add the verbose option

pyxtal/__init__.py

@@ -276,6 +276,29 @@ def from_random(
  tm = None,
  use_hall = False,
  ):
+ """
+ The main function to generate random crystals.
+ It calls `block_crysstal` or `random_crystal` internally.
+
+
+ Args:
+ dim (int): dimenion (0, 1, 2, 3)
+ group (int): the group number (1-56, 1-75, 1-80, 1-230)
+ species (list): a list of atomic symbols for each ion type, e.g., `["Ti", "O"]`
+ numIons (list): a list of the number of each type of atom within the
+ primitive cell (NOT the conventional cell), e.g., `[4, 2]`
+ factor (optional): volume factor used to generate the crystal
+ thickness:
+ area (float):
+ lattice (optional): `Lattice <pyxtal.lattice.Lattice.html>`_ to define the cell
+ sites (optional): pre-assigned wyckoff sites (e.g., `[["4a"], ["2b"]]`)
+ conventional (bool): whether or not use the conventional setting
+ t_factor ():
+ max_count ():
+ tm (optional): `Tol_matrix <pyxtal.tolerance.Tol_matrix.html>`_ object
+ to define the distances
+
+ """
  if self.molecular:
  prototype = "molecular"
  else:

pyxtal/crystal.py

@@ -258,7 +258,7 @@ def set_crystal(self):
  else:
  self.lattice_attempts = 40
  self.coord_attempts = 10
- 
+
  #QZ: Maybe we no longer need this tag
  #if not self.lattice.allow_volume_reset:
  # self.lattice_attempts = 1
@@ -368,7 +368,7 @@ def _set_ion_wyckoffs(self, numIon, specie, cell, wyks):
  # Generate a list of coords from ops
  pt = self.lattice.generate_point()
  pt, wp, _ = wp.merge(pt, cell, tol, group=self.group)
- #print('good pt', pt) 
+ #print('good pt', pt)
  if wp is not False:
  # For pure planar structure
  if self.dim == 2 and self.thickness is not None and \

pyxtal/db.py

@@ -1164,6 +1164,8 @@ def export_structures(self, fmt='vasp', folder='mof_out', criteria=None,
  eng = float(vasp_eng)
  elif ff_eng is not None:
  eng = float(ff_eng)
+ else:
+ eng = None
  #if True:
  try:
  xtal = self.get_pyxtal(id, use_relaxed)
@@ -1264,9 +1266,14 @@ def get_db_unique(self, db_name=None, etol=2e-3):
  db.write(row.toatoms(), key_value_pairs=kvp)
  print("Created {:s} with {:d} strucs".format(db_name, db.count()))
 
- def check_overlap(self, reference_db, etol=2e-3):
+ def check_overlap(self, reference_db, etol=2e-3, verbose=True):
  """
  Check the overlap w.r.t the reference database
+
+ Args:
+ reference_db (str): path of reference database
+ etol (float): energy tolerence to distinguish the identical structure
+ verbose (bool): whether or not print out details
  """
 
  db_ref = database_topology(reference_db)
@@ -1294,13 +1301,22 @@ def check_overlap(self, reference_db, etol=2e-3):
  strs += "/{:d}/{:d}".format(self.db.count(), db_ref.db.count())
  print(strs)
  sorted_overlaps = sorted(overlaps, key=lambda x: x[-1])
- for entry in sorted_overlaps:
- print('{:4d} {:6s} {:4d} {:20s} {:10.3f}'.format(*entry))
+ if verbose:
+ for entry in sorted_overlaps:
+ print('{:4d} {:6s} {:4d} {:20s} {:10.3f}'.format(*entry))
 
  return overlaps
 
  def print_info(self, excluded_ids=[], cutoff=100):
+ """
+ Print out the summary of the database based on the calculated energy
+ Mostly used to quickly view the most interesting low-energy structures.
+ Todo: show vasp_energy if available
 
+ Args:
+ excluded_ids (list): list of unwanted row ids
+ cutoff (int): the cutoff value for the print
+ """
  print("\nCurrent database {:s}: {:d}".format(self.db_name, self.db.count()))
  output = []
  for row in self.db.select():
@@ -1312,7 +1328,7 @@ def print_info(self, excluded_ids=[], cutoff=100):
  for entry in sorted_output[:cutoff]:
  print('{:4d} {:6s} {:4d} {:20s} {:10.3f}'.format(*entry))
 
- strs = "Output structures: {:d}/{:d}".format(len(sorted_output), self.db.count())
+ strs = "Showed structures: {:d}/{:d}".format(len(sorted_output), self.db.count())
  print(strs)