def init_common(
self,
molecules,
numMols,
volume_factor,
select_high,
allow_inversion,
orientations,
group,
lattice,
tm,
sites,
):
# init functionality which is shared by 3D, 2D, and 1D crystals
self.valid = False
self.numattempts = 0 # number of attempts to generate the crystal.
if type(group) == Group:
self.group = group
"""A pyxtal.symmetry.Group object storing information about the space/layer
/Rod/point group, and its Wyckoff positions."""
else:
self.group = Group(group, dim=self.dim)
self.number = self.group.number
"""
The international group number of the crystal:
1-230 for 3D space groups
1-80 for 2D layer groups
1-75 for 1D Rod groups
1-32 for crystallographic point groups
None otherwise
"""
self.Msgs()
self.factor = volume_factor # volume factor for the unit cell.
numMols = np.array(numMols) # must convert it to np.array
self.numMols0 = numMols # in the PRIMITIVE cell
self.numMols = self.numMols0 * cellsize(
self.group) # in the CONVENTIONAL cell
# boolean numbers
self.allow_inversion = allow_inversion
self.select_high = select_high
# Set the tolerance matrix
# The Tol_matrix object for checking inter-atomic distances within the structure.
if type(tm) == Tol_matrix:
self.tol_matrix = tm
else:
try:
self.tol_matrix = Tol_matrix(prototype=tm)
# TODO remove bare except
except:
msg = "Error: tm must either be a Tol_matrix object +\n"
msg += "or a prototype string for initializing one."
printx(msg, priority=1)
return
self.molecules = [] # A pyxtal_molecule objects,
for mol in molecules:
self.molecules.append(pyxtal_molecule(mol, self.tol_matrix))
self.sites = {}
for i, mol in enumerate(self.molecules):
if sites is not None and sites[i] is not None:
self.check_consistency(sites[i], self.numMols[i])
self.sites[i] = sites[i]
else:
self.sites[i] = None
# if seeds, directly parse the structure from cif
# At the moment, we only support one specie
if self.seed is not None:
seed = structure_from_ext(self.seed,
self.molecules[0].mol,
relax_h=self.relax_h)
if seed.match():
self.mol_sites = [seed.make_mol_site()]
self.group = Group(seed.wyc.number)
self.lattice = seed.lattice
self.molecules = [pyxtal_molecule(seed.molecule)]
self.diag = seed.diag
self.valid = True # Need to add a check function
else:
raise ValueError("Cannot extract the structure from cif")
# The valid orientations for each molecule and Wyckoff position.
# May be copied when generating a new molecular_crystal to save a
# small amount of time
if orientations is None:
self.get_orientations()
else:
self.valid_orientations = orientations
if self.seed is None:
if lattice is not None:
# Use the provided lattice
self.lattice = lattice
self.volume = lattice.volume
# Make sure the custom lattice PBC axes are correct.
if lattice.PBC != self.PBC:
self.lattice.PBC = self.PBC
printx("\n Warning: converting custom lattice PBC to " +
str(self.PBC))
else:
# Determine the unique axis
if self.dim == 2:
if self.number in range(3, 8):
unique_axis = "c"
else:
unique_axis = "a"
elif self.dim == 1:
if self.number in range(3, 8):
unique_axis = "a"
else:
unique_axis = "c"
else:
unique_axis = "c"
# Generate a Lattice instance
self.volume = self.estimate_volume()
# The Lattice object used to generate lattice matrices
if self.dim == 3 or self.dim == 0:
self.lattice = Lattice(
self.group.lattice_type,
self.volume,
PBC=self.PBC,
unique_axis=unique_axis,
)
elif self.dim == 2:
self.lattice = Lattice(
self.group.lattice_type,
self.volume,
PBC=self.PBC,
unique_axis=unique_axis,
thickness=self.thickness,
)
elif self.dim == 1:
self.lattice = Lattice(
self.group.lattice_type,
self.volume,
PBC=self.PBC,
unique_axis=unique_axis,
area=self.area,
)
self.generate_crystal()
import pymatgen.analysis.structure_matcher as sm
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
import numpy as np
from pyxtal.lattice import cellsize
for G in range(1, 231):
#for G in [90, 99, 105, 107, 203, 210, 224, 226, 227, 228]:
g = Group(G)
subs = g.get_max_t_subgroup()
indices = subs['index']
hs = subs['subgroup']
relations = subs['relations']
tran = subs['transformation']
letter = str(g[0].multiplicity) + g[0].letter
print(G)
C1 = random_crystal(G, ['C'], [int(g[0].multiplicity / cellsize(g))],
sites=[[letter]])
pmg_s1 = C1.to_pymatgen()
sga1 = SpacegroupAnalyzer(pmg_s1).get_space_group_symbol()
# each subgroup
for i in range(len(relations)):
C2 = C1.subgroup(eps=0, idx=[i], once=True)
pmg_s2 = C2.to_pymatgen()
try:
sga2 = SpacegroupAnalyzer(pmg_s2,
symprec=1e-4).get_space_group_symbol()
except:
#print("unable to find the space group")
sga2 = None
print(G, hs[i], g.symbol, sga1, Group(hs[i]).symbol, sga2, i)
if not sm.StructureMatcher().fit(pmg_s1, pmg_s2):
def init_common(self, species, numIons, factor, group, lattice, sites,
conventional, tm):
"""
Common init functionality for 0D-3D cases of random_crystal.
"""
self.source = 'Random'
self.valid = False
# Check that numIons are integers greater than 0
for num in numIons:
if int(num) != num or num < 1:
printx("Error: composition must be positive integers.",
priority=1)
return False
if type(group) == Group:
self.group = group
else:
self.group = Group(group, dim=self.dim)
self.number = self.group.number
"""
The international group number of the crystal:
1-230 for 3D space groups
1-80 for 2D layer groups
1-75 for 1D Rod groups
1-32 for crystallographic point groups
None otherwise
"""
# The number of attempts to generate the crystal
# number of atoms
# volume factor for the unit cell.
# The number of atom in the PRIMITIVE cell
# The number of each type of atom in the CONVENTIONAL cell.
# A list of atomic symbols for the types of atoms
# A list of warning messages
self.numattempts = 0
numIons = np.array(numIons)
self.factor = factor
if not conventional:
mul = cellsize(self.group)
else:
mul = 1
self.numIons = numIons * mul
formula = ""
for i, s in zip(self.numIons, species):
formula += "{:s}{:d}".format(s, int(i))
self.formula = formula
self.species = species
# Use the provided lattice
if lattice is not None:
self.lattice = lattice
self.volume = lattice.volume
# Make sure the custom lattice PBC axes are correct.
if lattice.PBC != self.PBC:
self.lattice.PBC = self.PBC
printx("\n Warning: converting custom lattice PBC to " +
str(self.PBC))
# Generate a Lattice instance based on a given volume estimation
elif lattice is None:
# Determine the unique axis
if self.dim == 2:
if self.number in range(3, 8):
unique_axis = "c"
else:
unique_axis = "a"
elif self.dim == 1:
if self.number in range(3, 8):
unique_axis = "a"
else:
unique_axis = "c"
else:
unique_axis = "c"
self.volume = self.estimate_volume()
if self.dim == 3 or self.dim == 0:
self.lattice = Lattice(
self.group.lattice_type,
self.volume,
PBC=self.PBC,
unique_axis=unique_axis,
)
elif self.dim == 2:
self.lattice = Lattice(
self.group.lattice_type,
self.volume,
PBC=self.PBC,
unique_axis=unique_axis,
# NOTE self.thickness is part of 2D class
thickness=self.thickness,
)
elif self.dim == 1:
self.lattice = Lattice(
self.group.lattice_type,
self.volume,
PBC=self.PBC,
unique_axis=unique_axis,
# NOTE self.area is part of 1D class
area=self.area,
)
# Set the tolerance matrix for checking inter-atomic distances
if type(tm) == Tol_matrix:
self.tol_matrix = tm
else:
try:
self.tol_matrix = Tol_matrix(prototype=tm)
# TODO Remove bare except
except:
printx(
("Error: tm must either be a Tol_matrix object or "
"a prototype string for initializing one."),
priority=1,
)
self.valid = False
return
self.sites = {}
for i, specie in enumerate(self.species):
if sites is not None and sites[i] is not None:
self.check_consistency(sites[i], self.numIons[i])
self.sites[specie] = sites[i]
else:
self.sites[specie] = None
# QZ: needs to check if it is compatible
self.generate_crystal()
def init_common(
self,
molecules,
numMols,
volume_factor,
select_high,
allow_inversion,
orientations,
group,
lattice,
sites,
conventional,
tm,
):
# init functionality which is shared by 3D, 2D, and 1D crystals
self.valid = False
self.numattempts = 0 # number of attempts to generate the crystal.
if type(group) == Group:
self.group = group
else:
self.group = Group(group, dim=self.dim)
self.number = self.group.number
"""
The international group number of the crystal:
1-230 for 3D space groups
1-80 for 2D layer groups
1-75 for 1D Rod groups
1-32 for crystallographic point groups
None otherwise
"""
self.factor = volume_factor # volume factor for the unit cell.
numMols = np.array(numMols) # must convert it to np.array
if not conventional:
mul = cellsize(self.group)
else:
mul = 1
self.numMols = numMols * mul
# boolean numbers
self.allow_inversion = allow_inversion
self.select_high = select_high
# Set the tolerance matrix
# The Tol_matrix object for checking inter-atomic distances within the structure.
if type(tm) == Tol_matrix:
self.tol_matrix = tm
else:
try:
self.tol_matrix = Tol_matrix(prototype=tm)
# TODO remove bare except
except:
msg = "Error: tm must either be a Tol_matrix object +\n"
msg += "or a prototype string for initializing one."
printx(msg, priority=1)
return
self.molecules = [] # A pyxtal_molecule objects,
for mol in molecules:
self.molecules.append(pyxtal_molecule(mol, self.tol_matrix))
self.sites = {}
for i, mol in enumerate(self.molecules):
if sites is not None and sites[i] is not None:
self.check_consistency(sites[i], self.numMols[i])
self.sites[i] = sites[i]
else:
self.sites[i] = None
# The valid orientations for each molecule and Wyckoff position.
# May be copied when generating a new molecular_crystal to save a
# small amount of time
if orientations is None:
self.get_orientations()
else:
self.valid_orientations = orientations
if lattice is not None:
# Use the provided lattice
self.lattice = lattice
self.volume = lattice.volume
# Make sure the custom lattice PBC axes are correct.
if lattice.PBC != self.PBC:
self.lattice.PBC = self.PBC
printx("\n Warning: converting custom lattice PBC to " + str(self.PBC))
else:
# Determine the unique axis
if self.dim == 2:
if self.number in range(3, 8):
unique_axis = "c"
else:
unique_axis = "a"
elif self.dim == 1:
if self.number in range(3, 8):
unique_axis = "a"
else:
unique_axis = "c"
else:
unique_axis = "c"
# Generate a Lattice instance
self.volume = self.estimate_volume()
# The Lattice object used to generate lattice matrices
if self.dim == 3 or self.dim == 0:
self.lattice = Lattice(
self.group.lattice_type,
self.volume,
PBC=self.PBC,
unique_axis=unique_axis,
)
elif self.dim == 2:
self.lattice = Lattice(
self.group.lattice_type,
self.volume,
PBC=self.PBC,
unique_axis=unique_axis,
thickness=self.thickness,
)
elif self.dim == 1:
self.lattice = Lattice(
self.group.lattice_type,
self.volume,
PBC=self.PBC,
unique_axis=unique_axis,
area=self.area,
)
self.generate_crystal()