complete substitute_1_2 function

pyxtal/__init__.py

@@ -664,7 +664,8 @@ def supergroups(self, G=None, d_tol=1.0):
  sup = supergroups(self, G=G, d_tol=d_tol)
  return sup.strucs
 
- def subgroup(self, perms=None, H=None, eps=0.05, idx=None, group_type='t', max_cell=4, min_cell=0):
+ def subgroup(self, perms=None, H=None, eps=0.05, idx=None, group_type='t',
+ max_cell=4, min_cell=0, N_groups=None):
  """
  Generate a structure with lower symmetry
 
@@ -676,13 +677,20 @@ def subgroup(self, perms=None, H=None, eps=0.05, idx=None, group_type='t', max_c
  group_type (string): `t`, `k` or `t+k`
  max_cell (float): maximum cell reconstruction
  min_cell (float): maximum cell reconstruction
-
+ max_subgroups (int): maximum number of trial subgroups
  Returns:
  a list of pyxtal structures with lower symmetries
  """
 
+ idx, sites, t_types, k_types = self._get_subgroup_ids(H,
+ group_type,
+ idx,
+ max_cell,
+ min_cell)
  #randomly choose a subgroup from the available list
- idx, sites, t_types, k_types = self._get_subgroup_ids(H, group_type, idx, max_cell, min_cell)
+ if N_groups is not None and len(idx) >= N_groups:
+ idx = sample(idx, N_groups)
+ #print('max_sub_group', len(idx), max_subgroups)
 
  valid_splitters = []
  bad_splitters = []
@@ -2664,7 +2672,9 @@ def show_mol_cluster(self, id, factor=1.5, max_d=4.0, plot=True, ignore_E=False,
 
  return display_cluster(molecules, self.lattice.matrix, engs, cmap, **kwargs)
 
- def substitute_1_2(self, dicts, ratio=[1, 1], group_type='t+k', max_cell=4, min_cell=0, max_wp=None):
+ def substitute_1_2(self, dicts, ratio=[1, 1], group_type='t+k', max_cell=4,
+ min_cell=0, max_wp=None, N_groups=None,
+ N_max=10, criteria=None):
  """
  Derive the BC compounds from A via subgroup relation
  For example, from C to BN or from SiO2 to AlPO3.
@@ -2678,16 +2688,24 @@ def substitute_1_2(self, dicts, ratio=[1, 1], group_type='t+k', max_cell=4, min_
  max_cell (float): maximum cell reconstruction
  min_cell (float): maximum cell reconstruction
  max_wp (int): maximum number of wp
+ N_groups (int): maximum number of trial subgroups
+ N_max (int): maximum number of structures
+ criteria (dict): dictionary criteria
 
  Returns:
  A list of pyxtal structures
  """
  from pyxtal.util import new_struc_wo_energy
 
  xtals = self._substitute_1_2(dicts, ratio)
+ xtals = [xtal for xtal in xtals if criteria is None or xtal.check_validity(criteria)]
+
  if len(xtals) == 0:
  #print("\nCannot split, look for subgroup representation")
- subs = self.subgroup(group_type=group_type, max_cell=max_cell, min_cell=min_cell)
+ subs = self.subgroup(group_type=group_type,
+ max_cell=max_cell,
+ min_cell=min_cell,
+ N_groups=N_groups)
  #print("Found {:d} subgroup representatios".format(len(subs)))
  for sub in subs:
  #print(sub)
@@ -2697,12 +2715,20 @@ def substitute_1_2(self, dicts, ratio=[1, 1], group_type='t+k', max_cell=4, min_
  continue
  else:
  if new_struc_wo_energy(_xtal, xtals):
- xtals.append(_xtal)
- print('Add substitution', _xtal.get_xtal_string())
+ add = True
+
+ if criteria is not None and not _xtal.check_validity(criteria):
+ add = False
+
+ if add:
+ xtals.append(_xtal)
+ print('Add substitution', _xtal.get_xtal_string())
+ if len(xtals) == N_max:
+ break
  #print('Add {:d} substitutions in subgroup {:d}'.format(len(_xtals), sub.group.number))
  else:
  print('Good representation ({:d})'.format(len(xtals)), self.get_xtal_string())
- print('Found {:d} substitutions in total\n'.format(len(xtals)))
+ print('Found {:d} substitutions in total'.format(len(xtals)))
  return xtals
 
  def _substitute_1_2(self, dicts, ratio=[1, 1]): #, group_type='t', max_cell=4, min_cell=0):