Merge pull request #1787 from amcadmus/master

Merge devel into master

Author: amcadmus

.github/labeler.yml

@@ -0,0 +1,13 @@
+Python:
+- deepmd/**/*
+- source/tests/**/*
+Docs: doc/**/*
+Examples: examples/**/*
+Core: source/lib/**/*
+CUDA: source/lib/src/cuda/**/*
+ROCM: source/lib/src/rocm/**/*
+OP: source/op/**/*
+C++: source/api_cc/**/*
+LAMMPS: source/lmp/**/*
+Gromacs: source/gmx/**/*
+i-Pi: source/ipi/**/*

.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
@@ -26,7 +28,7 @@ jobs:
       - name: Build wheels
         env:
           CIBW_BUILD: "cp36-* cp37-* cp38-* cp39-* cp310-*"
-          CIBW_MANYLINUX_X86_64_IMAGE: ghcr.io/deepmodeling/manylinux2010_x86_64_tensorflow
+          CIBW_MANYLINUX_X86_64_IMAGE: ghcr.io/deepmodeling/manylinux2014_x86_64_tensorflow
           CIBW_BEFORE_BUILD: pip install tensorflow
           CIBW_SKIP: "*-win32 *-manylinux_i686 *-musllinux*"
         run: |

.github/workflows/labeler.yml

@@ -0,0 +1,14 @@
+name: "Pull Request Labeler"
+on:
+- pull_request_target
+
+jobs:
+  triage:
+    permissions:
+      contents: read
+      pull-requests: write
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/labeler@v4
+      with:
+        repo-token: "${{ secrets.GITHUB_TOKEN }}"

.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

@@ -51,6 +51,8 @@ jobs:
 
     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
     - name: pip cache
       uses: actions/cache@v2

README.md

@@ -86,7 +86,8 @@ 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)
@@ -99,6 +100,7 @@ A full [document](doc/train/train-input-auto.rst) on options in the training inp
     - [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)
     - [Deep potential long-range](doc/model/dplr.md)
+    - [Deep Potential - Range Correction (DPRc)](doc/model/dprc.md)
 - [Training](doc/train/index.md)
     - [Training a model](doc/train/training.md)
     - [Advanced options](doc/train/training-advanced.md)
@@ -121,37 +123,31 @@ 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/common.py

@@ -95,6 +95,7 @@ def add_data_requirement(
     high_prec: bool = False,
     type_sel: bool = None,
     repeat: int = 1,
+    default: float = 0.,
 ):
     """Specify data requirements for training.
 
@@ -116,6 +117,8 @@ def add_data_requirement(
         select only certain type of atoms, by default None
     repeat : int, optional
         if specify repaeat data `repeat` times, by default 1
+    default : float, optional, default=0.
+        default value of data
     """
     data_requirement[key] = {
         "ndof": ndof,
@@ -124,6 +127,7 @@ def add_data_requirement(
         "high_prec": high_prec,
         "type_sel": type_sel,
         "repeat": repeat,
+        "default": default,
     }
 
 
@@ -444,28 +448,6 @@ def expand_sys_str(root_dir: Union[str, Path]) -> List[str]:
     return matches
 
 
-def docstring_parameter(*sub: Tuple[str, ...]):
-    """Add parameters to object docstring.
-
-    Parameters
-    ----------
-    sub: Tuple[str, ...]
-        list of strings that will be inserted into prepared locations in docstring.
-
-    Note
-    ----
-    Can be used on both object and classes.
-    """
-
-    @wraps
-    def dec(obj: "_OBJ") -> "_OBJ":
-        if obj.__doc__ is not None:
-            obj.__doc__ = obj.__doc__.format(*sub)
-        return obj
-
-    return dec
-
-
 def get_np_precision(precision: "_PRECISION") -> np.dtype:
     """Get numpy precision constant from string.