first release

Author: Yihao-Shi

.gitignore

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+*.vtu
+!**images/*.png
+!**images/*.eps
+*.xls
+*.npz
+*.tiff
+*.txt
+*.pyc
+*.vtr
+*.vtp
+*.svg
+src/efem/
+src/iga/
+src/igadem/
+src/igampdem/
+src/tlsmpm/
+examples/***/draw?.py
+research/
+!images/*.gif
+*.ini
+
+

LICENSE

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+import imageio.v2, os
+GIF = []
+filepath = "examples/mpm/column_collapse/Newtonian/animation"
+filenames = sorted((fn for fn in os.listdir(filepath) if fn.endswith('.png')))
+for filename in filenames:
+    GIF.append(imageio.v2.imread(filepath + "/" + filename))
+imageio.mimsave(filepath + "/" + 'mpdem.gif', GIF, fps=10)

PNGtoGIF.py

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+# GeoTaichi
+
+![Github License](https://img.shields.io/github/license/Yihao-Shi/GeoTaichi)          ![Github stars](https://img.shields.io/github/stars/Yihao-Shi/GeoTaichi)          ![Github forks](https://img.shields.io/github/forks/Yihao-Shi/GeoTaichi)          ![Github Downloads (all assets, latest release)](https://img.shields.io/github/downloads/Yihao-Shi/GeoTaichi/latest/total)
+
+## Breif description
+
+A [Taichi](https://github.com/taichi-dev/taichi)-based numerical package for high-performance simulations of multiscale and multiphysics geophysical problems. 
+Developed by [Multiscale Geomechanics Lab](https://person.zju.edu.cn/en/nguo), Zhejiang University.
+
+## Overview
+
+GeoTaichi is a collection of several numerical tools, currently including __Discrete Element Method (DEM)__, __Material Point Method (MPM)__, __Material Point-Discrete element method (MPDEM)__, and __Finite Element Method (FEM)__, that cover the analysis of the __Soil-Gravel-Structure-Interaction__ in geotechnical engineering. The main components of GeoTaichi is illustrated as follows:
+<p align="center">
+    <img src="https://github.com/Yihao-Shi/GeoTaichi/blob/main/images/main_component.png" width="50%" height="50%" />
+</p>
+
+GeoTaichi is a research project that is currently __under development__. Our vision is to share with the geotechnical community a free, open-source (under the GPL-3.0 License) software that facilitates the relevant computational research. In the Taichi ecosystem, we hope to emphasize the potential of Taichi for scientific computing. Furthermore, GeoTaichi is high parallelized, multi-platform (supporting for Windows, Linux and Macs) and multi-architecture (supporting for both CPU and GPU).
+
+## Examples
+### Material point method (MPM)
+- Soil and fluid dynamics
+<p align="center">
+    <img src="https://github.com/Yihao-Shi/GeoTaichi/blob/main/images/soil.gif" width="50%" height="50%" /><img src="https://github.com/Yihao-Shi/GeoTaichi/blob/main/images/newtonian.gif" width="50%" height="50%" />
+</p>
+
+- Strip footing penetration
+<p align="center">
+    <img src="https://github.com/Yihao-Shi/GeoTaichi/blob/main/images/footing.gif" width="50%" height="50%" />
+</p>
+
+### Discrete element method (DEM)
+- Granular packings (more than 1.6 milloin particles)
+<p align="center">
+    <img src="https://github.com/Yihao-Shi/GeoTaichi/blob/main/images/clump.gif" width="50%" height="50%" /><img src="https://github.com/Yihao-Shi/GeoTaichi/blob/main/images/heap_formation.gif" width="50%" height="50%" />
+</p>
+
+- Triaxial shear test
+<p align="center">
+    <img src="https://github.com/Yihao-Shi/GeoTaichi/blob/main/images/shear.gif" width="50%" height="50%" /><img src="https://github.com/Yihao-Shi/GeoTaichi/blob/main/images/force_chain.gif" width="50%" height="50%" />
+</p>
+
+### Coupled material point-discrete element method (MPDEM)
+<p align="center">
+  <img src="https://github.com/Yihao-Shi/GeoTaichi/blob/main/images/mpdem1.gif" width="50%" height="50%" /><img src="https://github.com/Yihao-Shi/GeoTaichi/blob/main/images/mpdem2.gif" width="50%" height="50%" />
+</p>
+
+## Quick start
+### Dependencies
+
+- Python packages
+
+|Package name|Version|Features|
+|:----------:|:-----:|:------:|
+|[python](https://www.python.org/)|>=3.8|Programming language|
+|[psutil](https://pypi.org/project/psutil/)|lastest|Get GPU memory|
+|[taichi](https://pypi.org/project/taichi/)|>=1.6.0|High performance computing|
+|[numpy](https://pypi.org/project/numpy/)|==1.23.5|Pre-processing|
+|[scipy](https://pypi.org/project/SciPy/)|==1.10.1|Pre-processing|
+|[pybind11](https://pypi.org/project/pybind11/)|==2.10.4|Warp C++ code|
+|[trimesh](https://pypi.org/project/trimesh/)|==3.20.1|Import stl/obj files|
+
+- C++ packages
+
+|Package name|Version|Features|
+|:----------:|:-----:|:------:|
+|[cmake](https://cmake.org/)|==3.18.2|/|
+|[eigen](https://eigen.tuxfamily.org/)|==3.4.0|Nurbs function|
+
+### Installation
+
+1. Change the current working directory to the desired location and download the GeoTaichi code:
+```
+cd /path/to/desired/location/
+git clone https://github.com/Yihao-Shi/GeoTaichi
+cd GeoTaichi
+```
+2. Install essential dependencies
+```
+# Install python and pip
+sudo apt-get install python3.8
+sudo apt-get install python3-pip
+
+# Install python packages
+python3 -m pip install taichi imageio pybind11 numpy trimesh psutil -i https://pypi.douban.com/simple
+
+# Install Eigen in C++
+sudo apt-get install libeigen3-dev cmake==3.18.2
+
+# Install pybind11
+git clone https://github.com/pybind/pybind11.git
+cd  pybind11
+mkdir build
+cd build
+cmake ..
+make check -j 4 
+sudo make install
+```
+3. Install CUDA, detailed information can be referred to [official installation guide](https://docs.nvidia.com/cuda/cuda-installation-guide-linux/index.html)
+4. Set up environment variables
+```
+sudo gedit ~/.bashrc
+$ export PYTHONPATH="$PYTHONPATH:/path/to/desired/location/GeoTaichi"
+source ~/.bashrc
+```
+5. If you want to use IGA (Isogeometric analysis) modulus. Note that some of programs are written in C++, which need to be compiled for your architecture:
+```
+python src/utils/NURBS/setup.py install --user
+```
+
+### Working with vtu files
+
+To visualize the VTS files produced by some of the scripts, it is recommended to use Paraview. It can be
+freely downloaded from: http://www.paraview.org/ To visualize the output in ParaView, use the following
+procedure:
+1. Open the .vts or .vtu file in ParaView
+2. Click on the "Apply" button on the left side of the screen
+3. Make sure under "Representation" that "Surface" or "Surface with Edges" is selected
+4. Under "Coloring" select variables and the approriate measure (i.e. "Magnitude", X-direction displacement, etc.)
+
+### Document
+
+Currently, only the tutorial of DEM in Chinese version is available in [doc](https://github.com/Yihao-Shi/GeoTaichi/blob/main/docs/GeoTaichi_tutorial_DEM_Chinese_version.pdf). 
+Users can set up simulations by specifying numerical parameters and configuring the desired simulation settings in a Python script. More detailed about Python scripts can be found in the [example floder](https://github.com/Yihao-Shi/GeoTaichi/tree/main/example).
+
+## Features
+### Discrete Element Method 
+Discrete element method is a powerful tool to simulate the movement of granular materials through a series of calculations that trace individual particles constituting the granular material.
+  - Sphere and multisphere particles
+  - Generating particle packings by specifying initial void ratio or particle number in a box/cylinder/sphere/triangular prism
+  - Two neighbor search algorithms, brust search/linked-cell
+  - Two velocity updating schemes, symlectic Euler/velocity Verlet
+  - Three contact models, including linear elastic, hertz-mindlin and linear rolling
+  - Supporting plane (infinite plane)/facet (servo wall)/triangle patch (suitable for complex boundary condition)
+
+### Material Point Method 
+The material point method (MPM) is a numerical technique used to simulate the behavior of solids, liquids, gases, and any other continuum material. Unlike other mesh-based methods like the finite element method, MPM does not encounter the drawbacks of mesh-based methods (high deformation tangling, advection errors etc.) which makes it a promising and powerful tool in computational mechanics. 
+  - Nine Constitutive Models, including linear elastic/neo-hookean/Von-Mises/isotropic hardening plastic/Mohr-Coulomb/Drucker-Prager/(cohesive) modified cam-clay/Newtonian fluid/Bingham fluid
+  - Two improved velocity projection techniques, including MLS/APIC
+  - Three stress update schemes, including USF/USL/MUSL/APIC
+  - Three stabilization techniques, including mix integration/B-bar method/F-bar method
+  - Two smoothing mehod, including strain/stress smoothing
+  - Supporting Dirichlet (Fix/Reflect/Friction)/Neumann boundary conditions
+  - Supporting total/updating Lagrangian explicit MPM and implicit MPM (Newmark-$\beta$ method)
+  - Free surface detection
+
+### MPDEM coupling
+  - Two contact models, including linear elastic, hertz-mindlin
+  - Support DEM-MPM-Mesh contact, feasible simulating complex boundary conditions 
+  - Multilevel neighbor search
+  - Two way or one way coupling
+
+### Postprocessing
+  - Restart from a specific time step
+  - A simple GUI powered by [Taichi](https://github.com/taichi-dev/taichi)
+  - VTU([Paraview](http://www.paraview.org/)) and NPZ(binary files) files are generated in the process of simualtion
+  - Supporting force chain visualization
+
+## Under development
+  - Developing level set DEM modulus
+  - Developing a well-structured IGA modulus
+  - Optimizing code structures
+  - Simulating soil-gravel-structure problems in geotechnical engineering
+  
+## License
+This project is licensed under the GNU General Public License v3 - see the [LICENSE](https://www.gnu.org/licenses/) for details.
+
+## Citation
+If you find GeoTaichi is helpful, you can [star it](https://github.com/Yihao-Shi/GeoTaichi).
+
+## Acknowledgements
+This is the release version of GeoTaichi, if you need more features such as implicit material point/level set DEM, please contact authors.
+We thank all contributors for their great work and open source spirit.
+
+## Release Notes
+V0.1 (January 21, 2024)
+
+- First release GeoTaichi