Merge branch 'devel' into modify_post_fp_cp2k

.git_archival.txt

@@ -1,4 +1,3 @@
 node: $Format:%H$
 node-date: $Format:%cI$
 describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
-ref-names: $Format:%D$

.pre-commit-config.yaml

@@ -28,7 +28,7 @@ repos:
 
 # Python
 - repo: https://github.com/astral-sh/ruff-pre-commit
- rev: v0.4.7
+ rev: v0.5.1
  hooks:
  - id: ruff
  args: ["--fix"]

dpgen/generator/arginfo.py

@@ -79,7 +79,14 @@ def data_args() -> list[Argument]:
 # Training
 
 
-def training_args() -> list[Argument]:
+def training_args_common() -> list[Argument]:
+ doc_numb_models = "Number of models to be trained in 00.train. 4 is recommend."
+ return [
+ Argument("numb_models", int, optional=False, doc=doc_numb_models),
+ ]
+
+
+def training_args_dp() -> list[Argument]:
  """Traning arguments.
 
  Returns
@@ -90,7 +97,6 @@ def training_args() -> list[Argument]:
  doc_train_backend = (
  "The backend of the training. Currently only support tensorflow and pytorch."
  )
- doc_numb_models = "Number of models to be trained in 00.train. 4 is recommend."
  doc_training_iter0_model_path = "The model used to init the first iter training. Number of element should be equal to numb_models."
  doc_training_init_model = "Iteration > 0, the model parameters will be initilized from the model trained at the previous iteration. Iteration == 0, the model parameters will be initialized from training_iter0_model_path."
  doc_default_training_param = "Training parameters for deepmd-kit in 00.train. You can find instructions from `DeePMD-kit documentation <https://docs.deepmodeling.org/projects/deepmd/>`_."
@@ -133,7 +139,6 @@ def training_args() -> list[Argument]:
  default="tensorflow",
  doc=doc_train_backend,
  ),
- Argument("numb_models", int, optional=False, doc=doc_numb_models),
  Argument(
  "training_iter0_model_path",
  list[str],
@@ -224,6 +229,19 @@ def training_args() -> list[Argument]:
  ]
 
 
+def training_args() -> Variant:
+ doc_mlp_engine = "Machine learning potential engine. Currently, only DeePMD-kit (defualt) is supported."
+ doc_dp = "DeePMD-kit."
+ return Variant(
+ "mlp_engine",
+ [
+ Argument("dp", dict, training_args_dp(), doc=doc_dp),
+ ],
+ default_tag="dp",
+ doc=doc_mlp_engine,
+ )
+
+
 # Exploration
 def model_devi_jobs_template_args() -> Argument:
  doc_template = (
@@ -987,7 +1005,11 @@ def run_jdata_arginfo() -> Argument:
  return Argument(
  "run_jdata",
  dict,
- sub_fields=basic_args() + data_args() + training_args() + fp_args(),
- sub_variants=model_devi_args() + [fp_style_variant_type_args()],
+ sub_fields=basic_args() + data_args() + training_args_common() + fp_args(),
+ sub_variants=[
+ training_args(),
+ *model_devi_args(),
+ fp_style_variant_type_args(),
+ ],
  doc=doc_run_jdata,
  )

dpgen/generator/run.py

@@ -128,15 +128,19 @@
 
 def _get_model_suffix(jdata) -> str:
  """Return the model suffix based on the backend."""
- suffix_map = {"tensorflow": ".pb", "pytorch": ".pth"}
- backend = jdata.get("train_backend", "tensorflow")
- if backend in suffix_map:
- suffix = suffix_map[backend]
+ mlp_engine = jdata.get("mlp_engine", "dp")
+ if mlp_engine == "dp":
+ suffix_map = {"tensorflow": ".pb", "pytorch": ".pth"}
+ backend = jdata.get("train_backend", "tensorflow")
+ if backend in suffix_map:
+ suffix = suffix_map[backend]
+ else:
+ raise ValueError(
+ f"The backend {backend} is not available. Supported backends are: 'tensorflow', 'pytorch'."
+ )
+ return suffix
  else:
- raise ValueError(
- f"The backend {backend} is not available. Supported backends are: 'tensorflow', 'pytorch'."
- )
- return suffix
+ raise ValueError(f"Unsupported engine: {mlp_engine}")
 
 
 def get_job_names(jdata):
@@ -270,6 +274,14 @@ def dump_to_deepmd_raw(dump, deepmd_raw, type_map, fmt="gromacs/gro", charge=Non
 
 
 def make_train(iter_index, jdata, mdata):
+ mlp_engine = jdata.get("mlp_engine", "dp")
+ if mlp_engine == "dp":
+ return make_train_dp(iter_index, jdata, mdata)
+ else:
+ raise ValueError(f"Unsupported engine: {mlp_engine}")
+
+
+def make_train_dp(iter_index, jdata, mdata):
  # load json param
  # train_param = jdata['train_param']
  train_input_file = default_train_input_file
@@ -714,6 +726,14 @@ def get_nframes(system):
 
 
 def run_train(iter_index, jdata, mdata):
+ mlp_engine = jdata.get("mlp_engine", "dp")
+ if mlp_engine == "dp":
+ return run_train_dp(iter_index, jdata, mdata)
+ else:
+ raise ValueError(f"Unsupported engine: {mlp_engine}")
+
+
+def run_train_dp(iter_index, jdata, mdata):
  # print("debug:run_train:mdata", mdata)
  # load json param
  numb_models = jdata["numb_models"]
@@ -899,6 +919,14 @@ def run_train(iter_index, jdata, mdata):
 
 
 def post_train(iter_index, jdata, mdata):
+ mlp_engine = jdata.get("mlp_engine", "dp")
+ if mlp_engine == "dp":
+ return post_train_dp(iter_index, jdata, mdata)
+ else:
+ raise ValueError(f"Unsupported engine: {mlp_engine}")
+
+
+def post_train_dp(iter_index, jdata, mdata):
  # load json param
  numb_models = jdata["numb_models"]
  # paths

dpgen/simplify/arginfo.py

@@ -12,6 +12,7 @@
  fp_style_siesta_args,
  fp_style_vasp_args,
  training_args,
+ training_args_common,
 )
 
 
@@ -201,10 +202,11 @@ def simplify_jdata_arginfo() -> Argument:
  *data_args(),
  *general_simplify_arginfo(),
  # simplify use the same training method as run
- *training_args(),
+ *training_args_common(),
  *fp_args(),
  ],
  sub_variants=[
+ training_args(),
  fp_style_variant_type_args(),
  ],
  doc=doc_run_jdata,

dpgen/simplify/simplify.py

@@ -103,6 +103,14 @@ def get_multi_system(path: Union[str, list[str]], jdata: dict) -> dpdata.MultiSy
 
 
 def init_model(iter_index, jdata, mdata):
+ mlp_engine = jdata.get("mlp_engine", "dp")
+ if mlp_engine == "dp":
+ init_model_dp(iter_index, jdata, mdata)
+ else:
+ raise TypeError(f"unsupported engine {mlp_engine}")
+
+
+def init_model_dp(iter_index, jdata, mdata):
  training_init_model = jdata.get("training_init_model", False)
  if not training_init_model:
  return

pyproject.toml

@@ -27,6 +27,7 @@ dependencies = [
  'paramiko',
  'custodian',
  'GromacsWrapper>=0.8.0',
+ 'GromacsWrapper>=0.9.0; python_version >= "3.12"',
  'dpdispatcher>=0.3.11',
  'netCDF4',
  'dargs>=0.4.0',
@@ -64,8 +65,9 @@ test = [
  "dpgui",
  "coverage",
  "pymatgen-analysis-defects<2023.08.22",
- # To be fixed: https://github.com/Becksteinlab/GromacsWrapper/issues/263
- 'setuptools; python_version >= "3.12"',
+ # https://github.com/materialsproject/pymatgen/issues/3882
+ # https://github.com/kuelumbus/rdkit-pypi/issues/102
+ "numpy<2",
 ]
 gui = [
  "dpgui",