def getSupercell(self, atoms):
from pyspglib import spglib
s = spglib.get_symmetry(atoms)
symmetry = []
print "building symmetry"
for i, rot in enumerate(s['rotations'][:100]):
print "symetry :", i
trans = s['translations'][i]
map0 = self.getMap(atoms, rot, trans)
symmetry.append([rot, map0])
return symmetry
def getSupercell(self, atoms):
from pyspglib import spglib
s = spglib.get_symmetry(atoms)
symmetry = []
print("building symmetry")
for i, rot in enumerate(s['rotations'][:100]):
print("symetry :", i)
trans = s['translations'][i]
map0 = self.getMap(atoms, rot, trans)
symmetry.append([rot, map0])
return symmetry
def get_unique_wyckoff(prim):
""" Function to find unique wyckoff sites in the primitive cell
Parameters
prim = pylada primitive cell
Returns
unique_list = unique list of sites (as numpy array) in primitive cell
"""
p = deepcopy(prim)
#Anuj_04/07/17: To make sure unique wyckoff is done on primitive
# p = primitive(pp)
# compute space group for the given primitive cell using spglib
sym = spglib.get_symmetry(p, 0.1)
# compute inverce cell of the primitive cell
inverse_cell = np.linalg.inv(p.cell)
dummy_list = []
wyckoff_list = []
for i in range(len(p)):
a = p[i].pos
a3 = get_pos_in_prim_cell(p, a)
frac_a = np.dot(inverse_cell, a3)
symm_list = []
for j in range(len(sym['rotations'])):
# rotation matrix from sym
R = sym['rotations'][j]
# translation vector from sym
Tt = sym['translations'][j]
frac_symm_a = np.dot(R, frac_a) + Tt
symm_a = np.dot(p.cell, frac_symm_a)
symm_list.append(symm_a)
symm_a2 = get_pos_in_prim_cell(p, symm_a)
symm_list.append(symm_a2)
# loop to find symmetrical equivalent positions
for k in range(i + 1, len(p)):
b = p[k].pos
b2 = get_pos_in_prim_cell(p, b)
# check distance between positions in pos and symm_list
if any(distance.euclidean(b2, c) < 0.1 for c in symm_list):
p[k].pos = p[i].pos
dummy_list = a.tolist()
dummy_list.append(p[i].type)
wyckoff_list.append(dummy_list)
### getting unique array of positions
unique_list = [list(t) for t in set(map(tuple, wyckoff_list))]
return unique_list
def get_unique_ints(prim, int_pos, ttol=0.5):
""" Function to find unique interstitial sites in the primitive cell
Parameters
prim = pylada primitive cell
int_pos = list of interstitial positions in primitive cell
ttol = tolerance, default = 0.5
Returns
unique_int_list = list of unique intestital sites (cartesian (x,y,z) as list) in primitive cell
"""
prim2 = deepcopy(prim)
pos2 = deepcopy(int_pos)
sym2 = spglib.get_symmetry(prim2, 0.1)
inverse_cell2 = np.linalg.inv(prim2.cell)
int_list2 = []
for i in range(len(pos2)):
# numpy 1D array into column vector with shape listed as (3,)
a4 = pos2[i]
frac_a4 = np.dot(inverse_cell2, a4)
symm_list2 = []
for j in range(len(sym2['rotations'])):
R = sym2['rotations'][j]
Tt = sym2['translations'][j]
frac_symm_a4 = np.dot(R, frac_a4) + Tt
symm_a4 = np.dot(prim2.cell, frac_symm_a4)
symm_list2.append(symm_a4)
symm_a5 = get_pos_in_prim_cell(prim2, symm_a4)
symm_list2.append(symm_a5)
# loop to find symmetrical equivalent positions
for k in range(i + 1, len(pos2)):
b2 = pos2[k]
# check distance between positions in pos and symm_list
if any(distance.euclidean(b2, c2) < ttol for c2 in symm_list2):
pos2[k] = pos2[i]
int_list2.append(pos2[i])
### getting the unique list of interstitials
unique_int_list = [list(t) for t in set(map(tuple, int_list2))]
return unique_int_list
# import vasp
# bulk = vasp.read_vasp(sys.argv[1])
print "[get_spacegroup]"
print " Spacegroup of Silicon is ", spglib.get_spacegroup(silicon)
print ""
print "[get_spacegroup]"
print " Spacegroup of Rutile is ", spglib.get_spacegroup(rutile)
print ""
print "[get_spacegroup]"
print " Spacegroup of MgB2 is ", spglib.get_spacegroup(MgB2)
print ""
print "[get_symmetry]"
print " Symmetry operations of Rutile unitcell are:"
print ""
symmetry = spglib.get_symmetry(rutile)
for i in range(symmetry['rotations'].shape[0]):
print " --------------- %4d ---------------" % (i + 1)
rot = symmetry['rotations'][i]
trans = symmetry['translations'][i]
print " rotation:"
for x in rot:
print " [%2d %2d %2d]" % (x[0], x[1], x[2])
print " translation:"
print " (%8.5f %8.5f %8.5f)" % (trans[0], trans[1], trans[2])
print ""
print "[get_pointgroup]"
print " Pointgroup of Rutile is", spglib.get_pointgroup(
symmetry['rotations'])[0]
print ""
# import vasp
# bulk = vasp.read_vasp(sys.argv[1])
print "[get_spacegroup]"
print " Spacegroup of Silicon is ", spglib.get_spacegroup(silicon)
print ""
print "[get_spacegroup]"
print " Spacegroup of Rutile is ", spglib.get_spacegroup(rutile)
print ""
print "[get_spacegroup]"
print " Spacegroup of MgB2 is ", spglib.get_spacegroup(MgB2)
print ""
print "[get_symmetry]"
print " Symmetry operations of Rutile unitcell are:"
print ""
symmetry = spglib.get_symmetry( rutile )
for i in range(symmetry['rotations'].shape[0]):
print " --------------- %4d ---------------" % (i+1)
rot = symmetry['rotations'][i]
trans = symmetry['translations'][i]
print " rotation:"
for x in rot:
print " [%2d %2d %2d]" % (x[0], x[1], x[2])
print " translation:"
print " (%8.5f %8.5f %8.5f)" % (trans[0], trans[1], trans[2])
print ""
print "[get_pointgroup]"
print " Pointgroup of Rutile is", spglib.get_pointgroup(symmetry['rotations'])[0]
print ""
dataset = spglib.get_symmetry_dataset( rutile )
def get_periodic_symmetry_operations(atoms, error_tolerance=0.01, debug=False):
from ase.utils import irotate
from ase.visualize import view
from pyspglib import spglib
#symmetry = spglib.get_symmetry(atoms, symprec=1e-5)
symmetry = spglib.get_symmetry(atoms, symprec=1e-2)
dataset = spglib.get_symmetry_dataset(atoms, symprec=1e-2)
result = []
if debug:
cell, scaled_positions, numbers = spglib.find_primitive(atoms,
symprec=1e-5)
a = Atoms(symbols='O4',
cell=cell,
scaled_positions=scaled_positions,
pbc=True)
#symmetry = spglib.get_symmetry(a, symprec=1e-2)
#dataset = spglib.get_symmetry_dataset(a, symprec=1e-2)
print dataset['equivalent_atoms']
print dataset['international']
print dataset['hall']
print dataset['wyckoffs']
print dataset['transformation_matrix']
print "Number of symmetry operations %i" % len(dataset['rotations'])
for i in range(dataset['rotations'].shape[0]):
new_atoms = atoms.copy()
test = atoms.copy()
rot = dataset['rotations'][i]
trans = dataset['translations'][i]
if debug:
x, y, z = irotate(rot)
#print x, y, z
print "------------------- %i -----------------------" % i
print "Rotation"
print rot
print "Translation"
print trans
new_pos = new_atoms.get_scaled_positions()
for l, pos in enumerate(new_atoms.get_scaled_positions()):
#print new_pos[l]
new_pos[l] = (numpy.dot(rot, pos))
new_pos[l] += trans
#print new_pos[l]
new_atoms.set_scaled_positions(new_pos)
equals = get_equals_periodic(atoms,
new_atoms,
error_tolerance=error_tolerance,
debug=debug)
if equals != None:
so = SymmetryOperation(str(i),
equals,
None,
vector=None,
magnitude=1,
rotation_matrix=rot,
translation_vector=trans)
#if debug:
# print so
result.append(so)
else:
print "Equivalent not found"
#view(test)
#view(new_atoms)
#raw_input()
return result
#!/usr/bin/evn python
import sys
from atoms import Atoms
from vasp import read_vasp
from pyspglib import spglib
import numpy as np
def get_magmom(text):
magmom = []
for numxmag in text.split():
num, mag = numxmag.split('*')
magmom += [float(mag)] * int(num)
return magmom
def parse_incar(filename):
for line in open(filename):
for conf in line.split(';'):
if 'MAGMOM' in conf:
return get_magmom(conf.split('=')[1])
cell = read_vasp(sys.argv[1]) # POSCAR
magmoms = parse_incar(sys.argv[2]) # INCAR
cell.set_magnetic_moments(magmoms)
symmetry = spglib.get_symmetry(cell, symprec=1e-3)
print len(symmetry['rotations'])
#!/usr/bin/evn python
import sys
from atoms import Atoms
from vasp import read_vasp
from pyspglib import spglib
import numpy as np
def get_magmom(text):
magmom = []
for numxmag in text.split():
num, mag = numxmag.split('*')
magmom += [float(mag)] * int(num)
return magmom
def parse_incar(filename):
for line in open(filename):
for conf in line.split(';'):
if 'MAGMOM' in conf:
return get_magmom(conf.split('=')[1])
cell = read_vasp(sys.argv[1]) # POSCAR
magmoms = parse_incar(sys.argv[2]) # INCAR
cell.set_magnetic_moments(magmoms)
symmetry = spglib.get_symmetry(cell, symprec=1e-3)
print len(symmetry['rotations'])
