merge devel to master (v3.0.0) (#4407)

Author: njzjz

.devcontainer/Dockerfile

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

.devcontainer/README.md

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

.devcontainer/build_cxx.sh

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

.devcontainer/build_py.sh

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

.devcontainer/devcontainer.json

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

.devcontainer/download_libtorch.sh

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

.devcontainer/gdb_lmp

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

.devcontainer/gdb_pytest_lmp

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

.devcontainer/lmp

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

.devcontainer/pytest_lmp

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