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merge devel to master (v3.0.0) (deepmodeling#4407)
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‎.devcontainer/Dockerfile

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FROM mcr.microsoft.com/devcontainers/cpp:1-ubuntu-24.04
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COPY --from=ghcr.io/astral-sh/uv:latest /uv /uvx /bin/

‎.devcontainer/README.md

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# DeePMD-kit devcontainer environment
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This [devcontainer](https://vscode.js.cn/docs/devcontainers/devcontainer-cli) environment setups Python and C++ environment to develop DeePMD-kit.
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One can setup locally or use [GitHub Codespaces](https://docs.github.com/en/codespaces) by clicking the Code button on the DeePMD-kit repository page.
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The whole setup process requires about 10 minutes, so one needs to be patient.
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## Python environment
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The following packages are installed into the Python environment `.venv`:
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- DeePMD-kit (in edit mode)
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- Backends including TensorFlow, PyTorch, JAX
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- LAMMPS
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- MPICH
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- CMake
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- pre-commit (including hooks)
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- Test packages including pytest
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- Doc packages including sphinx
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## C++ interface
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The C++ interface with TensorFlow and PyTorch support is installed into `dp` directory.
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When calling and debuging LAMMPS with DeePMD-kit, use the following scripts instead of the regular `lmp`:
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- `.devcontainer/lmp`
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- `.devcontainer/gdb_lmp`
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Use the following scripts for `pytest` with LAMMPS:
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- `.devcontainer/pytest_lmp`
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- `.devcontainer/gdb_pytest_lmp`
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## Rebuild
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Usually the Python package does not need to reinstall.
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But when one wants to recompile the C++ code, the following scripts can be executed.
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- `.devcontainer/build_cxx.sh`
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- `.devcontainer/build_py.sh`

‎.devcontainer/build_cxx.sh

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#!/bin/bash
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set -ev
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NPROC=$(nproc --all)
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SCRIPT_PATH=$(dirname $(realpath -s $0))
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export CMAKE_PREFIX_PATH=${SCRIPT_PATH}/../libtorch
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TENSORFLOW_ROOT=$(python -c 'import importlib,pathlib;print(pathlib.Path(importlib.util.find_spec("tensorflow").origin).parent)')
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mkdir -p ${SCRIPT_PATH}/../buildcxx/
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cd ${SCRIPT_PATH}/../buildcxx/
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cmake -D ENABLE_TENSORFLOW=ON \
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-D ENABLE_PYTORCH=ON \
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-D CMAKE_INSTALL_PREFIX=${SCRIPT_PATH}/../dp/ \
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-D LAMMPS_VERSION=stable_29Aug2024_update1 \
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-D CMAKE_BUILD_TYPE=Debug \
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-D BUILD_TESTING:BOOL=TRUE \
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-D TENSORFLOW_ROOT=${TENSORFLOW_ROOT} \
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${SCRIPT_PATH}/../source
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cmake --build . -j${NPROC}
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cmake --install .

‎.devcontainer/build_py.sh

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#!/bin/bash
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set -ev
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SCRIPT_PATH=$(dirname $(realpath -s $0))
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cd ${SCRIPT_PATH}/..
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uv sync --dev --python 3.12 --extra cpu --extra torch --extra jax --extra lmp --extra test --extra docs
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pre-commit install

‎.devcontainer/devcontainer.json

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{
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"name": "DeePMD-kit",
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"build": {
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"dockerfile": "Dockerfile"
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},
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"features": {
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"ghcr.io/devcontainers/features/github-cli:1": {}
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},
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"postCreateCommand": ".devcontainer/build_py.sh && .devcontainer/download_libtorch.sh && .devcontainer/build_cxx.sh && pre-commit install-hooks",
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"remoteEnv": {
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"PATH": "${containerEnv:PATH}:${containerWorkspaceFolder}/.venv/bin",
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"DP_ENABLE_PYTORCH": "1",
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"DP_VARIANT": "cpu",
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"LMP_CXX11_ABI_0": "1",
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"UV_EXTRA_INDEX_URL": "https://download.pytorch.org/whl/cpu"
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}
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}

‎.devcontainer/download_libtorch.sh

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#!/bin/bash
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set -ev
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SCRIPT_PATH=$(dirname $(realpath -s $0))
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cd ${SCRIPT_PATH}/..
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wget https://download.pytorch.org/libtorch/cpu/libtorch-cxx11-abi-shared-with-deps-2.5.0%2Bcpu.zip -O ~/libtorch.zip
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unzip ~/libtorch.zip

‎.devcontainer/gdb_lmp

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#!/bin/bash
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SCRIPT_PATH=$(dirname $(realpath -s $0))
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export CMAKE_PREFIX_PATH=${SCRIPT_PATH}/../libtorch
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TENSORFLOW_ROOT=$(python -c 'import importlib,pathlib;print(pathlib.Path(importlib.util.find_spec("tensorflow").origin).parent)')
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env LAMMPS_PLUGIN_PATH=${SCRIPT_PATH}/../dp/lib/deepmd_lmp \
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LD_LIBRARY_PATH=${SCRIPT_PATH}/../dp/lib:${CMAKE_PREFIX_PATH}/lib:${TENSORFLOW_ROOT} \
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gdb ${SCRIPT_PATH}/../.venv/lib/python3.12/site-packages/lammps/lmp "$@"

‎.devcontainer/gdb_pytest_lmp

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#!/bin/bash
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SCRIPT_PATH=$(dirname $(realpath -s $0))/../..
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export CMAKE_PREFIX_PATH=${SCRIPT_PATH}/../libtorch
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TENSORFLOW_ROOT=$(python -c 'import importlib,pathlib;print(pathlib.Path(importlib.util.find_spec("tensorflow").origin).parent)')
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env LAMMPS_PLUGIN_PATH=${SCRIPT_PATH}/../dp/lib/deepmd_lmp \
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LD_LIBRARY_PATH=${SCRIPT_PATH}/../dp/lib:${CMAKE_PREFIX_PATH}/lib:${TENSORFLOW_ROOT} \
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gdb --args python -m pytest -s "$@"

‎.devcontainer/lmp

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#!/bin/bash
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SCRIPT_PATH=$(dirname $(realpath -s $0))
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export CMAKE_PREFIX_PATH=${SCRIPT_PATH}/../libtorch
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TENSORFLOW_ROOT=$(python -c 'import importlib,pathlib;print(pathlib.Path(importlib.util.find_spec("tensorflow").origin).parent)')
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env LAMMPS_PLUGIN_PATH=${SCRIPT_PATH}/../dp/lib/deepmd_lmp \
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LD_LIBRARY_PATH=${SCRIPT_PATH}/../dp/lib:${CMAKE_PREFIX_PATH}/lib:${TENSORFLOW_ROOT} \
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${SCRIPT_PATH}/../.venv/bin/lmp "$@"

‎.devcontainer/pytest_lmp

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#!/bin/bash
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SCRIPT_PATH=$(dirname $(realpath -s $0))/../..
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export CMAKE_PREFIX_PATH=${SCRIPT_PATH}/../libtorch
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TENSORFLOW_ROOT=$(python -c 'import importlib,pathlib;print(pathlib.Path(importlib.util.find_spec("tensorflow").origin).parent)')
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env LAMMPS_PLUGIN_PATH=${SCRIPT_PATH}/../dp/lib/deepmd_lmp \
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LD_LIBRARY_PATH=${SCRIPT_PATH}/../dp/lib:${CMAKE_PREFIX_PATH}/lib:${TENSORFLOW_ROOT} \
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python -m pytest "$@"

‎.git_archival.txt

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node: $Format:%H$
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node-date: $Format:%cI$
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describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$

‎.gitattributes

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# do not show up detailed difference on GitHub
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source/3rdparty/* linguist-generated=true
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source/3rdparty/README.md linguist-generated=false
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.git_archival.txt export-subst

‎.github/ISSUE_TEMPLATE/bug-report.yml

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validations:
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required: true
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- type: input
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id: tf-version
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id: backend-version
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attributes:
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label: TensorFlow Version
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description: "The version will be printed when running DeePMD-kit."
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label: Backend and its version
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description: "The backend and its version will be printed when running DeePMD-kit, e.g. TensorFlow v2.15.0."
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validations:
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required: true
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- type: dropdown

‎.github/ISSUE_TEMPLATE/generic-issue.yml

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validations:
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required: true
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- type: input
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id: tf-version
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id: backend-version
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attributes:
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label: TensorFlow Version
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description: "The version will be printed when running DeePMD-kit."
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label: Backend and its version
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description: "The backend and its version will be printed when running DeePMD-kit, e.g. TensorFlow v2.15.0."
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validations:
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required: true
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- type: textarea

‎.github/labeler.yml

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Python:
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- changed-files:
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- any-glob-to-any-file:
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- deepmd/**/*
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- deepmd_utils/**/*
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- source/tests/**/*
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Docs:
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- changed-files:
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- any-glob-to-any-file: doc/**/*
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Examples:
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- changed-files:
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- any-glob-to-any-file: examples/**/*
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Core:
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- changed-files:
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- any-glob-to-any-file: source/lib/**/*
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CUDA:
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- changed-files:
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- any-glob-to-any-file: source/lib/src/gpu/**/*
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ROCM:
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- changed-files:
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- any-glob-to-any-file: source/lib/src/gpu/**/*
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OP:
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- changed-files:
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- any-glob-to-any-file: source/op/**/*
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C++:
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- changed-files:
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- any-glob-to-any-file: source/api_cc/**/*
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C:
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- changed-files:
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- any-glob-to-any-file: source/api_c/**/*
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LAMMPS:
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- changed-files:
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- any-glob-to-any-file: source/lmp/**/*
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Gromacs:
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- changed-files:
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- any-glob-to-any-file: source/gmx/**/*
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i-Pi:
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- changed-files:
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- any-glob-to-any-file: source/ipi/**/*
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Python:
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- changed-files:
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- any-glob-to-any-file:
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- deepmd/**/*
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- source/tests/**/*
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Docs:
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- changed-files:
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- any-glob-to-any-file: doc/**/*
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Examples:
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- changed-files:
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- any-glob-to-any-file: examples/**/*
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Core:
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- changed-files:
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- any-glob-to-any-file: source/lib/**/*
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CUDA:
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- changed-files:
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- any-glob-to-any-file: source/lib/src/gpu/**/*
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ROCM:
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- changed-files:
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- any-glob-to-any-file: source/lib/src/gpu/**/*
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OP:
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- changed-files:
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- any-glob-to-any-file: source/op/**/*
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C++:
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- changed-files:
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- any-glob-to-any-file: source/api_cc/**/*
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C:
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- changed-files:
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- any-glob-to-any-file: source/api_c/**/*
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LAMMPS:
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- changed-files:
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- any-glob-to-any-file: source/lmp/**/*
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Gromacs:
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- changed-files:
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- any-glob-to-any-file: source/gmx/**/*
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i-PI:
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- changed-files:
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- any-glob-to-any-file: source/ipi/**/*

‎.github/workflows/build_cc.yml

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on:
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push:
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branches-ignore:
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- "gh-readonly-queue/**"
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pull_request:
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merge_group:
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref || github.run_id }}
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cancel-in-progress: true
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name: Build C++
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jobs:
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buildcc:
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name: Build C++
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runs-on: ubuntu-latest
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runs-on: ubuntu-22.04
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strategy:
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matrix:
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include:
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- uses: actions/setup-python@v5
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with:
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python-version: '3.11'
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cache: 'pip'
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- uses: lukka/get-cmake@latest
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- run: python -m pip install tensorflow
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- run: python -m pip install uv
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- run: source/install/uv_with_retry.sh pip install --system tensorflow
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- name: Download libtorch
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run: |
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wget https://download.pytorch.org/libtorch/cpu/libtorch-cxx11-abi-shared-with-deps-2.1.2%2Bcpu.zip -O libtorch.zip
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unzip libtorch.zip
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- run: |
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wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2204/x86_64/cuda-keyring_1.0-1_all.deb \
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&& sudo dpkg -i cuda-keyring_1.0-1_all.deb \
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&& sudo apt-get update \
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&& sudo apt-get install -y rocm-dev hipcub-dev
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if: matrix.variant == 'rocm'
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- run: source/install/build_cc.sh
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- run: |
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export CMAKE_PREFIX_PATH=$GITHUB_WORKSPACE/libtorch
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source/install/build_cc.sh
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env:
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DP_VARIANT: ${{ matrix.dp_variant }}
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DOWNLOAD_TENSORFLOW: "FALSE"
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CMAKE_GENERATOR: Ninja
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if: matrix.variant != 'clang'
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- run: source/install/build_cc.sh
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- run: |
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export CMAKE_PREFIX_PATH=$GITHUB_WORKSPACE/libtorch
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source/install/build_cc.sh
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env:
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DP_VARIANT: cpu
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DOWNLOAD_TENSORFLOW: "FALSE"

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