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 _prepare_next(self, cell):
self._stage = 1
self._status = "phonons"
if self._supercell_matrix is None:
self._supercell_matrix = estimate_supercell_matrix(
cell,
max_num_atoms=self._max_num_atoms)
self._qh_tasks += self._get_phonon_tasks(cell)
self._tasks = self._qh_tasks[1:]
def _prepare_mode_gruneisen(self):
self._stage = 2
self._status = "mode_gruneisen"
if self._supercell_matrix is None:
cell = self.get_cell()
self._supercell_matrix = estimate_supercell_matrix(
cell,
max_num_atoms=self._max_num_atoms)
cells = [task.get_cell()
for task in self._all_tasks[1].get_all_tasks()[2:5]]
tasks = self._get_phonon_tasks(cells,
is_cell_relaxed=True,
directory="gruneisen")
self._all_tasks += tasks
self._tasks = tasks
def _prepare_phonons(self):
self._stage = 3
self._status = "phonons"
if self._supercell_matrix is None:
self._supercell_matrix = estimate_supercell_matrix(
cell,
max_num_atoms=self._max_num_atoms)
if self._estimate_strain:
self._strains = self._get_estimated_strains()
cell = self.get_cell()
cells = get_strained_cells(cell, self._strains)
tasks = self._get_phonon_tasks(cells)
self._all_tasks += tasks
self._tasks = tasks
def _set_phonon(self):
cell = self.get_cell()
if self._supercell_matrix is None:
self._supercell_matrix = estimate_supercell_matrix(
cell,
max_num_atoms=self._max_num_atoms)
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)
#!/usr/bin/env python import sys import numpy as np from cogue.interface.vasp_io import read_poscar from cogue.crystal.cell import symbols2formula from cogue.crystal.supercell import estimate_supercell_matrix cell = read_poscar(sys.argv[1]) supercell_matrix = estimate_supercell_matrix(cell, 120)
