sourcetdbIndexes set of thermodynamic data sets indexes - * @return map of thermodynamic data sets names and indexes - */ - auto sourcetdbNamesIndexes(const std::set &sourcetdbIndexes) -> std::map; - - /** - * @brief sourcetdbNamesComments returns a map with all available thermodynamic data sets names and associated comments - * from the json schema - * @param sourcetdbIndexes set of thermodynamic data sets indexes - * @return map of thermodynamic data sets names and comments - */ - auto sourcetdbNamesComments(const std::set &sourcetdbIndexes) -> std::map; - - /** - * @brief sourcetdbListAll returns the indexes and name of all available thermodynamic data sets - * @return a list of -- - */ - auto sourcetdbListAll() -> std::vector; - - /** - * @brief sourcetdbNamesIndexes returns a map with all available thermodynamic data sets names and their indexes - * @return map of thermodynamic data sets names and indexes - */ - auto sourcetdbNamesIndexes() -> std::map - { - return sourcetdbNamesIndexes(sourcetdbIndexes()); - } - - /** - * @brief availableElements returns the set of available element symbols, for a given thermodynamic data set index - * @param sourcetdb thermodynamic data set index - * @return set of element symbols - */ - auto availableElements(int sourcetdb) -> std::set; - - /** - * @brief availableElementsKey returns a vector of all available elements (ElementKey object), for a given thermodynamic data set index - * @param sourcetdb thermodynamic data set index - * @return vector of ElementKey objects - */ - auto availableElementsKey(int sourcetdb) -> std::vector; - - /** - * @brief availableElementsSet returns a set of all available elements (Element object), for a given thermodynamic data set index - * @param sourcetdb thermodynamic data set index - * @return set of Element objects - */ - auto availableElementsSet(int sourcetdb) -> std::set; - - - /** - * @brief elementIds returns a vector of element ids from ElementKeys - * @param elements vector of ElementKeys - * @return vector of Element ids - */ - auto elementIds( const std::vector& elements) -> std::vector; - - /** - * @brief availableSubstances returns the list of available substance symbols - * @param sourcetdb thermodynamic data set index - * @return vector of substance symbols - */ - auto availableSubstances(int sourcetdb) -> std::vector; - - /** - * @brief availableReactions returns the list of available reaction symbols - * @param sourcetdb thermodynamic data set index - * @return vector of reaction symbols - */ - auto availableReactions(int sourcetdb) -> std::vector; - - /** - * @brief substData returns a SubstanceData object for reading substance data from the database - * @return SubstanceData object - */ - auto substData() const -> SubstanceData_&; - - /** - * @brief reactData returns a ReactionData object for reading reaction data from the database - * @return ReactionData object - */ - auto reactData() const -> ReactionData_&; - - /** - * @brief reactSetData returns a ReactionSetData_ object - * @return - */ - auto reactSetData() const -> ReactionSetData_&; - - /** - * @brief thermoDataSet returns a ThermoDataSet object - * @return - */ - auto thermoDataSet() const -> ThermoSetData&; - - /** - * @brief getTraversal returns a TraversalData object - * @return - */ - auto getTraversal() const -> TraversalData&; - - /// Output record and all incoming to json file - auto BackupAllIncoming( const std::vector& ids, const std::string fileName ) -> void; - - /// Collect record and all incoming _ids - auto TraverseAllIncomingEdges( const std::string& id ) -> List_VertexId_VertexType; - - auto recordsFromThermoDataSet(const std::string& ThermoDataSetSymbol ) -> List_VertexId_VertexType; - - auto databaseFromThermoDataSet( const std::string& ThermoDataSetSymbol ) -> Database; - -private: - - auto extractFieldValuesFromQueryResult(std::vector resultQuery, std::string fieldName) -> std::vector; - - struct Impl; - - std::shared_ptr pimpl; -}; -} - -#endif // DATABASECLIENT_H diff --git a/ThermoHubClient/ElementData.cpp b/ThermoHubClient/ElementData.cpp deleted file mode 100644 index 70e58f13..00000000 --- a/ThermoHubClient/ElementData.cpp +++ /dev/null @@ -1,371 +0,0 @@ -#include -#include "ElementData.h" -#include "jsonio/io_settings.h" -#include "jsonio/jsondomfree.h" -#include "sourcetdb.h" - -// ThermoFun includes -#ifdef FROM_SRC -#include "../ThermoFun/Common/formuladata.h" -#include "../ThermoFun/Element.h" -#include "../ThermoFun/Database.h" -#include "../ThermoFun/Common/ParseJsonToData.h" -#else -#include "ThermoFun/Common/formuladata.h" -#include "ThermoFun/Element.h" -#include "ThermoFun/Common/ParseJsonToData.h" -#include "ThermoFun/Database.h" -#endif - -#include - -using json = nlohmann::json; - -using namespace std; -using namespace jsonio; - -namespace ThermoFun -{ - -//const DBQueryData reactQuery( "{\"_label\": \"element\" }", DBQueryData:: qTemplate ); -const DBQueryData elementQuery("FOR u IN elements ", DBQueryData::qAQL); -const vector elementFieldPaths = { "properties.symbol", "properties.name", "properties.number", "properties.sourcetdb", "properties.class_", "properties.isotope_mass", "_id" }; -const vector elementDataNames = {"symbol", "name", "number", "sourcetdb", "class_", "mass", "_id" }; // should have the same size as FieldPaths !! -const vector elementColumnHeaders = { "symbol", "name", "number"/*, "sourcetdb" */ }; - -struct ElementData_::Impl -{ - ValuesTable valuesTable; - - Impl( ) - { - } - -}; - -ElementData_::ElementData_(const TDataBase* dbconnect) - : AbstractData( dbconnect, "VertexElement", elementQuery, - elementFieldPaths, elementColumnHeaders, elementDataNames), pimpl(new Impl()) -{ -} - -ElementData_::ElementData_(const ElementData_& other) -: AbstractData(other), pimpl(new Impl(*other.pimpl)) -{} - -auto ElementData_::operator=(ElementData_ other) -> ElementData_ & -{ - pimpl = std::move(other.pimpl); - return *this; -} - -ElementData_::~ElementData_() -{ -} - -const jsonio::ValuesTable& ElementData_::getValuesTable() -{ - return pimpl->valuesTable; -} - -set ElementData_::getElementsList( const string& id ) -{ - set elements; - string jsonrecord = getJsonRecordVertex(id); - - ElementKey elem("",0,0); - auto node = jsonio::unpackJson(jsonrecord); - elem = fromElementNode( node->field("properties") ); - elements.insert(elem); - return elements; -} - -void ElementData_::updateTableByElementsList( jsonio::ValuesTable& dataQueryMatr, const vector& elements ) -{ - if( !elements.empty() ) - { - jsonio::ValuesTable dataMatr; - for (const auto& subitem : dataQueryMatr) - { - int class_ = 0; - json j = json::parse(subitem[getDataName_DataIndex().at("class_")]); - if (!j.is_null() && !j.empty() && j.is_object()) - class_ = stoi(j.begin().key()); - ElementKey elkey( subitem[getDataName_DataIndex().at("symbol")], - class_, - 0 ); - if( std::find( elements.begin(), elements.end(), elkey) != elements.end() ) - dataMatr.push_back(subitem); - } - dataQueryMatr = move(dataMatr); - } - } - -// return all record, no only fields if not default -ValuesTable ElementData_::loadRecordsValues( const DBQueryData& aquery, - int sourcetdb, const vector& elements ) -{ - auto fields = getDataFieldPaths(); - - // get records by query - auto query = aquery; - if (query.empty()) - { - query = getQuery(); - // only here we have subset fields to extract - query.setQueryFields(makeQueryFields()); - fields = getDataNames(); - } - if( !elements.empty() ) - addFieldsToQueryAQL( query, { make_pair( string("properties.sourcetdb"), sourceTDB_from_index(sourcetdb)) } ); - ValuesTable reactQueryMatr = getDB()->downloadDocuments( query, fields ); - - // get record by elements list - ValuesTable elemQueryMatr = getDB()->downloadDocuments(query, fields); - - // get record by elements list - updateTableByElementsList( elemQueryMatr, elements ); - pimpl->valuesTable = elemQueryMatr; - return elemQueryMatr; -} - -ValuesTable ElementData_::loadRecordsValues( const string& idrcset ) -{ - // extract sourcetdb and elements list from - string AQLreq = "FOR u IN reactionsets\n" - "FILTER u._id == '"; - AQLreq += idrcset; - AQLreq += "'\n RETURN { \"elements\": u.properties.elements, \"sourcetdb\":u.properties.sourcetdb}"; - - DBQueryData query( AQLreq, DBQueryData::qAQL ); - ValuesTable resMatr = getDB()->downloadDocuments( query, { "elements", "sourcetdb" }); - - // read elements by sourcetdb and elements list - if( resMatr.size() > 0) - { - set elementset; - ElementsKeysFromJson( resMatr[0][0], elementset ); - vector elements(elementset.begin(), elementset.end()); - int sourcetdb = index_from_map( resMatr[0][1] ); - - return loadRecordsValues( jsonio::emptyQuery, sourcetdb, elements ); - } - return ValuesTable(); -} - - -// Extract data defined sourcetdbs and elements -std::vector ElementData_::selectGiven( const std::vector& sourcetdbs, const std::vector& elements ) -{ - string AQLreq = "FOR u IN elements \n" - " FILTER u.properties.sourcetdb IN @sourcetdbs\n" - " SORT u.properties.symbol "; - - // generate bind values - shared_ptr domdata(JsonDomFree::newObject()); - auto arr = domdata->appendArray( "sourcetdbs"); - sourceTDB_from_indexes( sourcetdbs, arr ); - // make query - DBQueryData query( AQLreq, DBQueryData::qAQL ); - query.setBindVars( domdata.get() ); - query.setQueryFields( makeQueryFields() ); - - ValuesTable elmQueryMatr = getDB()->downloadDocuments(query, getDataNames()); - - updateTableByElementsList( elmQueryMatr, elements ); - - vector elmKeys; - for (const auto& elitem : elmQueryMatr) - { - int class_ = 0; - json j = json::parse(elitem[getDataName_DataIndex().at("class_")]); - if (!j.is_null() && !j.empty() && j.is_object()) - class_ = stoi(j.begin().key()); - elmKeys.push_back( ElementKey( elitem[getDataName_DataIndex().at("symbol")], - class_, - 0)); - } - - pimpl->valuesTable = move(elmQueryMatr); - return elmKeys; -} - - -vector ElementData_::selectGiven( const vector& idThermoDataSets, bool /*unique*/ ) -{ - string qrAQL = "FOR vertex IN " + vectorToJson( idThermoDataSets); - qrAQL += "\n FOR v,e IN 1..5 INBOUND vertex \n"; - qrAQL += " basis"; - qrAQL += "\n FILTER v._label == 'element' "; - qrAQL += "\n SORT v.properties.symbol "; - qrAQL += DBQueryData::generateReturn( true, makeQueryFields(), "v"); - DBQueryData query( qrAQL, DBQueryData::qAQL ); - ValuesTable resMatr = getDB()->downloadDocuments( query, getDataNames()); - - vector elmSymbols; - for (const auto& subitem : resMatr) - elmSymbols.push_back(subitem[getDataName_DataIndex().at("symbol")]); - - setDefaultLevelForReactionDefinedSubst(resMatr); - pimpl->valuesTable = move(resMatr); - return elmSymbols; -} - -// Reads data from JsonDom (fromm real record) -auto fromElementNode( const jsonio::JsonDom *object ) -> ElementKey -{ - std::string symbol; int isotope, class_; - if(!object->findValue( "symbol", symbol ) ) - jsonio::jsonioErr( "ElementKey: ", "Undefined symbol."); - if(!object->findValue( "isotope_mass", isotope ) ) - isotope = 0; - std::map map_; - if(!object->findObject("class_", map_ ) || map_.size() < 1 ) - class_ = 0; - else - class_ = atoi(map_.begin()->first.c_str()); - return ElementKey(symbol,class_,isotope); -} - -// Reads data from JsonDom (only key) -auto fromKeyNode( const jsonio::JsonDom *object ) -> ElementKey -{ - std::string symbol; int isotope, class_; - if(!object->findValue( "symbol", symbol ) ) - jsonio::jsonioErr( "ElementKey: ", "Undefined symbol."); - if(!object->findValue( "isotope_mass", isotope ) ) - isotope = 0; - if(!object->findValue("class_", class_ ) ) - class_ = 0; - return ElementKey(symbol,class_,isotope); -} - -// Work only with internal elements list (wihout map) -void ElementsKeysFromJsonDom( const jsonio::JsonDom *object, set& elements ) -{ - ElementKey elem("",0,0); - size_t objsize = object->getChildrenCount(); - - for( size_t ii=0; iigetChild( ii); - if( childobj->getType() != jsonio::JSON_OBJECT ) - continue; - elem = fromKeyNode(childobj); - elements.insert(elem); - } - } - -bool ElementsKeysFromJson( const string elmsjson, set& elements ) -{ - try{ - auto arrobject = jsonio::unpackJson( elmsjson ); - elements.clear(); - ElementsKeysFromJsonDom( arrobject.get(), elements ); - return true; - } - catch(...) - { - return false; - } -} - -int index_from_map(std::string map) -{ - if( map.empty() ) - return 0; - auto first = map.find("\""); - jsonio::jsonioErrIf( first == string::npos, map, "Illegal class value."); - auto second = map.find("\"", first+1); - jsonio::jsonioErrIf( second == string::npos, map, "Illegal class value."); - string strNew = map.substr (first+1,second-(first+1)); - return stoi(strNew); -} - -bool ElementsKeysFromJsonDomArray( const string& keypath, const jsonio::JsonDom *object, set& elements ) -{ - elements.clear(); - auto elmobj = object->field(keypath); - if(elmobj==nullptr) - return false; - ElementsKeysFromJsonDom( elmobj, elements ); - return true; -} - -auto ElementKeyFromDB( jsonio::TDBVertexDocument* elementDB ) -> ElementKey -{ - //std::string symbol; int isotope, class_; - - return fromElementNode(elementDB->getDom()->field("properties")); - /*elementDB->getValue( "properties.symbol" , symbol ); - std::string class_str; - elementDB->getValue( "properties.class_" , class_str ); - class_ = index_from_map(class_str); - elementDB->getValue( "properties.isotope_mass" , isotope ); - return ElementKey(symbol,class_,isotope);*/ -} - -// Writes data to json (only key) -void toKeyNode( Element el, jsonio::JsonDom *object ) -{ - object->appendString( "symbol", el.name() ); - if( el.isotopeMass() != 0 ) - object->appendInt( "isotope_mass", el.isotopeMass() ); - if( el.class_()!= 0 ) - object->appendInt( "class_", el.class_() ); -} - -void ElementsKeysToJsonDom( jsonio::JsonDom *object, const set& elements ) -{ - int ndx=0; - for( auto el: elements) - { - auto objel = object->appendObject(to_string(ndx++)); - toKeyNode(elementKeyToElement(el), objel); - } -} - -shared_ptr ElementsKeysToJsonArray( const set& elements ) -{ - shared_ptr domdata(jsonio::JsonDomFree::newArray()); - ElementsKeysToJsonDom( domdata.get(), elements ); - return domdata; -} - -string ElementsKeysToJson( const set& elements ) -{ - auto domarray = ElementsKeysToJsonArray( elements ); - string elmsjson; - printNodeToJson( elmsjson, domarray.get() ); - return elmsjson; -} - -void setDBElements( jsonio::TDBVertexDocument* elementDB, const jsonio::DBQueryData& query ) -{ - vector resultData = elementDB->runQuery( query ); - - ElementsMap elements_map; - for(std::size_t ii=0; ii0) - ChemicalFormula::setDBElements( elements_map ); -} - -vector getElementKeys( jsonio::TDBVertexDocument* elementDB, const vector& idList ) -{ - vector elements; - - for(uint ii=0; iiRead( idList[ii] ); - elements.push_back(ElementKeyFromDB(elementDB)); - } - - return elements; -} - -} diff --git a/ThermoHubClient/ElementData.h b/ThermoHubClient/ElementData.h deleted file mode 100644 index e844fee4..00000000 --- a/ThermoHubClient/ElementData.h +++ /dev/null @@ -1,56 +0,0 @@ -#ifndef ELEMENTDATA_H -#define ELEMENTDATA_H - -#include "AbstractData.h" - -namespace ThermoFun -{ - -class ElementData_ : public AbstractData -{ - public: - ElementData_(const jsonio::TDataBase* dbconnect); - - /// Construct a copy of an ReactionData instance - ElementData_(const ElementData_& other); - - auto operator=(ElementData_ other) -> ElementData_ &; - - virtual ~ElementData_(); - - /// Extract data connected to ReactionSet - virtual jsonio::ValuesTable loadRecordsValues( const std::string& idReactionSet ); - /// Extract data by condition - virtual jsonio::ValuesTable loadRecordsValues(const jsonio::DBQueryData& query, int sourcetdb, - const std::vector &elements = {}); - /// Extract data connected to ThermoDataSet - virtual std::vector selectGiven( const std::vector& idThermoDataSets, bool unique = true ); - - /// Extract data defined sourcetdbs and elements - std::vector selectGiven( const std::vector& sourcetdbs, const std::vector& elements ); - - /// Get Elements list from reactions - virtual std::set getElementsList(const std::string &id); - - /// Link to table of fields values loaded before - const jsonio::ValuesTable& getValuesTable(); - - private: - - struct Impl; - std::shared_ptr pimpl; - - void updateTableByElementsList( jsonio::ValuesTable& dataQueryMatr, const std::vector& elements ); -}; - -auto fromElementNode( const jsonio::JsonDom *object ) -> ElementKey; -bool ElementsKeysFromJson( const std::string elmsjson, std::set& elements ); -auto index_from_map(std::string map) -> int; -bool ElementsKeysFromJsonDomArray( const std::string& keypath, const jsonio::JsonDom *object, std::set& elements ); -auto ElementsKeysToJson( const std::set& elements ) -> std::string; -void setDBElements( jsonio::TDBVertexDocument* elementDB, - const jsonio::DBQueryData& query = jsonio::DBQueryData("{\"_label\": \"element\" }",jsonio::DBQueryData::qTemplate ) ); -auto getElementKeys( jsonio::TDBVertexDocument* elementDB, const std::vector& idList ) -> std::vector; -} - -#endif // ELEMENTDATA_H diff --git a/ThermoHubClient/ParseDbcToData.cpp b/ThermoHubClient/ParseDbcToData.cpp deleted file mode 100644 index 82fe964b..00000000 --- a/ThermoHubClient/ParseDbcToData.cpp +++ /dev/null @@ -1,103 +0,0 @@ -#include "ParseDbcToData.h" -#include "SubstanceData.h" -#include "ReactionData.h" -#include "DatabaseClient.h" - -// ThermoFun includes -#ifdef FROM_SRC -#include "../ThermoFun/Common/ParseJsonToData.h" -#include "../ThermoFun/Common/Exception.h" -#include "../ThermoFun/Database.h" -#include "../ThermoFun/Substance.h" -#include "../ThermoFun/Reaction.h" -#else -#include "ThermoFun/Common/ParseJsonToData.h" -#include "ThermoFun/Common/Exception.h" -#include "ThermoFun/Database.h" -#include "ThermoFun/Substance.h" -#include "ThermoFun/Reaction.h" -#endif - -namespace ThermoFun { - -auto databaseFromRecordList(const DatabaseClient &dbc, const List_VertexId_VertexType &recordList, DefinesSubstLevelOptions levelOptions ) -> Database -{ - std::string _idSubst, _idReact, substSymb; - std::string level_; - Database tdb; - - // The set of all aqueous species in the database - SubstancesMap substances_map; - // The set of all gaseous species in the database - ReactionsMap reactions_map; - - // get substances and the reaction symbol if necessary - for(auto iterator = recordList.begin(); iterator != recordList.end(); iterator++) - { - if (iterator->second == "substance") - { - _idSubst = iterator->first; - std::string jsonrecord = dbc.substData().getJsonRecordVertex(_idSubst); - auto domdata = jsonio::unpackJson( jsonrecord, "VertexSubstance" ); // with default values - domdata->findValue("properties.symbol", substSymb); - // record = dbc.substData().getJsonBsonRecordVertex(_idSubst).second; - // bsonio::bson_to_key( record.data, "properties.symbol", substSymb ); - - auto mode = levelOptions.definesSubstLevelMode; - - switch(mode) - { - case DefinesSubstLevelMode::followAll : level_ = "-1"; // follows all connected data - break; - case DefinesSubstLevelMode::followGiven : level_ = levelOptions.level; // follows edges defines with level - break; - case DefinesSubstLevelMode::followDiefferentPerSubstance : { - if (levelOptions.substSymbol_definesLevel.find(substSymb) != levelOptions.substSymbol_definesLevel.end()) // follows edges defines with specific leveles for substSymbols - level_ = levelOptions.substSymbol_definesLevel[substSymb]; // if the substance symbol is not found in the map, it uses the default level - else - level_ = levelOptions.level; - } - break; - } - - Substance substance = parseSubstance(jsonrecord); - - // get reaction symbol which define substance with _idSubst - std::string definesReactSymb = dbc.substData().definesReactionSymbol(_idSubst, level_); - if (definesReactSymb != "") - { - substance.setReactionSymbol(definesReactSymb); - substance.setThermoCalculationType(ThermoFun::SubstanceThermoCalculationType::type::REACDC); - } - - if ( substances_map.find(substance.symbol()) == substances_map.end() ) { - substances_map[substance.symbol()] = substance; - } else { - errorSameSymbol("substance", substance.symbol(), __LINE__, __FILE__ ); - } - } else - if (iterator->second == "reaction") - { - _idReact = iterator->first; - std::string jsonrecord = dbc.reactData().getJsonRecordVertex(_idReact); - auto domdata = jsonio::unpackJson( jsonrecord, "VertexReaction" ); // with default values - // record = dbc.reactData().getJsonBsonRecordVertex(_idReact).second; - - Reaction reaction = parseReaction(jsonrecord); - - // get reactants by following reaction incoming takes edge - reaction.setReactants(dbc.reactData().reactantsCoeff(_idReact)); - - if ( reactions_map.find(reaction.symbol()) == reactions_map.end() ) { - reactions_map[reaction.symbol()] = reaction; - } else { - errorSameSymbol("reaction", reaction.symbol(), __LINE__, __FILE__ ); - } - } - } - tdb.addMapReactions(reactions_map); - tdb.addMapSubstances(substances_map); - return tdb; -} - -} diff --git a/ThermoHubClient/ParseDbcToData.h b/ThermoHubClient/ParseDbcToData.h deleted file mode 100644 index a1ded29f..00000000 --- a/ThermoHubClient/ParseDbcToData.h +++ /dev/null @@ -1,36 +0,0 @@ -// C++ includes -#include -#include -#include -//#include - -namespace ThermoFun { - -class DatabaseClient; -class Database; - -using List_VertexId_VertexType = std::vector>; - -enum DefinesSubstLevelMode { - followAll= 0, - followGiven, - followDiefferentPerSubstance -}; - -struct DefinesSubstLevelOptions { - /// map of substance symbol and level for the edge defines connected to the substance - std::map substSymbol_definesLevel; - - /// current level for the traversal operation - std::string level = "0"; - - /// mode of using levels for traversal (all: collect all connected; single: collect all connected using one - /// defines level for all substances; multiple: collect all connectec using different levels for different - /// substances (from map substSymbol_definesLevel) - DefinesSubstLevelMode definesSubstLevelMode = DefinesSubstLevelMode::followAll; -}; - -auto databaseFromRecordList(const DatabaseClient &dbc, const List_VertexId_VertexType &recordList, DefinesSubstLevelOptions levelOptions = DefinesSubstLevelOptions()) -> Database; - - -} diff --git a/ThermoHubClient/ReactionData.cpp b/ThermoHubClient/ReactionData.cpp deleted file mode 100644 index 1bd7c1fe..00000000 --- a/ThermoHubClient/ReactionData.cpp +++ /dev/null @@ -1,347 +0,0 @@ -#include "ReactionData.h" -#include "ElementData.h" -#include "sourcetdb.h" - -// C++ includes -#include -#include -#include "jsonio/jsondomfree.h" - -// ThermoFun includes -#ifdef FROM_SRC -#include "../ThermoFun/OptimizationUtils.h" -#else -#include "ThermoFun/OptimizationUtils.h" -#endif - -using namespace std; -using namespace jsonio; - -namespace ThermoFun -{ - -//const DBQueryData reactQuery("{\"_label\": \"reaction\" }", DBQueryData::qTemplate); -const DBQueryData reactQuery("FOR u IN reactions ", DBQueryData::qAQL); -const vector reactFieldPaths = {"properties.symbol", "properties.equation", "properties.reactyp", "properties.sourcetdb", "properties.level", "properties.name", "_id" }; -const vector reactDataNames = {"symbol", "equation", "type", "sourcetdb", "level", "name", "_id"}; // should have the same size as FieldPaths !! -const vector reactColumnHeaders = {"symbol", "equation"/*, "type", "sourcetdb", "level"*/}; - -using QueryVertexReaction = std::function)>; - - -struct ReactionData_::Impl -{ - ValuesTable valuesTable; - - Impl( ) - { - } - -}; - -ReactionData_::ReactionData_(const TDataBase* dbconnect) - : AbstractData(dbconnect, "VertexReaction", reactQuery, reactFieldPaths, - reactColumnHeaders, reactDataNames), pimpl(new Impl()) -{ -} - -ReactionData_::ReactionData_(const ReactionData_& other) -: AbstractData(other), pimpl(new Impl(*other.pimpl)) -{} - -auto ReactionData_::operator=(ReactionData_ other) -> ReactionData_ & -{ - pimpl = std::move(other.pimpl); - return *this; -} - -ReactionData_::~ReactionData_() -{ -} - -const jsonio::ValuesTable& ReactionData_::getValuesTable() -{ - return pimpl->valuesTable; -} - -auto ReactionData_::queryInEdgesTakes(string idReact) -> vector -{ - return queryInEdgesTakes_(idReact); -} - -auto ReactionData_::reactantsCoeff(string idReact) -> std::map -{ - return reactantsCoeff_(idReact); -} - -void ReactionData_::updateTableByElementsList( ValuesTable& reactQueryMatr, const vector& elements ) -{ - if( !elements.empty() ) - { - ValuesTable reactMatr; - for (const auto& subitem : reactQueryMatr) - { - string idreac = subitem[getDataName_DataIndex().at("_id")]; - if (testElements(idreac, elements)) - reactMatr.push_back(subitem); - } - reactQueryMatr = move(reactMatr); - } - } - -// return all record, no only fields if not default -ValuesTable ReactionData_::loadRecordsValues(const DBQueryData& aquery, - int sourcetdb, const vector &elements) -{ - auto fields = getDataFieldPaths(); - - // get records by query - auto query = aquery; - if (query.empty()) - { - query = getQuery(); - // only here we have subset fields to extract - query.setQueryFields(makeQueryFields()); - fields = getDataNames(); - } - //if (!elements.empty()) - addFieldsToQueryAQL(query, {make_pair(string(getDataName_DataFieldPath().at("sourcetdb")), sourceTDB_from_index(sourcetdb))}); - ValuesTable reactQueryMatr = getDB()->downloadDocuments(query, fields); - - // get record by elements list - updateTableByElementsList( reactQueryMatr, elements ); - setDefaultLevelForReactionDefinedSubst(reactQueryMatr); - pimpl->valuesTable = reactQueryMatr; - return reactQueryMatr; -} - -ValuesTable ReactionData_::loadRecordsValues( const string& idReactionSet ) -{ - string qrAQL = "FOR u,e IN 1..1 INBOUND '"; - qrAQL += idReactionSet + "' \n prodreac\n"; - //qrAQL += "RETURN u"; - - DBQueryData query( qrAQL, DBQueryData::qAQL ); - query.setQueryFields(makeQueryFields()); - ValuesTable reactMatr = getDB()->downloadDocuments( query, getDataNames()); - setDefaultLevelForReactionDefinedSubst(reactMatr); - pimpl->valuesTable = reactMatr; - return reactMatr; -} - -bool ReactionData_::testElements(const string &idReaction, - const vector &elements) -{ - set reactelements = getElementsList(idReaction); - - /* if user fogot insert elements property - if( reactelements.empty() ) - { - vector formulalst = getSubstanceFormulas( idReaction ); - reactelements = elements::ChemicalFormula::extractElements(formulalst ); - }*/ - - for (auto formelm : reactelements) - { - auto itr = elements.begin(); - while (itr != elements.end()) - { - if (formelm == *itr) - break; - itr++; - } - if (itr == elements.end()) - return false; - } - return true; -} - -vector ReactionData_::getReactantsFormulas(const string &idReaction) -{ - string qrJson = "FOR v,e IN 1..1 INBOUND '"; - qrJson += idReaction + "' \n takes\n"; - qrJson += "RETURN DISTINCT v.properties.formula"; - - vector formulas = getDB()->runQuery( DBQueryData( qrJson, DBQueryData::qAQL ) ); - return formulas; -} - -set ReactionData_::getElementsList(const string &idReaction) -{ - set elements; - string jsonrecord = getJsonRecordVertex(idReaction); - auto domdata = jsonio::unpackJson( jsonrecord ); - ElementsKeysFromJsonDomArray("properties.elements", domdata.get(), elements); - - // if user fogot insert elements property - if (elements.empty()) - { - vector formulalst = getReactantsFormulas(idReaction); - elements = ChemicalFormula::extractElements(formulalst); - } - return elements; -} - -void ReactionData_::resetRecordElements(const string& idReact ) -{ - string _id; - try{ - getDB()->Read(idReact); - getDB()->getValue("_id",_id); - - vector formulalst = getReactantsFormulas( _id ); - set elements = ThermoFun::ChemicalFormula::extractElements(formulalst ); - - string elementsJsonArray = ElementsKeysToJson( elements ); - getDB()->setValue("properties.elements",elementsJsonArray); - getDB()->UpdateWithTestValues(); - } - catch(jsonio_exception& e) - { - cout << "ResetElementsintoReactionRecord " << e.title() << e.what() << endl; - } - catch(std::exception& e) - { - cout << "std::exception" << e.what() << endl; - } -} - -vector ReactionData_::getKeys(string symbol, int sourcetdb) -{ - string qrAQL = "FOR u IN reactions \nFILTER u.properties.symbol == '"; - qrAQL += symbol + "' and u.properties.sourcetdb == " + sourceTDB_from_index(sourcetdb) + " "; - //qrAQL += "RETURN u"; - - DBQueryData query( qrAQL, DBQueryData::qAQL ); - return getDB()->getKeysByQuery( query ); -} - -bool ReactionData_::checkReactSymbolLevel (int sourcetdb, string &symbol, string &level) -{ - vector levels; - vector levelQueryMatr; - string reactSymbol = symbol; - vector reactKeys = getKeys(symbol, sourcetdb); - level = "0"; - while (reactKeys.size() > 0) - { - levels.clear(); - - for (auto key_: reactKeys) - { - string qrJson = "FOR v,e IN 1..1 OUTBOUND '"; - qrJson += key_ + "' \n defines\n"; - qrJson += "RETURN e.properties.level"; - levelQueryMatr = getDB()->runQuery( DBQueryData( qrJson, DBQueryData::qAQL ) ); - if (levelQueryMatr.size()>0) - levels.push_back(std::stoi(levelQueryMatr[0])); - else - levels.push_back(std::stoi(level)); - } - - if (levels.size()>0) - { - level = std::to_string((*std::max_element(levels.begin(), levels.end())+1)); - symbol = reactSymbol + "_"+level; - } - reactKeys = getKeys(symbol, sourcetdb); - } - - if (symbol == reactSymbol) - return false; - else - return true; -} - -vector ReactionData_::selectGiven( const vector& sourcetdbs, - const vector& substanceSymbols, bool unique ) -{ - // define query string - string AQLreq = "FOR u IN reactions\n" - " FILTER u.properties.sourcetdb IN @sourcetdbs\n" - " LET takessub = ( FOR v,e IN 1..1 INBOUND u._id takes RETURN v.properties.symbol ) \n" - " FILTER takessub ALL IN @substanceSymbols \n" - " SORT u.properties.symbol "; - AQLreq += DBQueryData::generateReturn( false, makeQueryFields()); - - // generate bind values - shared_ptr domdata(JsonDomFree::newObject()); - auto arr = domdata->appendArray( "sourcetdbs"); - sourceTDB_from_indexes( sourcetdbs, arr ); - domdata->appendArray( "substanceSymbols", substanceSymbols ); - // make query - DBQueryData query( AQLreq, DBQueryData::qAQL ); - query.setBindVars( domdata.get() ); - query.setQueryFields( makeQueryFields() ); - - ValuesTable reactQueryMatr = getDB()->downloadDocuments(query, getDataNames()); - - // delete not unique - if( unique ) - deleteNotUnique( reactQueryMatr, getDataName_DataIndex().at("symbol") ); - - vector reactSymbols; - for (const auto& subitem : reactQueryMatr) - reactSymbols.push_back(subitem[getDataName_DataIndex().at("symbol")]); - - setDefaultLevelForReactionDefinedSubst(reactQueryMatr); - pimpl->valuesTable = move(reactQueryMatr); - return reactSymbols; -} - -vector ReactionData_::selectGiven( const vector& idThermoDataSets, bool unique ) -{ - string qrAQL = "FOR vertex IN " + vectorToJson( idThermoDataSets); - qrAQL += "\n FOR v,e IN 1..5 INBOUND vertex \n"; - qrAQL += ThermoDataSetQueryEdges; - qrAQL += "\n FILTER v._label == 'reaction' "; - qrAQL += "\n SORT v.properties.symbol "; - qrAQL += DBQueryData::generateReturn( true, makeQueryFields(), "v"); - DBQueryData query( qrAQL, DBQueryData::qAQL ); - ValuesTable resMatr = getDB()->downloadDocuments( query, getDataNames()); - - if( unique ) - deleteNotUnique( resMatr, getDataName_DataIndex().at("symbol") ); - - vector reacSymbols; - for (const auto& subitem : resMatr) - reacSymbols.push_back(subitem[getDataName_DataIndex().at("symbol")]); - - setDefaultLevelForReactionDefinedSubst(resMatr); - pimpl->valuesTable = move(resMatr); - return reacSymbols; - -} - - -vector ReactionData_::selectGiven( const string& idThermoDataSet, - const vector& substanceSymbols ) -{ - string qrAQL = "FOR v,e IN 1..5 INBOUND '" + idThermoDataSet+ "' \n"; - qrAQL += ThermoDataSetQueryEdges; - qrAQL += "\n FILTER v._label == 'reaction' "; - qrAQL += "\n LET takessub = ( FOR v1 IN 1..1 INBOUND v._id takes RETURN v1.properties.symbol )"; - qrAQL += "\n FILTER takessub ALL IN @substanceSymbols \n"; - qrAQL += "\n SORT v.properties.symbol "; - qrAQL += DBQueryData::generateReturn( true, makeQueryFields(), "v"); - - //cout << "qrAQL: " << qrAQL << endl; - // generate bind values - shared_ptr domdata(JsonDomFree::newObject()); - domdata->appendArray( "substanceSymbols", substanceSymbols ); - // make query - DBQueryData query( qrAQL, DBQueryData::qAQL ); - query.setBindVars( domdata.get() ); - - ValuesTable resMatr = getDB()->downloadDocuments( query, getDataNames()); - - vector reacSymbols; - for (const auto& subitem : resMatr) - reacSymbols.push_back(subitem[getDataName_DataIndex().at("symbol")]); - - setDefaultLevelForReactionDefinedSubst(resMatr); - pimpl->valuesTable = move(resMatr); - return reacSymbols; -} - -} diff --git a/ThermoHubClient/ReactionData.h b/ThermoHubClient/ReactionData.h deleted file mode 100644 index bb4c9699..00000000 --- a/ThermoHubClient/ReactionData.h +++ /dev/null @@ -1,93 +0,0 @@ -#ifndef REACTIONDATA_H -#define REACTIONDATA_H - -// C++ includes -#include -#include "AbstractData.h" - -namespace ThermoFun -{ - -class ReactionData_ : public AbstractData -{ - public: - ReactionData_(const jsonio::TDataBase* dbconnect); - - /// Construct a copy of an ReactionData instance - ReactionData_(const ReactionData_& other); - - auto operator=(ReactionData_ other) -> ReactionData_ &; - - virtual ~ReactionData_(); - - /// Extract data connected to ReactionSet - virtual jsonio::ValuesTable loadRecordsValues( const std::string& idReactionSet ); - /// Extract data by condition - virtual jsonio::ValuesTable loadRecordsValues(const jsonio::DBQueryData& query, int sourcetdb, - const std::vector &elements = {}); - /// Extract data connected to ThermoDataSet - virtual std::vector selectGiven( const std::vector& idThermoDataSets, bool unique = true ); - - /// Select reactions belonging to sourcetdbs and containing given substance symbols - std::vector selectGiven( const std::vector& sourcetdbs, - const std::vector& substanceSymbols, bool unique=true ); - /// Extract data connected to ThermoDataSet and containing given substance symbols - std::vector selectGiven( const std::string& idThermoDataSet, const std::vector& substanceSymbols ); - - /// Get Elements list from reactions - virtual std::set getElementsList(const std::string &id); - - /// Link to table of fields values loaded before - const jsonio::ValuesTable& getValuesTable(); - - /// Return all formulas from all connected substances - std::vector getReactantsFormulas(const std::string &idReaction); - - /** - * @brief queryIncomingEdgesTakes returns data of the incoming edges of type takes - * @param idReact reaction id - * @return list of extracted data for each edge - */ - auto queryInEdgesTakes(std::string idReact) -> std::vector; - - /** - * @brief mapReactantsCoeff returns the map of reactants symbols and coefficients - * connected to a reaction with an edge of type takes - * @param _idReac reaction id - * @return - */ - auto reactantsCoeff(std::string idReact) -> std::map; - - /** - * @brief resetRecordElements resets elements list in record - * @param idReact - */ - auto resetRecordElements(const std::string& idReact) -> void; - - /** - * @brief checkReactSymbolLevel checks if reaction with the same symbol / level exists. If exists the level is increased and the - * symbol is annotated with _#level - * @param sourcetdb - * @param symbol - * @param level - * @return - */ - bool checkReactSymbolLevel (int sourcetdb, std::string &symbol, std::string &level); - - - private: - - // tests if elements are present in the reaction - bool testElements(const std::string &idReaction, const std::vector &elements); - - // returns a list of ids for all reaction with symbol and sourcetdb present in the database - std::vector getKeys(std::string symbol, int sourcetdb); - - void updateTableByElementsList( jsonio::ValuesTable& reactQueryMatr, const std::vector& elements ); - - struct Impl; - std::shared_ptr pimpl; -}; -} - -#endif // REACTIONDATA_H diff --git a/ThermoHubClient/ReactionSetData.cpp b/ThermoHubClient/ReactionSetData.cpp deleted file mode 100644 index 2c613306..00000000 --- a/ThermoHubClient/ReactionSetData.cpp +++ /dev/null @@ -1,314 +0,0 @@ -#include "ReactionSetData.h" -#include "jsonio/io_settings.h" -#include "jsonio/jsondomfree.h" -#include "sourcetdb.h" -#include "ElementData.h" - -using namespace std; -using namespace jsonio; - -namespace ThermoFun -{ - -//const DBQueryData reactQuery( "{\"_label\": \"reactionset\" }", DBQueryData:: qTemplate ); -const DBQueryData reactQuery("FOR u IN reactionsets ", DBQueryData::qAQL); -const vector reactFieldPaths = {"properties.symbol", "properties.name", "properties.stype", "properties.sourcetdb", "properties.level", "_id"}; -const vector reactDataNames = {"symbol", "name", "type" , "sourcetdb", "level", "_id"}; // should have the same size as FieldPaths !! -const vector reactColumnHeaders = { "symbol", "name", "type"/*, "sourcetdb", "level", "_id"*/ }; - -struct ReactionSetData_::Impl -{ - ValuesTable valuesTable; - - Impl( ) - { - } - -}; - -ReactionSetData_::ReactionSetData_(const TDataBase* dbconnect) - : AbstractData( dbconnect, "VertexReactionSet", reactQuery, - reactFieldPaths, reactColumnHeaders, reactDataNames), pimpl(new Impl()) -{ -} - -ReactionSetData_::ReactionSetData_(const ReactionSetData_& other) -: AbstractData(other), pimpl(new Impl(*other.pimpl)) -{} - -auto ReactionSetData_::operator=(ReactionSetData_ other) -> ReactionSetData_ & -{ - pimpl = std::move(other.pimpl); - return *this; -} - -ReactionSetData_::~ReactionSetData_() -{ -} - -const jsonio::ValuesTable& ReactionSetData_::getValuesTable() -{ - return pimpl->valuesTable; -} - -set ReactionSetData_::getElementsList( const string& idrcset ) -{ - set elements; - string jsonrecord = getJsonRecordVertex(idrcset); - auto domdata = jsonio::unpackJson( jsonrecord ); - ElementsKeysFromJsonDomArray("properties.elements", domdata.get(), elements); - - // if user fogot tnsert elements property - if( elements.empty() ) - { - vector formulalst = getSubstanceFormulas( idrcset ); - elements = ThermoFun::ChemicalFormula::extractElements(formulalst ); - } - return elements; -} - -// return all record, no only fields if not default -ValuesTable ReactionSetData_::loadRecordsValues( const DBQueryData& aquery, - int sourcetdb, const vector& elements ) -{ - auto fields = getDataFieldPaths(); - - // get records by query - auto query = aquery; - if (query.empty()) - { - query = getQuery(); - // only here we have subset fields to extract - query.setQueryFields(makeQueryFields()); - fields = getDataNames(); - } - if( !elements.empty() ) - addFieldsToQueryAQL( query, { make_pair( string("properties.sourcetdb"), sourceTDB_from_index(sourcetdb)) } ); - ValuesTable reactQueryMatr = getDB()->downloadDocuments( query, fields ); - - // get record by elements list - ValuesTable reactMatr; - if( elements.empty() ) - { - reactMatr = move(reactQueryMatr); - } - else - { - for( const auto& subitem: reactQueryMatr ) - { - string idreac = subitem[getDataName_DataIndex().at("_id")]; - if( testElements( idreac, elements) ) - reactMatr.push_back(subitem); - } - } - return reactMatr; -} - -ValuesTable ReactionSetData_::loadRecordsValues( const string& idrcset ) -{ - vector ids; - ids.push_back(idrcset); - return getDB()->downloadDocuments(ids, getDataFieldPaths()); -} - -vector ReactionSetData_::getSubstanceIds( const string& idrcset ) -{ - // Select substance ids connected to reactionSet - auto subIds = getInVertexIds( "product, master", idrcset ); - //auto subIds2 = getInVertexIds( "master", idrcset ); - //subIds.insert( subIds.end(), subIds2.begin(), subIds2.end() ); - return subIds; -} - - -vector ReactionSetData_::getSubstanceFormulas( const string& idrcset ) -{ - string qrJson = "FOR v,e IN 1..1 INBOUND '"; - qrJson += idrcset + "' \n product, master\n"; - qrJson += "RETURN DISTINCT v.properties.formula"; - - vector formulas = getDB()->runQuery( DBQueryData( qrJson, DBQueryData::qAQL ) ); - return formulas; -} - -bool ReactionSetData_::testElements( const string& idrcset, - const vector& elements ) -{ - set reactelements = getElementsList( idrcset ); - - if(reactelements.empty()) - return false; - - for( auto formelm: reactelements ) - { - auto itr = elements.begin(); - while( itr != elements.end() ) - { - if( formelm == *itr ) - break; - itr++; - } - if( itr == elements.end() ) - return false; - } - return true; -} - -void ReactionSetData_::resetRecordElements( const string& aKey ) -{ - string _id; - try{ - auto graphdb = getDB(); - graphdb->Read( aKey ); - graphdb->getValue("_id",_id); - - vector formulalst = getSubstanceFormulas( _id ); - set elements = ThermoFun::ChemicalFormula::extractElements(formulalst ); - - string elementsJsonArray = ThermoFun::ElementsKeysToJson( elements ); - graphdb->setValue("properties.elements",elementsJsonArray); - graphdb->UpdateWithTestValues(); - } - catch(jsonio_exception& e) - { - cout << "ResetElementsintoReactionRecord " << e.title() << e.what() << endl; - } - catch(std::exception& e) - { - cout << "std::exception" << e.what() << endl; - } -} - -bool ReactionSetData_::getSpeciesMap( const string& RcSid, std::map& specmap ) -{ - // extract data from reaction record - getDB()->Read( RcSid ); - bool iret = getDB()->getDom()->findObject( "properties.species_map", specmap ); - //bool iret = bson_read_map_path( reobj.data, "properties.species_map", specmap ); - return iret; -} - -vector ReactionSetData_::selectGivenSubstances( const vector& sourcetdbs, - const vector& substanceSymbols, bool unique ) -{ - // define query string - string AQLreq = "FOR u IN reactionsets \n" - " FILTER u.properties.sourcetdb IN @sourcetdbs\n" - " LET takesreac = ( FOR v,e IN 1..1 INBOUND u._id prodreac RETURN v.properties.symbol ) \n" - " FILTER takesreac ALL IN @substanceSymbols \n" - " SORT u.properties.symbol "; - AQLreq += DBQueryData::generateReturn( false, makeQueryFields()); - - // generate bind values - shared_ptr domdata(JsonDomFree::newObject()); - auto arr = domdata->appendArray( "sourcetdbs"); - sourceTDB_from_indexes( sourcetdbs, arr ); - domdata->appendArray( "substanceSymbols", substanceSymbols); - // make query - DBQueryData query( AQLreq, DBQueryData::qAQL ); - query.setBindVars( domdata.get() ); - query.setQueryFields( makeQueryFields() ); - - ValuesTable reactSetQueryMatr = getDB()->downloadDocuments(query, getDataNames()); - - // delete not unique - if( unique ) - deleteNotUnique( reactSetQueryMatr, getDataName_DataIndex().at("symbol") ); - - vector reactSetSymbols; - for (const auto& subitem : reactSetQueryMatr) - reactSetSymbols.push_back(subitem[getDataName_DataIndex().at("symbol")]); - - setDefaultLevelForReactionDefinedSubst(reactSetQueryMatr); - pimpl->valuesTable = move(reactSetQueryMatr); - return reactSetSymbols; -} - -vector ReactionSetData_::selectGiven(const vector& sourcetdbs, - const vector& reactionSymbols, bool unique ) -{ - // define query string - string AQLreq = "FOR u IN reactionsets \n" - " FILTER u.properties.sourcetdb IN @sourcetdbs\n" - " LET prodreac = ( FOR v,e IN 1..1 INBOUND u._id prodreac RETURN v.properties.symbol ) \n" - " FILTER prodreac ALL IN @reactionSymbols \n" - " SORT u.properties.symbol "; - AQLreq += DBQueryData::generateReturn( false, makeQueryFields()); - - // generate bind values - shared_ptr domdata(JsonDomFree::newObject()); - auto arr = domdata->appendArray( "sourcetdbs"); - sourceTDB_from_indexes( sourcetdbs, arr ); - domdata->appendArray( "reactionSymbols", reactionSymbols); - // make query - DBQueryData query( AQLreq, DBQueryData::qAQL ); - query.setBindVars( domdata.get() ); - query.setQueryFields( makeQueryFields() ); - - ValuesTable reactSetQueryMatr = getDB()->downloadDocuments(query, getDataNames()); - - // delete not unique - if( unique ) - deleteNotUnique( reactSetQueryMatr, getDataName_DataIndex().at("symbol") ); - - vector reactSetSymbols; - for (const auto& subitem : reactSetQueryMatr) - reactSetSymbols.push_back(subitem[getDataName_DataIndex().at("symbol")]); - - setDefaultLevelForReactionDefinedSubst(reactSetQueryMatr); - pimpl->valuesTable = move(reactSetQueryMatr); - return reactSetSymbols; -} - -vector ReactionSetData_::selectGiven( const vector& idThermoDataSets, bool unique ) -{ - string qrAQL = "FOR vertex IN " + vectorToJson( idThermoDataSets); - qrAQL += "\n FOR v,e IN 1..5 INBOUND vertex \n"; - qrAQL += ThermoDataSetQueryEdges; - qrAQL += "\n FILTER v._label == 'reactionset' "; - qrAQL += "\n SORT v.properties.symbol "; - qrAQL += DBQueryData::generateReturn( true, makeQueryFields(), "v"); - DBQueryData query( qrAQL, DBQueryData::qAQL ); - ValuesTable resMatr = getDB()->downloadDocuments( query, getDataNames()); - - if( unique ) - deleteNotUnique( resMatr, getDataName_DataIndex().at("symbol") ); - - vector reacSymbols; - for (const auto& subitem : resMatr) - reacSymbols.push_back(subitem[getDataName_DataIndex().at("symbol")]); - - setDefaultLevelForReactionDefinedSubst(resMatr); - pimpl->valuesTable = move(resMatr); - return reacSymbols; -} - -vector ReactionSetData_::selectGiven( const string& idThermoDataSet, const vector& reactionSymbols ) -{ - string qrAQL = "FOR v IN 1..5 INBOUND '" + idThermoDataSet + "'\n"; - qrAQL += ThermoDataSetQueryEdges; - qrAQL += "\n FILTER v._label == 'reactionset' "; - qrAQL += "\n LET prodreac = ( FOR v1 IN 1..1 INBOUND v._id prodreac RETURN v1.properties.symbol )"; - qrAQL += "\n FILTER prodreac ALL IN @reactionSymbols"; - qrAQL += "\n SORT v.properties.symbol "; - qrAQL += DBQueryData::generateReturn( true, makeQueryFields(), "v"); - - // generate bind values - shared_ptr domdata(JsonDomFree::newObject()); - domdata->appendArray( "reactionSymbols", reactionSymbols); - // make query - DBQueryData query( qrAQL, DBQueryData::qAQL ); - query.setBindVars( domdata.get() ); - ValuesTable resMatr = getDB()->downloadDocuments( query, getDataNames()); - - vector reacSymbols; - for (const auto& subitem : resMatr) - reacSymbols.push_back(subitem[getDataName_DataIndex().at("symbol")]); - - setDefaultLevelForReactionDefinedSubst(resMatr); - pimpl->valuesTable = move(resMatr); - return reacSymbols; -} - - -} diff --git a/ThermoHubClient/ReactionSetData.h b/ThermoHubClient/ReactionSetData.h deleted file mode 100644 index 1f570038..00000000 --- a/ThermoHubClient/ReactionSetData.h +++ /dev/null @@ -1,73 +0,0 @@ -#ifndef REACTIONSETDATA_H -#define REACTIONSETDATA_H - -#include "AbstractData.h" - -namespace ThermoFun -{ - -class ReactionSetData_ : public AbstractData -{ - public: - ReactionSetData_(const jsonio::TDataBase* dbconnect); - - /// Construct a copy of an ReactionData instance - ReactionSetData_(const ReactionSetData_& other); - - auto operator=(ReactionSetData_ other) -> ReactionSetData_ &; - - virtual ~ReactionSetData_(); - - /// Extract data connected to ReactionSet - virtual jsonio::ValuesTable loadRecordsValues( const std::string& idReactionSet ); - /// Extract data by condition - virtual jsonio::ValuesTable loadRecordsValues(const jsonio::DBQueryData& query, int sourcetdb, - const std::vector &elements = {}); - /// Extract data connected to ThermoDataSet - virtual std::vector selectGiven( const std::vector& idThermoDataSets, bool unique = true ); - - std::vector selectGivenSubstances( const std::vector& sourcetdbs, - const std::vector& substanceSymbols, bool unique = true ); - - /// Select reaction sets belonging to sourcetdbs and containing given reaction symbols - std::vector selectGiven( const std::vector& sourcetdbs, - const std::vector& reactionSymbols, bool unique = true ); - - /// Extract data connected to ThermoDataSet and containing given reaction symbols - std::vector selectGiven( const std::string& idThermoDataSet, const std::vector& reactionSymbols ); - - /// Get Elements list from reactions - virtual std::set getElementsList(const std::string &id); - - /// Link to table of fields values loaded before - const jsonio::ValuesTable& getValuesTable(); - - /** - * @brief resetRecordElements resets elements list in record - * @param aKey record key - */ - void resetRecordElements( const std::string& aKey ); - - /// Return all ids from all connected substances - std::vector getSubstanceIds( const std::string& idrcset ); - - /// Return all formulas from all connected substances - std::vector getSubstanceFormulas( const std::string& idreaction ); - - /// Read species map from record - bool getSpeciesMap( const std::string& RcSid, std::map& specmap ); - - private: - - - /// Test record all elements exist into list - bool testElements( const std::string& idrecord, - const std::vector& elements ); - - struct Impl; - std::shared_ptr pimpl; -}; - -} - -#endif // REACTIONSETDATA_H diff --git a/ThermoHubClient/SubstanceData.cpp b/ThermoHubClient/SubstanceData.cpp deleted file mode 100644 index 7bbf9761..00000000 --- a/ThermoHubClient/SubstanceData.cpp +++ /dev/null @@ -1,311 +0,0 @@ -#include -#include "SubstanceData.h" -#include "jsonio/jsondomfree.h" -#include "sourcetdb.h" - -using namespace std; -using namespace jsonio; - -namespace ThermoFun { - -//const DBQueryData substQuery("{\"_label\": \"substance\" }", DBQueryData::qTemplate); -const DBQueryData substQuery("FOR u IN substances ", DBQueryData::qAQL); -const vector substFieldPaths = { "properties.symbol", "properties.formula", "properties.class_", "properties.sourcetdb", "properties.name", "_id"}; -const vector substDataNames = { "symbol", "formula", "class_", "sourcetdb", "name", "_id" }; // should have the same size as FieldPaths !! -const vector datsetColumnHeaders = { "symbol", "formula", "class", "sourcetdb", "name" }; - -struct SubstanceData_::Impl -{ - ValuesTable valuesTable; - - Impl( ) - { - } - -}; - - -SubstanceData_::SubstanceData_( const TDataBase* adbconnect ) - : AbstractData( adbconnect, "VertexSubstance", substQuery, - substFieldPaths, datsetColumnHeaders, substDataNames), pimpl(new Impl()) -{ } - -SubstanceData_::SubstanceData_(const SubstanceData_& other) -: AbstractData(other), pimpl(new Impl(*other.pimpl)) -{ } - -auto SubstanceData_::operator=(SubstanceData_ other) -> SubstanceData_& -{ - pimpl = std::move(other.pimpl); - return *this; -} - -SubstanceData_::~SubstanceData_() -{ } - -const jsonio::ValuesTable& SubstanceData_::getValuesTable() -{ - return pimpl->valuesTable; -} - -auto SubstanceData_::queryInEdgesDefines(string idSubst, string level) -> vector -{ - return queryInEdgesDefines_(idSubst, level); -} - -auto SubstanceData_::definesReactionSymbol(string idSubst, string level) -> std::string -{ - return definesReactionSymbol_(idSubst, level); -} - -auto SubstanceData_::getSubstanceLevel(string substSymbol) const -> string -{ - return getSubstanceLevel_(substSymbol); -} - -auto SubstanceData_::setSubstanceLevel(string substSymbol, string level) -> void -{ - setSubstanceLevel_(substSymbol, level); -} - -set SubstanceData_::getElementsList( const string& idSubstance ) -{ - string formula; - // get record - string jsonrecord = getJsonRecordVertex(idSubstance); - auto domdata = jsonio::unpackJson( jsonrecord ); - - // Extract data from fields - domdata->findValue(getDataName_DataFieldPath().at("formula"), formula); - //bsonio::bson_to_key( record.data, getDataName_DataFieldPath()["formula"], formula); - - FormulaToken parser(formula); - return parser.getElements(); -} - - -void SubstanceData_::updateTableByElementsList( ValuesTable& substQueryMatr, const vector& elements ) -{ - if( !elements.empty() ) - { - ValuesTable substMatr; - for (const auto& subitem : substQueryMatr) - { - string formula = subitem[getDataName_DataIndex().at("formula")]; - if (testElementsFormula(formula, elements)) - substMatr.push_back(subitem); - } - substQueryMatr = move(substMatr); - } - } - -// return all record, no only fields if not default -ValuesTable SubstanceData_::loadRecordsValues( const DBQueryData& aquery, - int sourcetdb, const vector& elements ) -{ - auto fields = getDataFieldPaths(); - - // get records by query - auto query = aquery; - if (query.empty()) - { - query = getQuery(); - // only here we have subset fields to extract - query.setQueryFields(makeQueryFields()); - fields = getDataNames(); - } - //if (!elements.empty()) - addFieldsToQueryAQL( query, { make_pair( string(getDataName_DataFieldPath().at("sourcetdb")), sourceTDB_from_index(sourcetdb)) } ); - - ValuesTable substQueryMatr = getDB()->downloadDocuments(query, fields); - - // get record by elements list - updateTableByElementsList( substQueryMatr, elements ); - setDefaultLevelForReactionDefinedSubst(substQueryMatr); - pimpl->valuesTable = substQueryMatr; - return substQueryMatr; -} - -ValuesTable SubstanceData_::loadRecordsValues( const string& idReactionSet ) -{ - string qrAQL = "FOR u,e IN 1..1 INBOUND '"; - qrAQL += idReactionSet + "' \n product, master "; - // qrAQL += "RETURN u"; - DBQueryData query( qrAQL, DBQueryData::qAQL ); - query.setQueryFields(makeQueryFields()); - ValuesTable substMatr = getDB()->downloadDocuments( query, getDataNames()); - setDefaultLevelForReactionDefinedSubst(substMatr); - pimpl->valuesTable = substMatr; - return substMatr; -} - -auto SubstanceData_::querySolvents(int sourcetdb) -> vector> -{ - string aqlStr = "FOR u IN substances\n FILTER u.properties.class_ == {'3' : 'SC_AQSOLVENT'} && u.properties.sourcetdb == "; - aqlStr += sourceTDB_from_index(sourcetdb) + " "; - auto qrJson = DBQueryData( aqlStr, DBQueryData::qAQL ); - qrJson.setQueryFields(makeQueryFields()); - - ValuesTable solventMatr = getDB()->downloadDocuments(qrJson, getDataNames() ); - return solventMatr; -} - -auto SubstanceData_::nextValueForDefinesLevel (string idSubst) const -> string -{ - // maybe use query edge defines memoized? - string level = "0"; ValuesTable levelQueryMatr; - vector levels; - - auto queryJson = getDB_edgeAccessMode()->inEdgesQuery( "defines", idSubst); - queryJson.setQueryFields( {{ "level", "properties.level" }} ); - levelQueryMatr = getDB_edgeAccessMode()->downloadDocuments( queryJson, {"level"} ); - for (std::size_t i = 0; i < levelQueryMatr.size(); i++) - { - levels.push_back(std::stoi(levelQueryMatr[i][0])); - } - if (levels.size() > 0) - level = std::to_string((*std::max_element(levels.begin(), levels.end())+1)); - return level; -} - -MapSubstSymbol_MapLevel_IdReaction SubstanceData_::recordsMapLevelDefinesReaction( ) -{ - string level, idreact, idsub; - MapSubstSymbol_MapLevel_IdReaction recordsLevelReact; - for (auto value : pimpl->valuesTable) - { - MapLevel_IdReaction levelReact; - idsub = value[getDataName_DataIndex().at("_id")]; - string qrJson = "FOR v,e IN 1..1 INBOUND '"; - qrJson += idsub + "' \n defines\n"; - qrJson += "RETURN { 'level': e.properties.level, 'reaction': v._id }"; - - vector resultsQuery = getDB()->runQuery( DBQueryData( qrJson, DBQueryData::qAQL ) ); - - for( auto result: resultsQuery ) - { - auto domdata = jsonio::unpackJson( result ); - domdata->findValue("level", level); - domdata->findValue("reaction", idreact); - levelReact[level] = idreact; - } -// if (!levelReact.empty()) - recordsLevelReact[value[getDataName_DataIndex().at("symbol")]] = levelReact; - } - return recordsLevelReact; -} - - -MapSubstSymbol_MapLevel_IdReaction SubstanceData_::recordsMapLevelDefinesReaction(vector connectedSubstIds, vector connectedSubstSymbols ) -{ - string level, idreact, idsub; - MapSubstSymbol_MapLevel_IdReaction recordsLevelReact; - - for (std::size_t i = 0; i < connectedSubstIds.size(); i++) - { - MapLevel_IdReaction levelReact; - idsub = connectedSubstIds[i]; - string qrJson = "FOR v,e IN 1..1 INBOUND '"; - qrJson += idsub + "' \n defines\n"; - qrJson += "RETURN { 'level': e.properties.level, 'reaction': v._id }"; - - vector resultsQuery = getDB()->runQuery( DBQueryData( qrJson, DBQueryData::qAQL ) ); - - for( auto result: resultsQuery ) - { - auto domdata = jsonio::unpackJson( result ); - domdata->findValue("level", level); - domdata->findValue("reaction", idreact); - levelReact[level] = idreact; - } -// if (!levelReact.empty()) - recordsLevelReact[connectedSubstSymbols[i]] = levelReact; - } - return recordsLevelReact; -} - -vector SubstanceData_::selectGiven( const vector& sourcetdbs, - const vector& elements, bool unique ) -{ - // define query string - string AQLreq = "FOR u IN substances \n" - " FILTER u.properties.sourcetdb IN @sourcetdbs\n" - " SORT u.properties.symbol "; - - // generate bind values - shared_ptr domdata(JsonDomFree::newObject()); - auto arr = domdata->appendArray( "sourcetdbs"); - sourceTDB_from_indexes( sourcetdbs, arr ); - // make query - DBQueryData query( AQLreq, DBQueryData::qAQL ); - query.setBindVars( domdata.get() ); - query.setQueryFields( makeQueryFields() ); - - ValuesTable substQueryMatr = getDB()->downloadDocuments(query, getDataNames()); - - // delete not unique - if( unique ) - deleteNotUnique( substQueryMatr, getDataName_DataIndex().at("symbol")); - - updateTableByElementsList( substQueryMatr, elements ); - - vector substanceSymbols; - for (const auto& subitem : substQueryMatr) - substanceSymbols.push_back(subitem[getDataName_DataIndex().at("symbol")]); - - setDefaultLevelForReactionDefinedSubst(substQueryMatr); - pimpl->valuesTable = move(substQueryMatr); - return substanceSymbols; -} - -vector SubstanceData_::selectGiven( const vector& idThermoDataSets, bool unique ) -{ - string qrAQL = "FOR vertex IN " + vectorToJson( idThermoDataSets); - qrAQL += "\n FOR v,e IN 1..5 INBOUND vertex \n"; - qrAQL += ThermoDataSetQueryEdges; - qrAQL += "\n FILTER v._label == 'substance' "; - qrAQL += "\n SORT v.properties.symbol "; - qrAQL += DBQueryData::generateReturn( true, makeQueryFields(), "v"); - DBQueryData query( qrAQL, DBQueryData::qAQL ); - ValuesTable resMatr = getDB()->downloadDocuments( query, getDataNames()); - - if( unique ) - deleteNotUnique( resMatr, getDataName_DataIndex().at("symbol") ); - - vector substanceSymbols; - for (const auto& subitem : resMatr) - substanceSymbols.push_back(subitem[getDataName_DataIndex().at("symbol")]); - - setDefaultLevelForReactionDefinedSubst(resMatr); - pimpl->valuesTable = move(resMatr); - return substanceSymbols; -} - -vector SubstanceData_::selectGiven( const string& idThermoDataSet, - const vector& elements, bool unique ) -{ - string qrAQL = "FOR v,e IN 1..5 INBOUND '" + idThermoDataSet + "' \n"; - qrAQL += ThermoDataSetQueryEdges; - qrAQL += "\n FILTER v._label == 'substance' "; - qrAQL += "\n SORT v.properties.symbol "; - qrAQL += DBQueryData::generateReturn( true, makeQueryFields(), "v"); - //cout << "qrAQL: " << qrAQL << endl; - DBQueryData query( qrAQL, DBQueryData::qAQL ); - ValuesTable resMatr = getDB()->downloadDocuments( query, getDataNames()); - - if( unique ) - deleteNotUnique( resMatr, getDataName_DataIndex().at("symbol") ); - - updateTableByElementsList( resMatr, elements ); - - vector substanceSymbols; - for (const auto& subitem : resMatr) - substanceSymbols.push_back(subitem[getDataName_DataIndex().at("symbol")]); - - setDefaultLevelForReactionDefinedSubst(resMatr); - pimpl->valuesTable = move(resMatr); - return substanceSymbols; -} - - -} diff --git a/ThermoHubClient/SubstanceData.h b/ThermoHubClient/SubstanceData.h deleted file mode 100644 index e0f51d9a..00000000 --- a/ThermoHubClient/SubstanceData.h +++ /dev/null @@ -1,120 +0,0 @@ -#ifndef SUBSTANCEDATA_H -#define SUBSTANCEDATA_H - -// C++ includes -#include -#include "AbstractData.h" - -namespace ThermoFun { - -//struct ThermoDataAbstract; -using MapLevel_IdReaction = std::map; -using MapSubstSymbol_MapLevel_IdReaction = std::map; - -class SubstanceData_ : public AbstractData -{ -public: - - SubstanceData_( const jsonio::TDataBase* dbconnect ); - - /// Construct a copy of an SubstanceData instance - SubstanceData_(const SubstanceData_& other); - - auto operator=(SubstanceData_ other) -> SubstanceData_&; - - virtual ~SubstanceData_(); - - /// Extract data connected to ReactionSet - virtual jsonio::ValuesTable loadRecordsValues( const std::string& idReactionSet ); - /// Extract data by condition - virtual jsonio::ValuesTable loadRecordsValues( const jsonio::DBQueryData& query, int sourcetdb, - const std::vector& elements = {} ); - /// Extract data connected to ThermoDataSet - virtual std::vector selectGiven( const std::vector& idThermoDataSets, bool unique = true ); - std::vector selectGiven( const std::vector& sourcetdbs, const std::vector& elements, bool unique = true ); - std::vector selectGiven( const std::string& idThermoDataSet, - const std::vector& elements, bool unique = true ); - /// Get Elements list from reaction record - virtual std::set getElementsList( const std::string& idSubstance ); - - /// Link to table of fields values loaded before - const jsonio::ValuesTable& getValuesTable(); - - /** - * @brief queryIncomingEdgesDefines query the ids of incoming edges of type defines - * @param idSubst substance id - * @param level level of the edge - * @return list of ids - */ - auto queryInEdgesDefines(std::string idSubst, std::string level) -> std::vector; - - /** - * @brief definesReactionSymbol returns the reaction symbol which defines a substance - * @param idSubst substance id - * @param level edge defines level - * @return reaction symbol - */ - auto definesReactionSymbol(std::string idSubst, std::string level) -> std::string; - - /** - * @brief querySolvents returns the solvents data - * @param sourcetdb - * @return solvents data determind by the dataFieldPaths of the object - * { "properties.symbol","properties.name","properties.formula","_id", "properties.class_", "properties.sourcetdb"}; - */ - auto querySolvents(int sourcetdb) -> std::vector>; - - /** - * @brief getSubstanceLevel returns the level which is set for the substance - * @param substSymbol substance symbol - * @return level value - */ - auto getSubstanceLevel(std::string substSymbol) const -> std::string; - - /** - * @brief setSubstanceLevel - * @param substSymbol - * @param level value - */ - auto setSubstanceLevel(std::string substSymbol, std::string level) -> void; - - /** - * @brief nextValueForDefinesLevel looks through the database for all eges defines incoming towards the substance - * and returns the maximum level+1, found for the defines edges - * @param idSubst substance id - * @return level value - */ - auto nextValueForDefinesLevel (std::string idSubst) const -> std::string; - - /** - * @brief recordsMapLevelDefinesReaction returns the map of substances and map of levels and id reactions - * e.g. CaCO3@ can be defined on level one by the aragonite solubility reaction and on level 2 by the - * calcite solubility reaction - * @return - */ - MapSubstSymbol_MapLevel_IdReaction recordsMapLevelDefinesReaction( ); - - /** - * @brief recordsMapLevelDefinesReaction returns the map of substances and map of levels and id reactions, for a given - * list of substances - * e.g. CaCO3@ can be defined on level one by the aragonite solubility reaction and on level 2 by the - * calcite solubility reaction - * @param connectedSubstIds list of substances ids - * @param connectedSubstSymbols list of substances symbols - * @return - */ - MapSubstSymbol_MapLevel_IdReaction recordsMapLevelDefinesReaction(std::vector connectedSubstIds, std::vector connectedSubstSymbols ); - - - -private: - struct Impl; - std::shared_ptr pimpl; - void updateTableByElementsList( jsonio::ValuesTable& substQueryMatr, const std::vector& elements ); -}; - -} - - - -#endif // SUBSTANCEDATA_H diff --git a/ThermoHubClient/ThermoHubClient.pri b/ThermoHubClient/ThermoHubClient.pri deleted file mode 100644 index 0e9ef94a..00000000 --- a/ThermoHubClient/ThermoHubClient.pri +++ /dev/null @@ -1,22 +0,0 @@ -HEADERS += $$PWD/SubstanceData.h \ - $$PWD/AQLqueries.h \ - $$PWD/DatabaseClient.h \ - $$PWD/ReactionData.h \ - $$PWD/TraversalData.h \ - $$PWD/ElementData.h \ - $$PWD/AbstractData.h \ - $$PWD/ThermoSetData.h \ - $$PWD/ReactionSetData.h \ - $$PWD/sourcetdb.h \ - $$PWD/ParseDbcToData.h - -SOURCES += $$PWD/AbstractData.cpp \ - $$PWD/SubstanceData.cpp \ - $$PWD/ReactionData.cpp \ - $$PWD/ReactionSetData.cpp \ - $$PWD/TraversalData.cpp \ - $$PWD/DatabaseClient.cpp \ - $$PWD/ThermoSetData.cpp \ - $$PWD/sourcetdb.cpp \ - $$PWD/ElementData.cpp \ - $$PWD/ParseDbcToData.cpp diff --git a/ThermoHubClient/ThermoSetData.cpp b/ThermoHubClient/ThermoSetData.cpp deleted file mode 100644 index b2bf9722..00000000 --- a/ThermoHubClient/ThermoSetData.cpp +++ /dev/null @@ -1,207 +0,0 @@ -#include "ThermoSetData.h" -#include "ElementData.h" -#include "jsonio/jsondomfree.h" -#include - -using namespace std; -using namespace jsonio; - -namespace ThermoFun { - -//const DBQueryData datsetQuery( "{\"_label\": \"thermodataset\" }", DBQueryData::qTemplate ); -const DBQueryData datsetQuery("FOR u IN thermodatasets ", DBQueryData::qAQL); -const vector datsetFieldPaths = {"properties.symbol", "properties.name", "properties.stype","_id"}; -const vector datsetDataNames = {"symbol", "name", "stype", "_id"}; // should have the same size as FieldPaths !! -const vector datsetColumnHeaders = {"symbol", "name", "stype"}; - -struct ThermoSetData::Impl -{ - ValuesTable valuesTable; - - Impl( ) - { - } - -}; - -ThermoSetData::ThermoSetData( const TDataBase* adbconnect ) - : AbstractData( adbconnect, "VertexThermoDataSet", datsetQuery, - datsetFieldPaths, datsetColumnHeaders, datsetDataNames), pimpl(new Impl()) -{ } - -ThermoSetData::ThermoSetData(const ThermoSetData& other) -: AbstractData(other), pimpl(new Impl(*other.pimpl)) -{} - -auto ThermoSetData::operator=(ThermoSetData other) -> ThermoSetData& -{ - pimpl = std::move(other.pimpl); - return *this; -} - -ThermoSetData::~ThermoSetData() -{} - -const jsonio::ValuesTable& ThermoSetData::getValuesTable() -{ - return pimpl->valuesTable; -} - -set ThermoSetData::getElementsList( const string& idthermo ) -{ - set elements; - string jsonrecord = getJsonRecordVertex(idthermo); - auto domdata = jsonio::unpackJson( jsonrecord ); - - // query elements - vector jElements; - string qrAQL = "FOR v,e IN 1..1 INBOUND '" + idthermo + "' \n"; - qrAQL += "basis"; - qrAQL += "\n FILTER v._label == 'element' "; - qrAQL += "\nRETURN DISTINCT v"; - - jElements = getDB()->runQuery( DBQueryData( qrAQL, DBQueryData::qAQL ) ); - - ElementKey elem("",0,0); - for (auto jel : jElements) - { - auto node = jsonio::unpackJson(jel); - elem = fromElementNode( node->field("properties")); - elements.insert(elem); - } - //ElementsFromJsonDomArray("properties.elements", domdata.get(), elements); - - // if user fogot tnsert elements property - if( elements.empty() ) - { - vector formulalst = getSubstanceFormulas( idthermo ); - elements = ThermoFun::ChemicalFormula::extractElements(formulalst ); - } - return elements; -} - -vector ThermoSetData::getSubstanceFormulas( const string& idthermo ) -{ - string qrAQL = "FOR v,e IN 1..5 INBOUND '" + idthermo + "' \n"; - qrAQL += ThermoDataSetQueryEdges; - qrAQL += "\n FILTER v._label == 'substance' "; - qrAQL += "\nRETURN DISTINCT v.properties.formula"; - - vector formulas = getDB()->runQuery( DBQueryData( qrAQL, DBQueryData::qAQL ) ); - return formulas; -} - -ValuesTable ThermoSetData::loadRecordsValues( const DBQueryData& aquery, - int sourcetdb, const vector& elements ) -{ - auto fields = getDataFieldPaths(); - - // get records by query - auto query = aquery; - if (query.empty()) - { - query = getQuery(); - // only here we have subset fields to extract - query.setQueryFields(makeQueryFields()); - fields = getDataNames(); - } - //?? if (!elements.empty()) - //?? addFieldsToQueryAQL( query, { make_pair( string(getDataName_DataFieldPath()["sourcetdb"]), to_string(sourcetdb)) } ); - - ValuesTable substQueryMatr = getDB()->downloadDocuments(query, fields); - - // get record by elements list - //updateTableByElementsList( substQueryMatr, elements ); - pimpl->valuesTable = substQueryMatr; - return substQueryMatr; -} - -ValuesTable ThermoSetData::loadRecordsValues( const string& idReactionSet ) -{ - ValuesTable substQueryMatr; - return substQueryMatr; -} - -auto ThermoSetData::idRecordFromSymbol (const string &symbol) -> string -{ - string qrJson = "FOR u IN thermodatasets "; - qrJson += "FILTER u.properties.symbol == \""+symbol+"\" "; - qrJson += "RETURN u._id"; - - vector ids = getDB()->runQuery( DBQueryData( qrJson, DBQueryData::qAQL ) ); - for (auto &i:ids) - while (std::find(i.begin(), i.end(), '"') != i.end()) - i.erase(std::find(i.begin(), i.end(), '"')); - if ( ids.size() == 1) - return ids[0]; - else return ""; -} - -vector ThermoSetData::selectGiven( const vector& idThermoDataSets, bool ) -{ - auto resMatr = getDB()->downloadDocuments(idThermoDataSets, getDataFieldPaths()); - - vector thermoSymbols; - for (const auto& subitem : resMatr) - thermoSymbols.push_back(subitem[getDataName_DataIndex().at("symbol")]); - - pimpl->valuesTable = move(resMatr); - return thermoSymbols; -} - - -// Visit all linked Vertexes -void ThermoSetData::traverceVertexes( const string& idThermoDataSet, jsonio::GraphElementFunction afunc ) -{ - string qrAQL = "FOR v,e IN 1..5 INBOUND '" + idThermoDataSet + "' \n"; - qrAQL += ThermoDataSetQueryEdges; - qrAQL += "\n SORT v._label "; - qrAQL += " \n RETURN DISTINCT v"; - - DBQueryData query( qrAQL, DBQueryData::qAQL ); - vector resultsQuery = getDB()->runQuery( query ); - - for( auto result: resultsQuery ) - afunc( true, result ); -} - -// Visit all linked Edges -void ThermoSetData::traverceEdges( const string& idThermoDataSet, jsonio::GraphElementFunction afunc ) -{ - string qrAQL = "FOR v,e IN 1..5 INBOUND '" + idThermoDataSet + "' \n"; - qrAQL += ThermoDataSetQueryEdges; - qrAQL += "\n SORT e._label "; - qrAQL += " \n RETURN DISTINCT e"; - - DBQueryData query( qrAQL, DBQueryData::qAQL ); - vector resultsQuery = getDB()->runQuery( query ); - - for( auto result: resultsQuery ) - afunc( false, result ); -} - -std::vector ThermoSetData::sourceTDBs(const string &idThermoDataSet) const -{ - std::vector srcs; - string qrAQL = "FOR u IN thermodatasets "; - qrAQL += "\nFILTER u._id == \""+idThermoDataSet+"\" ";; - qrAQL += "\nRETURN u.properties.sourcetdbs"; - - DBQueryData query( qrAQL, DBQueryData::qAQL ); - vector resultsQuery = getDB()->runQuery( query ); - - if( resultsQuery.size() > 0) - { - //cout << resultsQuery[0] << endl; - auto domdata = jsonio::unpackJson( resultsQuery[0] ); - std::map newmap; - domdata->findObject( "", newmap ); - for( auto row: newmap ) - srcs.push_back( stoi(row.first) ); - } - return srcs; -} - - - -} diff --git a/ThermoHubClient/ThermoSetData.h b/ThermoHubClient/ThermoSetData.h deleted file mode 100644 index ddb580d3..00000000 --- a/ThermoHubClient/ThermoSetData.h +++ /dev/null @@ -1,59 +0,0 @@ -#ifndef THERMOSETDATA_H -#define THERMOSETDATA_H - -#include "AbstractData.h" -#include "jsonio/traversal.h" - -namespace ThermoFun { - -class ThermoSetData : public AbstractData -{ -public: - - ThermoSetData( const jsonio::TDataBase* dbconnect ); - - /// Construct a copy of an SubstanceData instance - ThermoSetData(const ThermoSetData& other); - - auto operator=(ThermoSetData other) -> ThermoSetData&; - - virtual ~ThermoSetData(); - - /// Extract data connected to ReactionSet - virtual jsonio::ValuesTable loadRecordsValues( const std::string& idReactionSet ); - /// Extract data by condition - virtual jsonio::ValuesTable loadRecordsValues( const jsonio::DBQueryData& query, int sourcetdb, - const std::vector& elements = {} ); - /// Extract data connected to ThermoDataSet - virtual std::vector selectGiven( const std::vector& idThermoDataSets, bool unique = true ); - - /// Get Elements list from reaction record - virtual std::set getElementsList( const std::string& idThermoDataSet); - - /// Link to table of fields values loaded before - const jsonio::ValuesTable& getValuesTable(); - - /// Return all formulas from all connected substances - std::vector getSubstanceFormulas( const std::string& idThermoDataSet ); - - - auto idRecordFromSymbol (const std::string &symbol) -> std::string; - - /// Visit all linked Vertexes - void traverceVertexes( const std::string& idThermoDataSet, jsonio::GraphElementFunction afunc ); - /// Visit all linked Edges - void traverceEdges( const std::string& idThermoDataSet, jsonio::GraphElementFunction afunc ); - - /// Get all sourceTDBs from record - std::vector sourceTDBs(const std::string& idThermoDataSet) const; - -private: - - struct Impl; - std::shared_ptr pimpl; -}; - - -} - -#endif // THERMOSETDATA_H diff --git a/ThermoHubClient/TraversalData.cpp b/ThermoHubClient/TraversalData.cpp deleted file mode 100644 index 6d2a7298..00000000 --- a/ThermoHubClient/TraversalData.cpp +++ /dev/null @@ -1,641 +0,0 @@ -#include "TraversalData.h" -#include "AQLqueries.h" - -// ThermoFun includes -#include "jsonio/jsondomfree.h" -#include "jsonio/jsondomschema.h" -#include "SubstanceData.h" -#include "ReactionData.h" -#include "Database.h" -#include "Substance.h" -#include "Reaction.h" -//#include "Common/ParseBsonTraversalData.h" -#include "Common/Exception.h" -#include "OptimizationUtils.h" -#include "Common/ParseJsonToData.h" - -#include - -#include // for high_resolution_clock -#include "nlohmann/json.hpp" - -using namespace jsonio; -using json = nlohmann::json; - -namespace ThermoFun -{ - -//const std::vector queryFieldsVertex = {"_id", "_label", "_type", "properties.symbol"}; -//const std::vector queryFieldsEdgeDefines = { "_from", "_label"}; -//const std::vector queryFieldsEdgeTakes = { "_from", "_label", "properties.stoi_coeff" }; - -using GetlinkedDataFromId = std::function; -using GetlinkedDataFromIds = std::function)>; - -template -bool isEqual(std::vector const &v1, std::vector const &v2) -{ - return (v1.size() == v2.size() && - std::equal(v1.begin(), v1.end(), v2.begin())); -} - -enum DefinesLevelMode { - all= 0, - single, - multiple -}; - -struct TraversalData::Impl -{ - /// map of substance symbol and level for the edge defines connected to the substance - std::map substSymbol_definesLevel; - - /// current level for the traversal operation - std::string level = "0"; - - /// mode of using levels for traversal (all: collect all connected; single: collect all connected using one - /// defines level for all substances; multiple: collect all connectec using different levels for different - /// substances (from map substSymbol_definesLevel) - DefinesLevelMode definesLevelMode = DefinesLevelMode::single; - - /// map of database ids and bson record of vertexes -// std::map idBsonRec; - - /// pointer to substance data for access to substance records - SubstanceData_ *substData; - - /// pointer to reaction data for access to reaction records - ReactionData_ *reactData; - - GetlinkedDataFromId get_linked_data_from_id_fn; - GetlinkedDataFromIds get_linked_data_from_ids_fn; - - Impl(SubstanceData_ *asubstData, ReactionData_ *areactData ): - substData( asubstData ), reactData( areactData ) - { - get_linked_data_from_id_fn = [=](string idRecord) { - return getlinkedDataFromId(idRecord); - }; - - get_linked_data_from_id_fn = memoize(get_linked_data_from_id_fn); - - get_linked_data_from_ids_fn = [=](vector idList) { - return getLinkedDataFromIds(idList); - }; - - get_linked_data_from_ids_fn = memoize(get_linked_data_from_ids_fn); - } - - auto getDefinesLevel (std::string jsonrecord) -> std::string - { - std::string level_; - - switch(definesLevelMode) - { - case DefinesLevelMode::all : level_ = "-1"; // follows all connected data - break; - case DefinesLevelMode::single : level_ = level;; // follows edges defines with level - break; - case DefinesLevelMode::multiple : { - std::string substSymb; -// std::string key = idSubst; - -// string jsonrecord = substData->getJsonRecordVertex(key); - auto domdata = jsonio::unpackJson( jsonrecord ); - domdata->findValue("properties.symbol", substSymb); - - //record = pimpl->substData->getJsonBsonRecordVertex(key).second; - //bsonio::bson_to_key( record.data, "properties.symbol", substSymb ); - if (substSymbol_definesLevel.find(substSymb) != substSymbol_definesLevel.end()) // follows edges defines with specific leveles for substSymbols - level_ = substSymbol_definesLevel[substSymb]; // if the substance symbol is not found in the map, it uses the default level - else - level_ = level; - } - break; - } - - return level_; - } - - auto getlinkedDataFromId(std::string id_) -> VertexId_VertexType - { - string _idRecord, _label, /*_type, _symbol,*/ level_; - VertexId_VertexType result; - - string jsonrecord = substData->getJsonRecordVertex(id_); - auto domdata = jsonio::unpackJson( jsonrecord ); - domdata->findValue("_id", _idRecord); - domdata->findValue("_label", _label); - - // if not in the database proceed - if (!result.count(_idRecord)) - { - if (_label == "substance") - { - // get level mode - level_ = getDefinesLevel(jsonrecord); - result.insert(std::pair(_idRecord, "substance")); - followIncomingEdgeDefines(_idRecord, result, level_); - } - if (_label == "reaction") - { - result.insert(std::pair(_idRecord, "reaction")); - followIncomingEdgeTakes(_idRecord, result); - } - } - return result; - } - - void followIncomingEdgeDefines(std::string _idSubst, VertexId_VertexType &result, string level_) - { - string _idReact = ""; - string _resultDataReac; - vector _resultDataEdge = substData->queryInEdgesDefines(_idSubst, level_ ); - - //std::cout << "incoming defines: "<< _idSubst << endl; - - for(std::size_t i = 0; i < _resultDataEdge.size(); i++) - { - _idReact = _resultDataEdge[i]; - _resultDataReac = reactData->getJsonRecordVertex(_idReact); - - // if not in the database - if (!result.count(_idReact)) - { - result.insert((std::pair(_idReact, "reaction"))); - followIncomingEdgeTakes(_idReact, result); - } - } - } - - void followIncomingEdgeTakes(std::string _idReact, VertexId_VertexType &result) - { - string _idSubst = ""; string level_ = "0"; - string _resultDataSubst; - vector _resultDataEdge = reactData->queryInEdgesTakes(_idReact ); - - //std::cout << "incoming takes: "<< _idReact << endl; - - for(std::size_t i = 0; i < _resultDataEdge.size(); i++) - { - _idSubst = extractStringField("_from", _resultDataEdge[i]); - _resultDataSubst = substData->getJsonRecordVertex(_idSubst); - - // if not in the database - if (!result.count(_idSubst)) - { - level_ = getDefinesLevel(_resultDataSubst); - result.insert((std::pair(_idSubst, "substance"))); - followIncomingEdgeDefines(_idSubst, result, level_); - } - } - } - - auto queryIdLabel(vector idList, string AQLreq, string bindValues) -> ValuesTable - { - shared_ptr domdata(JsonDomFree::newObject()); - auto arr = domdata->appendArray(bindValues); - - jsonio::JsonDom *object; - - for(std::size_t ii=0; iiappendValue(std::to_string(ii), idList[ii]); - } - - // make query - DBQueryData query( AQLreq, DBQueryData::qAQL ); - query.setBindVars( domdata.get() ); - jsonio::QueryFields qfields; - qfields["_id"] = "_id"; - qfields["_label"] = "_label"; - query.setQueryFields(qfields); - return substData->getDB()->downloadDocuments(query, {"_id", "_label"}); - } - - auto querySubstancesReactionIds(vector idList, string AQLreq, string bindValues) -> ValuesTable - { - shared_ptr domdata(JsonDomFree::newObject()); - auto arr = domdata->appendArray(bindValues); - - jsonio::JsonDom *object; - - for(std::size_t ii=0; iiappendValue(std::to_string(ii), idList[ii]); - } - - // make query - DBQueryData query( AQLreq, DBQueryData::qAQL ); - query.setBindVars( domdata.get() ); - jsonio::QueryFields qfields; - qfields["substances"] = "substances"; - qfields["reactions"] = "reactions"; - qfields["ids"]="ids"; - query.setQueryFields(qfields); - return substData->getDB()->downloadDocuments(query, {"substances", "reactions", "ids"}); - } - - auto getLinkedDefines(vector idList) -> ValuesTable - { - string AQLreq = "FOR r IN @records \n" - " FOR v IN 1..1 INBOUND r defines \n" - " RETURN {_id : v._id, _label : v._label}"; - - return queryIdLabel(idList, AQLreq, "records"); - } - - auto getLinkedTakes(vector idList) -> ValuesTable - { - string AQLreq = "FOR r IN @records \n" - " FOR v IN 1..1 INBOUND r takes \n" - " RETURN {_id : v._id, _label : v._label}"; - - return queryIdLabel(idList, AQLreq, "records"); - } - - auto getIdListData(vector idList) -> ValuesTable - { - string AQLreq = "FOR r IN substances OR reactions \n" - " FILTER r._id IN @records \n" - " RETURN {_id : r._id, _label : r._label}"; - - return queryIdLabel(idList, AQLreq, "records"); - } - - auto getLinkedDataFromIds(vector idList) -> VertexId_VertexType - { - VertexId_VertexType result; - ValuesTable queryMatr; - std::vector::iterator it; - auto s = idList.size(); - - queryMatr = getIdListData(idList); - for (auto q : queryMatr) - { - result[q[0]] = q[1]; - } - - do { - s = idList.size(); - queryMatr = getLinkedDefines(idList); - - for (auto q : queryMatr) - { - result[q[0]] = q[1]; - it = std::find (idList.begin(), idList.end(), q[0]); - if (it == idList.end()) - idList.push_back(q[0]); - } - - queryMatr = getLinkedTakes(idList); - - for (auto q : queryMatr) - { - result[q[0]] = q[1]; - it = std::find (idList.begin(), idList.end(), q[0]); - if (it == idList.end()) - idList.push_back(q[0]); - } - - } while( idList.size() != s ); - - return result; - } - - auto getConnectedData(vector idList) -> ValuesTable - { - ValuesTable queryMatr; - auto s = idList.size(); - - std::vector::iterator itl; - - do { - s = idList.size(); - queryMatr = querySubstancesReactionIds(idList, aql_fun_substances_reactions_ids, "ids"); - json jarr = json::parse(queryMatr[0][2]); - - if (s != jarr.size()) - for (auto it = jarr.begin(); it != jarr.end(); ++it) - { - itl = std::find (idList.begin(), idList.end(), it.value().get()); - if (itl == idList.end()) - idList.push_back(it.value().get()); - } - } while( idList.size() != s ); - - return queryMatr; - } - - auto getResult(vector idList, vector selNdx ={}) -> VertexId_VertexType - { - VertexId_VertexType result, result2, r; - // Record start time - auto start = std::chrono::high_resolution_clock::now(); - -// if (selNdx.size() == 0) -// { -// for (std::size_t ii=0; ii0) - result = get_linked_data_from_ids_fn(idList); - - // Record end time - auto finish = std::chrono::high_resolution_clock::now(); - std::chrono::duration elapsed = finish - start; - - cout << "finished getresult, in: " << elapsed.count() << endl; - - auto start2 = std::chrono::high_resolution_clock::now(); - - auto data = getConnectedData(idList); - - // Record end time - auto finish2 = std::chrono::high_resolution_clock::now(); - std::chrono::duration elapsed2 = finish2 - start2; - cout << "finished getConnectedData, in: " << elapsed2.count() << endl; - - auto start3 = std::chrono::high_resolution_clock::now(); - - json jSubstances = json::parse(data[0][0]); - json jReactions = json::parse(data[0][1]); - Database tdb; - // The set of all aqueous species in the database - SubstancesMap substances_map; - // The set of all gaseous species in the database - ReactionsMap reactions_map; - - for (auto it = jSubstances.begin(); it != jSubstances.end(); ++it) - { - Substance substance = parseSubstance(it.value().dump()); - json jSubst = it.value(); - if (jSubst.contains("reaction")) - { - substance.setReactionSymbol(jSubst["reaction"]); - substance.setThermoCalculationType(ThermoFun::SubstanceThermoCalculationType::type::REACDC); - } - if ( substances_map.find(substance.symbol()) == substances_map.end() ) { - substances_map[substance.symbol()] = substance; - } else { - errorSameSymbol("substance", substance.symbol(), __LINE__, __FILE__ ); - } - } - - for (auto it = jReactions.begin(); it != jReactions.end(); ++it) - { - Reaction reaction = parseReaction(it.value().dump()); - - if ( reactions_map.find(reaction.symbol()) == reactions_map.end() ) { - reactions_map[reaction.symbol()] = reaction; - } else { - errorSameSymbol("reaction", reaction.symbol(), __LINE__, __FILE__ ); - } - } - - // Record end time - auto finish3 = std::chrono::high_resolution_clock::now(); - std::chrono::duration elapsed3 = finish3 - start3; - cout << "finished getDatabase, in: " << elapsed3.count() << endl; - - return result; - } - - auto getDatabase(const std::vector idList) -> Database - { - auto start2 = std::chrono::high_resolution_clock::now(); - - auto data = getConnectedData(idList); - - // Record end time - auto finish2 = std::chrono::high_resolution_clock::now(); - std::chrono::duration elapsed2 = finish2 - start2; - cout << "finished getConnectedData, in: " << elapsed2.count() << endl; - - auto start3 = std::chrono::high_resolution_clock::now(); - - json jSubstances = json::parse(data[0][0]); // [0] substances - json jReactions = json::parse(data[0][1]); // [1] reactions; [2] list of ids - Database tdb; - // The set of all aqueous species in the database - SubstancesMap substances_map; - // The set of all gaseous species in the database - ReactionsMap reactions_map; - - for (auto it = jSubstances.begin(); it != jSubstances.end(); ++it) - { - Substance substance = parseSubstance(it.value().dump()); - json jSubst = it.value(); - if (jSubst.contains("reaction")) - { - substance.setReactionSymbol(jSubst["reaction"]); - substance.setThermoCalculationType(ThermoFun::SubstanceThermoCalculationType::type::REACDC); - } - if ( substances_map.find(substance.symbol()) == substances_map.end() ) { - substances_map[substance.symbol()] = substance; - } else { - errorSameSymbol("substance", substance.symbol(), __LINE__, __FILE__ ); - } - } - - for (auto it = jReactions.begin(); it != jReactions.end(); ++it) - { - Reaction reaction = parseReaction(it.value().dump()); - - if ( reactions_map.find(reaction.symbol()) == reactions_map.end() ) { - reactions_map[reaction.symbol()] = reaction; - } else { - errorSameSymbol("reaction", reaction.symbol(), __LINE__, __FILE__ ); - } - } - - // Record end time - auto finish3 = std::chrono::high_resolution_clock::now(); - std::chrono::duration elapsed3 = finish3 - start3; - cout << "finished getDatabase, in: " << elapsed3.count() << endl; - - tdb.addMapReactions(reactions_map); - tdb.addMapSubstances(substances_map); - - return tdb; - } - - auto getDatabase(VertexId_VertexType resultTraversal) -> Database - { - string _idSubst, _idReact, substSymb; string level_ = level; - Database tdb; - auto result = resultTraversal; - // Record start time - auto start = std::chrono::high_resolution_clock::now(); - - // The set of all aqueous species in the database - SubstancesMap substances_map; - // The set of all gaseous species in the database - ReactionsMap reactions_map; - - // get substances and the reaction symbol if necessary - for(auto iterator = result.begin(); iterator != result.end(); iterator++) - { - if (iterator->second == "substance") - { - _idSubst = iterator->first; - - string jsonrecord = substData->getJsonRecordVertex(_idSubst); - auto domdata = jsonio::unpackJson( jsonrecord, "VertexSubstance" ); // with default values - domdata->findValue("properties.symbol", substSymb); - //record = pimpl->substData->getJsonBsonRecordVertex(_idSubst).second; - //bsonio::bson_to_key( record.data, "properties.symbol", substSymb ); - - level_ = getDefinesLevel(jsonrecord); - Substance substance = parseSubstance(jsonrecord); - - // get reaction symbol which define substance with _idSubst - string definesReactSymb = substData->definesReactionSymbol(_idSubst, level_); - if (definesReactSymb != "") - { - substance.setReactionSymbol(definesReactSymb); - substance.setThermoCalculationType(ThermoFun::SubstanceThermoCalculationType::type::REACDC); - } - - if ( substances_map.find(substance.symbol()) == substances_map.end() ) { - substances_map[substance.symbol()] = substance; - } else { - errorSameSymbol("substance", substance.symbol(), __LINE__, __FILE__ ); - } - } else - if (iterator->second == "reaction") - { - _idReact = iterator->first; - string jsonrecord = reactData->getJsonRecordVertex(_idReact); - auto domdata = jsonio::unpackJson( jsonrecord, "VertexReaction" ); // with default values - //record = pimpl->reactData->getJsonBsonRecordVertex(_idReact).second; - - Reaction reaction = ThermoFun::parseReaction(jsonrecord); - - // get reactants by following reaction incoming takes edge - reaction.setReactants(reactData->reactantsCoeff(_idReact)); - - if ( reactions_map.find(reaction.symbol()) == reactions_map.end() ) { - reactions_map[reaction.symbol()] = reaction; - } else { - errorSameSymbol("reaction", reaction.symbol(), __LINE__, __FILE__ ); - } - } - } - tdb.addMapReactions(reactions_map); - tdb.addMapSubstances(substances_map); - - // Record end time - auto finish = std::chrono::high_resolution_clock::now(); - std::chrono::duration elapsed = finish - start; - - cout << "finished database, in: " << elapsed.count() << endl; - return tdb; - } -}; - -TraversalData::TraversalData(SubstanceData_ *substData, ReactionData_ *reactData) : - pimpl(new Impl(substData, reactData )) -{ } - -auto TraversalData::operator=(TraversalData other) -> TraversalData& -{ - pimpl = std::move(other.pimpl); - return *this; -} - -//TraversalData::TraversalData(const TraversalData& other) -//: pimpl(new Impl(*other.pimpl)) -//{} - -TraversalData::~TraversalData() -{ } - -// Public -auto TraversalData::getMapOfConnectedIds(vector selNdx, vector idsList, string level_) -> VertexId_VertexType -{ - pimpl->level = level_; - pimpl->definesLevelMode = DefinesLevelMode::single; - - return pimpl->getResult(idsList, selNdx); -} - -auto TraversalData::getMapOfConnectedIds( vector idList, string level_) -> VertexId_VertexType -{ - pimpl->level = level_; - pimpl->definesLevelMode = DefinesLevelMode::single; - - return pimpl->getResult(idList); -} - -auto TraversalData::getMapOfConnectedIds(vector idList, std::map substSymbol_definesLevel) -> VertexId_VertexType -{ - pimpl->definesLevelMode = DefinesLevelMode::multiple; - - if (!substSymbol_definesLevel.empty()) - { - pimpl->substSymbol_definesLevel = substSymbol_definesLevel; - } else - { - pimpl->definesLevelMode = DefinesLevelMode::single; - } - return pimpl->getResult(idList);; -} - -auto TraversalData::getDatabaseFromMapOfIds(VertexId_VertexType resultTraversal, string level_) -> Database -{ - pimpl->level = level_; - pimpl->definesLevelMode = DefinesLevelMode::single; - return pimpl->getDatabase(resultTraversal); -} - -auto TraversalData::getDatabaseFromMapOfIds(VertexId_VertexType resultTraversal, std::map substSymbol_definesLevel) -> Database -{ - if (!substSymbol_definesLevel.empty()) - { - pimpl->definesLevelMode = DefinesLevelMode::multiple; - pimpl->substSymbol_definesLevel = substSymbol_definesLevel; - } else - { - pimpl->definesLevelMode = DefinesLevelMode::single; - } - return pimpl->getDatabase(resultTraversal); -} - -VertexId_VertexType TraversalData::getMapOfConnectedIds( vector idList ) -{ - pimpl->definesLevelMode = DefinesLevelMode::all; - return pimpl->getResult(idList); -} - -auto TraversalData::linkedDataIds(const std::vector aKeyList, std::vector &substIds, std::vector &reactIds) -> void -{ - reactIds.clear(); substIds.clear(); - for (auto idType : getMapOfConnectedIds(aKeyList)) - { - if (idType.second == "reaction") - reactIds.push_back((idType.first)); - if (idType.second == "substance") - substIds.push_back((idType.first)); - } -} - -auto TraversalData::getDatabase(const std::vector &idList) -> Database -{ - return pimpl->getDatabase(idList); -} - -// Private - -} diff --git a/ThermoHubClient/TraversalData.h b/ThermoHubClient/TraversalData.h deleted file mode 100644 index 6ea6e82a..00000000 --- a/ThermoHubClient/TraversalData.h +++ /dev/null @@ -1,120 +0,0 @@ -#ifndef GRAPHTRAVERSAL_H -#define GRAPHTRAVERSAL_H - -// C++ includes -#include -#include -#include -#include -#include - -namespace ThermoFun -{ - -class Database; -class SubstanceData_; -class ReactionData_; - -using VertexId_VertexType = std::map; -using VertexId_DefinesLevel = std::map>; - -class TraversalData -{ -public: - - TraversalData(SubstanceData_ *substData, ReactionData_ *reactData); - - auto operator=(TraversalData other) -> TraversalData&; - - virtual ~TraversalData(); - - /// - /// \brief getLinkedBsonFromSelectedData returns the linked data strting form the selected id list - /// \param selNdx Indexes of the selected ids from aKeyList - /// \param aKeyList List of ids - /// \param level of edge defines - /// \return a map of [id, vertex type] - /// - auto getMapOfConnectedIds(std::vector selNdx, std::vector idsList, std::string level_) -> VertexId_VertexType; - - /// - /// \brief getLinkedBsonFromIdList returns a map of vertex ids and vertex type which is linked to the idList, for a given level - /// \param idList list of ids - /// \param level of edge defines - /// \return a map of [vertex id, vertex type] - /// - auto getMapOfConnectedIds(std::vector idList, std::string level_) -> VertexId_VertexType; - - /** - * @brief getMapOfConnectedIds returns a map of vertex ids and vertex type which is linked to the idList, following the level specified for - * individual substances defined by a reaction - * @param idList list of vertex ids - * @param substSymbolLevel_ map of substance symbol and level - * @return a map of [vertex id, vertex type] - */ - auto getMapOfConnectedIds(std::vector idList, std::map substSymbol_definesLevel) -> VertexId_VertexType; - - /** - * @brief getMapOfConnectedIds returns a map of vertex ids and vertex type which is linked to the idList, for all levels - * @param idList list of vertex ids - * @return a map of [vertex id, vertex type] - */ - auto getMapOfConnectedIds(std::vector idList) -> VertexId_VertexType; - - /** - * @brief getDatabase returns a ThermoFun Database from a pre selected list of ids or hub record keys - * @param idList list of record keys - * @return ThermoFun::Database object - */ - auto getDatabase(const std::vector &idList) -> Database; - - /// - /// \brief getDatabaseFromTraversal returns a ThermoFun::Database object from a map of [vertex id, vertex type], for a given level - /// \param resultTraversal the map of [id, vertex type] resulted from traversal (all connected vertexes) - /// \param level of edge defines - /// \return ThermoFun::Database object - /// - auto getDatabaseFromMapOfIds(VertexId_VertexType resultTraversal, std::string level_) -> Database; - - /** - * @brief getDatabaseFromMapOfIds returns a ThermoFun::Database object from a map of [vertex id, vertex type], following the level specified for - * individual substances defined by a reaction - * @param resultTraversal the map of [id, vertex type] resulted from traversal (all connected vertexes) - * @param substSymbolLevel_ map of substance symbol and level - * @return ThermoFun::Database object - */ - auto getDatabaseFromMapOfIds(VertexId_VertexType resultTraversal, std::map substSymbol_definesLevel) -> Database; - - /** - * @brief linkedDataIds sets the list of substsnce and reactio ids which are connected to a given list of database record keys - * @param aKeyList record key list - * @param substIds the list of substance ids resulted from the search - * @param reactIds the list of reaction ids resulted from the search - */ - auto linkedDataIds(const std::vector aKeyList, std::vector &substIds, std::vector &reactIds) -> void; - -private: - -// // follows the incoming Defines edge for substance with _idSubst -// void followIncomingEdgeDefines(std::string idSubst, VertexId_VertexType &result, std::string level_); -// // follows the incoming Takes edges for reaction with _idReac -// void followIncomingEdgeTakes(std::string idReact, VertexId_VertexType &result); -// // fills the map MapIdType with all vertexes connected to the vertex with id_ -// auto linkedDataFromId(std::string id_) -> VertexId_VertexType; -// // returns the symbol of the reaction which defines the substance with _idSubst -// auto level (std::string idSubst) -> std::string; -// // returns a map of [id, vertex type] with all vertexes connected to the idList -// auto getResult(std::vector idList, std::vector selNdx = {}) -> VertexId_VertexType; -// // returns a ThermoFun::Database object from a map of [id, vertex type] resulted from traversal (all connected vertexes) -// auto getDatabase(VertexId_VertexType resultTraversal) -> Database; - - // auto getJsonRecord(string idRecord) -> string; - - struct Impl; - std::shared_ptr pimpl; -}; - - -} - -#endif // GRAPHTRAVERSAL_H diff --git a/ThermoHubClient/sourcetdb.cpp b/ThermoHubClient/sourcetdb.cpp deleted file mode 100644 index cd3919a8..00000000 --- a/ThermoHubClient/sourcetdb.cpp +++ /dev/null @@ -1,71 +0,0 @@ -#include "sourcetdb.h" - -using namespace jsonio; - -namespace ThermoFun -{ - -auto sourceTDB_from_indexes(std::vector ndx) -> std::vector -{ - std::vector sourcetdbs; - for (auto x : ndx) - sourcetdbs.push_back(sourceTDB_from_index(x)); - return sourcetdbs; -} - -auto sourceTDB_from_names(std::vector names) -> std::vector -{ - std::vector sourcetdbs; - for (auto n : names) - sourcetdbs.push_back(sourceTDB_from_name(n)); - return sourcetdbs; -} - -auto sourceTDB_from_indexes( std::vector ndx, jsonio::JsonDom *arr ) -> void -{ - ThriftEnumDef *enumdef = ioSettings().Schema()->getEnum("SourceTDB"); - jsonio::JsonDom *object; - - for(std::size_t ii=0; iiappendObject( std::to_string(ii) ); - object->appendString( std::to_string(ndx[ii]), enumdef->getNamebyId(ndx[ii]) ); - } -} - -auto sourceTDB_from_names(std::vector names, jsonio::JsonDom *arr ) -> void -{ - ThriftEnumDef *enumdef = ioSettings().Schema()->getEnum("SourceTDB"); - jsonio::JsonDom *object; - - for(std::size_t ii=0; iiappendObject( std::to_string(ii) ); - object->appendString( std::to_string(enumdef->getId(names[ii])), names[ii] ); - } -} - - -auto sourceTDB_from_index(int ndx) -> std::string -{ - std::string _sourcetdb = "{\""; - _sourcetdb += std::to_string(ndx); - _sourcetdb += "\":\""; - ThriftEnumDef *enumdef = ioSettings().Schema()->getEnum("SourceTDB"); - _sourcetdb += enumdef->getNamebyId(ndx); - _sourcetdb += "\"}"; - return _sourcetdb; -} - -auto sourceTDB_from_name(std::string name) -> std::string -{ - ThriftEnumDef *enumdef = ioSettings().Schema()->getEnum("SourceTDB"); - std::string _sourcetdb = "{\""; - int ndx = enumdef->getId(name); - _sourcetdb += std::to_string(ndx); - _sourcetdb += "\":\""; - _sourcetdb += name; - _sourcetdb += "\"}"; - return _sourcetdb; -} -} diff --git a/ThermoHubClient/sourcetdb.h b/ThermoHubClient/sourcetdb.h deleted file mode 100644 index 803ac8eb..00000000 --- a/ThermoHubClient/sourcetdb.h +++ /dev/null @@ -1,23 +0,0 @@ -#ifndef SOURCETDB_H -#define SOURCETDB_H - -#include "jsonio/io_settings.h" - -namespace ThermoFun -{ -auto sourceTDB_from_index(int ndx) -> std::string; - -auto sourceTDB_from_name(std::string name) -> std::string; - -auto sourceTDB_from_names(std::vector names) -> std::vector; - -auto sourceTDB_from_indexes(std::vector ndx) -> std::vector; - -auto sourceTDB_from_indexes( std::vector ndx, jsonio::JsonDom *arr ) -> void; - -auto sourceTDB_from_names(std::vector names, jsonio::JsonDom *arr ) -> void; - -} - - -#endif // SOURCETDB_H diff --git a/a-build-win-dependencies.bat b/a-build-win-dependencies.bat deleted file mode 100644 index 231e24aa..00000000 --- a/a-build-win-dependencies.bat +++ /dev/null @@ -1,253 +0,0 @@ -@echo off -setlocal EnableDelayedExpansion - -set PROGFILES=%ProgramFiles% -if not "%ProgramFiles(x86)%" == "" set PROGFILES=%ProgramFiles(x86)% - -REM Check if Visual Studio 2017 comunity is installed -set MSVCDIR="%PROGFILES%\Microsoft Visual Studio\2017\Community" -set VCVARSALLPATH="%PROGFILES%\Microsoft Visual Studio\2017\Community\VC\Auxiliary\Build\vcvarsall.bat" -if exist %MSVCDIR% ( - if exist %VCVARSALLPATH% ( - set COMPILER_VER="2017" - echo Using Visual Studio 2017 Community - goto setup_env - ) -) - -REM Check if Visual Studio 2019 comunity is installed -set MSVCDIR="%PROGFILES%\Microsoft Visual Studio\2019\Community" -set VCVARSALLPATH="%PROGFILES%\Microsoft Visual Studio\2019\Community\VC\Auxiliary\Build\vcvarsall.bat" -if exist %MSVCDIR% ( - if exist %VCVARSALLPATH% ( - set COMPILER_VER="2019" - echo Using Visual Studio 2019 Community - goto setup_env - ) -) - - -echo No compiler : Microsoft Visual Studio 2017 or 2019 Community is not installed. -goto end - -:setup_env - -:begin - -REM Setup path to helper bin -set ROOT_DIR="%CD%" -set FART="%CD%\bin\fart\fart.exe" -set RM="%CD%\bin\unxutils\rm.exe" -set CP="%CD%\bin\unxutils\cp.exe" -set MKDIR="%CD%\bin\unxutils\mkdir.exe" -set SEVEN_ZIP="%CD%\bin\7-zip\7za.exe" -set WGET="%CD%\bin\unxutils\wget.exe" -set XIDEL="%CD%\bin\xidel\xidel.exe" -set DEP_DIR="%ROOT_DIR%\..\dependencies" - -REM Housekeeping -del /F /S /Q tmp_* -%RM% -rf tmp_* -REM %RM% -rf dependencies -REM %RM% -rf curl.zip -%RM% -rf build_*.txt - -echo -echo ****** ****** -echo ****** Compiling Curl ****** -echo ****** ****** -echo - - -mkdir tmp_libcurl - -cd tmp_libcurl - -echo Get Curl from git... - -git clone https://github.com/curl/curl.git -cd curl* -git checkout tags/curl-7_62_0 - -cd src - -rename "tool_hugehelp.c.cvs" "tool_hugehelp.c" - -cd .. - -cd winbuild - -if %COMPILER_VER% == "2017" ( - set VCVERSION = 14.1 - goto buildnow -) - -:buildnow -REM Build! - -if [%1]==[-static] ( - set RTLIBCFG=static - echo Using /MT instead of /MD -) - -echo "%MSVCDIR%\VC\Auxiliary\Build\vcvarsall.bat" -REM call %MSVCDIR%\VC\Auxiliary\Build\vcvarsall.bat x86 -REM echo Compiling dll-debug-x86 version... -REM nmake /f Makefile.vc mode=dll VC=%VCVERSION% DEBUG=yes - -REM echo Compiling dll-release-x86 version... -REM nmake /f Makefile.vc mode=dll VC=%VCVERSION% DEBUG=no GEN_PDB=yes - -REM echo Compiling static-debug-x86 version... -REM nmake /f Makefile.vc mode=static VC=%VCVERSION% DEBUG=yes - -REM echo Compiling static-release-x86 version... -REM nmake /f Makefile.vc mode=static VC=%VCVERSION% DEBUG=no - -call %MSVCDIR%\VC\Auxiliary\Build\vcvarsall.bat x64 -echo Compiling dll-debug-x64 version... -nmake /f Makefile.vc mode=dll VC=%VCVERSION% DEBUG=yes MACHINE=x64 - -echo Compiling dll-release-x64 version... -nmake /f Makefile.vc mode=dll VC=%VCVERSION% DEBUG=no GEN_PDB=yes MACHINE=x64 - -REM echo Compiling static-debug-x64 version... -REM nmake /f Makefile.vc mode=static VC=%VCVERSION% DEBUG=yes MACHINE=x64 -REM -REM echo Compiling static-release-x64 version... -REM nmake /f Makefile.vc mode=static VC=%VCVERSION% DEBUG=no MACHINE=x64 - -REM REM Copy compiled .*lib, *.pdb, *.dll files folder to dependencies\lib\dll-debug folder -REM cd %ROOT_DIR%\tmp_libcurl\curl*\builds\libcurl-vc-x86-debug-dll-ipv6-sspi-winssl -REM %MKDIR% -p %ROOT_DIR%\dependencies\lib-dll-debug-x86 -REM %CP% lib\*.pdb %ROOT_DIR%\dependencies\lib-dll-debug-x86 -REM %CP% lib\*.lib %ROOT_DIR%\dependencies\lib-dll-debug-x86 -REM %CP% bin\*.dll %ROOT_DIR%\dependencies\lib-dll-debug-x86 -REM -REM REM Copy compiled .*lib, *.pdb, *.dll files to dependencies\lib\dll-release folder -REM cd %ROOT_DIR%\tmp_libcurl\curl*\builds\libcurl-vc-x86-release-dll-ipv6-sspi-winssl -REM %MKDIR% -p %ROOT_DIR%\dependencies\lib-dll-release-x86 -REM %CP% lib\*.pdb %ROOT_DIR%\dependencies\lib-dll-release-x86 -REM %CP% lib\*.lib %ROOT_DIR%\dependencies\lib-dll-release-x86 -REM %CP% bin\*.dll %ROOT_DIR%\dependencies\lib-dll-release-x86 -REM -REM REM Copy compiled .*lib file in lib-release folder to dependencies\lib\static-debug folder -REM cd %ROOT_DIR%\tmp_libcurl\curl*\builds\libcurl-vc-x86-debug-static-ipv6-sspi-winssl -REM %MKDIR% -p %ROOT_DIR%\dependencies\lib-static-debug-x86 -REM %CP% lib\*.lib %ROOT_DIR%\dependencies\lib-static-debug-x86 -REM -REM REM Copy compiled .*lib files in lib-release folder to dependencies\lib\static-release folder -REM cd %ROOT_DIR%\tmp_libcurl\curl*\builds\libcurl-vc-x86-release-static-ipv6-sspi-winssl -REM %MKDIR% -p %ROOT_DIR%\dependencies\lib-static-release-x86 -REM %CP% lib\*.lib %ROOT_DIR%\dependencies\lib-static-release-x86 - -echo Copy compiled .*lib, *.pdb, *.dll files folder to dependencies\lib\dll-debug folder -cd %ROOT_DIR%\tmp_libcurl\curl*\builds\libcurl-vc-x64-debug-dll-ipv6-sspi-winssl -%MKDIR% -p %DEP_DIR%\lib-dll-debug-x64 -%CP% lib\*.pdb %DEP_DIR%\lib-dll-debug-x64 -%CP% lib\*.lib %DEP_DIR%\lib-dll-debug-x64 -%CP% bin\*.dll %DEP_DIR%\lib-dll-debug-x64 - -echo Copy compiled .*lib, *.pdb, *.dll files to dependencies\lib\dll-release folder -cd %ROOT_DIR%\tmp_libcurl\curl*\builds\libcurl-vc-x64-release-dll-ipv6-sspi-winssl -%MKDIR% -p %DEP_DIR%\lib-dll-release-x64 -%CP% lib\*.pdb %DEP_DIR%\lib-dll-release-x64 -%CP% lib\*.lib %DEP_DIR%\lib-dll-release-x64 -%CP% bin\*.dll %DEP_DIR%\lib-dll-release-x64 - -echo Copy compiled .*lib file in lib-release folder to dependencies\lib\static-debug folder -cd %ROOT_DIR%\tmp_libcurl\curl*\builds\libcurl-vc-x64-debug-static-ipv6-sspi-winssl -%MKDIR% -p %DEP_DIR%\lib-static-debug-x64 -%CP% lib\*.lib %DEP_DIR%\lib-static-debug-x64 - -echo Copy compiled .*lib files in lib-release folder to dependencies\lib\static-release folder -cd %ROOT_DIR%\tmp_libcurl\curl*\builds\libcurl-vc-x64-release-static-ipv6-sspi-winssl -%MKDIR% -p %DEP_DIR%\lib-static-release-x64 -%CP% lib\*.lib %DEP_DIR%\lib-static-release-x64 - - -echo Copy include folder to dependencies folder -%CP% -rf include %DEP_DIR% - -echo Cleanup temporary file/folders -cd %ROOT_DIR% -del /F /S /Q tmp_libcurl -%RM% -rf tmp_libcurl -REM %RM% -rf tmp_* - - -echo -echo ****** ****** -echo ****** Compiling Velocypack ****** -echo ****** ****** -echo - -mkdir tmp_velo -cd tmp_velo - -echo Get velocypack from git... - -git clone https://github.com/arangodb/velocypack.git -cd velo* -git checkout ce7c5fec3ec54c46ff4adbadfd4519540895e096 -cd .. - -echo Setting velocypack build examples and tests OFF -%FART% -w "%ROOT_DIR%\tmp_velo\velocypack\CMakeLists.txt" ON OFF - -echo Setting linker settings from /MT to /MD -%FART% "%ROOT_DIR%\tmp_velo\velocypack\cmake\Modules\AR_CompilerSettings.cmake" MTd MDd -%FART% "%ROOT_DIR%\tmp_velo\velocypack\cmake\Modules\AR_CompilerSettings.cmake" MT MD - -cd velo* -git checkout ce7c5fec3ec54c46ff4adbadfd4519540895e096 -mkdir build -cd build - -echo "%MSVCDIR%\VC\Auxiliary\Build\vcvarsall.bat" -call %MSVCDIR%\VC\Auxiliary\Build\vcvarsall.bat x64 -echo Compiling lib-release-x64 version... -cmake -G "NMake Makefiles" -DCMAKE_BUILD_TYPE=Release -DBuildTools=OFF -DBuildExamples=OFF -DBuildTests=OFF .. -nmake /f Makefile - -cd %ROOT_DIR%\tmp_velo\velo*\build\ -%MKDIR% -p %DEP_DIR%\lib-static-release-x64 -REM %CP% *.lib %ROOT_DIR%\dependencies\lib-static-release-x64 -%CP% *.lib %DEP_DIR%\lib-static-release-x64 - -cd .. -del /F /S /Q build -cd build - -echo Compiling lib-debug-x64 version... -cmake -G "NMake Makefiles" -DCMAKE_BUILD_TYPE=debug -DBuildTools=OFF -DBuildExamples=OFF -DBuildTests=OFF .. -nmake /f Makefile - -cd %ROOT_DIR%\tmp_velo\velo*\build\ -%MKDIR% -p %DEP_DIR%\lib-static-debug-x64 -REM %CP% *.lib %ROOT_DIR%\dependencies\lib-static-debug-x64 -%CP% *.lib %DEP_DIR%\lib-static-debug-x64 - -echo Copy include folder to dependencies folder -cd .. -%CP% -rf include %DEP_DIR% - -echo Cleanup temporary file/folders -cd %ROOT_DIR% -del /F /S /Q tmp_velo - -%RM% -rf tmp_velo - -%MKDIR% -p %ROOT_DIR%\..\build-fun-gui\debug -%MKDIR% -p %ROOT_DIR%\..\build-fun-gui\release - -%CP% -rf %ROOT_DIR%\Resources %ROOT_DIR%\..\build-fun-gui\debug -%CP% -rf %ROOT_DIR%\Resources %ROOT_DIR%\..\build-fun-gui\release - -%CP% %DEP_DIR%\lib-dll-release-x64\libcurl*.dll %ROOT_DIR%\..\build-fun-gui\release -%CP% %DEP_DIR%\lib-dll-debug-x64\libcurl*.dll %ROOT_DIR%\..\build-fun-gui\debug - -echo Finished a-build-win-dependencies.bat scrip! - -:end -exit /b diff --git a/b-build-win-boost.bat b/b-build-win-boost.bat deleted file mode 100644 index 13e2083f..00000000 --- a/b-build-win-boost.bat +++ /dev/null @@ -1,102 +0,0 @@ -@echo off -setlocal EnableDelayedExpansion - -set PROGFILES=%ProgramFiles% -if not "%ProgramFiles(x86)%" == "" set PROGFILES=%ProgramFiles(x86)% - -REM Check if Visual Studio 2017 comunity is installed -set MSVCDIR="%PROGFILES%\Microsoft Visual Studio\2017\Community" -set VCVARSALLPATH="%PROGFILES%\Microsoft Visual Studio\2017\Community\VC\Auxiliary\Build\vcvarsall.bat" -if exist %MSVCDIR% ( - if exist %VCVARSALLPATH% ( - set COMPILER_VER="2017" - echo Using Visual Studio 2017 Community - goto setup_env - ) -) - -REM Check if Visual Studio 2019 comunity is installed -set MSVCDIR="%PROGFILES%\Microsoft Visual Studio\2019\Community" -set VCVARSALLPATH="%PROGFILES%\Microsoft Visual Studio\2019\Community\VC\Auxiliary\Build\vcvarsall.bat" -if exist %MSVCDIR% ( - if exist %VCVARSALLPATH% ( - set COMPILER_VER="2019" - echo Using Visual Studio 2019 Community - goto setup_env - ) -) - - -echo No compiler : Microsoft Visual Studio 2017 or 2019 Community is not installed. -goto end - -:setup_env - -:begin - -REM Setup path to helper bin -set ROOT_DIR="%CD%" -set FART="%CD%\bin\fart\fart.exe" -set RM="%CD%\bin\unxutils\rm.exe" -set CP="%CD%\bin\unxutils\cp.exe" -set MKDIR="%CD%\bin\unxutils\mkdir.exe" -set SEVEN_ZIP="%CD%\bin\7-zip\7za.exe" -set WGET="%CD%\bin\unxutils\wget.exe" -set XIDEL="%CD%\bin\xidel\xidel.exe" -set DEP_DIR="%ROOT_DIR%\..\dependencies" - -mkdir tmp_libboost -cd tmp_libboost - -REM Get download url .Look under
-echo Get download url... -%XIDEL% https://www.boost.org/users/download/ -e "//a[ends-with(@href, '.zip')]/@href" > tmp_url -set /p url= - - - -Disclaimer - - - - -

Disclaimer

- -

THIS SOFTWARE IS PROVIDED "AS IS" AND ANY EXPRESSED OR IMPLIED -WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND -FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE  CONTRIBUTORS -BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL -DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS -OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
-HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR -TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

- -

Karl M. Syring

- - diff --git a/bin/unxutils/UnxUtilsDist.html b/bin/unxutils/UnxUtilsDist.html deleted file mode 100644 index 1669fe94..00000000 --- a/bin/unxutils/UnxUtilsDist.html +++ /dev/null @@ -1,660 +0,0 @@ - - - - - - -Native Win32 ports of some GNU utilities - - - - - - - - -
- - - - -
GNU utilities for Win32
-


- This are some ports of common GNU utilities to native - Win32. In this context, native means the executables do only depend on the Microsoft - C-runtime (msvcrt.dll) and not an emulation layer like that provided by Cygwin tools.
-

-

Download:

-
-

by http: UnxUtils.zip
- latest updates (after 14-04-03):  UnxUpdates.zip

-
-

Source code:

-
-

I have started an Open source project at http://unxutils.sourceforge.net. There is a -   CVS repository of all sources, even if the changes to the - original GNU code are trivial. The repository can be accessed via anonymous CVS with the - command
- cvs - -d:pserver:anonymous@cvs.UnxUtils.sourceforge.net:/cvsroot/unxutils login

-
-
-

The following program versions are covered:

-
-

bc-1.05
- bison-1.28
- bzip2-1.0.2
- diffutils-2.7
- fileutils-3.16
- findutils-4.1
- flex-2.5.4
- gawk-3.1.0
- grep-2.4.2
- gsar110
- gzip-1.2.4
- indent-2.2.9
- jwhois-2.4.1
- less-340
- m4-1.4
- make-3.78.1
- patch-2.5
- recode-3.6
- rman-3.0.7
- sed-3.02
- shellutils-1.9.4
- tar-1.12
- textutils-2.1
- unrar-3.00
- wget-1.8.2
- which-2.4

-
-

Standard behavior:

-
    -

  • forward as well as backward slashes in file - paths are accepted.

    -
    • -
-

What is new:

-


-    14-04-03

-
    -

  • New edition

    -
    • -

  • The programs are in use on all continents of - earth, including Antarctica. Still no users on Mars.

    -
    • -
-

 

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Program

-

Notes

-
agrep.exegot it from here: http://www.tgries.de/agrep/
ansi2knr.exe
basename.exe
bison.exe
bzip2.exeJulian Sewards alternative - compressor
bunzip2.exe
bzip2recover.exe
cat.exe
chgrp.exedummy
chmod.exe
chown.exedummy
cksum.exe
cmp.exe
comm.exe
compress.exefor (de)compressing .Z files; this is actually a program - called ncompress and was found on one of  the Linux mirrors
cp.exeworks only on NT, does real hardlinks on NTFS
csplit.exe
cut.exe
date.exe
dd.exe
df.exedummy
diff.exe
diff3.exe
dirname.exe
du.exe
echo.exe
egrep.exe
env.exedummy
expand.exe
expr.exe
factor.exe
fgrep.exe
find.exe
    -
  • Example of command line under Cmd/Command shell:
    - find -name *.txt -exec cat {} ;
    • -
-
flex.exe
fmt.exe
fold.exe
gawk.exeinput files are opened in text mode
make.exeFrom v3.77 upwards, make searches for a sh.exe on the path. If - it does not find one, it switches to win32 make mode that is it uses intermediate batch - files for command processing.
- This is fine until your makefile tries to execute something like mkdir, which will invoke - the internal mkdir from cmd.exe or command.com. As the results may not be to your liking, - you may prefer to use the sh.exe provide here.
grep.exe
gsar.exe
gunzip.exe
gzip.exe
head.exe
id.exedummy
install.exe
join.exe
less.exe
ln.exeworks only on NT, does real hardlinks on NTFS
logname.exe
ls.exe
m4.exe
md5sum.exe
mkdir.exe
mkfifo.exedummy
mknod.exedummy
mv.exe
mvdir.exe
nl.exe
od.exe
paste.exe
patch.exe
pathchk.exe
pr.exe
printenv.exe
printf.exe
ptx.exe
recode.exe
rm.exe
rman.exePolyglotMan by Thomas A. Phelps ( source)
rmdir.exe
sdiff.exe
sed.exe
seq.exe
sleep.exe
sort.exe
sh.exerenamed zsh - this is no replacement for the Cygwin bash
shar.exeonly works with -T (text) option
split.exe
stego.exestego -E encode.me -T words.txt
- Encodes file encode.me as gibberish text using words from the words.txt file to - stdout. If the -T option is omitted, stego looks for a file called "words" in - the current directory. Of course, the -D option will decode the input file; remember to - redistribute words.txt together with the encoded file.
- The purpose of this program is to disguise binary files as a kind of text file or to drive - your coworkers mad.
su.exedummy
sum.exe
sync.exe
tac.exe
tail.exe
tar.exe
    -
  • only forward slashes are accepted
    • -
  • the -z option (compression) does not work
    • -
  • no remote archives
    • -
  • works only on NT, does real hardlinks on NTFS
    • -
-
tee.exe
test.exe
touch.exe
tr.exe
uname.exe
unexpand.exe
uniq.exe
unrar.exeThis is unrar 3.00 beta 7, which seems to have been - "free". Works good enough.
unshar.exe
uudecode.exe
uuencode.exe
wc.exe
wget.exewget 1.8.2 builds out of the box with MS Visual C
which.exedoes not search the current directory
whoami.exe
xargs.exe
yes.exe
zcat.exe

Additional - programs

pclip.exeput the Windows clipboard text to stdout
gclip.exeget  the Windows clipboard text from stdin
- Example: run the text from the clipboard through sed and put the result back
-                - pclip | sed "s/string1/string2/g" | gclip
gplay.exeMy minimalist console multimedia player using DirectShow. With
- gplay filename | URL
- you should be able to play just everything, as long as Microsoft supports it.
-
- -

md5 sums

- -
- -

Links:

- -

The gcc compiler for Win32:
-   http://www.mingw.org
-Digital Mars compiler:
-   http://www.digitalmars.com
-A zsh shell for Win32:
-   ftp://ftp.blarg.net/users/amol/zsh
-The home of vim, has a Win32 version:
-   http://www.vim.org
-An emacs for NT:
-   http://www.gnu.org/software/emacs/windows/ntemacs.html
-The CVS version control system:
-   http://www.cvshome.org
-   http://www.cvsnt.org
-A free IDE for the Win32 gcc:
-  VIDE

- -

José Fonsecas site with related stuff:
-     http://jrfonseca.dyndns.org/projects/gnu-win32
-HTML man pages for the GNU utilities:
-     http://www.fsf.org/manual/manual.html
-An Un*x shell scripting resource:
-     http://www.shelldorado.com/
-Another source of unixish stuff:
-     http://virtunix.itribe.net

- -

Useful free NT system utilities:
-     http://www.sysinternals.com
-Some hints on cloning your system with dd:
-     http://www.rajeevnet.com/hacks_hints/os_clone/os_cloning.html
-Programs missing from this distribution, especially a command line registry editor.
-     http://www.dmst.aueb.gr/dds/sw/outwit
-
-The GNU Privacy Guard:
-     http://www.gnupg.org
-zip and unzip from the Infozip distribution:
-     http://www.info-zip.org/pub/infozip

- -

An Un*x emulation on Win32:
-     http://www.cygwin.com
-Another Un*x emulation on Win32:
-     http://www.research.att.com/sw/tools/uwin/
-Windows Services for UNIX, integrates the Interix subsystem:
-     http://www.microsoft.com/windows/sfu/productinfo/overview/default.asp

- -
- -

Read my standard disclaimer: (really?)
-Last change on 15-04-03 by Karl M. Syring (bug reports -are welcome)
-Original location of this page: http://www.weihenstephan.de/~syring/win32/UnxUtils.html

- - - - - - - diff --git a/bin/unxutils/cp.exe b/bin/unxutils/cp.exe deleted file mode 100644 index 7130bbb1..00000000 Binary files a/bin/unxutils/cp.exe and /dev/null differ diff --git a/bin/unxutils/mkdir.exe b/bin/unxutils/mkdir.exe deleted file mode 100644 index 239b4437..00000000 Binary files a/bin/unxutils/mkdir.exe and /dev/null differ diff --git a/bin/unxutils/rm.exe b/bin/unxutils/rm.exe deleted file mode 100644 index 8258af4a..00000000 Binary files a/bin/unxutils/rm.exe and /dev/null differ diff --git a/bin/unxutils/wget.exe b/bin/unxutils/wget.exe deleted file mode 100644 index f4b85e7d..00000000 Binary files a/bin/unxutils/wget.exe and /dev/null differ diff --git a/bin/xidel/readme.txt b/bin/xidel/readme.txt deleted file mode 100644 index 6d413f76..00000000 --- a/bin/xidel/readme.txt +++ /dev/null @@ -1,445 +0,0 @@ - -================================================ Basics ================================================ - - -The trivial usage is to extract an expression from a webpage like: - - xidel http://www.example.org --extract //title - -Instead of one or more urls, you can also pass file names or the xml data itself (xidel ".." ...). -The --extract option can be abbreviated as -e, and there are five different kind of extract expressions: - - 1 ) XPath 2 expressions, with some changes and additional functions. - - 2 ) XQuery 1 expressions - - 3 ) CSS 3 selectors. - - 4 ) Templates, a simplified version of the page which is pattern matched against the input - - 5 ) Multipage templates, i.e. a file that contains templates for several pages - -The different kinds except multipage templates are usually automatically detected, but -a certain type can be forced with the extract-kind option. -Or by using the shorter --xpath "..", --xquery "..", --css ".." options. -Especially XQuery and template expressions are easily confused by the auto detector. -(Xidel assumes templates, if the expression starts with a "<" ) - -See the sections below for a more detailed description of each expression kind. - - - -The next important option is --follow (abbreviated as -f) to follow links on a page. E.g: - - xidel http://www.example.org --follow //a --extract //title - -This will print the titles of all pages that are linked from http://www.example.org. - ---follow supports the same expressions as --extract, and it will follow the href or src attributes of the -usual elements, or the contained text if there are no such attributes. - - - -============================== Recursion / Argument order and grouping =============================== - - -You can specify multiple --extract (-e) and --follow (-f) arguments to extract values from one page, -follow the links to the next pages and extract values from there as well ... -Then it becomes important in which order the arguments are given, so it extracts before following, -or the other way around. -You can usually read it left-to-right like an English sentence, extracting from the current page, -or following to a new one, which will then become the next current page. -For example: - -a) xidel http://site1 -e "select content 1" http://site2 -e "select content 2" - - This will extract content 1 from site 1 and content 2 from site 2 - -b) xidel http://site1 http://site2 -e "select content 1" -e "select content 2" - - This will extract content 1 and 2 from site 1 as well as from site 2 - -c) xidel http://site1 -e "select content 1" -f "//a (:select links:)" -e "select content 2" - - This will extract the "content 1" from site1, and "content 2" from all sites the first site has links to. - -d) xidel http://site1 -f "//a (:select links:)" -e "select content 1" -e "select content 2" - - This will extract "content 1" and "content 2" from all sites the first site links to, and will not - extract anything from site1. - -e) xidel http://site1 -e "select content 1" -e "select content 2" -f "//a (:select links:)" - - This is some kind of special case. Since -f is the last option, it will repeat the previous operation, i.e. - it will extract content 1 and 2 from site1 and ALL sites that can be reached by an selected link on site1 - or any other of the processed sites. - Only if there were another -e after -f, it would extract that from the first set of followed links and stop. - -In some kinds of extract expression you can create new variables, if you assign values to a variable called -"_follow", that value will be included in the next follow expression. -If you assign an object to _follow, its properties will override the command line parameters with the same -value. - -Generally an option modifier (like --extract-kind) affects all succeeding options, unless there are none, -then it affects the immediate preceding option. - - - - -You can always override the argument order by using [ and ] to group the options. -For example: - -f) xidel http://site1 [ -f "//a (:select links:)" -e "select content 1" ] -e "select content 2" - - This will extract content 1 from all sites linked by site1 and content 2 from site1 itself. - I.e. the extract of content 2 is not affected by the follow-option within the [..] brackets. - -g) xidel http://site1 [ -f //a[@type1] --download type1/ ] - [ -f //a[@type2] --download type2/ ] - [ -f //a[@type3] --download type3/ ] - - This will download all links of type 1 in a directory type1, all links of type2 in directory type2... - (if written on one line) - -[ and ] must be surrounded by a space. - - - - - - -========================================== XPath 2.0 / XQuery =========================================== - -XPath expressions provide an easy way to extract calculated values from x/html. -See http://en.wikipedia.org/wiki/XPath_2.0 for details. - -Xidel also supports JSONiq and some custom extensions, so it deviates in a few ways from the standard. -However, you can disable this differences with the respective options (see link below or the -command line parameter listing printed by --help). -Switched to full standard compatible mode, its implementation passes 99.3% of the XPath 2 only tests and -97.8% of the XQuery 1 tests in the XQuery Testsuite (skipping tests for invalid input queries) - -However, in the default mode, there are the following important extensions: - - Syntax: - - Variable assignment: $var := value - - adds $var to a set of global variables, which can be created and accessed - everywhere - - JSONiq literals true, false, null - - true and false are evaluated as true(), false(), null becomes jn:null() - - JSONiq arrays: [a,b,c] - - Arrays store a list of values and can be nested with each other and - within sequences. - jn:members converts an array to a sequence. - - JSONiq objects: {"name": value, ...} - - Object stores a set of values as associative map. The values can be - accessed similar to a function call, e.g.: {"name": value, ...}("name"). - Xidel also has {"name": value, ..}.name as an additional syntax to - access properties. - jn:keys returns a sequence of all property names, libjn:values a sequence - of values. - Used with global variables, you can copy an object with obj2 := obj - (objects are immutable, but properties can be changed with - obj2.foo := 12, which will create a new object with the changed property) - - Extended strings: x"..{..}.." - - If a string is prefixed by an "x", all expressions inside {}-parentheses - are evaluated, like in the value of a direct attribute constructor. - (Warning: This was changed in Xidel 0.7. Xidel <= 0.6 used - "foo$var;bar" without prefix for this) - - - Semantic: - - All string comparisons are case insensitive, and "clever", e.g.: - '9xy' = '9XY' < '10XY' < 'xy' - This is more useful for html (think of @class = 'foobar'), but can be - disabled by passing collation urls to the string functions. - - Everything is weakly typed, e.g 'false' = false() is true, and 1+"2" is 3. - - Unknown namespace prefixes are resolved with the namespace bindings of the - input data. - Therefore //a always finds all links, independent of any xmlns-attributes. - (however, if you explicitly declare a namespace like - 'declare default element namespace "..."' in XQuery, it will only find - elements in that namespace) - - XML Schemas, error codes and static type checking are not supported. - - Certain additional functions: - - jn:*, libjn:* The standard JSONiq and JSONlib functions - json("str.") Parses a string as json, or downloads json from an url.(only use with trusted input) - serialize-json(value) - Converts a value to JSON - extract("string","regex"[,,[]]) - This applies the regex "regex" to "string" and returns only the matching part. - If the argument is used, only the -th submatch will be returned. - (this function used to be called "filter") - css("sel") This returns the nodes below the context node matched by the specified css 3 selector. - You can use this to combine css and XPath, like in 'css("a.aclass")/@href'. - eval("xpath") This will evaluate the string "xpath" as an XPath expression - system("..") Runs a certain program and returns its stdout result as string - deep-text() This is the concatenated plain text of the every tag inside the current text. - You can also pass a separator like deep-text(' ') to separate text of different nodes. - inner-html() This is the html content of node ., like innerHTML in javascript. - outer-html() This is the same as inner-html, but includes the node itself - inner-xml() This is the xml content of node, similar to inner-html() - outer-xml() Like outer-html(), but xml-serialized - split-equal("list", "string"[, "sep" = " "]) - Treats the string "list" as a list of strings separated by "sep" and tests if - "string" is contained in that list. (just like css class matching) - form(form, [overridden parameters = ()]) - Converts a html form in a http request, by url encoding all inputs descendants - of the given form node. You can give a sequence of parameters to override. - e.g. form(//form[1], "foo=bar&xyz=123") returns a request for the first form, - with the foo and xyz parameters overriden by bar and 123. - You can also use a JSON object to set the override parameters, e.g. - {"foo": "bar", "xyz": 123}, in that case they are url encoded. - It returns an object with .url, .method and .post properties. - match(