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):
# In some cases, interface mode falls back to phonopy_yaml mode.
fallback_reason = _fallback_to_phonopy_yaml(supercell_matrix,
interface_mode, cell_filename)
if fallback_reason:
_interface_mode = 'phonopy_yaml'
elif interface_mode is None:
_interface_mode = None
else:
_interface_mode = interface_mode.lower()
unitcell, optional_structure_info = read_crystal_structure(
filename=cell_filename,
interface_mode=_interface_mode,
chemical_symbols=chemical_symbols,
command_name=command_name)
# Error check
if unitcell is None:
err_msg = _get_error_message(optional_structure_info, interface_mode,
fallback_reason, cell_filename,
command_name)
return err_msg
# Retrieve more information on cells
(interface_mode_out, supercell_matrix_out,
primitive_matrix_out) = _collect_cells_info(
_interface_mode, optional_structure_info, command_name,
interface_mode, supercell_matrix, primitive_matrix,
enforce_primitive_matrix_auto)
# Another error check
msg_list = [
"Crystal structure was read from \"%s\"." % optional_structure_info[0],
]
if supercell_matrix_out is None:
msg_list.append(
"Supercell matrix (DIM or --dim) information was not found.")
return "\n".join(msg_list)
if np.linalg.det(unitcell.get_cell()) < 0.0:
msg_list.append("Lattice vectors have to follow the right-hand rule.")
return "\n".join(msg_list)
# Succeeded!
if _interface_mode == 'phonopy_yaml':
phpy_yaml = optional_structure_info[1]
else:
phpy_yaml = None
return (unitcell, supercell_matrix_out, primitive_matrix_out,
optional_structure_info, interface_mode_out, phpy_yaml)
def test_phonopy_atoms_behavior(sc_structure, tmpdir):
print(tmpdir)
tmpdir.chdir()
# actual = structure_to_phonopy_atoms(sc_structure)
sc_structure.to(fmt="poscar", filename="POSCAR")
a, _ = read_crystal_structure("POSCAR")
b = PhonopyAtoms(atoms=a)
print(type(a.get_cell()))
print(a.get_atomic_numbers())
assert_same_phonopy_atoms(a, b)
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, optional_structure_info = 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, optional_structure_info = 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:
filename = optional_structure_info[0]
msg = "'%s' could not be found." % filename
raise FileNotFoundError(msg)
pmat = _get_primitive_matrix(pmat, cell, symprec)
return cell, smat, pmat
def get_cell_settings(
supercell_matrix=None,
primitive_matrix=None,
unitcell=None,
supercell=None,
unitcell_filename=None,
supercell_filename=None,
calculator=None,
symprec=1e-5,
log_level=0,
):
"""Return crystal structures."""
optional_structure_info = None
if primitive_matrix is None or (type(primitive_matrix) is str and
primitive_matrix == "auto"): # noqa E129
pmat = "auto"
else:
pmat = primitive_matrix
if unitcell_filename is not None:
cell, optional_structure_info = _read_crystal_structure(
filename=unitcell_filename, interface_mode=calculator)
smat = supercell_matrix
if log_level:
print('Unit cell structure was read from "%s".' %
optional_structure_info[0])
elif supercell_filename is not None:
cell, optional_structure_info = read_crystal_structure(
filename=supercell_filename, interface_mode=calculator)
smat = np.eye(3, dtype="intc", order="C")
if log_level:
print('Supercell structure was read from "%s".' %
optional_structure_info[0])
elif unitcell is not None:
cell = PhonopyAtoms(atoms=unitcell)
smat = supercell_matrix
elif supercell is not None:
cell = PhonopyAtoms(atoms=supercell)
smat = np.eye(3, dtype="intc", order="C")
else:
raise RuntimeError("Cell has to be specified.")
if optional_structure_info is not None and cell is None:
filename = optional_structure_info[0]
msg = "'%s' could not be found." % filename
raise FileNotFoundError(msg)
pmat = get_primitive_matrix(pmat, symprec=symprec)
return cell, smat, pmat
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,
log_level=0):
optional_structure_info = None
if (primitive_matrix is None
or (type(primitive_matrix) is str and primitive_matrix == "auto")):
pmat = 'auto'
else:
pmat = primitive_matrix
if unitcell_filename is not None:
cell, optional_structure_info = _read_crystal_structure(
filename=unitcell_filename, interface_mode=calculator)
smat = supercell_matrix
if log_level:
print("Unit cell structure was read from \"%s\"." %
optional_structure_info[0])
elif supercell_filename is not None:
cell, optional_structure_info = read_crystal_structure(
filename=supercell_filename, interface_mode=calculator)
smat = np.eye(3, dtype='intc', order='C')
if log_level:
print("Supercell structure was read from \"%s\"." %
optional_structure_info[0])
elif unitcell is not None:
cell = PhonopyAtoms(atoms=unitcell)
smat = supercell_matrix
elif supercell is not None:
cell = PhonopyAtoms(atoms=supercell)
smat = np.eye(3, dtype='intc', order='C')
else:
raise RuntimeError("Cell has to be specified.")
if optional_structure_info is not None and cell is None:
filename = optional_structure_info[0]
msg = "'%s' could not be found." % filename
raise FileNotFoundError(msg)
pmat = _get_primitive_matrix(pmat, cell, symprec)
return cell, smat, pmat
def _read_crystal_structure(filename=None, interface_mode=None):
try:
return read_crystal_structure(filename=filename,
interface_mode=interface_mode)
except FileNotFoundError:
raise
except Exception:
msg = [
"============================ phonopy.load "
"============================",
" Reading crystal structure file failed in phonopy.load.",
" Maybe phonopy.load(..., calculator='<calculator name>') "
"expected?",
"============================ phonopy.load "
"============================",
]
raise RuntimeError("\n".join(msg))
def _read_crystal_structure(filename=None, interface_mode=None):
try:
return read_crystal_structure(filename=filename,
interface_mode=interface_mode)
except FileNotFoundError:
raise
except:
print(
"============================ phonopy.load ============================"
)
print(" Reading crystal structure file failed in phonopy.load.")
print(
" Maybe phonopy.load(..., calculator='<calculator name>') expected?"
)
print(
"============================ phonopy.load ============================"
)
raise
import numpy as np
import seekpath
from phonopy import Phonopy
from phonopy.structure.atoms import PhonopyAtoms
from phonopy.interface.calculator import read_crystal_structure
unitcell, _ = read_crystal_structure("POSCAR", interface_mode='vasp')
cell=unitcell.get_cell()
positions = unitcell.get_scaled_positions()
numbers = np.unique(unitcell.get_chemical_symbols(), return_inverse=True)[1]
path_data = seekpath.get_path((cell, positions, numbers))
labels = path_data['point_coords']
band_ranges = []
for set in path_data['path']:
band_ranges.append([labels[set[0]], labels[set[1]]])
dict= {'ranges': band_range , 'labels': path_data['path']}
with open("output.txt","w") as f :
for i in range(len(dict['labels'])):
f.writelines(str(dict['labels'][i])+":"+str(dict['ranges'][i]))
def collect_cell_info(
supercell_matrix=None,
primitive_matrix=None,
interface_mode=None,
cell_filename=None,
chemical_symbols=None,
enforce_primitive_matrix_auto=False,
phonopy_yaml_cls=None,
):
"""Collect crystal structure information from inputs.
Note
----
When the crystal structure is read from phonopy.yaml like file,
``supercell_matrix`` and ``primitive_matrix`` are ignored.
Parameters
----------
supercell_matrix : array_like or None
3x3 transformation matrix or when it is a diagonal matrix,
three diagonal elements. Default is None.
See also shape_supercell_matrix.
primitive_matrix : array_like, str, or None
3x3 transformation matrix or a character representing centring
or None. Default is None. See also get_primitive_matrix.
interface_mode : str or None
Force calculator or crystal structure format name.
cell_filename : str or None
Input cell filename.
chemical_symbols : list of str
List of chemical symbols or unit cell.
enforce_primitive_matrix_auto : bool
Enforce primitive_matrix='auto' when True. Default is False.
phonopy_yaml_cls : Class object
PhonopyYaml like class name. This is used to return its instance
when needed.
Returns
-------
dict :
"unitcell": PhonopyAtoms
Unit cell.
"supercell_matrix": ndarray
"primitive_matrix": ndarray
"optional_structure_info": list
See read_crystal_structure.
"interface_mode": str
Force calculator or crystal structure format name.
"phonopy_yaml": None or instance of the class given by phonopy_yaml_cls
Not None when crystal structure was read phonopy.yaml like file.
"error_message" : str
Unless error exists, this entry should not be in this dict.
Otherwise, some error exists. The error message is storedin the
string.
"""
# In some cases, interface mode falls back to phonopy_yaml mode.
fallback_reason = _fallback_to_phonopy_yaml(supercell_matrix,
interface_mode, cell_filename)
if fallback_reason:
_interface_mode = "phonopy_yaml"
elif interface_mode is None:
_interface_mode = None
else:
_interface_mode = interface_mode.lower()
if phonopy_yaml_cls is None:
_phonopy_yaml_cls = PhonopyYaml
else:
_phonopy_yaml_cls = phonopy_yaml_cls
unitcell, optional_structure_info = read_crystal_structure(
filename=cell_filename,
interface_mode=_interface_mode,
chemical_symbols=chemical_symbols,
phonopy_yaml_cls=_phonopy_yaml_cls,
)
# Error check
if unitcell is None:
err_msg = _get_error_message(
optional_structure_info,
fallback_reason,
cell_filename,
_phonopy_yaml_cls,
)
return {"error_message": err_msg}
# Retrieve more information on cells
(
interface_mode_out,
supercell_matrix_out,
primitive_matrix_out,
) = _collect_cells_info(
_interface_mode,
optional_structure_info,
interface_mode,
supercell_matrix,
primitive_matrix,
)
err_msg = []
unitcell_filename = optional_structure_info[0]
if supercell_matrix_out is None:
err_msg.append(
"Supercell matrix (DIM or --dim) information was not found.")
if cell_filename is None and (
unitcell_filename
== get_default_cell_filename(interface_mode_out)):
err_msg += [
"",
"Phonopy read the crystal structure from the file having the default "
"filename ",
"of each calculator. In this case, supercell matrix has to be "
"specified.",
"Because this is the old style way of using %s," %
_phonopy_yaml_cls.command_name,
]
filenames = [
'"%s"' % name
for name in _phonopy_yaml_cls.default_filenames[:-1]
]
err_msg += [
'"%s" was read being prefered to files such as ' %
unitcell_filename,
'%s, or "%s".' % (", ".join(filenames),
_phonopy_yaml_cls.default_filenames[-1]),
]
err_msg += [
"",
'If crystal structure is expected to be read from some "*.yaml" file,',
'Please rename "%s" to something else.' % unitcell_filename,
]
if np.linalg.det(unitcell.cell) < 0.0:
err_msg.append("Lattice vectors have to follow the right-hand rule.")
if len(err_msg) > 0:
err_msg = [
'Crystal structure was read from "%s".' % unitcell_filename
] + err_msg
return {"error_message": "\n".join(err_msg)}
if enforce_primitive_matrix_auto:
primitive_matrix_out = "auto"
if _interface_mode == "phonopy_yaml":
phpy_yaml: PhonopyYaml = optional_structure_info[1]
else:
phpy_yaml = None
return {
"unitcell": unitcell,
"supercell_matrix": supercell_matrix_out,
"primitive_matrix": primitive_matrix_out,
"optional_structure_info": optional_structure_info,
"interface_mode": interface_mode_out,
"phonopy_yaml": phpy_yaml,
}
parser.add_argument("--calc",
action="store",
type=str,
dest="calc",
default='vasp',
help="Calculator (vasp,abinit,castep)")
parser.add_argument("--tolerance",
action="store",
type=float,
dest="tol",
default=1e-05,
help="Symmetry tolerance")
args = parser.parse_args()
cell, optional_structure_info = read_crystal_structure(
filename=args.in_fn, interface_mode=args.calc)
print("Cell:")
for v in cell.cell:
print("% 9.7f % 9.7f % 9.7f" % (v[0], v[1], v[2]))
print("Species:")
print(cell.get_chemical_symbols())
print('Atomic positions:')
print(cell.get_scaled_positions())
structure = [cell.cell, cell.get_scaled_positions(), cell.get_atomic_numbers()]
res = seekpath.getpaths.get_path(structure,
with_time_reversal=True,
recipe='hpkot',
