first commit

Author: corochann

.flexci/build_and_push.sh

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+#!/bin/bash -uex
+
+IMAGE_BASE="${1:-}"
+IMAGE_PUSH=1
+if [ "${IMAGE_BASE}" = "" ]; then
+  IMAGE_BASE="torch-dftd3"
+  IMAGE_PUSH=0
+fi
+
+TEST_PIP_PACKAGES="
+flake8 pytest pytest-cov pytest-xdist pytest-benchmark
+"
+
+SRC_ROOT="$(cd "$(dirname "${BASH_SOURCE}")/.."; pwd)"
+
+docker_build_and_push() {
+
+  IMAGE_TAG="${1}"; shift
+  IMAGE_NAME="${IMAGE_BASE}:${IMAGE_TAG}"
+
+  pushd "$(dirname ${0})"
+  docker build -f ${SRC_ROOT}/docker/Dockerfile -t "${IMAGE_NAME}" "$@" .
+  popd
+
+  if [ "${IMAGE_PUSH}" = "0" ]; then
+    echo "Skipping docker push."
+  else
+    docker push "${IMAGE_NAME}"
+  fi
+}
+
+WAIT_PIDS=""
+
+# PyTorch 1.5 + Python 3.6
+docker_build_and_push torch15 \
+    --build-arg base_image="nvidia/cuda:10.2-cudnn7-devel-ubuntu18.04" \
+    --build-arg python_version="3.6.12" \
+    --build-arg pip_packages="torch==1.5.* torchvision==0.6.* ${TEST_PIP_PACKAGES}" &
+WAIT_PIDS="$! ${WAIT_PIDS}"
+
+# Wait until the build complete.
+for P in ${WAIT_PIDS}; do
+    wait ${P}
+done

.flexci/config.pbtxt

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+configs {
+  # Project name.
+  key: "torch-dftd.pytest"
+  value {
+    requirement {
+      cpu: 4
+      memory: 16
+      disk: 10
+      gpu: 1
+    }
+    command:
+        "bash -x .flexci/pytest_script.sh"
+  }
+}

.flexci/pytest_script.sh

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+#!/bin/bash
+set -eu
+
+#IMAGE=pytorch/pytorch:1.5.1-cuda10.1-cudnn7-devel
+IMAGE=asia.gcr.io/pfn-public-ci/torch-dftd3-ci:torch15
+
+
+main() {
+  SRC_ROOT="$(cd "$(dirname "${BASH_SOURCE}")/../.."; pwd)"
+
+  prepare_docker &
+  wait
+
+# Build and push docker images for unit tests.
+#  bash -x -c "${SRC_ROOT}/.flexci/build_and_push.sh" \
+#      "${IMAGE}"
+
+# 1st pytest: when xdist is enabled with `-n $(nproc)`, benchmark is not executed.
+# 2nd pytest: only execute pytest-benchmark.
+  docker run --runtime=nvidia --rm --volume="$(pwd)":/workspace -w /workspace \
+    ${IMAGE} \
+    bash -x -c "pip install flake8 pytest pytest-cov pytest-xdist pytest-benchmark && \
+      pip install cupy-cuda102 pytorch-pfn-extras && \
+      pip install -e . && \
+      pysen run lint && \
+      pytest --cov=torch_dftd -n $(nproc) -m 'not slow' tests &&
+      pytest --benchmark-only tests"
+}
+
+
+# prepare_docker makes docker use tmpfs to speed up.
+# CAVEAT: Do not use docker during this is running.
+prepare_docker() {
+  service docker stop
+  mount -t tmpfs -o size=100% tmpfs /var/lib/docker
+  service docker start
+  gcloud auth configure-docker
+}
+
+
+main "$@"

.gitignore

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+# 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/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# 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
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# 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/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# 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/
+
+# PyCharm
+.idea/
+tests/ase_dftd3.out
+tests/ase_dftd3.xyz

LICENSE

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+MIT License
+
+Copyright (c) 2021 Preferred Networks, Inc.
+
+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 the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

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+# torch-dftd
+pytorch implementation of dftd2 [1] & dftd3 [2, 3]
+
+## Install
+
+```bash
+git clone https://github.com/pfnet-research/torch-dftd
+pip install -e .
+```
+
+## Quick start
+
+```python
+from ase.build import molecule
+from torch_dftd.torch_dftd3_calculator import TorchDFTD3Calculator
+
+atoms = molecule("CH3CH2OCH3")
+# device="cuda:0" for fast GPU computation.
+calc = TorchDFTD3Calculator(atoms=atoms, device="cpu", damping="bj")
+
+energy = atoms.get_potential_energy()
+forces = atoms.get_forces()
+
+print(f"energy {energy} eV")
+print(f"forces {forces}")
+```
+
+## Dependency
+
+The library is tested under following environment.
+ - python: 3.6
+ - CUDA: 10.2
+```bash
+torch==1.5.1
+ase==3.21.1
+# Below is only for 3-body term
+cupy-cuda102==8.6.0
+pytorch-pfn-extras==0.3.2
+```
+
+## Development tips
+### Formatting & Linting
+[pysen](https://github.com/pfnet/pysen) is used to format the python code of this repository.<br/>
+You can simply run below to get your code formatted :)
+```bash
+# Format the code
+$ pysen run format
+# Check the code format
+$ pysen run lint
+```
+
+### CUDA Kernel function implementation with cupy
+[cupy](https://github.com/cupy/cupy) supports users to implement CUDA kernels within python code, 
+and it can be easily linked with pytorch tensor calculations.<br/>
+Element wise kernel is implemented and used in some pytorch functions to accelerate speed with GPU.
+
+See [document](https://docs.cupy.dev/en/stable/user_guide/kernel.html) for details about user defined kernel.
+
+## Citation
+
+Please always cite original paper of DFT-D2 [1] or DFT-D3 [2, 3], if you used this software for your publication.
+
+DFT-D2:<br/>
+[1] S. Grimme, J. Comput. Chem, 27 (2006), 1787-1799.
+DOI: [10.1002/jcc.20495](https://doi.org/10.1002/jcc.20495)
+
+DFT-D3:<br/>
+[2] S. Grimme, J. Antony, S. Ehrlich and H. Krieg, J. Chem. Phys, 132 (2010), 154104.
+DOI: [10.1063/1.3382344](https://doi.org/10.1063/1.3382344)
+
+If BJ-damping is used in DFT-D3:<br/> 
+[3] S. Grimme, S. Ehrlich and L. Goerigk, J. Comput. Chem, 32 (2011), 1456-1465.
+DOI: [10.1002/jcc.21759](https://doi.org/10.1002/jcc.21759)

docker/Dockerfile

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+# FROM nvidia/cuda:10.2-cudnn7-devel-ubuntu18.04
+ARG base_image
+FROM ${base_image}
+
+# Install pyenv requirements.
+# https://github.com/pyenv/pyenv/wiki/Common-build-problems#requirements
+RUN export DEBIAN_FRONTEND=noninteractive && \
+    apt-get -y update && \
+    apt-get -y install \
+        build-essential libssl-dev zlib1g-dev libbz2-dev \
+        libreadline-dev libsqlite3-dev wget curl llvm libncurses5-dev libncursesw5-dev \
+        xz-utils tk-dev libffi-dev liblzma-dev git gfortran && \
+    rm -rf /var/lib/apt/lists/* /var/cache/apt/archives/*
+
+# Install pyenv.
+RUN git clone https://github.com/pyenv/pyenv.git /opt/pyenv
+ENV PYENV_ROOT=/opt/pyenv
+ENV PATH ${PYENV_ROOT}/shims:${PYENV_ROOT}/bin:${PATH}
+
+# Install Python.
+ARG python_version
+RUN pyenv install ${python_version} && \
+    pyenv global ${python_version}
+
+# Install test dependencies.
+ARG pip_packages
+RUN pip install -U pip && \
+    pip install ${pip_packages} && \
+    pip list
+
+# Install DFTD3
+RUN cd /tmp && \
+  wget https://www.chemie.uni-bonn.de/pctc/mulliken-center/software/dft-d3/dftd3.tgz && \
+  tar zxvf dftd3.tgz && \
+  make && \
+  mv dftd3 /usr/local/bin && \
+  rm dftd3.tgz