Merge branch 'devel' into add_dpa1

deepmodeling · Nov 29, 2024 · 3e64196 · 3e64196
2 parents ac479ed + a11f264
commit 3e64196
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -29,7 +29,7 @@ repos:
         exclude: ^source/3rdparty
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.7.4
+    rev: v0.8.0
     hooks:
       - id: ruff
         args: ["--fix"]
@@ -60,18 +60,18 @@ repos:
       - id: blacken-docs
   # C++
   - repo: https://github.com/pre-commit/mirrors-clang-format
-    rev: v19.1.3
+    rev: v19.1.4
     hooks:
       - id: clang-format
         exclude: ^(source/3rdparty|source/lib/src/gpu/cudart/.+\.inc|.+\.ipynb$)
   # markdown, yaml, CSS, javascript
-  # - repo: https://github.com/pre-commit/mirrors-prettier
-  #   rev: v4.0.0-alpha.8
-  #   hooks:
-  #     - id: prettier
-  #       types_or: [markdown, yaml, css]
-  #       # workflow files cannot be modified by pre-commit.ci
-  #       exclude: ^(source/3rdparty|\.github/workflows|\.clang-format)
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v4.0.0-alpha.8
+    hooks:
+      - id: prettier
+        types_or: [markdown, yaml, css]
+        # workflow files cannot be modified by pre-commit.ci
+        exclude: ^(source/3rdparty|\.github/workflows|\.clang-format)
   # Shell
   - repo: https://github.com/scop/pre-commit-shfmt
     rev: v3.10.0-1
@@ -83,25 +83,25 @@ repos:
     hooks:
       - id: cmake-format
       #- id: cmake-lint
-  # - repo: https://github.com/njzjz/mirrors-bibtex-tidy
-  #   rev: v1.13.0
-  #   hooks:
-  #     - id: bibtex-tidy
-  #       args:
-  #         - --curly
-  #         - --numeric
-  #         - --align=13
-  #         - --blank-lines
-  #         # disable sort: the order of keys and fields has explict meanings
-  #         #- --sort=key
-  #         - --duplicates=key,doi,citation,abstract
-  #         - --merge=combine
-  #         #- --sort-fields
-  #         #- --strip-comments
-  #         - --trailing-commas
-  #         - --encode-urls
-  #         - --remove-empty-fields
-  #         - --wrap=80
+  - repo: https://github.com/njzjz/mirrors-bibtex-tidy
+    rev: v1.13.0
+    hooks:
+      - id: bibtex-tidy
+        args:
+          - --curly
+          - --numeric
+          - --align=13
+          - --blank-lines
+          # disable sort: the order of keys and fields has explict meanings
+          #- --sort=key
+          - --duplicates=key,doi,citation,abstract
+          - --merge=combine
+          #- --sort-fields
+          #- --strip-comments
+          - --trailing-commas
+          - --encode-urls
+          - --remove-empty-fields
+          - --wrap=80
   # license header
   - repo: https://github.com/Lucas-C/pre-commit-hooks
     rev: v1.5.5

diff --git a/deepmd/__init__.py b/deepmd/__init__.py
@@ -40,6 +40,6 @@ def DeepPotential(*args, **kwargs):
 
 
 __all__ = [
-    "__version__",
     "DeepPotential",
+    "__version__",
 ]
diff --git a/deepmd/common.py b/deepmd/common.py
@@ -35,13 +35,13 @@
 )
 
 __all__ = [
-    "select_idx_map",
-    "make_default_mesh",
-    "j_loader",
+    "VALID_ACTIVATION",
+    "VALID_PRECISION",
     "expand_sys_str",
     "get_np_precision",
-    "VALID_PRECISION",
-    "VALID_ACTIVATION",
+    "j_loader",
+    "make_default_mesh",
+    "select_idx_map",
 ]
 
 _PRECISION = Literal["default", "float16", "float32", "float64"]
@@ -63,9 +63,9 @@
 if TYPE_CHECKING:
     _DICT_VAL = TypeVar("_DICT_VAL")
     __all__ += [
+        "_ACTIVATION",
         "_DICT_VAL",
         "_PRECISION",
-        "_ACTIVATION",
     ]
 
 

diff --git a/deepmd/dpmodel/__init__.py b/deepmd/dpmodel/__init__.py
@@ -23,18 +23,18 @@
 )
 
 __all__ = [
-    "DPModelCommon",
-    "PRECISION_DICT",
     "DEFAULT_PRECISION",
-    "NativeOP",
-    "ModelOutputDef",
+    "PRECISION_DICT",
+    "DPModelCommon",
     "FittingOutputDef",
+    "ModelOutputDef",
+    "NativeOP",
     "OutputVariableDef",
-    "model_check_output",
     "fitting_check_output",
-    "get_reduce_name",
     "get_deriv_name",
     "get_hessian_name",
+    "get_reduce_name",
+    "model_check_output",
 ]
 
 

diff --git a/deepmd/dpmodel/atomic_model/__init__.py b/deepmd/dpmodel/atomic_model/__init__.py
@@ -44,14 +44,14 @@
 )
 
 __all__ = [
-    "make_base_atomic_model",
     "BaseAtomicModel",
     "DPAtomicModel",
-    "DPEnergyAtomicModel",
-    "PairTabAtomicModel",
-    "LinearEnergyAtomicModel",
-    "DPZBLLinearEnergyAtomicModel",
     "DPDOSAtomicModel",
-    "DPPolarAtomicModel",
     "DPDipoleAtomicModel",
+    "DPEnergyAtomicModel",
+    "DPPolarAtomicModel",
+    "DPZBLLinearEnergyAtomicModel",
+    "LinearEnergyAtomicModel",
+    "PairTabAtomicModel",
+    "make_base_atomic_model",
 ]
diff --git a/deepmd/dpmodel/common.py b/deepmd/dpmodel/common.py
@@ -221,10 +221,10 @@ def safe_cast_array(
 
 
 __all__ = [
-    "GLOBAL_NP_FLOAT_PRECISION",
+    "DEFAULT_PRECISION",
     "GLOBAL_ENER_FLOAT_PRECISION",
+    "GLOBAL_NP_FLOAT_PRECISION",
     "PRECISION_DICT",
     "RESERVED_PRECISON_DICT",
-    "DEFAULT_PRECISION",
     "NativeOP",
 ]
diff --git a/deepmd/dpmodel/descriptor/__init__.py b/deepmd/dpmodel/descriptor/__init__.py
@@ -28,13 +28,13 @@
 )
 
 __all__ = [
+    "DescrptDPA1",
+    "DescrptDPA2",
+    "DescrptHybrid",
     "DescrptSeA",
+    "DescrptSeAttenV2",
     "DescrptSeR",
     "DescrptSeT",
     "DescrptSeTTebd",
-    "DescrptDPA1",
-    "DescrptSeAttenV2",
-    "DescrptDPA2",
-    "DescrptHybrid",
     "make_base_descriptor",
 ]
diff --git a/deepmd/dpmodel/fitting/__init__.py b/deepmd/dpmodel/fitting/__init__.py
@@ -22,11 +22,11 @@
 )
 
 __all__ = [
-    "InvarFitting",
-    "make_base_fitting",
+    "DOSFittingNet",
     "DipoleFitting",
     "EnergyFittingNet",
+    "InvarFitting",
     "PolarFitting",
-    "DOSFittingNet",
     "PropertyFittingNet",
+    "make_base_fitting",
 ]
diff --git a/deepmd/dpmodel/model/__init__.py b/deepmd/dpmodel/model/__init__.py
@@ -29,9 +29,9 @@
 )
 
 __all__ = [
+    "DPModelCommon",
     "EnergyModel",
     "PropertyModel",
-    "DPModelCommon",
     "SpinModel",
     "make_model",
 ]
diff --git a/deepmd/dpmodel/utils/__init__.py b/deepmd/dpmodel/utils/__init__.py
@@ -36,27 +36,27 @@
 )
 
 __all__ = [
-    "EnvMat",
-    "make_multilayer_network",
-    "make_embedding_network",
-    "make_fitting_network",
+    "AtomExcludeMask",
     "EmbeddingNet",
+    "EnvMat",
     "FittingNet",
     "NativeLayer",
     "NativeNet",
     "NetworkCollection",
-    "load_dp_model",
-    "save_dp_model",
-    "traverse_model_dict",
-    "build_neighbor_list",
-    "nlist_distinguish_types",
-    "get_multiple_nlist_key",
+    "PairExcludeMask",
     "build_multiple_neighbor_list",
+    "build_neighbor_list",
     "extend_coord_with_ghosts",
-    "normalize_coord",
+    "get_multiple_nlist_key",
     "inter2phys",
+    "load_dp_model",
+    "make_embedding_network",
+    "make_fitting_network",
+    "make_multilayer_network",
+    "nlist_distinguish_types",
+    "normalize_coord",
     "phys2inter",
+    "save_dp_model",
     "to_face_distance",
-    "AtomExcludeMask",
-    "PairExcludeMask",
+    "traverse_model_dict",
 ]
diff --git a/deepmd/entrypoints/test.py b/deepmd/entrypoints/test.py
@@ -704,9 +704,9 @@ def test_dos(
             frame_output = np.hstack((test_out, pred_out))
 
             save_txt_file(
-                detail_path.with_suffix(".dos.out.%.d" % ii),
+                detail_path.with_suffix(f".dos.out.{ii}"),
                 frame_output,
-                header="%s - %.d: data_dos pred_dos" % (system, ii),
+                header=f"{system} - {ii}: data_dos pred_dos",
                 append=append_detail,
             )
 
@@ -718,9 +718,9 @@ def test_dos(
                 frame_output = np.hstack((test_out, pred_out))
 
                 save_txt_file(
-                    detail_path.with_suffix(".ados.out.%.d" % ii),
+                    detail_path.with_suffix(f".ados.out.{ii}"),
                     frame_output,
-                    header="%s - %.d: data_ados pred_ados" % (system, ii),
+                    header=f"{system} - {ii}: data_ados pred_ados",
                     append=append_detail,
                 )
 
@@ -860,9 +860,9 @@ def test_property(
             frame_output = np.hstack((test_out, pred_out))
 
             save_txt_file(
-                detail_path.with_suffix(".property.out.%.d" % ii),
+                detail_path.with_suffix(f".property.out.{ii}"),
                 frame_output,
-                header="%s - %.d: data_property pred_property" % (system, ii),
+                header=f"{system} - {ii}: data_property pred_property",
                 append=append_detail,
             )
 
@@ -874,9 +874,9 @@ def test_property(
                 frame_output = np.hstack((test_out, pred_out))
 
                 save_txt_file(
-                    detail_path.with_suffix(".aproperty.out.%.d" % ii),
+                    detail_path.with_suffix(f".aproperty.out.{ii}"),
                     frame_output,
-                    header="%s - %.d: data_aproperty pred_aproperty" % (system, ii),
+                    header=f"{system} - {ii}: data_aproperty pred_aproperty",
                     append=append_detail,
                 )
 

diff --git a/deepmd/env.py b/deepmd/env.py
@@ -13,12 +13,12 @@
 import deepmd.lib
 
 __all__ = [
-    "GLOBAL_NP_FLOAT_PRECISION",
-    "GLOBAL_ENER_FLOAT_PRECISION",
-    "global_float_prec",
     "GLOBAL_CONFIG",
-    "SHARED_LIB_MODULE",
+    "GLOBAL_ENER_FLOAT_PRECISION",
+    "GLOBAL_NP_FLOAT_PRECISION",
     "SHARED_LIB_DIR",
+    "SHARED_LIB_MODULE",
+    "global_float_prec",
 ]
 
 log = logging.getLogger(__name__)

diff --git a/deepmd/infer/__init__.py b/deepmd/infer/__init__.py
@@ -10,10 +10,10 @@
 )
 
 __all__ = [
-    "DeepPot",
-    "calc_model_devi",
     "DeepEval",
+    "DeepPot",
     "DeepPotential",
+    "calc_model_devi",
 ]
 
 

diff --git a/deepmd/infer/deep_eval.py b/deepmd/infer/deep_eval.py
@@ -503,8 +503,7 @@ def _standard_input(self, coords, cells, atom_types, fparam, aparam, mixed_type)
                 fparam = np.tile(fparam.reshape([-1]), [nframes, 1])
             else:
                 raise RuntimeError(
-                    "got wrong size of frame param, should be either %d x %d or %d"
-                    % (nframes, fdim, fdim)
+                    f"got wrong size of frame param, should be either {nframes} x {fdim} or {fdim}"
                 )
         if aparam is not None:
             fdim = self.get_dim_aparam()
@@ -516,8 +515,7 @@ def _standard_input(self, coords, cells, atom_types, fparam, aparam, mixed_type)
                 aparam = np.tile(aparam.reshape([-1]), [nframes, natoms])
             else:
                 raise RuntimeError(
-                    "got wrong size of frame param, should be either %d x %d x %d or %d x %d or %d"
-                    % (nframes, natoms, fdim, natoms, fdim, fdim)
+                    f"got wrong size of frame param, should be either {nframes} x {natoms} x {fdim} or {natoms} x {fdim} or {fdim}"
                 )
         return coords, cells, atom_types, fparam, aparam, nframes, natoms
 

diff --git a/deepmd/infer/model_devi.py b/deepmd/infer/model_devi.py
@@ -204,16 +204,16 @@ def write_model_devi_out(
         assert devi.shape[1] == 8
     else:
         assert devi.shape[1] > 8
-    header = "%s\n%10s" % (header, "step")
+    header = f"{header}\n{'step':10s}"
     for item in "vf":
-        header += "%19s%19s%19s" % (
+        header += "{:19s}{:19s}{:19s}".format(
             f"max_devi_{item}",
             f"min_devi_{item}",
             f"avg_devi_{item}",
         )
-    header += "%19s" % "devi_e"
+    header += f'{"devi_e":19s}'
     if atomic:
-        header += "%19s" % "atm_devi_f(N)"
+        header += f"{'atm_devi_f(N)':19s}"
     with open(fname, "ab") as fp:
         np.savetxt(
             fp,

diff --git a/deepmd/jax/descriptor/__init__.py b/deepmd/jax/descriptor/__init__.py
@@ -25,12 +25,12 @@
 )
 
 __all__ = [
+    "DescrptDPA1",
+    "DescrptDPA2",
+    "DescrptHybrid",
     "DescrptSeA",
+    "DescrptSeAttenV2",
     "DescrptSeR",
     "DescrptSeT",
     "DescrptSeTTebd",
-    "DescrptDPA1",
-    "DescrptSeAttenV2",
-    "DescrptDPA2",
-    "DescrptHybrid",
 ]