def next(self):
if self._stage == 0:
if "next" in self._status:
self._energy = self._tasks[0].get_energy()
self._comment = "%s\\n%f" % (
self._tasks[0].get_space_group()['international'],
self._energy)
self._set_stage1()
return self._tasks
elif "terminate" in self._status and self._traverse == "restart":
self._traverse = False
self._set_stage0()
return self._tasks
else:
raise StopIteration
elif self._stage == 1:
if "next" in self._status:
disp_dataset = self._phonon_fc3.get_displacement_dataset()
for disp1, task in zip(disp_dataset['first_atoms'], self._tasks):
disp1['forces'] = task.get_properties()['forces'][-1]
write_FORCE_SETS(disp_dataset)
self._phonon.set_displacement_dataset(disp_dataset)
self._phonon.produce_force_constants(
calculate_full_force_constants=False)
if self._exist_imaginary_mode():
self._status = "imaginary_mode"
self._write_yaml()
self._tasks = []
raise StopIteration
else:
self._set_stage2()
return self._tasks
elif "terminate" in self._status and self._traverse == "restart":
self._reset_stage1()
return self._tasks
else:
raise StopIteration
elif self._stage == 2:
if "next" in self._status:
self._status = "done"
forces_fc3 = []
for i, task in enumerate(self._phonon_fc3_tasks[1:]):
forces_fc3.append(task.get_properties()['forces'][-1])
disp_dataset = self._phonon_fc3.get_displacement_dataset()
write_FORCES_FC3(disp_dataset, forces_fc3)
self._tasks = []
raise StopIteration
elif "terminate" in self._status and self._traverse == "restart":
self._reset_stage2()
return self._tasks
else:
raise StopIteration
else: # stage2
pass
def get_forces_txt(force_sets):
w = StringIO.StringIO()
from phono3py.file_IO import write_FORCES_FC3
write_FORCES_FC3(force_sets.get_datasets3(),
force_sets.get_forces3(),
fp=w)
w.seek(0)
lines = w.read()
w.close()
return lines
def create_supercells_with_displacements(phono3py):
phono3py.generate_displacements(distance=0.03)
scells_with_disps = phono3py.get_supercells_with_displacements()
# from phonopy.interface.vasp import write_vasp
# for i, scell in enumerate(scells_with_disps):
# write_vasp("POSCAR-%05d" % (i + 1), scell)
# # print(scell)
# A dataset of displacements. The dictionary format is shown at
# phono3py.phonon3.displacement_fc3.get_third_order_displacements.
print("Displacement sets")
disp_dataset = phono3py.get_displacement_dataset()
count = 0
for i, disp1 in enumerate(disp_dataset['first_atoms']):
print("%4d: %4d %s" % (
count + 1,
disp1['number'] + 1,
np.around(disp1['displacement'], decimals=3)))
count += 1
distances = []
for i, disp1 in enumerate(disp_dataset['first_atoms']):
for j, disp2 in enumerate(disp1['second_atoms']):
print("%4d: %4d-%4d (%6.3f) %s %s" % (
count + 1,
disp1['number'] + 1,
disp2['number'] + 1,
disp2['pair_distance'],
np.around(disp1['displacement'], decimals=3),
np.around(disp2['displacement'], decimals=3)))
distances.append(disp2['pair_distance'])
count += 1
# Find unique pair distances
distances = np.array(distances)
distances_int = (distances * 1e5).astype(int)
unique_distances = np.unique(distances_int) * 1e-5 # up to 5 decimals
print("Unique pair distances")
print(unique_distances)
# FORCES_FC3 is created as follows:
from phono3py.file_IO import write_FORCES_FC3
# force_sets is a simple force array:
# [len(scells_with_disps), num_supercell_atoms, 3].
force_sets = parse_FORCES_FC3(disp_dataset, filename="FORCES_FC3")
write_FORCES_FC3(disp_dataset, force_sets, filename="FORCES_FC3_new")
def create_supercells_with_displacements(phono3py):
phono3py.generate_displacements(distance=0.03)
scells_with_disps = phono3py.get_supercells_with_displacements()
print(len(scells_with_disps))
# from phonopy.interface.vasp import write_vasp
# for i, scell in enumerate(scells_with_disps):
# write_vasp("POSCAR-%05d" % (i + 1), scell)
# # print(scell)
# A dataset of displacements. The dictionary format is shown at
# phono3py.phonon3.displacement_fc3.get_third_order_displacements.
disp_dataset = phono3py.get_displacement_dataset()
# FORCES_FC3 is created as follows:
from phono3py.file_IO import write_FORCES_FC3
# force_sets is a simple force array:
# [len(scells_with_disps), num_supercell_atoms, 3].
force_sets = parse_FORCES_FC3(disp_dataset, filename="FORCES_FC3")
write_FORCES_FC3(disp_dataset, force_sets, filename="FORCES_FC3_new")
def create_FORCES_FC3_and_FORCES_FC2_then_exit(settings, input_filename,
output_filename, log_level):
interface_mode = settings.calculator
#####################
# Create FORCES_FC3 #
#####################
if settings.create_forces_fc3 or settings.create_forces_fc3_file:
if input_filename is None:
disp_fc3_filename = 'disp_fc3.yaml'
else:
disp_fc3_filename = 'disp_fc3.' + input_filename + '.yaml'
ph3py_yaml = None
disp_filenames = files_exist(['phono3py_disp.yaml', disp_fc3_filename],
log_level,
is_any=True)
if disp_filenames[0] == 'phono3py_disp.yaml':
try:
ph3py_yaml = Phono3pyYaml()
ph3py_yaml.read('phono3py_disp.yaml')
if ph3py_yaml.calculator is not None:
interface_mode = ph3py_yaml.calculator # overwrite
disp_filename = 'phono3py_disp.yaml'
except KeyError:
file_exists('disp_fc3.yaml', log_level)
if log_level > 0:
print("\"phono3py_disp.yaml\" was found but wasn't used.")
disp_filename = disp_fc3_filename
else:
disp_filename = disp_filenames[0]
if ph3py_yaml is None:
file_exists(disp_filename, log_level)
disp_dataset = parse_disp_fc3_yaml(filename=disp_filename)
else:
disp_dataset = ph3py_yaml.dataset
if log_level:
print('')
print("Displacement dataset was read from \"%s\"." % disp_filename)
num_atoms = disp_dataset['natom']
num_disps = len(disp_dataset['first_atoms'])
for d1 in disp_dataset['first_atoms']:
for d2 in d1['second_atoms']:
if 'included' not in d2 or d2['included']:
num_disps += 1
if settings.create_forces_fc3_file:
file_exists(settings.create_forces_fc3_file, log_level)
force_filenames = [
x.strip() for x in open(settings.create_forces_fc3_file)
]
else:
force_filenames = settings.create_forces_fc3
for filename in force_filenames:
file_exists(filename, log_level)
if log_level > 0:
print("Number of displacements: %d" % num_disps)
print("Number of supercell files: %d" % len(force_filenames))
if not check_number_of_force_files(num_disps, force_filenames,
disp_filename):
force_sets = []
else:
force_sets = get_force_sets(interface_mode,
num_atoms,
num_disps,
force_filenames,
disp_filename=disp_filename,
verbose=(log_level > 0))
if settings.subtract_forces:
force_filename = settings.subtract_forces
file_exists(force_filename, log_level)
force_set_zero = get_force_sets(interface_mode,
num_atoms,
1, [
force_filename,
],
verbose=(log_level > 0))[0]
for fs in force_sets:
fs -= force_set_zero
if log_level > 0:
print(
"Forces in \'%s\' were subtracted from supercell forces." %
force_filename)
if force_sets:
write_FORCES_FC3(disp_dataset, force_sets, filename="FORCES_FC3")
if log_level:
print("")
print("%s has been created." % "FORCES_FC3")
print_end()
sys.exit(0)
else:
if log_level:
print("")
print("%s could not be created." % "FORCES_FC3")
print_error()
sys.exit(1)
#####################
# Create FORCES_FC2 #
#####################
if settings.create_forces_fc2:
if input_filename is None:
disp_filename = 'disp_fc2.yaml'
else:
disp_filename = 'disp_fc2.' + input_filename + '.yaml'
file_exists(disp_filename, log_level)
disp_dataset = parse_disp_fc2_yaml(filename=disp_filename)
if log_level:
print("Displacement dataset was read from \"%s\"." % disp_filename)
num_atoms = disp_dataset['natom']
num_disps = len(disp_dataset['first_atoms'])
force_filenames = settings.create_forces_fc2
for filename in force_filenames:
file_exists(filename, log_level)
if log_level > 0:
print("Number of displacements: %d" % num_disps)
print("Number of supercell files: %d" % len(force_filenames))
force_sets = get_force_sets(interface_mode,
num_atoms,
num_disps,
force_filenames,
disp_filename,
verbose=(log_level > 0))
if settings.subtract_forces:
force_filename = settings.subtract_forces
file_exists(force_filename, log_level)
force_set_zero = get_force_sets(interface_mode,
num_atoms,
1, [
force_filename,
],
verbose=(log_level > 0))[0]
for fs in force_sets:
fs -= force_set_zero
if log_level > 0:
print(
"Forces in \'%s\' were subtracted from supercell forces." %
force_filename)
if force_sets:
write_FORCES_FC2(disp_dataset,
forces_fc2=force_sets,
filename="FORCES_FC2")
if log_level:
print("")
print("%s has been created." % "FORCES_FC2")
print_end()
sys.exit(0)
else:
if log_level:
print("")
print("%s could not be created." % "FORCES_FC2")
print_error()
sys.exit(1)
# get phono3py data from database
force_sets = wc.out.force_sets
structure = wc.out.final_structure
ph_settings = wc.inp.ph_settings
supercell = get_supercell(phonopy_bulk_from_structure(structure),
ph_settings.dict.supercell,
symprec=ph_settings.dict.symmetry_precision)
write_disp_fc3_yaml(force_sets.get_data_sets3(),
supercell,
filename='disp_fc3.yaml')
write_FORCES_FC3(force_sets.get_data_sets3(),
force_sets.get_forces3(),
filename='FORCES_FC3')
with open('POSCAR-unitcell', mode='w') as f:
f.writelines(get_poscar_txt(structure))
if 'nac_data' in wc.get_outputs_dict():
nac_data = wc.out.nac_data
print('Writing BORN file')
with open('BORN', mode='w') as f:
f.writelines(
get_BORN_txt(nac_data, structure=structure,
parameters=ph_settings))
if 'force_constants_2order' and 'force_constants_3order' in wc.get_outputs_dict(
):
def create_FORCES_FC3_and_FORCES_FC2_then_exit(settings, input_filename,
log_level):
"""Create FORCES_FC3 and FORCES_FC2 from files."""
interface_mode = settings.calculator
ph3py_yaml = None
#####################
# Create FORCES_FC3 #
#####################
if settings.create_forces_fc3 or settings.create_forces_fc3_file:
if input_filename is None:
disp_fc3_filename = "disp_fc3.yaml"
else:
disp_fc3_filename = "disp_fc3." + input_filename + ".yaml"
disp_filenames = files_exist(["phono3py_disp.yaml", disp_fc3_filename],
log_level,
is_any=True)
disp_filename = disp_filenames[0]
if "phono3py_disp.yaml" in disp_filename:
ph3py_yaml = Phono3pyYaml()
ph3py_yaml.read(disp_filename)
if ph3py_yaml.calculator is not None:
interface_mode = ph3py_yaml.calculator # overwrite
disp_dataset = ph3py_yaml.dataset
else:
file_exists(disp_filename, log_level)
disp_dataset = parse_disp_fc3_yaml(filename=disp_filename)
if log_level:
print("")
print('Displacement dataset was read from "%s".' % disp_filename)
num_atoms = disp_dataset["natom"]
num_disps = len(disp_dataset["first_atoms"])
for d1 in disp_dataset["first_atoms"]:
for d2 in d1["second_atoms"]:
if "included" not in d2 or d2["included"]:
num_disps += 1
if settings.create_forces_fc3_file:
file_exists(settings.create_forces_fc3_file, log_level)
force_filenames = [
x.strip() for x in open(settings.create_forces_fc3_file)
]
else:
force_filenames = settings.create_forces_fc3
for filename in force_filenames:
file_exists(filename, log_level)
if log_level > 0:
print("Number of displacements: %d" % num_disps)
print("Number of supercell files: %d" % len(force_filenames))
if not check_number_of_force_files(num_disps, force_filenames,
disp_filename):
force_sets = []
else:
force_sets = get_force_sets(
interface_mode,
num_atoms,
force_filenames,
verbose=(log_level > 0),
)
if settings.subtract_forces:
force_filename = settings.subtract_forces
file_exists(force_filename, log_level)
force_set_zero = get_force_sets(
interface_mode,
num_atoms,
[
force_filename,
],
verbose=(log_level > 0),
)[0]
for fs in force_sets:
fs -= force_set_zero
if log_level > 0:
print("Forces in '%s' were subtracted from supercell forces." %
force_filename)
if force_sets:
write_FORCES_FC3(disp_dataset,
forces_fc3=force_sets,
filename="FORCES_FC3")
if log_level:
print("")
print("%s has been created." % "FORCES_FC3")
print_end()
sys.exit(0)
else:
if log_level:
print("")
print("%s could not be created." % "FORCES_FC3")
print_error()
sys.exit(1)
#####################
# Create FORCES_FC2 #
#####################
if settings.create_forces_fc2:
if input_filename is None:
disp_fc2_filename = "disp_fc2.yaml"
else:
disp_fc2_filename = "disp_fc2." + input_filename + ".yaml"
disp_filenames = files_exist(["phono3py_disp.yaml", disp_fc2_filename],
log_level,
is_any=True)
if "phono3py_disp.yaml" in disp_filenames[0]:
# ph3py_yaml is not None, phono3py_disp.yaml is already read.
if ph3py_yaml is None:
disp_filename = disp_filenames[0]
ph3py_yaml = Phono3pyYaml()
ph3py_yaml.read(disp_filename)
if ph3py_yaml.calculator is not None:
interface_mode = ph3py_yaml.calculator # overwrite
disp_dataset = ph3py_yaml.phonon_dataset
else:
disp_filename = disp_filenames[0]
file_exists(disp_filename, log_level)
disp_dataset = parse_disp_fc2_yaml(filename=disp_filename)
if log_level:
print('Displacement dataset was read from "%s".' % disp_filename)
num_atoms = disp_dataset["natom"]
num_disps = len(disp_dataset["first_atoms"])
force_filenames = settings.create_forces_fc2
for filename in force_filenames:
file_exists(filename, log_level)
if log_level > 0:
print("Number of displacements: %d" % num_disps)
print("Number of supercell files: %d" % len(force_filenames))
force_sets = get_force_sets(
interface_mode,
num_atoms,
force_filenames,
verbose=(log_level > 0),
)
if settings.subtract_forces:
force_filename = settings.subtract_forces
file_exists(force_filename, log_level)
force_set_zero = get_force_sets(
interface_mode,
num_atoms,
[
force_filename,
],
verbose=(log_level > 0),
)[0]
for fs in force_sets:
fs -= force_set_zero
if log_level > 0:
print("Forces in '%s' were subtracted from supercell forces." %
force_filename)
if force_sets:
write_FORCES_FC2(disp_dataset,
forces_fc2=force_sets,
filename="FORCES_FC2")
if log_level:
print("")
print("%s has been created." % "FORCES_FC2")
print_end()
sys.exit(0)
else:
if log_level:
print("")
print("%s could not be created." % "FORCES_FC2")
print_error()
sys.exit(1)