Merge branch 'develop' into collisionFilter

pshriwise · Apr 7, 2021 · ab32931 · ab32931
2 parents 754d215 + e9c91fc
commit ab32931
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diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -3,8 +3,8 @@ project(openmc C CXX)
 
 # Set version numbers
 set(OPENMC_VERSION_MAJOR 0)
-set(OPENMC_VERSION_MINOR 12)
-set(OPENMC_VERSION_RELEASE 1)
+set(OPENMC_VERSION_MINOR 13)
+set(OPENMC_VERSION_RELEASE 0)
 set(OPENMC_VERSION ${OPENMC_VERSION_MAJOR}.${OPENMC_VERSION_MINOR}.${OPENMC_VERSION_RELEASE})
 configure_file(include/openmc/version.h.in "${CMAKE_BINARY_DIR}/include/openmc/version.h" @ONLY)
 
@@ -54,13 +54,13 @@ endif()
 #===============================================================================
 
 # If not found, we just pull appropriate versions from github and build them.
-find_package(fmt QUIET)
+find_package(fmt QUIET NO_SYSTEM_ENVIRONMENT_PATH)
 if(fmt_FOUND)
   message(STATUS "Found fmt: ${fmt_DIR} (version ${fmt_VERSION})")
 else()
   message(STATUS "Did not find fmt, will use submodule instead")
 endif()
-find_package(pugixml QUIET)
+find_package(pugixml QUIET NO_SYSTEM_ENVIRONMENT_PATH)
 if(pugixml_FOUND)
   message(STATUS "Found pugixml: ${pugixml_DIR}")
 else()
@@ -87,7 +87,9 @@ endif()
 find_package(HDF5 REQUIRED COMPONENTS C HL)
 if(HDF5_IS_PARALLEL)
   if(NOT MPI_ENABLED)
-    message(FATAL_ERROR "Parallel HDF5 must be used with MPI.")
+    message(FATAL_ERROR "Parallel HDF5 was detected, but the detected compiler,\
+     ${CMAKE_CXX_COMPILER}, does not support MPI. An MPI-capable compiler must \
+     be used with parallel HDF5.")
   endif()
   message(STATUS "Using parallel HDF5")
 endif()

diff --git a/Dockerfile b/Dockerfile
@@ -65,7 +65,7 @@ RUN if [ "$include_dagmc" = "true" ] ; \
 
 # Clone and install Embree
 RUN if [ "$include_dagmc" = "true" ] ; \
-    then git clone --single-branch --branch master https://github.com/embree/embree.git ; \
+    then git clone --single-branch --branch v3.12.2 https://github.com/embree/embree.git ; \
     cd embree ; \
     mkdir build ; \
     cd build ; \
@@ -81,7 +81,7 @@ RUN if [ "$include_dagmc" = "true" ] ; \
     mkdir MOAB ; \
     cd MOAB ; \
     mkdir build ; \
-    git clone  --single-branch --branch master https://bitbucket.org/fathomteam/moab.git ; \
+    git clone  --single-branch --branch 5.2.1 https://bitbucket.org/fathomteam/moab.git ; \
     cd build ; \
     cmake ../moab -DENABLE_HDF5=ON \
                   -DENABLE_NETCDF=ON \
@@ -117,7 +117,7 @@ RUN if [ "$include_dagmc" = "true" ] ; \
 RUN if [ "$include_dagmc" = "true" ] ; \
     then mkdir DAGMC ; \
     cd DAGMC ; \
-    git clone --single-branch --branch develop https://github.com/svalinn/DAGMC.git ; \
+    git clone --single-branch --branch 3.2.0 https://github.com/svalinn/DAGMC.git ; \
     mkdir build ; \
     cd build ; \
     cmake ../DAGMC -DBUILD_TALLY=ON \

diff --git a/LICENSE b/LICENSE
@@ -1,4 +1,4 @@
-Copyright (c) 2011-2020 Massachusetts Institute of Technology and OpenMC contributors
+Copyright (c) 2011-2021 Massachusetts Institute of Technology and OpenMC contributors
 
 Permission is hereby granted, free of charge, to any person obtaining a copy of
 this software and associated documentation files (the "Software"), to deal in

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -63,16 +63,16 @@
 
 # General information about the project.
 project = 'OpenMC'
-copyright = '2011-2020, Massachusetts Institute of Technology and OpenMC contributors'
+copyright = '2011-2021, Massachusetts Institute of Technology and OpenMC contributors'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = "0.12"
+version = "0.13"
 # The full version, including alpha/beta/rc tags.
-release = "0.12.1-dev"
+release = "0.13.0-dev"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -215,6 +215,7 @@ def setup(app):
 \hypersetup{bookmarksdepth=3}
 \setcounter{tocdepth}{2}
 \numberwithin{equation}{section}
+\DeclareUnicodeCharacter{03B1}{$\alpha$}
 """,
 'printindex': r""
 }

diff --git a/docs/source/devguide/styleguide.rst b/docs/source/devguide/styleguide.rst
@@ -215,7 +215,7 @@ Documentation
 -------------
 
 Classes, structs, and functions are to be annotated for the `Doxygen
-<http://www.doxygen.nl/>`_ documentation generation tool. Use the ``\`` form of
+<https://www.doxygen.nl/>`_ documentation generation tool. Use the ``\`` form of
 Doxygen commands, e.g., ``\brief`` instead of ``@brief``.
 
 ------

diff --git a/docs/source/devguide/tests.rst b/docs/source/devguide/tests.rst
@@ -14,7 +14,7 @@ functions/classes in the OpenMC Python API.
 Prerequisites
 -------------
 
-- The test suite relies on the third-party `pytest <https://pytest.org>`_
+- The test suite relies on the third-party `pytest <https://docs.pytest.org>`_
   package. To run either or both the regression and unit test suites, it is
   assumed that you have OpenMC fully installed, i.e., the :ref:`scripts_openmc`
   executable is available on your :envvar:`PATH` and the :mod:`openmc` Python
@@ -46,7 +46,7 @@ To execute the test suite, go to the ``tests/`` directory and run::
     pytest
 
 If you want to collect information about source line coverage in the Python API,
-you must have the `pytest-cov <https://pypi.python.org/pypi/pytest-cov>`_ plugin
+you must have the `pytest-cov <https://pypi.org/project/pytest-cov>`_ plugin
 installed and run::
 
     pytest --cov=../openmc --cov-report=html

diff --git a/docs/source/devguide/user-input.rst b/docs/source/devguide/user-input.rst
@@ -65,7 +65,7 @@ developer or send a message to the `developers mailing list`_.
 .. _property attribute: https://docs.python.org/3.6/library/functions.html#property
 .. _XML Schema Part 2: http://www.w3.org/TR/xmlschema-2/
 .. _boolean: http://www.w3.org/TR/xmlschema-2/#boolean
-.. _RELAX NG: http://relaxng.org/
-.. _compact syntax: http://relaxng.org/compact-tutorial-20030326.html
-.. _trang: http://www.thaiopensource.com/relaxng/trang.html
+.. _RELAX NG: https://relaxng.org/
+.. _compact syntax: https://relaxng.org/compact-tutorial-20030326.html
+.. _trang: https://relaxng.org/jclark/trang.html
 .. _developers mailing list: https://groups.google.com/forum/?fromgroups=#!forum/openmc-dev
diff --git a/docs/source/devguide/workflow.rst b/docs/source/devguide/workflow.rst
@@ -122,11 +122,11 @@ can interfere with virtual environments.
 
 .. _git: http://git-scm.com/
 .. _GitHub: https://github.com/
-.. _git flow: http://nvie.com/git-model
-.. _valgrind: http://valgrind.org/
+.. _git flow: https://nvie.com/git-model
+.. _valgrind: https://www.valgrind.org/
 .. _style guide: https://docs.openmc.org/en/latest/devguide/styleguide.html
-.. _pull request: https://help.github.com/articles/using-pull-requests
+.. _pull request: https://docs.github.com/en/github/collaborating-with-issues-and-pull-requests/about-pull-requests
 .. _openmc-dev/openmc: https://github.com/openmc-dev/openmc
-.. _paid plan: https://github.com/plans
+.. _paid plan: https://github.com/pricing
 .. _Bitbucket: https://bitbucket.org
 .. _pip: https://pip.pypa.io/en/stable/
diff --git a/docs/source/examples/capi.ipynb b/docs/source/examples/capi.ipynb
@@ -0,0 +1 @@
+../../../examples/jupyter/capi.ipynb
diff --git a/docs/source/examples/index.rst b/docs/source/examples/index.rst
@@ -19,7 +19,7 @@ General Usage
     post-processing
     pandas-dataframes
     tally-arithmetic
-    CAPI
+    capi
     expansion-filters
     search
     nuclear-data

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -13,8 +13,8 @@ programming model.
 
 OpenMC was originally developed by members of the `Computational Reactor Physics
 Group <http://crpg.mit.edu>`_ at the `Massachusetts Institute of Technology
-<http://web.mit.edu>`_ starting in 2011. Various universities, laboratories, and
-other organizations now contribute to the development of OpenMC. For more
+<https://web.mit.edu>`_ starting in 2011. Various universities, laboratories,
+and other organizations now contribute to the development of OpenMC. For more
 information on OpenMC, feel free to post a message on the `OpenMC Discourse
 Forum <https://openmc.discourse.group/>`_.
 

diff --git a/docs/source/io_formats/data_wmp.rst b/docs/source/io_formats/data_wmp.rst
@@ -49,4 +49,4 @@ Windowed Multipole Library Format
         windows[i, 1] are, respectively, the indexes (1-based) of the first and
         last pole in window i.
 
-.. _h5py: http://docs.h5py.org/en/latest/
+.. _h5py: https://docs.h5py.org/en/latest/
diff --git a/docs/source/io_formats/index.rst b/docs/source/io_formats/index.rst
@@ -44,7 +44,6 @@ Output Files
 
    statepoint
    source
-   surface_source
    summary
    depletion_results
    particle_restart

diff --git a/docs/source/io_formats/mgxs_library.rst b/docs/source/io_formats/mgxs_library.rst
@@ -21,7 +21,7 @@ nuclides or materials.
 
 The current version of the multi-group library file format is 1.0.
 
-.. _HDF5: http://www.hdfgroup.org/HDF5/
+.. _HDF5: https://www.hdfgroup.org/solutions/hdf5/
 
 .. _mgxs_lib_spec:
 

diff --git a/docs/source/io_formats/statepoint.rst b/docs/source/io_formats/statepoint.rst
@@ -162,5 +162,5 @@ All values are given in seconds and are measured on the master process.
              source sites between processes for load balancing.
            - **accumulating tallies** (*double*) -- Time spent communicating
              tally results and evaluating their statistics.
-          - **writing statepoints** (*double*) -- Time spent writing statepoint
-            files
+           - **writing statepoints** (*double*) -- Time spent writing statepoint
+             files
diff --git a/docs/source/license.rst b/docs/source/license.rst
@@ -4,7 +4,7 @@
 License Agreement
 =================
 
-Copyright © 2011-2020 Massachusetts Institute of Technology and OpenMC contributors
+Copyright © 2011-2021 Massachusetts Institute of Technology and OpenMC contributors
 
 Permission is hereby granted, free of charge, to any person obtaining a copy of
 this software and associated documentation files (the "Software"), to deal in

diff --git a/docs/source/methods/cross_sections.rst b/docs/source/methods/cross_sections.rst
@@ -186,10 +186,10 @@ The data governing the interaction of particles with various nuclei or materials
 are represented using a multi-group library format specific to the OpenMC code.
 The format is described in the :ref:`mgxs_lib_spec`. The data itself can be
 prepared via traditional paths or directly from a continuous-energy OpenMC
-calculation by use of the Python API as is shown in the
-:ref:`notebook_mg_mode_part_i` example notebook. This multi-group library
-consists of meta-data (such as the energy group structure) and multiple `xsdata`
-objects which contains the required microscopic or macroscopic multi-group data.
+calculation by use of the Python API as is shown in an `example notebook
+<../examples/mg-mode-part-i.ipynb>`_. This multi-group library consists of
+meta-data (such as the energy group structure) and multiple `xsdata` objects
+which contains the required microscopic or macroscopic multi-group data.
 
 At a minimum, the library must contain the absorption cross section
 (:math:`\sigma_{a,g}`) and a scattering matrix. If the problem is an eigenvalue
@@ -269,12 +269,12 @@ or even isotropic scattering.
 
 .. _logarithmic mapping technique:
    https://laws.lanl.gov/vhosts/mcnp.lanl.gov/pdf_files/la-ur-14-24530.pdf
-.. _Hwang: http://www.ans.org/pubs/journals/nse/a_16381
+.. _Hwang: https://doi.org/10.13182/NSE87-A16381
 .. _Josey: https://doi.org/10.1016/j.jcp.2015.08.013
 .. _WMP Library: https://github.com/mit-crpg/WMP_Library
-.. _MCNP: http://mcnp.lanl.gov
+.. _MCNP: https://mcnp.lanl.gov
 .. _Serpent: http://montecarlo.vtt.fi
-.. _NJOY: http://t2.lanl.gov/codes.shtml
-.. _ENDF/B data: http://www.nndc.bnl.gov/endf
+.. _NJOY: https://www.njoy21.io/NJOY21/
+.. _ENDF/B data: https://www.nndc.bnl.gov/endf/b8.0/
 .. _Leppanen: https://doi.org/10.1016/j.anucene.2009.03.019
 .. _algorithms: http://ab-initio.mit.edu/wiki/index.php/Faddeeva_Package
diff --git a/docs/source/methods/geometry.rst b/docs/source/methods/geometry.rst
@@ -962,6 +962,6 @@ surface is known as in :ref:`reflection`.
 
 .. _constructive solid geometry: https://en.wikipedia.org/wiki/Constructive_solid_geometry
 .. _surfaces: https://en.wikipedia.org/wiki/Surface
-.. _MCNP: http://mcnp.lanl.gov
+.. _MCNP: https://mcnp.lanl.gov
 .. _Serpent: http://montecarlo.vtt.fi
 .. _Monte Carlo Performance benchmark: https://github.com/mit-crpg/benchmarks/tree/master/mc-performance/openmc
diff --git a/docs/source/methods/neutron_physics.rst b/docs/source/methods/neutron_physics.rst
@@ -76,10 +76,11 @@ absorption cross section (this includes fission), and :math:`\sigma_f` is the
 total fission cross section. If this condition is met, then the neutron is
 killed and we proceed to simulate the next neutron from the source bank.
 
-No secondary particles from disappearance reactions such as photons or
-alpha-particles are produced or tracked. To truly capture the affects of gamma
-heating in a problem, it would be necessary to explicitly track photons
-originating from :math:`(n,\gamma)` and other reactions.
+Note that photons arising from :math:`(n,\gamma)` and other neutron reactions
+are not produced in a microscopically correct manner. Instead, photons are
+sampled probabilistically at each neutron collision, regardless of what reaction
+actually takes place. This is described in more detail in
+:ref:`photon_production`.
 
 ------------------
 Elastic Scattering
@@ -1694,31 +1695,31 @@ another.
 
 .. _SIGMA1 method: https://doi.org/10.13182/NSE76-1
 
-.. _scaled interpolation: http://www.ans.org/pubs/journals/nse/a_26575
+.. _scaled interpolation: https://doi.org/10.13182/NSE73-A26575
 
 .. _probability table method: https://doi.org/10.13182/NSE72-3
 
 .. _Watt fission spectrum: https://doi.org/10.1103/PhysRev.87.1037
 
 .. _Foderaro: http://hdl.handle.net/1721.1/1716
 
-.. _OECD: http://www.oecd-nea.org/tools/abstract/detail/NEA-1792
+.. _OECD: https://www.oecd-nea.org/tools/abstract/detail/NEA-1792
 
 .. _NJOY: https://www.njoy21.io/NJOY2016/
 
-.. _PREPRO: http://www-nds.iaea.org/ndspub/endf/prepro/
+.. _PREPRO: https://www-nds.iaea.org/ndspub/endf/prepro/
 
 .. _endf102: https://www.oecd-nea.org/dbdata/data/manual-endf/endf102.pdf
 
-.. _Monte Carlo Sampler: https://laws.lanl.gov/vhosts/mcnp.lanl.gov/pdf_files/la-9721.pdf
+.. _Monte Carlo Sampler: https://permalink.lanl.gov/object/tr?what=info:lanl-repo/lareport/LA-09721-MS
 
-.. _LA-UR-14-27694: http://permalink.lanl.gov/object/tr?what=info:lanl-repo/lareport/LA-UR-14-27694
+.. _LA-UR-14-27694: https://permalink.lanl.gov/object/tr?what=info:lanl-repo/lareport/LA-UR-14-27694
 
-.. _MC21: http://www.osti.gov/bridge/servlets/purl/903083-HT5p1o/903083.pdf
+.. _MC21: https://www.osti.gov/biblio/903083
 
 .. _Romano: https://doi.org/10.1016/j.cpc.2014.11.001
 
-.. _Sutton and Brown: http://www.osti.gov/bridge/product.biblio.jsp?osti_id=307911
+.. _Sutton and Brown: https://www.osti.gov/biblio/307911
 
 .. _lectures: https://laws.lanl.gov/vhosts/mcnp.lanl.gov/pdf_files/la-ur-05-4983.pdf
 

diff --git a/docs/source/methods/parallelization.rst b/docs/source/methods/parallelization.rst
@@ -251,8 +251,8 @@ depending on how many nodes are communicating and the size of the message. Using
 multiple algorithms allows one to minimize latency for small messages and
 minimize bandwidth for long messages.
 
-We will focus here on the implementation of broadcast in the MPICH2_
-implementation. For short messages, MPICH2 uses a `binomial tree`_ algorithm. In
+We will focus here on the implementation of broadcast in the MPICH_
+implementation. For short messages, MPICH uses a `binomial tree`_ algorithm. In
 this algorithm, the root process sends the data to one node in the first step,
 and then in the subsequent, both the root and the other node can send the data
 to other nodes. Thus, it takes a total of :math:`\lceil \log_2 p \rceil` steps
@@ -266,7 +266,7 @@ to complete the communication. The time to complete the communication is
 This algorithm works well for short messages since the latency term scales
 logarithmically with the number of nodes. However, for long messages, an
 algorithm that has lower bandwidth has been proposed by Barnett_ and implemented
-in MPICH2. Rather than using a binomial tree, the broadcast is divided into a
+in MPICH. Rather than using a binomial tree, the broadcast is divided into a
 scatter and an allgather. The time to complete the scatter is :math:` \log_2 p
 \: \alpha + \frac{p-1}{p} N\beta` using a binomial tree algorithm. The allgather
 is performed using a ring algorithm that completes in :math:`p-1) \alpha +
@@ -613,7 +613,7 @@ is actually independent of the number of nodes:
 
 .. _Brissenden and Garlick: https://doi.org/10.1016/0306-4549(86)90095-2
 
-.. _MPICH2: http://www.mcs.anl.gov/mpi/mpich
+.. _MPICH: http://www.mpich.org
 
 .. _binomial tree: https://www.mcs.anl.gov/~thakur/papers/ijhpca-coll.pdf
 
@@ -629,19 +629,19 @@ is actually independent of the number of nodes:
 
 .. _message-passing interface: https://en.wikipedia.org/wiki/Message_Passing_Interface
 
-.. _PVM: http://www.csm.ornl.gov/pvm/pvm_home.html
+.. _PVM: https://www.csm.ornl.gov/pvm/pvm_home.html
 
-.. _MPI: http://www.mcs.anl.gov/research/projects/mpi/
+.. _MPI: https://www.mcs.anl.gov/research/projects/mpi/
 
 .. _embarrassingly parallel: https://en.wikipedia.org/wiki/Embarrassingly_parallel
 
-.. _sends: http://www.mcs.anl.gov/research/projects/mpi/www/www3/MPI_Send.html
+.. _sends: https://www.mpich.org//static/docs/latest/www3/MPI_Send.html
 
-.. _broadcasts: http://www.mcs.anl.gov/research/projects/mpi/www/www3/MPI_Bcast.html
+.. _broadcasts: https://www.mpich.org//static/docs/latest/www3/MPI_Bcast.html
 
-.. _scatter: http://www.mcs.anl.gov/research/projects/mpi/www/www3/MPI_Scatter.html
+.. _scatter: https://www.mpich.org//static/docs/latest/www3/MPI_Scatter.html
 
-.. _allgather: http://www.mcs.anl.gov/research/projects/mpi/www/www3/MPI_Allgather.html
+.. _allgather: https://www.mpich.org//static/docs/latest/www3/MPI_Allgather.html
 
 .. _Cauchy distribution: https://en.wikipedia.org/wiki/Cauchy_distribution
 

diff --git a/docs/source/methods/photon_physics.rst b/docs/source/methods/photon_physics.rst
@@ -1004,6 +1004,8 @@ direction of the incident charged particle, which is a reasonable approximation
 at higher energies when the bremsstrahlung radiation is emitted at small
 angles.
 
+.. _photon_production:
+
 -----------------
 Photon Production
 -----------------
@@ -1067,6 +1069,6 @@ emitted photon.
 
 .. _Kaltiaisenaho: https://aaltodoc.aalto.fi/bitstream/handle/123456789/21004/master_Kaltiaisenaho_Toni_2016.pdf
 
-.. _Salvat: http://www.oecd-nea.org/globalsearch/download.php?doc=77434
+.. _Salvat: https://www.oecd-nea.org/globalsearch/download.php?doc=77434
 
 .. _Sternheimer: https://doi.org/10.1103/PhysRevB.26.6067