merge devel into master (deepmodeling#2917)

Prepare v2.2.6.

.gitattributes

@@ -0,0 +1,2 @@
+# do not show up detailed difference on GitHub
+source/3rdparty/* linguist-generated=true

.github/workflows/build_wheel.yml

@@ -76,6 +76,8 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
       - uses: actions/setup-python@v4
         name: Install Python
         with:

.github/workflows/test_cuda.yml

@@ -9,13 +9,19 @@ jobs:
   test_cuda:
     name: Test Python and C++ on CUDA
     runs-on: nvidia
+    # https://github.com/deepmodeling/deepmd-kit/pull/2884#issuecomment-1744216845
+    container:
+      image: nvidia/cuda:11.8.0-cudnn8-devel-ubuntu22.04
+      options: --gpus all
     if: github.repository_owner == 'deepmodeling' && github.event.label.name == 'Test CUDA' || github.event_name == 'workflow_dispatch'
     steps:
+    - name: Make sudo and git work
+      run: apt-get update && apt-get install -y sudo git
     - uses: actions/checkout@v4
     - uses: actions/setup-python@v4
       with:
         python-version: '3.11'
-        cache: 'pip'
+        # cache: 'pip'
     - name: Setup MPI
       uses: mpi4py/setup-mpi@v1
       with:
@@ -26,14 +32,17 @@ jobs:
          && sudo dpkg -i cuda-keyring_1.0-1_all.deb \
          && sudo apt-get update \
          && sudo apt-get -y install cuda-11-8 libcudnn8=8.9.5.*-1+cuda11.8
+      if: false  # skip as we use nvidia image
+    - name: Set PyPI mirror for Aliyun cloud machine
+      run: python -m pip config --user set global.index-url https://mirrors.aliyun.com/pypi/simple/
     - run: python -m pip install -U "pip>=21.3.1,!=23.0.0"
-    - run: pip install -v -e .[gpu,test,lmp,cu11] "ase @ https://github.com/rosswhitfield/ase/archive/edd03571aff6944b77b4a4b055239f3c3e4eeb66.zip"
+    - run: python -m pip install -v -e .[gpu,test,lmp,cu11] "ase @ https://github.com/rosswhitfield/ase/archive/edd03571aff6944b77b4a4b055239f3c3e4eeb66.zip"
       env:
         DP_BUILD_TESTING: 1
         DP_VARIANT: cuda
         CUDA_PATH: /usr/local/cuda-11.8
     - run: dp --version
-    - run: pytest -s --cov=deepmd --cov=deepmd_cli source/tests --durations=0
+    - run: python -m pytest -s --cov=deepmd --cov=deepmd_cli source/tests --durations=0
     - run: source/install/test_cc_local.sh
       env:
         OMP_NUM_THREADS: 1
@@ -45,10 +54,10 @@ jobs:
         DP_USE_MPICH2: 1
         CUDA_PATH: /usr/local/cuda-11.8
     - run: |
-        export LD_LIBRARY_PATH=${{ github.workspace }}/dp_test/lib:$CUDA_PATH/lib64:$LD_LIBRARY_PATH
-        export PATH=${{ github.workspace }}/dp_test/bin:$PATH
-        pytest -s --cov=deepmd source/lmp/tests
-        pytest -s --cov=deepmd source/ipi/tests
+        export LD_LIBRARY_PATH=$GITHUB_WORKSPACE/dp_test/lib:$CUDA_PATH/lib64:$LD_LIBRARY_PATH
+        export PATH=$GITHUB_WORKSPACE/dp_test/bin:$PATH
+        python -m pytest -s --cov=deepmd source/lmp/tests
+        python -m pytest -s --cov=deepmd source/ipi/tests
       env:
         OMP_NUM_THREADS: 1
         TF_INTRA_OP_PARALLELISM_THREADS: 1

.pre-commit-config.yaml

@@ -2,7 +2,7 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
     -   id: trailing-whitespace
         exclude: "^.+\\.pbtxt$"
@@ -27,22 +27,26 @@ repos:
     hooks:
     - id: isort
       files: \.py$
+      exclude: ^source/3rdparty
 -   repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.0.291
+    rev: v0.0.292
     hooks:
     - id: ruff
       args: ["--fix"]
+      exclude: ^source/3rdparty
 -   repo: https://github.com/psf/black-pre-commit-mirror
     rev: 23.9.1
     hooks:
     -   id: black-jupyter
+        exclude: ^source/3rdparty
 # numpydoc
 -   repo: https://github.com/Carreau/velin
     rev: 0.0.12
     hooks:
     - id: velin
       args: ["--write"]
+      exclude: ^source/3rdparty
 # Python inside docs
 -   repo: https://github.com/asottile/blacken-docs
     rev: 1.16.0
@@ -102,6 +106,7 @@ repos:
         - --comment-style
         - "#"
         - --no-extra-eol
+        exclude: ^source/3rdparty
     # HTML
     -   id: insert-license
         files: \.(html|vue|xml)$

README.md

@@ -92,6 +92,7 @@ A full [document](doc/train/train-input-auto.rst) on options in the training inp
     - [Install GROMACS](doc/install/install-gromacs.md)
     - [Building conda packages](doc/install/build-conda.md)
     - [Install Node.js interface](doc/install/install-nodejs.md)
+    - [Easy install the latest development version](doc/install/easy-install-dev.md)
 - [Data](doc/data/index.md)
     - [System](doc/data/system.md)
     - [Formats of a system](doc/data/data-conv.md)

backend/dynamic_metadata.py

@@ -38,6 +38,7 @@ def dynamic_metadata(
                 "pytest",
                 "pytest-cov",
                 "pytest-sugar",
+                "dpgui",
             ],
             "docs": [
                 "sphinx>=3.1.1",
@@ -62,6 +63,9 @@ def dynamic_metadata(
                 "i-PI",
                 *find_libpython_requires,
             ],
+            "gui": [
+                "dpgui",
+            ],
             **get_tf_requirement(tf_version),
             "cu11": [
                 "nvidia-cuda-runtime-cu11",

deepmd/descriptor/__init__.py

@@ -14,6 +14,9 @@
 from .se_a_ebd import (
     DescrptSeAEbd,
 )
+from .se_a_ebd_v2 import (
+    DescrptSeAEbdV2,
+)
 from .se_a_ef import (
     DescrptSeAEf,
     DescrptSeAEfLower,
@@ -39,6 +42,7 @@
     "DescrptHybrid",
     "DescrptLocFrame",
     "DescrptSeA",
+    "DescrptSeAEbdV2",
     "DescrptSeAEbd",
     "DescrptSeAEf",
     "DescrptSeAEfLower",

deepmd/descriptor/descriptor.py

@@ -66,16 +66,20 @@ class SomeDescript(Descriptor):
         """
         return Descriptor.__plugins.register(key)
 
+    @classmethod
+    def get_class_by_input(cls, input: dict):
+        try:
+            descrpt_type = input["type"]
+        except KeyError:
+            raise KeyError("the type of descriptor should be set by `type`")
+        if descrpt_type in Descriptor.__plugins.plugins:
+            return Descriptor.__plugins.plugins[descrpt_type]
+        else:
+            raise RuntimeError("Unknown descriptor type: " + descrpt_type)
+
     def __new__(cls, *args, **kwargs):
         if cls is Descriptor:
-            try:
-                descrpt_type = kwargs["type"]
-            except KeyError:
-                raise KeyError("the type of descriptor should be set by `type`")
-            if descrpt_type in Descriptor.__plugins.plugins:
-                cls = Descriptor.__plugins.plugins[descrpt_type]
-            else:
-                raise RuntimeError("Unknown descriptor type: " + descrpt_type)
+            cls = cls.get_class_by_input(kwargs)
         return super().__new__(cls)
 
     @abstractmethod
@@ -489,3 +493,19 @@ def build_type_exclude_mask(
     def explicit_ntypes(self) -> bool:
         """Explicit ntypes with type embedding."""
         return False
+
+    @classmethod
+    @abstractmethod
+    def update_sel(cls, global_jdata: dict, local_jdata: dict):
+        """Update the selection and perform neighbor statistics.
+
+        Parameters
+        ----------
+        global_jdata : dict
+            The global data, containing the training section
+        local_jdata : dict
+            The local data refer to the current class
+        """
+        # call subprocess
+        cls = cls.get_class_by_input(local_jdata)
+        return cls.update_sel(global_jdata, local_jdata)

deepmd/descriptor/hybrid.py

@@ -416,3 +416,21 @@ def pass_tensors_from_frz_model(
     def explicit_ntypes(self) -> bool:
         """Explicit ntypes with type embedding."""
         return any(ii.explicit_ntypes for ii in self.descrpt_list)
+
+    @classmethod
+    def update_sel(cls, global_jdata: dict, local_jdata: dict):
+        """Update the selection and perform neighbor statistics.
+
+        Parameters
+        ----------
+        global_jdata : dict
+            The global data, containing the training section
+        local_jdata : dict
+            The local data refer to the current class
+        """
+        local_jdata_cpy = local_jdata.copy()
+        local_jdata_cpy["list"] = [
+            Descriptor.update_sel(global_jdata, sub_jdata)
+            for sub_jdata in local_jdata["list"]
+        ]
+        return local_jdata_cpy

deepmd/descriptor/loc_frame.py

@@ -430,3 +430,16 @@ def init_variables(
         self.dstd = get_tensor_by_name_from_graph(
             graph, "descrpt_attr%s/t_std" % suffix
         )
+
+    @classmethod
+    def update_sel(cls, global_jdata: dict, local_jdata: dict):
+        """Update the selection and perform neighbor statistics.
+
+        Parameters
+        ----------
+        global_jdata : dict
+            The global data, containing the training section
+        local_jdata : dict
+            The local data refer to the current class
+        """
+        return local_jdata

deepmd/descriptor/se.py

@@ -141,3 +141,22 @@ def init_variables(
     def precision(self) -> tf.DType:
         """Precision of filter network."""
         return self.filter_precision
+
+    @classmethod
+    def update_sel(cls, global_jdata: dict, local_jdata: dict):
+        """Update the selection and perform neighbor statistics.
+
+        Parameters
+        ----------
+        global_jdata : dict
+            The global data, containing the training section
+        local_jdata : dict
+            The local data refer to the current class
+        """
+        from deepmd.entrypoints.train import (
+            update_one_sel,
+        )
+
+        # default behavior is to update sel which is a list
+        local_jdata_cpy = local_jdata.copy()
+        return update_one_sel(global_jdata, local_jdata_cpy, False)