def prepare_for_submission(self, folder):
"""
This is the routine to be called when you want to create
the input files and related stuff with a plugin.
:param folder: a aiida.common.folders.Folder subclass where
the plugin should put all its files.
"""
if 'structure' in self.inputs:
pmg_structure = self.inputs.structure.get_pymatgen_molecule()
else:
# If structure is not specified, it is read from the chk file
pmg_structure = None
# Generate the input file
input_string = GaussianCalculation._render_input_string_from_params(
self.inputs.parameters.get_dict(), pmg_structure)
with open(folder.get_abs_path(self.INPUT_FILE), "w") as out_file:
out_file.write(input_string)
settings = self.inputs.settings.get_dict(
) if "settings" in self.inputs else {}
# create code info
codeinfo = CodeInfo()
codeinfo.cmdline_params = settings.pop("cmdline", [])
codeinfo.code_uuid = self.inputs.code.uuid
codeinfo.stdin_name = self.INPUT_FILE
codeinfo.stdout_name = self.OUTPUT_FILE
codeinfo.withmpi = self.inputs.metadata.options.withmpi
# create calculation info
calcinfo = CalcInfo()
calcinfo.remote_copy_list = []
calcinfo.local_copy_list = []
calcinfo.uuid = self.uuid
calcinfo.cmdline_params = codeinfo.cmdline_params
calcinfo.stdin_name = self.INPUT_FILE
calcinfo.stdout_name = self.OUTPUT_FILE
calcinfo.codes_info = [codeinfo]
calcinfo.retrieve_list = [self.OUTPUT_FILE]
# symlink or copy to parent calculation
calcinfo.remote_symlink_list = []
calcinfo.remote_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.PARENT_FOLDER_NAME)
if (self.inputs.code.computer.uuid == comp_uuid):
# if running on the same computer - make a symlink
# if not - copy the folder
calcinfo.remote_symlink_list.append(copy_info)
else:
calcinfo.remote_copy_list.append(copy_info)
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
"""
from aiida_orca.utils import OrcaInput
# create input structure(s)
if 'structure' in self.inputs:
self._write_structure(self.inputs.structure, folder,
self._INPUT_COORDS_FILE)
settings = self.inputs.settings.get_dict(
) if 'settings' in self.inputs else {}
# create code info
codeinfo = CodeInfo()
codeinfo.cmdline_params = settings.pop('cmdline',
[]) + [self._INPUT_FILE]
codeinfo.stdout_name = self._OUTPUT_FILE
codeinfo.join_files = True
codeinfo.code_uuid = self.inputs.code.uuid
# create calc info
calcinfo = CalcInfo()
calcinfo.uuid = self.uuid
calcinfo.cmdline_params = codeinfo.cmdline_params
calcinfo.stdin_name = self._INPUT_FILE
calcinfo.stdout_name = self._OUTPUT_FILE
calcinfo.codes_info = [codeinfo]
# files or additional structures
if 'file' in self.inputs:
calcinfo.local_copy_list = []
for name, obj in self.inputs.file.items():
if name == 'gbw':
calcinfo.local_copy_list.append(
(obj.uuid, obj.filename, 'aiida_old.gbw'))
else:
calcinfo.local_copy_list.append(
(obj.uuid, obj.filename, obj.filename))
# Retrive list
calcinfo.retrieve_list = [
self._OUTPUT_FILE, self._GBW_FILE, self._HESSIAN_FILE,
self._RELAX_COORDS_FILE
]
calcinfo.retrieve_list += settings.pop('additional_retrieve_list', [])
# create ORCA input file
# inp = OrcaInput(self.inputs.parameters.get_dict(), remote_path=remote_path)
inp = OrcaInput(self.inputs.parameters.get_dict())
with io.open(folder.get_abs_path(self._INPUT_FILE), mode='w') as fobj:
fobj.write(inp.render())
return calcinfo
def prepare_for_submission(self, folder):
"""
This is the routine to be called when you want to create
the input files and related stuff with a plugin.
:param folder: a aiida.common.folders.Folder subclass where
the plugin should put all its files.
"""
# create calc info
calcinfo = CalcInfo()
calcinfo.remote_copy_list = []
calcinfo.local_copy_list = []
# The main input
try:
input_string = GaussianCalculation._render_input_string_from_params(
self.inputs.parameters.get_dict(), self.inputs.structure
)
# If structure is not specified the user might want to restart from a chk
except AttributeError:
input_string = GaussianCalculation._render_input_string_from_params(
self.inputs.parameters.get_dict(), None
)
# Parse additional link1 sections
if "extra_link1_sections" in self.inputs:
for l1_name, l1_params in self.inputs.extra_link1_sections.items():
input_string += "--Link1--\n"
# The link1 secions don't support their own geometries.
input_string += GaussianCalculation._render_input_string_from_params(
l1_params.get_dict(), None
)
with open(folder.get_abs_path(self.INPUT_FILE), "w") as out_file:
out_file.write(input_string)
settings = self.inputs.settings.get_dict() if "settings" in self.inputs else {}
# create code info
codeinfo = CodeInfo()
codeinfo.cmdline_params = settings.pop("cmdline", [])
codeinfo.code_uuid = self.inputs.code.uuid
codeinfo.stdin_name = self.INPUT_FILE
codeinfo.stdout_name = self.OUTPUT_FILE
codeinfo.withmpi = self.inputs.metadata.options.withmpi
# create calculation info
calcinfo.uuid = self.uuid
calcinfo.cmdline_params = codeinfo.cmdline_params
calcinfo.stdin_name = self.INPUT_FILE
calcinfo.stdout_name = self.OUTPUT_FILE
calcinfo.codes_info = [codeinfo]
calcinfo.retrieve_list = [self.OUTPUT_FILE]
# symlink or copy to parent calculation
calcinfo.remote_symlink_list = []
calcinfo.remote_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, "parent_calc")
if (
self.inputs.code.computer.uuid == comp_uuid
): # if running on the same computer - make a symlink
# if not - copy the folder
calcinfo.remote_symlink_list.append(copy_info)
else:
calcinfo.remote_copy_list.append(copy_info)
return calcinfo
def prepare_for_submission(self, tempfolder):
# Setup template
with open(self.inputs.template, 'r') as tempfile:
temp_contents = tempfile.read()
lmp_template = Template(temp_contents)
# # check variables
# for variable in self.inputs.variables.values():
# if not isinstance(variable, list):
# raise TypeError('Values in variables must be list')
# check kinds
if 'kinds' in self.inputs:
kind_var = {
kind: kind_index + 1
for kind_index, kind in enumerate(self.inputs.kinds)
}
lmp_template = Template(lmp_template.safe_substitute(**kind_var))
for i, case in enumerate(self.inputs.cases):
structure = case.pop('structure')
if isinstance(structure, StructureData):
structure_txt, struct_transform = generate_lammps_structure(
structure, kinds=self.inputs.kinds)
elif isinstance(structure, SinglefileData):
structure_txt = structure.get_content()
else:
raise TypeError(
'Input structure must be StructureData or SinglefileData')
input_txt = lmp_template.safe_substitute(**case)
# ========================= dump to file ===========================
tempfolder.get_subfolder(i, create=True)
input_filename = tempfolder.get_abs_path(
f'{i}/{self._INPUT_FILE_NAME}')
with open(input_filename, 'w') as infile:
infile.write(input_txt)
structure_filename = tempfolder.get_abs_path(
f'{i}/{self._INPUT_STRUCTURE}')
with open(structure_filename, 'w') as infile:
infile.write(structure_txt)
case_filename = tempfolder.get_abs_path(f'{i}/case.json')
case.update({'structure pk': structure.pk})
with open(case_filename, 'w') as infile:
json.dump(case, infile, sort_keys=True, indent=2)
# ============================ calcinfo ================================
settings = self.inputs.settings.get_dict() \
if 'settings' in self.inputs else {}
codeinfo = CodeInfo()
codeinfo.cmdline_params = self._cmdline_params
codeinfo.code_uuid = self.inputs.code.uuid
codeinfo.stdout_name = self._stdout_name
codeinfo.join_files = True
calcinfo = CalcInfo()
calcinfo.uuid = self.uuid
calcinfo.prepend_text = (f'for i in $(seq 0 {i})\n'
'do\n'
'cd "${i}" || exit')
calcinfo.append_text = ('cd ..\n' 'done')
calcinfo.cmdline_params = codeinfo.cmdline_params
calcinfo.stdin_name = self._INPUT_FILE_NAME
calcinfo.stdout_name = self._stdout_name
calcinfo.retrieve_list = self._retrieve_list + [
self.options.output_filename
]
calcinfo.retrieve_list += settings.pop('additional_retrieve_list', [])
calcinfo.retrieve_temporary_list = self._retrieve_temporary_list
calcinfo.codes_info = [codeinfo]
# =========================== local_copy_list ==========================
if 'file' in self.inputs:
calcinfo.local_copy_list = []
for name, obj in self.inputs.file.items():
calcinfo.local_copy_list.append(
(obj.uuid, obj.filename, f'{name}.pb'))
return calcinfo
def prepare_for_submission(self, tempfolder):
# Setup structure
if isinstance(self.inputs.structure, StructureData):
structure_txt, struct_transform = generate_lammps_structure(
self.inputs.structure, kinds=self.inputs.kinds)
elif isinstance(self.inputs.structure, SinglefileData):
structure_txt = self.inputs.structure.get_content()
else:
raise TypeError(
'Input structure must be StructureData or SinglefileData')
with open(self.inputs.template, 'r') as tempfile:
temp_contents = tempfile.read()
init_temp = Template(temp_contents)
input_txt = init_temp.safe_substitute(**self.inputs.variables)
if 'kinds' in self.inputs:
kind_temp = Template(input_txt)
kind_var = {
kind: kind_index + 1
for kind_index, kind in enumerate(self.inputs.kinds)
}
input_txt = kind_temp.safe_substitute(**kind_var)
# =========================== dump to file =============================
input_filename = tempfolder.get_abs_path(self._INPUT_FILE_NAME)
with open(input_filename, 'w') as infile:
infile.write(input_txt)
structure_filename = tempfolder.get_abs_path(self._INPUT_STRUCTURE)
with open(structure_filename, 'w') as infile:
infile.write(structure_txt)
# ============================ calcinfo ================================
settings = self.inputs.settings.get_dict() \
if 'settings' in self.inputs else {}
codeinfo = CodeInfo()
codeinfo.cmdline_params = self._cmdline_params
codeinfo.code_uuid = self.inputs.code.uuid
codeinfo.stdout_name = self._stdout_name
codeinfo.join_files = True
calcinfo = CalcInfo()
calcinfo.uuid = self.uuid
calcinfo.cmdline_params = codeinfo.cmdline_params
calcinfo.stdin_name = self._INPUT_FILE_NAME
calcinfo.stdout_name = self._stdout_name
calcinfo.retrieve_list = self._retrieve_list + [
self.options.output_filename
]
calcinfo.retrieve_list += settings.pop('additional_retrieve_list', [])
calcinfo.retrieve_temporary_list = self._retrieve_temporary_list
calcinfo.codes_info = [codeinfo]
# =========================== local_copy_list ==========================
if 'file' in self.inputs:
calcinfo.local_copy_list = []
for name, obj in self.inputs.file.items():
calcinfo.local_copy_list.append(
(obj.uuid, obj.filename, f'{name}.pb'))
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
"""
from aiida_cp2k.utils import Cp2kInput
# create cp2k input file
inp = Cp2kInput(self.inputs.parameters.get_dict())
inp.add_keyword("GLOBAL/PROJECT", self._DEFAULT_PROJECT_NAME)
# create input structure(s)
if 'structure' in self.inputs:
# As far as I understand self.inputs.structure can't deal with tags
# self.inputs.structure.export(folder.get_abs_path(self._DEFAULT_COORDS_FILE_NAME), fileformat="xyz")
self._write_structure(self.inputs.structure, folder,
self._DEFAULT_COORDS_FILE_NAME)
# modify the input dictionary accordingly
for i, letter in enumerate('ABC'):
inp.add_keyword('FORCE_EVAL/SUBSYS/CELL/' + letter,
'{:<15} {:<15} {:<15}'.format(
*self.inputs.structure.cell[i]),
override=False,
conflicting_keys=[
'ABC', 'ALPHA_BETA_GAMMA', 'CELL_FILE_NAME'
])
topo = "FORCE_EVAL/SUBSYS/TOPOLOGY"
inp.add_keyword(topo + "/COORD_FILE_NAME",
self._DEFAULT_COORDS_FILE_NAME,
override=False)
inp.add_keyword(topo + "/COORD_FILE_FORMAT",
"XYZ",
override=False,
conflicting_keys=['COORDINATE'])
with io.open(folder.get_abs_path(self._DEFAULT_INPUT_FILE),
mode="w",
encoding="utf-8") as fobj:
try:
fobj.write(inp.render())
except ValueError as exc:
six.raise_from(
InputValidationError(
"invalid keys or values in input parameters found"),
exc)
settings = self.inputs.settings.get_dict(
) if 'settings' in self.inputs else {}
# create code info
codeinfo = CodeInfo()
codeinfo.cmdline_params = settings.pop(
'cmdline', []) + ["-i", self._DEFAULT_INPUT_FILE]
codeinfo.stdout_name = self._DEFAULT_OUTPUT_FILE
codeinfo.join_files = True
codeinfo.code_uuid = self.inputs.code.uuid
# create calc info
calcinfo = CalcInfo()
calcinfo.uuid = self.uuid
calcinfo.cmdline_params = codeinfo.cmdline_params
calcinfo.stdin_name = self._DEFAULT_INPUT_FILE
calcinfo.stdout_name = self._DEFAULT_OUTPUT_FILE
calcinfo.codes_info = [codeinfo]
# files or additional structures
if 'file' in self.inputs:
calcinfo.local_copy_list = []
for name, obj in self.inputs.file.items():
if isinstance(obj, SinglefileData):
calcinfo.local_copy_list.append(
(obj.uuid, obj.filename, obj.filename))
elif isinstance(obj, StructureData):
self._write_structure(obj, folder, name + '.xyz')
calcinfo.retrieve_list = [
self._DEFAULT_OUTPUT_FILE, self._DEFAULT_RESTART_FILE_NAME,
self._DEFAULT_TRAJECT_FILE_NAME
]
calcinfo.retrieve_list += settings.pop('additional_retrieve_list', [])
# symlinks
calcinfo.remote_symlink_list = []
calcinfo.remote_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 self.inputs.code.computer.uuid == comp_uuid: # if running on the same computer - make a symlink
# if not - copy the folder
calcinfo.remote_symlink_list.append(copy_info)
else:
calcinfo.remote_copy_list.append(copy_info)
# check for left over settings
if settings:
raise InputValidationError(
"The following keys have been found " +
"in the settings input node {}, ".format(self.pk) +
"but were not understood: " + ",".join(settings.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
"""
from .utils import Cp2kInput
# create input structure
if "structure" in self.inputs:
self.inputs.structure.export(folder.get_abs_path(
self._DEFAULT_COORDS_FILE_NAME),
fileformat="xyz")
# create cp2k input file
inp = Cp2kInput(self.inputs.parameters.get_dict())
inp.add_keyword("GLOBAL/PROJECT", self._DEFAULT_PROJECT_NAME)
if "structure" in self.inputs:
for i, letter in enumerate("ABC"):
inp.add_keyword(
"FORCE_EVAL/SUBSYS/CELL/" + letter,
"{:<15} {:<15} {:<15}".format(
*self.inputs.structure.cell[i]),
)
topo = "FORCE_EVAL/SUBSYS/TOPOLOGY"
inp.add_keyword(topo + "/COORD_FILE_NAME",
self._DEFAULT_COORDS_FILE_NAME)
inp.add_keyword(topo + "/COORD_FILE_FORMAT", "XYZ")
with io.open(folder.get_abs_path(self._DEFAULT_INPUT_FILE),
mode="w",
encoding="utf-8") as fobj:
try:
inp.to_file(fobj)
except ValueError as exc:
six.raise_from(
InputValidationError(
"invalid keys or values in input parameters found"),
exc,
)
if "settings" in self.inputs:
settings = self.inputs.settings.get_dict()
else:
settings = {}
# create code info
codeinfo = CodeInfo()
codeinfo.cmdline_params = settings.pop("cmdline", []) + [
"-i",
self._DEFAULT_INPUT_FILE,
]
codeinfo.stdout_name = self._DEFAULT_OUTPUT_FILE
codeinfo.join_files = True
codeinfo.code_uuid = self.inputs.code.uuid
# create calc info
calcinfo = CalcInfo()
calcinfo.stdin_name = self._DEFAULT_INPUT_FILE
calcinfo.uuid = self.uuid
calcinfo.cmdline_params = codeinfo.cmdline_params
calcinfo.stdin_name = self._DEFAULT_INPUT_FILE
calcinfo.stdout_name = self._DEFAULT_OUTPUT_FILE
calcinfo.codes_info = [codeinfo]
# file lists
calcinfo.remote_symlink_list = []
if "file" in self.inputs:
calcinfo.local_copy_list = []
for fobj in self.inputs.file.values():
calcinfo.local_copy_list.append(
(fobj.uuid, fobj.filename, fobj.filename))
calcinfo.remote_copy_list = []
calcinfo.retrieve_list = [
self._DEFAULT_OUTPUT_FILE,
self._DEFAULT_RESTART_FILE_NAME,
]
calcinfo.retrieve_list += settings.pop("additional_retrieve_list", [])
# symlinks
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()
symlink = (comp_uuid, remote_path,
self._DEFAULT_PARENT_CALC_FLDR_NAME)
calcinfo.remote_symlink_list.append(symlink)
# check for left over settings
if settings:
raise InputValidationError(
"The following keys have been found " +
"in the settings input node {}, ".format(self.pk) +
"but were not understood: " + ",".join(settings.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
"""
# pylint: disable=too-many-statements,too-many-branches
# Create cp2k input file.
inp = Cp2kInput(self.inputs.parameters.get_dict())
inp.add_keyword("GLOBAL/PROJECT", self._DEFAULT_PROJECT_NAME)
# Create input structure(s).
if 'structure' in self.inputs:
# As far as I understand self.inputs.structure can't deal with tags
# self.inputs.structure.export(folder.get_abs_path(self._DEFAULT_COORDS_FILE_NAME), fileformat="xyz")
self._write_structure(self.inputs.structure, folder, self._DEFAULT_COORDS_FILE_NAME)
# modify the input dictionary accordingly
for i, letter in enumerate('ABC'):
inp.add_keyword('FORCE_EVAL/SUBSYS/CELL/' + letter,
'{:<15} {:<15} {:<15}'.format(*self.inputs.structure.cell[i]),
override=False,
conflicting_keys=['ABC', 'ALPHA_BETA_GAMMA', 'CELL_FILE_NAME'])
topo = "FORCE_EVAL/SUBSYS/TOPOLOGY"
inp.add_keyword(topo + "/COORD_FILE_NAME", self._DEFAULT_COORDS_FILE_NAME, override=False)
inp.add_keyword(topo + "/COORD_FILE_FORMAT", "XYZ", override=False, conflicting_keys=['COORDINATE'])
if 'basissets' in self.inputs:
validate_basissets(inp, self.inputs.basissets,
self.inputs.structure if 'structure' in self.inputs else None)
write_basissets(inp, self.inputs.basissets, folder)
if 'pseudos' in self.inputs:
validate_pseudos(inp, self.inputs.pseudos, self.inputs.structure if 'structure' in self.inputs else None)
write_pseudos(inp, self.inputs.pseudos, folder)
# Kpoints.
if 'kpoints' in self.inputs:
try:
mesh, _ = self.inputs.kpoints.get_kpoints_mesh()
except AttributeError:
raise InputValidationError("K-point sampling for SCF must be given in mesh form.")
inp.add_keyword('FORCE_EVAL/DFT/KPOINTS', {'WAVEFUNCTIONS': ' COMPLEX', 'FULL_GRID': '.TRUE.'})
inp.add_keyword('FORCE_EVAL/DFT/KPOINTS/SCHEME MONKHORST-PACK', f'{mesh[0]} {mesh[1]} {mesh[2]}')
with io.open(folder.get_abs_path(self._DEFAULT_INPUT_FILE), mode="w", encoding="utf-8") as fobj:
try:
fobj.write(inp.render())
except ValueError as exc:
raise InputValidationError("Invalid keys or values in input parameters found") from exc
settings = self.inputs.settings.get_dict() if 'settings' in self.inputs else {}
# Create code info.
codeinfo = CodeInfo()
codeinfo.cmdline_params = settings.pop('cmdline', []) + ["-i", self._DEFAULT_INPUT_FILE]
codeinfo.stdout_name = self._DEFAULT_OUTPUT_FILE
codeinfo.join_files = True
codeinfo.code_uuid = self.inputs.code.uuid
# Create calc info.
calcinfo = CalcInfo()
calcinfo.uuid = self.uuid
calcinfo.cmdline_params = codeinfo.cmdline_params
calcinfo.stdin_name = self._DEFAULT_INPUT_FILE
calcinfo.stdout_name = self._DEFAULT_OUTPUT_FILE
calcinfo.codes_info = [codeinfo]
# Files or additional structures.
if 'file' in self.inputs:
calcinfo.local_copy_list = []
for name, obj in self.inputs.file.items():
if isinstance(obj, SinglefileData):
calcinfo.local_copy_list.append((obj.uuid, obj.filename, obj.filename))
elif isinstance(obj, StructureData):
self._write_structure(obj, folder, name + '.xyz')
calcinfo.retrieve_list = [
self._DEFAULT_OUTPUT_FILE, self._DEFAULT_RESTART_FILE_NAME, self._DEFAULT_TRAJECT_FILE_NAME
]
calcinfo.retrieve_list += settings.pop('additional_retrieve_list', [])
# Symlinks.
calcinfo.remote_symlink_list = []
calcinfo.remote_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)
# Check for left over settings.
if settings:
raise InputValidationError(
f"The following keys have been found in the settings input node {self.pk}, but were not understood: " +
",".join(settings.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
"""
# from aiida_deepmd.utils import DpInput
# create json input file
# input = DpInput(self.inputs.model.get_dict(), self.inputs.learning_rate.get_dict(), self.inputs.loss.get_dict(), self.inputs.training.get_dict())
input = dict()
input['model'] = self.inputs.model.get_dict()
input['learning_rate'] = self.inputs.learning_rate.get_dict()
input['loss'] = self.inputs.loss.get_dict()
input['training'] = self.inputs.training.get_dict()
json_str = json.dumps(input, indent=4, sort_keys=False)
with io.open(folder.get_abs_path(self._DEFAULT_INPUT_FILE), mode="w", encoding="utf-8") as fobj:
try:
fobj.write(json_str)
except ValueError as exc:
raise InputValidationError("invalid keys or values in input parameters found")
local_copy_list = []
# Create the subfolder that will contain the train data
folder.get_subfolder(self._TRAIN_DATA_SUBFOLDER, create=True)
for fn in self.inputs.file:
fobj = self.inputs.file[fn]
src_path = fobj.filename
dst_path = os.path.join(self._TRAIN_DATA_SUBFOLDER, fobj.filename)
local_copy_list.append((fobj.uuid, src_path, dst_path))
def create_array_from_files(files):
for f in files:
content = f.get_content()
# function from aiida_ce
pass
return data_array
# create train set and store the data in
data_array = create_array_from_files(self.inputs.file)
# for simplicity do not split the folder
n = 0
set_folder = folder.get_subfolder(os.path.join(self._TRAIN_DATA_SUBFOLDER, self._TRAIN_SET_PRFIX + str(n)), create=True)
with io.open(set_folder.get_abs_path(coord.npy), mode="w") as fobj:
try:
np.dump(fobj, array=data_array)
except ValueError as exc:
raise InputValidationError("invalid keys or values in input parameters found")
# settings = self.inputs.settings.get_dict() if 'settings' in self.inputs else {}
# create code info
codeinfo = CodeInfo()
codeinfo.cmdline_params = ["train", self._DEFAULT_INPUT_FILE]
codeinfo.stdout_name = self._DEFAULT_OUTPUT_FILE
codeinfo.join_files = True
codeinfo.code_uuid = self.inputs.code.uuid
# create calc info
calcinfo = CalcInfo()
calcinfo.uuid = self.uuid
calcinfo.cmdline_params = codeinfo.cmdline_params
calcinfo.stdin_name = self._DEFAULT_INPUT_FILE
calcinfo.stdout_name = self._DEFAULT_OUTPUT_FILE
calcinfo.local_copy_list = local_copy_list
calcinfo.codes_info = [codeinfo]
calcinfo.retrieve_list = [
# self._DEFAULT_OUTPUT_FILE,
# self._DEFAULT_OUTPUT_INFO_FILE,
# self._DEFAULT_CHECK_META_FILE,
# self._DEFAULT_CHECK_INDEX_FILE,
]
return calcinfo
def prepare_for_submission(self, tempfolder):
"""
Create the input files from the input nodes passed to this instance of the `CalcJob`.
:param tempfolder: an `aiida.common.folders.Folder` to temporarily write files on disk
:return: `aiida.common.datastructures.CalcInfo` instance
"""
#####################################################
# BEGINNING OF INITIAL INPUT CHECK #
# All input ports that are defined via spec.input #
# are checked by default, only need to asses their #
# presence in case they are optional #
#####################################################
code = self.inputs.code
structure = self.inputs.structure
parameters = self.inputs.parameters
if 'kpoints' in self.inputs:
kpoints = self.inputs.kpoints
else:
kpoints = None
if 'basis' in self.inputs:
basis = self.inputs.basis
else:
basis = None
if 'settings' in self.inputs:
settings = self.inputs.settings.get_dict()
settings_dict = _uppercase_dict(settings, dict_name='settings')
else:
settings_dict = {}
if 'bandskpoints' in self.inputs:
bandskpoints = self.inputs.bandskpoints
else:
bandskpoints = None
if 'parent_calc_folder' in self.inputs:
parent_calc_folder = self.inputs.parent_calc_folder
else:
parent_calc_folder = None
pseudos = self.inputs.pseudos
kinds = [kind.name for kind in structure.kinds]
if set(kinds) != set(pseudos.keys()):
raise ValueError(
'Mismatch between the defined pseudos and the list of kinds of the structure.\n',
'Pseudos: {} \n'.format(', '.join(list(pseudos.keys()))),
'Kinds: {}'.format(', '.join(list(kinds))),
)
# List of the file to copy in the folder where the calculation
# runs, for instance pseudo files
local_copy_list = []
# List of files for restart
remote_copy_list = []
##############################
# END OF INITIAL INPUT CHECK #
##############################
# ============== Preprocess of input parameters ===============
# There should be a warning for duplicated (canonicalized) keys
# in the original dictionary in the script
input_params = FDFDict(parameters.get_dict())
# Look for blocked keywords and
# add the proper values to the dictionary
for blocked_key in self._aiida_blocked_keywords:
canonical_blocked = FDFDict.translate_key(blocked_key)
for key in input_params:
if key == canonical_blocked:
raise InputValidationError(
"You cannot specify explicitly the '{}' flag in the "
"input parameters".format(
input_params.get_last_key(key)))
input_params.update({'system-name': self._PREFIX})
input_params.update({'system-label': self._PREFIX})
input_params.update({'use-tree-timer': 'T'})
input_params.update({'xml-write': 'T'})
input_params.update({'number-of-species': len(structure.kinds)})
input_params.update({'number-of-atoms': len(structure.sites)})
# Regarding the lattice-constant parameter:
# -- The variable "alat" is not typically kept anywhere, and
# has already been used to define the vectors.
# We need to specify that the units of these vectors are Ang...
input_params.update({'lattice-constant': '1.0 Ang'})
# Note that this will break havoc with the band-k-points "pi/a"
# option. The use of this option should be banned.
# Note that the implicit coordinate convention of the Structure
# class corresponds to the "Ang" convention in Siesta.
# That is why the "atomic-coordinates-format" keyword is blocked
# and reset.
input_params.update({'atomic-coordinates-format': 'Ang'})
# ============== Preparation of input data ===============
# ---------------- CELL_PARAMETERS ------------------------
cell_parameters_card = "%block lattice-vectors\n"
for vector in structure.cell:
cell_parameters_card += ("{0:18.10f} {1:18.10f} {2:18.10f}"
"\n".format(*vector))
cell_parameters_card += "%endblock lattice-vectors\n"
# --------------ATOMIC_SPECIES & PSEUDOS-------------------
# I create the subfolder that will contain the pseudopotentials
tempfolder.get_subfolder(self._PSEUDO_SUBFOLDER, create=True)
# I create the subfolder with the output data
tempfolder.get_subfolder(self._OUTPUT_SUBFOLDER, create=True)
atomic_species_card_list = []
# Dictionary to get the atomic number of a given element
datmn = dict([(v['symbol'], k) for k, v in six.iteritems(elements)])
spind = {}
spcount = 0
for kind in structure.kinds:
spcount += 1 # species count
spind[kind.name] = spcount
atomic_species_card_list.append("{0:5} {1:5} {2:5}\n".format(
spind[kind.name], datmn[kind.symbol], kind.name.rjust(6)))
ps = pseudos[kind.name]
# Add this pseudo file to the list of files to copy, with
# the appropiate name. In the case of sub-species
# (different kind.name but same kind.symbol, e.g.,
# 'C_surf', sharing the same pseudo with 'C'), we will
# copy the file ('C.psf') twice, once as 'C.psf', and once
# as 'C_surf.psf'. This is required by Siesta.
# ... list of tuples with format ('node_uuid', 'filename', relativedestpath')
# We probably should be pre-pending 'self._PSEUDO_SUBFOLDER' in the
# last slot, for generality...
if isinstance(ps, PsfData):
local_copy_list.append((ps.uuid, ps.filename,
kind.name + ".psf"))
elif isinstance(ps, PsmlData):
local_copy_list.append((ps.uuid, ps.filename,
kind.name + ".psml"))
else:
pass
atomic_species_card_list = (["%block chemicalspecieslabel\n"] +
list(atomic_species_card_list))
atomic_species_card = "".join(atomic_species_card_list)
atomic_species_card += "%endblock chemicalspecieslabel\n"
# Free memory
del atomic_species_card_list
# --------------------- ATOMIC_POSITIONS -----------------------
atomic_positions_card_list = [
"%block atomiccoordinatesandatomicspecies\n"
]
countatm = 0
for site in structure.sites:
countatm += 1
atomic_positions_card_list.append(
"{0:18.10f} {1:18.10f} {2:18.10f} {3:4} {4:6} {5:6}\n".format(
site.position[0], site.position[1], site.position[2],
spind[site.kind_name], site.kind_name.rjust(6), countatm))
atomic_positions_card = "".join(atomic_positions_card_list)
del atomic_positions_card_list # Free memory
atomic_positions_card += "%endblock atomiccoordinatesandatomicspecies\n"
# -------------------- K-POINTS ----------------------------
# It is optional, if not specified, gamma point only is performed,
# this is default of siesta
if kpoints is not None:
#
# Get a mesh for sampling
# NOTE that there is not yet support for the 'kgrid-cutoff'
# option in Siesta.
#
try:
mesh, offset = kpoints.get_kpoints_mesh()
has_mesh = True
except AttributeError:
raise InputValidationError("K-point sampling for scf "
"must be given in mesh form")
kpoints_card_list = ["%block kgrid_monkhorst_pack\n"]
#
# This will fail if has_mesh is False (for the case of a list),
# since in that case 'offset' is undefined.
#
kpoints_card_list.append("{0:6} {1:6} {2:6} {3:18.10f}\n".format(
mesh[0], 0, 0, offset[0]))
kpoints_card_list.append("{0:6} {1:6} {2:6} {3:18.10f}\n".format(
0, mesh[1], 0, offset[1]))
kpoints_card_list.append("{0:6} {1:6} {2:6} {3:18.10f}\n".format(
0, 0, mesh[2], offset[2]))
kpoints_card = "".join(kpoints_card_list)
kpoints_card += "%endblock kgrid_monkhorst_pack\n"
del kpoints_card_list
# ----------------- K-POINTS-FOR-BANDS ----------------------
#Two possibility are supported in Siesta: BandLines ad BandPoints
#At the moment the user can't choose directly one of the two options
#BandsLine is set automatically if bandskpoints has labels,
#BandsPoints if bandskpoints has no labels
#BandLinesScale =pi/a is not supported at the moment because currently
#a=1 always. BandLinesScale ReciprocalLatticeVectors is always set
if bandskpoints is not None:
bandskpoints_card_list = [
"BandLinesScale ReciprocalLatticeVectors\n"
]
if bandskpoints.labels == None:
bandskpoints_card_list.append("%block BandPoints\n")
for s in bandskpoints.get_kpoints():
bandskpoints_card_list.append(
"{0:8.3f} {1:8.3f} {2:8.3f} \n".format(
s[0], s[1], s[2]))
fbkpoints_card = "".join(bandskpoints_card_list)
fbkpoints_card += "%endblock BandPoints\n"
else:
bandskpoints_card_list.append("%block BandLines\n")
savs = []
listforbands = bandskpoints.get_kpoints()
for s, m in bandskpoints.labels:
savs.append(s)
rawindex = 0
for s, m in bandskpoints.labels:
rawindex = rawindex + 1
x, y, z = listforbands[s]
if rawindex == 1:
bandskpoints_card_list.append(
"{0:3} {1:8.3f} {2:8.3f} {3:8.3f} {4:1} \n".format(
1, x, y, z, m))
else:
bandskpoints_card_list.append(
"{0:3} {1:8.3f} {2:8.3f} {3:8.3f} {4:1} \n".format(
s - savs[rawindex - 2], x, y, z, m))
fbkpoints_card = "".join(bandskpoints_card_list)
fbkpoints_card += "%endblock BandLines\n"
del bandskpoints_card_list
# ================ Operations for restart =======================
# The presence of a 'parent_calc_folder' input node signals
# that we want to get something from there, as indicated in the
# self._restart_copy_from attribute.
# In Siesta's case, for now, it is just the density-matrix file
#
# It will be copied to the current calculation's working folder.
# NOTE: This mechanism is not flexible enough.
# Maybe we should pass the information about which file(s) to
# copy in the metadata 'options' dictionary
if parent_calc_folder is not None:
remote_copy_list.append(
(parent_calc_folder.computer.uuid,
os.path.join(parent_calc_folder.get_remote_path(),
self._restart_copy_from), self._restart_copy_to))
input_params.update({'dm-use-save-dm': "T"})
# ====================== FDF file creation ========================
# To have easy access to inputs metadata options
metadataoption = self.inputs.metadata.options
# input_filename = self.inputs.metadata.options.input_filename
input_filename = tempfolder.get_abs_path(metadataoption.input_filename)
with open(input_filename, 'w') as infile:
# here print keys and values tp file
# for k, v in sorted(six.iteritems(input_params)):
for k, v in sorted(input_params.get_filtered_items()):
infile.write("%s %s\n" % (k, v))
# Basis set info is processed just like the general
# parameters section. Some discipline is needed to
# put any basis-related parameters (including blocks)
# in the basis dictionary in the input script.
#
if basis is not None:
infile.write("#\n# -- Basis Set Info follows\n#\n")
for k, v in six.iteritems(basis.get_dict()):
infile.write("%s %s\n" % (k, v))
# Write previously generated cards now
infile.write("#\n# -- Structural Info follows\n#\n")
infile.write(atomic_species_card)
infile.write(cell_parameters_card)
infile.write(atomic_positions_card)
if kpoints is not None:
infile.write("#\n# -- K-points Info follows\n#\n")
infile.write(kpoints_card)
if bandskpoints is not None:
infile.write("#\n# -- Bandlines/Bandpoints Info follows\n#\n")
infile.write(fbkpoints_card)
# Write max wall-clock time
infile.write("#\n# -- Max wall-clock time block\n#\n")
infile.write("max.walltime {}".format(
metadataoption.max_wallclock_seconds))
# ====================== Code and Calc info ========================
# Code information object and Calc information object are now
# only used to set up the CMDLINE (the bash line that launches siesta)
# and to set up the list of files to retrieve.
cmdline_params = settings_dict.pop('CMDLINE', [])
codeinfo = CodeInfo()
codeinfo.cmdline_params = list(cmdline_params)
codeinfo.stdin_name = metadataoption.input_filename
codeinfo.stdout_name = metadataoption.output_filename
codeinfo.code_uuid = code.uuid
calcinfo = CalcInfo()
calcinfo.uuid = str(self.uuid)
if cmdline_params:
calcinfo.cmdline_params = list(cmdline_params)
calcinfo.local_copy_list = local_copy_list
calcinfo.remote_copy_list = remote_copy_list
calcinfo.stdin_name = metadataoption.input_filename
calcinfo.stdout_name = metadataoption.output_filename
calcinfo.codes_info = [codeinfo]
# Retrieve by default: the output file, the xml file, the
# messages file, and the json timing file.
# If bandskpoints, also the bands file is added to the retrieve list.
calcinfo.retrieve_list = []
calcinfo.retrieve_list.append(metadataoption.output_filename)
calcinfo.retrieve_list.append(self._DEFAULT_XML_FILE)
calcinfo.retrieve_list.append(self._DEFAULT_JSON_FILE)
calcinfo.retrieve_list.append(self._DEFAULT_MESSAGES_FILE)
if bandskpoints is not None:
calcinfo.retrieve_list.append(self._DEFAULT_BANDS_FILE)
# Any other files specified in the settings dictionary
settings_retrieve_list = settings_dict.pop('ADDITIONAL_RETRIEVE_LIST',
[])
calcinfo.retrieve_list += settings_retrieve_list
return calcinfo