def prepare_extra_files(self, tempfolder, potential_object):
if 'fore_constants' in self.inputs:
force_constants = self.inputs.force_constants
else:
force_constants = None
if 'fore_constants' in self.inputs:
force_sets = self.inputs.force_sets
else:
force_sets = None
cell_txt = get_poscar_txt(self.inputs.structure)
cell_filename = tempfolder(self._POSCAR_NAME)
with open(cell_filename, 'w') as infile:
infile.write(cell_txt)
if force_constants is not None:
force_constants_txt = get_FORCE_CONSTANTS_txt(force_constants)
force_constants_filename = tempfolder.get_abs_path(
self._INPUT_FORCE_CONSTANTS)
with open(force_constants_filename, 'w') as infile:
infile.write(force_constants_txt)
elif force_sets is not None:
force_sets_txt = get_FORCE_SETS_txt(force_sets)
force_sets_filename = tempfolder.get_abs_path(
self._INPUT_FORCE_SETS)
with open(force_sets_filename, 'w') as infile:
infile.write(force_sets_txt)
else:
raise InputValidationError(
"no force_sets nor force_constants are specified for this calculation"
)
try:
parameters_data_dynaphopy = Dict.pop(
self.get_linkname('parameters_dynaphopy'))
except KeyError:
raise InputValidationError(
"No dynaphopy parameters specified for this calculation")
parameters_dynaphopy_txt = generate_dynaphopy_input(
parameters_data_dynaphopy,
poscar_name=self._POSCAR_NAME,
force_constants_name=self._INPUT_FORCE_CONSTANTS,
force_sets_filename=self._INPUT_FORCE_SETS,
use_sets=force_sets is not None)
dynaphopy_filename = tempfolder.get_abs_path(
self._INPUT_FILE_NAME_DYNA)
with open(dynaphopy_filename, 'w') as infile:
infile.write(parameters_dynaphopy_txt)
md_supercell = parameters_data_dynaphopy.dict.md_supercell
time_step = self._parameters_data.dict.timestep
equilibrium_time = self._parameters_data.dict.equilibrium_steps * time_step
total_time = self._parameters_data.dict.total_steps * time_step
self._cmdline_params = [
self._INPUT_FILE_NAME_DYNA,
'--run_lammps',
self._INPUT_FILE_NAME,
'{}'.format(total_time),
'{}'.format(time_step),
'{}'.format(equilibrium_time),
'--dim',
'{}'.format(md_supercell[0]),
'{}'.format(md_supercell[1]),
'{}'.format(md_supercell[2]),
'--silent',
'-sfc',
self._OUTPUT_FORCE_CONSTANTS,
'-thm', # '--resolution 0.01',
'-psm',
'2',
'--normalize_dos',
'-sdata',
'--velocity_only',
'--temperature',
'{}'.format(self._parameters_data.dict.temperature)
]
if 'md_commensurate' in parameters_data_dynaphopy.get_dict():
if parameters_data_dynaphopy.dict.md_commensurate:
self._cmdline_params.append('--MD_commensurate')
def _prepare_for_submission(self, tempfolder, inputdict):
"""
This is the routine to be called when you want to create
the input files and related stuff with a plugin.
:param tempfolder: a aiida.common.folders.Folder subclass where
the plugin should put all its files.
:param inputdict: a dictionary with the input nodes, as they would
be returned by get_inputdata_dict (without the Code!)
"""
try:
parameters_data = inputdict.pop(self.get_linkname('parameters'))
except KeyError:
pass
#raise InputValidationError("No parameters specified for this "
# "calculation")
if not isinstance(parameters_data, ParameterData):
raise InputValidationError("parameters is not of type "
"ParameterData")
try:
structure = inputdict.pop(self.get_linkname('structure'))
except KeyError:
raise InputValidationError(
"no structure is specified for this calculation")
try:
trajectory = inputdict.pop(self.get_linkname('trajectory'))
except KeyError:
raise InputValidationError(
"trajectory is specified for this calculation")
try:
force_constants = inputdict.pop(
self.get_linkname('force_constants'))
except KeyError:
raise InputValidationError(
"no force_constants is specified for this calculation")
try:
code = inputdict.pop(self.get_linkname('code'))
except KeyError:
raise InputValidationError(
"no code is specified for this calculation")
time_step = trajectory.get_times()[1] - trajectory.get_times()[0]
##############################
# END OF INITIAL INPUT CHECK #
##############################
# =================== prepare the python input files =====================
cell_txt = get_poscar_txt(structure)
input_txt = parameters_to_input_file(parameters_data)
force_constants_txt = get_FORCE_CONSTANTS_txt(force_constants)
trajectory_txt = get_trajectory_txt(trajectory)
# =========================== dump to file =============================
input_filename = tempfolder.get_abs_path(self._INPUT_FILE_NAME)
with open(input_filename, 'w') as infile:
infile.write(input_txt)
cell_filename = tempfolder.get_abs_path(self._INPUT_CELL)
with open(cell_filename, 'w') as infile:
infile.write(cell_txt)
force_constants_filename = tempfolder.get_abs_path(
self._INPUT_FORCE_CONSTANTS)
with open(force_constants_filename, 'w') as infile:
infile.write(force_constants_txt)
trajectory_filename = tempfolder.get_abs_path(self._INPUT_TRAJECTORY)
with open(trajectory_filename, 'w') as infile:
infile.write(trajectory_txt)
# ============================ calcinfo ================================
local_copy_list = []
remote_copy_list = []
# additional_retrieve_list = settings_dict.pop("ADDITIONAL_RETRIEVE_LIST",[])
calcinfo = CalcInfo()
calcinfo.uuid = self.uuid
# Empty command line by default
calcinfo.local_copy_list = local_copy_list
calcinfo.remote_copy_list = remote_copy_list
# Retrieve files
calcinfo.retrieve_list = [
self._OUTPUT_FILE_NAME, self._OUTPUT_FORCE_CONSTANTS,
self._OUTPUT_QUASIPARTICLES
]
codeinfo = CodeInfo()
codeinfo.cmdline_params = [
self._INPUT_FILE_NAME,
self._INPUT_TRAJECTORY,
'-ts',
'{}'.format(time_step),
'--silent',
'-sfc',
self._OUTPUT_FORCE_CONSTANTS,
'-thm', # '--resolution 0.01',
'-psm',
'2',
'--normalize_dos',
'-sdata'
]
if 'temperature' in parameters_data.get_dict():
codeinfo.cmdline_params.append('--temperature')
codeinfo.cmdline_params.append('{}'.format(
parameters_data.dict.temperature))
if 'md_commensurate' in parameters_data.get_dict():
if parameters_data.dict.md_commensurate:
codeinfo.cmdline_params.append('--MD_commensurate')
codeinfo.stdout_name = self._OUTPUT_FILE_NAME
codeinfo.code_uuid = code.uuid
codeinfo.withmpi = False
calcinfo.codes_info = [codeinfo]
return calcinfo
def _prepare_for_submission(self, tempfolder, inputdict):
"""
This is the routine to be called when you want to create
the input files and related stuff with a plugin.
:param tempfolder: a aiida.common.folders.Folder subclass where
the plugin should put all its files.
:param inputdict: a dictionary with the input nodes, as they would
be returned by get_inputdata_dict (without the Code!)
"""
try:
parameters_data = inputdict[self.get_linkname('parameters')]
except KeyError:
raise InputValidationError(
"No parameters specified for this calculation")
try:
structure = inputdict[self.get_linkname('structure')]
except KeyError:
raise InputValidationError(
"no structure is specified for this calculation")
try:
code = inputdict.pop(self.get_linkname('code'))
except KeyError:
raise InputValidationError(
"no code is specified for this calculation")
nac_data = inputdict.pop(self.get_linkname('nac_data'), None)
bands = inputdict.pop(self.get_linkname('bands'), None)
##############################
# END OF INITIAL INPUT CHECK #
##############################
# =================== prepare the python input files =====================
self._create_additional_files(tempfolder, inputdict)
cell_txt = get_poscar_txt(structure)
input_txt = get_phonopy_conf_file_txt(parameters_data, bands=bands)
input_filename = tempfolder.get_abs_path(self._INPUT_FILE_NAME)
with open(input_filename, 'w') as infile:
infile.write(input_txt)
cell_filename = tempfolder.get_abs_path(self._INPUT_CELL)
with open(cell_filename, 'w') as infile:
infile.write(cell_txt)
if nac_data is not None:
born_txt = get_BORN_txt(nac_data,
structure=structure,
parameters=parameters_data)
nac_filename = tempfolder.get_abs_path(self._INPUT_NAC)
with open(nac_filename, 'w') as infile:
infile.write(born_txt)
self._additional_cmdline_params += ['--nac']
# ============================ calcinfo ================================
local_copy_list = []
remote_copy_list = []
# additional_retrieve_list = settings_dict.pop("ADDITIONAL_RETRIEVE_LIST",[])
calcinfo = CalcInfo()
calcinfo.uuid = self.uuid
# Empty command line by default
calcinfo.local_copy_list = local_copy_list
calcinfo.remote_copy_list = remote_copy_list
# Retrieve files
calcinfo.retrieve_list = self._internal_retrieve_list
calcinfo.codes_info = []
for property_cmd in self._calculation_cmd:
codeinfo = CodeInfo()
codeinfo.cmdline_params = [
self._INPUT_FILE_NAME
] + self._additional_cmdline_params + property_cmd
codeinfo.code_uuid = code.uuid
codeinfo.withmpi = False
calcinfo.codes_info += [codeinfo]
return calcinfo
def prepare_for_submission(self, folder):
"""Create the input files from the input nodes passed to this instance of the `CalcJob`.
:param folder: an `aiida.common.folders.Folder` to temporarily write files on disk
:return: `aiida.common.datastructures.CalcInfo` instance
"""
self.logger.info("prepare_for_submission")
self._internal_retrieve_list = []
self._additional_cmd_params = []
self._calculation_cmd = []
settings = self.inputs.settings
structure = self.inputs.structure
code = self.inputs.code
##############################
# END OF INITIAL INPUT CHECK #
##############################
# ================= prepare the python input files =================
self._create_additional_files(folder)
cell_txt = get_poscar_txt(structure)
input_txt = get_phonopy_conf_file_txt(settings)
input_filename = folder.get_abs_path(
self.inputs.metadata.options.input_filename)
with open(input_filename, 'w') as infile:
infile.write(input_txt)
cell_filename = folder.get_abs_path(self._INPUT_CELL)
with open(cell_filename, 'w') as infile:
infile.write(cell_txt)
if ('nac_params' in self.inputs and 'primitive' in self.inputs):
born_txt = get_BORN_txt(self.inputs.nac_params,
self.inputs.primitive,
settings['symmetry_tolerance'])
nac_filename = folder.get_abs_path(self._INPUT_NAC)
with open(nac_filename, 'w') as infile:
infile.write(born_txt)
for params in self._additional_cmd_params:
params.append('--nac')
# ============================ calcinfo ===============================
local_copy_list = []
remote_copy_list = []
calcinfo = CalcInfo()
calcinfo.uuid = self.uuid
# Empty command line by default
calcinfo.local_copy_list = local_copy_list
calcinfo.remote_copy_list = remote_copy_list
# Retrieve files
calcinfo.retrieve_list = self._internal_retrieve_list
calcinfo.codes_info = []
for default_params, additional_params in zip(
self._calculation_cmd, self._additional_cmd_params):
codeinfo = CodeInfo()
codeinfo.cmdline_params = ([
self.inputs.metadata.options.input_filename,
] + default_params + additional_params)
codeinfo.code_uuid = code.uuid
codeinfo.stdout_name = self.inputs.metadata.options.output_filename
codeinfo.withmpi = False
calcinfo.codes_info.append(codeinfo)
return calcinfo
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(
):
from phono3py.file_IO import write_fc2_to_hdf5, write_fc3_to_hdf5
print('Writing FC2 and FC3 into HDF5 files')
fc2 = wc.out.force_constants_2order.get_data()