def from_pymatgen(self, structure):
"""
Load the seed structure from Pymatgen/ASE/POSCAR/CIFs
"""
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer as sga
try:
# needs to do it twice in order to get the conventional cell
s = sga(structure)
structure = s.get_refined_structure()
s = sga(structure)
sym_struc = s.get_symmetrized_structure()
number = s.get_space_group_number()
except:
print("Failed to load the Pymatgen structure")
self.valid = False
if self.valid:
d = sym_struc.composition.as_dict()
species = [key for key in d.keys()]
numIons = []
for ele in species:
numIons.append(int(d[ele]))
self.numIons = numIons
self.species = species
self.group = Group(number)
atom_sites = []
for i, site in enumerate(sym_struc.equivalent_sites):
pos = site[0].frac_coords
wp = Wyckoff_position.from_group_and_index(
number, sym_struc.wyckoff_symbols[i])
specie = site[0].specie.number
atom_sites.append(atom_site(wp, pos, specie))
self.atom_sites = atom_sites
self.lattice = Lattice.from_matrix(sym_struc.lattice.matrix,
ltype=self.group.lattice_type)
def subgroup_by_splitter(self, splitter, eps=0.05):
lat1 = np.dot(splitter.R[:3, :3].T, self.lattice.matrix)
multiples = np.linalg.det(splitter.R[:3, :3])
split_sites = []
for i, site in enumerate(self.atom_sites):
pos = site.position
for ops1, ops2 in zip(splitter.G2_orbits[i], splitter.H_orbits[i]):
pos0 = apply_ops(pos, ops1)[0]
pos0 -= np.floor(pos0)
pos0 += eps * (np.random.sample(3) - 0.5)
wp, _ = Wyckoff_position.from_symops(ops2,
group=splitter.H.number,
permutation=False)
split_sites.append(atom_site(wp, pos0, site.specie))
new_struc = deepcopy(self)
new_struc.group = splitter.H
lattice = Lattice.from_matrix(lat1, ltype=new_struc.group.lattice_type)
new_struc.lattice = lattice.mutate(degree=0.01, frozen=True)
new_struc.atom_sites = split_sites
new_struc.numIons = [
int(multiples * numIon) for numIon in self.numIons
]
new_struc.source = 'Wyckoff Split'
return new_struc
def make_supergroup(self, solutions, once=False, show_detail=True):
"""
create supergroup structures based on the list of solutions
Args:
solutions: list of tuples (splitter, mapping, disp)
show_detail (bool): print out the detail
Returns:
list of pyxtal structures
"""
G_strucs = []
if len(solutions) > 0:
if once:
disps = np.array([sol[-1] for sol in solutions])
ID = np.argmin(disps)
solutions = [solutions[ID]]
for solution in solutions:
(sp, mapping, disp, mae) = solution
lat1 = np.dot(np.linalg.inv(sp.R[:3,:3]).T, self.struc.lattice.matrix)
lattice = Lattice.from_matrix(lat1, ltype=sp.G.lattice_type)
details = self.symmetrize(sp, mapping, disp)
coords_G1, coords_G2, coords_H1, elements = details
G_struc = self.struc.copy()
G_struc.group = sp.G
G_sites = []
for i, wp in enumerate(sp.wp1_lists):
pos = coords_G1[i]
pos -= np.floor(pos)
pos1 = sym.search_matched_position(sp.G, wp, pos)
if pos1 is not None:
site = atom_site(wp, pos1, sp.elements[i])
G_sites.append(site)
else:
print(">>>>>>>>>>>>>>")
print(self.struc.group.number)
print(pos)
print(wp)
print(">>>>>>>>>>>>>>")
raise RuntimeError("cannot assign the right wp")
G_struc.atom_sites = G_sites
G_struc.source = 'supergroup {:6.3f}'.format(mae)
G_struc.lattice = lattice
G_struc.numIons *= round(np.abs(np.linalg.det(sp.R[:3,:3])))
G_struc._get_formula()
G_struc.disp = mae
if new_structure(G_struc, G_strucs):
G_strucs.append(G_struc)
if show_detail:
G = sp.G.number
self.print_detail(G, coords_H1, coords_G2, elements, disp)
print(G_struc)
return G_strucs
def read_cif(filename):
"""
read the cif, mainly for pyxtal cif output
Be cautious in using it to read other cif files
Args:
filename: path of the structure file
Return:
pyxtal structure
"""
species = []
coords = []
with open(filename, 'r') as f:
lines = f.readlines()
for i, line in enumerate(lines):
if line.startswith('_symmetry_Int_Tables_number'):
sg = int(line.split()[-1])
elif line.startswith('_cell_length_a'):
a = float(lines[i].split()[-1])
b = float(lines[i+1].split()[-1])
c = float(lines[i+2].split()[-1])
alpha = float(lines[i+3].split()[-1])
beta = float(lines[i+4].split()[-1])
gamma = float(lines[i+5].split()[-1])
elif line.startswith('_symmetry_cell_setting'):
lat_type = line.split()[-1]
elif line.startswith('_symmetry_space_group_name_H-M '):
symbol = line.split()[-1]
if eval(symbol) in ["Pn", "P21/n", "C2/n"]:
diag = True
else:
diag = False
elif line.find('_atom_site') >= 0:
s = i
while True:
s += 1
if lines[s].find('_atom_site') >= 0:
pass
elif len(lines[s].split()) <= 3:
break
else:
tmp = lines[s].split()
pos = [float(tmp[-4]), float(tmp[-3]), float(tmp[-2])]
species.append(tmp[0])
coords.append(pos)
break
wp0 = Group(sg)[0]
lattice = Lattice.from_para(a, b, c, alpha, beta, gamma, lat_type)
sites = []
for specie, coord in zip(species, coords):
pt, wp, _ = WP_merge(coord, lattice.matrix, wp0, tol=0.1)
sites.append(atom_site(wp, pt, specie, diag))
return lattice, sites
def optimize_lattice(self, iterations=3):
"""
optimize the lattice if the cell has a bad inclination angles
"""
#if self.molecular:
count = 0
for i in range(iterations):
lattice, trans, opt = self.lattice.optimize()
#print(self.lattice, "->", lattice)
if opt:
if self.molecular:
sites = self.mol_sites
else:
sites = self.atom_sites
for j, site in enumerate(sites):
count += 1
pos_abs = np.dot(site.position, self.lattice.matrix)
pos_frac = pos_abs.dot(lattice.inv_matrix)
pos_frac -= np.floor(pos_frac)
if self.molecular:
site.lattice = lattice
# for P21/c, Pc, C2/c, check if opt the inclination angle
ops = site.wp.ops.copy()
diag = False
if self.group.number in [7, 14, 15]:
for k, op in enumerate(ops):
vec = op.translation_vector.dot(trans)
#print(vec)
vec -= np.floor(vec)
op1 = op.from_rotation_and_translation(
op.rotation_matrix, vec)
ops[k] = op1
wp, perm = Wyckoff_position.from_symops(
ops, self.group.number)
if not isinstance(perm, list):
diag = True
else:
diag = False
pos_frac = pos_frac[perm]
sites[j] = atom_site(wp, pos_frac, site.specie, diag)
#print(sites[j].wp)
#site.update()
self.lattice = lattice
self.diag = diag
else:
break
def make_supergroup(self, solutions, show_detail=True):
"""
create supergroup structures based on the list of solutions
Args:
solutions: list of tuples (splitter, mapping, disp)
Returns:
list of pyxtal structures
"""
G_strucs = []
for solution in solutions:
(sp, mapping, disp, mae) = solution
G = sp.G.number
#print(disp)
details = self.symmetrize(sp, mapping, disp)
coords_G1, coords_G2, coords_H1, elements, mults = details
G_struc = self.struc.copy()
G_struc.group = sp.G
G_sites = []
for i, wp in enumerate(sp.wp1_lists):
site = atom_site(wp, coords_G1[i], sp.elements[i])
G_sites.append(site)
G_struc.atom_sites = G_sites
G_struc.source = 'supergroup {:6.3f}'.format(mae)
lat1 = np.dot(sp.inv_R[:3, :3].T, self.struc.lattice.matrix)
lattice = Lattice.from_matrix(lat1, ltype=sp.G.lattice_type)
#lattice.reset_matrix() #make it has a regular shape
#G_struc.lattice = self.struc.lattice.supergroup(sp.G.lattice_type)
G_struc.lattice = lattice
G_struc.numIons *= round(np.abs(np.linalg.det(sp.R[:3, :3])))
G_struc._get_formula()
if new_structure(G_struc, G_strucs):
G_strucs.append(G_struc)
if show_detail:
details = self.symmetrize(sp, mapping, disp)
_, coords_G2, coords_H1, elements, mults = details
self.print_detail(G, coords_H1, coords_G2, elements, mults,
disp)
print(G_struc)
#print(sp.R)
return G_strucs
def _from_pymatgen(self, struc, tol=1e-3, a_tol=5.0):
"""
Load structure from Pymatgen
should not be used directly
"""
from pyxtal.util import get_symmetrized_pmg
#import pymatgen.analysis.structure_matcher as sm
self.valid = True
try:
sym_struc, number = get_symmetrized_pmg(struc, tol, a_tol)
#print(sym_struc)
#import sys; sys.exit()
except TypeError:
print("Failed to load the Pymatgen structure")
# print(struc)
# self.valid = False
if self.valid:
d = sym_struc.composition.as_dict()
species = [key for key in d.keys()]
numIons = []
for ele in species:
numIons.append(int(d[ele]))
self.numIons = numIons
self.species = species
self.group = Group(number)
matrix, ltype = sym_struc.lattice.matrix, self.group.lattice_type
self.lattice = Lattice.from_matrix(matrix, ltype=ltype)
atom_sites = []
for i, site in enumerate(sym_struc.equivalent_sites):
pos = site[0].frac_coords
wp = Wyckoff_position.from_group_and_index(number, sym_struc.wyckoff_symbols[i])
specie = site[0].specie.number
pos1 = search_matched_position(self.group, wp, pos)
if pos1 is not None:
atom_sites.append(atom_site(wp, pos1, specie))
else:
break
if len(atom_sites) != len(sym_struc.equivalent_sites):
raise RuntimeError("Cannot extract the right mapping from spglib")
else:
self.atom_sites = atom_sites
def _from_pymatgen(self, struc, tol=1e-3):
"""
Load structure from Pymatgen
should not be used directly
"""
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer as sga
from pyxtal.util import symmetrize
#import pymatgen.analysis.structure_matcher as sm
self.valid = True
try:
# needs to do it twice in order to get the conventional cell
pmg = symmetrize(struc, tol)
s = sga(pmg, symprec=tol)
sym_struc = s.get_symmetrized_structure()
number = s.get_space_group_number()
#print(sym_struc)
except:
print("Failed to load the Pymatgen structure")
self.valid = False
if self.valid:
d = sym_struc.composition.as_dict()
species = [key for key in d.keys()]
numIons = []
for ele in species:
numIons.append(int(d[ele]))
self.numIons = numIons
self.species = species
self.group = Group(number)
atom_sites = []
for i, site in enumerate(sym_struc.equivalent_sites):
pos = site[0].frac_coords
wp = Wyckoff_position.from_group_and_index(
number, sym_struc.wyckoff_symbols[i])
specie = site[0].specie.number
atom_sites.append(atom_site(wp, pos, specie, search=True))
self.atom_sites = atom_sites
matrix, ltype = sym_struc.lattice.matrix, self.group.lattice_type
self.lattice = Lattice.from_matrix(matrix, ltype=ltype)
def _get_alternative(self, wyc_set, index):
"""
get alternative structure representations
Args:
tran: affine matrix
index: the list of transformed wps
Returns:
a new pyxtal structure after transformation
"""
new_struc = self.copy()
# xyz_string like 'x+1/4,y+1/4,z+1/4'
xyz_string = wyc_set['Coset Representative'][index]
op = get_inverse(SymmOp.from_xyz_string(xyz_string))
#op = SymmOp.from_xyz_string(xyz_string)
ids = []
for i, site in enumerate(new_struc.atom_sites):
id = len(self.group) - site.wp.index - 1
letter = wyc_set['Transformed WP'][index].split()[id]
ids.append(letters.index(letter))
wp = Wyckoff_position.from_group_and_index(self.group.number, letter)
pos = op.operate(site.position)
pos1 = search_matched_position(self.group, wp, pos)
if pos1 is not None:
new_struc.atom_sites[i] = atom_site(wp, pos1, site.specie)
else:
print(pos)
print(wp)
raise RuntimeError("Cannot find the right pos")
# switch lattice
R = op.affine_matrix[:3,:3] #rotation
matrix = np.dot(R, self.lattice.matrix)
new_struc.lattice = Lattice.from_matrix(matrix, ltype=self.group.lattice_type)
new_struc.source = "Alt. Wyckoff Set: " + xyz_string
return new_struc, ids
def _generate_ion_wyckoffs(self, numIon, specie, cell_matrix, wyks):
"""
generates a set of wyckoff positions to accomodate a given number
of ions
Args:
numIon: Number of ions to accomodate
specie: Type of species being placed on wyckoff site
cell_matrix: Matrix of lattice vectors
wyks: current wyckoff sites
Returns:
Sucess:
wyckoff_sites_tmp: list of wyckoff sites for valid sites
Failue:
None
"""
numIon_added = 0
tol = self.tol_matrix.get_tol(specie, specie)
tol_matrix = self.tol_matrix
wyckoff_sites_tmp = []
# Now we start to add the specie to the wyckoff position
sites_list = deepcopy(self.sites[specie]) # the list of Wyckoff site
if sites_list is not None:
wyckoff_attempts = max(len(sites_list) * 2, 10)
else:
# the minimum numattempts is to put all atoms to the general WPs
min_wyckoffs = int(numIon /
len(self.group.wyckoffs_organized[0][0]))
wyckoff_attempts = max(2 * min_wyckoffs, 10)
cycle = 0
while cycle < wyckoff_attempts:
# Choose a random WP for given multiplicity: 2a, 2b
if sites_list is not None:
site = sites_list[0]
else: # Selecting the merging
site = None
wp = choose_wyckoff(self.group, numIon - numIon_added, site,
self.dim)
if wp is not False:
# Generate a list of coords from ops
mult = wp.multiplicity # remember the original multiplicity
pt = self.lattice.generate_point()
# Merge coordinates if the atoms are close
pt, wp, _ = WP_merge(pt, cell_matrix, wp, tol)
# For pure planar structure
if self.dim == 2 and self.thickness is not None and self.thickness < 0.1:
pt[-1] = 0.5
# If site the pre-assigned, do not accept merge
if wp is not False:
if site is not None and mult != wp.multiplicity:
cycle += 1
continue
# Use a Wyckoff_site object for the current site
new_site = atom_site(wp, pt, specie)
# Check current WP against existing WP's
passed_wp_check = True
for ws in wyckoff_sites_tmp + wyks:
if not new_site.check_with_ws2(ws, cell_matrix,
tol_matrix):
passed_wp_check = False
if passed_wp_check:
if sites_list is not None:
sites_list.pop(0)
wyckoff_sites_tmp.append(new_site)
numIon_added += new_site.multiplicity
# Check if enough atoms have been added
if numIon_added == numIon:
return wyckoff_sites_tmp
cycle += 1
self.numattempts += 1
return None
def subgroup_by_splitter(self, splitter, eps=0.05):
"""
transform the crystal to subgroup symmetry from a splitter object
"""
lat1 = np.dot(splitter.R[:3, :3].T, self.lattice.matrix)
multiples = np.linalg.det(splitter.R[:3, :3])
new_struc = deepcopy(self)
new_struc.group = splitter.H
lattice = Lattice.from_matrix(lat1, ltype=new_struc.group.lattice_type)
lattice = lattice.mutate(degree=eps, frozen=True)
h = splitter.H.number
split_sites = []
if self.molecular:
# below only works when the cell does not change
for i, site in enumerate(self.mol_sites):
pos = site.position
mol = site.molecule
ori = site.orientation
coord0 = mol.mol.cart_coords.dot(ori.matrix.T)
wp1 = site.wp
ori.reset_matrix(np.eye(3))
for ops1, ops2 in zip(splitter.G2_orbits[i],
splitter.H_orbits[i]):
#reset molecule
coord1 = np.dot(coord0, ops1[0].affine_matrix[:3, :3].T)
_mol = mol.copy()
_mol.reset_positions(coord1)
pos0 = apply_ops(pos, ops1)[0]
pos0 -= np.floor(pos0)
pos0 += eps * (np.random.sample(3) - 0.5)
wp, _ = Wyckoff_position.from_symops(ops2,
h,
permutation=False)
split_sites.append(mol_site(_mol, pos0, ori, wp, lattice))
new_struc.mol_sites = split_sites
new_struc.numMols = [
int(multiples * numMol) for numMol in self.numMols
]
else:
for i, site in enumerate(self.atom_sites):
pos = site.position
for ops1, ops2 in zip(splitter.G2_orbits[i],
splitter.H_orbits[i]):
pos0 = apply_ops(pos, ops1)[0]
pos0 -= np.floor(pos0)
pos0 += eps * (np.random.sample(3) - 0.5)
wp, _ = Wyckoff_position.from_symops(ops2,
h,
permutation=False)
split_sites.append(atom_site(wp, pos0, site.specie))
new_struc.atom_sites = split_sites
new_struc.numIons = [
int(multiples * numIon) for numIon in self.numIons
]
new_struc.lattice = lattice
new_struc.source = 'Wyckoff Split'
return new_struc
def _subgroup_by_splitter(self, splitter, eps=0.05, mut_lat=True):
"""
transform the crystal to subgroup symmetry from a splitter object
Args:
splitter: wyckoff splitter object
eps (float): maximum atomic displacement in Angstrom
mut_lat (bool): whether or not mutate the lattice
"""
lat1 = np.dot(splitter.R[:3,:3].T, self.lattice.matrix)
multiples = np.linalg.det(splitter.R[:3,:3])
new_struc = self.copy()
new_struc.group = splitter.H
lattice = Lattice.from_matrix(lat1, ltype=new_struc.group.lattice_type)
if mut_lat:
lattice=lattice.mutate(degree=eps, frozen=True)
h = splitter.H.number
split_sites = []
if self.molecular:
# below only works when the cell does not change
for i, site in enumerate(self.mol_sites):
pos = site.position
mol = site.molecule
ori = site.orientation
coord0 = mol.mol.cart_coords.dot(ori.matrix.T)
coord0 = np.dot(coord0, splitter.R[:3,:3])
wp1 = site.wp
ori.reset_matrix(np.eye(3))
id = 0
for ops1, ops2 in zip(splitter.G2_orbits[i], splitter.H_orbits[i]):
#reset molecule
rot = wp1.generators_m[id].affine_matrix[:3,:3].T
coord1 = np.dot(coord0, rot)
_mol = mol.copy()
_mol.reset_positions(coord1)
pos0 = apply_ops(pos, ops1)[0]
pos0 -= np.floor(pos0)
dis = (np.random.sample(3) - 0.5).dot(self.lattice.matrix)
dis /= np.linalg.norm(dis)
pos0 += eps*dis*(np.random.random()-0.5)
wp, _ = Wyckoff_position.from_symops(ops2, h, permutation=False)
if h in [7, 14] and self.group.number == 31:
diag = True
else:
diag = self.diag
split_sites.append(mol_site(_mol, pos0, ori, wp, lattice, diag))
id += wp.multiplicity
new_struc.mol_sites = split_sites
new_struc.numMols = [int(multiples*numMol) for numMol in self.numMols]
else:
for i, site in enumerate(self.atom_sites):
pos = site.position
for ops1, ops2 in zip(splitter.G2_orbits[i], splitter.H_orbits[i]):
pos0 = apply_ops(pos, ops1)[0]
pos0 -= np.floor(pos0)
dis = (np.random.sample(3) - 0.5).dot(self.lattice.matrix)
dis /= np.linalg.norm(dis)
pos0 += np.dot(eps*dis*(np.random.random()-0.5), self.lattice.inv_matrix)
wp, _ = Wyckoff_position.from_symops(ops2, h, permutation=False)
split_sites.append(atom_site(wp, pos0, site.specie))
new_struc.atom_sites = split_sites
new_struc.numIons = [int(multiples*numIon) for numIon in self.numIons]
new_struc.lattice = lattice
new_struc.source = 'subgroup'
return new_struc