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 test_read_poscar_yaml(self):
filename = "POSCAR.yaml"
cell, poscar_order = read_poscar_yaml(filename)
for s, p in zip(cell.get_symbols(), cell.get_points().T):
print s, p
print write_poscar(cell)
print poscar_order
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 next(self):
if self._stage == 0:
task = self._phr_tasks[0]
if self._status == "next":
imag_modes = task.get_imaginary_modes()
self._comment += " --> %s" % task.get_space_group_type()
self._energy = task.get_energy()
if self._energy:
num_atom = len(task.get_cell().get_symbols())
self._comment += "\\n%f/%d" % (self._energy, num_atom)
if imag_modes: # Next phonon-relaxes
self._stage = 1
self._status = "offspring"
self._set_offsprings(imag_modes)
return self._tasks
else: # No imaginary mode
self._status = "done"
self._tasks = []
elif self._status == "terminate":
pass
elif ("confluence" in self._status or
self._status == "low_symmetry" or
self._status == "max_iteration"):
self._comment += " --> %s" % task.get_space_group_type()
self._tasks = []
else:
print("It is something wrong happening in PhononRelaxBase.")
else:
if self._status == "next":
self._log += "# phonon_relax: task ID %d\n" % self._tid
self._log += write_poscar(self._cell)
self._log += "#\n"
self._status = "done"
self._write_yaml()
raise StopIteration
def get_unstable_modulations(phonon,
supercell_dimension,
degeneracy_tolerance=DEGENERACY_TOLERANCE,
symmetry_tolerance=0.1,
max_displacement=0.2,
cutoff_eigenvalue=0.0,
ndiv=180,
excluded_qpoints=[]):
qpoints, weigths, frequencies, eigvecs = phonon.get_mesh()
eigenvalues = frequencies ** 2 * np.sign(frequencies)
imag_modes = []
for i, (q, eigs_at_q) in enumerate(zip(qpoints, eigenvalues)):
qpt_exists = False
for qpt in excluded_qpoints:
if (abs(q - qpt) < 1e-10).all():
qpt_exists = True
break
if qpt_exists:
continue
indices_imaginary = np.where(eigs_at_q < cutoff_eigenvalue)[0]
degeneracy_sets = get_degeneracy_sets(eigs_at_q,
indices_imaginary,
degeneracy_tolerance)
if degeneracy_sets:
phonon.write_animation(q, filename="anime-d%d%d%d-q%d.ascii" %
(tuple(supercell_dimension) + (i + 1,)))
for deg_set in degeneracy_sets:
j = deg_set[0]
eig = eigs_at_q[j]
modulation_dimension = []
for a, multi in zip(q, supercell_dimension):
if abs(a) < CUTOFF_ZERO:
modulation_dimension.append(1)
else:
modulation_dimension.append(multi)
phononMod = PhononModulation(
phonon,
q,
deg_set,
modulation_dimension,
ndiv=ndiv,
symmetry_tolerance=symmetry_tolerance,
max_displacement=max_displacement)
modulation_cells = phononMod.get_modulation_cells()
supercell = phononMod.get_supercell()
write_poscar(supercell,
"SPOSCAR-d%d%d%d" % tuple(modulation_dimension))
write_cif_P1(supercell,
"supercell-d%d%d%d.cif" % tuple(modulation_dimension))
write_v_sim(supercell,
"supercell-d%d%d%d.ascii" % tuple(modulation_dimension))
for k, modcell in enumerate(modulation_cells):
write_poscar(modcell,
"POSCAR-d%d%d%d-q%db%d-%d" %
(tuple(modulation_dimension) + (i + 1, j + 1, k + 1)))
write_cif_P1(modcell,
"mod-d%d%d%d-q%db%d-%d.cif" %
(tuple(modulation_dimension) + (i + 1, j + 1, k + 1)))
write_v_sim(modcell,
"mod-d%d%d%d-q%db%d-%d.ascii" %
(tuple(modulation_dimension) + (i + 1, j + 1, k + 1)))
imag_modes.append(
(modcell, q, np.sqrt(-eig), i, j, k,
len(deg_set), modulation_dimension))
return imag_modes
'icsd_ids': get_icsd_ids,
'e_above_hull': get_e_above_hull,
'pretty_formula': get_pretty_formula,
'created_at': get_created_at,
'is_hubbard': get_is_hubbard,
'nsites': get_nsites,
'elasticity': get_elasticity,
'final_structure': get_final_structure,
'initial_structure': get_initial_structure,
'icsd_id': get_icsd_id,
'spacegroup': get_spacegroup,
'magnetic_type': get_magnetic_type,
'exp_lattice': get_exp_lattice}
functions = {'band_gap': get_band_gap,
'e_above_hull': get_e_above_hull,
'is_hubbard': get_is_hubbard,
'final_structure': get_final_structure,
'initial_structure': get_initial_structure,
'magnetic_type': get_magnetic_type}
mid = sys.argv[2]
for line in open(sys.argv[1]):
words = line.partition(':')
key = words[0].strip()
if key in functions:
if key == 'final_structure':
retval = functions[key](words[2].strip(), show=False)
brv_cell = get_crystallographic_cell(retval, tolerance=1e-1)
write_poscar(brv_cell, filename="BPOSCAR-%s" % mid)
def get_unstable_modulations(phonon,
supercell_dimension,
degeneracy_tolerance=DEGENERACY_TOLERANCE,
symmetry_tolerance=0.1,
max_displacement=0.2,
cutoff_eigenvalue=None,
ndiv=180,
excluded_qpoints=None):
qpoints, weigths, frequencies, eigvecs = phonon.get_mesh()
eigenvalues = frequencies**2 * np.sign(frequencies)
imag_modes = []
for i, (q, eigs_at_q) in enumerate(zip(qpoints, eigenvalues)):
qpt_exists = False
for qpt in excluded_qpoints:
if (abs(q - qpt) < 1e-10).all():
qpt_exists = True
break
if qpt_exists:
continue
indices_imaginary = np.where(eigs_at_q < cutoff_eigenvalue)[0]
degeneracy_sets = get_degeneracy_sets(eigs_at_q, indices_imaginary,
degeneracy_tolerance)
if degeneracy_sets:
phonon.write_animation(q,
filename="anime-d%d%d%d-q%d.ascii" %
(tuple(supercell_dimension) + (i + 1, )))
for deg_set in degeneracy_sets:
j = deg_set[0]
eig = eigs_at_q[j]
modulation_dimension = []
for a, multi in zip(q, supercell_dimension):
if abs(a) < CUTOFF_ZERO:
modulation_dimension.append(1)
else:
modulation_dimension.append(multi)
phononMod = PhononModulation(phonon,
q,
deg_set,
modulation_dimension,
ndiv=ndiv,
symmetry_tolerance=symmetry_tolerance,
max_displacement=max_displacement)
modulation_cells = phononMod.get_modulation_cells()
supercell = phononMod.get_supercell()
write_poscar(supercell,
"SPOSCAR-d%d%d%d" % tuple(modulation_dimension))
write_cif_P1(supercell,
"supercell-d%d%d%d.cif" % tuple(modulation_dimension))
write_v_sim(
supercell,
"supercell-d%d%d%d.ascii" % tuple(modulation_dimension))
for k, modcell in enumerate(modulation_cells):
write_poscar(
modcell, "POSCAR-d%d%d%d-q%db%d-%d" %
(tuple(modulation_dimension) + (i + 1, j + 1, k + 1)))
write_cif_P1(
modcell, "mod-d%d%d%d-q%db%d-%d.cif" %
(tuple(modulation_dimension) + (i + 1, j + 1, k + 1)))
write_v_sim(
modcell, "mod-d%d%d%d-q%db%d-%d.ascii" %
(tuple(modulation_dimension) + (i + 1, j + 1, k + 1)))
imag_modes.append((modcell, q, np.sqrt(-eig), i, j, k,
len(deg_set), modulation_dimension))
return imag_modes