chore: ban module-level import of pymatgen

dpgen/auto_test/Elastic.py

@@ -4,11 +4,6 @@
 from shutil import copyfile
 
 from monty.serialization import dumpfn, loadfn
-from pymatgen.analysis.elasticity.elastic import ElasticTensor
-from pymatgen.analysis.elasticity.strain import DeformedStructureSet, Strain
-from pymatgen.analysis.elasticity.stress import Stress
-from pymatgen.core.structure import Structure
-from pymatgen.io.vasp import Incar, Kpoints
 
 import dpgen.auto_test.lib.abacus as abacus
 import dpgen.auto_test.lib.vasp as vasp
@@ -53,6 +48,9 @@
  self.inter_param = inter_param if inter_param is not None else {"type": "vasp"}
 
  def make_confs(self, path_to_work, path_to_equi, refine=False):
+ from pymatgen.analysis.elasticity.strain import DeformedStructureSet, Strain
+ from pymatgen.core.structure import Structure
+
  path_to_work = os.path.abspath(path_to_work)
  if os.path.exists(path_to_work):
  dlog.warning(f"{path_to_work} already exists")
@@ -189,6 +187,8 @@
  return task_list
 
  def post_process(self, task_list):
+ from pymatgen.io.vasp import Incar, Kpoints
+
  if self.inter_param["type"] == "abacus":
  POSCAR = "STRU"
  INCAR = "INPUT"
@@ -250,6 +250,9 @@
  return self.parameter
 
  def _compute_lower(self, output_file, all_tasks, all_res):
+ from pymatgen.analysis.elasticity.elastic import ElasticTensor
+ from pymatgen.analysis.elasticity.stress import Stress
+
  output_file = os.path.abspath(output_file)
  res_data = {}
  ptr_data = os.path.dirname(output_file) + "\n"

dpgen/auto_test/Gamma.py

@@ -8,8 +8,6 @@
 from ase.lattice.cubic import BodyCenteredCubic as bcc
 from ase.lattice.cubic import FaceCenteredCubic as fcc
 from monty.serialization import dumpfn, loadfn
-from pymatgen.core.structure import Structure
-from pymatgen.io.ase import AseAtomsAdaptor
 
 import dpgen.auto_test.lib.abacus as abacus
 import dpgen.auto_test.lib.vasp as vasp
@@ -94,6 +92,8 @@ def __init__(self, parameter, inter_param=None):
  self.inter_param = inter_param if inter_param is not None else {"type": "vasp"}
 
  def make_confs(self, path_to_work, path_to_equi, refine=False):
+ from pymatgen.core.structure import Structure
+
  path_to_work = os.path.abspath(path_to_work)
  if os.path.exists(path_to_work):
  dlog.warning(f"{path_to_work} already exists")
@@ -287,6 +287,8 @@ def return_direction(self):
  return directions
 
  def __gen_slab_ase(self, symbol, lat_param):
+ from pymatgen.io.ase import AseAtomsAdaptor
+
  if not self.lattice_type:
  raise RuntimeError("Error! Please provide the input lattice type!")
  elif self.lattice_type == "bcc":

dpgen/auto_test/Interstitial.py

@@ -5,8 +5,6 @@
 
 import numpy as np
 from monty.serialization import dumpfn, loadfn
-from pymatgen.analysis.defects.generators import InterstitialGenerator
-from pymatgen.core.structure import Structure
 
 import dpgen.auto_test.lib.abacus as abacus
 import dpgen.auto_test.lib.lammps as lammps
@@ -78,6 +76,9 @@ def __init__(self, parameter, inter_param=None):
  self.inter_param = inter_param if inter_param is not None else {"type": "vasp"}
 
  def make_confs(self, path_to_work, path_to_equi, refine=False):
+ from pymatgen.analysis.defects.generators import InterstitialGenerator
+ from pymatgen.core.structure import Structure
+
  path_to_work = os.path.abspath(path_to_work)
  path_to_equi = os.path.abspath(path_to_equi)
 

dpgen/auto_test/Surface.py

@@ -6,8 +6,6 @@
 import dpdata
 import numpy as np
 from monty.serialization import dumpfn, loadfn
-from pymatgen.core.structure import Structure
-from pymatgen.core.surface import generate_all_slabs
 
 import dpgen.auto_test.lib.abacus as abacus
 import dpgen.auto_test.lib.vasp as vasp
@@ -85,6 +83,9 @@ def __init__(self, parameter, inter_param=None):
  self.inter_param = inter_param if inter_param is not None else {"type": "vasp"}
 
  def make_confs(self, path_to_work, path_to_equi, refine=False):
+ from pymatgen.core.structure import Structure
+ from pymatgen.core.surface import generate_all_slabs
+
  path_to_work = os.path.abspath(path_to_work)
  if os.path.exists(path_to_work):
  dlog.warning(f"{path_to_work} already exists")

dpgen/auto_test/VASP.py

@@ -2,8 +2,6 @@
 
 from dpdata import LabeledSystem
 from monty.serialization import dumpfn
-from pymatgen.core.structure import Structure
-from pymatgen.io.vasp import Incar, Kpoints
 
 import dpgen.auto_test.lib.vasp as vasp
 from dpgen import dlog
@@ -22,6 +20,8 @@ def __init__(self, inter_parameter, path_to_poscar):
  self.path_to_poscar = path_to_poscar
 
  def make_potential_files(self, output_dir):
+ from pymatgen.core.structure import Structure
+
  potcar_not_link_list = ["vacancy", "interstitial"]
  task_type = output_dir.split("/")[-2].split("_")[0]
 
@@ -69,6 +69,8 @@ def make_potential_files(self, output_dir):
  dumpfn(self.inter, os.path.join(output_dir, "inter.json"), indent=4)
 
  def make_input_file(self, output_dir, task_type, task_param):
+ from pymatgen.io.vasp import Incar, Kpoints
+
  sepline(ch=output_dir)
  dumpfn(task_param, os.path.join(output_dir, "task.json"), indent=4)
 

dpgen/auto_test/Vacancy.py

@@ -5,8 +5,6 @@
 
 import numpy as np
 from monty.serialization import dumpfn, loadfn
-from pymatgen.analysis.defects.generators import VacancyGenerator
-from pymatgen.core.structure import Structure
 
 import dpgen.auto_test.lib.abacus as abacus
 from dpgen import dlog
@@ -77,6 +75,9 @@ def __init__(self, parameter, inter_param=None):
  self.inter_param = inter_param if inter_param is not None else {"type": "vasp"}
 
  def make_confs(self, path_to_work, path_to_equi, refine=False):
+ from pymatgen.analysis.defects.generators import VacancyGenerator
+ from pymatgen.core.structure import Structure
+
  path_to_work = os.path.abspath(path_to_work)
  if os.path.exists(path_to_work):
  dlog.warning(f"{path_to_work} already exists")

dpgen/auto_test/gen_confs.py

@@ -4,9 +4,6 @@
 import os
 import re
 
-from pymatgen.analysis.structure_matcher import StructureMatcher
-from pymatgen.ext.matproj import MPRester
-
 import dpgen.auto_test.lib.crys as crys
 
 global_std_crystal = {
@@ -20,6 +17,8 @@
 
 
 def test_fit(struct, data):
+ from pymatgen.analysis.structure_matcher import StructureMatcher
+
  m = StructureMatcher()
  for ii in data:
  if m.fit(ii["structure"], struct):
@@ -50,6 +49,9 @@
 
 
 def gen_element(ele_name, key):
+ from pymatgen.analysis.structure_matcher import StructureMatcher
+ from pymatgen.ext.matproj import MPRester
+
  assert isinstance(ele_name, str)
  mpr = MPRester(key)
  data = mpr.query(
@@ -93,6 +95,8 @@
 
 
 def gen_alloy(eles, key):
+ from pymatgen.ext.matproj import MPRester
+
  mpr = MPRester(key)
 
  data = mpr.query(

dpgen/auto_test/lib/abacus.py

@@ -7,7 +7,6 @@
 from dpdata.abacus.scf import make_unlabeled_stru
 from dpdata.utils import uniq_atom_names
 from dpdata.vasp import poscar as dpdata_poscar
-from pymatgen.core.structure import Structure
 
 import dpgen.generator.lib.abacus_scf as abacus_scf
 
@@ -343,6 +342,8 @@ def final_stru(abacus_path):
 
 
 def stru2Structure(struf):
+ from pymatgen.core.structure import Structure
+
  stru = dpdata.System(struf, fmt="stru")
  stru.to("poscar", "POSCAR.tmp")
  ss = Structure.from_file("POSCAR.tmp")

dpgen/auto_test/lib/crys.py

@@ -1,15 +1,18 @@
 import numpy as np
-from pymatgen.core.lattice import Lattice
-from pymatgen.core.structure import Structure
 
 
 def fcc(ele_name="ele", a=4.05):
+ from pymatgen.core.structure import Structure
+
  box = np.array([[0.0, 0.5, 0.5], [0.5, 0.0, 0.5], [0.5, 0.5, 0.0]])
  box *= a
  return Structure(box, [ele_name], [[0, 0, 0]])
 
 
 def fcc1(ele_name="ele", a=4.05):
+ from pymatgen.core.lattice import Lattice
+ from pymatgen.core.structure import Structure
+
  latt = Lattice.cubic(a)
  return Structure(
  latt,
@@ -19,11 +22,17 @@
 
 
 def sc(ele_name="ele", a=2.551340126037118):
+ from pymatgen.core.lattice import Lattice
+ from pymatgen.core.structure import Structure
+
  latt = Lattice.cubic(a)
  return Structure(latt, [ele_name], [[0, 0, 0]])
 
 
 def bcc(ele_name="ele", a=3.2144871302356037):
+ from pymatgen.core.lattice import Lattice
+ from pymatgen.core.structure import Structure
+
  latt = Lattice.cubic(a)
  return Structure(
  latt,
@@ -38,6 +47,9 @@
 def hcp(
  ele_name="ele", a=4.05 / np.sqrt(2), c=4.05 / np.sqrt(2) * 2.0 * np.sqrt(2.0 / 3.0)
 ):
+ from pymatgen.core.lattice import Lattice
+ from pymatgen.core.structure import Structure
+
  box = np.array([[1, 0, 0], [0.5, 0.5 * np.sqrt(3), 0], [0, 0, 1]])
  box[0] *= a
  box[1] *= a
@@ -51,6 +63,9 @@
 def dhcp(
  ele_name="ele", a=4.05 / np.sqrt(2), c=4.05 / np.sqrt(2) * 4.0 * np.sqrt(2.0 / 3.0)
 ):
+ from pymatgen.core.lattice import Lattice
+ from pymatgen.core.structure import Structure
+
  box = np.array([[1, 0, 0], [0.5, 0.5 * np.sqrt(3), 0], [0, 0, 1]])
  box[0] *= a
  box[1] *= a
@@ -69,6 +84,9 @@
 
 
 def diamond(ele_name="ele", a=2.551340126037118):
+ from pymatgen.core.lattice import Lattice
+ from pymatgen.core.structure import Structure
+
  box = np.array([[0.0, 1.0, 1.0], [1.0, 0.0, 1.0], [1.0, 1.0, 0.0]])
  box *= a
  latt = Lattice(box)

dpgen/auto_test/lib/vasp.py

@@ -3,7 +3,6 @@
 import warnings
 
 import numpy as np
-from pymatgen.io.vasp import Incar, Kpoints
 
 import dpgen.auto_test.lib.util as util
 from dpgen.generator.lib.vasp import incar_upper
@@ -503,6 +502,8 @@
 
 
 def make_vasp_kpoints_from_incar(work_dir, jdata):
+ from pymatgen.io.vasp import Incar, Kpoints
+
  cwd = os.getcwd()
  fp_aniso_kspacing = jdata.get("fp_aniso_kspacing")
  os.chdir(work_dir)

dpgen/auto_test/mpdb.py

@@ -1,13 +1,13 @@
 import os
 
-from pymatgen.ext.matproj import MPRester, MPRestError
-
 from dpgen import dlog
 
 web = "materials.org"
 
 
 def check_apikey():
+ from pymatgen.ext.matproj import MPRester, MPRestError
+
  try:
  apikey = os.environ["MAPI_KEY"]
  except KeyError:

dpgen/data/gen.py

@@ -10,8 +10,6 @@
 
 import dpdata
 import numpy as np
-from pymatgen.core import Structure
-from pymatgen.io.vasp import Incar
 
 import dpgen.data.tools.bcc as bcc
 import dpgen.data.tools.diamond as diamond
@@ -300,6 +298,8 @@
 
 
 def make_super_cell(jdata):
+ from pymatgen.core import Structure
+
  out_dir = jdata["out_dir"]
  super_cell = jdata["super_cell"]
  path_uc = os.path.join(out_dir, global_dirname_02)
@@ -342,6 +342,8 @@
 
 
 def make_super_cell_poscar(jdata):
+ from pymatgen.core import Structure
+
  out_dir = jdata["out_dir"]
  super_cell = jdata["super_cell"]
  path_sc = os.path.join(out_dir, global_dirname_02)
@@ -1444,6 +1446,8 @@
 
 
 def gen_init_bulk(args):
+ from pymatgen.io.vasp import Incar
+
  jdata = load_file(args.PARAM)
  if args.MACHINE is not None:
  mdata = load_file(args.MACHINE)

dpgen/data/surf.py

@@ -12,12 +12,7 @@
 from ase.build import general_surface
 
 # -----ASE-------
-from pymatgen.core import Element, Structure
-from pymatgen.io.ase import AseAtomsAdaptor
-
 # -----PMG---------
-from pymatgen.io.vasp import Poscar
-
 import dpgen.data.tools.bcc as bcc
 import dpgen.data.tools.diamond as diamond
 import dpgen.data.tools.fcc as fcc
@@ -168,6 +163,8 @@ def poscar_scale_direct(str_in, scale):
 
 
 def poscar_elong(poscar_in, poscar_out, elong, shift_center=True):
+ from pymatgen.core import Structure
+
  with open(poscar_in) as fin:
  lines = list(fin)
  if lines[7][0].upper() != "C":
@@ -215,6 +212,9 @@ def make_unit_cell(jdata):
 
 
 def make_super_cell_pymatgen(jdata):
+ from pymatgen.core import Element, Structure
+ from pymatgen.io.ase import AseAtomsAdaptor
+
  make_unit_cell(jdata)
  out_dir = jdata["out_dir"]
  path_uc = os.path.join(out_dir, global_dirname_02)
@@ -401,6 +401,8 @@ def poscar_scale_cartesian(str_in, scale):
 
 
 def poscar_scale(poscar_in, poscar_out, scale):
+ from pymatgen.io.vasp import Poscar
+
  with open(poscar_in) as fin:
  lines = list(fin)
  if "D" == lines[7][0] or "d" == lines[7][0]: