def _create_supercell(self, unitcell, symprec):
mat = self._supercell_matrix
frame = self._get_surrounding_frame(mat)
sur_cell, u2sur_map = self._get_simple_supercell(frame, unitcell)
# Trim the simple supercell by the supercell matrix
trim_frame = np.array([mat[0] / float(frame[0]),
mat[1] / float(frame[1]),
mat[2] / float(frame[2])])
supercell, sur2s_map = trim_cell(trim_frame,
sur_cell,
symprec)
multi = supercell.get_number_of_atoms() / unitcell.get_number_of_atoms()
if multi != determinant(self._supercell_matrix):
print "Supercell creation failed."
Atoms.__init__(self)
else:
Atoms.__init__(self,
numbers=supercell.get_atomic_numbers(),
masses=supercell.get_masses(),
magmoms=supercell.get_magnetic_moments(),
scaled_positions=supercell.get_scaled_positions(),
cell=supercell.get_cell(),
pbc=True)
self._u2s_map = np.arange(unitcell.get_number_of_atoms()) * multi
self._u2u_map = dict([(j, i) for i, j in enumerate(self._u2s_map)])
self._s2u_map = np.array(u2sur_map)[sur2s_map] * multi
def _create_supercell(self, unitcell, symprec):
mat = self._supercell_matrix
frame = self._get_surrounding_frame(mat)
sur_cell, u2sur_map = self._get_simple_supercell(frame, unitcell)
# Trim the simple supercell by the supercell matrix
trim_frame = np.array([
mat[0] / float(frame[0]), mat[1] / float(frame[1]),
mat[2] / float(frame[2])
])
supercell, sur2s_map = trim_cell(trim_frame, sur_cell, symprec)
multi = supercell.get_number_of_atoms() / unitcell.get_number_of_atoms(
)
if multi != determinant(self._supercell_matrix):
print "Supercell creation failed."
Atoms.__init__(self)
else:
Atoms.__init__(self,
numbers=supercell.get_atomic_numbers(),
masses=supercell.get_masses(),
magmoms=supercell.get_magnetic_moments(),
scaled_positions=supercell.get_scaled_positions(),
cell=supercell.get_cell(),
pbc=True)
self._u2s_map = np.arange(unitcell.get_number_of_atoms()) * multi
self._u2u_map = dict([(j, i) for i, j in enumerate(self._u2s_map)])
self._s2u_map = np.array(u2sur_map)[sur2s_map] * multi
class TestCell(unittest.TestCase):
def setUp(self):
symbols = ['Si'] * 2 + ['O'] * 4
lattice = [[4.65, 0, 0],
[0, 4.75, 0],
[0, 0, 3.25]]
points = [[0.0, 0.0, 0.0],
[0.5, 0.5, 0.5],
[0.3, 0.3, 0.0],
[0.7, 0.7, 0.0],
[0.2, 0.8, 0.5],
[0.8, 0.2, 0.5]]
self._cell = Atoms(cell=lattice,
scaled_positions=points,
symbols=symbols)
def tearDown(self):
pass
def test_atoms(self):
print(self._cell.get_cell())
for s, p in zip(self._cell.get_chemical_symbols(),
self._cell.get_scaled_positions()):
print("%s %s" % (s, p))
def test_phonopy_atoms(self):
print(PhonopyAtoms(atoms=self._cell))
def read_pwscf(filename):
pwscf_in = PwscfIn(open(filename).readlines())
tags = pwscf_in.get_tags()
lattice = tags['cell_parameters']
positions = [pos[1] for pos in tags['atomic_positions']]
species = [pos[0] for pos in tags['atomic_positions']]
mass_map = {}
pp_map = {}
for vals in tags['atomic_species']:
mass_map[vals[0]] = vals[1]
pp_map[vals[0]] = vals[2]
masses = [mass_map[x] for x in species]
pp_all_filenames = [pp_map[x] for x in species]
unique_species = []
for x in species:
if x not in unique_species:
unique_species.append(x)
numbers = []
is_unusual = False
for x in species:
if x in symbol_map:
numbers.append(symbol_map[x])
else:
numbers.append(-unique_species.index(x))
is_unusual = True
if is_unusual:
positive_numbers = []
for n in numbers:
if n > 0:
if n not in positive_numbers:
positive_numbers.append(n)
available_numbers = range(1, 119)
for pn in positive_numbers:
available_numbers.remove(pn)
for i, n in enumerate(numbers):
if n < 1:
numbers[i] = available_numbers[-n]
cell = Atoms(numbers=numbers,
masses=masses,
cell=lattice,
scaled_positions=positions)
else:
cell = Atoms(numbers=numbers,
cell=lattice,
scaled_positions=positions)
unique_symbols = []
pp_filenames = {}
for i, symbol in enumerate(cell.get_chemical_symbols()):
if symbol not in unique_symbols:
unique_symbols.append(symbol)
pp_filenames[symbol] = pp_all_filenames[i]
return cell, pp_filenames
def read_pwscf(filename):
pwscf_in = PwscfIn(open(filename).readlines())
tags = pwscf_in.get_tags()
lattice = tags['cell_parameters']
positions = [pos[1] for pos in tags['atomic_positions']]
species = [pos[0] for pos in tags['atomic_positions']]
mass_map = {}
pp_map = {}
for vals in tags['atomic_species']:
mass_map[vals[0]] = vals[1]
pp_map[vals[0]] = vals[2]
masses = [mass_map[x] for x in species]
pp_all_filenames = [pp_map[x] for x in species]
unique_species = []
for x in species:
if x not in unique_species:
unique_species.append(x)
numbers = []
is_unusual = False
for x in species:
if x in symbol_map:
numbers.append(symbol_map[x])
else:
numbers.append(-unique_species.index(x))
is_unusual = True
if is_unusual:
positive_numbers = []
for n in numbers:
if n > 0:
if n not in positive_numbers:
positive_numbers.append(n)
available_numbers = range(1, 119)
for pn in positive_numbers:
available_numbers.remove(pn)
for i, n in enumerate(numbers):
if n < 1:
numbers[i] = available_numbers[-n]
cell = Atoms(numbers=numbers,
masses=masses,
cell=lattice,
scaled_positions=positions)
else:
cell = Atoms(numbers=numbers,
cell=lattice,
scaled_positions=positions)
unique_symbols = []
pp_filenames = {}
for i, symbol in enumerate(cell.get_chemical_symbols()):
if symbol not in unique_symbols:
unique_symbols.append(symbol)
pp_filenames[symbol] = pp_all_filenames[i]
return cell, pp_filenames
def setUp(self):
self._cells = []
symbols = ['Si'] * 2 + ['O'] * 4
lattice = [[4.65, 0, 0],
[0, 4.75, 0],
[0, 0, 3.25]]
points = [[0.0, 0.0, 0.0],
[0.5, 0.5, 0.5],
[0.3, 0.3, 0.0],
[0.7, 0.7, 0.0],
[0.2, 0.8, 0.5],
[0.8, 0.2, 0.5]]
self._cells.append(Atoms(cell=lattice,
scaled_positions=points,
symbols=symbols))
symbols = ['Si'] * 2
lattice = [[0, 2.73, 2.73],
[2.73, 0, 2.73],
[2.73, 2.73, 0]]
points = [[0.75, 0.75, 0.75],
[0.5, 0.5, 0.5]]
self._cells.append(Atoms(cell=lattice,
scaled_positions=points,
symbols=symbols))
self._smats = []
self._smats.append(np.diag([1, 2, 3]))
self._smats.append([[-1, 1, 1],
[1, -1, 1],
[1, 1, -1]])
self._fnames = ("SiO2-123.yaml", "Si-conv.yaml")
def get_data_from_dir(directory, i_volume):
data_sets = file_IO.parse_FORCE_SETS(
filename=directory + '/phonon-{0:02d}/FORCE_SETS'.format(i_volume))
yaml_file = open(
directory + '/phonon-{0:02d}/phonon.yaml'.format(i_volume), 'r')
data = yaml.load_all(yaml_file).next()
unit_cell = PhonopyAtoms(
symbols=[item['symbol'] for item in data['points']],
scaled_positions=[item['coordinates'] for item in data['points']],
cell=data['lattice'])
phonon = Phonopy(unit_cell, data['supercell_matrix'])
phonon.set_displacement_dataset(data_sets)
phonon.produce_force_constants()
force_constants = phonon.get_force_constants()
supercell = phonon.get_supercell()
volume = unit_cell.get_volume()
energy = data['electric_total_energy']
return supercell, volume, energy, force_constants, data['supercell_matrix']
class TestCell(unittest.TestCase):
def setUp(self):
symbols = ['Si'] * 2 + ['O'] * 4
lattice = [[4.65, 0, 0],
[0, 4.75, 0],
[0, 0, 3.25]]
points = [[0.0, 0.0, 0.0],
[0.5, 0.5, 0.5],
[0.3, 0.3, 0.0],
[0.7, 0.7, 0.0],
[0.2, 0.8, 0.5],
[0.8, 0.2, 0.5]]
self._cell = Atoms(cell=lattice,
scaled_positions=points,
symbols=symbols)
def tearDown(self):
pass
def test_atoms(self):
print(self._cell.get_cell())
for s, p in zip(self._cell.get_chemical_symbols(),
self._cell.get_scaled_positions()):
print s, p
def test_phonopy_atoms(self):
print(PhonopyAtoms(atoms=self._cell))
def __init__( self, supercell, supercell_to_unitcell_map ):
Atoms.__init__( self,
numbers = supercell.get_atomic_numbers(),
masses = supercell.get_masses(),
scaled_positions = supercell.get_scaled_positions(),
cell = supercell.get_cell(),
pbc = True )
self.s2u_map = supercell_to_unitcell_map
def __init__(self, supercell, supercell_to_unitcell_map):
Atoms.__init__(self,
numbers = supercell.get_atomic_numbers(),
masses = supercell.get_masses(),
magmoms = supercell.get_magnetic_moments(),
scaled_positions = supercell.get_scaled_positions(),
cell = supercell.get_cell(),
pbc = True)
self.s2u_map = supercell_to_unitcell_map
def setUp(self):
symbols = ['Si'] * 2 + ['O'] * 4
lattice = [[4.65, 0, 0], [0, 4.75, 0], [0, 0, 3.25]]
points = [[0.0, 0.0, 0.0], [0.5, 0.5, 0.5], [0.3, 0.3, 0.0],
[0.7, 0.7, 0.0], [0.2, 0.8, 0.5], [0.8, 0.2, 0.5]]
self._cell = Atoms(cell=lattice,
scaled_positions=points,
symbols=symbols)
def get_phonopy(structure):
from phonopy import Phonopy
from phonopy.structure.atoms import Atoms as PhonopyAtoms
phon_atoms = PhonopyAtoms(symbols=[str(s.specie) for s in structure],
scaled_positions=structure.frac_coords)
phon_atoms.set_cell(structure.lattice.matrix)
# supercell size
scell = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
return Phonopy(phon_atoms, scell)
def get_phonopy(structure):
from phonopy import Phonopy
from phonopy.structure.atoms import Atoms as PhonopyAtoms
phon_atoms = PhonopyAtoms(symbols=[str(s.specie) for s in structure],
scaled_positions=structure.frac_coords)
phon_atoms.set_cell(structure.lattice.matrix)
# supercell size
scell = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
return Phonopy(phon_atoms, scell)
def _primitive_cell(self, supercell):
trimed_cell, p2s_map = trim_cell(self.frame, supercell, self.symprec)
Atoms.__init__(self,
numbers=trimed_cell.get_atomic_numbers(),
masses=trimed_cell.get_masses(),
magmoms=trimed_cell.get_magnetic_moments(),
scaled_positions=trimed_cell.get_scaled_positions(),
cell=trimed_cell.get_cell(),
pbc=True)
self.p2s_map = p2s_map
def _primitive_cell(self, supercell):
trimed_cell, p2s_map = trim_cell(self._primitive_matrix, supercell,
self._symprec)
Atoms.__init__(self,
numbers=trimed_cell.get_atomic_numbers(),
masses=trimed_cell.get_masses(),
magmoms=trimed_cell.get_magnetic_moments(),
scaled_positions=trimed_cell.get_scaled_positions(),
cell=trimed_cell.get_cell(),
pbc=True)
self._p2s_map = np.array(p2s_map, dtype='intc')
def __primitive_cell(self, supercell):
trimed_cell, p2s_map = trim_cell( self.frame,
supercell,
self.symprec )
Atoms.__init__( self,
numbers = trimed_cell.get_atomic_numbers(),
masses = trimed_cell.get_masses(),
scaled_positions = trimed_cell.get_scaled_positions(),
cell = trimed_cell.get_cell(),
pbc = True )
self.p2s_map = p2s_map
def _primitive_cell(self, supercell):
trimed_cell, p2s_map = trim_cell(self._primitive_matrix,
supercell,
self._symprec)
Atoms.__init__(self,
numbers=trimed_cell.get_atomic_numbers(),
masses=trimed_cell.get_masses(),
magmoms=trimed_cell.get_magnetic_moments(),
scaled_positions=trimed_cell.get_scaled_positions(),
cell=trimed_cell.get_cell(),
pbc=True)
self._p2s_map = np.array(p2s_map, dtype='intc')
def get_phonopy(structure):
try:
from phonopy import Phonopy
from phonopy.structure.atoms import Atoms as PhonopyAtoms
except ImportError:
print("Install phonopy. Exiting.")
sys.exit()
phon_atoms = PhonopyAtoms(symbols=[str(s.specie) for s in structure],
scaled_positions=structure.frac_coords)
phon_atoms.set_cell(structure.lattice.matrix)
# supercell size
scell = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
return Phonopy(phon_atoms, scell)
def get_phonopy(structure):
try:
from phonopy import Phonopy
from phonopy.structure.atoms import Atoms as PhonopyAtoms
except ImportError:
print("Install phonopy. Exiting.")
sys.exit()
phon_atoms = PhonopyAtoms(symbols=[str(s.specie) for s in structure],
scaled_positions=structure.frac_coords)
phon_atoms.set_cell(structure.lattice.matrix)
# supercell size
scell = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
return Phonopy(phon_atoms, scell)
def read_aims(filename):
"""Read FHI-aims geometry files in phonopy context."""
lines = open(filename, "r").readlines()
cell = []
is_frac = []
positions = []
symbols = []
magmoms = []
for line in lines:
fields = line.split()
if not len(fields):
continue
if fields[0] == "lattice_vector":
vec = lmap(float, fields[1:4])
cell.append(vec)
elif fields[0][0:4] == "atom":
if fields[0] == "atom":
frac = False
elif fields[0] == "atom_frac":
frac = True
pos = lmap(float, fields[1:4])
sym = fields[4]
is_frac.append(frac)
positions.append(pos)
symbols.append(sym)
magmoms.append(None)
# implicitly assuming that initial_moments line adhere to FHI-aims geometry.in
# specification, i.e. two subsequent initial_moments lines do not occur
# if they do, the value specified in the last line is taken here - without
# any warning
elif fields[0] == "initial_moment":
magmoms[-1] = float(fields[1])
for (n, frac) in enumerate(is_frac):
if frac:
pos = [
sum([positions[n][ll] * cell[ll][i] for ll in range(3)])
for i in range(3)
]
positions[n] = pos
if None in magmoms:
atoms = Atoms(cell=cell, symbols=symbols, positions=positions)
else:
atoms = Atoms(cell=cell,
symbols=symbols,
positions=positions,
magmoms=magmoms)
return atoms
def _build_supercells_with_displacements(self):
supercells = []
magmoms = self._supercell.get_magnetic_moments()
masses = self._supercell.get_masses()
numbers = self._supercell.get_atomic_numbers()
lattice = self._supercell.get_cell()
for disp1 in self._displacement_dataset['first_atoms']:
disp_cart1 = disp1['displacement']
positions = self._supercell.get_positions()
positions[disp1['number']] += disp_cart1
supercells.append(
Atoms(numbers=numbers,
masses=masses,
magmoms=magmoms,
positions=positions,
cell=lattice,
pbc=True))
for disp1 in self._displacement_dataset['first_atoms']:
for disp2 in disp1['second_atoms']:
positions = self._supercell.get_positions()
positions[disp1['number']] += disp_cart1
positions[disp2['number']] += disp2['displacement']
supercells.append(
Atoms(numbers=numbers,
masses=masses,
magmoms=magmoms,
positions=positions,
cell=lattice,
pbc=True))
for disp1 in self._displacement_dataset['first_atoms']:
for disp2 in disp1['second_atoms']:
for disp3 in disp2['third_atoms']:
positions = self._supercell.get_positions()
positions[disp1['number']] += disp_cart1
positions[disp2['number']] += disp2['displacement']
positions[disp3['number']] += disp3['displacement']
supercells.append(
Atoms(numbers=numbers,
masses=masses,
magmoms=magmoms,
positions=positions,
cell=lattice,
pbc=True))
self._supercells_with_displacements = supercells
def ReadBORN(structure, filePath="BORN"):
"""
Read a Phonopy BORN file, and expand the charges for the supplied structure, and return a list of Born effective-charge tensors for each atom in the structure.
Arguments:
structure -- a tuple of (lattice_vectors, atomic_symbols, atom_positions) specifying the structure to be used to expand the Born charges to the full set of atoms.
Keyword arguments:
filePath -- path to the Phonopy BORN-format file to read (default: BORN).
Return value:
A list of 3x3 Born effective-charge tensors for each atom in the supplied structure.
Notes:
The atom positions supplied with structure are assumed to be in fractional coordinates.
"""
# Convert the supplied structure to a Phonopy Atoms object.
latticeVectors, atomicSymbols, atomPositions = structure
cell = Atoms(symbols=atomicSymbols,
cell=latticeVectors,
scaled_positions=atomPositions)
# Read the BORN file.
bornData = parse_BORN(cell, filename=filePath)
# Return the Born effective-charge tensors from the dictionary returned by parse_BORN.
return [becTensor for becTensor in bornData['born']]
def get_simple_supercell(multi, unitcell):
# Scaled positions within the frame, i.e., create a supercell that
# is made simply to multiply the input cell.
positions = unitcell.get_scaled_positions()
numbers = unitcell.get_atomic_numbers()
masses = unitcell.get_masses()
magmoms = unitcell.get_magnetic_moments()
lattice = unitcell.get_cell()
positions_multi = []
numbers_multi = []
masses_multi = []
if magmoms == None:
magmoms_multi = None
else:
magmoms_multi = []
for l, pos in enumerate(positions):
for i in range(multi[2]):
for j in range(multi[1]):
for k in range(multi[0]):
positions_multi.append([(pos[0] + k) / multi[0],
(pos[1] + j) / multi[1],
(pos[2] + i) / multi[2]])
numbers_multi.append(numbers[l])
masses_multi.append(masses[l])
if not magmoms == None:
magmoms_multi.append(magmoms[l])
return Atoms(numbers = numbers_multi,
masses = masses_multi,
magmoms = magmoms_multi,
scaled_positions = positions_multi,
cell = np.dot(np.diag(multi), lattice),
pbc=True)
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_siesta(filename):
siesta_in = SiestaIn(open(filename).read())
numbers = siesta_in._tags["atomicnumbers"]
lattice = siesta_in._tags["latticevectors"]
positions = siesta_in._tags["atomiccoordinates"]
atypes = siesta_in._tags["chemicalspecieslabel"]
cell = Atoms(numbers=numbers, cell=lattice, scaled_positions=positions)
coordformat = siesta_in._tags["atomiccoordinatesformat"]
if coordformat == "fractional" or coordformat == "scaledbylatticevectors":
cell.set_scaled_positions(positions)
elif coordformat == "scaledcartesian":
if siesta_in._tags['latticeconstant'] == 'ang':
cell.set_positions(np.array(positions) / Bohr)
else:
cell.set_positions(np.array(positions))
elif coordformat == "notscaledcartesianang" or coordformat == "ang":
cell.set_positions(np.array(positions) / Bohr)
elif coordformat == "notscaledcartesianbohr" or coordformat == "bohr":
cell.set_positions(np.array(positions))
else:
print("The format %s for the AtomicCoordinatesFormat is not "
"implemented." % coordformat)
sys.exit(1)
return cell, atypes
def _get_supercell(self):
"""Attention
This method will be removed after
new get_delta method is well checked.
"""
dim = self._dimension
scaled_positions = []
masses = []
magmoms_prim = self._primitive.get_magnetic_moments()
if magmoms_prim is None:
magmoms = None
else:
magmoms = []
symbols = []
for a, b, c in list(np.ndindex(tuple(dim))):
for i in range(self._primitive.get_number_of_atoms()):
p = self._primitive.get_scaled_positions()[i]
scaled_positions.append(p + np.array([a, b, c]))
masses.append(self._primitive.get_masses()[i])
symbols.append(self._primitive.get_chemical_symbols()[i])
if magmoms_prim is not None:
magmoms.append(magmoms_prim[i])
lattice = np.dot(np.diag(dim), self._primitive.get_cell())
positions = np.dot(scaled_positions, self._primitive.get_cell())
from phonopy.structure.atoms import Atoms
return Atoms(cell=lattice,
positions=positions,
masses=masses,
magmoms=magmoms,
symbols=symbols,
pbc=True)
def get_born_vasprunxml(filename="vasprun.xml",
primitive_matrix=None,
supercell_matrix=None,
is_symmetry=True,
symmetrize_tensors=False,
symprec=1e-5):
import io
borns = []
epsilon = []
with io.open(filename, "rb") as f:
vasprun = VasprunxmlExpat(f)
if vasprun.parse():
epsilon = vasprun.get_epsilon()
borns = vasprun.get_born()
lattice = vasprun.get_lattice()[-1]
points = vasprun.get_points()[-1]
symbols = vasprun.get_symbols()
ucell = Atoms(symbols=symbols,
scaled_positions=points,
cell=lattice)
else:
return None
return elaborate_borns_and_epsilon(ucell,
borns,
epsilon,
primitive_matrix=primitive_matrix,
supercell_matrix=supercell_matrix,
is_symmetry=is_symmetry,
symmetrize_tensors=symmetrize_tensors,
symprec=symprec)
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 read_fleur(filename):
fleur_in = FleurIn(open(filename).readlines())
tags = fleur_in.get_variables()
avec = [tags['avec'][i] for i in range(3)]
speci = tags['atoms']['speci']
symbols = [
list(symbol_map.keys())[list(symbol_map.values()).index(
math.floor(float(x)))] for x in speci
]
numbers = [math.floor(float(x)) for x in speci]
for i, n in enumerate(numbers):
if n == 0:
for j in range(1, 119):
if not (j in numbers):
numbers[i] = j
break
pos_all = []
num_all = []
for num, pos in zip(numbers, tags['atoms']['positions']):
pos_all += pos
num_all = [symbol_map[s] for s in symbols]
return Atoms(numbers=num_all, cell=avec,
scaled_positions=pos_all), speci, fleur_in._restlines
def _get_cell(self, lattice, points, symbols, masses=None):
if lattice:
_lattice = lattice
else:
_lattice = None
if points:
_points = points
else:
_points = None
if symbols:
_symbols = symbols
else:
_symbols = None
if masses:
_masses = masses
else:
_masses = None
if _lattice and _points and _symbols:
return Atoms(symbols=_symbols,
cell=_lattice,
masses=_masses,
scaled_positions=_points)
else:
return None
def get_commensurate_points(supercell_matrix): # wrt primitive cell
rec_primitive = Atoms(numbers=[1],
scaled_positions=[[0, 0, 0]],
cell=np.diag([1, 1, 1]),
pbc=True)
rec_supercell = get_supercell(rec_primitive, supercell_matrix.T)
return rec_supercell.get_scaled_positions()
def check_symmetry(input_cell,
primitive_axis=np.eye(3, dtype=float),
symprec=1e-5,
phonopy_version=None):
cell = Primitive(input_cell, primitive_axis, symprec)
symmetry = Symmetry(cell, symprec)
print get_symmetry_yaml(cell, symmetry, phonopy_version),
if input_cell.get_magnetic_moments() == None:
primitive = find_primitive(cell, symprec)
if not primitive == None:
print "# Primitive cell was found. It is written into PPOSCAR."
write_vasp('PPOSCAR', primitive)
# Overwrite symmetry and cell
symmetry = Symmetry(primitive, symprec)
cell = primitive
bravais_lattice, bravais_pos, bravais_numbers = \
spg.refine_cell(cell, symprec)
bravais = Atoms(numbers=bravais_numbers,
scaled_positions=bravais_pos,
cell=bravais_lattice,
pbc=True)
print "# Bravais lattice is written into BPOSCAR."
write_vasp('BPOSCAR', bravais)
def parse_disp_yaml_with_supercell(filename='disp.yaml'):
try:
import yaml
except ImportError:
print "You need to install python-yaml."
exit(1)
try:
from yaml import CLoader as Loader
from yaml import CDumper as Dumper
except ImportError:
from yaml import Loader, Dumper
data = yaml.load(open(filename).read(), Loader=Loader)
lattice = data['lattice']
displacements = []
for x in data['displacements']:
displacements.append([x['atom'] - 1, x['displacement']])
positions = [x['position'] for x in data['atoms']]
symbols = [x['symbol'] for x in data['atoms']]
cell = Atoms(cell=lattice,
scaled_positions=positions,
symbols=symbols,
pbc=True)
return displacements, cell
def check_symmetry(input_cell,
primitive_axis=None,
symprec=1e-5,
distance_to_A=1.0,
phonopy_version=None):
if primitive_axis is None:
cell = get_primitive(input_cell, np.eye(3), symprec=symprec)
else:
cell = get_primitive(input_cell, primitive_axis, symprec=symprec)
lattice = cell.get_cell() * distance_to_A
cell.set_cell(lattice)
symmetry = Symmetry(cell, symprec)
print(_get_symmetry_yaml(cell, symmetry, phonopy_version))
if input_cell.get_magnetic_moments() is None:
primitive = find_primitive(cell, symprec)
if primitive is not None:
print("# Primitive cell was found. It is written into PPOSCAR.")
write_vasp('PPOSCAR', primitive)
# Overwrite symmetry and cell
symmetry = Symmetry(primitive, symprec)
cell = primitive
(bravais_lattice, bravais_pos,
bravais_numbers) = spg.refine_cell(cell, symprec)
bravais = Atoms(numbers=bravais_numbers,
scaled_positions=bravais_pos,
cell=bravais_lattice,
pbc=True)
print("# Bravais lattice is written into BPOSCAR.")
write_vasp('BPOSCAR', bravais)
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_elk(filename):
"""Read crystal structure."""
elk_in = ElkIn(open(filename).readlines())
tags = elk_in.get_variables()
avec = [tags["scale"][i] * np.array(tags["avec"][i]) for i in range(3)]
spfnames = tags["atoms"]["spfnames"]
symbols = [x.split(".")[0] for x in spfnames]
numbers = []
for s in symbols:
if s in symbols:
numbers.append(symbol_map[s])
else:
numbers.append(0)
for i, n in enumerate(numbers):
if n == 0:
for j in range(1, 119):
if not (j in numbers):
numbers[i] = j
break
pos_all = []
num_all = []
for num, pos in zip(numbers, tags["atoms"]["positions"]):
pos_all += pos
num_all += [num] * len(pos)
return Atoms(numbers=num_all, cell=avec,
scaled_positions=pos_all), spfnames
def _build_supercells_with_displacements(self):
supercells = []
magmoms = self._supercell.get_magnetic_moments()
masses = self._supercell.get_masses()
numbers = self._supercell.get_atomic_numbers()
lattice = self._supercell.get_cell()
supercells = self._build_phonon_supercells_with_displacements(
self._supercell,
self._displacement_dataset)
for disp1 in self._displacement_dataset['first_atoms']:
disp_cart1 = disp1['displacement']
for disp2 in disp1['second_atoms']:
if 'included' in disp2:
included = disp2['included']
else:
included = True
if included:
positions = self._supercell.get_positions()
positions[disp1['number']] += disp_cart1
positions[disp2['number']] += disp2['displacement']
supercells.append(Atoms(numbers=numbers,
masses=masses,
magmoms=magmoms,
positions=positions,
cell=lattice,
pbc=True))
else:
supercells.append(None)
self._supercells_with_displacements = supercells
def _get_supercell(self):
dim = self._dimension
scaled_positions = []
masses = []
magmoms_prim = self._cell.get_magnetic_moments()
if magmoms_prim == None:
magmoms = None
else:
magmoms = []
symbols = []
for a in range(dim[0]):
for b in range(dim[1]):
for c in range(dim[2]):
for i in range(self._cell.get_number_of_atoms()):
p = self._cell.get_scaled_positions()[i]
scaled_positions.append(p + np.array([a,b,c]))
masses.append(self._cell.get_masses()[i])
symbols.append(self._cell.get_chemical_symbols()[i])
if not magmoms_prim == None:
magmoms.append(magmoms_prim[i])
lattice = np.dot(np.diag(dim), self._cell.get_cell())
positions = np.dot(scaled_positions, self._cell.get_cell())
return Atoms(cell=lattice,
positions=positions,
masses=masses,
magmoms=magmoms,
symbols=symbols,
pbc=True)
def setUp(self):
symbols = ['Si'] * 2 + ['O'] * 4
lattice = [[4.65, 0, 0],
[0, 4.75, 0],
[0, 0, 3.25]]
points = [[0.0, 0.0, 0.0],
[0.5, 0.5, 0.5],
[0.3, 0.3, 0.0],
[0.7, 0.7, 0.0],
[0.2, 0.8, 0.5],
[0.8, 0.2, 0.5]]
self._cell = Atoms(cell=lattice,
scaled_positions=points,
symbols=symbols)
def read_siesta(filename):
siesta_in = SiestaIn(open(filename).read())
numbers = siesta_in._tags["atomicnumbers"]
lattice = siesta_in._tags["latticevectors"]
positions = siesta_in._tags["atomiccoordinates"]
atypes = siesta_in._tags["chemicalspecieslabel"]
cell = Atoms(numbers=numbers,
cell=lattice)
coordformat = siesta_in._tags["atomiccoordinatesformat"]
if coordformat == "fractional" or coordformat == "scaledbylatticevectors":
cell.set_scaled_positions(positions)
elif coordformat == "scaledcartesian":
if siesta_in._tags['latticeconstant'] == 'ang':
cell.set_positions(np.array(positions) / Bohr)#convert from angstroem to Bohr
else:
cell.set_positions(np.array(positions))
elif coordformat == "notscaledcartesianang" or coordformat == "ang":
cell.set_positions(np.array(positions) / Bohr) #convert from angstroem to Bohr
elif coordformat == "notscaledcartesianbohr" or coordformat == "bohr":
cell.set_positions(np.array(positions))
else:
print "The format %s for the AtomicCoordinatesFormat is not implemented"%coordformat
exit()
return cell, atypes
def __init__(self, numbatom=125, supercell=5):
#species = 'WRe_0.25_conv'
species = 'WRe_0.00'
#species = 'Re'
###read force constants from vasprun.xml###
vasprun = etree.iterparse('vasprun.xml', tag='varray')
#fc = vasp.get_force_constants_vasprun_xml(vasprun,1) #pass xml input and species atomic weight.
###########################################
########### read positionsl ###############
primitive = vasp.get_atoms_from_poscar(open('POSCAR-p'),'W')
superc = vasp.get_atoms_from_poscar(open('POSCAR'),'W')
###########################################
numbatom = superc.get_number_of_atoms()
#print primitive.get_cell()
#print primitive.get_scaled_positions()
#print superc.get_scaled_positions()
print numbatom, species, os.getcwd()
if species=='W':
#Tungsten
fc = vasp.get_force_constants_vasprun_xml(vasprun,1,0,64)
s = 4.
a = superc.get_cell()[0][0]*2.
print a
bulk = PhonopyAtoms(symbols=['W'] * 1,
scaled_positions= primitive.get_scaled_positions())
bulk.set_cell(np.diag((a, a, a)))
phonon = Phonopy(bulk,
[[s,0.,0.],[0.,s,0.],[0.,0.,s]],
primitive_matrix=[[-0.5, 0.5, 0.5],[0.5, -0.5, 0.5],[0.5, 0.5, -0.5]],
distance=0.01, factor=15.633302)
print fc
phonon.set_force_constants(fc[0])
phonon.set_dynamical_matrix()
#print phonon.get_dynamical_matrix_at_q([0,0,0])
mesh = [100, 100, 100]
phonon.set_mesh(mesh)
qpoints, weights, frequencies, eigvecs = phonon.get_mesh()
print frequencies
phonon.set_total_DOS()
phonon.set_thermal_properties(t_step=10,
t_max=3700,
t_min=0)
elif species=='W_conv_2x2x2':
#Tungsten
fc = vasp.get_force_constants_vasprun_xml(vasprun,1,2)
s = 2.
a = superc.get_cell()[0][0]*2.
print a
bulk = PhonopyAtoms(symbols=['W','W'] * 1,
scaled_positions= primitive.get_scaled_positions())
bulk.set_cell(np.diag((a, a, a)))
phonon = Phonopy(bulk,
[[s,0.,0.],[0.,s,0.],[0.,0.,s]],
primitive_matrix=[[-0.5, 0.5, 0.5],[0.5, -0.5, 0.5],[0.5, 0.5, -0.5]],
distance=0.01, factor=15.633302)
print fc
phonon.set_force_constants(fc[0])
phonon.set_dynamical_matrix()
#print phonon.get_dynamical_matrix_at_q([0,0,0])
mesh = [100, 100, 100]
phonon.set_mesh(mesh)
qpoints, weights, frequencies, eigvecs = phonon.get_mesh()
print frequencies
phonon.set_total_DOS()
phonon.set_thermal_properties(t_step=10,
t_max=3700,
t_min=0)
elif species=='W_conv':
#Tungsten
fc = vasp.get_force_constants_vasprun_xml(vasprun,1,2)
s = 4.
a = superc.get_cell()[0][0]*2.
print a
bulk = PhonopyAtoms(symbols=['W','W'] * 1,
scaled_positions= primitive.get_scaled_positions())
bulk.set_cell(np.diag((a, a, a)))
phonon = Phonopy(bulk,
[[s,0.,0.],[0.,s,0.],[0.,0.,s]],
primitive_matrix=[[-0.5, 0.5, 0.5],[0.5, -0.5, 0.5],[0.5, 0.5, -0.5]],
distance=0.01, factor=15.633302)
print fc
phonon.set_force_constants(fc[0])
phonon.set_dynamical_matrix()
#print phonon.get_dynamical_matrix_at_q([0,0,0])
mesh = [100, 100, 100]
phonon.set_mesh(mesh)
qpoints, weights, frequencies, eigvecs = phonon.get_mesh()
print frequencies
phonon.set_total_DOS()
phonon.set_thermal_properties(t_step=10,
t_max=3700,
t_min=0)
elif species=='WRe_0.25_conv':
#Tungsten
fc = vasp.get_force_constants_vasprun_xml(vasprun,8,2,64)
s = 4.
a = superc.get_cell()[0][0]*2.
print a, primitive.get_scaled_positions()
bulk = PhonopyAtoms(symbols=['W','W'] * 1,
scaled_positions= primitive.get_scaled_positions())
bulk.set_cell(np.diag((a, a, a)))
phonon = Phonopy(bulk,
[[s,0.,0.],[0.,s,0.],[0.,0.,s]],
primitive_matrix=[[-0.5, 0.5, 0.5],[0.5, -0.5, 0.5],[0.5, 0.5, -0.5]],
distance=0.01, factor=15.633302)
print fc
phonon.set_force_constants(fc[0])
phonon.set_dynamical_matrix()
#print phonon.get_dynamical_matrix_at_q([0,0,0])
mesh = [100, 100, 100]
phonon.set_mesh(mesh)
qpoints, weights, frequencies, eigvecs = phonon.get_mesh()
#print frequencies
phonon.set_total_DOS()
phonon.set_thermal_properties(t_step=10,
t_max=3700,
t_min=0)
elif species == 'WRe_B2':
fc = vasp.get_force_constants_vasprun_xml(vasprun,1,1)
s = 5.
a = superc.get_cell()[0][0]*2.
print a
bulk = PhonopyAtoms(symbols=['W','Re'] * 1,
scaled_positions= primitive.get_scaled_positions())
bulk.set_cell(np.diag((a, a, a)))
phonon = Phonopy(bulk,
[[s,0.,0.],[0.,s,0.],[0.,0.,s]],
primitive_matrix=[[-0.5, 0.5, 0.5],[0.5, -0.5, 0.5],[0.5, 0.5, -0.5]],
distance=0.01, factor=15.633302)
print fc
phonon.set_force_constants(fc[0])
phonon.set_dynamical_matrix()
#print phonon.get_dynamical_matrix_at_q([0,0,0])
mesh = [100, 100, 100]
phonon.set_mesh(mesh)
qpoints, weights, frequencies, eigvecs = phonon.get_mesh()
print frequencies
phonon.set_total_DOS()
phonon.set_thermal_properties(t_step=10,
t_max=3700,
t_min=0)
elif species == 'WRe_0.00':
fc = vasp.get_force_constants_vasprun_xml(vasprun,1,0,numbatom)
s = supercell
a = superc.get_cell()[0][0]*2.
print a
bulk = PhonopyAtoms(symbols=['W'] * 1,
scaled_positions= primitive.get_scaled_positions())
bulk.set_cell(np.diag((a, a, a)))
phonon = Phonopy(bulk,
[[s,0.,0.],[0.,s,0.],[0.,0.,s]],
primitive_matrix=[[-0.5, 0.5, 0.5],[0.5, -0.5, 0.5],[0.5, 0.5, -0.5]],
distance=0.01, factor=15.633302)
print fc
phonon.set_force_constants(fc[0])
phonon.set_dynamical_matrix()
#print phonon.get_dynamical_matrix_at_q([0,0,0])
mesh = [200, 200, 200]
phonon.set_mesh(mesh)
qpoints, weights, frequencies, eigvecs = phonon.get_mesh()
print frequencies
phonon.set_total_DOS()
phonon.set_thermal_properties(t_step=10,
t_max=3700,
t_min=0)
elif species == 'WRe_0.03':
fc = vasp.get_force_constants_vasprun_xml(vasprun,2,0)
s = 2.
a = superc.get_cell()[0][0]*2.
print a
bulk = PhonopyAtoms(symbols=['W'] * 1,
scaled_positions= primitive.get_scaled_positions())
bulk.set_cell(np.diag((a, a, a)))
phonon = Phonopy(bulk,
[[s,0.,0.],[0.,s,0.],[0.,0.,s]],
primitive_matrix=[[-0.5, 0.5, 0.5],[0.5, -0.5, 0.5],[0.5, 0.5, -0.5]],
distance=0.01, factor=15.633302)
print fc
phonon.set_force_constants(fc[0])
phonon.set_dynamical_matrix()
#print phonon.get_dynamical_matrix_at_q([0,0,0])
mesh = [100, 100, 100]
phonon.set_mesh(mesh)
qpoints, weights, frequencies, eigvecs = phonon.get_mesh()
print frequencies
phonon.set_total_DOS()
phonon.set_thermal_properties(t_step=10,
t_max=3700,
t_min=0)
elif species == 'WRe_0.06':
fc = vasp.get_force_constants_vasprun_xml(vasprun,3,0)
s = 2.
a = superc.get_cell()[0][0]*2.
print a
bulk = PhonopyAtoms(symbols=['W'] * 1,
scaled_positions= primitive.get_scaled_positions())
bulk.set_cell(np.diag((a, a, a)))
phonon = Phonopy(bulk,
[[s,0.,0.],[0.,s,0.],[0.,0.,s]],
primitive_matrix=[[-0.5, 0.5, 0.5],[0.5, -0.5, 0.5],[0.5, 0.5, -0.5]],
distance=0.01, factor=15.633302)
print fc
phonon.set_force_constants(fc[0])
phonon.set_dynamical_matrix()
#print phonon.get_dynamical_matrix_at_q([0,0,0])
mesh = [100, 100, 100]
phonon.set_mesh(mesh)
qpoints, weights, frequencies, eigvecs = phonon.get_mesh()
print frequencies
phonon.set_total_DOS()
phonon.set_thermal_properties(t_step=10,
t_max=3700,
t_min=0)
elif species == 'WRe_0.09':
fc = vasp.get_force_constants_vasprun_xml(vasprun,4,0)
s = 2.
a = superc.get_cell()[0][0]*2.
print a
bulk = PhonopyAtoms(symbols=['W'] * 1,
scaled_positions= primitive.get_scaled_positions())
bulk.set_cell(np.diag((a, a, a)))
phonon = Phonopy(bulk,
[[s,0.,0.],[0.,s,0.],[0.,0.,s]],
primitive_matrix=[[-0.5, 0.5, 0.5],[0.5, -0.5, 0.5],[0.5, 0.5, -0.5]],
distance=0.01, factor=15.633302)
print fc
phonon.set_force_constants(fc[0])
phonon.set_dynamical_matrix()
#print phonon.get_dynamical_matrix_at_q([0,0,0])
mesh = [100, 100, 100]
phonon.set_mesh(mesh)
qpoints, weights, frequencies, eigvecs = phonon.get_mesh()
print frequencies
phonon.set_total_DOS()
phonon.set_thermal_properties(t_step=10,
t_max=3700,
t_min=0)
elif species == 'WRe_0.12':
fc = vasp.get_force_constants_vasprun_xml(vasprun,5,0)
s = 2.
a = superc.get_cell()[0][0]*2.
print a
bulk = PhonopyAtoms(symbols=['W'] * 1,
scaled_positions= primitive.get_scaled_positions())
bulk.set_cell(np.diag((a, a, a)))
phonon = Phonopy(bulk,
[[s,0.,0.],[0.,s,0.],[0.,0.,s]],
primitive_matrix=[[-0.5, 0.5, 0.5],[0.5, -0.5, 0.5],[0.5, 0.5, -0.5]],
distance=0.01, factor=15.633302)
print fc
phonon.set_force_constants(fc[0])
phonon.set_dynamical_matrix()
#print phonon.get_dynamical_matrix_at_q([0,0,0])
mesh = [100, 100, 100]
phonon.set_mesh(mesh)
qpoints, weights, frequencies, eigvecs = phonon.get_mesh()
print frequencies
phonon.set_total_DOS()
phonon.set_thermal_properties(t_step=10,
t_max=3700,
t_min=0)
elif species == 'WRe_0.18':
fc = vasp.get_force_constants_vasprun_xml(vasprun,6,0)
s = 2.
a = superc.get_cell()[0][0]*2.
print a
bulk = PhonopyAtoms(symbols=['W'] * 1,
scaled_positions= primitive.get_scaled_positions())
bulk.set_cell(np.diag((a, a, a)))
phonon = Phonopy(bulk,
[[s,0.,0.],[0.,s,0.],[0.,0.,s]],
primitive_matrix=[[-0.5, 0.5, 0.5],[0.5, -0.5, 0.5],[0.5, 0.5, -0.5]],
distance=0.01, factor=15.633302)
print fc
phonon.set_force_constants(fc[0])
phonon.set_dynamical_matrix()
#print phonon.get_dynamical_matrix_at_q([0,0,0])
mesh = [100, 100, 100]
phonon.set_mesh(mesh)
qpoints, weights, frequencies, eigvecs = phonon.get_mesh()
print frequencies
phonon.set_total_DOS()
phonon.set_thermal_properties(t_step=10,
t_max=3700,
t_min=0)
elif species == 'WRe_0.25':
fc = vasp.get_force_constants_vasprun_xml(vasprun,7,0)
s = 2.
a = primitive.get_cell()[0][0]*2.
print a, primitive.get_scaled_positions()
bulk = PhonopyAtoms(symbols=['W'] * 1,
scaled_positions= primitive.get_scaled_positions())
bulk.set_cell(np.diag((a, a, a)))
phonon = Phonopy(bulk,
[[s,0.,0.],[0.,s,0.],[0.,0.,s]],
primitive_matrix=[[-0.5, 0.5, 0.5],[0.5, -0.5, 0.5],[0.5, 0.5, -0.5]],
distance=0.01, factor=15.633302)
print fc
phonon.set_force_constants(fc[0])
phonon.set_dynamical_matrix()
#print phonon.get_dynamical_matrix_at_q([0,0,0])
mesh = [100, 100, 100]
phonon.set_mesh(mesh)
qpoints, weights, frequencies, eigvecs = phonon.get_mesh()
print frequencies
phonon.set_total_DOS()
#phonon.set_partial_DOS()
phonon.set_thermal_properties(t_step=10,
t_max=3700,
t_min=0)
elif species == 'WRe_0.50':
fc = vasp.get_force_constants_vasprun_xml(vasprun,8,0)
s = 2.
a = superc.get_cell()[0][0]*2.
print a
bulk = PhonopyAtoms(symbols=['W'] * 1,
scaled_positions= primitive.get_scaled_positions())
bulk.set_cell(np.diag((a, a, a)))
phonon = Phonopy(bulk,
[[s,0.,0.],[0.,s,0.],[0.,0.,s]],
primitive_matrix=[[-0.5, 0.5, 0.5],[0.5, -0.5, 0.5],[0.5, 0.5, -0.5]],
distance=0.01, factor=15.633302)
#print fc
phonon.set_force_constants(fc[0])
phonon.set_dynamical_matrix()
#print phonon.get_dynamical_matrix_at_q([0,0,0])
mesh = [100, 100, 100]
phonon.set_mesh(mesh)
qpoints, weights, frequencies, eigvecs = phonon.get_mesh()
#print frequencies
phonon.set_total_DOS()
#phonon.set_partial_DOS()
phonon.set_thermal_properties(t_step=10,
t_max=3700,
t_min=0)
elif species == 'Au':
fc = vasp.get_force_constants_vasprun_xml(vasprun,1,0)
#Gold
s = 5.
a = superc.get_cell()[0][0]
bulk = PhonopyAtoms(symbols=['Au'] * 1,
scaled_positions= primitive.get_scaled_positions())
bulk.set_cell(np.diag((a, a, a)))
phonon = Phonopy(bulk,
[[s,0.,0.],[0.,s,0.],[0.,0.,s]],
primitive_matrix=[[0.5, 0.5, 0.0],[0.0, 0.5, 0.5],[0.5, 0.0, 0.5]],
distance=0.01, factor=15.633302)
phonon.set_force_constants(fc[0])
phonon.set_dynamical_matrix()
#print phonon.get_dynamical_matrix_at_q([0,0,0])
mesh = [100, 100, 100]
phonon.set_mesh(mesh)
qpoints, weights, frequencies, eigvecs = phonon.get_mesh()
print frequencies
phonon.set_total_DOS()
phonon.set_partial_DOS()
phonon.set_thermal_properties(t_step=10,
t_max=1300,
t_min=0)
elif species == 'Mo':
fc = vasp.get_force_constants_vasprun_xml(vasprun,10,0)
s = 5.
a = superc.get_cell()[0][0]*2.
print a
bulk = PhonopyAtoms(symbols=['Mo'] * 1,
scaled_positions= primitive.get_scaled_positions())
bulk.set_cell(np.diag((a, a, a)))
phonon = Phonopy(bulk,
[[s,0.,0.],[0.,s,0.],[0.,0.,s]],
primitive_matrix=[[-0.5, 0.5, 0.5],[0.5, -0.5, 0.5],[0.5, 0.5, -0.5]],
distance=0.01, factor=15.633302)
print fc
phonon.set_force_constants(fc[0])
phonon.set_dynamical_matrix()
#print phonon.get_dynamical_matrix_at_q([0,0,0])
mesh = [100, 100, 100]
phonon.set_mesh(mesh)
qpoints, weights, frequencies, eigvecs = phonon.get_mesh()
print frequencies
phonon.set_total_DOS()
phonon.set_thermal_properties(t_step=10,
t_max=2500,
t_min=0)
elif species == 'Re':
fc = vasp.get_force_constants_vasprun_xml(vasprun,9,0)
s = 5.
a = superc.get_cell()[0][0]*2.
print a
bulk = PhonopyAtoms(symbols=['Re'] * 1,
scaled_positions= primitive.get_scaled_positions())
bulk.set_cell(np.diag((a, a, a)))
phonon = Phonopy(bulk,
[[s,0.,0.],[0.,s,0.],[0.,0.,s]],
primitive_matrix=[[-0.5, 0.5, 0.5],[0.5, -0.5, 0.5],[0.5, 0.5, -0.5]],
distance=0.01, factor=15.633302)
print fc
phonon.set_force_constants(fc[0])
phonon.set_dynamical_matrix()
#print phonon.get_dynamical_matrix_at_q([0,0,0])
mesh = [100, 100, 100]
phonon.set_mesh(mesh)
qpoints, weights, frequencies, eigvecs = phonon.get_mesh()
print frequencies
phonon.set_total_DOS()
phonon.set_thermal_properties(t_step=10,
t_max=2500,
t_min=0)
f = open('F_TV','w')
for t, free_energy, entropy, cv in np.array(phonon.get_thermal_properties()).T:
#print t, cv
#print ("%12.3f " + "%15.7f" * 3) % ( t, free_energy, entropy, cv )
f.write(("%12.3f " + "%15.7f" + "\n") % ( t, free_energy))
f.close()
fc = open('thermal_properties','w')
for t, free_energy, entropy, cv in np.array(phonon.get_thermal_properties()).T:
fc.write(("%12.3f " + "%15.7f" *3 + "\n") % ( t, free_energy, entropy, cv ))
fc.close()
#phonon.plot_thermal_properties().show()
#phonon.plot_total_DOS().show()
phonon.write_total_DOS()
#phonon.write_partial_DOS()
phonon.write_yaml_thermal_properties()
bands = []
#### PRIMITIVE
q_start = np.array([0.0, 0.0, 0.0])
#q_start = np.array([0.5, 0.5, 0.0])
q_end = np.array([-0.5, 0.5, 0.5])
#q_end = np.array([0., 0., 0.])
band = []
for i in range(101):
band.append(q_start + (q_end - q_start) / 100 * i)
bands.append(band)
band = []
q_start = np.array([-0.5, 0.5, 0.5])
#q_start = np.array([0., 0., 0.])
q_end = np.array([0.25, 0.25, 0.25])
#q_end = np.array([1., 0., 0.])
for i in range(101):
#band.append([-0.5+3*1/400*i, 0.5-1/400*i, 0.5-1/400*i])
band.append(q_start + (q_end - q_start) / 100 * i)
bands.append(band)
#print band
q_start = np.array([0.25, 0.25, 0.25])
q_end = np.array([0., 0., 0.])
band = []
for i in range(101):
band.append(q_start + (q_end - q_start) / 100 * i)
bands.append(band)
q_start = np.array([0., 0., 0.])
q_end = np.array([0.0, 0., 0.5])
band = []
for i in range(101):
band.append(q_start + (q_end - q_start) / 100 * i)
bands.append(band)
#q_start = np.array([0.0, 0.0, 0.0])
#q_end = np.array([0.5, 0.5, 0.5])
#band = []
#for i in range(101):
# band.append(q_start + (q_end - q_start) / 100 * i)
#bands.append(band)
"""
###### CONVENTIONAL CELL ######
q_start = np.array([0.0, 0.0, 0.0])
q_end = np.array([-0.5, 0.5, 0.5])
band = []
for i in range(101):
band.append(q_start + (q_end - q_start) / 100 * i)
bands.append(band)
q_start = np.array([-0.5, 0.5, 0.5])
q_end = np.array([1./4., 1./4., 1./4.])
band = []
for i in range(101):
band.append(q_start + (q_end - q_start) / 100 * i)
bands.append(band)
q_start = np.array([1./4., 1./4., 1./4.])
q_end = np.array([0.0, 0.0, 0.0])
band = []
for i in range(101):
band.append(q_start + (q_end - q_start) / 100 * i)
bands.append(band)
q_start = np.array([0.0, 0.0, 0.0])
q_end = np.array([0.5, 0.0, 0.0])
band = []
for i in range(101):
band.append(q_start + (q_end - q_start) / 100 * i)
bands.append(band)
"""
phonon.set_band_structure(bands)
#phonon.plot_band_structure().show()
q_points, distances, frequencies, eigvecs = phonon.get_band_structure()
disp = {'q':q_points, 'distances':distances, 'frequencies':frequencies, 'eigvecs':eigvecs}
f = open('ph_dispersion.pkl','w')
pickle.dump(disp, f)
f.close()
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
import phonopy.interface.vasp as vasp
import numpy as np
import lxml.etree as etree
from phonopy import Phonopy
from phonopy.structure.atoms import Atoms as PhonopyAtoms
vasprun = etree.iterparse('vasprun.xml', tag='varray')
fc = vasp.get_force_constants_vasprun_xml(vasprun)
primitive = vasp.get_atoms_from_poscar(open('POSCAR-p'),'W')
superc = vasp.get_atoms_from_poscar(open('POSCAR'),'W')
print superc.get_scaled_positions()
a = 5.404
bulk = PhonopyAtoms(symbols=['W'] * 216,
positions=superc.get_scaled_positions())
bulk.set_cell(np.diag((a, a, a)))
phonon = Phonopy(bulk,[[1,0,0],[0,1,0],[0,0,1]],primitive_matrix=[[-0.5, 0.5, 0.5],[0.5, -0.5, 0.5],[0.5, 0.5, -0.5]])
phonon.set_force_constants(fc)
mesh = [3, 3, 3]
phonon.set_mesh(mesh)
qpoints, weights, frequencies, eigvecs = phonon.get_mesh()
phonon.set_total_DOS()
phonon.plot_total_DOS().show()