def _get_cell_settings(unitcell_filename, supercell_filename, unitcell,
supercell, calculator, pmat, smat, symprec):
if unitcell_filename is not None:
cell, filename = read_crystal_structure(filename=unitcell_filename,
interface_mode=calculator)
_smat = _get_supercell_matrix(smat)
_pmat = pmat
elif supercell_filename is not None:
cell, filename = read_crystal_structure(filename=supercell_filename,
interface_mode=calculator)
_smat = np.eye(3, dtype='intc', order='C')
if pmat is None:
_pmat = 'auto'
elif unitcell is not None:
cell = unitcell
elif supercell is not None:
cell = supercell
_smat = np.eye(3, dtype='intc', order='C')
if pmat is None:
_pmat = 'auto'
else:
raise RuntimeError("Cell has to be specified.")
if cell is None:
msg = "'%s' could not be found." % filename
raise FileNotFoundError(msg)
_pmat = _get_primitive_matrix(_pmat, cell, symprec)
return cell, _smat, _pmat
def get_data(args, interface_mode=None):
args = parse_args()
cell, _ = read_crystal_structure(args.filenames[0],
interface_mode=interface_mode)
f = h5py.File(args.filenames[1])
primitive_matrix = np.reshape(
[fracval(x) for x in args.primitive_matrix.split()], (3, 3))
primitive = get_primitive(cell, primitive_matrix)
symmetry = Symmetry(primitive)
data = {}
data['cell'] = primitive
data['symmetry'] = symmetry
data['mesh'] = np.array(f['mesh'][:], dtype='intc') # (3)
data['weight'] = f['weight'][:] # (gp)
data['group_velocity'] = f['group_velocity'][:] # (gp, band, 3)
data['qpoint'] = f['qpoint'][:] # (gp, 3)
data['frequency'] = f['frequency'][:] # (gp, band)
if 'gamma_N' in f:
data['gamma_N'] = f['gamma_N'][:] # (temps, gp, band)
data['gamma_U'] = f['gamma_U'][:] # (temps, gp, band)
if 'gamma_isotope' in f:
data['gamma_isotope'] = f['gamma_isotope'][:] # (gp, band)
data['heat_capacity'] = f['heat_capacity'][:] # (temps, gp, band)
data['temperature'] = np.array(f['temperature'][:],
dtype='double') # (temps)
ir_grid_points, grid_address, _ = get_grid_symmetry(data)
data['ir_grid_points'] = ir_grid_points
data['grid_address'] = grid_address
return data
def load(supercell_matrix,
primitive_matrix=None,
nac_params=None,
unitcell=None,
calculator="vasp",
unitcell_filename=None,
born_filename=None,
force_sets_filename=None,
force_constants_filename=None,
factor=VaspToTHz,
frequency_scale_factor=None,
symprec=1e-5,
is_symmetry=True,
log_level=0):
if unitcell is None:
_unitcell, _ = read_crystal_structure(filename=unitcell_filename,
interface_mode=calculator)
else:
_unitcell = unitcell
# units keywords: factor, nac_factor, distance_to_A
units = get_default_physical_units(calculator)
phonon = Phonopy(_unitcell,
supercell_matrix,
primitive_matrix=primitive_matrix,
factor=units['factor'])
if nac_params is None:
if born_filename is None:
_nac_params = None
else:
_nac_params = parse_BORN(phonon.primitive, filename=born_filename)
else:
_nac_params = nac_params
if _nac_params is not None:
if _nac_params['factor'] is None:
_nac_params['factor'] = units['nac_factor']
phonon.set_nac_params(_nac_params)
if force_constants_filename is not None:
dot_split = force_constants_filename.split('.')
p2s_map = phonon.primitive.get_primitive_to_supercell_map()
if len(dot_split) > 1 and dot_split[-1] == 'hdf5':
fc = read_force_constants_hdf5(filename=force_constants_filename,
p2s_map=p2s_map)
else:
fc = parse_FORCE_CONSTANTS(filename=force_constants_filename,
p2s_map=p2s_map)
phonon.set_force_constants(fc)
elif force_sets_filename is not None:
force_sets = parse_FORCE_SETS(filename=force_sets_filename)
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants()
return phonon
def get_cell_settings(phonopy_yaml=None,
supercell_matrix=None,
primitive_matrix=None,
unitcell=None,
supercell=None,
unitcell_filename=None,
supercell_filename=None,
calculator=None,
symprec=1e-5):
if unitcell_filename is not None:
cell, filename = read_crystal_structure(
filename=unitcell_filename, interface_mode=calculator)
smat = _get_supercell_matrix(supercell_matrix)
pmat = primitive_matrix
elif supercell_filename is not None:
cell, filename = read_crystal_structure(
filename=supercell_filename, interface_mode=calculator)
smat = np.eye(3, dtype='intc', order='C')
if primitive_matrix is None or primitive_matrix == "auto":
pmat = 'auto'
elif unitcell is not None:
cell = PhonopyAtoms(atoms=unitcell)
smat = _get_supercell_matrix(supercell_matrix)
pmat = primitive_matrix
elif supercell is not None:
cell = PhonopyAtoms(atoms=supercell)
smat = np.eye(3, dtype='intc', order='C')
if primitive_matrix is None or primitive_matrix == "auto":
pmat = 'auto'
else:
raise RuntimeError("Cell has to be specified.")
if cell is None:
msg = "'%s' could not be found." % filename
raise FileNotFoundError(msg)
pmat = _get_primitive_matrix(pmat, cell, symprec)
return cell, smat, pmat
def collect_cell_info(supercell_matrix=None,
primitive_matrix=None,
interface_mode=None,
cell_filename=None,
chemical_symbols=None,
enforce_primitive_matrix_auto=False,
command_name="phonopy",
symprec=1e-5):
if supercell_matrix is None:
_interface_mode = "phonopy_yaml"
elif interface_mode is None:
try:
read_vasp(cell_filename)
_interface_mode = None
except (ValueError, TypeError):
# TypeError occurs when cell_filename is None.
# ValueError occurs in parsing POSCAR like file.
_interface_mode = "phonopy_yaml"
else:
_interface_mode = interface_mode
unitcell, optional_structure_info = read_crystal_structure(
filename=cell_filename,
interface_mode=_interface_mode,
chemical_symbols=chemical_symbols,
command_name=command_name)
unitcell_filename = optional_structure_info[0]
if _interface_mode == 'phonopy_yaml' and unitcell is not None:
if optional_structure_info[1] is None:
interface_mode_out = interface_mode
else:
interface_mode_out = optional_structure_info[1]
if optional_structure_info[2] is None:
_supercell_matrix = supercell_matrix
else:
_supercell_matrix = optional_structure_info[2]
if primitive_matrix is not None:
_primitive_matrix = primitive_matrix
elif optional_structure_info[3] is not None:
_primitive_matrix = optional_structure_info[3]
else:
_primitive_matrix = 'auto'
has_read_phonopy_yaml = True
else:
interface_mode_out = _interface_mode
_supercell_matrix = supercell_matrix
_primitive_matrix = primitive_matrix
has_read_phonopy_yaml = False
if enforce_primitive_matrix_auto:
_primitive_matrix = 'auto'
if _supercell_matrix is None and _primitive_matrix == 'auto':
supercell_matrix_out = np.eye(3, dtype='intc')
else:
supercell_matrix_out = _supercell_matrix
primitive_matrix_out = _primitive_matrix
if unitcell is None:
fname_list = optional_structure_info
if len(fname_list) == 1:
msg = "Crystal structure file of \"%s\"" % fname_list[0]
msg_list = [
"%s was not found." % msg,
]
elif len(fname_list) == 2:
msg = "Crystal structure file of \"%s\" %s" % fname_list
msg_list = [
"%s was not found." % msg,
]
elif len(fname_list) == 4:
msg_list = []
if cell_filename is None:
msg = (
"\"%s\" or \"%s\" should exist in the current directory" %
fname_list[:2])
msg_list.append(msg)
msg = "to run without setting supercell matrix (DIM or --dim)."
msg_list.append(msg)
else:
msg_list.append("Supercell matrix (DIM or --dim) may be "
"forgotten to be specified.")
return "\n".join(msg_list)
if supercell_matrix_out is None:
return "Supercell matrix (DIM or --dim) is not specified."
# Check unit cell
if np.linalg.det(unitcell.get_cell()) < 0.0:
return "Lattice vectors have to follow the right-hand rule."
return (unitcell, supercell_matrix_out, primitive_matrix_out,
unitcell_filename, optional_structure_info, interface_mode_out,
has_read_phonopy_yaml)
option_list=option_list)
settings = phonopy_conf.get_settings()
else:
phonopy_conf = PhonopyConfParser(options=options, option_list=option_list)
settings = phonopy_conf.get_settings()
if options.is_graph_save:
import matplotlib
matplotlib.use('Agg')
##################
# Initialization #
##################
unitcell, optional_structure_file_information = read_crystal_structure(
filename=settings.get_cell_filename(),
interface_mode=interface_mode,
chemical_symbols=settings.get_chemical_symbols(),
yaml_mode=settings.get_yaml_mode())
unitcell_filename = optional_structure_file_information[0]
if unitcell is None:
print_error_message("Crystal structure file of %s could not be found." %
unitcell_filename)
if log_level > 0:
print_error()
sys.exit(1)
# Check unit cell
if np.linalg.det(unitcell.get_cell()) < 0.0:
print_error_message("Determinant of the lattice vector matrix "
"has to be positive.")
def collect_cell_info(supercell_matrix=None,
primitive_matrix=None,
interface_mode=None,
cell_filename=None,
chemical_symbols=None,
enforce_primitive_matrix_auto=False,
command_name="phonopy",
symprec=1e-5):
if supercell_matrix is None:
_interface_mode = "phonopy_yaml"
elif interface_mode is None:
try:
if cell_filename is None:
read_vasp(get_default_cell_filename('vasp'))
else:
read_vasp(cell_filename)
_interface_mode = None
except (ValueError, TypeError):
# TypeError occurs when cell_filename is None.
# ValueError occurs in parsing POSCAR like file.
_interface_mode = "phonopy_yaml"
else:
_interface_mode = interface_mode
unitcell, optional_structure_info = read_crystal_structure(
filename=cell_filename,
interface_mode=_interface_mode,
chemical_symbols=chemical_symbols,
command_name=command_name)
unitcell_filename = optional_structure_info[0]
if _interface_mode == 'phonopy_yaml' and unitcell is not None:
if optional_structure_info[1] is None:
interface_mode_out = interface_mode
else:
interface_mode_out = optional_structure_info[1]
if optional_structure_info[2] is None:
_supercell_matrix = supercell_matrix
else:
_supercell_matrix = optional_structure_info[2]
if primitive_matrix is not None:
_primitive_matrix = primitive_matrix
elif optional_structure_info[3] is not None:
_primitive_matrix = optional_structure_info[3]
else:
_primitive_matrix = 'auto'
has_read_phonopy_yaml = True
else:
interface_mode_out = _interface_mode
_supercell_matrix = supercell_matrix
_primitive_matrix = primitive_matrix
has_read_phonopy_yaml = False
if enforce_primitive_matrix_auto:
_primitive_matrix = 'auto'
if _supercell_matrix is None and _primitive_matrix == 'auto':
supercell_matrix_out = np.eye(3, dtype='intc')
else:
supercell_matrix_out = _supercell_matrix
primitive_matrix_out = _primitive_matrix
if unitcell is None:
fname_list = optional_structure_info
if len(fname_list) == 1:
msg = "Crystal structure file of \"%s\"" % fname_list[0]
msg_list = ["%s was not found." % msg, ]
elif len(fname_list) == 2:
msg = "Crystal structure file of \"%s\" %s" % fname_list
msg_list = ["%s was not found." % msg, ]
elif len(fname_list) == 4:
msg_list = []
if supercell_matrix is None:
if cell_filename is None:
msg = ["Supercell matrix (DIM or --dim) is not specified. "
"To run phonopy without",
"explicitly setting supercell matrix, \"%s\" or \"%s\" "
% fname_list[:2],
"must exist in the current directory."]
msg_list += msg
else:
msg_list.append("Supercell matrix (DIM or --dim) may be "
"forgotten to be specified.")
elif cell_filename is None:
msg_list = ["Any crystal structure file was not found.", ""]
return "\n".join(msg_list)
if supercell_matrix_out is None:
return "Supercell matrix (DIM or --dim) is not specified."
# Check unit cell
if np.linalg.det(unitcell.get_cell()) < 0.0:
return "Lattice vectors have to follow the right-hand rule."
return (unitcell, supercell_matrix_out, primitive_matrix_out,
unitcell_filename, optional_structure_info, interface_mode_out,
has_read_phonopy_yaml)