def prepare_for_submission(self, folder):
"""
Create input files.
:param folder: an `aiida.common.folders.Folder` where the plugin should temporarily place all files needed by
the calculation.
:return: `aiida.common.datastructures.CalcInfo` instance
"""
codeinfo = datastructures.CodeInfo()
codeinfo.cmdline_params = [self.inputs.script.filename]
codeinfo.code_uuid = self.inputs.code.uuid
#codeinfo.stdout_name = self.metadata.options.output_filename
codeinfo.withmpi = self.inputs.metadata.options.withmpi
# Prepare a `CalcInfo` to be returned to the engine
calcinfo = datastructures.CalcInfo()
calcinfo.codes_info = [codeinfo]
local_copy_list = [ (self.inputs.script.uuid, self.inputs.script.filename, self.inputs.script.filename) ]
# this is minimalistic - one could add things here like:
# * if something is passed to the top-level "structure" input, write the file out in a given format
# * if type of file is X, pre-process using procedure Y
# * ...
if 'files' in self.inputs:
for f in self.inputs.files:
node = self.inputs.files[f]
local_copy_list.append( (node.uuid, node.filename, node.filename) )
calcinfo.local_copy_list = local_copy_list
calcinfo.retrieve_list = ['*']
return calcinfo
def prepare_for_submission(self, folder):
"""
Create input files.
:param folder: an `aiida.common.folders.Folder` where the plugin should temporarily place all files needed by
the calculation.
:return: `aiida.common.datastructures.CalcInfo` instance
"""
codeinfo = datastructures.CodeInfo()
codeinfo.code_uuid = self.inputs.code.uuid
if not self.inputs.code.can_run_on(
self.inputs.bigdft_data_folder.computer):
self.report("This post-processing script {}\
can't run on {} where data resides" ,
format(self.inputs.code, self.inputs.bigdft_data_folder.get_computer_name()))
return self.exit_codes.ERROR_SCRIPT
codeinfo.withmpi = False
codeinfo.cmdline_params = [self.inputs.bigdft_data_folder.get_remote_path()]
# Prepare a `CalcInfo` to be returned to the engine
calcinfo = datastructures.CalcInfo()
calcinfo.codes_info = [codeinfo]
calcinfo.local_copy_list = []
calcinfo.retrieve_list = []
calcinfo.retrieve_list.extend(self.inputs.retrieved_files)
return calcinfo
def prepare_for_submission(self, folder):
"""
Create input files.
:param folder: an `aiida.common.folders.Folder` where the plugin should temporarily place all files needed by
the calculation.
:return: `aiida.common.datastructures.CalcInfo` instance
"""
codeinfo = datastructures.CodeInfo()
codeinfo.cmdline_params = self.inputs.parameters.cmdline_params(
file1_name=self.inputs.file1.filename,
file2_name=self.inputs.file2.filename)
codeinfo.code_uuid = self.inputs.code.uuid
codeinfo.stdout_name = self.metadata.options.output_filename
codeinfo.withmpi = self.inputs.metadata.options.withmpi
# Prepare a `CalcInfo` to be returned to the engine
calcinfo = datastructures.CalcInfo()
calcinfo.codes_info = [codeinfo]
calcinfo.local_copy_list = [
(self.inputs.file1.uuid, self.inputs.file1.filename, self.inputs.file1.filename),
(self.inputs.file2.uuid, self.inputs.file2.filename, self.inputs.file2.filename),
]
calcinfo.retrieve_list = [self.metadata.options.output_filename]
return calcinfo
def prepare_for_submission(self, folder):
"""
Create input files.
:param folder: an `aiida.common.folders.Folder` where the plugin should temporarily place all files needed by
the calculation.
:return: `aiida.common.datastructures.CalcInfo` instance
"""
codeinfo = datastructures.CodeInfo()
codeinfo.code_uuid = self.inputs.code.uuid
codeinfo.withmpi = self.inputs.metadata.options.withmpi
codeinfo.cmdline_params = ['PreModRun.txt']
# Prepare a `CalcInfo` to be returned to the engine
calcinfo = datastructures.CalcInfo()
calcinfo.codes_info = [codeinfo]
calcinfo.local_copy_list = [
(self.inputs.alloy.uuid, self.inputs.alloy.filename, self.inputs.alloy.filename),
(self.inputs.solver.uuid, self.inputs.solver.filename, self.inputs.solver.filename),
(self.inputs.temperature.uuid, self.inputs.temperature.filename, self.inputs.temperature.filename),
(self.inputs.models.uuid, self.inputs.models.filename, self.inputs.models.filename),
(self.inputs.libphases.uuid, self.inputs.libphases.filename, self.inputs.libphases.filename),
(self.inputs.libmodel.uuid, self.inputs.libmodel.filename, self.inputs.libmodel.filename),
]
calcinfo.retrieve_list = ['PreModRun','PreModRun.log']
# write input file
parameter_parser = ParameterParser(data=self.inputs.parameters)
parameter_parser.write(folder.get_abs_path('PreModRun.txt'))
return calcinfo
def prepare_for_submission(self, folder):
"""
Create input files.
:param folder: an `aiida.common.folders.Folder` where the plugin should temporarily place all files needed by
the calculation.
:return: `aiida.common.datastructures.CalcInfo` instance
"""
codeinfo = datastructures.CodeInfo()
codeinfo.code_uuid = self.inputs.code.uuid
codeinfo.stdout_name = self.metadata.options.output_filename
codeinfo.withmpi = self.inputs.metadata.options.withmpi
# Prepare a `CalcInfo` to be returned to the engine
calcinfo = datastructures.CalcInfo()
calcinfo.codes_info = [codeinfo]
local_copy_list = []
retrieve_list = []
# Define which datafiles to analyze
for item in self.inputs.datafiles.values():
local_copy_list.append((item.uuid, item.filename, item.filename))
retrieve_list.append(item.filename)
calcinfo.local_copy_list = local_copy_list
calcinfo.retrieve_list = retrieve_list
return calcinfo
def prepare_for_submission(self, folder):
"""
Create input files.
sirius.json,
input.yml
:param folder: an `aiida.common.folders.Folder` where the plugin should temporarily place all files needed by
the calculation.
:return: `aiida.common.datastructures.CalcInfo` instance
"""
codeinfo = datastructures.CodeInfo()
output_filename = self.metadata.options.output_filename
codeinfo.cmdline_params = ['--input=input.yml']
codeinfo.code_uuid = self.inputs.code.uuid
codeinfo.stdout_name = self.metadata.options.output_filename
codeinfo.withmpi = self.inputs.metadata.options.withmpi
# with config from input
structure = self.inputs.structure
kpoints = self.inputs.kpoints
magnetization = self.inputs.magnetization
# sirius_json = make_sirius_json(self.inputs.sirius_config.get_dict()['parameters'],
sirius_json = self.inputs.sirius_config.get_dict()
with tempfile.NamedTemporaryFile(mode='w',
suffix='.json',
delete=False) as sirius_tmpfile:
# insert Pseudopotentials directly into json
sirius_json = self._read_pseudos(sirius_json)
# dump to file
json.dump(sirius_json, sirius_tmpfile)
sirius_config = SinglefileData(file=sirius_tmpfile.name)
sirius_config.store()
# prepare YAML input for NLCG
with tempfile.NamedTemporaryFile(mode='w', suffix='.yml',
delete=False) as sirius_md_yaml:
out = yaml.dump(
{'parameters': self.inputs.sirius_md_params.get_dict()})
md_tmpfile_name = sirius_md_yaml.name
sirius_md_yaml.write(out)
sirius_md_config = SinglefileData(file=md_tmpfile_name)
sirius_md_config.store()
# Prepare a `CalcInfo` to be returned to the engine
calcinfo = datastructures.CalcInfo()
calcinfo.codes_info = [codeinfo]
calcinfo.local_copy_list = [
(sirius_config.uuid, sirius_config.filename, 'sirius.json'),
(sirius_md_config.uuid, sirius_md_config.filename, 'input.yml')
]
calcinfo.retrieve_list = [
self.metadata.options.output_filename, 'md_results.json'
]
return calcinfo
def prepare_for_submission(self, folder):
codeinfo = datastructures.CodeInfo()
codeinfo.code_uuid = self.inputs.code.uuid
codeinfo.withmpi = self.inputs.metadata.options.withmpi
if self.inputs.metadata.options.command_line != '':
codeinfo.cmdline_params = \
self.inputs.metadata.options.command_line.split()
# Prepare a `CalcInfo` to be returned to the engine
calcinfo = datastructures.CalcInfo()
calcinfo.codes_info = [codeinfo]
calcinfo.local_copy_list = \
self.inputs.metadata.options.local_copy_list.get_list()
calcinfo.retrieve_list = \
self.inputs.metadata.options.retrieve_list.get_list()
return calcinfo
def prepare_for_submission(self, folder: folders.Folder):
"""Create 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._validate_inputs()
dos_filenames = OpenmxCalculation.dos_filenames
remote_symlink_list = [
(self.inputs.openmx_output_folder.computer.uuid,
os.path.join(self.inputs.openmx_output_folder.get_remote_path(),
dos_filenames['val']),
os.path.join(self._DATA_PATH, dos_filenames['val'])),
(self.inputs.openmx_output_folder.computer.uuid,
os.path.join(self.inputs.openmx_output_folder.get_remote_path(),
dos_filenames['vec']),
os.path.join(self._DATA_PATH, dos_filenames['vec'])),
]
retrieve_list = self._generate_retrieve_list()
input_file_content = self._write_input_file()
with folder.open(self._INPUT_FILE, 'w') as handle:
handle.write(input_file_content)
# Fill out the `CodeInfo`
codeinfo = datastructures.CodeInfo()
codeinfo.cmdline_params = ([
dos_filenames['val'], dos_filenames['vec']
])
codeinfo.stdin_name = self._INPUT_FILE
codeinfo.stdout_name = self._OUTPUT_FILE
codeinfo.code_uuid = self.inputs.code.uuid
codeinfo.with_mpi = True
# Fill out the `CalcInfo`
calcinfo = datastructures.CalcInfo()
calcinfo.uuid = str(self.uuid)
calcinfo.codes_info = [codeinfo]
calcinfo.remote_symlink_list = remote_symlink_list
calcinfo.retrieve_list = retrieve_list
calcinfo.retrieve_list.append(self._OUTPUT_FILE)
return calcinfo
def prepare_for_submission(self, folder):
"""This method is called prior to job submission with a set of calculation input nodes.
The inputs will be validated and sanitized, after which the necessary input files will be written to disk in a
temporary folder. A CalcInfo instance will be returned that contains lists of files that need to be copied to
the remote machine before job submission, as well as file lists that are to be retrieved after job completion.
:param folder: an aiida.common.folders.Folder to temporarily write files on disk
:returns: CalcInfo instance
"""
from aiida_codtools.cli.utils.parameters import CliParameters
try:
parameters = self.inputs.parameters.get_dict()
except AttributeError:
parameters = {}
# The input file should simply contain the relative filename that contains the CIF to be deposited
with folder.open(self.options.input_filename, 'w') as handle:
handle.write(u'{}\n'.format(self.filename_cif))
# Write parameters that relate to the config file to that file and remove them from the CLI parameters
with folder.open(self.filename_config, 'w') as handle:
for key in self._config_keys:
if key in parameters:
handle.write(u'{}={}\n'.format(key, parameters.pop(key)))
cli_parameters = copy.deepcopy(self._default_cli_parameters)
cli_parameters.update(parameters)
codeinfo = datastructures.CodeInfo()
codeinfo.code_uuid = self.inputs.code.uuid
codeinfo.cmdline_params = CliParameters.from_dictionary(cli_parameters).get_list()
codeinfo.stdin_name = self.options.input_filename
codeinfo.stdout_name = self.options.output_filename
codeinfo.stderr_name = self.options.error_filename
calcinfo = datastructures.CalcInfo()
calcinfo.uuid = str(self.uuid)
calcinfo.codes_info = [codeinfo]
calcinfo.retrieve_list = [self.options.output_filename, self.options.error_filename]
calcinfo.local_copy_list = [(self.inputs.cif.uuid, self.inputs.cif.filename, self.filename_cif)]
calcinfo.remote_copy_list = []
return calcinfo
def prepare_for_submission(self, folder):
"""
"""
self.write_input_files(folder)
# Code
codeinfo = datastructures.CodeInfo()
codeinfo.cmdline_params = [self.options.input_filename]
codeinfo.code_uuid = self.inputs.code.uuid
codeinfo.stdout_name = self.metadata.options.output_filename
# Prepare a `CalaInfo` to be returned to the engine
calcinfo = datastructures.CalcInfo()
calcinfo.codes_info = [codeinfo]
retrieve_list = ['sqs.out']
calcinfo.retrieve_list = retrieve_list + [self.metadata.options.output_filename]
return calcinfo
def prepare_for_submission(self, folder):
"""
Create input files.
:param folder: an `aiida.common.folders.Folder` where the plugin should temporarily place all files needed by
the calculation.
:return: `aiida.common.datastructures.CalcInfo` instance
"""
# Add the used defined input parameters to the input file
inp = self.inputs.parameters.get_dict()
# Add the structure related variables to the dictionary
if 'structure' in self.inputs:
inp.update(structure_to_abivars(self.inputs.structure.get_pymatgen()))
lines = []
for inp_var, value in inp.items():
lines.append(str(InputVariable(inp_var, value)))
with io.open(folder.get_abs_path(self._DEFAULT_INPUT_FILE), mode="w", encoding="utf-8") as fobj:
fobj.writelines(lines)
# Create code info
codeinfo = datastructures.CodeInfo()
codeinfo.code_uuid = self.inputs.code.uuid
# codeinfo.stdin_name = self.options.input_filename
# This gives the path to the input file to Abinit rather than passing the input from standard input
#codeinfo.cmdline_params = ['<', self.options.input_filename]
codeinfo.cmdline_params = [self.options.input_filename]
codeinfo.stdout_name = self.metadata.options.output_filename
codeinfo.withmpi = self.inputs.metadata.options.withmpi
# Prepare a `CalcInfo` to be returned to the engine
calcinfo = datastructures.CalcInfo()
calcinfo.codes_info = [codeinfo]
calcinfo.stdin_name = self.options.input_filename
calcinfo.stdout_name = self.options.output_filename
calcinfo.retrieve_list = [self.metadata.options.output_filename]
calcinfo.retrieve_list = [self._DEFAULT_OUTPUT_FILE, self._DEFAULT_GSR_FILE_NAME]
#calcinfo.retrieve_list += settings.pop('additional_retrieve_list', [])
return calcinfo
def prepare_for_submission(self, folder):
"""
Create input files.
:param folder: an `aiida.common.folders.Folder` where the plugin should temporarily place all files needed by
the calculation.
:return: `aiida.common.datastructures.CalcInfo` instance
"""
codeinfo = datastructures.CodeInfo()
output_filename = self.metadata.options.output_filename
codeinfo.code_uuid = self.inputs.code.uuid
codeinfo.stdout_name = self.metadata.options.output_filename
codeinfo.withmpi = self.inputs.metadata.options.withmpi
# with config from input
structure = self.inputs.structure
kpoints = self.inputs.kpoints
magnetization = self.inputs.magnetization
sirius_json = self.inputs.sirius_config.get_dict()
sirius_json = add_cell_kpoints_mag_to_sirius(sirius_json, structure,
magnetization, kpoints)
# TODO check schema
Schema(sirius_options)(sirius_json)
with tempfile.NamedTemporaryFile(mode='w', suffix='.json', delete=False) as sirius_tmpfile:
# insert Pseudopotentials directly into json
sirius_json = self._read_pseudos(sirius_json)
# dump to file
json.dump(sirius_json, sirius_tmpfile)
sirius_config = SinglefileData(file=sirius_tmpfile.name)
sirius_config.store()
# Prepare a `CalcInfo` to be returned to the engine
calcinfo = datastructures.CalcInfo()
calcinfo.codes_info = [codeinfo]
calcinfo.local_copy_list = [
(sirius_config.uuid, sirius_config.filename, 'sirius.json')
]
calcinfo.retrieve_list = [self.metadata.options.output_filename, 'nlcg.out']
return calcinfo
def prepare_for_submission(self, folder):
"""
Create input files.
sirius.json,
nlcg.yaml
:param folder: an `aiida.common.folders.Folder` where the plugin should temporarily place all files needed by
the calculation.
:return: `aiida.common.datastructures.CalcInfo` instance
"""
codeinfo = datastructures.CodeInfo()
output_filename = self.metadata.options.output_filename
codeinfo.cmdline_params = ['--output=output.json']
codeinfo.code_uuid = self.inputs.code.uuid
codeinfo.stdout_name = self.metadata.options.output_filename
codeinfo.withmpi = self.inputs.metadata.options.withmpi
# with config from input
structure = self.inputs.structure
kpoints = self.inputs.kpoints
magnetization = self.inputs.magnetization
sirius_json = make_sirius_json(self.inputs.sirius_config.get_dict()['parameters'],
structure, kpoints, magnetization)
with tempfile.NamedTemporaryFile(mode='w', suffix='.json', delete=False) as sirius_tmpfile:
sirius_json = self._read_pseudos(sirius_json)
sirius_tmpfile_name = sirius_tmpfile.name
# merge with settings given from outside
sirius_json = {**sirius_json, **self.inputs.sirius_config.get_dict()}
# dump to file
json.dump(sirius_json, sirius_tmpfile)
sirius_config = SinglefileData(file=sirius_tmpfile_name)
sirius_config.store()
# Prepare a `CalcInfo` to be returned to the engine
calcinfo = datastructures.CalcInfo()
calcinfo.codes_info = [codeinfo]
calcinfo.local_copy_list = [
(sirius_config.uuid, sirius_config.filename, 'sirius.json')
]
calcinfo.retrieve_list = [self.metadata.options.output_filename, 'output.json']
return calcinfo
def prepare_for_submission(self, folder):
"""This method is called prior to job submission with a set of calculation input nodes.
The inputs will be validated and sanitized, after which the necessary input files will be written to disk in a
temporary folder. A CalcInfo instance will be returned that contains lists of files that need to be copied to
the remote machine before job submission, as well as file lists that are to be retrieved after job completion.
:param folder: an aiida.common.folders.Folder to temporarily write files on disk
:returns: CalcInfo instance
"""
from aiida_codtools.cli.utils.parameters import CliParameters
try:
parameters = self.inputs.parameters.get_dict()
except AttributeError:
parameters = {}
self._validate_resources()
cli_parameters = copy.deepcopy(self._default_cli_parameters)
cli_parameters.update(parameters)
codeinfo = datastructures.CodeInfo()
codeinfo.code_uuid = self.inputs.code.uuid
codeinfo.cmdline_params = CliParameters.from_dictionary(cli_parameters).get_list()
codeinfo.stdin_name = self.options.input_filename
codeinfo.stdout_name = self.options.output_filename
codeinfo.stderr_name = self.options.error_filename
calcinfo = datastructures.CalcInfo()
calcinfo.uuid = str(self.uuid)
calcinfo.codes_info = [codeinfo]
calcinfo.retrieve_list = [self.options.output_filename, self.options.error_filename]
calcinfo.local_copy_list = [(self.inputs.cif.uuid, self.inputs.cif.filename, self.options.input_filename)]
calcinfo.remote_copy_list = []
return calcinfo
def prepare_for_submission(self, folder):
"""
Create input files.
:param folder: an `aiida.common.folders.Folder` where the plugin should temporarily place all files needed by
the calculation.
:return: `aiida.common.datastructures.CalcInfo` instance
"""
# set up the mkm file
with folder.open(self.inputs.mkm_filename.value, 'w', encoding='utf8') as handle:
## Writing the reaction conditions
handle.write(f"scaler = '{self.inputs.scaler.value}' \n")
handle.write(f'rxn_expressions = {self.inputs.rxn_expressions.get_list()} \n')
handle.write(f'surface_names = {self.inputs.surface_names.get_list()} \n')
handle.write(f'descriptor_names = {self.inputs.descriptor_names.get_list()} \n')
handle.write(f'descriptor_ranges = {self.inputs.descriptor_ranges.get_list()} \n')
handle.write(f'resolution = {self.inputs.resolution.value} \n')
handle.write(f'temperature = {self.inputs.temperature.value} \n')
handle.write(f'species_definitions = {self.inputs.species_definitions.get_dict()} \n')
handle.write(f"data_file = '{self.inputs.data_file.value}' \n")
handle.write(f"input_file = '{self.inputs.energies.filename}' \n")
handle.write(f"gas_thermo_mode = '{self.inputs.gas_thermo_mode.value}' \n")
handle.write(f"adsorbate_thermo_mode = '{self.inputs.adsorbate_thermo_mode.value}' \n")
# handle.write('ideal_gas_params = {d} \n'.format(d=self.inputs.ideal_gas_params.get_dict()))
handle.write(f'scaling_constraint_dict = {self.inputs.scaling_constraint_dict.get_dict()} \n')
## Only related to electrochemistry
if self.inputs.electrocatal.value == True: #pylint: disable=singleton-comparison
if self.inputs.scaler.value == 'GeneralizedLinearScaler': #pylint: disable=singleton-comparison
handle.write(f'voltage = {self.inputs.voltage.value} \n')
handle.write(f'pH = {self.inputs.pH.value} \n')
elif self.inputs.scaler.value != 'GeneralizedLinearScaler':
handle.write(f"potential_reference_scale = '{self.inputs.potential_reference_scale.value}' \n")
handle.write(f'extrapolated_potential = {self.inputs.extrapolated_potential.value} \n')
handle.write(f'voltage_diff_drop = {self.inputs.voltage_diff_drop.value} \n')
handle.write(f'sigma_input = {self.inputs.sigma_input.get_list()} \n')
handle.write(f'Upzc = {self.inputs.Upzc.value} \n')
handle.write(f'beta = {self.inputs.beta.value} \n')
for val in self.inputs.electrochemical_thermo_mode.get_list():
handle.write(f"electrochemical_thermo_mode = '{val}' \n")
## Write numerical data last
handle.write(f'decimal_precision = {self.inputs.decimal_precision.value} \n')
handle.write(f'tolerance = {self.inputs.tolerance.value} \n')
handle.write(f'max_rootfinding_iterations = {self.inputs.max_rootfinding_iterations.value} \n')
handle.write(f'max_bisections = {self.inputs.max_bisections.value} \n')
handle.write(f"numerical_solver = '{self.inputs.numerical_solver.value}' \n")
# write the simplest run command
with folder.open(self.options.input_filename, 'w', encoding='utf8') as handle:
handle.write('from catmap import ReactionModel \n')
handle.write(f"mkm_file = '{self.inputs.mkm_filename.value}' \n")
handle.write('model = ReactionModel(setup_file=mkm_file) \n')
handle.write("model.output_variables += ['production_rate'] \n")
handle.write('model.run() \n')
codeinfo = datastructures.CodeInfo()
codeinfo.code_uuid = self.inputs.code.uuid
codeinfo.stdout_name = self.options.output_filename
codeinfo.stdin_name = self.options.input_filename
codeinfo.withmpi = self.inputs.metadata.options.withmpi
# Prepare a `CalcInfo` to be returned to the engine
calcinfo = datastructures.CalcInfo()
calcinfo.codes_info = [codeinfo]
calcinfo.local_copy_list = [
(self.inputs.energies.uuid, self.inputs.energies.filename, self.inputs.energies.filename),
]
calcinfo.retrieve_list = [self.metadata.options.output_filename, self.inputs.data_file.value]
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
"""
if 'settings' in self.inputs:
settings = _uppercase_dict(self.inputs.settings.get_dict(), dict_name='settings')
else:
settings = {}
# Check that a pseudo potential was specified for each kind present in the `StructureData`
kinds = [kind.name for kind in self.inputs.structure.kinds]
if set(kinds) != set(self.inputs.pseudos.keys()):
raise exceptions.InputValidationError(
'Mismatch between the defined pseudos and the list of kinds of the structure.\n'
'Pseudos: {};\nKinds: {}'.format(', '.join(list(self.inputs.pseudos.keys())), ', '.join(list(kinds))))
local_copy_list = []
remote_copy_list = []
remote_symlink_list = []
# Create the subfolder that will contain the pseudopotentials
folder.get_subfolder(self._PSEUDO_SUBFOLDER, create=True)
# Create the subfolder for the output data (sometimes Quantum ESPRESSO codes crash if the folder does not exist)
folder.get_subfolder(self._OUTPUT_SUBFOLDER, create=True)
# If present, add also the Van der Waals table to the pseudo dir. Note that the name of the table is not checked
# but should be the one expected by Quantum ESPRESSO.
if 'vdw_table' in self.inputs:
uuid = self.inputs.vdw_table.uuid
src_path = self.inputs.vdw_table.filename
dst_path = os.path.join(self._PSEUDO_SUBFOLDER, self.inputs.vdw_table.filename)
local_copy_list.append((uuid, src_path, dst_path))
if 'hubbard_file' in self.inputs:
uuid = self.inputs.hubbard_file.filename
src_path = self.inputs.hubbard_file.filename
dst_path = self.input_file_name_hubbard_file
local_copy_list.append((uuid, src_path, dst_path))
arguments = [
self.inputs.parameters,
settings,
self.inputs.pseudos,
self.inputs.structure,
]
if self._use_kpoints:
arguments.append(self.inputs.kpoints)
input_filecontent, local_copy_pseudo_list = self._generate_PWCPinputdata(*arguments)
local_copy_list += local_copy_pseudo_list
with folder.open(self.metadata.options.input_filename, 'w') as handle:
handle.write(input_filecontent)
# operations for restart
symlink = settings.pop('PARENT_FOLDER_SYMLINK', self._default_symlink_usage) # a boolean
if symlink:
if 'parent_folder' in self.inputs:
# I put the symlink to the old parent ./out folder
remote_symlink_list.append((
self.inputs.parent_folder.computer.uuid,
os.path.join(self.inputs.parent_folder.get_remote_path(), self._restart_copy_from),
self._restart_copy_to
))
else:
# copy remote output dir, if specified
if 'parent_folder' in self.inputs:
remote_copy_list.append((
self.inputs.parent_folder.computer.uuid,
os.path.join(self.inputs.parent_folder.get_remote_path(), self._restart_copy_from),
self._restart_copy_to
))
# Create an `.EXIT` file if `only_initialization` flag in `settings` is set to `True`
if settings.pop('ONLY_INITIALIZATION', False):
with folder.open('{}.EXIT'.format(self._PREFIX), 'w') as handle:
handle.write('\n')
# Check if specific inputs for the ENVIRON module where specified
environ_namelist = settings.pop('ENVIRON', None)
if environ_namelist is not None:
if not isinstance(environ_namelist, dict):
raise exceptions.InputValidationError('ENVIRON namelist should be specified as a dictionary')
# We first add the environ flag to the command-line options (if not already present)
try:
if '-environ' not in settings['CMDLINE']:
settings['CMDLINE'].append('-environ')
except KeyError:
settings['CMDLINE'] = ['-environ']
# To create a mapping from the species to an incremental fortran 1-based index
# we use the alphabetical order as in the inputdata generation
kind_names = sorted([kind.name for kind in self.inputs.structure.kinds])
mapping_species = {kind_name: (index + 1) for index, kind_name in enumerate(kind_names)}
with folder.open(self._ENVIRON_INPUT_FILE_NAME, 'w') as handle:
handle.write('&ENVIRON\n')
for k, v in sorted(six.iteritems(environ_namelist)):
handle.write(convert_input_to_namelist_entry(k, v, mapping=mapping_species))
handle.write('/\n')
# Check for the deprecated 'ALSO_BANDS' setting and if present fire a deprecation log message
also_bands = settings.pop('ALSO_BANDS', None)
if also_bands:
self.node.logger.warning(
"The '{}' setting is deprecated as bands are now parsed by default. "
"If you do not want the bands to be parsed set the '{}' to True {}. "
'Note that the eigenvalue.xml files are also no longer stored in the repository'
.format('also_bands', 'no_bands', type(self))
)
calcinfo = datastructures.CalcInfo()
calcinfo.uuid = str(self.uuid)
# Empty command line by default
cmdline_params = settings.pop('CMDLINE', [])
# we commented calcinfo.stin_name and added it here in cmdline_params
# in this way the mpirun ... pw.x ... < aiida.in
# is replaced by mpirun ... pw.x ... -in aiida.in
# in the scheduler, _get_run_line, if cmdline_params is empty, it
# simply uses < calcinfo.stin_name
calcinfo.cmdline_params = (list(cmdline_params) + ['-in', self.metadata.options.input_filename])
codeinfo = datastructures.CodeInfo()
codeinfo.cmdline_params = (list(cmdline_params) + ['-in', self.metadata.options.input_filename])
codeinfo.stdout_name = self.metadata.options.output_filename
codeinfo.code_uuid = self.inputs.code.uuid
calcinfo.codes_info = [codeinfo]
calcinfo.local_copy_list = local_copy_list
calcinfo.remote_copy_list = remote_copy_list
calcinfo.remote_symlink_list = remote_symlink_list
# Retrieve by default the output file and the xml file
calcinfo.retrieve_list = []
calcinfo.retrieve_list.append(self.metadata.options.output_filename)
calcinfo.retrieve_list.extend(self.xml_filepaths)
calcinfo.retrieve_list += settings.pop('ADDITIONAL_RETRIEVE_LIST', [])
calcinfo.retrieve_list += self._internal_retrieve_list
# Retrieve the k-point directories with the xml files to the temporary folder
# to parse the band eigenvalues and occupations but not to have to save the raw files
# if and only if the 'no_bands' key was not set to true in the settings
no_bands = settings.pop('NO_BANDS', False)
if no_bands is False:
xmlpaths = os.path.join(self._OUTPUT_SUBFOLDER, self._PREFIX + '.save', 'K*[0-9]', 'eigenval*.xml')
calcinfo.retrieve_temporary_list = [[xmlpaths, '.', 2]]
# We might still have parser options in the settings dictionary: pop them.
_pop_parser_options(self, settings)
if settings:
unknown_keys = ', '.join(list(settings.keys()))
raise exceptions.InputValidationError('`settings` contained unexpected keys: {}'.format(unknown_keys))
return calcinfo
def prepare_for_submission(self, folder):
"""
Create input files.
:param folder: an `aiida.common.folders.Folder` where the plugin should temporarily place all files needed by
the calculation.
:return: `aiida.common.datastructures.CalcInfo` instance
"""
### SETUP ###
local_copy_list = []
### INPUT CHECK ###
# PSEUDOS
for kind in self.inputs.structure.get_kind_names():
if kind not in self.inputs.pseudos:
raise ValueError(f'no pseudo available for element {kind}')
elif not isinstance(self.inputs.pseudos[kind], (Psp8Data, JthXmlData)):
raise ValueError(f'pseudo for element {kind} is not of type Psp8Data or JthXmlData')
# KPOINTS
if 'ngkpt' in self.inputs.parameters.keys():
raise ValueError('`ngkpt` should not be specified in input parameters')
if 'kptopt' in self.inputs.parameters.keys():
raise ValueError('`kptopt` should not be specified in input parameters')
### PREPARATION ###
# PSEUDOS
folder.get_subfolder(self._DEFAULT_PSEUDO_SUBFOLDER, create=True)
for kind in self.inputs.structure.get_kind_names():
psp = self.inputs.pseudos[kind]
local_copy_list.append((psp.uuid, psp.filename, self._DEFAULT_PSEUDO_SUBFOLDER + kind + '.psp8'))
# KPOINTS
kpoints_mesh = self.inputs.kpoints.get_kpoints_mesh()[0]
### INPUTS ###
input_parameters = self.inputs.parameters.get_dict()
shiftk = input_parameters.pop('shiftk', [0.0, 0.0, 0.0])
# TODO: There must be a better way to do this
# maybe we can convert the PseudoPotential objects into pymatgen Pseudo objects?
znucl = structure_to_abivars(self.inputs.structure.get_pymatgen())['znucl']
pseudo_parameters = {
'pseudos': '"' + ', '.join([Element.from_Z(Z).symbol + '.psp8' for Z in znucl]) + '"',
'pp_dirpath': '"' + self._DEFAULT_PSEUDO_SUBFOLDER + '"'
}
input_parameters = {**input_parameters, **pseudo_parameters}
abin = AbinitInput(
structure=self.inputs.structure.get_pymatgen(),
pseudos=HGH_TABLE,
abi_kwargs=input_parameters
)
abin.set_kmesh(
ngkpt=kpoints_mesh,
shiftk=shiftk
)
with io.open(folder.get_abs_path(self._DEFAULT_INPUT_FILE), mode='w', encoding='utf-8') as f:
f.write(abin.to_string(with_pseudos=False))
### CODE ###
codeinfo = datastructures.CodeInfo()
codeinfo.code_uuid = self.inputs.code.uuid
codeinfo.cmdline_params = [self.options.input_filename]
codeinfo.stdout_name = self.metadata.options.output_filename
codeinfo.withmpi = self.inputs.metadata.options.withmpi
### CALC INFO ###
calcinfo = datastructures.CalcInfo()
calcinfo.codes_info = [codeinfo]
calcinfo.stdin_name = self.options.input_filename
calcinfo.stdout_name = self.options.output_filename
calcinfo.retrieve_list = [self.metadata.options.output_filename]
calcinfo.retrieve_list = [self._DEFAULT_OUTPUT_FILE, self._DEFAULT_GSR_FILE_NAME, self._DEFAULT_TRAJECT_FILE_NAME]
calcinfo.remote_symlink_list = []
calcinfo.remote_copy_list = []
calcinfo.local_copy_list = local_copy_list
if 'parent_calc_folder' in self.inputs:
comp_uuid = self.inputs.parent_calc_folder.computer.uuid
remote_path = self.inputs.parent_calc_folder.get_remote_path()
copy_info = (comp_uuid, remote_path, self._DEFAULT_PARENT_CALC_FLDR_NAME)
# If running on the same computer - make a symlink.
if self.inputs.code.computer.uuid == comp_uuid:
calcinfo.remote_symlink_list.append(copy_info)
# If not - copy the folder.
else:
calcinfo.remote_copy_list.append(copy_info)
return calcinfo
def prepare_for_submission(self, folder):
"""Create the input file(s) from the input nodes.
:param folder: an `aiida.common.folders.Folder` where the plugin should temporarily place all files needed by
the calculation.
:return: `aiida.common.datastructures.CalcInfo` instance
"""
# process the settings so that capitalization isn't an issue
settings = uppercase_dict(self.inputs.settings.get_dict()) if 'settings' in self.inputs else {}
# validate the input parameters and pseudopotentials
self._validate_parameters()
self._validate_pseudos()
# create lists which specify files to copy and symlink
local_copy_list = []
remote_copy_list = []
remote_symlink_list = []
# create the subfolder which will contain the pseudopotential files
folder.get_subfolder(self._PSEUDO_SUBFOLDER, create=True)
# set the input and stdout filenames from the prefix
self.metadata.options.input_filename = f'{self.metadata.options.prefix}.in'
self.metadata.options.output_filename = f'{self.metadata.options.prefix}.out'
# generate the input file content and list of pseudopotential files to copy
arguments = [
self.inputs.parameters,
self.inputs.pseudos,
self.inputs.structure,
self.inputs.kpoints
]
input_filecontent, local_copy_pseudo_list = self._generate_inputdata(*arguments)
# merge the pseudopotential copy list with the overall copylist and write the input file
local_copy_list += local_copy_pseudo_list
with io.open(folder.get_abs_path(self.metadata.options.input_filename), mode='w', encoding='utf-8') as stream:
stream.write(input_filecontent)
# list the files to copy or symlink in the case of a restart
if 'parent_folder' in self.inputs:
# symlink by default if on the same computer, otherwise copy by default
same_computer = self.inputs.code.computer.uuid == self.inputs.parent_folder.computer.uuid
if settings.pop('PARENT_FOLDER_SYMLINK', same_computer):
remote_symlink_list.append((
self.inputs.parent_folder.computer.uuid,
os.path.join(self.inputs.parent_folder.get_remote_path(), '*'),
'./')
)
else:
remote_copy_list.append((
self.inputs.parent_folder.computer.uuid,
os.path.join(self.inputs.parent_folder.get_remote_path(), '*'),
'./')
)
# generate the commandline parameters
cmdline_params = self._generate_cmdline_params(settings)
# generate list of files to retrieve from wherever the calculation is run
retrieve_list = self._generate_retrieve_list(self.inputs.parameters, settings)
# set up the code info to pass to `CalcInfo`
codeinfo = datastructures.CodeInfo()
codeinfo.code_uuid = self.inputs.code.uuid
codeinfo.cmdline_params = cmdline_params
codeinfo.stdout_name = self.metadata.options.output_filename
codeinfo.withmpi = self.inputs.metadata.options.withmpi
# set up the calc info so AiiDA knows what to do with everything
calcinfo = datastructures.CalcInfo()
calcinfo.codes_info = [codeinfo]
calcinfo.stdin_name = self.metadata.options.input_filename
calcinfo.stdout_name = self.metadata.options.output_filename
calcinfo.retrieve_list = retrieve_list
calcinfo.remote_symlink_list = remote_symlink_list
calcinfo.remote_copy_list = remote_copy_list
calcinfo.local_copy_list = local_copy_list
return calcinfo
def prepare_for_submission(self, folder):
"""
Create input files.
:param folder: an `aiida.common.folders.Folder` where the plugin should temporarily place all files needed by
the calculation.
:return: `aiida.common.datastructures.CalcInfo` instance
"""
# check that either structure or structurefile are set
# if both are set, fail.
# if self.inputs.structurefile is None and self.inputs.structure is None:
# raise exceptions.InputValidationError("either structure or structurefile must be set")
# if self.inputs.structurefile is not None and self.inputs.structure is not None:
# raise exceptions.InputValidationError("Only one of structure or structurefile must be set")
# somehow aiida sends back unicode strings here
dico = BigDFT_files.Inputfile()
dico.update(self.inputs.parameters.dict)
bigdft_calc = PluginSystemCalculator()
local_copy_list = []
# if the structure is not already inside input dict
if 'posinp' not in dico:
posinp_filename = self.inputs.structurefile.value
if self.inputs.structure is not None:
print("writing input posinp file")
posinp_string = self.inputs.structure._prepare_xyz()[0]
if "jobname" not in self.inputs.metadata.options:
posinp_filename = self._POSINP_FILE_NAME
else:
posinp_filename = self.inputs.metadata.options.jobname + ".xyz"
# bigdft_calc.update_global_options(units="angstroem")
posinp_file = open(posinp_filename, "wb")
posinp_file.write(posinp_string)
posinp_file.close()
posinp_filedata = SinglefileData(
file=os.path.abspath(posinp_filename)).store()
# BigDFT_input.set_atomic_positions(dico, posinp_filename)
# bigdft_calc._run_options(posinp={})
local_copy_list = [
(posinp_filedata.uuid, posinp_filedata.filename, posinp_filedata.filename)]
# setup pseudopotentials if needed
if self.inputs.pseudos is not None:
for filename in self.inputs.pseudos:
pseudo_filedata = SinglefileData(
file=os.path.abspath(filename)).store()
local_copy_list.append(
(pseudo_filedata.uuid, pseudo_filedata.filename, pseudo_filedata.filename))
# generate yaml input file from dict and whatever
if "jobname" in self.inputs.metadata.options:
bigdft_calc.update_global_options(
name=self.inputs.metadata.options.jobname)
bigdft_calc._run_options(input=dico, run_dir=folder.abspath)
bigdft_calc.pre_processing()
if "jobname" not in self.inputs.metadata.options:
input_filename = self._INPUT_FILE_NAME
else:
input_filename = self.inputs.metadata.options.jobname + ".yaml"
input_filedata = SinglefileData(
file=folder.get_abs_path(input_filename)).store()
local_copy_list.append(
(input_filedata.uuid, input_filedata.filename, input_filename))
codeinfo = datastructures.CodeInfo()
codeinfo.code_uuid = self.inputs.code.uuid
outfile = self.inputs.metadata.options.output_filename
timefile = self._TIMING_FILE_NAME
if "jobname" in self.inputs.metadata.options:
outfile = "log-" + self.inputs.metadata.options.jobname + ".yaml"
timefile = "time-" + self.inputs.metadata.options.jobname + ".yaml"
# codeinfo.stdout_name = outfile
codeinfo.withmpi = self.inputs.metadata.options.withmpi
if "jobname" in self.inputs.metadata.options:
codeinfo.cmdline_params = ["--name=" +
self.inputs.metadata.options.jobname]
#local_copy_list = []
# Prepare a `CalcInfo` to be returned to the engine
calcinfo = datastructures.CalcInfo()
calcinfo.codes_info = [codeinfo]
calcinfo.local_copy_list = local_copy_list
calcinfo.retrieve_list = [outfile,
timefile,
"forces_posinp.yaml",
"final_posinp.yaml",
["./debug/bigdft-err*", ".", 2]]
calcinfo.retrieve_list.extend(self.inputs.extra_retrieved_files)
return calcinfo
def prepare_for_submission(self, folder):
"""
Create input file: inpsd.dat
:param folder: an `aiida.common.folders.Folder` where the plugin should temporarily place all files needed by
the calculation.
:return: `aiida.common.datastructures.CalcInfo` instance
"""
# Create input file: inpsd.dat
input_dmdata = self.inputs.dmdata
input_jij = self.inputs.jij
input_momfile = self.inputs.momfile
input_posfile = self.inputs.posfile
input_qfile = self.inputs.qfile
input_simid = self.inputs.simid
input_ncell = self.inputs.ncell
input_BC = self.inputs.BC
input_cell = self.inputs.cell
input_do_prnstruct = self.inputs.do_prnstruct
input_maptype = self.inputs.maptype
input_SDEalgh = self.inputs.SDEalgh
input_Initmag = self.inputs.Initmag
input_ip_mode = self.inputs.ip_mode
input_qm_svec = self.inputs.qm_svec
input_qm_nvec = self.inputs.qm_nvec
input_mode = self.inputs.mode
input_temp = self.inputs.temp
input_damping = self.inputs.damping
input_Nstep = self.inputs.Nstep
input_timestep = self.inputs.timestep
input_qpoints = self.inputs.qpoints
input_plotenergy = self.inputs.plotenergy
input_do_avrg = self.inputs.do_avrg
input_retrieve_list_name = self.inputs.retrieve_list_name
# write inpsd.dat
# it seems we don's need to put it in local_copy_list ?
with folder.open(self.options.input_filename, 'a+') as f:
f.write(f'simid {input_simid.value}\n')
f.write(f"ncell {input_ncell.get_array('matrix')[0]} {input_ncell.get_array('matrix')[1]} {input_ncell.get_array('matrix')[2]} \n")
# we set the default array name is "matrix"
#np.savetxt(f, input_ncell.get_array('matrix'))
f.write(f'BC {input_BC.value}\n')
f.write("cell ")
np.savetxt(f, input_cell.get_array('matrix'))
f.write(f'do_prnstruct {input_do_prnstruct.value}\n')
f.write(f'input_posfile ./{input_posfile.filename}\n')
f.write(f'exchange ./{input_jij.filename}\n')
f.write(f'momfile ./{input_momfile.filename}\n')
f.write(f'dm ./{input_dmdata.filename}\n')
f.write(f'maptype {input_maptype.value}\n')
f.write(f'SDEalgh {input_SDEalgh.value}\n')
f.write(f'Initmag {input_Initmag.value}\n')
f.write(f'ip_mode {input_ip_mode.value}\n')
f.write(f"qm_svec {input_qm_svec.get_array('matrix')[0]} {input_qm_svec.get_array('matrix')[1]} {input_qm_svec.get_array('matrix')[2]} \n")
f.write(f"qm_nvec {input_qm_nvec.get_array('matrix')[0]} {input_qm_nvec.get_array('matrix')[1]} {input_qm_nvec.get_array('matrix')[2]} \n")
f.write(f'mode {input_mode.value}\n')
f.write(f'temp {input_temp.value}\n')
f.write(f'damping {input_damping.value}\n')
f.write(f'Nstep {input_Nstep.value}\n')
f.write(f'timestep {input_timestep.value}\n')
f.write(f'qpoints {input_qpoints.value}\n')
f.write(f'qfile ./{input_qfile.filename}\n')
f.write(f'plotenergy {input_plotenergy.value}\n')
f.write(f'do_avrg {input_do_avrg.value}\n')
codeinfo = datastructures.CodeInfo()
codeinfo.cmdline_params = []# note that nothing need here for SD
codeinfo.code_uuid = self.inputs.code.uuid
#codeinfo.stdout_name = self.metadata.options.output_filename
#codeinfo.withmpi = self.inputs.metadata.options.withmpi
# Prepare a `CalcInfo` to be returned to the engine
calcinfo = datastructures.CalcInfo()
calcinfo.codes_info = [codeinfo]
calcinfo.local_copy_list = [
(self.inputs.dmdata.uuid, self.inputs.dmdata.filename,
self.inputs.dmdata.filename),
(self.inputs.jij.uuid, self.inputs.jij.filename, self.inputs.jij.filename),
(self.inputs.momfile.uuid, self.inputs.momfile.filename,
self.inputs.momfile.filename),
(self.inputs.posfile.uuid, self.inputs.posfile.filename,
self.inputs.posfile.filename),
(self.inputs.qfile.uuid, self.inputs.qfile.filename,
self.inputs.qfile.filename),
]
#calc_info.remote_copy_list[(self.inputs.parent_folder.computer.uuid, 'output_folder', 'restart_folder')]
calcinfo.retrieve_list =input_retrieve_list_name.get_list()
return calcinfo
def prepare_for_submission(self, folder):
"""Prepare the calculation job for submission by transforming input nodes into input files.
In addition to the input files being written to the sandbox folder, a `CalcInfo` instance will be returned that
contains lists of files that need to be copied to the remote machine before job submission, as well as file
lists that are to be retrieved after job completion.
:param folder: a sandbox folder to temporarily write files on disk.
:return: :py:`~aiida.common.datastructures.CalcInfo` instance.
"""
# pylint: disable=too-many-branches,too-many-statements
if 'settings' in self.inputs:
settings = _uppercase_dict(self.inputs.settings.get_dict(),
dict_name='settings')
else:
settings = {}
following_text = self._get_following_text()
# Put the first-level keys as uppercase (i.e., namelist and card names) and the second-level keys as lowercase
if 'parameters' in self.inputs:
parameters = _uppercase_dict(self.inputs.parameters.get_dict(),
dict_name='parameters')
parameters = {
k: _lowercase_dict(v, dict_name=k)
for k, v in parameters.items()
}
else:
parameters = {}
# =================== NAMELISTS AND CARDS ========================
try:
namelists_toprint = settings.pop('NAMELISTS')
if not isinstance(namelists_toprint, list):
raise exceptions.InputValidationError(
"The 'NAMELISTS' value, if specified in the settings input node, must be a list of strings"
)
except KeyError: # list of namelists not specified; do automatic detection
namelists_toprint = self._default_namelists
parameters = self.set_blocked_keywords(parameters)
parameters = self.filter_namelists(parameters, namelists_toprint)
file_content = self.generate_input_file(parameters)
file_content += '\n' + following_text
input_filename = self.inputs.metadata.options.input_filename
with folder.open(input_filename, 'w') as infile:
infile.write(file_content)
symlink = settings.pop('PARENT_FOLDER_SYMLINK', False)
remote_copy_list = []
local_copy_list = []
remote_symlink_list = []
ptr = remote_symlink_list if symlink else remote_copy_list
# copy remote output dir, if specified
parent_calc_folder = self.inputs.get('parent_folder', None)
if parent_calc_folder is not None:
if isinstance(parent_calc_folder, RemoteData):
parent_calc_out_subfolder = settings.pop(
'PARENT_CALC_OUT_SUBFOLDER', self._INPUT_SUBFOLDER)
ptr.append((parent_calc_folder.computer.uuid,
os.path.join(parent_calc_folder.get_remote_path(),
parent_calc_out_subfolder),
self._OUTPUT_SUBFOLDER))
elif isinstance(parent_calc_folder, FolderData):
for filename in parent_calc_folder.list_object_names():
local_copy_list.append(
(parent_calc_folder.uuid, filename,
os.path.join(self._OUTPUT_SUBFOLDER, filename)))
elif isinstance(parent_calc_folder, SinglefileData):
single_file = parent_calc_folder
local_copy_list.append((single_file.uuid, single_file.filename,
single_file.filename))
codeinfo = datastructures.CodeInfo()
codeinfo.cmdline_params = settings.pop('CMDLINE', [])
codeinfo.stdin_name = self.inputs.metadata.options.input_filename
codeinfo.stdout_name = self.inputs.metadata.options.output_filename
codeinfo.code_uuid = self.inputs.code.uuid
calcinfo = datastructures.CalcInfo()
calcinfo.uuid = str(self.uuid)
calcinfo.codes_info = [codeinfo]
calcinfo.local_copy_list = local_copy_list
calcinfo.remote_copy_list = remote_copy_list
calcinfo.remote_symlink_list = remote_symlink_list
# Retrieve by default the output file and the xml file
calcinfo.retrieve_list = []
calcinfo.retrieve_list.append(
self.inputs.metadata.options.output_filename)
settings_retrieve_list = settings.pop('ADDITIONAL_RETRIEVE_LIST', [])
calcinfo.retrieve_list += settings_retrieve_list
calcinfo.retrieve_list += self._internal_retrieve_list
calcinfo.retrieve_singlefile_list = self._retrieve_singlefile_list
# We might still have parser options in the settings dictionary: pop them.
_pop_parser_options(self, settings)
if settings:
unknown_keys = ', '.join(list(settings.keys()))
raise exceptions.InputValidationError(
f'`settings` contained unexpected keys: {unknown_keys}')
return calcinfo
def prepare_for_submission(self, folder): # pylint: disable=too-many-statements,too-many-branches
"""Prepare the calculation job for submission by transforming input nodes into input files.
In addition to the input files being written to the sandbox folder, a `CalcInfo` instance will be returned that
contains lists of files that need to be copied to the remote machine before job submission, as well as file
lists that are to be retrieved after job completion.
:param folder: a sandbox folder to temporarily write files on disk.
:return: :py:`~aiida.common.datastructures.CalcInfo` instance.
"""
def test_offset(offset):
"""Check if the grid has an offset."""
if any([i != 0. for i in offset]):
raise NotImplementedError(
'Computation of electron-phonon on a mesh with non zero offset is not implemented, '
'at the level of epw.x')
# pylint: disable=too-many-statements,too-many-branches
local_copy_list = []
remote_copy_list = []
remote_symlink_list = []
if 'settings' in self.inputs:
settings = _uppercase_dict(self.inputs.settings.get_dict(), dict_name='settings')
else:
settings = {}
# Copy nscf folder
parent_folder_nscf = self.inputs.parent_folder_nscf
parent_calc_nscf = parent_folder_nscf.creator
if parent_calc_nscf is None:
raise exceptions.NotExistent('parent_folder<{}> has no parent calculation'.format(parent_folder_nscf.pk))
# Also, the parent calculation must be on the same computer
if not self.node.computer.uuid == parent_calc_nscf.computer.uuid:
raise exceptions.InputValidationError(
'Calculation has to be launched on the same computer as that of the parent: {}'.format(
parent_calc_nscf.computer.get_name()))
# put by default, default_parent_output_folder = ./out
parent_calc_out_subfolder_nscf = parent_calc_nscf.process_class._OUTPUT_SUBFOLDER # pylint: disable=protected-access
# Now phonon folder
parent_folder_ph = self.inputs.parent_folder_ph
parent_calc_ph = parent_folder_ph.creator
# Also, the parent calculation must be on the same computer
if not self.node.computer.uuid == parent_calc_ph.computer.uuid:
raise exceptions.InputValidationError(
'Calculation has to be launched on the same computer as that of the parent: {}'.format(
parent_calc_ph.computer.get_name()))
# I put the first-level keys as uppercase (i.e., namelist and card names) and the second-level keys as lowercase
parameters = _uppercase_dict(self.inputs.parameters.get_dict(), dict_name='parameters')
parameters = {k: _lowercase_dict(v, dict_name=k) for k, v in parameters.items()}
if 'INPUTEPW' not in parameters:
raise exceptions.InputValidationError('required namelist INPUTEPW not specified')
parameters['INPUTEPW']['outdir'] = self._OUTPUT_SUBFOLDER
parameters['INPUTEPW']['iverbosity'] = 1
parameters['INPUTEPW']['prefix'] = self._PREFIX
try:
mesh, offset = self.inputs.qpoints.get_kpoints_mesh()
test_offset(offset)
parameters['INPUTEPW']['nq1'] = mesh[0]
parameters['INPUTEPW']['nq2'] = mesh[1]
parameters['INPUTEPW']['nq3'] = mesh[2]
postpend_text = None
except NotImplementedError as exception:
raise exceptions.InputValidationError('Cannot get the coarse q-point grid') from exception
try:
mesh, offset = self.inputs.kpoints.get_kpoints_mesh()
test_offset(offset)
parameters['INPUTEPW']['nk1'] = mesh[0]
parameters['INPUTEPW']['nk2'] = mesh[1]
parameters['INPUTEPW']['nk3'] = mesh[2]
postpend_text = None
except NotImplementedError as exception:
raise exceptions.InputValidationError('Cannot get the coarse k-point grid') from exception
try:
mesh, offset = self.inputs.qfpoints.get_kpoints_mesh()
test_offset(offset)
parameters['INPUTEPW']['nqf1'] = mesh[0]
parameters['INPUTEPW']['nqf2'] = mesh[1]
parameters['INPUTEPW']['nqf3'] = mesh[2]
postpend_text = None
except NotImplementedError as exception:
raise exceptions.InputValidationError('Cannot get the fine q-point grid') from exception
try:
mesh, offset = self.inputs.kfpoints.get_kpoints_mesh()
test_offset(offset)
parameters['INPUTEPW']['nkf1'] = mesh[0]
parameters['INPUTEPW']['nkf2'] = mesh[1]
parameters['INPUTEPW']['nkf3'] = mesh[2]
postpend_text = None
except NotImplementedError as exception:
raise exceptions.InputValidationError('Cannot get the fine k-point grid') from exception
# customized namelists, otherwise not present in the distributed epw code
try:
namelists_toprint = settings.pop('NAMELISTS')
if not isinstance(namelists_toprint, list):
raise exceptions.InputValidationError(
"The 'NAMELISTS' value, if specified in the settings input "
'node, must be a list of strings')
except KeyError: # list of namelists not specified in the settings; do automatic detection
namelists_toprint = self._compulsory_namelists
# create the save folder with dvscf and dyn files.
folder.get_subfolder(self._FOLDER_SAVE, create=True)
# List of IBZ q-point to be added below EPW. To be removed when removed from EPW.
qibz_ar = []
for key, value in sorted(parent_folder_ph.creator.outputs.output_parameters.get_dict().items()):
if key.startswith('dynamical_matrix_'):
qibz_ar.append(value['q_point'])
qibz_node = orm.ArrayData()
qibz_node.set_array('qibz', np.array(qibz_ar))
list_of_points = qibz_node.get_array('qibz')
# Number of q-point in the irreducible Brillouin Zone.
nqpt = len(list_of_points[0, :])
# add here the list of point coordinates
if len(list_of_points) > 1:
postpend_text = '{} cartesian\n'.format(len(list_of_points))
for points in list_of_points:
postpend_text += '{0:18.10f} {1:18.10f} {2:18.10f} \n'.format(*points)
with folder.open(self.metadata.options.input_filename, 'w') as infile:
for namelist_name in namelists_toprint:
infile.write('&{0}\n'.format(namelist_name))
# namelist content; set to {} if not present, so that we leave an empty namelist
namelist = parameters.pop(namelist_name, {})
for key, value in sorted(namelist.items()):
infile.write(convert_input_to_namelist_entry(key, value))
infile.write('/\n')
# add list of qpoints if required
if postpend_text is not None:
infile.write(postpend_text)
if parameters:
raise exceptions.InputValidationError(
'The following namelists are specified in parameters, but are '
'not valid namelists for the current type of calculation: '
'{}'.format(','.join(list(parameters.keys()))))
# copy the parent scratch
symlink = settings.pop('PARENT_FOLDER_SYMLINK', self._default_symlink_usage) # a boolean
if symlink:
# I create a symlink to each file/folder in the parent ./out
folder.get_subfolder(self._OUTPUT_SUBFOLDER, create=True)
remote_symlink_list.append((
parent_folder_nscf.computer.uuid,
os.path.join(parent_folder_nscf.get_remote_path(), parent_calc_out_subfolder_nscf, '*'),
self._OUTPUT_SUBFOLDER
))
else:
# here I copy the whole folder ./out
remote_copy_list.append((
parent_folder_nscf.computer.uuid,
os.path.join(parent_folder_nscf.get_remote_path(), parent_calc_out_subfolder_nscf),
self._OUTPUT_SUBFOLDER
))
prefix = self._PREFIX
for iqpt in range(1, nqpt+1):
label = str(iqpt)
tmp_path = os.path.join(self._FOLDER_DYNAMICAL_MATRIX, 'dynamical-matrix-0')
remote_copy_list.append((
parent_folder_ph.computer.uuid,
os.path.join(parent_folder_ph.get_remote_path(), tmp_path),
'save/'+prefix+'.dyn_q0'))
tmp_path = os.path.join(self._FOLDER_DYNAMICAL_MATRIX, 'dynamical-matrix-'+label)
remote_copy_list.append((
parent_folder_ph.computer.uuid,
os.path.join(parent_folder_ph.get_remote_path(), tmp_path),
'save/'+prefix+'.dyn_q'+label))
if iqpt == 1:
tmp_path = os.path.join(self._OUTPUT_SUBFOLDER, '_ph0/'+prefix+'.dvscf*')
remote_copy_list.append((
parent_folder_ph.computer.uuid,
os.path.join(parent_folder_ph.get_remote_path(), tmp_path),
'save/'+prefix+'.dvscf_q'+label))
tmp_path = os.path.join(self._OUTPUT_SUBFOLDER, '_ph0/'+prefix+'.phsave')
remote_copy_list.append((
parent_folder_ph.computer.uuid,
os.path.join(parent_folder_ph.get_remote_path(), tmp_path),
'save/'))
else:
tmp_path = os.path.join(self._OUTPUT_SUBFOLDER, '_ph0/'+prefix+'.q_'+label+'/'+prefix+'.dvscf*')
remote_copy_list.append((
parent_folder_ph.computer.uuid,
os.path.join(parent_folder_ph.get_remote_path(), tmp_path),
'save/'+prefix+'.dvscf_q'+label))
codeinfo = datastructures.CodeInfo()
codeinfo.cmdline_params = (list(settings.pop('CMDLINE', [])) + ['-in', self.metadata.options.input_filename])
codeinfo.stdout_name = self.metadata.options.output_filename
codeinfo.code_uuid = self.inputs.code.uuid
calcinfo = datastructures.CalcInfo()
calcinfo.codes_info = [codeinfo]
calcinfo.local_copy_list = local_copy_list
calcinfo.remote_copy_list = remote_copy_list
calcinfo.remote_symlink_list = remote_symlink_list
# Retrieve by default the output file
calcinfo.retrieve_list = []
calcinfo.retrieve_list.append(self.metadata.options.output_filename)
calcinfo.retrieve_list += settings.pop('ADDITIONAL_RETRIEVE_LIST', [])
if settings:
unknown_keys = ', '.join(list(settings.keys()))
raise exceptions.InputValidationError('`settings` contained unexpected keys: {}'.format(unknown_keys))
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
"""
if 'settings' in self.inputs:
settings = _uppercase_dict(self.inputs.settings.get_dict(),
dict_name='settings')
else:
settings = {}
following_text = self._get_following_text()
# Put the first-level keys as uppercase (i.e., namelist and card names) and the second-level keys as lowercase
if 'parameters' in self.inputs:
parameters = _uppercase_dict(self.inputs.parameters.get_dict(),
dict_name='parameters')
parameters = {
k: _lowercase_dict(v, dict_name=k)
for k, v in six.iteritems(parameters)
}
else:
parameters = {}
# Force default values for blocked keywords. NOTE: this is different from PW/CP
for blocked in self._blocked_keywords:
namelist = blocked[0].upper()
key = blocked[1].lower()
value = blocked[2]
if namelist in parameters:
if key in parameters[namelist]:
raise exceptions.InputValidationError(
"You cannot specify explicitly the '{}' key in the '{}' "
'namelist.'.format(key, namelist))
else:
parameters[namelist] = {}
parameters[namelist][key] = value
# =================== NAMELISTS AND CARDS ========================
try:
namelists_toprint = settings.pop('NAMELISTS')
if not isinstance(namelists_toprint, list):
raise exceptions.InputValidationError(
"The 'NAMELISTS' value, if specified in the settings input node, must be a list of strings"
)
except KeyError: # list of namelists not specified; do automatic detection
namelists_toprint = self._default_namelists
input_filename = self.inputs.metadata.options.input_filename
with folder.open(input_filename, 'w') as infile:
for namelist_name in namelists_toprint:
infile.write(u'&{0}\n'.format(namelist_name))
# namelist content; set to {} if not present, so that we leave an empty namelist
namelist = parameters.pop(namelist_name, {})
for key, value in sorted(six.iteritems(namelist)):
infile.write(convert_input_to_namelist_entry(key, value))
infile.write(u'/\n')
# Write remaning text now, if any
infile.write(following_text)
# Check for specified namelists that are not expected
if parameters:
raise exceptions.InputValidationError(
'The following namelists are specified in parameters, but are '
'not valid namelists for the current type of calculation: '
'{}'.format(','.join(list(parameters.keys()))))
remote_copy_list = []
local_copy_list = []
# copy remote output dir, if specified
parent_calc_folder = self.inputs.get('parent_folder', None)
if parent_calc_folder is not None:
if isinstance(parent_calc_folder, RemoteData):
parent_calc_out_subfolder = settings.pop(
'PARENT_CALC_OUT_SUBFOLDER', self._INPUT_SUBFOLDER)
remote_copy_list.append(
(parent_calc_folder.computer.uuid,
os.path.join(parent_calc_folder.get_remote_path(),
parent_calc_out_subfolder),
self._OUTPUT_SUBFOLDER))
elif isinstance(parent_calc_folder, FolderData):
# TODO: test me, especially with deep relative paths.
for filename in parent_calc_folder.list_object_names():
local_copy_list.append(
(parent_calc_folder.uuid, filename,
os.path.join(self._OUTPUT_SUBFOLDER, filename)))
elif isinstance(parent_calc_folder, SinglefileData):
# TODO: test me
single_file = parent_calc_folder
local_copy_list.append((single_file.uuid, single_file.filename,
single_file.filename))
codeinfo = datastructures.CodeInfo()
codeinfo.cmdline_params = settings.pop('CMDLINE', [])
codeinfo.stdin_name = self.inputs.metadata.options.input_filename
codeinfo.stdout_name = self.inputs.metadata.options.output_filename
codeinfo.code_uuid = self.inputs.code.uuid
calcinfo = datastructures.CalcInfo()
calcinfo.uuid = str(self.uuid)
calcinfo.codes_info = [codeinfo]
calcinfo.local_copy_list = local_copy_list
calcinfo.remote_copy_list = remote_copy_list
# Retrieve by default the output file and the xml file
calcinfo.retrieve_list = []
calcinfo.retrieve_list.append(
self.inputs.metadata.options.output_filename)
settings_retrieve_list = settings.pop('ADDITIONAL_RETRIEVE_LIST', [])
calcinfo.retrieve_list += settings_retrieve_list
calcinfo.retrieve_list += self._internal_retrieve_list
calcinfo.retrieve_singlefile_list = self._retrieve_singlefile_list
# We might still have parser options in the settings dictionary: pop them.
_pop_parser_options(self, settings)
if settings:
unknown_keys = ', '.join(list(settings.keys()))
raise exceptions.InputValidationError(
'`settings` contained unexpected keys: {}'.format(
unknown_keys))
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
"""
local_copy_list = []
remote_copy_list = []
remote_symlink_list = []
if 'settings' in self.inputs:
settings = _uppercase_dict(self.inputs.settings.get_dict(),
dict_name='settings')
else:
settings = {}
parent_folder = self.inputs.parent_folder
parent_calcs = parent_folder.get_incoming(
node_class=orm.CalcJobNode).all()
if not parent_calcs:
raise exceptions.NotExistent(
'parent_folder<{}> has no parent calculation'.format(
parent_folder.pk))
elif len(parent_calcs) > 1:
raise exceptions.UniquenessError(
'parent_folder<{}> has multiple parent calculations'.format(
parent_folder.pk))
parent_calc = parent_calcs[0].node
# If the parent calculation is a `PhCalculation` we are restarting
restart_flag = parent_calc.process_type == 'aiida.calculations:quantumespresso.ph'
# Also, the parent calculation must be on the same computer
if not self.node.computer.uuid == parent_calc.computer.uuid:
raise exceptions.InputValidationError(
'Calculation has to be launched on the same computer as that of the parent: {}'
.format(parent_calc.computer.get_name()))
# put by default, default_parent_output_folder = ./out
try:
default_parent_output_folder = parent_calc.process_class._OUTPUT_SUBFOLDER
except AttributeError:
try:
default_parent_output_folder = parent_calc._get_output_folder()
except AttributeError:
raise exceptions.InputValidationError(
'parent calculation does not have a default output subfolder'
)
parent_calc_out_subfolder = settings.pop('PARENT_CALC_OUT_SUBFOLDER',
default_parent_output_folder)
# I put the first-level keys as uppercase (i.e., namelist and card names) and the second-level keys as lowercase
parameters = _uppercase_dict(self.inputs.parameters.get_dict(),
dict_name='parameters')
parameters = {
k: _lowercase_dict(v, dict_name=k)
for k, v in six.iteritems(parameters)
}
prepare_for_d3 = settings.pop('PREPARE_FOR_D3', False)
if prepare_for_d3:
self._blocked_keywords += [('INPUTPH', 'fildrho'),
('INPUTPH', 'drho_star%open'),
('INPUTPH', 'drho_star%ext'),
('INPUTPH', 'drho_star%dir')]
for namelist, flag in self._blocked_keywords:
if namelist in parameters:
if flag in parameters[namelist]:
raise exceptions.InputValidationError(
"Cannot specify explicitly the '{}' flag in the '{}' namelist or card."
.format(flag, namelist))
if 'INPUTPH' not in parameters:
raise exceptions.InputValidationError(
'required namelist INPUTPH not specified')
parameters['INPUTPH']['outdir'] = self._OUTPUT_SUBFOLDER
parameters['INPUTPH']['iverbosity'] = 1
parameters['INPUTPH']['prefix'] = self._PREFIX
parameters['INPUTPH']['fildyn'] = self._OUTPUT_DYNAMICAL_MATRIX_PREFIX
if prepare_for_d3:
parameters['INPUTPH']['fildrho'] = self._DRHO_PREFIX
parameters['INPUTPH']['drho_star%open'] = True
parameters['INPUTPH']['drho_star%ext'] = self._DRHO_STAR_EXT
parameters['INPUTPH']['drho_star%dir'] = self._FOLDER_DRHO
try:
mesh, offset = self.inputs.qpoints.get_kpoints_mesh()
if any([i != 0. for i in offset]):
raise NotImplementedError(
'Computation of phonons on a mesh with non zero offset is not implemented, at the level of ph.x'
)
parameters['INPUTPH']['ldisp'] = True
parameters['INPUTPH']['nq1'] = mesh[0]
parameters['INPUTPH']['nq2'] = mesh[1]
parameters['INPUTPH']['nq3'] = mesh[2]
postpend_text = None
except AttributeError:
# this is the case where no mesh was set. Maybe it's a list
try:
list_of_points = self.inputs.qpoints.get_kpoints(
cartesian=True)
except AttributeError:
# In this case, there are no info on the qpoints at all
raise exceptions.InputValidationError(
'Input `qpoints` contains neither a mesh nor a list of points'
)
# change to 2pi/a coordinates
lattice_parameter = numpy.linalg.norm(self.inputs.qpoints.cell[0])
list_of_points *= lattice_parameter / (2. * numpy.pi)
# add here the list of point coordinates
if len(list_of_points) > 1:
parameters['INPUTPH']['qplot'] = True
parameters['INPUTPH']['ldisp'] = True
postpend_text = u'{}\n'.format(len(list_of_points))
for points in list_of_points:
postpend_text += u'{0:18.10f} {1:18.10f} {2:18.10f} 1\n'.format(
*points)
# Note: the weight is fixed to 1, because ph.x calls these
# things weights but they are not such. If they are going to
# exist with the meaning of weights, they will be supported
else:
parameters['INPUTPH']['ldisp'] = False
postpend_text = u''
for points in list_of_points:
postpend_text += u'{0:18.10f} {1:18.10f} {2:18.10f}\n'.format(
*points)
# customized namelists, otherwise not present in the distributed ph code
try:
namelists_toprint = settings.pop('NAMELISTS')
if not isinstance(namelists_toprint, list):
raise exceptions.InputValidationError(
"The 'NAMELISTS' value, if specified in the settings input "
'node, must be a list of strings')
except KeyError: # list of namelists not specified in the settings; do automatic detection
namelists_toprint = self._compulsory_namelists
# create a folder for the dynamical matrices
if not restart_flag: # if it is a restart, it will be copied over
folder.get_subfolder(self._FOLDER_DYNAMICAL_MATRIX, create=True)
with folder.open(self.metadata.options.input_filename, 'w') as infile:
for namelist_name in namelists_toprint:
infile.write(u'&{0}\n'.format(namelist_name))
# namelist content; set to {} if not present, so that we leave an empty namelist
namelist = parameters.pop(namelist_name, {})
for key, value in sorted(six.iteritems(namelist)):
infile.write(convert_input_to_namelist_entry(key, value))
infile.write(u'/\n')
# add list of qpoints if required
if postpend_text is not None:
infile.write(postpend_text)
if parameters:
raise exceptions.InputValidationError(
'The following namelists are specified in parameters, but are '
'not valid namelists for the current type of calculation: '
'{}'.format(','.join(list(parameters.keys()))))
# copy the parent scratch
symlink = settings.pop('PARENT_FOLDER_SYMLINK',
self._default_symlink_usage) # a boolean
if symlink:
# I create a symlink to each file/folder in the parent ./out
folder.get_subfolder(self._OUTPUT_SUBFOLDER, create=True)
remote_symlink_list.append(
(parent_folder.computer.uuid,
os.path.join(parent_folder.get_remote_path(),
parent_calc_out_subfolder,
'*'), self._OUTPUT_SUBFOLDER))
# I also create a symlink for the ./pseudo folder
# TODO: suppress this when the recover option of QE will be fixed
# (bug when trying to find pseudo file)
remote_symlink_list.append(
(parent_folder.computer.uuid,
os.path.join(parent_folder.get_remote_path(),
self._get_pseudo_folder()),
self._get_pseudo_folder()))
else:
# here I copy the whole folder ./out
remote_copy_list.append(
(parent_folder.computer.uuid,
os.path.join(parent_folder.get_remote_path(),
parent_calc_out_subfolder),
self._OUTPUT_SUBFOLDER))
# I also copy the ./pseudo folder
# TODO: suppress this when the recover option of QE will be fixed
# (bug when trying to find pseudo file)
remote_copy_list.append(
(parent_folder.computer.uuid,
os.path.join(parent_folder.get_remote_path(),
self._get_pseudo_folder()),
self._get_pseudo_folder()))
if restart_flag: # in this case, copy in addition also the dynamical matrices
if symlink:
remote_symlink_list.append(
(parent_folder.computer.uuid,
os.path.join(parent_folder.get_remote_path(),
self._FOLDER_DYNAMICAL_MATRIX),
self._FOLDER_DYNAMICAL_MATRIX))
else:
# copy the dynamical matrices
# no need to copy the _ph0, since I copied already the whole ./out folder
remote_copy_list.append(
(parent_folder.computer.uuid,
os.path.join(parent_folder.get_remote_path(),
self._FOLDER_DYNAMICAL_MATRIX), '.'))
# Create an `.EXIT` file if `only_initialization` flag in `settings` is set to `True`
if settings.pop('ONLY_INITIALIZATION', False):
with folder.open('{}.EXIT'.format(self._PREFIX), 'w') as handle:
handle.write('\n')
codeinfo = datastructures.CodeInfo()
codeinfo.cmdline_params = (
list(settings.pop('CMDLINE', [])) +
['-in', self.metadata.options.input_filename])
codeinfo.stdout_name = self.metadata.options.output_filename
codeinfo.code_uuid = self.inputs.code.uuid
calcinfo = datastructures.CalcInfo()
calcinfo.uuid = str(self.uuid)
calcinfo.codes_info = [codeinfo]
calcinfo.local_copy_list = local_copy_list
calcinfo.remote_copy_list = remote_copy_list
calcinfo.remote_symlink_list = remote_symlink_list
# Retrieve by default the output file and the xml file
filepath_xml_tensor = os.path.join(self._OUTPUT_SUBFOLDER, '_ph0',
'{}.phsave'.format(self._PREFIX))
calcinfo.retrieve_list = []
calcinfo.retrieve_list.append(self.metadata.options.output_filename)
calcinfo.retrieve_list.append(self._FOLDER_DYNAMICAL_MATRIX)
calcinfo.retrieve_list.append(
os.path.join(filepath_xml_tensor,
self._OUTPUT_XML_TENSOR_FILE_NAME))
calcinfo.retrieve_list += settings.pop('ADDITIONAL_RETRIEVE_LIST', [])
if settings:
unknown_keys = ', '.join(list(settings.keys()))
raise exceptions.InputValidationError(
'`settings` contained unexpected keys: {}'.format(
unknown_keys))
return calcinfo
def prepare_for_submission(self, folder: folders.Folder):
"""Create 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
"""
# To be filled out below
local_copy_list = []
remote_copy_list = []
remote_symlink_list = []
# Create the subfolders for pseudopotentials and orbitals
folder.get_subfolder(self._PSEUDO_SUBFOLDER, create=True)
folder.get_subfolder(self._ORBITAL_SUBFOLDER, create=True)
# Get an uppercase-key-only version of the settings dictionary (also check for case-insensitive duplicates)
if 'settings' in self.inputs:
settings = uppercase_dict_keys(self.inputs.settings.get_dict(),
dict_name='settings')
else:
settings = {}
# Get an uppercase-key-only verion of the parameters dictionary (also check for case-insensitive duplicates)
parameters = uppercase_dict_keys(self.inputs.parameters.get_dict(),
dict_name='parameters')
# No reserved parameter keywords should be provided
self._check_reserved_keywords(parameters)
# Load parameter schema
with open(self._INPUT_SCHEMA, 'r') as stream:
schema = json.load(stream)
# Automatically generate input parameters for derived fields, e.g. structure -> Atoms.Unitvectors, etc.
parameters = self._generate_input_parameters(
self.inputs.structure, self.inputs.kpoints, parameters,
self.inputs.pseudos, self.inputs.orbitals,
self.inputs.orbital_configurations)
# Get a lowercase-value-only version of the parameters dictionary
parameters = lowercase_dict_values(parameters)
# Validate input parameters
self._validate_inputs(self.inputs.structure, self.inputs.kpoints,
parameters, self.inputs.pseudos,
self.inputs.orbitals,
self.inputs.orbital_configurations, schema)
# Get input file contents and lists of the pseudopotential and orbital files which need to be copied
input_file_content = write_input_file(parameters, schema)
local_copy_pseudo_list, local_copy_orbital_list = self._generate_local_copy_lists(
self.inputs.pseudos, self.inputs.orbitals)
local_copy_list += local_copy_pseudo_list
local_copy_list += local_copy_orbital_list
# Add output files to retrieve which have been specified to write in the input parameters
retrieve_list = []
if parameters.get('BAND_NKPATH', 0) > 0 and parameters.get(
'SCF_EIGENVALUESOLVER', 'band') == 'band':
retrieve_list.append(self._DATAFILE_BAND_FILE)
if parameters.get('MD_TYPE', 'nomd') != 'nomd':
retrieve_list.append(self._DATAFILE_MD_FILE)
retrieve_list.append(self._DATAFILE_MD2_FILE)
# Write input file
with folder.open(self._INPUT_FILE, 'w') as handle:
handle.write(input_file_content)
# Fill out the `CodeInfo`
codeinfo = datastructures.CodeInfo()
codeinfo.code_uuid = self.inputs.code.uuid
codeinfo.withmpi = True
codeinfo.cmdline_params = ([self._INPUT_FILE] +
list(settings.pop('CMDLINE', [])))
codeinfo.stdout_name = self._OUTPUT_FILE
# Fill out the `CalcInfo`
calcinfo = datastructures.CalcInfo()
calcinfo.uuid = str(self.uuid)
calcinfo.codes_info = [codeinfo]
calcinfo.local_copy_list = local_copy_list
calcinfo.remote_copy_list = remote_copy_list
calcinfo.remote_symlink_list = remote_symlink_list
calcinfo.retrieve_list = retrieve_list
calcinfo.retrieve_list.append(self._OUTPUT_FILE)
calcinfo.retrieve_list += settings.pop('ADDITIONAL_RETRIEVE_LIST', [])
# TODO: pop parser settings and report remaining unknown settings
return calcinfo
def prepare_for_submission(self, folder): #pylint: disable=too-many-locals, too-many-statements # noqa: disable=MC0001
"""
Routine which creates the input file of Wannier90
:param folder: a aiida.common.folders.Folder subclass where
the plugin should put all its files.
"""
self._validate_input_output_names()
param_dict = self.inputs.parameters.get_dict()
self._validate_lowercase(param_dict)
self._validate_input_parameters(param_dict)
if 'settings' in self.inputs:
settings_dict = self.inputs.settings.get_dict()
else:
settings_dict = {}
self._validate_lowercase(settings_dict)
pp_setup = settings_dict.pop('postproc_setup', False)
if pp_setup:
param_dict.update({'postproc_setup': True})
has_local_input = 'local_input_folder' in self.inputs
has_remote_input = 'remote_input_folder' in self.inputs
if pp_setup:
if has_local_input or has_local_input:
raise exc.InputValidationError(
"Can not set 'local_input_folder' or 'remote_input_folder' "
"with the 'postproc_setup' option.")
else:
if has_local_input and has_remote_input:
raise exc.InputValidationError(
"Both the 'local_input_folder' and 'remote_input_folder' "
"inputs are set, but they are exclusive. Exactly one of "
"the two must be given.")
if not (has_local_input or has_remote_input):
raise exc.InputValidationError(
"None of the 'local_input_folder' and 'remote_input_folder' "
"inputs is set. Exactly one of the two must be given.")
############################################################
# End basic check on inputs
############################################################
random_projections = settings_dict.pop('random_projections', False)
write_win(
filename=folder.get_abs_path('{}.win'.format(self._SEEDNAME)),
parameters=param_dict,
structure=self.inputs.structure,
kpoints=self.inputs.kpoints,
kpoint_path=getattr(self.inputs, 'kpoint_path', None),
projections=getattr(self.inputs, 'projections', None),
random_projections=random_projections,
)
input_file_lists = self._get_input_file_lists(pp_setup=pp_setup)
#######################################################################
calcinfo = datastructures.CalcInfo()
calcinfo.uuid = self.uuid
calcinfo.local_copy_list = input_file_lists.local_copy_list + settings_dict.pop(
"additional_local_copy_list", [])
calcinfo.remote_copy_list = input_file_lists.remote_copy_list + settings_dict.pop(
"additional_remote_copy_list", [])
calcinfo.remote_symlink_list = input_file_lists.remote_symlink_list + settings_dict.pop(
"additional_remote_symlink_list", [])
codeinfo = datastructures.CodeInfo()
codeinfo.code_uuid = self.inputs.code.uuid
codeinfo.cmdline_params = [self._SEEDNAME]
calcinfo.codes_info = [codeinfo]
calcinfo.codes_run_mode = datastructures.CodeRunMode.SERIAL
retrieve_list = [
self._SEEDNAME + suffix
for suffix in self._DEFAULT_RETRIEVE_SUFFIXES
]
exclude_retrieve_list = settings_dict.pop("exclude_retrieve_list", [])
retrieve_list = [
filename for filename in retrieve_list if not any(
fnmatch.fnmatch(filename, pattern)
for pattern in exclude_retrieve_list)
]
calcinfo.retrieve_list = retrieve_list
calcinfo.retrieve_temporary_list = []
if pp_setup:
# The parser will then put this in a SinglefileData (if present)
calcinfo.retrieve_temporary_list.append('{}.nnkp'.format(
self._SEEDNAME))
# Retrieves bands automatically, if they are calculated
calcinfo.retrieve_list += settings_dict.pop("additional_retrieve_list",
[])
# pop input keys not used here
settings_dict.pop('seedname', None)
if settings_dict:
raise exc.InputValidationError(
"The following keys in settings are unrecognized: {}".format(
list(settings_dict.keys())))
return calcinfo
def prepare_for_submission(self, folder): # pylint: disable=too-many-branches,too-many-statements
"""Prepare the calculation job for submission by transforming input nodes into input files.
In addition to the input files being written to the sandbox folder, a `CalcInfo` instance will be returned that
contains lists of files that need to be copied to the remote machine before job submission, as well as file
lists that are to be retrieved after job completion.
:param folder: a sandbox folder to temporarily write files on disk.
:return: :py:`~aiida.common.datastructures.CalcInfo` instance.
"""
# Put the first-level keys as uppercase (i.e., namelist and card names) and the second-level keys as lowercase
parameters = _uppercase_dict(self.inputs.parameters.get_dict(), dict_name='parameters')
parameters = {k: _lowercase_dict(v, dict_name=k) for k, v in parameters.items()}
# Same for settings.
if 'settings' in self.inputs:
settings = _uppercase_dict(self.inputs.settings.get_dict(), dict_name='settings')
else:
settings = {}
# Set default values. NOTE: this is different from PW/CP
for blocked in self._blocked_keywords:
namelist = blocked[0].upper()
key = blocked[1].lower()
value = blocked[2]
if namelist in parameters:
if key in parameters[namelist]:
raise exceptions.InputValidationError(
"You cannot specify explicitly the '{}' key in the '{}' "
'namelist.'.format(key, namelist))
else:
parameters[namelist] = {}
parameters[namelist][key] = value
# Restrict the plot output to the file types that we want to be able to parse
dimension_to_output_format = {
0: 0, # Spherical integration -> Gnuplot, 1D
1: 0, # 1D -> Gnuplot, 1D
2: 7, # 2D -> Gnuplot, 2D
3: 6, # 3D -> Gaussian cube
4: 0, # Polar on a sphere -> # Gnuplot, 1D
}
parameters['PLOT']['output_format'] = dimension_to_output_format[parameters['PLOT']['iflag']]
namelists_toprint = self._default_namelists
input_filename = self.inputs.metadata.options.input_filename
with folder.open(input_filename, 'w') as infile:
for namelist_name in namelists_toprint:
infile.write('&{0}\n'.format(namelist_name))
# namelist content; set to {} if not present, so that we leave an empty namelist
namelist = parameters.pop(namelist_name, {})
for key, value in sorted(namelist.items()):
infile.write(convert_input_to_namelist_entry(key, value))
infile.write('/\n')
# Check for specified namelists that are not expected
if parameters:
raise exceptions.InputValidationError(
'The following namelists are specified in parameters, but are '
'not valid namelists for the current type of calculation: '
'{}'.format(','.join(list(parameters.keys()))))
remote_copy_list = []
local_copy_list = []
# Copy remote output dir
parent_calc_folder = self.inputs.get('parent_folder', None)
if isinstance(parent_calc_folder, orm.RemoteData):
remote_copy_list.append((
parent_calc_folder.computer.uuid,
os.path.join(parent_calc_folder.get_remote_path(), self._INPUT_SUBFOLDER),
self._OUTPUT_SUBFOLDER
))
remote_copy_list.append((
parent_calc_folder.computer.uuid,
os.path.join(parent_calc_folder.get_remote_path(), self._PSEUDO_SUBFOLDER),
self._PSEUDO_SUBFOLDER
))
elif isinstance(parent_calc_folder, orm.FolderData):
for filename in parent_calc_folder.list_object_names():
local_copy_list.append((
parent_calc_folder.uuid,
filename,
os.path.join(self._OUTPUT_SUBFOLDER, filename)
))
local_copy_list.append((
parent_calc_folder.uuid,
filename,
os.path.join(self._PSEUDO_SUBFOLDER, filename)
))
codeinfo = datastructures.CodeInfo()
codeinfo.cmdline_params = settings.pop('CMDLINE', [])
codeinfo.stdin_name = self.inputs.metadata.options.input_filename
codeinfo.stdout_name = self.inputs.metadata.options.output_filename
codeinfo.code_uuid = self.inputs.code.uuid
calcinfo = datastructures.CalcInfo()
calcinfo.codes_info = [codeinfo]
calcinfo.local_copy_list = local_copy_list
calcinfo.remote_copy_list = remote_copy_list
# Retrieve by default the output file
calcinfo.retrieve_list = [self.inputs.metadata.options.output_filename]
calcinfo.retrieve_temporary_list = []
# Depending on the `plot_num` and the corresponding parameters, more than one pair of `filplot` + `fileout`
# files may be written. In that case, the data files will have `filplot` as a prefix with some suffix to
# distinguish them from one another. The `fileout` filename will be the full data filename with the `fileout`
# value as a suffix.
retrieve_tuples = [
self._FILEOUT,
('{}_*{}'.format(self._FILPLOT, self._FILEOUT), '.', 0)
]
if self.inputs.metadata.options.keep_plot_file:
calcinfo.retrieve_list.extend(retrieve_tuples)
else:
calcinfo.retrieve_temporary_list.extend(retrieve_tuples)
return calcinfo
def prepare_for_submission(self, folder):
"""
Create the input files from the input nodes passed to this instance of the `CalcJob`.
"""
# pylint: disable=too-many-locals
# Generate the content of the structure file based on the input
# structure
structure_filecontent, _ = generate_lammps_structure(
self.inputs.structure,
self.inputs.potential.atom_style,
)
# Get the name of the structure file and write it to the remote folder
_structure_filename = self.inputs.metadata.options.structure_filename
with folder.open(_structure_filename, 'w') as handle:
handle.write(structure_filecontent)
# Get the parameters dictionary so that they can be used for creating
# the input file
_parameters = self.inputs.parameters.get_dict()
# Get the name of the trajectory file
_trajectory_filename = self.inputs.metadata.options.trajectory_filename
# Get the name of the variables file
_variables_filename = self.inputs.metadata.options.variables_filename
# Get the name of the restart file
_restart_filename = self.inputs.metadata.options.restart_filename
# Get the name of the output file
_output_filename = self.inputs.metadata.options.output_filename
# Get the name of the logfile file
_logfile_filename = self.inputs.metadata.options.logfile_filename
# If there is a restartfile set its name to the input variables and
# write it in the remote folder
if 'input_restartfile' in self.inputs:
_read_restart_filename = self._DEFAULT_READ_RESTART_FILENAME
with folder.open(_read_restart_filename, 'wb') as handle:
handle.write(self.inputs.input_restartfile.get_content())
else:
_read_restart_filename = None
# Write the input file content. This function will also check the
# sanity of the passed paremters when comparing it to a schema
input_filecontent = generate_input_file(
potential=self.inputs.potential,
structure=self.inputs.structure,
parameters=_parameters,
restart_filename=_restart_filename,
trajectory_filename=_trajectory_filename,
variables_filename=_variables_filename,
read_restart_filename=_read_restart_filename,
)
# Get the name of the input file, and write it to the remote folder
_input_filename = self.inputs.metadata.options.input_filename
with folder.open(_input_filename, 'w') as handle:
handle.write(input_filecontent)
# Write the potential to the remote folder
with folder.open(self._DEFAULT_POTENTIAL_FILENAME, 'w') as handle:
handle.write(self.inputs.potential.get_content())
codeinfo = datastructures.CodeInfo()
# Command line variables to ensure that the input file from LAMMPS can
# be read
codeinfo.cmdline_params = [
'-in', _input_filename, '-log', _logfile_filename
]
# Set the code uuid
codeinfo.code_uuid = self.inputs.code.uuid
# Set the name of the stdout
codeinfo.stdout_name = _output_filename
# Set whether or not one is running with MPI
codeinfo.withmpi = self.inputs.metadata.options.withmpi
# Generate the datastructure for the calculation information
calcinfo = datastructures.CalcInfo()
calcinfo.uuid = str(self.uuid)
# Set the files that must be retrieved
calcinfo.retrieve_list = []
calcinfo.retrieve_list.append(_output_filename)
calcinfo.retrieve_list.append(_logfile_filename)
calcinfo.retrieve_list.append(_restart_filename)
calcinfo.retrieve_list.append(_variables_filename)
calcinfo.retrieve_list.append(_trajectory_filename)
# Set the information of the code into the calculation datastructure
calcinfo.codes_info = [codeinfo]
return calcinfo
def prepare_for_submission(self, folder):
self.inputs.metadata.options.parser_name = 'z2pack.z2pack'
self.inputs.metadata.options.output_filename = self._OUTPUT_Z2PACK_FILE
self.inputs.metadata.options.input_filename = self._INPUT_Z2PACK_FILE
calcinfo = datastructures.CalcInfo()
codeinfo = datastructures.CodeInfo()
codeinfo.stdout_name = self._OUTPUT_Z2PACK_FILE
codeinfo.stdin_name = self._INPUT_Z2PACK_FILE
codeinfo.code_uuid = self.inputs.code.uuid
calcinfo.codes_info = [codeinfo]
calcinfo.codes_run_mode = datastructures.CodeRunMode.SERIAL
calcinfo.cmdline_params = []
calcinfo.retrieve_list = []
calcinfo.retrieve_temporary_list = []
calcinfo.local_copy_list = []
calcinfo.remote_copy_list = []
calcinfo.remote_symlink_list = []
inputs = [
self._INPUT_PW_NSCF_FILE,
self._INPUT_OVERLAP_FILE,
self._INPUT_W90_FILE,
]
outputs = [
self._OUTPUT_Z2PACK_FILE,
self._OUTPUT_SAVE_FILE,
self._OUTPUT_RESULT_FILE,
]
errors = [
os.path.join('build', a)
for a in [self._ERROR_W90_FILE, self._ERROR_PW_FILE]
]
calcinfo.retrieve_list.extend(outputs)
calcinfo.retrieve_list.extend(errors)
parent = self.inputs.parent_folder
rpath = parent.get_remote_path()
uuid = parent.computer.uuid
parent_type = parent.creator.process_class
if parent_type == Z2packCalculation:
self._set_inputs_from_parent_z2pack()
elif parent_type == PwCalculation:
self._set_inputs_from_parent_scf()
pw_dct = _lowercase_dict(self.inputs.pw_parameters.get_dict(),
'pw_dct')
sys = pw_dct['system']
if sys.get('noncolin', False) and sys.get('lspinorb', False):
self._blocked_keywords_wannier90.append(('spinors', True))
try:
settings = _lowercase_dict(self.inputs.z2pack_settings.get_dict(),
'z2pack_settings')
except AttributeError:
raise exceptions.InputValidationError(
'Must provide `z2pack_settings` input for `scf` calculation.')
symlink = settings.get('parent_folder_symlink', False)
self.restart_mode = settings.get('restart_mode', True)
ptr = calcinfo.remote_symlink_list if symlink else calcinfo.remote_copy_list
if parent_type == PwCalculation:
prepare_nscf(self, folder)
prepare_overlap(self, folder)
prepare_wannier90(self, folder)
elif parent_type == Z2packCalculation:
if self.restart_mode:
calcinfo.remote_copy_list.append((
uuid,
os.path.join(rpath, self._OUTPUT_SAVE_FILE),
self._OUTPUT_SAVE_FILE,
))
calcinfo.remote_copy_list.extend([(uuid, os.path.join(rpath,
inp), inp)
for inp in inputs])
else:
raise exceptions.ValidationError(
'parent node must be either from a PWscf or a Z2pack calculation.'
)
parent_files = [self._PSEUDO_SUBFOLDER, self._OUTPUT_SUBFOLDER]
ptr.extend([(uuid, os.path.join(rpath, fname), fname)
for fname in parent_files])
prepare_z2pack(self, folder)
return calcinfo