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

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

dpgen2/entrypoint/submit.py

@@ -5,7 +5,9 @@
 import os
 import pickle
 import re
-from copy import deepcopy
+from copy import (
+ deepcopy,
+)
 from pathlib import (
  Path,
 )
@@ -71,9 +73,9 @@
  ExplorationScheduler,
 )
 from dpgen2.exploration.selector import (
- conf_filter_styles,
  ConfFilters,
  ConfSelectorFrames,
+ conf_filter_styles,
 )
 from dpgen2.exploration.task import (
  CustomizedLmpTemplateTaskGroup,

dpgen2/exploration/selector/__init__.py

@@ -9,10 +9,9 @@
  ConfSelectorFrames,
 )
 from .distance_conf_filter import (
- DistanceConfFilter
+ DistanceConfFilter,
 )
 
-
 conf_filter_styles = {
  "distance": DistanceConfFilter,
 }

dpgen2/exploration/selector/distance_conf_filter.py

@@ -1,16 +1,111 @@
-import dpdata
-import numpy as np
 import os
 import shutil
-from . import ConfFilter
+
+import dpdata
+import numpy as np
+
+from . import (
+ ConfFilter,
+)
 
 safe_dist_dict = {
- "H": 1.2255, "He": 0.936, "Li": 1.8, "Be": 1.56, "B": 1.32, "C": 1.32, "N": 1.32, "O": 1.32, "F": 1.26, "Ne": 1.92,
- "Na": 1.595, "Mg": 1.87, "Al": 1.87, "Si": 1.76, "P": 1.65, "S": 1.65, "Cl": 1.65, "Ar": 2.09,
- "K": 2.3, "Ca": 2.3, "Sc": 2.0, "Ti": 2.0, "V": 2.0, "Cr": 1.9, "Mn": 1.95, "Fe": 1.9, "Co": 1.9, "Ni": 1.9, "Cu": 1.9, "Zn": 1.9, "Ga": 2.0, "Ge": 2.0, "As": 2.0, "Se": 2.1, "Br": 2.1, "Kr": 2.3,
- "Rb": 2.5, "Sr": 2.5, "Y": 2.1, "Zr": 2.1, "Nb": 2.1, "Mo": 2.1, "Tc": 2.1, "Ru": 2.1, "Rh": 2.1, "Pd": 2.1, "Ag": 2.1, "Cd": 2.1, "In": 2.0, "Sn": 2.0, "Sb": 2.0, "Te": 2.0, "I": 2.0, "Xe": 2.0,
- "Cs": 2.5, "Ba": 2.8, "La": 2.5, "Ce": 2.55, "Pr": 2.7, "Nd": 2.8, "Pm": 2.8, "Sm": 2.8, "Eu": 2.8, "Gd": 2.8, "Tb": 2.8, "Dy": 2.8, "Ho": 2.8, "Er": 2.6, "Tm": 2.8, "Yb": 2.8, "Lu": 2.8, "Hf": 2.4, "Ta": 2.5, "W": 2.3, "Re": 2.3, "Os": 2.3, "Ir": 2.3,
- "Pt": 2.3, "Au": 2.3, "Hg": 2.3, "Tl": 2.3, "Pb": 2.3, "Bi": 2.3, "Po": 2.3, "At": 2.3, "Rn": 2.3, "Fr": 2.9, "Ra": 2.9, "Ac": 2.9, "Th": 2.8, "Pa": 2.8, "U": 2.8, "Np": 2.8, "Pu": 2.8, "Am": 2.8, "Cm": 2.8, "Cf": 2.3
+ "H": 1.2255,
+ "He": 0.936,
+ "Li": 1.8,
+ "Be": 1.56,
+ "B": 1.32,
+ "C": 1.32,
+ "N": 1.32,
+ "O": 1.32,
+ "F": 1.26,
+ "Ne": 1.92,
+ "Na": 1.595,
+ "Mg": 1.87,
+ "Al": 1.87,
+ "Si": 1.76,
+ "P": 1.65,
+ "S": 1.65,
+ "Cl": 1.65,
+ "Ar": 2.09,
+ "K": 2.3,
+ "Ca": 2.3,
+ "Sc": 2.0,
+ "Ti": 2.0,
+ "V": 2.0,
+ "Cr": 1.9,
+ "Mn": 1.95,
+ "Fe": 1.9,
+ "Co": 1.9,
+ "Ni": 1.9,
+ "Cu": 1.9,
+ "Zn": 1.9,
+ "Ga": 2.0,
+ "Ge": 2.0,
+ "As": 2.0,
+ "Se": 2.1,
+ "Br": 2.1,
+ "Kr": 2.3,
+ "Rb": 2.5,
+ "Sr": 2.5,
+ "Y": 2.1,
+ "Zr": 2.1,
+ "Nb": 2.1,
+ "Mo": 2.1,
+ "Tc": 2.1,
+ "Ru": 2.1,
+ "Rh": 2.1,
+ "Pd": 2.1,
+ "Ag": 2.1,
+ "Cd": 2.1,
+ "In": 2.0,
+ "Sn": 2.0,
+ "Sb": 2.0,
+ "Te": 2.0,
+ "I": 2.0,
+ "Xe": 2.0,
+ "Cs": 2.5,
+ "Ba": 2.8,
+ "La": 2.5,
+ "Ce": 2.55,
+ "Pr": 2.7,
+ "Nd": 2.8,
+ "Pm": 2.8,
+ "Sm": 2.8,
+ "Eu": 2.8,
+ "Gd": 2.8,
+ "Tb": 2.8,
+ "Dy": 2.8,
+ "Ho": 2.8,
+ "Er": 2.6,
+ "Tm": 2.8,
+ "Yb": 2.8,
+ "Lu": 2.8,
+ "Hf": 2.4,
+ "Ta": 2.5,
+ "W": 2.3,
+ "Re": 2.3,
+ "Os": 2.3,
+ "Ir": 2.3,
+ "Pt": 2.3,
+ "Au": 2.3,
+ "Hg": 2.3,
+ "Tl": 2.3,
+ "Pb": 2.3,
+ "Bi": 2.3,
+ "Po": 2.3,
+ "At": 2.3,
+ "Rn": 2.3,
+ "Fr": 2.9,
+ "Ra": 2.9,
+ "Ac": 2.9,
+ "Th": 2.8,
+ "Pa": 2.8,
+ "U": 2.8,
+ "Np": 2.8,
+ "Pu": 2.8,
+ "Am": 2.8,
+ "Cm": 2.8,
+ "Cf": 2.3,
 }
 for k in safe_dist_dict:
  safe_dist_dict[k] *= 0.441
@@ -23,7 +118,9 @@ def check_multiples(a, b, c, multiple):
  for j in range(len(values)):
  if i != j:
  if values[i] > multiple * values[j]:
- print(f"Value {values[i]} is {multiple} times greater than {values[j]}")
+ print(
+ f"Value {values[i]} is {multiple} times greater than {values[j]}"
+ )
  return True
  return False
 
@@ -39,15 +136,28 @@ def check(
  atom_types: np.ndarray,
  nopbc: bool,
  ):
- from ase import Atoms
- from ase.build import make_supercell
+ from ase import (
+ Atoms,
+ )
+ from ase.build import (
+ make_supercell,
+ )
 
  atom_names = list(safe_dist_dict)
- structure = Atoms(positions=coords, numbers=[atom_names.index(n)+1 for n in atom_types], cell=cell, pbc=(not nopbc))
+ structure = Atoms(
+ positions=coords,
+ numbers=[atom_names.index(n) + 1 for n in atom_types],
+ cell=cell,
+ pbc=(not nopbc),
+ )
 
  cell = structure.get_cell()
 
- if (cell[1][0]>1.732*cell[1][1] or cell[2][0]>1.732*cell[2][2] or cell[2][1]>1.732*cell[2][2]):
+ if (
+ cell[1][0] > 1.732 * cell[1][1]
+ or cell[2][0] > 1.732 * cell[2][2]
+ or cell[2][1] > 1.732 * cell[2][2]
+ ):
  print("Inclined box")
  return False
 
@@ -67,14 +177,16 @@ def check(
 
  num_atoms = len(coords)
  for i in range(num_atoms):
- for j in range(i+1, num_atoms):
+ for j in range(i + 1, num_atoms):
  dist = extended_structure.get_distance(i, j, mic=True)
  type_i = symbols[i]
  type_j = symbols[j]
  dr = safe_dist_dict[type_i] + safe_dist_dict[type_j]
 
  if dist < dr:
- print(f"Dangerous close for {type_i} - {type_j}, {dist:.5f} less than {dr:.5f}")
+ print(
+ f"Dangerous close for {type_i} - {type_j}, {dist:.5f} less than {dr:.5f}"
+ )
  return False
 
  print("Valid structure")

tests/exploration/test_distance_conf_filter.py

@@ -1,15 +1,16 @@
-import dpdata
 import os
-import numpy as np
 import unittest
 
-from .context import (
- dpgen2,
-)
+import dpdata
+import numpy as np
+
 from dpgen2.exploration.selector import (
  DistanceConfFilter,
 )
 
+from .context import (
+ dpgen2,
+)
 
 POSCAR_1 = """ Er
 1.0