[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

Author: pre-commit-ci[bot]

dpgen2/entrypoint/args.py

@@ -261,7 +261,11 @@ def lmp_args():
  doc=doc_filters,
  ),
  Argument(
- "lammps_input_file", str, optional=True, default=None, doc=doc_lammps_input_file
+ "lammps_input_file",
+ str,
+ optional=True,
+ default=None,
+ doc=doc_lammps_input_file,
  ),
  ]
 

dpgen2/entrypoint/submit.py

@@ -81,8 +81,8 @@
  CustomizedLmpTemplateTaskGroup,
  ExplorationStage,
  ExplorationTask,
- LmpTemplateTaskGroup,
  LmpSpinTaskGroup,
+ LmpTemplateTaskGroup,
  NPTTaskGroup,
  caly_normalize,
  diffcsp_normalize,
@@ -319,7 +319,9 @@ def make_naive_exploration_scheduler_without_conf(config, explore_style):
  conv_style = convergence.pop("type")
  report = conv_styles[conv_style](**convergence)
  # trajectory render, the format of the output trajs are assumed to be lammps/dump
- render = TrajRenderLammps(nopbc=output_nopbc,lammps_input_file=config["explore"]["lammps_input_file"])
+ render = TrajRenderLammps(
+ nopbc=output_nopbc, lammps_input_file=config["explore"]["lammps_input_file"]
+ )
  # selector
  selector = ConfSelectorFrames(
  render,
@@ -379,7 +381,11 @@ def make_lmp_naive_exploration_scheduler(config):
  # report
  conv_style = convergence.pop("type")
  report = conv_styles[conv_style](**convergence)
- render = TrajRenderLammps(nopbc=output_nopbc, use_ele_temp=use_ele_temp, lammps_input_file=config["explore"]["lammps_input_file"])
+ render = TrajRenderLammps(
+ nopbc=output_nopbc,
+ use_ele_temp=use_ele_temp,
+ lammps_input_file=config["explore"]["lammps_input_file"],
+ )
  # selector
  selector = ConfSelectorFrames(
  render,

dpgen2/exploration/render/traj_render_lammps.py

@@ -42,7 +42,7 @@ def __init__(
  self,
  nopbc: bool = False,
  use_ele_temp: int = 0,
- lammps_input_file: str = None, # type: ignore
+ lammps_input_file: str = None,  # type: ignore
  ):
  self.nopbc = nopbc
  self.use_ele_temp = use_ele_temp
@@ -80,10 +80,10 @@ def _load_one_model_devi(self, fname, model_devi):
  model_devi.add(DeviManager.MIN_DEVI_F, dd[:, 5]) # type: ignore
  model_devi.add(DeviManager.AVG_DEVI_F, dd[:, 6]) # type: ignore
  # assume the 7-9 columns are for MF
- if dd.shape[1] >= 10: # type: ignore
- model_devi.add(DeviManager.MAX_DEVI_MF, dd[:, 7]) # type: ignore
- model_devi.add(DeviManager.MIN_DEVI_MF, dd[:, 8]) # type: ignore
- model_devi.add(DeviManager.AVG_DEVI_MF, dd[:, 9]) # type: ignore
+ if dd.shape[1] >= 10:  # type: ignore
+ model_devi.add(DeviManager.MAX_DEVI_MF, dd[:, 7])  # type: ignore
+ model_devi.add(DeviManager.MIN_DEVI_MF, dd[:, 8])  # type: ignore
+ model_devi.add(DeviManager.AVG_DEVI_MF, dd[:, 9])  # type: ignore
 
  def get_ele_temp(self, optional_outputs):
  ele_temp = []
@@ -139,7 +139,9 @@ def get_confs(
  else:
  traj = trajs[ii]
  # for spin job, need to read input file to get the key of the spin data
- ss = dpdata.System(traj, fmt=traj_fmt, type_map=type_map, input_file=lammps_input_file)
+ ss = dpdata.System(
+ traj, fmt=traj_fmt, type_map=type_map, input_file=lammps_input_file
+ )
  ss.nopbc = self.nopbc
  if ele_temp:
  self.set_ele_temp(ss, ele_temp[ii])

dpgen2/exploration/report/report_adaptive_lower.py

@@ -175,8 +175,12 @@ def make_class_doc_link(key):
  rate_candi_v_link = make_class_doc_link("rate_candi_v")
  numb_candi_mf_link = make_class_doc_link("numb_candi_mf")
  rate_candi_mf_link = make_class_doc_link("rate_candi_mf")
- numb_candi_s = f"{numb_candi_f_link} or {numb_candi_v_link} or {numb_candi_mf_link}"
- rate_candi_s = f"{rate_candi_f_link} or {rate_candi_v_link} or {rate_candi_mf_link}"
+ numb_candi_s = (
+ f"{numb_candi_f_link} or {numb_candi_v_link} or {numb_candi_mf_link}"
+ )
+ rate_candi_s = (
+ f"{rate_candi_f_link} or {rate_candi_v_link} or {rate_candi_mf_link}"
+ )
  level_f_hi_link = make_class_doc_link("level_f_hi")
  level_v_hi_link = make_class_doc_link("level_v_hi")
  level_mf_hi_link = make_class_doc_link("level_mf_hi")
@@ -232,7 +236,11 @@ def args() -> List[Argument]:
  "numb_candi_mf", int, optional=True, default=0, doc=doc_numb_candi_mf
  ),
  Argument(
- "rate_candi_mf", float, optional=True, default=0.0, doc=doc_rate_candi_mf
+ "rate_candi_mf",
+ float,
+ optional=True,
+ default=0.0,
+ doc=doc_rate_candi_mf,
  ),
  Argument(
  "n_checked_steps", int, optional=True, default=2, doc=doc_n_check_steps
@@ -286,9 +294,14 @@ def record(
  coll_mf = []
  # loop over trajs
  for ii in range(ntraj):
- add_nframes, add_accur, add_failed, add_f, add_v, add_mf = self._record_one_traj(
- ii, md_f[ii], md_v[ii], md_mf[ii]
- )
+ (
+ add_nframes,
+ add_accur,
+ add_failed,
+ add_f,
+ add_v,
+ add_mf,
+ ) = self._record_one_traj(ii, md_f[ii], md_v[ii], md_mf[ii])
  self.nframes += add_nframes
  self.accur.update(add_accur)
  self.failed += add_failed
@@ -319,14 +332,14 @@ def record(
  self.level_v_lo = coll_v[-numb_candi_v][0]
  if not self.has_virial:
  self.level_v_lo = None
- 
+
  if numb_candi_mf == 0:
  self.level_mf_lo = self.level_mf_hi
  else:
  self.level_mf_lo = coll_mf[-numb_candi_mf][0]
  if not self.has_mf:
  self.level_mf_lo = None
- 
+
  if numb_candi_f == 0:
  self.level_f_lo = self.level_f_hi
  else:
@@ -385,7 +398,11 @@ def _record_one_traj(
  coll_v = []
  coll_mf = []
  for ii in range(nframes):
- if md_f[ii] > self.level_f_hi or md_v[ii] > self.level_v_hi or md_mf[ii] > self.level_mf_hi:
+ if (
+ md_f[ii] > self.level_f_hi
+ or md_v[ii] > self.level_v_hi
+ or md_mf[ii] > self.level_mf_hi
+ ):
  failed.append((tt, ii))
  else:
  coll_f.append([md_f[ii], tt, ii])

dpgen2/exploration/report/report_trust_levels_base.py

@@ -44,7 +44,9 @@ def __init__(
  self.conv_accuracy = conv_accuracy
  self.clear()
  self.v_level = (self.level_v_lo is not None) and (self.level_v_hi is not None)
- self.mf_level = (self.level_mf_lo is not None) and (self.level_mf_hi is not None)
+ self.mf_level = (self.level_mf_lo is not None) and (
+ self.level_mf_hi is not None
+ )
  self.model_devi = None
 
  print_tuple = (
@@ -242,16 +244,18 @@ def _record_one_traj(
  set_mf_accu = set_full if nomagforce else set(id_mf_accu)
  set_mf_cand = set([]) if nomagforce else set(id_mf_cand)
  set_mf_fail = set([]) if nomagforce else set(id_mf_fail)
- 
+
  # check consistency
  assert set_full == set_f_accu | set_f_cand | set_f_fail
- for accu, cand, fail in [[set_f_accu, set_f_cand, set_f_fail], 
- [set_v_accu, set_v_cand, set_v_fail], 
- [set_mf_accu, set_mf_cand, set_mf_fail]]:
+ for accu, cand, fail in [
+ [set_f_accu, set_f_cand, set_f_fail],
+ [set_v_accu, set_v_cand, set_v_fail],
+ [set_mf_accu, set_mf_cand, set_mf_fail],
+ ]:
  assert 0 == len(accu & cand)
  assert 0 == len(accu & fail)
  assert 0 == len(cand & fail)
- 
+
  # accu, cand, fail
  set_accu = set_f_accu & set_v_accu & set_mf_accu
  set_fail = set_f_fail | set_v_fail | set_mf_fail

dpgen2/exploration/task/__init__.py

@@ -10,12 +10,12 @@
 from .diffcsp_task_group import (
  DiffCSPTaskGroup,
 )
-from .lmp_template_task_group import (
- LmpTemplateTaskGroup,
-)
 from .lmp_spin_task_group import (
  LmpSpinTaskGroup,
 )
+from .lmp_template_task_group import (
+ LmpTemplateTaskGroup,
+)
 from .make_task_group_from_config import (
  caly_normalize,
  caly_task_group_args,

dpgen2/exploration/task/lmp_spin_task_group.py

@@ -41,7 +41,7 @@ def set_lmp(
  numb_models: int,
  lmp_template_fname: str,
  plm_template_fname: Optional[str] = None,
- revisions: dict = {}
+ revisions: dict = {},
  ) -> None:
  self.lmp_template = Path(lmp_template_fname).read_text().split("\n")
  self.revisions = revisions
@@ -104,6 +104,7 @@ def _make_lmp_task(
  )
  return task
 
+
 def revise_by_keys(lmp_lines, keys, values):
  for kk, vv in zip(keys, values): # type: ignore
  for ii in range(len(lmp_lines)):

dpgen2/exploration/task/make_task_group_from_config.py

@@ -19,13 +19,12 @@
 from dpgen2.exploration.task.customized_lmp_template_task_group import (
  CustomizedLmpTemplateTaskGroup,
 )
-from dpgen2.exploration.task.lmp_template_task_group import (
- LmpTemplateTaskGroup,
-)
 from dpgen2.exploration.task.lmp_spin_task_group import (
  LmpSpinTaskGroup,
 )
-
+from dpgen2.exploration.task.lmp_template_task_group import (
+ LmpTemplateTaskGroup,
+)
 from dpgen2.exploration.task.npt_task_group import (
  NPTTaskGroup,
 )
@@ -180,6 +179,7 @@ def lmp_template_task_group_args():
  ),
  ]
 
+
 def lmp_spin_task_group_args():
  doc_lmp_template_fname = "The file name of lammps input template"
  doc_plm_template_fname = "The file name of plumed input template"
@@ -210,11 +210,12 @@ def lmp_spin_task_group_args():
  alias=["plm_template", "plm"],
  ),
  Argument(
- "revisions", 
- dict, 
- optional=True, 
- default={}, 
- doc=doc_revisions,)
+ "revisions",
+ dict,
+ optional=True,
+ default={},
+ doc=doc_revisions,
+ ),
  ]
 
 

dpgen2/op/run_dp_train.py

@@ -522,9 +522,7 @@ def training_args():
  doc_init_model_start_pref_fm = (
  "The start magnetic force prefactor in loss when init-model for spin job"
  )
- doc_spin = (
- "If is a spin job"
- )
+ doc_spin = "If is a spin job"
  doc_init_model_start_pref_v = (
  "The start virial prefactor in loss when init-model"
  )

tests/exploration/test_devi_manager.py

@@ -84,7 +84,7 @@ def test_devi_manager_std_check_data(self):
  model_devi.get,
  DeviManager.MAX_DEVI_V,
  )
- 
+
  self.assertRaisesRegex(
  AssertionError,
  "Error: the number of model deviation",
@@ -119,7 +119,7 @@ def test_devi_manager_std_check_data(self):
  model_devi.get,
  DeviManager.MAX_DEVI_V,
  )
- 
+
  model_devi = DeviManagerStd()
  model_devi.add(DeviManager.MAX_DEVI_F, np.array([1, 2, 3]))
  model_devi.add(DeviManager.MAX_DEVI_F, np.array([4, 5, 6]))