material model refactor - along with some other things (#17)

* restructured how to define macrscale loading in the input file * Delete 3d0_MFL_0.h5 * Delete sphere.h5 * refactored postprocess in solver.h * Add marimo notebook to create fans-input files * nc * Delete .gitignore * added marimo_inputs * v_u is initialized to 0 in the solver constructor only * material model refactor * added some stuff to Readme * added VonMisesPlasticLinearIsotropicHardening * added a FANS Dashboard * added postprocessing for VonMises and PseudoPlastic matmodels * phase-wise stress and strain averages can be written to the h5 file * updated dashboard utilities * LinearElasticIsotropic also expects bulk and shear modulus as input now * commit before merging dev PR * final commit before PR --------- Co-authored-by: Claudius Haag <[email protected]>
DataAnalyticsEngineering · Aug 20, 2024 · 99cafd2 · 99cafd2
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diff --git a/.gitignore b/.gitignore
@@ -60,13 +60,145 @@ Thumbs.db
 # Ignore package manager directories
 pip-wheel-metadata/
 
+!fans_input.grid.json
+!fans_input.slides.json
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+docs/_static/
+docs/_autosummary/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# MkDocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pyright type checker
+.pyright/
+
+# End of standard Python ignores
+
+
 # Extra
 *.xdmf
 FANS
 *.log
 run.sh
-
 *.h5
-!sphere.h5
 data_gen/
-*.json
+*.json
+
+
+# Test microstructure files
+!sphere.h5
+
+# Test input files
+!test_LinearElasticIsotropic.json
+!test_LinearThermalIsotropic.json
+!test_PseudoPlasticLinearHardening.json
+!test_VonMisesPlasticLinearIsotropicHardening.json
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -131,14 +131,19 @@ set_property(TARGET FANS_FANS PROPERTY PUBLIC_HEADER
         include/solverCG.h
         include/solverFP.h
         include/solver.h
+        include/setup.h
+
+        include/material_models/LinearThermalIsotropic.h
+        include/material_models/LinearElasticIsotropic.h
+        include/material_models/PseudoPlasticLinearHardening.h
+        include/material_models/VonMisesPlasticLinearIsotropicHardening.h
 )
 
 # ##############################################################################
 # SOURCES
 # ##############################################################################
 
 target_sources(FANS_FANS PRIVATE
-        src/matmodel.cpp
         src/reader.cpp
 )
 

diff --git a/README.md b/README.md
@@ -16,6 +16,38 @@ You can either build FANS yourself, or use one of our prebuilt packages (see [Ta
 
 ### Prerequisites
 
+Before proceeding with the installation, ensure that your system has the necessary dependencies. The prerequisites of FANS can be installed using Spack for a streamlined setup on high-performance computing systems, or through traditional package management for personal use.
+
+#### Spack Installation (Recommended for Clusters/Supercomputers)
+
+Spack is a package manager designed for high-performance computing environments. It simplifies the installation of complex software stacks, making it ideal for setting up FANS on large clusters or supercomputers.
+
+1. **Install Spack**: If you don’t have Spack installed, you can set it up with the following commands:
+    ```bash
+    git clone https://github.com/spack/spack.git
+    cd spack/bin
+    source ./spack
+    ```
+
+2. **Install Dependencies**: Once Spack is set up, you can install the required dependencies:
+    ```bash
+    spack install cmake
+    spack install mpi
+    spack install hdf5 +cxx +mpi
+    spack install eigen
+    spack install fftw +mpi
+    ```
+    You can also use alternative and optimized FFTW implementations depending on your system's architecture like amdfftw (For AMD systems) or cray-fftw (For Cray systems) or fujitsu-fftw (For Fujitsu systems).
+    
+3. **Load Dependencies** Once dependencies are installed, you can load them before building:
+    ```
+    spack load cmake mpi hdf5 eigen fftw
+    ```
+
+#### Traditional Installation
+
+If you're setting up FANS on a personal computer or in a non-HPC environment, follow these instructions:
+
 Please ensure you have the following dependencies installed on your system:
 
 - CMake (version 3.0 or higher)
@@ -38,7 +70,7 @@ If for some reason you are unable to install these packages directly on your hos
 
 1. Clone the repository:
     ```sh
-    git clone https://github.tik.uni-stuttgart.de/SanathKeshav/FANS.git
+    git clone https://github.tik.uni-stuttgart.de/DAE/FANS.git
     cd FANS
     ```
 2. Configure the project using CMake:
@@ -52,7 +84,7 @@ If for some reason you are unable to install these packages directly on your hos
     ```sh
     cmake --build . -j
     ```
-The compilation will symlink the generated FANS binary into the `test/` directory for convenience.
+The compilation will symlink the generated `FANS` binary into the `test/` directory for convenience.
 
 ### Build Options
 This project supports the following CMake build options:
@@ -84,16 +116,11 @@ After compiling, you can install FANS (system-wide) using the following options:
 
 ## Usage
 
-To run the FANS solver, you need to provide a JSON input file specifying the problem parameters. Here is the command to run FANS:
+To run the FANS solver, you need to provide a JSON input file specifying the problem parameters. 
 
-```sh
-nohup /usr/bin/time -v mpiexec -n 1 ./FANS path/to/your/input_file.json &
-```
-
-## Input File Format
+### Input File Format
 
 The input file is in JSON format and contains several fields to define the problem settings:
-- `comment`: Optional field for comments.
 - `ms_filename`: Path to the microstructure file (HDF5 format).
 - `ms_datasetname`: Path to the dataset inside the HDF5 file.
 - `ms_L`: List defining the domain size.
@@ -105,13 +132,80 @@ The input file is in JSON format and contains several fields to define the probl
 - `n_it`: Maximum number of iterations.
 - `g0`: Macroscale loading vector.
 
-## Example
+### Example
 
 To run a linear elastic mechanical homogenization problem for a single load case on a microstructure image of size `256 x 256 x 256` with a single spherical inclusion,
 
 ```sh
 mpiexec -n 1 ./FANS input_files/sphere_mech.json
 ```
 
+## Contributing
+
+We welcome contributions to FANS! Whether you're fixing bugs, adding features, or improving documentation, your help is appreciated. Please follow the guidelines below to ensure smooth collaboration.
+
+### How to Contribute
+
+1. **Fork and Clone**: Fork the repository on GitHub and clone your fork locally.
+    ```bash
+    git clone https://github.com/your-username/FANS.git
+    cd FANS
+    ```
+
+2. **Create a Branch**: Create a branch for your work, using a descriptive name.
+    ```bash
+    git checkout -b feature/my-feature
+    ```
+
+3. **Make Changes**: Implement your changes, adhering to the [Code Style Guidelines](#code-style-guidelines).
+
+4. **Write Tests**: Ensure new features or bug fixes are covered by tests.
+
+5. **Commit and Push**: Commit your changes with a clear message, then push to your fork.
+    ```bash
+    git add .
+    git commit -m "Describe your changes"
+    git push origin feature/my-feature
+    ```
+
+6. **Create a Pull Request**: Open a pull request to the `develop` branch. Include relevant details, such as the issue being fixed or the feature being added.
+
+### Code Style Guidelines
+
+- **C++ Standard**: Use C++17 or later.
+- **Indentation**: 4 spaces, no tabs.
+- **Naming**: 
+    - Functions: `camelCase`
+    - Classes: `PascalCase`
+    - Variables: `snake_case`
+    - Constants: `ALL_CAPS`
+- **Documentation**: Use Doxygen-style comments.
+
+### Branching and Merging
+
+- **`main`**: Latest stable release.
+- **`develop`**: Active development. Base your feature branches off `develop`.
+- **Feature branches**: Branch off `develop` and submit pull requests back to `develop`.
+- **Release branches**: Merged into `main` for new releases.
+
+### Issue Reporting
+
+Use GitHub Issues to report bugs or request features. Include a clear description, steps to reproduce, and relevant details (e.g., OS, compiler).
+
+### Code of Conduct
+
+Please review our [Code of Conduct](CODE_OF_CONDUCT.md) to ensure a respectful and inclusive community.
+
+### Contributor License Agreement (CLA)
+
+By contributing, you agree that your contributions will be licensed under the project's license. You may be asked to sign a Contributor License Agreement (CLA).
+
+Thank you for contributing to FANS! Your efforts help make this project better for everyone.
+
+
+## Acknowledgements
+Funded by Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy - EXC 2075 – 390740016. Contributions by Felix Fritzen are funded by Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) within the Heisenberg program - DFG-FR2702/8 - 406068690; DFG-FR2702/10 - 517847245 and through NFDI-MatWerk - NFDI 38/1 - 460247524. We acknowledge the support by the Stuttgart Center for Simulation Science (SimTech).
+
+
 
 
diff --git a/docker/README.md b/docker/README.md
@@ -60,7 +60,7 @@ For convenience we added some basic utilities to our `fans-dev` image including
 ### Attaching Visual Studio Code
 You can attach VS Code to the newly created container in order to actually work inside the container. This has the benefit that IntelliSense and other static analysis tools have access to all the headers of FANS' dependencies which would not be possible when developing on the host and only using the container for building FANS.
 
-To attach VS Code you need to install the `Remomte Development Extension Pack` and the `Docker` Extension. Then open the Docker menu, right click our newly created `fans-dev` container and select "Start" (if not running already) and then "Attach Visual Studio Code".
+To attach VS Code you need to install the `Remote Development Extension Pack` and the `Docker` Extension. Then open the Docker menu, right click our newly created `fans-dev` container and select "Start" (if not running already) and then "Attach Visual Studio Code".
 
 After attaching VS Code you unfortunately are user `root` in VS Code due to the way the UID and GID mapping is implemented: The container starts as root, executes the entrypoint script which changes UID and GID and only then drops privileges using `gosu`. VS Code though skips the entrypoint script and thus doesn't switch to the non-root user `develop`. You however can do so manually by typing `gosu develop bash` in your terminal sessions inside VS Code.