def check_symmetry(phonon, optional_structure_info):
# Assumed that primitive cell is the cell that user is interested in.
print(_get_symmetry_yaml(phonon.primitive,
phonon.primitive_symmetry,
phonon.version))
if phonon.unitcell.magnetic_moments is None:
base_fname = get_default_cell_filename(phonon.calculator)
symprec = phonon.primitive_symmetry.get_symmetry_tolerance()
(bravais_lattice,
bravais_pos,
bravais_numbers) = spglib.refine_cell(phonon.primitive, symprec)
bravais = PhonopyAtoms(numbers=bravais_numbers,
scaled_positions=bravais_pos,
cell=bravais_lattice)
filename = 'B' + base_fname
print("# Symmetrized conventional unit cell is written into %s."
% filename)
trans_mat = guess_primitive_matrix(bravais, symprec=symprec)
primitive = get_primitive(bravais, trans_mat, symprec=symprec)
write_crystal_structure(
filename,
bravais,
interface_mode=phonon.calculator,
optional_structure_info=optional_structure_info)
filename = 'P' + base_fname
print("# Symmetrized primitive is written into %s." % filename)
write_crystal_structure(
filename,
primitive,
interface_mode=phonon.calculator,
optional_structure_info=optional_structure_info)
def _get_error_message(optional_structure_info, interface_mode,
fallback_reason, cell_filename, command_name):
final_cell_filename = optional_structure_info[0]
if fallback_reason is None:
msg_list = []
if cell_filename != final_cell_filename:
msg_list.append("Crystal structure file \"%s\" was not found." %
cell_filename)
msg_list.append("Crystal structure file \"%s\" was not found." %
final_cell_filename)
return "\n".join(msg_list)
####################################
# Must be phonopy_yaml mode below. #
####################################
msg_list = []
if fallback_reason in [
"default file not found", "read_vasp parsing failed"
]:
if cell_filename:
vasp_filename = cell_filename
else:
vasp_filename = get_default_cell_filename('vasp')
if fallback_reason == "read_vasp parsing failed":
msg_list.append(
"Parsing crystal structure file of \"%s\" failed." %
vasp_filename)
else:
msg_list.append("Crystal structure file of \"%s\" was not found." %
vasp_filename)
elif fallback_reason == "no supercell matrix given":
msg_list.append("Supercell matrix (DIM or --dim) was not explicitly "
"specified.")
msg_list.append("By this reason, phonopy_yaml mode was invoked.")
if final_cell_filename is None: # No phonopy*.yaml file was found.
msg_list.append(
"But \"%s\" and \"%s\" could not be found." %
("%s_disp.yaml" % command_name, "%s.yaml" % command_name))
return "\n".join(msg_list)
phpy = optional_structure_info[1]
if phpy is None: # Failed to parse phonopy*.yaml.
msg_list.append("But parsing \"%s\" failed." % final_cell_filename)
return "\n".join(msg_list)
def _poscar_failed(cell_filename):
"""Determine if fall back happens
1) read_vasp (parsing POSCAR-style file) is failed. --> fallback
ValueError is raised by read_vasp when the POSCAR-style format
is broken. By this way, we assume the input crystal structure
is not in the POSCAR-style format and is in the phonopy.yaml
type.
2) The file given by get_default_cell_filename('vasp') is not
found at the current directory. --> fallback
This is the trigger to look for the phonopy.yaml type file.
3) The given file with cell_filename is not found. --> not fallback
This case will not invoke phonopy.yaml mode and here nothing
is done, i.e., fallback_reason = None.
This error will be caught in the following part again be
handled properly (read_crystal_structure).
"""
fallback_reason = None
try:
if cell_filename is None:
read_vasp(get_default_cell_filename('vasp'))
else:
read_vasp(cell_filename)
except ValueError:
# (1) see above
fallback_reason = "read_vasp parsing failed"
except FileNotFoundError:
if cell_filename is None:
# (2) see above
fallback_reason = "default file not found"
else:
# (3) see above
pass
return fallback_reason
def _get_error_message(optional_structure_info,
interface_mode,
fallback_reason,
cell_filename,
phonopy_yaml_cls):
final_cell_filename = optional_structure_info[0]
if phonopy_yaml_cls is None:
_phonopy_yaml_cls = PhonopyYaml
else:
_phonopy_yaml_cls = phonopy_yaml_cls
if fallback_reason is None:
msg_list = []
if cell_filename != final_cell_filename:
msg_list.append("Crystal structure file \"%s\" was not found."
% cell_filename)
msg_list.append("Crystal structure file \"%s\" was not found."
% final_cell_filename)
return "\n".join(msg_list)
####################################
# Must be phonopy_yaml mode below. #
####################################
msg_list = []
if fallback_reason in ["default file not found",
"read_vasp parsing failed"]:
if cell_filename:
vasp_filename = cell_filename
else:
vasp_filename = get_default_cell_filename('vasp')
if fallback_reason == "read_vasp parsing failed":
msg_list.append(
"Parsing crystal structure file of \"%s\" failed."
% vasp_filename)
else:
msg_list.append(
"Crystal structure file of \"%s\" was not found."
% vasp_filename)
elif fallback_reason == "no supercell matrix given":
msg_list.append("Supercell matrix (DIM or --dim) was not explicitly "
"specified.")
msg_list.append("By this reason, %s_yaml mode was invoked."
% _phonopy_yaml_cls.command_name)
if final_cell_filename is None: # No phonopy*.yaml file was found.
filenames = ["\"%s\"" % name
for name in _phonopy_yaml_cls.default_filenames]
if len(filenames) == 1:
text = filenames[0]
elif len(filenames) == 2:
text = " and ".join(filenames)
else:
tail = " and ".join(filenames[-2:])
head = ", ".join(filenames[:-2])
text = head + ", " + tail
msg_list.append("But %s could not be found." % text)
return "\n".join(msg_list)
phpy = optional_structure_info[1]
if phpy is None: # Failed to parse phonopy*.yaml.
msg_list.append("But parsing \"%s\" failed." % final_cell_filename)
return "\n".join(msg_list)
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,
}
