Merge pull request #4 from deepmodeling/devel

Devel update

.github/workflows/build_cc.yml

@@ -21,7 +21,8 @@ jobs:
     - uses: actions/checkout@master
       with:
         submodules: true
-    - run: sudo apt update && sudo apt install nvidia-cuda-toolkit
+    - run: sudo apt update && sudo apt install g++-7
+    - run: sudo apt install nvidia-cuda-toolkit
       if: matrix.variant == 'gpu'
     - run: source/install/build_cc.sh
       env:

deepmd/__main__.py

@@ -1,6 +1,6 @@
 """Package dp entry point."""
 
-from .main import main
+from .entrypoints.main import main
 
 if __name__ == '__main__':
     main()

source/train/calculator.py → deepmd/calculator.py

@@ -1,13 +1,12 @@
 """ASE calculator interface module."""
 
 from typing import TYPE_CHECKING, Dict, List, Optional, Union
+from pathlib import Path
 
 from deepmd import DeepPotential
 from ase.calculators.calculator import Calculator, all_changes
 
 if TYPE_CHECKING:
-    from pathlib import Path
-
     from ase import Atoms
 
 __all__ = ["DP"]
@@ -62,7 +61,7 @@ def __init__(
         **kwargs
     ) -> None:
         Calculator.__init__(self, label=label, **kwargs)
-        self.dp = DeepPot(str(Path(model).resolve()))
+        self.dp = DeepPotential(str(Path(model).resolve()))
         if type_dict:
             self.type_dict = type_dict
         else:

deepmd/common.py

@@ -20,7 +20,7 @@
 import yaml
 
 from deepmd.env import op_module, tf
-from deepmd.run_options import GLOBAL_TF_FLOAT_PRECISION, GLOBAL_NP_FLOAT_PRECISION
+from deepmd.env import GLOBAL_TF_FLOAT_PRECISION, GLOBAL_NP_FLOAT_PRECISION
 
 if TYPE_CHECKING:
     _DICT_VAL = TypeVar("_DICT_VAL")

deepmd/descriptor/hybrid.py

@@ -4,8 +4,8 @@
 from deepmd.env import tf
 from deepmd.common import ClassArg
 from deepmd.env import op_module
-from deepmd.run_options import GLOBAL_TF_FLOAT_PRECISION
-from deepmd.run_options import GLOBAL_NP_FLOAT_PRECISION
+from deepmd.env import GLOBAL_TF_FLOAT_PRECISION
+from deepmd.env import GLOBAL_NP_FLOAT_PRECISION
 # from deepmd.descriptor import DescrptLocFrame
 # from deepmd.descriptor import DescrptSeA
 # from deepmd.descriptor import DescrptSeAT

deepmd/descriptor/loc_frame.py

@@ -2,8 +2,8 @@
 from typing import Tuple, List
 
 from deepmd.env import tf
-from deepmd.run_options import GLOBAL_TF_FLOAT_PRECISION
-from deepmd.run_options import GLOBAL_NP_FLOAT_PRECISION
+from deepmd.env import GLOBAL_TF_FLOAT_PRECISION
+from deepmd.env import GLOBAL_NP_FLOAT_PRECISION
 from deepmd.env import op_module
 from deepmd.env import default_tf_session_config
 

deepmd/descriptor/se_a.py

@@ -5,8 +5,8 @@
 from deepmd.env import tf
 from deepmd.common import get_activation_func, get_precision, ACTIVATION_FN_DICT, PRECISION_DICT, docstring_parameter, get_np_precision
 from deepmd.utils.argcheck import list_to_doc
-from deepmd.run_options import GLOBAL_TF_FLOAT_PRECISION
-from deepmd.run_options import GLOBAL_NP_FLOAT_PRECISION
+from deepmd.env import GLOBAL_TF_FLOAT_PRECISION
+from deepmd.env import GLOBAL_NP_FLOAT_PRECISION
 from deepmd.env import op_module
 from deepmd.env import default_tf_session_config
 from deepmd.utils.network import embedding_net
@@ -112,7 +112,7 @@ def __init__ (self,
             self.place_holders['natoms_vec'] = tf.placeholder(tf.int32, [self.ntypes+2], name=name_pfx+'t_natoms')
             self.place_holders['default_mesh'] = tf.placeholder(tf.int32, [None], name=name_pfx+'t_mesh')
             self.stat_descrpt, descrpt_deriv, rij, nlist \
-                = op_module.descrpt_se_a(self.place_holders['coord'],
+                = op_module.prod_env_mat_a(self.place_holders['coord'],
                                          self.place_holders['type'],
                                          self.place_holders['natoms_vec'],
                                          self.place_holders['box'],
@@ -340,7 +340,7 @@ def build (self,
         atype = tf.reshape (atype_, [-1, natoms[1]])
 
         self.descrpt, self.descrpt_deriv, self.rij, self.nlist \
-            = op_module.descrpt_se_a (coord,
+            = op_module.prod_env_mat_a (coord,
                                        atype,
                                        natoms,
                                        box,

deepmd/descriptor/se_a_ebd.py

@@ -4,8 +4,8 @@
 from deepmd.env import tf
 from deepmd.common import ClassArg, get_activation_func, get_precision, add_data_requirement
 from deepmd.utils.network import one_layer
-from deepmd.run_options import GLOBAL_TF_FLOAT_PRECISION
-from deepmd.run_options import GLOBAL_NP_FLOAT_PRECISION
+from deepmd.env import GLOBAL_TF_FLOAT_PRECISION
+from deepmd.env import GLOBAL_NP_FLOAT_PRECISION
 from deepmd.env import op_module
 from deepmd.env import default_tf_session_config
 from deepmd.utils.network import embedding_net
@@ -27,7 +27,8 @@ def __init__ (self,
                   numb_aparam : int = 0,
                   set_davg_zero: bool = False,
                   activation_function: str = 'tanh',
-                  precision: str = 'default'
+                  precision: str = 'default',
+                  exclude_types: List[int] = [],
     ) -> None:
         """
         Constructor

deepmd/descriptor/se_a_ef.py

@@ -4,8 +4,8 @@
 from deepmd.env import tf
 from deepmd.common import add_data_requirement,get_activation_func, get_precision, ACTIVATION_FN_DICT, PRECISION_DICT, docstring_parameter
 from deepmd.utils.argcheck import list_to_doc
-from deepmd.run_options import GLOBAL_TF_FLOAT_PRECISION
-from deepmd.run_options import GLOBAL_NP_FLOAT_PRECISION
+from deepmd.env import GLOBAL_TF_FLOAT_PRECISION
+from deepmd.env import GLOBAL_NP_FLOAT_PRECISION
 from deepmd.env import op_module
 from deepmd.env import default_tf_session_config
 from .se_a import DescrptSeA

deepmd/descriptor/se_a_t.py

@@ -4,8 +4,8 @@
 from deepmd.env import tf
 from deepmd.common import get_activation_func, get_precision, ACTIVATION_FN_DICT, PRECISION_DICT, docstring_parameter
 from deepmd.utils.argcheck import list_to_doc
-from deepmd.run_options import GLOBAL_TF_FLOAT_PRECISION
-from deepmd.run_options import GLOBAL_NP_FLOAT_PRECISION
+from deepmd.env import GLOBAL_TF_FLOAT_PRECISION
+from deepmd.env import GLOBAL_NP_FLOAT_PRECISION
 from deepmd.env import op_module
 from deepmd.env import default_tf_session_config
 from deepmd.utils.network import embedding_net

deepmd/descriptor/se_r.py

@@ -4,8 +4,8 @@
 from deepmd.env import tf
 from deepmd.common import get_activation_func, get_precision, ACTIVATION_FN_DICT, PRECISION_DICT, docstring_parameter
 from deepmd.utils.argcheck import list_to_doc
-from deepmd.run_options import GLOBAL_TF_FLOAT_PRECISION
-from deepmd.run_options import GLOBAL_NP_FLOAT_PRECISION
+from deepmd.env import GLOBAL_TF_FLOAT_PRECISION
+from deepmd.env import GLOBAL_NP_FLOAT_PRECISION
 from deepmd.env import op_module
 from deepmd.env import default_tf_session_config
 from deepmd.utils.network import embedding_net
@@ -112,7 +112,7 @@ def __init__ (self,
             self.place_holders['natoms_vec'] = tf.placeholder(tf.int32, [self.ntypes+2], name=name_pfx+'t_natoms')
             self.place_holders['default_mesh'] = tf.placeholder(tf.int32, [None], name=name_pfx+'t_mesh')
             self.stat_descrpt, descrpt_deriv, rij, nlist \
-                = op_module.descrpt_se_r(self.place_holders['coord'],
+                = op_module.prod_env_mat_r(self.place_holders['coord'],
                                          self.place_holders['type'],
                                          self.place_holders['natoms_vec'],
                                          self.place_holders['box'],
@@ -285,7 +285,7 @@ def build (self,
         atype = tf.reshape (atype_, [-1, natoms[1]])
 
         self.descrpt, self.descrpt_deriv, self.rij, self.nlist \
-            = op_module.descrpt_se_r (coord,
+            = op_module.prod_env_mat_r(coord,
                                       atype,
                                       natoms,
                                       box,

deepmd/entrypoints/freeze.py

@@ -43,6 +43,7 @@ def _make_node_names(model_type: str, modifier_type: Optional[str] = None) -> Li
         "descrpt_attr/ntypes",
         "model_attr/tmap",
         "model_attr/model_type",
+        "model_attr/model_version",
     ]
 
     if model_type == "ener":
@@ -59,6 +60,7 @@ def _make_node_names(model_type: str, modifier_type: Optional[str] = None) -> Li
         nodes += [
             "o_wfc",
             "model_attr/sel_type",
+            "model_attr/output_dim",
         ]
     elif model_type == "dipole":
         nodes += [
@@ -76,11 +78,13 @@ def _make_node_names(model_type: str, modifier_type: Optional[str] = None) -> Li
         nodes += [
             "o_polar",
             "model_attr/sel_type",
+            "model_attr/output_dim",
         ]
     elif model_type == "global_polar":
         nodes += [
             "o_global_polar",
             "model_attr/sel_type",
+            "model_attr/output_dim",
         ]
     else:
         raise RuntimeError(f"unknow model type {model_type}")

source/train/main.py → deepmd/entrypoints/main.py

@@ -232,10 +232,10 @@ def parse_args(args: Optional[List[str]] = None):
     )
     parser_tst.add_argument(
         "-a",
-        "--atomic-energy",
+        "--atomic",
         action="store_true",
         default=False,
-        help="Test the accuracy of atomic energy",
+        help="Test the accuracy of atomic label, i.e. energy / dipole / polar",
     )
 
     # * compress model *****************************************************************