merge devel to master (v3.1.1)

.devcontainer/build_cxx.sh

@@ -5,15 +5,15 @@ 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)')
+TENSORFLOW_ROOT=$(python -c 'import importlib.util,pathlib;print(pathlib.Path(importlib.util.find_spec("tensorflow").origin).parent)')
 
 mkdir -p ${SCRIPT_PATH}/../buildcxx/
 cd ${SCRIPT_PATH}/../buildcxx/
 cmake -D ENABLE_TENSORFLOW=ON \
 	-D ENABLE_PYTORCH=ON \
 	-D ENABLE_PADDLE=ON \
 	-D CMAKE_INSTALL_PREFIX=${SCRIPT_PATH}/../dp/ \
-	-D LAMMPS_VERSION=stable_29Aug2024_update1 \
+	-D LAMMPS_VERSION=stable_22Jul2025_update1 \
 	-D CMAKE_BUILD_TYPE=Debug \
 	-D BUILD_TESTING:BOOL=TRUE \
 	-D TENSORFLOW_ROOT=${TENSORFLOW_ROOT} \

.devcontainer/devcontainer.json

@@ -11,7 +11,6 @@
     "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

@@ -4,5 +4,5 @@ set -ev
 SCRIPT_PATH=$(dirname $(realpath -s $0))
 cd ${SCRIPT_PATH}/..
 
-wget https://download.pytorch.org/libtorch/cpu/libtorch-cxx11-abi-shared-with-deps-2.7.0%2Bcpu.zip -O ~/libtorch.zip
+wget https://download.pytorch.org/libtorch/cpu/libtorch-cxx11-abi-shared-with-deps-2.8.0%2Bcpu.zip -O ~/libtorch.zip
 unzip ~/libtorch.zip

.devcontainer/gdb_lmp

@@ -2,7 +2,7 @@
 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)')
+TENSORFLOW_ROOT=$(python -c 'import importlib.util,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} \

.devcontainer/gdb_pytest_lmp

@@ -2,7 +2,7 @@
 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)')
+TENSORFLOW_ROOT=$(python -c 'import importlib.util,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} \

.devcontainer/lmp

@@ -2,7 +2,7 @@
 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)')
+TENSORFLOW_ROOT=$(python -c 'import importlib.util,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} \

.devcontainer/pytest_lmp

@@ -2,7 +2,7 @@
 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)')
+TENSORFLOW_ROOT=$(python -c 'import importlib.util,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} \

.github/workflows/build_cc.yml

@@ -2,6 +2,9 @@ on:
   push:
     branches-ignore:
       - "gh-readonly-queue/**"
+      - "copilot/**"
+      - "dependabot/**"
+      - "pre-commit-ci-update-config"
   pull_request:
   merge_group:
 concurrency:
@@ -26,14 +29,14 @@ jobs:
         - variant: clang
           dp_variant: clang
     steps:
-    - uses: actions/checkout@v4
-    - uses: actions/setup-python@v5
+    - uses: actions/checkout@v5
+    - uses: actions/setup-python@v6
       with:
         python-version: '3.11'
     - uses: lukka/get-cmake@latest
     - run: python -m pip install uv
     - run: source/install/uv_with_retry.sh pip install --system tensorflow
-    - run: source/install/uv_with_retry.sh pip install --system 'torch==2.7' --index-url https://download.pytorch.org/whl/cpu
+    - run: source/install/uv_with_retry.sh pip install --system 'torch==2.8.*' --index-url https://download.pytorch.org/whl/cpu
     - run: |
          wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2204/x86_64/cuda-keyring_1.0-1_all.deb \
          && sudo dpkg -i cuda-keyring_1.0-1_all.deb \

.github/workflows/build_wheel.yml

@@ -4,6 +4,9 @@ on:
   push:
     branches-ignore:
       - "gh-readonly-queue/**"
+      - "copilot/**"
+      - "dependabot/**"
+      - "pre-commit-ci-update-config"
     tags:
       - "v*"
   pull_request:
@@ -54,7 +57,7 @@ jobs:
             platform_id: manylinux_aarch64
             dp_variant: cpu
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           # https://github.com/pypa/setuptools_scm/issues/480
           fetch-depth: 0
@@ -70,7 +73,7 @@ jobs:
           rm -rf .git
         if: matrix.dp_pkg_name == 'deepmd-kit-cu11'
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.23
+        uses: pypa/cibuildwheel@v3.1
         env:
           CIBW_BUILD_VERBOSITY: 1
           CIBW_ARCHS: all
@@ -87,7 +90,7 @@ jobs:
     name: Build source distribution
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
       - name: Build sdist
@@ -106,7 +109,7 @@ jobs:
       id-token: write
     if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v')
     steps:
-      - uses: actions/download-artifact@v4
+      - uses: actions/download-artifact@v5
         with:
           pattern: cibw-*
           path: dist
@@ -128,8 +131,8 @@ jobs:
     steps:
       - name: Delete huge unnecessary tools folder
         run: rm -rf /opt/hostedtoolcache
-      - uses: actions/checkout@v4
-      - uses: actions/download-artifact@v4
+      - uses: actions/checkout@v5
+      - uses: actions/download-artifact@v5
         with:
           path: source/install/docker/dist
           pattern: cibw-*-manylinux_x86_64-cu${{ matrix.cuda_version }}*
@@ -162,12 +165,12 @@ jobs:
     needs: [build_wheels, build_sdist]
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/download-artifact@v4
+      - uses: actions/download-artifact@v5
         with:
           path: dist/packages
           pattern: cibw-*
           merge-multiple: true
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v6
         name: Install Python
         with:
           python-version: '3.11'
@@ -176,7 +179,7 @@ jobs:
           ls dist/packages > package_list.txt
           dumb-pypi --output-dir dist --packages-url ../../packages --package-list package_list.txt --title "DeePMD-kit Developed Packages"
       - name: Upload Pages artifact
-        uses: actions/upload-pages-artifact@v3
+        uses: actions/upload-pages-artifact@v4
         with:
           path: dist
   deploy_pypi_index:

.github/workflows/codeql.yml

@@ -4,6 +4,9 @@ on:
   push:
     branches-ignore:
       - "gh-readonly-queue/**"
+      - "copilot/**"
+      - "dependabot/**"
+      - "pre-commit-ci-update-config"
   pull_request:
   schedule:
     - cron: '45 2 * * 2'
@@ -27,8 +30,8 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v4
-    - uses: actions/setup-python@v5
+      uses: actions/checkout@v5
+    - uses: actions/setup-python@v6
       with:
         python-version: '3.11'
         cache: 'pip'
@@ -41,7 +44,7 @@ jobs:
          && sudo apt-get update \
          && sudo apt-get -y install cuda-cudart-dev-12-2 cuda-nvcc-12-2
         python -m pip install tensorflow
-        python -m pip install 'torch==2.7' --index-url https://download.pytorch.org/whl/cpu
+        python -m pip install 'torch==2.8.*' --index-url https://download.pytorch.org/whl/cpu
       env:
         DEBIAN_FRONTEND: noninteractive
     # Initializes the CodeQL tools for scanning.

.github/workflows/copilot-setup-steps.yml

@@ -0,0 +1,69 @@
+name: "Copilot Setup Steps"
+
+# Automatically run the setup steps when they are changed to allow for easy validation, and
+# allow manual testing through the repository's "Actions" tab
+on:
+  workflow_dispatch:
+  push:
+    branches-ignore:
+      - "copilot/**"
+      - "dependabot/**"
+      - "pre-commit-ci-update-config"
+    paths:
+      - .github/workflows/copilot-setup-steps.yml
+  pull_request:
+    paths:
+      - .github/workflows/copilot-setup-steps.yml
+
+jobs:
+  # The job MUST be called `copilot-setup-steps` or it will not be picked up by Copilot.
+  copilot-setup-steps:
+    runs-on: ubuntu-latest
+
+    # Set the permissions to the lowest permissions possible needed for your steps.
+    # Copilot will be given its own token for its operations.
+    permissions:
+      # If you want to clone the repository as part of your setup steps, for example to install dependencies, you'll need the `contents: read` permission. If you don't clone the repository in your setup steps, Copilot will do this for you automatically after the steps complete.
+      contents: read
+
+    # You can define any steps you want, and they will run before the agent starts.
+    # If you do not check out your code, Copilot will do this for you.
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v5
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.10"
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          enable-cache: true
+
+      - name: Create virtual environment
+        run: uv venv venv
+
+      - name: Activate virtual environment
+        run: echo "VIRTUAL_ENV=$PWD/venv" >> $GITHUB_ENV && echo "$PWD/venv/bin" >> $GITHUB_PATH
+
+      - name: Install base dependencies
+        run: uv pip install tensorflow-cpu
+
+      - name: Install PyTorch
+        run: uv pip install torch --index-url https://download.pytorch.org/whl/cpu
+
+      - name: Build Python package
+        run: uv pip install -e .[cpu,test]
+
+      - name: Install pre-commit tools
+        run: uv tool install pre-commit
+
+      - name: Install pre-commit hooks
+        run: pre-commit install --install-hooks
+
+      - name: Verify installation
+        run: |
+          dp --version
+          python -c "import deepmd; import deepmd.tf; print('DeePMD-kit installation verified')"

.github/workflows/labeler.yml

@@ -9,6 +9,6 @@ jobs:
       pull-requests: write
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/labeler@v5
+    - uses: actions/labeler@v6
       with:
         repo-token: "${{ secrets.GITHUB_TOKEN }}"

.github/workflows/mirror_gitee.yml

@@ -1,6 +1,13 @@
 name: Mirror to Gitee Repo
 
-on: [ push, delete, create ]
+on:
+  push:
+    branches-ignore:
+      - "copilot/**"
+      - "dependabot/**"
+      - "pre-commit-ci-update-config"
+  delete:
+  create:
 
 # Ensures that only one mirror task will run at a time.
 concurrency:

.github/workflows/package_c.yml

@@ -4,6 +4,9 @@ on:
   push:
     branches-ignore:
       - "gh-readonly-queue/**"
+      - "copilot/**"
+      - "dependabot/**"
+      - "pre-commit-ci-update-config"
     tags:
       - "v*"
   pull_request:
@@ -22,10 +25,10 @@ jobs:
             tensorflow_version: ""
             filename: libdeepmd_c.tar.gz
           - tensorflow_build_version: "2.14"
-            tensorflow_version: ">=2.5.0rc0,<2.15"
+            tensorflow_version: ">=2.5.0,<2.15"
             filename: libdeepmd_c_cu11.tar.gz
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
       - name: Package C library
@@ -53,9 +56,9 @@ jobs:
     needs: [build_c]
     runs-on: ubuntu-22.04
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - name: Download artifact
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v5
         with:
           pattern: libdeepmd_c-*
           merge-multiple: true

.github/workflows/test_cc.yml

@@ -2,6 +2,9 @@ on:
   push:
     branches-ignore:
       - "gh-readonly-queue/**"
+      - "copilot/**"
+      - "dependabot/**"
+      - "pre-commit-ci-update-config"
   pull_request:
   merge_group:
 concurrency:
@@ -16,23 +19,19 @@ jobs:
       matrix:
         check_memleak: [true, false]
     steps:
-    - uses: actions/checkout@v4
-    - uses: actions/setup-python@v5
+    - uses: actions/checkout@v5
+    - uses: actions/setup-python@v6
       with:
         python-version: '3.11'
         cache: 'pip'
-    - name: Setup MPI
-      uses: mpi4py/setup-mpi@v1
-      with:
-        mpi: mpich
     - uses: lukka/get-cmake@latest
     - run: python -m pip install uv
     - name: Install Python dependencies
       run: |
         source/install/uv_with_retry.sh pip install --system tensorflow-cpu~=2.18.0 jax==0.5.0
-        export TENSORFLOW_ROOT=$(python -c 'import importlib,pathlib;print(pathlib.Path(importlib.util.find_spec("tensorflow").origin).parent)')
-        source/install/uv_with_retry.sh pip install --system -e .[cpu,test,lmp,jax] mpi4py
-        source/install/uv_with_retry.sh pip install --system 'torch==2.7' --index-url https://download.pytorch.org/whl/cpu
+        export TENSORFLOW_ROOT=$(python -c 'import importlib.util,pathlib;print(pathlib.Path(importlib.util.find_spec("tensorflow").origin).parent)')
+        source/install/uv_with_retry.sh pip install --system -e .[cpu,test,lmp,jax] mpi4py mpich
+        source/install/uv_with_retry.sh pip install --system 'torch==2.8.*' --index-url https://download.pytorch.org/whl/cpu
     - name: Convert models
       run: source/tests/infer/convert-models.sh
     # https://github.com/actions/runner-images/issues/9491
@@ -45,7 +44,6 @@ jobs:
         OMP_NUM_THREADS: 1
         TF_INTRA_OP_PARALLELISM_THREADS: 1
         TF_INTER_OP_PARALLELISM_THREADS: 1
-        LMP_CXX11_ABI_0: 1
         CMAKE_GENERATOR: Ninja
         CXXFLAGS: ${{ matrix.check_memleak && '-fsanitize=leak' || '' }}
         LSAN_OPTIONS: suppressions=${{ github.workspace }}/.github/workflows/suppr.txt
@@ -54,13 +52,13 @@ jobs:
         cp ${{ github.workspace }}/source/build_tests/paddle_inference_install_dir/paddle/lib/*.so ${{ github.workspace }}/dp_test/lib/
         cp ${{ github.workspace }}/source/build_tests/paddle_inference_install_dir/third_party/install/onednn/lib/* ${{ github.workspace }}/dp_test/lib/
         cp ${{ github.workspace }}/source/build_tests/paddle_inference_install_dir/third_party/install/mklml/lib/* ${{ github.workspace }}/dp_test/lib/
+        export LD_LIBRARY_PATH=${{ github.workspace }}/dp_test/lib:$LD_LIBRARY_PATH
         pytest --cov=deepmd source/lmp/tests
       env:
         OMP_NUM_THREADS: 1
         TF_INTRA_OP_PARALLELISM_THREADS: 1
         TF_INTER_OP_PARALLELISM_THREADS: 1
         LAMMPS_PLUGIN_PATH: ${{ github.workspace }}/dp_test/lib/deepmd_lmp
-        LD_LIBRARY_PATH: ${{ github.workspace }}/dp_test/lib
       if: ${{ !matrix.check_memleak }}
     # test ipi
     - run: |