update doc and comment for ethresh in pme
#227
Workflow file for this run
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| name: OpenMM DMFF Plugin tests. | |
| on: | |
| push: | |
| pull_request: | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: [3.9] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install Dependencies | |
| run: | | |
| source $CONDA/bin/activate | |
| conda create -n dmff_omm -y python=${{ matrix.python-version }} numpy openmm=7.7 -c conda-forge | |
| conda activate dmff_omm | |
| conda install -y libtensorflow_cc=2.9.1 -c conda-forge | |
| pip install setuptools==59.5.0 | |
| mkdir /tmp/omm_dmff_working_dir | |
| cd /tmp/omm_dmff_working_dir | |
| wget https://github.com/tensorflow/tensorflow/archive/refs/tags/v2.9.1.tar.gz | |
| tar -xvf v2.9.1.tar.gz | |
| cp -r tensorflow-2.9.1/tensorflow/c ${CONDA_PREFIX}/include/tensorflow/ | |
| git clone https://github.com/serizba/cppflow.git | |
| cd cppflow | |
| git apply ${GITHUB_WORKSPACE}/backend/openmm_dmff_plugin/tests/cppflow_empty_constructor.patch | |
| mkdir ${CONDA_PREFIX}/include/cppflow | |
| cp -r include/cppflow ${CONDA_PREFIX}/include/ | |
| - name: Install OpenMM DMFF Plugin | |
| run: | | |
| source $CONDA/bin/activate dmff_omm | |
| cd ${GITHUB_WORKSPACE}/backend/openmm_dmff_plugin | |
| mkdir build && cd build | |
| export OPENMM_INSTALLED_DIR=$CONDA_PREFIX | |
| export CPPFLOW_INSTALLED_DIR=$CONDA_PREFIX | |
| export LIBTENSORFLOW_INSTALLED_DIR=$CONDA_PREFIX | |
| cmake .. -DOPENMM_DIR=${OPENMM_INSTALLED_DIR} -DCPPFLOW_DIR=${CPPFLOW_INSTALLED_DIR} -DTENSORFLOW_DIR=${LIBTENSORFLOW_INSTALLED_DIR} -DUSE_HIGH_PRECISION=OFF | |
| make && make install | |
| make PythonInstall | |
| - name: Run Tests | |
| run: | | |
| source $CONDA/bin/activate dmff_omm | |
| cd ${GITHUB_WORKSPACE}/backend/ | |
| python -m OpenMMDMFFPlugin.tests.test_dmff_plugin_nve -n 100 --pdb ../examples/water_fullpol/water_dimer.pdb --model ./openmm_dmff_plugin/python/OpenMMDMFFPlugin/data/admp_water_dimer_aux --has_aux True |