def read_crystal(filename):
f_crystal = open(filename)
crystal_in = CrystalIn(f_crystal.readlines())
f_crystal.close()
tags = crystal_in.get_tags()
cell = Atoms(cell=tags['lattice_vectors'],
symbols=tags['atomic_species'],
scaled_positions=tags['coordinates'])
magmoms = tags['magnetic_moments']
if magmoms is not None:
# Print out symmetry information for magnetic cases
# Original code from structure/symmetry.py
symmetry = Symmetry(cell, symprec=1e-5)
print(
"CRYSTAL-interface: Magnetic structure, number of operations without spin: %d"
% len(symmetry.get_symmetry_operations()['rotations']))
print("CRYSTAL-interface: Spacegroup without spin: %s" %
symmetry.get_international_table())
cell.set_magnetic_moments(magmoms)
symmetry = Symmetry(cell, symprec=1e-5)
print(
"CRYSTAL-interface: Magnetic structure, number of operations with spin: %d"
% len(symmetry.get_symmetry_operations()['rotations']))
print("")
return cell, tags['conv_numbers']
def read_castep(filename):
f_castep = open(filename)
castep_in = CastepIn(f_castep.readlines())
f_castep.close()
tags = castep_in.get_tags()
# 1st stage is to create Atoms object ignoring Spin polarization. General case.
cell = Atoms(cell=tags['lattice_vectors'],
symbols=tags['atomic_species'],
scaled_positions=tags['coordinates'])
# Analyse spin states and add data to Atoms instance "cell" if ones exist
magmoms = tags['magnetic_moments']
if magmoms is not None:
# Print out symmetry information for magnetic cases
# Original code from structure/symmetry.py
symmetry = Symmetry(cell, symprec=1e-5)
print(
"CASTEP-interface: Magnetic structure, number of operations without spin: %d"
% len(symmetry.get_symmetry_operations()['rotations']))
print("CASTEP-interface: Spacegroup without spin: %s" %
symmetry.get_international_table())
cell.set_magnetic_moments(magmoms)
symmetry = Symmetry(cell, symprec=1e-5)
print(
"CASTEP-interface: Magnetic structure, number of operations with spin: %d"
% len(symmetry.get_symmetry_operations()['rotations']))
print("")
return cell
def gencastep(fn, modenum, basis, natom, typatsym, symprec, atpos):
from phonopy import Phonopy
import phonopy.structure.spglib as spg
from phonopy.structure.atoms import PhonopyAtoms as Atoms
from phonopy.structure.symmetry import Symmetry, find_primitive, get_pointgroup
fh = open(fn, 'w')
unitcell = Atoms(symbols=typatsym, cell=basis, positions=atpos)
pbasis = np.eye(3)
for i in range(len(basis)):
pbasis[i] = basis[i] / np.linalg.norm(basis[i])
symmetry = Symmetry(unitcell, symprec)
rotations = symmetry.get_symmetry_operations()['rotations']
translations = symmetry.get_symmetry_operations()['translations']
print('Space group International symbol: %s' %
symmetry.get_international_table())
fh.write('%BLOCK LATTICE_CART\n')
for bl in basis:
fh.write('%s\n' % ''.join(' %12.8f' % b for b in bl))
fh.write('%ENDBLOCK LATTICE_CART\n\n')
fh.write('%BLOCK POSITIONS_ABS\n')
for i in range(len(typatsym)):
fh.write(" %3s " % typatsym[i])
fh.write('%s\n' % ''.join(' %12.8f' % p for p in atpos[i].tolist()))
fh.write('%ENDBLOCK POSITIONS_ABS\n\n')
fh.write('SYMMETRY_TOL : %f ang\n' % symprec)
fh.write('SYMMETRY_GENERATE \n')
fh.write('#KPOINT_MP_GRID : 4 4 4\n#KPOINT_MP_OFFSET : 0.5 0.5 0.5\n')
def read_crystal(filename):
f_crystal = open(filename)
crystal_in = CrystalIn(f_crystal.readlines())
f_crystal.close()
tags = crystal_in.get_tags()
cell = Atoms(cell=tags['lattice_vectors'],
symbols=tags['atomic_species'],
scaled_positions=tags['coordinates'])
magmoms = tags['magnetic_moments']
if magmoms is not None:
# Print out symmetry information for magnetic cases
# Original code from structure/symmetry.py
symmetry = Symmetry(cell, symprec=1e-5)
print("CRYSTAL-interface: Magnetic structure, number of operations without spin: %d" %
len(symmetry.get_symmetry_operations()['rotations']))
print("CRYSTAL-interface: Spacegroup without spin: %s" % symmetry.get_international_table())
cell.set_magnetic_moments(magmoms)
symmetry = Symmetry(cell, symprec=1e-5)
print("CRYSTAL-interface: Magnetic structure, number of operations with spin: %d" %
len(symmetry.get_symmetry_operations()['rotations']))
print("")
return cell, tags['conv_numbers']
def gencastep(fn,modenum,basis,natom,typatsym,symprec,atpos):
from phonopy import Phonopy
import phonopy.structure.spglib as spg
from phonopy.structure.atoms import PhonopyAtoms as Atoms
from phonopy.structure.symmetry import Symmetry, find_primitive, get_pointgroup
fh=open(fn,'w')
unitcell = Atoms(symbols=typatsym, cell=basis, positions=atpos)
pbasis=np.eye(3)
for i in range(len(basis)):
pbasis[i]=basis[i]/np.linalg.norm(basis[i])
symmetry = Symmetry(unitcell, symprec)
rotations = symmetry.get_symmetry_operations()['rotations']
translations = symmetry.get_symmetry_operations()['translations']
print('Space group International symbol: %s' % symmetry.get_international_table())
fh.write('%BLOCK LATTICE_CART\n')
for bl in basis:
fh.write('%s\n' % ''.join(' %12.8f' % b for b in bl))
fh.write('%ENDBLOCK LATTICE_CART\n\n')
fh.write('%BLOCK POSITIONS_ABS\n')
for i in range(len(typatsym)):
fh.write(" %3s " % typatsym[i])
fh.write('%s\n' % ''.join(' %12.8f' % p for p in atpos[i].tolist()))
fh.write('%ENDBLOCK POSITIONS_ABS\n\n')
fh.write('SYMMETRY_TOL : %f ang\n' % symprec)
fh.write('SYMMETRY_GENERATE \n')
fh.write('#KPOINT_MP_GRID : 4 4 4\n#KPOINT_MP_OFFSET : 0.5 0.5 0.5\n')
def test_parse_wien2k_struct(self):
cell, npts, r0s, rmts = parse_wien2k_struct("BaGa2.struct")
lattice = cell.get_cell().T
displacements, supercell = parse_disp_yaml("disp_BaGa2.yaml",
return_cell=True)
symmetry = Symmetry(cell)
print(PhonopyAtoms(atoms=cell))
sym_op = symmetry.get_symmetry_operations()
print(symmetry.get_international_table())
for i, (r, t) in enumerate(
zip(sym_op['rotations'], sym_op['translations'])):
print("--- %d ---" % (i + 1))
print(r)
print(t)
self._set_x_tags('xred')
def _set_x_tags(self, tagname):
xtag = []
natom = self._tags['natom']
for val in self._values:
xtag += self._get_numerical_values(val)
if len(xtag) >= natom * 3:
break
self._tags[tagname] = np.reshape(xtag[:natom * 3], (-1, 3))
def _set_znucl(self):
znucl = []
ntypat = self._tags['ntypat']
for val in self._values:
znucl += self._get_numerical_values(val, num_type='int')
if len(znucl) >= ntypat:
break
self._tags['znucl'] = znucl[:ntypat]
if __name__ == '__main__':
import sys
from phonopy.structure.symmetry import Symmetry
abinit = AbinitIn(open(sys.argv[1]).readlines())
cell = read_abinit(sys.argv[1])
symmetry = Symmetry(cell)
print("# %s" % symmetry.get_international_table())
print(get_abinit_structure(cell))
self._tags['plat'] = plat
def _set_alat(self, header):
hlist = header.split()
for j in hlist:
if j.startswith('alat'):
alat = float(j.split('=')[1])
break
self._tags['alat'] = alat
def _check_ord(self, header):
if not 'xpos' in header.split():
print('EXIT(1): LMTO Interface requires site', end=' ')
print('files to be in fractional co-ordinates')
sys.exit(1)
def get_variables(self, header, sites):
self._check_ord(header)
self._set_atoms(sites)
self._set_plat(header)
self._set_alat(header)
return self._tags
if __name__ == '__main__':
import sys
from phonopy.structure.symmetry import Symmetry
cell = read_lmto(sys.argv[1])
symmetry = Symmetry(cell)
print('# %s' % symmetry.get_international_table())
print(get_lmto_structure(cell))
self._tags["atoms"] = {"spfnames": spfnames, "positions": positions}
def _set_avec(self):
avec = []
for i in range(3):
avec.append([float(x) for x in self._lines.pop(0).split()[:3]])
self._tags["avec"] = avec
def _set_scale(self):
scale = float(self._lines.pop(0).split()[0])
for i in range(3):
self._tags["scale"][i] = scale
def _set_scale1(self):
self._tags["scale"][0] = float(self._lines.pop(0).split()[0])
def _set_scale2(self):
self._tags["scale"][1] = float(self._lines.pop(0).split()[0])
def _set_scale3(self):
self._tags["scale"][2] = float(self._lines.pop(0).split()[0])
if __name__ == "__main__":
from phonopy.structure.symmetry import Symmetry
cell, sp_filenames = read_elk(sys.argv[1])
symmetry = Symmetry(cell)
print("# %s" % symmetry.get_international_table())
print(get_elk_structure(cell, sp_filenames=sp_filenames))
def _set_alat(self, header):
hlist = header.split()
for j in hlist:
if j.startswith('alat'):
alat = float(j.split('=')[1])
break
self._tags['alat'] = alat
def _check_ord(self, header):
if not 'xpos' in header.split():
print('EXIT(1): LMTO Interface requires site', end=' ')
print('files to be in fractional co-ordinates')
sys.exit(1)
def get_variables(self, header, sites):
self._check_ord(header)
self._set_atoms(sites)
self._set_plat(header)
self._set_alat(header)
return self._tags
if __name__ == '__main__':
import sys
from phonopy.structure.symmetry import Symmetry
cell = read_lmto(sys.argv[1])
symmetry = Symmetry(cell)
print('# %s' % symmetry.get_international_table())
print(get_lmto_structure(cell))
elif tag == "atomiccoordinatesandatomicspecies":
lines = block.split('\n')[:-1]
self._tags["atomiccoordinates"] = [ [float(x) for x in atom.split()[:3]] for atom in lines ]
self._tags["atomicspecies"] = [ int(atom.split()[3]) for atom in lines]
#check if the block are present
self.check_present("atomicspecies")
self.check_present("atomiccoordinates")
self.check_present("latticevectors")
self.check_present("chemicalspecieslabel")
#translate the atomicspecies to atomic numbers
self._tags["atomicnumbers"] = [self._tags["atomicnumbers"][atype] for atype in self._tags["atomicspecies"]]
def check_present(self,tag):
if not self._tags[tag]:
print "%s not present"%tag
exit()
def __str__():
return self._tags
if __name__ == '__main__':
import sys
from phonopy.structure.symmetry import Symmetry
cell,atypes = read_siesta(sys.argv[1])
symmetry = Symmetry(cell)
print "#", symmetry.get_international_table()
print get_siesta_structure(cell,atypes)
]
#check if the block are present
self.check_present("atomicspecies")
self.check_present("atomiccoordinates")
self.check_present("latticevectors")
self.check_present("chemicalspecieslabel")
#translate the atomicspecies to atomic numbers
self._tags["atomicnumbers"] = [
self._tags["atomicnumbers"][atype]
for atype in self._tags["atomicspecies"]
]
def check_present(self, tag):
if not self._tags[tag]:
print "%s not present" % tag
exit()
def __str__():
return self._tags
if __name__ == '__main__':
import sys
from phonopy.structure.symmetry import Symmetry
cell, atypes = read_siesta(sys.argv[1])
symmetry = Symmetry(cell)
print "#", symmetry.get_international_table()
print get_siesta_structure(cell, atypes)
from anharmonic.phonon3.triplets import get_triplets_at_q
from phonopy.interface.vasp import read_vasp
from phonopy.structure.symmetry import Symmetry
import numpy as np
cell = read_vasp("POSCAR-unitcell")
symmetry = Symmetry(cell, 1e-2)
print symmetry.get_international_table()
reciprocal_lattice = np.linalg.inv(cell.get_cell())
mesh = [7, 7, 7]
print reciprocal_lattice
(triplets_at_q,
weights_at_q,
grid_address,
bz_map,
triplets_map_at_q,
ir_map_at_q)= get_triplets_at_q(74,
mesh,
symmetry.get_pointgroup_operations(),
reciprocal_lattice,
stores_triplets_map=True)
for triplet in triplets_at_q:
sum_q = (grid_address[triplet]).sum(axis=0)
if (sum_q % mesh != 0).any():
print "============= Warning =================="
print triplet
for tp in triplet:
print grid_address[tp], np.linalg.norm(np.dot(reciprocal_lattice, grid_address[tp] / mesh))
