def _set_phonon(self):
if self._supercell_matrix is None:
cell = sort_cell_by_symbols(
get_crystallographic_cell(self.get_cell()))
self._supercell_matrix = estimate_supercell_matrix(
cell,
max_num_atoms=self._max_num_atoms)
else:
cell = self.get_cell()
phonopy_cell = cell2atoms(cell)
self._phonon = Phonopy(phonopy_cell,
self._supercell_matrix,
primitive_matrix=self._primitive_matrix,
dynamical_matrix_decimals=14,
force_constants_decimals=14,
symprec=self._symmetry_tolerance)
self._phonon.generate_displacements(
distance=self._distance,
is_plusminus=self._displace_plusminus,
is_diagonal=self._displace_diagonal)
supercell = self._phonon.get_supercell()
displacements = self._phonon.get_displacements()
write_poscar(cell, filename="POSCAR-unitcell")
write_poscar_yaml(cell, filename="POSCAR-unitcell.yaml")
write_disp_yaml(displacements, supercell)
def get_displaced_structures(pmg_structure, atom_disp=0.01,
supercell_matrix=None, yaml_fname=None, **kwargs):
"""
Generate a set of symmetrically inequivalent displaced structures for
phonon calculations.
Args:
pmg_structure (Structure): A pymatgen structure object.
atom_disp (float): Atomic displacement. Default is 0.01 $\\AA$.
supercell_matrix (3x3 array): Scaling matrix for supercell.
yaml_fname (string): If not None, it represents the full path to
the outputting displacement yaml file, e.g. disp.yaml.
**kwargs: Parameters used in Phonopy.generate_displacement method.
Return:
A list of symmetrically inequivalent structures with displacements, in
which the first element is the perfect supercell structure.
"""
is_plusminus = kwargs.get("is_plusminus", "auto")
is_diagonal = kwargs.get("is_diagonal", True)
is_trigonal = kwargs.get("is_trigonal", False)
ph_structure = get_phonopy_structure(pmg_structure)
if supercell_matrix is None:
supercell_matrix = np.eye(3) * np.array((1, 1, 1))
phonon = Phonopy(unitcell=ph_structure, supercell_matrix=supercell_matrix)
phonon.generate_displacements(distance=atom_disp,
is_plusminus=is_plusminus,
is_diagonal=is_diagonal,
is_trigonal=is_trigonal)
if yaml_fname is not None:
displacements = phonon.get_displacements()
directions = phonon.get_displacement_directions()
write_disp_yaml(displacements=displacements,
supercell=phonon.get_supercell(),
directions=directions, filename=yaml_fname)
# Supercell structures with displacement
disp_supercells = phonon.get_supercells_with_displacements()
# Perfect supercell structure
init_supercell = phonon.get_supercell()
# Structure list to be returned
structure_list = [get_pmg_structure(init_supercell)]
for c in disp_supercells:
if c is not None:
structure_list.append(get_pmg_structure(c))
return structure_list
def _set_phonon(self):
cell = self.get_cell()
phonopy_cell = Atoms(cell=cell.get_lattice().T,
scaled_positions=cell.get_points().T,
symbols=cell.get_symbols())
self._phonon = Phonopy(phonopy_cell,
self._supercell_matrix,
is_auto_displacements=False)
self._phonon.generate_displacements(distance=self._distance,
is_diagonal=False)
supercell = self._phonon.get_supercell()
displacements = self._phonon.get_displacements()
write_poscar(cell, "POSCAR-unitcell")
write_disp_yaml(displacements, supercell)
def _set_phonon(self):
cell = self.get_cell()
phonopy_cell = cell2atoms(cell)
self._phonon = Phonopy(phonopy_cell,
self._supercell_matrix,
primitive_matrix=self._primitive_matrix,
is_auto_displacements=False,
dynamical_matrix_decimals=14,
force_constants_decimals=14)
self._phonon.generate_displacements(
distance=self._distance,
is_plusminus=self._displace_plusminus,
is_diagonal=self._displace_diagonal)
supercell = self._phonon.get_supercell()
displacements = self._phonon.get_displacements()
write_poscar(cell, "POSCAR-unitcell")
write_disp_yaml(displacements, supercell)
def _set_phonon(self):
cell = self.get_cell()
phonopy_cell = Atoms(
cell=cell.get_lattice().T,
scaled_positions=cell.get_points().T,
symbols=cell.get_symbols())
self._phonon = Phonopy(phonopy_cell,
self._supercell_matrix,
is_auto_displacements=False)
self._phonon.generate_displacements(distance=self._distance,
is_diagonal=False)
supercell = self._phonon.get_supercell()
displacements = self._phonon.get_displacements()
write_poscar(cell, "POSCAR-unitcell")
write_disp_yaml(displacements, supercell)
def _set_phonon_fc3(self):
cell = self.get_cell()
phonopy_cell = cell2atoms(cell)
self._phonon = Phonopy(phonopy_cell,
self._supercell_matrix,
primitive_matrix=self._primitive_matrix,
dynamical_matrix_decimals=14,
force_constants_decimals=14)
self._phonon_fc3 = Phono3py(phonopy_cell,
self._supercell_matrix,
primitive_matrix=self._primitive_matrix)
self._phonon_fc3.generate_displacements(distance=self._distance,
is_diagonal=self._is_diagonal)
supercell = self._phonon_fc3.get_supercell()
disp_dataset = self._phonon_fc3.get_displacement_dataset()
self._phonon.set_displacement_dataset(disp_dataset)
write_poscar(cell, "POSCAR-unitcell")
write_disp_yaml(self._phonon.get_displacements(),
supercell,
directions=self._phonon.get_displacement_directions())
write_disp_fc3_yaml(disp_dataset, supercell)
def on_all_ok(self):
"""
This method is called once the `Work` is completed i.e. when all the tasks
have reached status S_OK. Here we get the forces from the output files, and
we call phonopy to compute the inter-atomic force constants.
"""
phonon = self.phonon
# Write POSCAR with initial unit cell.
structure = structure_from_atoms(phonon.get_primitive())
structure.to(filename=self.outdir.path_in("POSCAR"))
# Write yaml file with displacements.
supercell = phonon.get_supercell()
displacements = phonon.get_displacements()
#directions = phonon.get_displacement_directions()
file_IO.write_disp_yaml(displacements, supercell, # directions=directions,
filename=self.outdir.path_in('disp.yaml'))
# Extract forces from the main Abinit output files.
forces_filenames = [task.output_file.path for task in self.phonopy_tasks]
num_atoms = supercell.get_number_of_atoms()
force_sets = parse_set_of_forces(num_atoms, forces_filenames)
# Write FORCE_SETS file.
displacements = file_IO.parse_disp_yaml(filename=self.outdir.path_in('disp.yaml'))
num_atoms = displacements['natom']
for forces, disp in zip(force_sets, displacements['first_atoms']):
disp['forces'] = forces
file_IO.write_FORCE_SETS(displacements, filename=self.outdir.path_in('FORCE_SETS'))
# Write README and configuration files.
examples_url = "http://atztogo.github.io/phonopy/examples.html"
doctags_url = "http://atztogo.github.io/phonopy/setting-tags.html#setting-tags"
kptbounds = np.array([k.frac_coords for k in structure.hsym_kpoints])
path_coords = " ".join(str(rc) for rc in kptbounds.flat)
path_labels = " ".join(k.name for k in structure.hsym_kpoints)
ngqpt = structure.calc_ngkpt(nksmall=30)
with open(self.outdir.path_in("band.conf"), "wt") as fh:
fh.write("#" + doctags_url + "\n")
fh.write("DIM = %d %d %d\n" % tuple(self.scdims))
fh.write("BAND = %s\n" % path_coords)
fh.write("BAND_LABELS = %s\n" % path_labels)
fh.write("BAND_POINTS = 101\n")
fh.write("#BAND_CONNECTION = .TRUE.\n")
with open(self.outdir.path_in("dos.conf"), "wt") as fh:
fh.write("#" + doctags_url + "\n")
fh.write("DIM = %d %d %d\n" % tuple(self.scdims))
fh.write("MP = %d %d %d\n" % tuple(ngqpt))
fh.write("#GAMMA_CENTER = .TRUE.\n")
with open(self.outdir.path_in("band-dos.conf"), "wt") as fh:
fh.write("#" + doctags_url + "\n")
fh.write("DIM = %d %d %d\n" % tuple(self.scdims))
fh.write("BAND = %s\n" % path_coords)
fh.write("BAND_LABELS = %s\n" % path_labels)
fh.write("BAND_POINTS = 101\n")
fh.write("#BAND_CONNECTION = .TRUE.\n")
fh.write("MP = %d %d %d\n" % tuple(ngqpt))
fh.write("#GAMMA_CENTER = .TRUE.\n")
with open(self.outdir.path_in("README.md"), "wt") as fh:
fh.write("To plot bands, use:\n\tphonopy -p band.conf\n\n")
fh.write("To plot phonon dos, use:\n\tphonopy -p dos.conf\n\n")
fh.write("To plot bands and dos, use:\n\tphonopy -p band-dos.conf\n\n")
fh.write("See also:\n")
fh.write("\t" + examples_url + "\n")
fh.write("\t" + doctags_url + "\n")
if self.cpdata2dst:
self.outdir.copy_r(self.cpdata2dst)
return super(PhonopyWork, self).on_all_ok()
