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crystal.py
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crystal.py
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#!/usr/bin/env python3
import CifFile
import numpy as np
import sys, os, io, re
from disorder.material import symmetry
from disorder.material import tables
def unitcell(folder, filename, tol=1e-2):
"""
Reads atom site information from a CIF file.
Parameters
----------
folder : str,
Name of path excluding filename.
filename : str
Name of filename excluding path.
tol : float, optional
Tolerance of unique atom coordinates.
Returns
-------
unit_cell : dict
Dictionary of unit cell information.
"""
cf = CifFile.ReadCif(os.path.join(folder, filename))
cb = cf[[key for key in cf.keys() \
if cf[key].get('_cell_length_a') is not None][0]]
cif_dict = dict(cb.items())
cif_dict = {k.replace('.','_'):v for k,v in cif_dict.items()}
loop_ops = ['_space_group_symop_operation_xyz',
'_symmetry_equiv_pos_as_xyz',
'_space_group_symop_magn_operation_xyz']
ind_ops = next((i for i, loop_key in enumerate(loop_ops) \
if loop_key in cif_dict), None)
symops = cif_dict[loop_ops[ind_ops]]
parity = False if len(symops[0].split(',')) == 3 else True
if ind_ops == 2:
add_symops = cif_dict['_space_group_symop_magn_centering_xyz']
combine = []
for symop in symops:
for add_symop in add_symops:
left_op = ','.join(symop.split(',')[:3])
right_op = ','.join(add_symop.split(',')[:3])
combine_op = symmetry.binary([left_op],[right_op])
par = int(symop.split(',')[-1])
add_par = int(add_symop.split(',')[-1])
parity = par*add_par
combine += [combine_op[0]+','+str(parity)]
symops = combine
atomic_sites = cif_dict['_atom_site_label']
if '_atom_site_moment_label' in cif_dict:
magnetic_sites = cif_dict['_atom_site_moment_label']
magnetic_atoms = [asite in magnetic_sites \
for asite in atomic_sites]
if parity:
parities = [int(symop.split(',')[-1]) for symop in symops]
else:
parities = [1 for symop in symops]
symops = [','.join(symop.split(',')[:3]) for symop in symops]
atomic_sites = [re.sub(r'[0-9]', '', asite) for asite in atomic_sites]
if '_atom_site_type_symbol' in cif_dict:
symbols = cif_dict['_atom_site_type_symbol']
elif '_atom_site_symbol' in cif_dict:
symbols = cif_dict['_atom_site_symbol']
else:
symbols = atomic_sites
symbols = [sym if sym != 'D' else '2H' for sym in symbols]
xs = cif_dict['_atom_site_fract_x']
ys = cif_dict['_atom_site_fract_y']
zs = cif_dict['_atom_site_fract_z']
xs = [re.sub(r'\([^()]*\)', '', x) for x in xs]
ys = [re.sub(r'\([^()]*\)', '', y) for y in ys]
zs = [re.sub(r'\([^()]*\)', '', z) for z in zs]
if '_atom_site_occupancy' in cif_dict:
occs = cif_dict['_atom_site_occupancy']
occs = [re.sub(r'\([^()]*\)', '', occ) for occ in occs]
else:
occs = [1.0]*len(atomic_sites)
iso = False
ani = False
if '_atom_site_aniso_label' in cif_dict:
adp_type, ani = 'ani', True
if '_atom_site_aniso_u_11' in cif_dict:
adp_U = True
U11s = cif_dict['_atom_site_aniso_u_11']
U22s = cif_dict['_atom_site_aniso_u_22']
U33s = cif_dict['_atom_site_aniso_u_33']
U23s = cif_dict['_atom_site_aniso_u_23']
U13s = cif_dict['_atom_site_aniso_u_13']
U12s = cif_dict['_atom_site_aniso_u_12']
U11s = [re.sub(r'\([^()]*\)', '', U11) for U11 in U11s]
U22s = [re.sub(r'\([^()]*\)', '', U22) for U22 in U22s]
U33s = [re.sub(r'\([^()]*\)', '', U33) for U33 in U33s]
U23s = [re.sub(r'\([^()]*\)', '', U23) for U23 in U23s]
U13s = [re.sub(r'\([^()]*\)', '', U13) for U13 in U13s]
U12s = [re.sub(r'\([^()]*\)', '', U12) for U12 in U12s]
else:
adp_U = False
B11s = cif_dict['_atom_site_aniso_b_11']
B22s = cif_dict['_atom_site_aniso_b_22']
B33s = cif_dict['_atom_site_aniso_b_33']
B23s = cif_dict['_atom_site_aniso_b_23']
B13s = cif_dict['_atom_site_aniso_b_13']
B12s = cif_dict['_atom_site_aniso_b_12']
B11s = [re.sub(r'\([^()]*\)', '', B11) for B11 in B11s]
B22s = [re.sub(r'\([^()]*\)', '', B22) for B22 in B22s]
B33s = [re.sub(r'\([^()]*\)', '', B33) for B33 in B33s]
B23s = [re.sub(r'\([^()]*\)', '', B23) for B23 in B23s]
B13s = [re.sub(r'\([^()]*\)', '', B13) for B13 in B13s]
B12s = [re.sub(r'\([^()]*\)', '', B12) for B12 in B12s]
if '_atom_site_u_iso_or_equiv' in cif_dict:
adp_type, iso = 'iso', True
adp_U = True
Uisos = cif_dict['_atom_site_u_iso_or_equiv']
Uisos = [re.sub(r'\([^()]*\)', '', Uiso) for Uiso in Uisos]
elif '_atom_site_b_iso_or_equiv' in cif_dict:
adp_type, iso = 'iso', True
adp_U = False
Bisos = cif_dict['_atom_site_b_iso_or_equiv']
Bisos = [re.sub(r'\([^()]*\)', '', Biso) for Biso in Bisos]
elif ani == False:
adp_type, iso = 'iso', True
adp_U = True
Uisos = [0.0]*len(atomic_sites)
if ani and iso:
adp_type = 'ani'
D = cartesian_displacement(*parameters(folder, filename))
iso = np.dot(np.linalg.inv(D), np.linalg.inv(D.T))
iso_labels = cif_dict['_atom_site_label']
ani_labels = cif_dict['_atom_site_aniso_label']
adp_types = cif_dict.get('_atom_site_adp_type')
if adp_types is None:
adp_types = ['uani']*len(iso_labels)
U11, U22, U33, U23, U13, U12 = [], [], [], [], [], []
B11, B22, B33, B23, B13, B12 = [], [], [], [], [], []
for adp, label in zip(adp_types, iso_labels):
if adp.lower() == 'uani':
index = ani_labels.index(label)
U11.append(U11s[index])
U22.append(U22s[index])
U33.append(U33s[index])
U23.append(U23s[index])
U13.append(U13s[index])
U12.append(U12s[index])
elif adp.lower() == 'bani':
index = ani_labels.index(label)
B11.append(B11s[index])
B22.append(B22s[index])
B33.append(B33s[index])
B23.append(B23s[index])
B13.append(B13s[index])
B12.append(B12s[index])
elif adp.lower() == 'uiso':
index = iso_labels.index(label)
Uani = iso*float(Uisos[index])
U11.append(str(Uani[0,0]))
U22.append(str(Uani[1,1]))
U33.append(str(Uani[2,2]))
U23.append(str(Uani[1,2]))
U13.append(str(Uani[0,2]))
U12.append(str(Uani[0,1]))
elif adp.lower() == 'biso':
index = iso_labels.index(label)
Bani = iso*float(Bisos[index])
B11.append(str(Bani[0,0]))
B22.append(str(Bani[1,1]))
B33.append(str(Bani[2,2]))
B23.append(str(Bani[1,2]))
B13.append(str(Bani[0,2]))
B12.append(str(Bani[0,1]))
U11s, U22s, U33s, U23s, U13s, U12s = U11, U22, U33, U23, U13, U12
B11s, B22s, B33s, B23s, B13s, B12s = B11, B22, B33, B23, B13, B12
Mxs = [0.0]*len(atomic_sites)
Mys = [0.0]*len(atomic_sites)
Mzs = [0.0]*len(atomic_sites)
mag_symops = ['mx,my,mz']*len(atomic_sites)
if '_atom_site_moment_label' in cif_dict:
mxs = cif_dict['_atom_site_moment_crystalaxis_x']
mys = cif_dict['_atom_site_moment_crystalaxis_y']
mzs = cif_dict['_atom_site_moment_crystalaxis_z']
symmform = cif_dict.get('_atom_site_moment_symmform')
if symmform is None:
symmform = ['mx,my,mz']*len(mzs)
mxs = [re.sub(r'\([^()]*\)', '', mx) for mx in mxs]
mys = [re.sub(r'\([^()]*\)', '', my) for my in mys]
mzs = [re.sub(r'\([^()]*\)', '', mz) for mz in mzs]
if len(magnetic_sites) != len(atomic_sites):
j = 0
for i, mag in enumerate(magnetic_atoms):
if mag:
Mxs[i], Mys[i], Mzs[i] = mxs[j], mys[j], mzs[j]
mag_symops[i] = symmform[j]
j += 1
else:
Mxs, Mys, Mzs = mxs, mys, mzs
mag_symops = symmform
c, d, m, s = [], [], [], []
total, types, operators, mag_operators = [], [], [], []
cf = 8*np.pi**2
for i, asite in enumerate(atomic_sites):
x, y, z = float(xs[i]), float(ys[i]), float(zs[i])
Mx, My, Mz = float(Mxs[i]), float(Mys[i]), float(Mzs[i])
occ = float(occs[i])
if adp_type == 'ani':
if adp_U is False:
B11 = float(B11s[i])
B22 = float(B22s[i])
B33 = float(B33s[i])
B23 = float(B23s[i])
B13 = float(B13s[i])
B12 = float(B12s[i])
U11, U22, U33 = B11/cf, B22/cf, B33/cf
U23, U13, U12 = B23/cf, B13/cf, B12/cf
else:
U11 = float(U11s[i])
U22 = float(U22s[i])
U33 = float(U33s[i])
U23 = float(U23s[i])
U13 = float(U13s[i])
U12 = float(U12s[i])
else:
if adp_U is False:
Biso = float(Bisos[i])
Uiso = Biso/(8*np.pi**2)
else:
Uiso = float(Uisos[i])
symbol = symbols[i]
mag_symop = mag_symops[i]
for symop, parity in zip(symops, parities):
transformed = symmetry.evaluate([symop], [x,y,z]).flatten()
mag_op = symmetry.generate_mag([symop], mag_symop, parity)
mom = symmetry.evaluate_mag([mag_op], [Mx,My,Mz]).flatten()
if adp_type == 'ani':
disp = symmetry.evaluate_disp([symop], [U11,U22,U33,
U23,U13,U12])
else:
disp = [Uiso]
transformed = [tf+(tf < 0)-(tf >= 1) for tf in transformed]
total.append(transformed)
types.append(symbol)
operators.append(symop)
mag_operators.append(mag_op)
c.append(occ)
d.append(disp)
m.append(mom)
s.append(i)
total = np.array(total)
types = np.array(types)
operators = np.array(operators)
mag_operators = np.array(mag_operators)
c = np.array(c)
d = np.array(d)
m = np.array(m)
s = np.array(s)
metric = np.round(np.round(total/tol, 1)).astype(int)
_, labels = np.unique(types, return_inverse=True)
metric = np.column_stack((metric, labels))
symmetries, indices = np.unique(metric, axis=0, return_index=True)
total = total[indices]
u, v, w = total[:,0], total[:,1], total[:,2]
n_atm = symmetries.shape[0]
atm = types[indices]
u = np.round(u, 4)
v = np.round(v, 4)
w = np.round(w, 4)
c = c[indices]
d = d[indices]
m = m[indices]
s = s[indices]
ops = operators[indices]
mag_ops = mag_operators[indices]
sort = np.lexsort(np.column_stack((u, v, w, s)).T)
u = u[sort]
v = v[sort]
w = w[sort]
c = c[sort]
d = d[sort]
m = m[sort]
s = s[sort]
ops = ops[sort]
mag_ops = mag_ops[sort]
atm = atm[sort]
ion = np.array([''.join(re.findall(r'[\d.+-]+$', a)) for a in atm])
iso = np.array([''.join(re.findall(r'^\d+\s*', a)) for a in atm])
atm = np.array([''.join(re.findall(r'[a-zA-Z]', a)) for a in atm])
unit_cell = {}
unit_cell['u'] = u
unit_cell['v'] = v
unit_cell['w'] = w
unit_cell['occupancy'] = c
unit_cell['displacement'] = d
unit_cell['moment'] = m
unit_cell['site'] = s
unit_cell['operator'] = ops
unit_cell['magnetic_operator'] = mag_ops
unit_cell['isotope'] = iso
unit_cell['ion'] = ion
unit_cell['atom'] = atm
unit_cell['n_atom'] = n_atm
return unit_cell
def supercell(atm, occ, disp, mom, u, v, w, nu, nv, nw,
name, folder, filename):
"""
Write average supercell information to a CIF file.
Parameters
----------
atm : 1d array, str
Atoms, ions, or isotopes.
occ : 1d array
Site occupancies.
disp : 1d array
Atomic displacements.
mom : 1d array
Magnetic moments.
u, v, w : 1d array
Fractional coordinates.
nu, nv, nw : int
Number of grid points :math:`N_1`, :math:`N_2`, :math:`N_3` along the
:math:`a`, :math:`b`, and :math:`c`-axis of the supercell.
folder : str,
Name of path excluding filename of reference CIF file.
filename : str
Name of filename excluding path of reference CIF file.
tol : float, optional
Tolerance of unique atom coordinates.
"""
cf = CifFile.ReadCif(os.path.join(folder, filename))
cb = cf[[key for key in cf.keys() \
if cf[key].get('_cell_length_a') is not None][0]]
cif_dict = dict(cb.items())
cif_dict = {k.replace('.','_'):v for k,v in cif_dict.items()}
loop_ops = ['_space_group_symop_operation_xyz',
'_symmetry_equiv_pos_as_xyz',
'_space_group_symop_magn_operation_xyz']
ind_ops = next((i for i, loop_key in enumerate(loop_ops) \
if loop_key in cif_dict), None)
symops = cif_dict[loop_ops[ind_ops]]
symops = [re.sub(r'[+/][0-9]', '', symop) for symop in symops]
for symop in symops:
cb.RemoveLoopItem(symop)
symops = [re.sub(r'[+/][0-9]', '', symop) for symop in symops]
atomic_sites = cb.GetLoopNames('_atom_site_label')
for asite in atomic_sites:
cb.RemoveLoopItem(asite)
#n_atm = atm.shape[0]
a = float(re.sub(r'\([^()]*\)', '', cif_dict['_cell_length_a']))
b = float(re.sub(r'\([^()]*\)', '', cif_dict['_cell_length_b']))
c = float(re.sub(r'\([^()]*\)', '', cif_dict['_cell_length_c']))
cb['_cell_length_a'] = str(a*nu)
cb['_cell_length_b'] = str(b*nv)
cb['_cell_length_c'] = str(c*nw)
alpha = float(re.sub(r'\([^()]*\)', '', cif_dict['_cell_angle_alpha']))
beta = float(re.sub(r'\([^()]*\)', '', cif_dict['_cell_angle_beta']))
gamma = float(re.sub(r'\([^()]*\)', '', cif_dict['_cell_angle_gamma']))
V = volume(a,
b,
c,
np.deg2rad(alpha),
np.deg2rad(beta),
np.deg2rad(gamma))
cb['_cell_volume'] = str(V)
i, j, k = np.meshgrid(np.arange(nu),
np.arange(nv),
np.arange(nw), indexing='ij')
i = i.flatten()
j = j.flatten()
k = k.flatten()
U = (i[:,np.newaxis]+u).flatten()
V = (j[:,np.newaxis]+v).flatten()
W = (k[:,np.newaxis]+w).flatten()
n_uvw = nu*nv*nw
atom = np.tile(atm, n_uvw)
occupancy = np.tile(occ, n_uvw)
if np.shape(disp)[1] == 1:
D = cartesian_displacement(a,
b,
c,
np.deg2rad(alpha),
np.deg2rad(beta),
np.deg2rad(gamma))
uiso = np.dot(np.linalg.inv(D), np.linalg.inv(D.T))
u11, u22, u33 = uiso[0,0], uiso[1,1], uiso[2,2]
u23, u13, u12 = uiso[1,2], uiso[0,2], uiso[0,1]
ani_disp = []
for i in range(len(disp)):
const = disp[i,0]
ani_disp.append([const*u11, const*u22, const*u33,
const*u23, const*u13, const*u12])
disp = np.array(ani_disp)
U11 = np.tile(disp[:,0], n_uvw)
U22 = np.tile(disp[:,1], n_uvw)
U33 = np.tile(disp[:,2], n_uvw)
U23 = np.tile(disp[:,3], n_uvw)
U13 = np.tile(disp[:,4], n_uvw)
U12 = np.tile(disp[:,5], n_uvw)
MU = np.tile(mom[:,0], n_uvw)
MV = np.tile(mom[:,1], n_uvw)
MW = np.tile(mom[:,2], n_uvw)
if '_atom_site_aniso_label' in cif_dict:
cb.RemoveLoopItem('_atom_site_aniso_label')
if '_atom_site_moment_label' in cif_dict:
cb.RemoveLoopItem('_atom_site_moment_label')
cb.RemoveLoopItem('_atom_site_moment.label')
cb.RemoveLoopItem('_space_group_symop.magn_id')
cb.RemoveLoopItem('_space_group_symop_magn_id')
cb.RemoveLoopItem('_space_group_symop.magn_operation_xyz')
cb.RemoveLoopItem('_space_group_symop_magn_operation_xyz')
cb.RemoveLoopItem('_space_group_symop.magn_operation_mxmymz')
cb.RemoveLoopItem('_space_group_symop_magn_operation_mxmymz')
cb.RemoveLoopItem('_space_group_symop.magn_centering_id')
cb.RemoveLoopItem('_space_group_symop_magn_centering_id')
cb.RemoveLoopItem('_space_group_symop.magn_centering_xyz')
cb.RemoveLoopItem('_space_group_symop_magn_centering_xyz')
cb.RemoveLoopItem('_space_group_symop.magn_centering_mxmymz')
cb.RemoveLoopItem('_space_group_symop_magn_centering_mxmymz')
site, aniso, magn = [], [], []
for i in range(atom.shape[0]):
site.append([atom[i]+str(i),
U[i]/nu,
V[i]/nv,
W[i]/nw,
atom[i],
occupancy[i]])
aniso.append([atom[i]+str(i),
U11[i],
U22[i],
U33[i],
U12[i],
U13[i],
U23[i]])
magn.append([atom[i]+str(i),
MU[i],
MV[i],
MW[i],
'mx,my,mz'])
cb.AddLoopItem((['_space_group_symop_operation_xyz'], ['']))
cb['_space_group_symop_operation_xyz'] = ['x, y, z']
cb.AddLoopItem((['_atom_site_label',
'_atom_site_fract_x',
'_atom_site_fract_y',
'_atom_site_fract_z',
'_atom_site_type_symbol',
'_atom_site_occupancy'],
map(list, zip(*site))))
cb.AddLoopItem((['_atom_site_aniso_label',
'_atom_site_aniso_U_11',
'_atom_site_aniso_U_22',
'_atom_site_aniso_U_33',
'_atom_site_aniso_U_12',
'_atom_site_aniso_U_13',
'_atom_site_aniso_U_23'],
map(list, zip(*aniso))))
if not np.allclose((MU,MV,MW), 0):
cb.AddLoopItem((['_atom_site_moment_label',
'_atom_site_moment_crystalaxis_x',
'_atom_site_moment_crystalaxis_y',
'_atom_site_moment_crystalaxis_z',
'_atom_site_moment_symmform'],
map(list, zip(*magn))))
if name.split('.')[-1] == 'cif':
name = name.replace('cif', 'mcif')
outfile = open(name, mode='w')
# supress cf.WriteOut() output
sys.stdout = io.StringIO()
sys.stderr = io.StringIO()
outfile.write(cf.WriteOut())
sys.stdout = sys.__stdout__
sys.stderr = sys.__stderr__
outfile.close()
def disordered(delta, Ux, Uy, Uz, Sx, Sy, Sz, rx, ry, rz,
nu, nv, nw, atm, A, name, folder, filename):
"""
Write disordered supercell information to a CIF file.
Parameters
----------
delta : 1d array
Relative occupancies.
Ux, Uy, Uz : 1d array
Atomic displacementsr in Cartesian coordinates.
Sx, Sy, Sz : 1d array
Magnetic momentsr in Cartesian coordinates.
rx, ry, rz : 1d array
Spatial vector in Cartesian coordinates.
nu, nv, nw : int
Number of grid points :math:`N_1`, :math:`N_2`, :math:`N_3` along the
:math:`a`, :math:`b`, and :math:`c`-axis of the supercell.
atm : 1d array, str
Atoms, ions, or isotopes.
A : 2d array
Transformation matrix from crystal to Cartesian coordinates.
folder : str,
Name of path excluding filename of reference CIF file.
filename : str
Name of filename excluding path of reference CIF file.
"""
cf = CifFile.ReadCif(os.path.join(folder, filename))
cb = cf[[key for key in cf.keys() \
if cf[key].get('_cell_length_a') is not None][0]]
cif_dict = dict(cb.items())
cif_dict = {k.replace('.','_'):v for k,v in cif_dict.items()}
loop_ops = ['_space_group_symop_operation_xyz',
'_symmetry_equiv_pos_as_xyz',
'_space_group_symop_magn_operation_xyz']
ind_ops = next((i for i, loop_key in enumerate(loop_ops) \
if loop_key in cif_dict), None)
symops = cif_dict[loop_ops[ind_ops]]
for symop in symops:
cb.RemoveLoopItem(symop)
atomic_sites = cb.GetLoopNames('_atom_site_label')
for asite in atomic_sites:
cb.RemoveLoopItem(asite)
if '_atom_site_aniso_label' in cif_dict:
atomic_disp = cb.GetLoopNames('_atom_site_aniso_label')
for adisp in atomic_disp:
cb.RemoveLoopItem(adisp)
a = float(re.sub(r'\([^()]*\)', '', cif_dict['_cell_length_a']))
b = float(re.sub(r'\([^()]*\)', '', cif_dict['_cell_length_b']))
c = float(re.sub(r'\([^()]*\)', '', cif_dict['_cell_length_c']))
cb['_cell_length_a'] = str(a*nu)
cb['_cell_length_b'] = str(b*nv)
cb['_cell_length_c'] = str(c*nw)
ux = rx+Ux
uy = ry+Uy
uz = rz+Uz
A_inv = np.linalg.inv(A)
u, v, w = transform(ux, uy, uz, A_inv)
mx = np.round(Sx,4)
my = np.round(Sy,4)
mz = np.round(Sz,4)
G = np.dot(A.T,A)
a, b, c = np.sqrt(G[0,0]), np.sqrt(G[1,1]), np.sqrt(G[2,2])
alpha = np.arccos(G[1,2]/(b*c))
beta = np.arccos(G[0,2]/(a*c))
gamma = np.arccos(G[0,1]/(a*b))
C = cartesian_moment(a, b, c, alpha, beta, gamma)
C_inv = np.linalg.inv(C)
mu, mv, mw = transform(mx, my, mz, C_inv)
atom = np.tile(atm, nu*nv*nw)
site = []
moment = []
for i in range(atom.shape[0]):
site.append([atom[i]+str(i),
u[i]/nu,
v[i]/nv,
w[i]/nw,
atom[i],
delta[i]])
moment.append([atom[i]+str(i), mu[i], mv[i], mw[i], 'mx, my, mz'])
cb.AddLoopItem((['_space_group_symop_operation_xyz'],['']))
cb['_space_group_symop_operation_xyz'] = ['x, y, z']
cb.AddLoopItem((['_atom_site_label',
'_atom_site_fract_x',
'_atom_site_fract_y',
'_atom_site_fract_z',
'_atom_site_type_symbol',
'_atom_site_occupancy'],
map(list, zip(*site))))
if not np.allclose((mx,my,mz), 0):
cb.AddLoopItem((['_atom_site_moment_label',
'_atom_site_moment_crystalaxis_x',
'_atom_site_moment_crystalaxis_y',
'_atom_site_moment_crystalaxis_z',
'_atom_site_moment_symmform'],
map(list, zip(*moment))))
if (name.split('.')[-1] == 'cif'):
name = name.replace('cif', 'mcif')
outfile = open(name, mode='w')
# supress cf.WriteOut() output
sys.stdout = io.StringIO()
sys.stderr = io.StringIO()
outfile.write(cf.WriteOut())
sys.stdout = sys.__stdout__
sys.stderr = sys.__stderr__
outfile.close()
def laue(folder, filename):
"""
Determines Laue class from a CIF file.
===== ==================
Laue Noncentrosymmetric
===== ==================
m-3m 432, -43m
m-3 23
6/mmm 622, -62m, 6mmm
6/m 6, -6
-3m 32, 3m
-3 3
4/mmm 422, -42m, 4mm
4/m 4, -4
mmm 222, 22m
2/m 2, m
-1 1
===== ==================
Parameters
----------
folder : str,
Name of path excluding filename.
filename : str
Name of filename excluding path.
Returns
-------
laue : str
One of ``'-1'``, ``'2/m'``, ``'mmm'``, ``'4/m'``,
``'4/mmm'``, ``'-3'``, ``'-3m'``, ``'6/m'``, ``'6/mmm'``, ``'m-3'``, or
``'m-3m'``.
"""
cf = CifFile.ReadCif(os.path.join(folder, filename))
cb = cf[[key for key in cf.keys() \
if cf[key].get('_cell_length_a') is not None][0]]
cif_dict = dict(cb.items())
cif_dict = {k.replace('.','_'):v for k,v in cif_dict.items()}
loop_ops = ['_space_group_symop_operation_xyz',
'_symmetry_equiv_pos_as_xyz',
'_space_group_symop_magn_operation_xyz']
ind_ops = next((i for i, loop_key in enumerate(loop_ops) \
if loop_key in cif_dict), None)
symops = cif_dict[loop_ops[ind_ops]]
symops = symmetry.inverse(symmetry.inverse(symops))
symops.append(u'-x,-y,-z')
symops = np.unique(symops)
laue_sym = symmetry.operators(invert=False)
symmetries = list(laue_sym.keys())
for symm in symmetries:
if set(laue_sym[symm]) == set(symops):
return symm
def twins(folder, filename):
"""
Reads twin matrices from a CIF file.
Parameters
----------
folder : str,
Name of path excluding filename.
filename : str
Name of filename excluding path.
Returns
-------
T : 3d array
Twin matrices with individual components along last two axes.
weights : 1d array
Twin mass fraction.
"""
cf = CifFile.ReadCif(os.path.join(folder, filename))
cb = cf[[key for key in cf.keys() \
if cf[key].get('_cell_length_a') is not None][0]]
cif_dict = dict(cb.items())
cif_dict = {k.replace('.','_'):v for k,v in cif_dict.items()}
if '_twin_individual_id' in cif_dict:
twin_ids = cif_dict['_twin_individual_id']
n_var = len(twin_ids)
else:
n_var = 1
if '_twin_individual_mass_fraction_refined' in cif_dict:
twin_mf = cif_dict['_twin_individual_mass_fraction_refined']
twin_mf = [float(re.sub(r'\([^()]*\)', '', mf)) for mf in twin_mf]
T11s = cif_dict['_twin_individual_twin_matrix_11']
T12s = cif_dict['_twin_individual_twin_matrix_12']
T13s = cif_dict['_twin_individual_twin_matrix_13']
T21s = cif_dict['_twin_individual_twin_matrix_21']
T22s = cif_dict['_twin_individual_twin_matrix_22']
T23s = cif_dict['_twin_individual_twin_matrix_23']
T31s = cif_dict['_twin_individual_twin_matrix_31']
T32s = cif_dict['_twin_individual_twin_matrix_32']
T33s = cif_dict['_twin_individual_twin_matrix_33']
T11s = [float(re.sub(r'\([^()]*\)', '', T11)) for T11 in T11s]
T12s = [float(re.sub(r'\([^()]*\)', '', T12)) for T12 in T12s]
T13s = [float(re.sub(r'\([^()]*\)', '', T13)) for T13 in T13s]
T21s = [float(re.sub(r'\([^()]*\)', '', T21)) for T21 in T21s]
T22s = [float(re.sub(r'\([^()]*\)', '', T22)) for T22 in T22s]
T23s = [float(re.sub(r'\([^()]*\)', '', T23)) for T23 in T23s]
T31s = [float(re.sub(r'\([^()]*\)', '', T31)) for T31 in T31s]
T32s = [float(re.sub(r'\([^()]*\)', '', T32)) for T32 in T32s]
T33s = [float(re.sub(r'\([^()]*\)', '', T33)) for T33 in T33s]
else:
twin_mf = [1.0]
T11s = [1.0]
T12s = [0.0]
T13s = [0.0]
T21s = [0.0]
T22s = [1.0]
T23s = [0.0]
T31s = [0.0]
T32s = [0.0]
T33s = [1.0]
weights = np.array(twin_mf)/np.sum(twin_mf)
T = np.stack((T11s,T12s,T13s,
T21s,T22s,T23s,
T31s,T32s,T33s)).T.reshape(n_var,3,3)
return T, weights
def parameters(folder=None, filename=None):
"""
Reads lattice parameters from a CIF file.
Parameters
----------
folder : str,
Name of path excluding filename.
filename : str
Name of filename excluding path.
Returns
-------
a, b, c, alpha, beta, gamma : float
Lattice constants and angles. Angles in radians.
"""
cf = CifFile.ReadCif(os.path.join(folder, filename))
cb = cf[[key for key in cf.keys() \
if cf[key].get('_cell_length_a') is not None][0]]
cif_dict = dict(cb.items())
a = float(re.sub(r'\([^()]*\)', '', cif_dict['_cell_length_a']))
b = float(re.sub(r'\([^()]*\)', '', cif_dict['_cell_length_b']))
c = float(re.sub(r'\([^()]*\)', '', cif_dict['_cell_length_c']))
alpha = float(re.sub(r'\([^()]*\)', '', cif_dict['_cell_angle_alpha']))
beta = float(re.sub(r'\([^()]*\)', '', cif_dict['_cell_angle_beta']))
gamma = float(re.sub(r'\([^()]*\)', '', cif_dict['_cell_angle_gamma']))
return a, b, c, np.deg2rad(alpha), np.deg2rad(beta), np.deg2rad(gamma)
def group(folder, filename):
"""
Reads space group information from a CIF file.
Parameters
----------
folder : str,
Name of path excluding filename.
filename : str
Name of filename excluding path.
Returns
-------
group : int
Space group number.
hm : str
Space group symbol in Hermann–Mauguin notation.
"""
cf = CifFile.ReadCif(os.path.join(folder, filename))
cb = cf[[key for key in cf.keys() \
if cf[key].get('_cell_length_a') is not None][0]]
cif_dict = dict(cb.items())
cif_dict = {k.replace('.','_'):v for k,v in cif_dict.items()}
loop_hms = ['_space_group_name_h-m_alt',
'_symmetry_space_group_name_h-m',
'_parent_space_group_name_h-m']
ind_hms = next((i for i, loop_key in enumerate(loop_hms) \
if loop_key in cif_dict), None)
if ind_hms is not None:
hm = cif_dict[loop_hms[ind_hms]]
else:
hm = ''
hm = hm.replace('_', '').replace(' ', '')
loop_gps = ['_space_group_it_number',
'_symmetry_int_tables_number',
'_parent_space_group_it_number']
ind_gps = next((i for i, loop_key in enumerate(loop_gps) \
if loop_key in cif_dict), None)
if ind_gps is not None:
group = int(cif_dict[loop_gps[ind_gps]])
else:
group = 0
if group == 0:
if hm in tables.sg:
group = tables.sg[hm]
return group, hm
def operators(folder, filename):
"""
Reads symmetry operators from a CIF file.
Parameters
----------
folder : str,
Name of path excluding filename.
filename : str
Name of filename excluding path.
Returns
-------
symops : list
Symmetry operators in Jones-faithful notation.
"""
cf = CifFile.ReadCif(os.path.join(folder, filename))
cb = cf[[key for key in cf.keys() \
if cf[key].get('_cell_length_a') is not None][0]]
cif_dict = dict(cb.items())
cif_dict = {k.replace('.','_'):v for k,v in cif_dict.items()}
loop_ops = ['_space_group_symop_operation_xyz',
'_symmetry_equiv_pos_as_xyz',
'_space_group_symop_magn_operation_xyz']
ind_ops = next((i for i, loop_key in enumerate(loop_ops) \
if loop_key in cif_dict), None)
symops = cif_dict[loop_ops[ind_ops]]
if ind_ops == 2: