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‎.github/workflows/test_openmm_dmff_plugin.yml‎

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

‎.github/workflows/ut.yml‎

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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: [3.8]
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python-version: [3.9]
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python ${{ matrix.python-version }}
@@ -19,17 +19,19 @@ jobs:
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- name: Install Dependencies
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run: |
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source $CONDA/bin/activate
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$CONDA/bin/conda update -n base -c defaults conda
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conda install pip
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conda update pip
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conda install numpy openmm pytest rdkit biopandas openbabel -c conda-forge
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pip install jax jax_md
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pip install mdtraj==1.9.7 pymbar==4.0.1
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conda create -n dmff -y python=${{ matrix.python-version }} numpy openmm==7.7.0 pytest rdkit openbabel mdtraj ambertools -c conda-forge
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conda activate dmff
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pip install --upgrade pip
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pip install jax jaxlib jaxopt networkx parmed pymbar==4.0.1 optax tqdm
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- name: Install DMFF
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run: |
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source $CONDA/bin/activate
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pip install .
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source $CONDA/bin/activate dmff && pip install .
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- name: Run Tests
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run: |
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source $CONDA/bin/activate
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pytest -vs tests/
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source $CONDA/bin/activate dmff
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pytest -vs tests/test_classical/test_*
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pytest -vs tests/test_common/test_*
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pytest -vs tests/test_admp/test_*
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pytest -vs tests/test_utils.py
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pytest -vs tests/test_mbar/test_*
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pytest -vs tests/test_sgnn/test_*

‎.gitignore‎

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*/_version.py
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# hmtff cache
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*.hmtff/
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*.hmtff/
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# debugging ipynb
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debug.ipynb
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test.xml
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# PyCharm Cache
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.idea/

‎README.md‎

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# DMFF
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3-
[![doi:10.26434/chemrxiv-2022-2c7gv](https://img.shields.io/badge/DOI-10.26434%2Fchemrxiv--2022--2c7gv-blue)](https://doi.org/10.26434/chemrxiv-2022-2c7gv)
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[![DOI: 10.1021/acs.jctc.2c01297](https://img.shields.io/badge/DOI-10.1021%2Facs.jctc.2c01297-blue)](https://pubs.acs.org/doi/10.1021/acs.jctc.2c01297)
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## About DMFF
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@@ -10,24 +10,34 @@ The behavior of organic molecular systems (e.g., protein folding, polymer struct
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### License and credits
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The project DMFF is licensed under [GNU LGPL v3.0](LICENSE). If you use this code in any future publications, please cite this using `Wang X, Li J, Yang L, Chen F, Wang Y, Chang J, et al. DMFF: An Open-Source Automatic
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Differentiable Platform for Molecular Force Field
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Development and Molecular Dynamics
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Simulation. ChemRxiv. Cambridge: Cambridge Open Engage; 2022; This content is a preprint and has not been peer-reviewed.`
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The project DMFF is licensed under [GNU LGPL v3.0](LICENSE). If you use this code in any future publications, please cite this using `Xinyan Wang, Jichen Li, Lan Yang, Feiyang Chen, Yingze Wang, Junhan Chang, Junmin Chen, Wei Feng, Linfeng Zhang, and Kuang Yu
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Journal of Chemical Theory and Computation 2023 19 (17), 5897-5909
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DOI: 10.1021/acs.jctc.2c01297`
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## User Guide
1918

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+ [1. Introduction](docs/user_guide/introduction.md)
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+ [2. Installation](docs/user_guide/installation.md)
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+ [3. Basic usage](docs/user_guide/usage.md)
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+ [4. XML format force field](docs/user_guide/xml_spec.md)
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+ [5. Theory](docs/user_guide/theory.md)
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+ [1. Introduction](docs/user_guide/1.introduction.md)
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+ [2. Installation](docs/user_guide/2.installation.md)
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+ [3. Basic Usage](docs/user_guide/3.usage.md)
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+ [4. Modules](docs/user_guide/4.modules.md)
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+ [Classical](docs/user_guide/4.1classical.md)
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+ [ADMP](docs/user_guide/4.2ADMPPmeForce.md)
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+ [Qeq](docs/user_guide/4.3ADMPQeqForce.md)
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+ [Machine Learning](docs/user_guide/4.4MLForce.md)
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+ [Optimization](docs/user_guide/4.5Optimization.md)
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+ [Mbar Estimator](docs/user_guide/4.6MBAR.md)
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+ [OpenMM Plugin](docs/user_guide/4.7OpenMMplugin.md)
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+ [5. Advanced examples](docs/user_guide/DMFF_example.ipynb)
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+ [And here is a tutorial notebook of the basic usage of DMFF. Welcome to read it and get started with DMFF!](docs/user_guide/test.ipynb)
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[And here is a tutorial notebook, which would tell you some basic usage of DMFF. Welcome to read it and get started witn DMFF！](docs/user_guide/test.ipynb)
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## Developer Guide
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+ [1. Introduction](docs/dev_guide/introduction.md)
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+ [2. Software architecture](docs/dev_guide/arch.md)
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+ [3. Coding conventions](docs/dev_guide/convention.md)
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+ [4. Document writing](docs/dev_guide/write_docs.md)
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+ [5. An example for developing: how to write a generator?](docs/dev_guide/generator.ipynb)
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## Code Structure
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+ `package`: files for constructing packages or images, such as conda recipe and docker files.
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+ `tests`: unit tests.
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+ `dmff`: DMFF python codes
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+ `dmff/api`: source code of application programming interface of DMFF.
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+ `dmff/admp`: source code of automatic differentiable multipolar polarizable (ADMP) force field module.
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+ `dmff/classical`: source code of classical force field module.
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+ `dmff/common`: source code of common functions, such as neighbor list.
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+ `dmff/generators`: source code of force generators.
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+ `dmff/sgnn`: source of subgragh neural network force field model.
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+ `dmff/eann`: source of embedded atom neural network force field model.
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+ `dmff/generators`: source code of force generators.
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+ `dmff/operators`: source code of operators.
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4761
## Support and Contribution
4862

‎backend/c_api/CMakeLists.txt‎

Whitespace-only changes.

‎backend/cpp_api/CMakeLists.txt‎

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‎backend/openmm_dmff_plugin/.gitignore‎

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**/build
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**/.vscode
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**/__pycache__
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*.dcd
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**/output
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**/.devcontainer

‎backend/openmm_dmff_plugin/CMakeLists.txt‎

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#---------------------------------------------------
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# OpenMM DMFF Plugin
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#----------------------------------------------------
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CMAKE_MINIMUM_REQUIRED(VERSION 3.5)
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SET(CMAKE_VERBOSE_MAKEFILE OFF)
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project(OpenMMDMFF)
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# We need to know where OpenMM is installed so we can access the headers and libraries.
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SET(OPENMM_DIR "/usr/local/openmm" CACHE PATH "Where OpenMM is installed")
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INCLUDE_DIRECTORIES("${OPENMM_DIR}/include")
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LINK_DIRECTORIES("${OPENMM_DIR}/lib" "${OPENMM_DIR}/lib/plugins")
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# Include the cppflow
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SET(CPPFLOW_DIR "/usr/local/cppflow/" CACHE PATH "Where cppflow is installed")
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INCLUDE_DIRECTORIES("${CPPFLOW_DIR}/include")
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LINK_DIRECTORIES("${CPPFLOW_DIR}/lib")
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# Include the tensorflow
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SET(TENSORFLOW_DIR "/usr/local/tensorflow/" CACHE PATH "Where libtensorflow is installed")
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INCLUDE_DIRECTORIES("${TENSORFLOW_DIR}/include")
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LINK_DIRECTORIES("${TENSORFLOW_DIR}/lib")
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# Specify the C++ version we are building for.
27+
SET (CMAKE_CXX_STANDARD 17)
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set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-ignored-attributes -Wl,--allow-multiple-definition -Wl,--no-as-needed")
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# Set if high precision (double) is used. By default, it is off.
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OPTION(USE_HIGH_PRECISION "Use high precision (double) for calculations" OFF)
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IF(USE_HIGH_PRECISION)
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message(STATUS "USE_HIGH_PRECISION is enabled")
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ADD_DEFINITIONS(-DUSE_HIGH_PRECISION)
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endif ()
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if (USE_HIGH_PRECISION)
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set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DHIGH_PRECISION")
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else ()
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set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
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endif ()
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# Select where to install
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IF(${CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT})
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IF(WIN32)
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SET(CMAKE_INSTALL_PREFIX "$ENV{ProgramFiles}/OpenMM" CACHE PATH "Where to install the plugin" FORCE)
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ELSE(WIN32)
50+
SET(CMAKE_INSTALL_PREFIX "${OPENMM_DIR}" CACHE PATH "Where to install the plugin" FORCE)
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ENDIF(WIN32)
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ENDIF(${CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT})
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# Put all the tests and libraries in a single output directory.
55+
IF(NOT EXECUTABLE_OUTPUT_PATH)
56+
SET(EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR}
57+
CACHE INTERNAL "Single output directory for building all executables.")
58+
ENDIF()
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IF(NOT LIBRARY_OUTPUT_PATH)
60+
SET(LIBRARY_OUTPUT_PATH ${PROJECT_BINARY_DIR}
61+
CACHE INTERNAL "Single output directory for building all libraries.")
62+
ENDIF()
63+
SET(${PROJECT_NAME}_EXECUTABLE_DIR ${EXECUTABLE_OUTPUT_PATH}/${CMAKE_CFG_INTDIR})
64+
SET(${PROJECT_NAME}_LIBRARY_DIR ${LIBRARY_OUTPUT_PATH}/${CMAKE_CFG_INTDIR})
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# The source is organized into subdirectories, but we handle them all from
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# this CMakeLists file rather than letting CMake visit them as SUBDIRS.
68+
SET(DMFF_PLUGIN_SOURCE_SUBDIRS openmmapi serialization)
69+
70+
# Set the library name
71+
SET(DMFF_LIBRARY_NAME OpenMMDMFF)
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SET(SHARED_DMFF_TARGET ${DMFF_LIBRARY_NAME})
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# These are all the places to search for header files that are to be part of the API.
75+
SET(API_INCLUDE_DIRS "openmmapi/include" "openmmapi/include/internal")
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# Locate header files.
78+
SET(API_INCLUDE_FILES)
79+
FOREACH(dir ${API_INCLUDE_DIRS})
80+
FILE(GLOB fullpaths ${dir}/*.h)
81+
SET(API_INCLUDE_FILES ${API_INCLUDE_FILES} ${fullpaths})
82+
ENDFOREACH(dir)
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# Collect source files
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SET(SOURCE_FILES) # empty
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SET(SOURCE_INCLUDE_FILES)
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FOREACH(subdir ${DMFF_PLUGIN_SOURCE_SUBDIRS})
88+
FILE(GLOB src_files ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/src/*.cpp)
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FILE(GLOB incl_files ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/src/*.h)
90+
SET(SOURCE_FILES ${SOURCE_FILES} ${src_files}) #append
91+
SET(SOURCE_INCLUDE_FILES ${SOURCE_INCLUDE_FILES} ${incl_files})
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93+
## Make sure we find these locally before looking in OpenMM/include if
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## OpenMM was previously installed there.
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INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include)
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ENDFOREACH(subdir)
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# Create the library.
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ADD_LIBRARY(${SHARED_DMFF_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_INCLUDE_FILES})
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SET_TARGET_PROPERTIES(${SHARED_DMFF_TARGET}
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PROPERTIES COMPILE_FLAGS "-DDMFF_BUILDING_SHARED_LIBRARY ${EXTRA_COMPILE_FLAGS}"
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LINK_FLAGS "${EXTRA_COMPILE_FLAGS}")
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TARGET_LINK_LIBRARIES(${SHARED_DMFF_TARGET} OpenMM)
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TARGET_LINK_LIBRARIES(${SHARED_DMFF_TARGET} tensorflow_cc)
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INSTALL_TARGETS(/lib RUNTIME_DIRECTORY /lib ${SHARED_DMFF_TARGET})
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# install headers
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FILE(GLOB API_ONLY_INCLUDE_FILES "openmmapi/include/*.h")
111+
INSTALL (FILES ${API_ONLY_INCLUDE_FILES} DESTINATION include)
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FILE(GLOB API_ONLY_INCLUDE_FILES_INTERNAL "openmmapi/include/internal/*.h")
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INSTALL (FILES ${API_ONLY_INCLUDE_FILES_INTERNAL} DESTINATION include/internal)
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# Enable testing
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# Set no testing here.
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ENABLE_TESTING()
118+
ADD_SUBDIRECTORY(serialization/tests)
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# Use reference platform default.
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ADD_SUBDIRECTORY(platforms/reference)
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FIND_PACKAGE(CUDA QUIET)
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IF(CUDA_FOUND)
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message(STATUS "CUDA found, building CUDA implementation")
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SET(PLUGIN_BUILD_CUDA_LIB ON CACHE BOOL "Build implementation for CUDA: ON")
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ELSE(CUDA_FOUND)
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message(STATUS "CUDA not found, not building CUDA implementation")
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SET(PLUGIN_BUILD_CUDA_LIB OFF CACHE BOOL "Build implementation for CUDA: OFF")
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ENDIF(CUDA_FOUND)
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IF(PLUGIN_BUILD_CUDA_LIB)
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ADD_SUBDIRECTORY(platforms/cuda)
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ENDIF(PLUGIN_BUILD_CUDA_LIB)
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# Build the Python API
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FIND_PROGRAM(PYTHON_EXECUTABLE python)
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FIND_PROGRAM(SWIG_EXECUTABLE swig)
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IF(PYTHON_EXECUTABLE AND SWIG_EXECUTABLE)
140+
message(STATUS "Python and SWIG found, building Python wrappers")
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SET(PLUGIN_BUILD_PYTHON_WRAPPERS ON CACHE BOOL "Build wrappers for Python")
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ELSE(PYTHON_EXECUTABLE AND SWIG_EXECUTABLE)
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message(FATAL_ERROR "Python or SWIG not found, not building Python wrappers")
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SET(PLUGIN_BUILD_PYTHON_WRAPPERS OFF CACHE BOOL "Build wrappers for Python")
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ENDIF(PYTHON_EXECUTABLE AND SWIG_EXECUTABLE)
146+
IF(PLUGIN_BUILD_PYTHON_WRAPPERS)
147+
ADD_SUBDIRECTORY(python)
148+
ENDIF(PLUGIN_BUILD_PYTHON_WRAPPERS)
149+

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