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 test_magmom(self):
symprec = 1e-5
cell = get_unitcell_from_phonopy_yaml(os.path.join(data_dir,"Cr.yaml"))
symmetry_nonspin = Symmetry(cell, symprec=symprec)
atom_map_nonspin = symmetry_nonspin.get_map_atoms()
len_sym_nonspin = len(
symmetry_nonspin.get_symmetry_operations()['rotations'])
spin = [1, -1]
cell_withspin = cell.copy()
cell_withspin.set_magnetic_moments(spin)
symmetry_withspin = Symmetry(cell_withspin, symprec=symprec)
atom_map_withspin = symmetry_withspin.get_map_atoms()
len_sym_withspin = len(
symmetry_withspin.get_symmetry_operations()['rotations'])
broken_spin = [1, -2]
cell_brokenspin = cell.copy()
cell_brokenspin = cell.copy()
cell_brokenspin.set_magnetic_moments(broken_spin)
symmetry_brokenspin = Symmetry(cell_brokenspin, symprec=symprec)
atom_map_brokenspin = symmetry_brokenspin.get_map_atoms()
len_sym_brokenspin = len(
symmetry_brokenspin.get_symmetry_operations()['rotations'])
self.assertTrue((atom_map_nonspin == atom_map_withspin).all())
self.assertFalse((atom_map_nonspin == atom_map_brokenspin).all())
self.assertTrue(len_sym_nonspin == len_sym_withspin)
self.assertFalse(len_sym_nonspin == len_sym_brokenspin)
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_magmom(convcell_cr):
symprec = 1e-5
cell = convcell_cr
symmetry_nonspin = Symmetry(cell, symprec=symprec)
atom_map_nonspin = symmetry_nonspin.get_map_atoms()
len_sym_nonspin = len(
symmetry_nonspin.get_symmetry_operations()['rotations'])
spin = [1, -1]
cell_withspin = cell.copy()
cell_withspin.set_magnetic_moments(spin)
symmetry_withspin = Symmetry(cell_withspin, symprec=symprec)
atom_map_withspin = symmetry_withspin.get_map_atoms()
len_sym_withspin = len(
symmetry_withspin.get_symmetry_operations()['rotations'])
broken_spin = [1, -2]
cell_brokenspin = cell.copy()
cell_brokenspin = cell.copy()
cell_brokenspin.set_magnetic_moments(broken_spin)
symmetry_brokenspin = Symmetry(cell_brokenspin, symprec=symprec)
atom_map_brokenspin = symmetry_brokenspin.get_map_atoms()
len_sym_brokenspin = len(
symmetry_brokenspin.get_symmetry_operations()['rotations'])
assert (atom_map_nonspin == atom_map_withspin).all()
assert (atom_map_nonspin != atom_map_brokenspin).any()
assert len_sym_nonspin == len_sym_withspin
assert len_sym_nonspin != len_sym_brokenspin
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 test_magmom(self):
symprec = 1e-5
cell = read_cell_yaml(os.path.join(data_dir, "Cr.yaml"))
symmetry_nonspin = Symmetry(cell, symprec=symprec)
atom_map_nonspin = symmetry_nonspin.get_map_atoms()
len_sym_nonspin = len(
symmetry_nonspin.get_symmetry_operations()['rotations'])
spin = [1, -1]
cell_withspin = cell.copy()
cell_withspin.set_magnetic_moments(spin)
symmetry_withspin = Symmetry(cell_withspin, symprec=symprec)
atom_map_withspin = symmetry_withspin.get_map_atoms()
len_sym_withspin = len(
symmetry_withspin.get_symmetry_operations()['rotations'])
broken_spin = [1, -2]
cell_brokenspin = cell.copy()
cell_brokenspin = cell.copy()
cell_brokenspin.set_magnetic_moments(broken_spin)
symmetry_brokenspin = Symmetry(cell_brokenspin, symprec=symprec)
atom_map_brokenspin = symmetry_brokenspin.get_map_atoms()
len_sym_brokenspin = len(
symmetry_brokenspin.get_symmetry_operations()['rotations'])
self.assertTrue((atom_map_nonspin == atom_map_withspin).all())
self.assertFalse((atom_map_nonspin == atom_map_brokenspin).all())
self.assertTrue(len_sym_nonspin == len_sym_withspin)
self.assertFalse(len_sym_nonspin == len_sym_brokenspin)
def _distribute_forces(supercell, disp, forces, filename, symprec):
natom = supercell.get_number_of_atoms()
lattice = supercell.get_cell()
symbols = supercell.get_chemical_symbols()
positions = supercell.get_positions()
positions[disp[0]] += disp[1]
cell = Atoms(cell=lattice, positions=positions, symbols=symbols, pbc=True)
symmetry = Symmetry(cell, symprec)
independent_atoms = symmetry.get_independent_atoms()
# Rotation matrices in Cartesian
rotations = []
for r in symmetry.get_symmetry_operations()["rotations"]:
rotations.append(similarity_transformation(lattice.T, r))
map_operations = symmetry.get_map_operations()
map_atoms = symmetry.get_map_atoms()
atoms_in_dot_scf = _get_independent_atoms_in_dot_scf(filename)
if len(forces) != len(atoms_in_dot_scf):
print("%s does not contain necessary information." % filename)
print('Plese check if there are "FGL" lines with')
print('"total forces" are required.')
return False
if len(atoms_in_dot_scf) == natom:
print("It is assumed that there is no symmetrically-equivalent " "atoms in ")
print("'%s' at wien2k calculation." % filename)
force_set = forces
elif len(forces) != len(independent_atoms):
print("Non-equivalent atoms of %s could not be recognized by phonopy." % filename)
return False
else:
# 1. Transform wien2k forces to those on independent atoms
indep_atoms_to_wien2k = []
forces_remap = []
for i, pos_wien2k in enumerate(atoms_in_dot_scf):
for j, pos in enumerate(cell.get_scaled_positions()):
diff = pos_wien2k - pos
diff -= np.rint(diff)
if (abs(diff) < symprec).all():
forces_remap.append(np.dot(rotations[map_operations[j]], forces[i]))
indep_atoms_to_wien2k.append(map_atoms[j])
break
if len(forces_remap) != len(forces):
print("Atomic position mapping between Wien2k and phonopy failed.")
print("If you think this is caused by a bug of phonopy")
print("please report it in the phonopy mainling list.")
return False
# 2. Distribute forces from independent to dependent atoms.
force_set = []
for i in range(natom):
j = indep_atoms_to_wien2k.index(map_atoms[i])
force_set.append(np.dot(rotations[map_operations[i]].T, forces_remap[j]))
return force_set
def test_get_map_operations(self):
symprec = 1e-5
cell = read_cell_yaml(os.path.join(data_dir, "..", "NaCl.yaml"))
scell = get_supercell(cell, np.diag([2, 2, 2]), symprec=symprec)
symmetry = Symmetry(scell, symprec=symprec)
# start = time.time()
symmetry._set_map_operations()
# end = time.time()
# print(end - start)
map_ops = symmetry.get_map_operations()
map_atoms = symmetry.get_map_atoms()
positions = scell.get_scaled_positions()
rotations = symmetry.get_symmetry_operations()['rotations']
translations = symmetry.get_symmetry_operations()['translations']
for i, (op_i, atom_i) in enumerate(zip(map_ops, map_atoms)):
r_pos = np.dot(rotations[op_i], positions[i]) + translations[op_i]
diff = positions[atom_i] - r_pos
diff -= np.rint(diff)
self.assertTrue((diff < symprec).all())
def get_crystal_structure(cell, conv_numbers, write_symmetry=False):
lattice = cell.get_cell()
positions = cell.get_positions()
numbers = cell.get_atomic_numbers()
# Create and EXTERNAL file (fort.34)
# Dimensionality, centring, crystal type
lines = "3 1 1\n"
# Cartesian components of the lattice vectors
for lattvec in lattice:
lines += ("%12.8f" * 3 + "\n") % tuple(lattvec)
# Symmetry operators
if write_symmetry:
symmetry = Symmetry(cell, symprec=1e-5)
rotations = symmetry.get_symmetry_operations()['rotations']
translations = symmetry.get_symmetry_operations()['translations']
N_symmops = 0
symmlines = ""
for i in range(0, len(rotations)):
N_symmops += 1
for j in range(0, 3):
symmlines += (" %5.2f" * 3 + "\n") % tuple(rotations[i][j])
symmlines += (" %5.2f" * 3 + "\n") % tuple(translations[i])
lines += ("%d\n" % N_symmops)
lines += symmlines
else:
lines += "1\n"
lines += " 1.00 0.00 0.00\n"
lines += " 0.00 1.00 0.00\n"
lines += " 0.00 0.00 1.00\n"
lines += " 0.00 0.00 0.00\n"
# Number of atoms in the unit cell (asymmetric unit)
lines += ("%d\n") % len(positions)
# Conventional atomic number and cartesian coordinates of the atoms
for i, pos in zip(conv_numbers, positions):
lines += (" %d " + "%16.12f" * 3 + "\n") % (i, pos[0], pos[1], pos[2])
return lines
def get_crystal_structure(cell, conv_numbers, write_symmetry=False):
lattice = cell.get_cell()
positions = cell.get_positions()
numbers = cell.get_atomic_numbers()
# Create and EXTERNAL file (fort.34)
# Dimensionality, centring, crystal type
lines = "3 1 1\n"
# Cartesian components of the lattice vectors
for lattvec in lattice:
lines += ("%12.8f" * 3 + "\n") % tuple(lattvec)
# Symmetry operators
if write_symmetry:
symmetry = Symmetry(cell, symprec=1e-5)
rotations = symmetry.get_symmetry_operations()['rotations']
translations = symmetry.get_symmetry_operations()['translations']
N_symmops = 0
symmlines = ""
for i in range(0, len(rotations)):
N_symmops += 1
for j in range(0, 3):
symmlines += (" %5.2f" * 3 + "\n") % tuple(rotations[i][j])
symmlines += (" %5.2f" * 3 + "\n") % tuple(translations[i])
lines += ("%d\n" % N_symmops)
lines += symmlines
else:
lines += "1\n"
lines += " 1.00 0.00 0.00\n"
lines += " 0.00 1.00 0.00\n"
lines += " 0.00 0.00 1.00\n"
lines += " 0.00 0.00 0.00\n"
# Number of atoms in the unit cell (asymmetric unit)
lines += ("%d\n") % len(positions)
# Conventional atomic number and cartesian coordinates of the atoms
for i, pos in zip(conv_numbers, positions):
lines += (" %d " + "%16.12f"*3 + "\n") % (i, pos[0], pos[1], pos[2])
return lines
def test_get_map_operations(self):
symprec = 1e-5
cell = get_unitcell_from_phonopy_yaml(
os.path.join(data_dir,"../NaCl.yaml"))
scell = get_supercell(cell, np.diag([2, 2, 2]), symprec=symprec)
symmetry = Symmetry(scell, symprec=symprec)
start = time.time()
symmetry._set_map_operations()
end = time.time()
# print(end - start)
map_ops = symmetry.get_map_operations()
map_atoms = symmetry.get_map_atoms()
positions = scell.get_scaled_positions()
rotations = symmetry.get_symmetry_operations()['rotations']
translations = symmetry.get_symmetry_operations()['translations']
for i, (op_i, atom_i) in enumerate(zip(map_ops, map_atoms)):
r_pos = np.dot(rotations[op_i], positions[i]) + translations[op_i]
diff = positions[atom_i] - r_pos
diff -= np.rint(diff)
self.assertTrue((diff < symprec).all())
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)
def get_born_parameters(f, primitive, is_symmetry):
# Read unit conversion factor, damping factor, ...
factors = [float(x) for x in f.readline().split()]
if len(factors) < 1:
print "BORN file format of line 1 is incorrect"
return False
if len(factors) < 2:
factors = factors[0]
# Read dielectric constant
line = f.readline().split()
if not len(line) == 9:
print "BORN file format of line 2 is incorrect"
return False
dielectric = np.reshape([float(x) for x in line], (3, 3))
# Read Born effective charge
symmetry = Symmetry(primitive, is_symmetry=is_symmetry)
independent_atoms = symmetry.get_independent_atoms()
born = np.zeros((primitive.get_number_of_atoms(), 3, 3), dtype=float)
for i in independent_atoms:
line = f.readline().split()
if len(line) == 0:
print "Number of lines for Born effect charge is not enough."
return False
if not len(line) == 9:
print "BORN file format of line %d is incorrect" % (i + 3)
return False
born[i] = np.reshape([float(x) for x in line], (3, 3))
# Expand Born effective charges to all atoms in the primitive cell
rotations = symmetry.get_symmetry_operations()['rotations']
map_operations = symmetry.get_map_operations()
map_atoms = symmetry.get_map_atoms()
for i in range(primitive.get_number_of_atoms()):
# R_cart = L R L^-1
rot_cartesian = similarity_transformation(
primitive.get_cell().transpose(), rotations[map_operations[i]])
# R_cart^T B R_cart^-T (inverse rotation is required to transform)
born[i] = similarity_transformation(rot_cartesian.transpose(),
born[map_atoms[i]])
non_anal = {'born': born,
'factor': factors,
'dielectric': dielectric }
return non_anal
def symmetrize_borns_and_epsilon(borns,
epsilon,
ucell,
symprec=1e-5,
is_symmetry=True):
lattice = ucell.get_cell()
positions = ucell.get_scaled_positions()
u_sym = Symmetry(ucell, is_symmetry=is_symmetry, symprec=symprec)
rotations = u_sym.get_symmetry_operations()['rotations']
translations = u_sym.get_symmetry_operations()['translations']
ptg_ops = get_pointgroup_operations(rotations)
epsilon_ = symmetrize_2nd_rank_tensor(epsilon, ptg_ops, lattice)
for i, Z in enumerate(borns):
site_sym = get_site_symmetry(i,
lattice,
positions,
rotations,
translations,
symprec)
Z = symmetrize_2nd_rank_tensor(Z, site_sym, lattice)
borns_ = np.zeros_like(borns)
for i in range(len(borns)):
count = 0
for r, t in zip(rotations, translations):
count += 1
diff = np.dot(positions, r.T) + t - positions[i]
diff -= np.rint(diff)
dist = np.sqrt(np.sum(np.dot(diff, lattice) ** 2, axis=1))
j = np.nonzero(dist < symprec)[0][0]
r_cart = similarity_transformation(lattice.T, r)
borns_[i] += similarity_transformation(r_cart, borns[j])
borns_[i] /= count
return borns_, epsilon_
def parse_BORN( primitive, filename = "BORN" ):
file = open( filename, 'r' )
# Read unit conversion factor, damping factor, ...
factors = [ float( x ) for x in file.readline().split() ]
if len( factors ) < 1:
print "BORN file format of line 1 is incorrect"
return None
if len( factors ) < 2:
factors.append( Damping_Factor )
# Read dielectric constant
line = file.readline().split()
if 9 < len( line ) or len( line ) < 9:
print "BORN file format of line 2 is incorrect"
return None
dielectric = np.reshape( [ float( x ) for x in line ], ( 3, 3 ) )
# Read Born effective charge
symmetry = Symmetry( primitive )
independent_atoms = symmetry.get_independent_atoms()
born = np.zeros( ( primitive.get_number_of_atoms(), 3, 3 ), dtype=float )
for i in independent_atoms:
line = file.readline().split()
if 9 < len( line ) or len( line ) < 9:
print "BORN file format of line %d is incorrect" % ( i + 3 )
return None
born[ i ] = np.reshape( [ float( x ) for x in line ], ( 3, 3 ) )
# Expand Born effective charges to all atoms in the primitive cell
rotations = symmetry.get_symmetry_operations()['rotations']
map_operations = symmetry.get_map_operations()
map_atoms = symmetry.get_map_atoms()
for i in range( primitive.get_number_of_atoms() ):
# R_cart = L R L^-1
rot_cartesian = similarity_transformation(
primitive.get_cell().transpose(), rotations[ map_operations[i] ] )
# R_cart^T B R_cart^-T ( inverse rotation is required to transform )
born[i] = similarity_transformation( rot_cartesian.transpose(),
born[ map_atoms[ i ] ] )
non_anal = {'born': born,
'factor': factors,
'dielectric': dielectric }
return non_anal
def get_born_parameters(f, primitive, is_symmetry):
# Read unit conversion factor, damping factor, ...
factors = [float(x) for x in f.readline().split()]
if len(factors) < 1:
print "BORN file format of line 1 is incorrect"
return False
if len(factors) < 2:
factors = factors[0]
# Read dielectric constant
line = f.readline().split()
if not len(line) == 9:
print "BORN file format of line 2 is incorrect"
return False
dielectric = np.reshape([float(x) for x in line], (3, 3))
# Read Born effective charge
symmetry = Symmetry(primitive, is_symmetry=is_symmetry)
independent_atoms = symmetry.get_independent_atoms()
born = np.zeros((primitive.get_number_of_atoms(), 3, 3), dtype=float)
for i in independent_atoms:
line = f.readline().split()
if len(line) == 0:
print "Number of lines for Born effect charge is not enough."
return False
if not len(line) == 9:
print "BORN file format of line %d is incorrect" % (i + 3)
return False
born[i] = np.reshape([float(x) for x in line], (3, 3))
# Expand Born effective charges to all atoms in the primitive cell
rotations = symmetry.get_symmetry_operations()['rotations']
map_operations = symmetry.get_map_operations()
map_atoms = symmetry.get_map_atoms()
for i in range(primitive.get_number_of_atoms()):
# R_cart = L R L^-1
rot_cartesian = similarity_transformation(
primitive.get_cell().transpose(), rotations[map_operations[i]])
# R_cart^T B R_cart^-T (inverse rotation is required to transform)
born[i] = similarity_transformation(rot_cartesian.transpose(),
born[map_atoms[i]])
non_anal = {'born': born, 'factor': factors, 'dielectric': dielectric}
return non_anal
def get_born_OUTCAR(poscar_filename="POSCAR",
outcar_filename="OUTCAR",
primitive_axis=np.eye(3),
supercell_matrix=np.eye(3, dtype='intc'),
is_symmetry=True,
symmetrize_tensors=False):
ucell = read_vasp(poscar_filename)
scell = get_supercell(ucell, supercell_matrix)
inv_smat = np.linalg.inv(supercell_matrix)
pcell = get_primitive(scell, np.dot(inv_smat, primitive_axis))
u_sym = Symmetry(ucell, is_symmetry=is_symmetry)
p_sym = Symmetry(pcell, is_symmetry=is_symmetry)
lattice = ucell.get_cell().T
outcar = open(outcar_filename)
borns = []
while True:
line = outcar.readline()
if not line:
break
if "NIONS" in line:
num_atom = int(line.split()[11])
if "MACROSCOPIC STATIC DIELECTRIC TENSOR" in line:
epsilon = []
outcar.readline()
epsilon.append([float(x) for x in outcar.readline().split()])
epsilon.append([float(x) for x in outcar.readline().split()])
epsilon.append([float(x) for x in outcar.readline().split()])
if "BORN" in line:
outcar.readline()
line = outcar.readline()
if "ion" in line:
for i in range(num_atom):
born = []
born.append([float(x)
for x in outcar.readline().split()][1:])
born.append([float(x)
for x in outcar.readline().split()][1:])
born.append([float(x)
for x in outcar.readline().split()][1:])
outcar.readline()
borns.append(born)
borns = np.array(borns, dtype='double')
epsilon = np.array(epsilon, dtype='double')
if symmetrize_tensors:
borns_orig = borns.copy()
point_sym = [similarity_transformation(lattice, r)
for r in u_sym.get_pointgroup_operations()]
epsilon = symmetrize_tensor(epsilon, point_sym)
for i in range(num_atom):
z = borns[i]
site_sym = [similarity_transformation(lattice, r)
for r in u_sym.get_site_symmetry(i)]
borns[i] = symmetrize_tensor(z, site_sym)
rotations = u_sym.get_symmetry_operations()['rotations']
map_atoms = u_sym.get_map_atoms()
borns_copy = np.zeros_like(borns)
for i, m_i in enumerate(map_atoms):
count = 0
for j, r_j in enumerate(u_sym.get_map_operations()):
if map_atoms[j] == m_i:
count += 1
r_cart = similarity_transformation(lattice, rotations[r_j])
borns_copy[i] += similarity_transformation(r_cart, borns[j])
borns_copy[i] /= count
borns = borns_copy
sum_born = borns.sum(axis=0) / len(borns)
borns -= sum_born
if (np.abs(borns_orig - borns) > 0.1).any():
sys.stderr.write(
"Born effective charge symmetrization might go wrong.\n")
p2s = np.array(pcell.get_primitive_to_supercell_map(), dtype='intc')
s_indep_atoms = p2s[p_sym.get_independent_atoms()]
u2u = scell.get_unitcell_to_unitcell_map()
u_indep_atoms = [u2u[x] for x in s_indep_atoms]
reduced_borns = borns[u_indep_atoms].copy()
return reduced_borns, epsilon
if '*' in numxmag:
num, mag = numxmag.split('*')
magmom += [float(mag)] * int(num)
else:
magmom.append(float(numxmag))
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("POSCAR")
symmetry = Symmetry(cell, symprec=1e-3)
map_nonspin = symmetry.get_map_atoms()
print("Number of operations w/o spin %d" %
len(symmetry.get_symmetry_operations()['rotations']))
magmoms = parse_incar("INCAR")
cell.set_magnetic_moments(magmoms)
symmetry = Symmetry(cell, symprec=1e-3)
print("Number of operations w spin %d" %
len(symmetry.get_symmetry_operations()['rotations']))
map_withspin = symmetry.get_map_atoms()
if ((map_nonspin - map_withspin) == 0).all():
print(True)
else:
print(False)
print(map_nonspin)
print(map_withspin)
def get_born_OUTCAR(poscar_filename="POSCAR",
outcar_filename=None,
primitive_matrix=None,
supercell_matrix=None,
is_symmetry=True,
symmetrize_tensors=False,
read_vasprunxml=False,
symprec=1e-5):
if outcar_filename is None:
if read_vasprunxml:
filename = "vasprun.xml"
else:
filename = "OUTCAR"
else:
filename = outcar_filename
if primitive_matrix is None:
pmat = np.eye(3)
else:
pmat = primitive_matrix
if supercell_matrix is None:
smat = np.eye(3, dtype='intc')
else:
smat = supercell_matrix
ucell = read_vasp(poscar_filename)
if read_vasprunxml:
import io
borns = []
epsilon = []
with io.open(outcar_filename, "rb") as f:
vasprun = VasprunxmlExpat(f)
if vasprun.parse():
epsilon = vasprun.get_epsilon()
borns = vasprun.get_born()
else:
borns, epsilon = _read_born_and_epsilon(filename)
num_atom = len(borns)
assert num_atom == ucell.get_number_of_atoms(), \
"num_atom %d != len(borns) %d" % (ucell.get_number_of_atoms(),
len(borns))
if symmetrize_tensors:
lattice = ucell.get_cell()
positions = ucell.get_scaled_positions()
u_sym = Symmetry(ucell, is_symmetry=is_symmetry, symprec=symprec)
rotations = u_sym.get_symmetry_operations()['rotations']
translations = u_sym.get_symmetry_operations()['translations']
ptg_ops = get_pointgroup_operations(rotations)
epsilon = symmetrize_2nd_rank_tensor(epsilon,
ptg_ops,
lattice)
borns = symmetrize_borns(borns,
rotations,
translations,
lattice,
positions,
symprec)
inv_smat = np.linalg.inv(smat)
scell = get_supercell(ucell, smat, symprec=symprec)
pcell = get_primitive(scell, np.dot(inv_smat, pmat), symprec=symprec)
p2s = np.array(pcell.get_primitive_to_supercell_map(), dtype='intc')
p_sym = Symmetry(pcell, is_symmetry=is_symmetry, symprec=symprec)
s_indep_atoms = p2s[p_sym.get_independent_atoms()]
u2u = scell.get_unitcell_to_unitcell_map()
u_indep_atoms = [u2u[x] for x in s_indep_atoms]
reduced_borns = borns[u_indep_atoms].copy()
return reduced_borns, epsilon, s_indep_atoms
magmom = []
for numxmag in text.split():
if '*' in numxmag:
num, mag = numxmag.split('*')
magmom += [float(mag)] * int(num)
else:
magmom.append(float(numxmag))
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("POSCAR")
symmetry = Symmetry(cell, symprec=1e-3)
map_nonspin = symmetry.get_map_atoms()
print "Number of operations w/o spin", len(symmetry.get_symmetry_operations()['rotations'])
magmoms = parse_incar("INCAR")
cell.set_magnetic_moments(magmoms)
symmetry = Symmetry(cell, symprec=1e-3)
print "Number of operations w spin", len(symmetry.get_symmetry_operations()['rotations'])
map_withspin = symmetry.get_map_atoms()
if ((map_nonspin - map_withspin) == 0).all():
print True
else:
print False
print map_nonspin
print map_withspin
if '*' in numxmag:
num, mag = numxmag.split('*')
magmom += [float(mag)] * int(num)
else:
magmom.append(float(numxmag))
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("POSCAR")
symmetry = Symmetry(cell, symprec=1e-3)
map_nonspin = symmetry.get_map_atoms()
print("Number of operations w/o spin %d" %
len(symmetry.get_symmetry_operations()['rotations']))
magmoms = parse_incar("INCAR")
cell.set_magnetic_moments(magmoms)
symmetry = Symmetry(cell, symprec=1e-3)
print("Number of operations w spin %d" %
len(symmetry.get_symmetry_operations()['rotations']))
map_withspin = symmetry.get_map_atoms()
if ((map_nonspin - map_withspin) == 0).all():
print(True)
else:
print(False)
print(map_nonspin)
print(map_withspin)
def distribute_forces(supercell, disp, forces, filename, symprec):
natom = supercell.get_number_of_atoms()
lattice = supercell.get_cell()
symbols = supercell.get_chemical_symbols()
positions = supercell.get_positions()
positions[disp[0]] += disp[1]
cell = Atoms(cell=lattice, positions=positions, symbols=symbols, pbc=True)
symmetry = Symmetry(cell, symprec)
independent_atoms = symmetry.get_independent_atoms()
# Rotation matrices in Cartesian
rotations = []
for r in symmetry.get_symmetry_operations()['rotations']:
rotations.append(similarity_transformation(lattice.T, r))
map_operations = symmetry.get_map_operations()
map_atoms = symmetry.get_map_atoms()
atoms_in_dot_scf = get_independent_atoms_in_dot_scf(filename)
if not len(forces) == len(atoms_in_dot_scf):
print "%s does not contain necessary information." % filename
print "Plese check if there are \"FGL\" lines with"
print "\"total forces\" are required."
return False
if len(atoms_in_dot_scf) == natom:
print "It is assumed that there is no symmetrically-equivalent atoms in "
print "\'%s\' at wien2k calculation." % filename
print ""
force_set = forces
elif not len(forces) == len(independent_atoms):
print "Non-equivalent atoms of %s could not be recognized by phonopy." % filename
return False
else:
# 1. Transform wien2k forces to those on independent atoms
indep_atoms_to_wien2k = []
forces_remap = []
for i, pos_wien2k in enumerate(atoms_in_dot_scf):
for j, pos in enumerate(cell.get_scaled_positions()):
diff = pos_wien2k - pos
diff -= np.rint(diff)
if (abs(diff) < 0.00001).all():
forces_remap.append(
np.dot(forces[i], rotations[map_operations[j]].T))
indep_atoms_to_wien2k.append(map_atoms[j])
break
if not len(forces_remap) == len(forces):
print "Atomic position mapping between Wien2k and phonopy failed."
print "If you think this is caused by a bug of phonopy"
print "please report it in the phonopy mainling list."
return False
# 2. Distribute forces from independent to dependent atoms.
force_set = []
for i in range(natom):
force_set.append(
np.dot(forces_remap[indep_atoms_to_wien2k.index(map_atoms[i])],
rotations[map_operations[i]]))
return force_set
magmom = []
for numxmag in text.split():
if '*' in numxmag:
num, mag = numxmag.split('*')
magmom += [float(mag)] * int(num)
else:
magmom.append(float(numxmag))
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("POSCAR")
symmetry = Symmetry(cell, symprec=1e-3)
map_nonspin = symmetry.get_map_atoms()
print "Number of operations w/o spin", len(symmetry.get_symmetry_operations()['rotations'])
magmoms = parse_incar("INCAR")
cell.set_magnetic_moments(magmoms)
symmetry = Symmetry(cell, symprec=1e-3)
print "Number of operations w spin", len(symmetry.get_symmetry_operations()['rotations'])
map_withspin = symmetry.get_map_atoms()
if ((map_nonspin - map_withspin) == 0).all():
print True
else:
print False
print map_nonspin
print map_withspin
