Devel update

.github/workflows/build_cc.yml

@@ -12,6 +12,8 @@ jobs:
         - variant: cpu
         - variant: cuda
     steps:
+    - name: work around permission issue
+      run: git config --global --add safe.directory /__w/deepmd-kit/deepmd-kit
     - uses: actions/checkout@master
       with:
         submodules: true

.github/workflows/build_wheel.yml

@@ -13,6 +13,8 @@ jobs:
         os: [ubuntu-18.04]  #, windows-latest, macos-latest]
 
     steps:
+      - name: work around permission issue
+        run: git config --global --add safe.directory /__w/deepmd-kit/deepmd-kit
       - uses: actions/checkout@v2
       - uses: actions/setup-python@v2
         name: Install Python
@@ -25,7 +27,7 @@ jobs:
 
       - name: Build wheels
         env:
-          CIBW_BUILD: "cp36-* cp37-* cp38-* cp39-*"
+          CIBW_BUILD: "cp36-* cp37-* cp38-* cp39-* cp310-*"
           CIBW_MANYLINUX_X86_64_IMAGE: ghcr.io/deepmodeling/manylinux2010_x86_64_tensorflow
           CIBW_BEFORE_BUILD: pip install tensorflow
           CIBW_SKIP: "*-win32 *-manylinux_i686 *-musllinux*"

.github/workflows/lint_python.yml

@@ -11,6 +11,8 @@ jobs:
         python-version: [3.8]
 
     steps:
+    - name: work around permission issue
+      run: git config --global --add safe.directory /__w/deepmd-kit/deepmd-kit
     - uses: actions/checkout@v1
     - uses: actions/setup-python@v2
       with:

.github/workflows/test_cc.yml

@@ -6,6 +6,12 @@ jobs:
   testpython:
     name: Test C++
     runs-on: ubuntu-latest
+    container: ghcr.io/deepmodeling/deepmd-kit-test-cc:latest
     steps:
+    - name: work around permission issue
+      run: git config --global --add safe.directory /__w/deepmd-kit/deepmd-kit
     - uses: actions/checkout@master
-    - run: source/install/test_cc.sh
+    - run: source/install/test_cc_local.sh
+      env:
+        tensorflow_root: /usr/local
+    - run: source/install/codecov.sh

.github/workflows/test_python.yml

@@ -42,18 +42,18 @@ jobs:
           - python: 3.7
             gcc: 8
             tf:
-          - python: 3.8
+          - python: "3.10"
             gcc: 5
             tf:
-          - python: 3.8
+          - python: "3.10"
             gcc: 8
             tf:
 
+    container: ghcr.io/deepmodeling/deepmd-kit-test-environment:py${{ matrix.python }}-gcc${{ matrix.gcc }}-tf${{ matrix.tf }}
     steps:
+    - name: work around permission issue
+      run: git config --global --add safe.directory /__w/deepmd-kit/deepmd-kit
     - uses: actions/checkout@master
-    - uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python }}
     - name: pip cache
       uses: actions/cache@v2
       with:
@@ -62,19 +62,11 @@ jobs:
           ${{ runner.os }}-pip-${{ hashFiles('**/setup.py') }}-${{ hashFiles('**/requirements.txt') }}
         restore-keys: |
           ${{ runner.os }}-pip-
-    - run: |
-        sudo apt update
-        sudo apt install gcc-${{ matrix.gcc }} g++-${{ matrix.gcc }}
     - run: python -m pip install -U pip>=21.3.1
     - run: pip install -e .[cpu,test] codecov
       env:
         CC: gcc-${{ matrix.gcc }}
         CXX: g++-${{ matrix.gcc }}
         TENSORFLOW_VERSION: ${{ matrix.tf }}
     - run: dp --version
-    - name: Prepare parallel runtime
-      if: ${{ matrix.tf == '' }}
-      run: |
-        sudo apt install libopenmpi-dev openmpi-bin
-        HOROVOD_WITHOUT_GLOO=1 HOROVOD_WITH_TENSORFLOW=1 pip install horovod mpi4py
     - run: pytest --cov=deepmd source/tests && codecov

README.md

@@ -86,14 +86,16 @@ 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)
 - [Data](doc/data/index.md)
-    - [Data conversion](doc/data/data-conv.md)
+    - [System](doc/data/system.md)
+    - [Formats of a system](doc/data/data-conv.md)
     - [Prepare data with dpdata](doc/data/dpdata.md)
 - [Model](doc/model/index.md)
     - [Overall](doc/model/overall.md)
     - [Descriptor `"se_e2_a"`](doc/model/train-se-e2-a.md)
     - [Descriptor `"se_e2_r"`](doc/model/train-se-e2-r.md)
     - [Descriptor `"se_e3"`](doc/model/train-se-e3.md)
     - [Descriptor `"hybrid"`](doc/model/train-hybrid.md)
+    - [Descriptor `sel`](doc/model/sel.md)
     - [Fit energy](doc/model/train-energy.md)
     - [Fit `tensor` like `Dipole` and `Polarizability`](doc/model/train-fitting-tensor.md)
     - [Train a Deep Potential model using `type embedding` approach](doc/model/train-se-e2-a-tebd.md)
@@ -120,37 +122,31 @@ A full [document](doc/train/train-input-auto.rst) on options in the training inp
     - [LAMMPS commands](doc/third-party/lammps-command.md)
     - [Run path-integral MD with i-PI](doc/third-party/ipi.md)
     - [Run MD with GROMACS](doc/third-party/gromacs.md)
+    - [Interfaces out of DeePMD-kit](doc/third-party/out-of-deepmd-kit.md)
 
 # Code structure
+
 The code is organized as follows:
 
 * `data/raw`: tools manipulating the raw data files.
-
 * `examples`: examples.
-
 * `deepmd`: DeePMD-kit python modules.
-
 * `source/api_cc`: source code of DeePMD-kit C++ API.
-
 * `source/ipi`: source code of i-PI client.
-
 * `source/lib`: source code of DeePMD-kit library.
-
 * `source/lmp`: source code of Lammps module.
-
 * `source/gmx`: source code of Gromacs plugin.
-
 * `source/op`: tensorflow op implementation. working with library.
 
 
 # Troubleshooting
 
-- [Model compatibility](doc/troubleshooting/model-compatability.md)
+- [Model compatibility](doc/troubleshooting/model_compatability.md)
 - [Installation](doc/troubleshooting/installation.md)
-- [The temperature undulates violently during early stages of MD](doc/troubleshooting/md-energy-undulation.md)
-- [MD: cannot run LAMMPS after installing a new version of DeePMD-kit](doc/troubleshooting/md-version-compatibility.md)
-- [Do we need to set rcut < half boxsize?](doc/troubleshooting/howtoset-rcut.md)
-- [How to set sel?](doc/troubleshooting/howtoset-sel.md)
+- [The temperature undulates violently during early stages of MD](doc/troubleshooting/md_energy_undulation.md)
+- [MD: cannot run LAMMPS after installing a new version of DeePMD-kit](doc/troubleshooting/md_version_compatibility.md)
+- [Do we need to set rcut < half boxsize?](doc/troubleshooting/howtoset_rcut.md)
+- [How to set sel?](doc/troubleshooting/howtoset_sel.md)
 - [How to control the number of nodes used by a job?](doc/troubleshooting/howtoset_num_nodes.md)
 - [How to tune Fitting/embedding-net size?](doc/troubleshooting/howtoset_netsize.md)
 

deepmd/calculator.py

@@ -54,7 +54,7 @@ class DP(Calculator):
     """
 
     name = "DP"
-    implemented_properties = ["energy", "forces", "virial", "stress"]
+    implemented_properties = ["energy", "free_energy", "forces", "virial", "stress"]
 
     def __init__(
         self,
@@ -102,6 +102,8 @@ def calculate(
         atype = [self.type_dict[k] for k in symbols]
         e, f, v = self.dp.eval(coords=coord, cells=cell, atom_types=atype)
         self.results['energy'] = e[0][0]
+        # see https://gitlab.com/ase/ase/-/merge_requests/2485
+        self.results['free_energy'] = e[0][0]
         self.results['forces'] = f[0]
         self.results['virial'] = v[0].reshape(3, 3)
 

deepmd/descriptor/descriptor.py

@@ -351,16 +351,19 @@ def get_feed_dict(self,
         return feed_dict
 
     def init_variables(self,
-                       model_file: str,
+                       graph: tf.Graph,
+                       graph_def: tf.GraphDef,
                        suffix : str = "",
     ) -> None:
         """
         Init the embedding net variables with the given dict
 
         Parameters
         ----------
-        model_file : str
-            The input model file
+        graph : tf.Graph
+            The input frozen model graph
+        graph_def : tf.GraphDef
+            The input frozen model graph_def
         suffix : str, optional
             The suffix of the scope
 

deepmd/descriptor/hybrid.py

@@ -279,21 +279,24 @@ def enable_mixed_precision(self, mixed_prec : dict = None) -> None:
 
 
     def init_variables(self,
-                       model_file : str,
+                       graph: tf.Graph,
+                       graph_def: tf.GraphDef,
                        suffix : str = "",
     ) -> None:
         """
         Init the embedding net variables with the given dict
 
         Parameters
         ----------
-        model_file : str
-            The input frozen model file
+        graph : tf.Graph
+            The input frozen model graph
+        graph_def : tf.GraphDef
+            The input frozen model graph_def
         suffix : str, optional
             The suffix of the scope
         """
         for idx, ii in enumerate(self.descrpt_list):
-            ii.init_variables(model_file, suffix=f"{suffix}_{idx}")
+            ii.init_variables(graph, graph_def, suffix=f"{suffix}_{idx}")
 
     def get_tensor_names(self, suffix : str = "") -> Tuple[str]:
         """Get names of tensors.

deepmd/descriptor/loc_frame.py

@@ -8,6 +8,7 @@
 from deepmd.env import default_tf_session_config
 from deepmd.utils.sess import run_sess
 from .descriptor import Descriptor
+from deepmd.utils.graph import get_tensor_by_name_from_graph
 
 @Descriptor.register("loc_frame")
 class DescrptLocFrame (Descriptor) :
@@ -367,4 +368,22 @@ def _compute_dstats_sys_nonsmth (self,
     def _compute_std (self,sumv2, sumv, sumn) :
         return np.sqrt(sumv2/sumn - np.multiply(sumv/sumn, sumv/sumn))
 
-
+    def init_variables(self,
+                       graph: tf.Graph,
+                       graph_def: tf.GraphDef,
+                       suffix : str = "",
+    ) -> None:
+        """
+        Init the embedding net variables with the given dict
+
+        Parameters
+        ----------
+        graph : tf.Graph
+            The input frozen model graph
+        graph_def : tf.GraphDef
+            The input frozen model graph_def
+        suffix : str, optional
+            The suffix of the scope
+        """
+        self.davg = get_tensor_by_name_from_graph(graph, 'descrpt_attr%s/t_avg' % suffix)
+        self.dstd = get_tensor_by_name_from_graph(graph, 'descrpt_attr%s/t_std' % suffix)

deepmd/descriptor/se.py

@@ -1,7 +1,7 @@
 from typing import Tuple, List
 
 from deepmd.env import tf
-from deepmd.utils.graph import get_embedding_net_variables
+from deepmd.utils.graph import get_embedding_net_variables_from_graph_def, get_tensor_by_name_from_graph
 from .descriptor import Descriptor
 
 
@@ -92,20 +92,25 @@ def pass_tensors_from_frz_model(self,
         self.descrpt_reshape = descrpt_reshape
 
     def init_variables(self,
-                       model_file : str,
+                       graph: tf.Graph,
+                       graph_def: tf.GraphDef,
                        suffix : str = "",
     ) -> None:
         """
-        Init the embedding net variables with the given frozen model
+        Init the embedding net variables with the given dict
 
         Parameters
         ----------
-        model_file : str
-            The input frozen model file
+        graph : tf.Graph
+            The input frozen model graph
+        graph_def : tf.GraphDef
+            The input frozen model graph_def
         suffix : str, optional
             The suffix of the scope
         """
-        self.embedding_net_variables = get_embedding_net_variables(model_file, suffix = suffix)
+        self.embedding_net_variables = get_embedding_net_variables_from_graph_def(graph_def, suffix = suffix)
+        self.davg = get_tensor_by_name_from_graph(graph, 'descrpt_attr%s/t_avg' % suffix)
+        self.dstd = get_tensor_by_name_from_graph(graph, 'descrpt_attr%s/t_std' % suffix)
 
     @property
     def precision(self) -> tf.DType: