def prepare_for_submission(self, folder):
# create code info
codeinfo = CodeInfo()
codeinfo.code_uuid = self.inputs.code.uuid
codeinfo.cmdline_params = [
self.PARENT_FOLDER_NAME + "/" + self.inputs.chk_name.value, self.DEFAULT_OUTPUT_FILE
]
codeinfo.withmpi = self.inputs.metadata.options.withmpi
# create calculation info
calcinfo = CalcInfo()
calcinfo.uuid = self.uuid
calcinfo.codes_info = [codeinfo]
calcinfo.retrieve_list = []
if self.inputs.retrieve_fchk:
calcinfo.retrieve_list.append(self.DEFAULT_OUTPUT_FILE)
# symlink or copy to parent calculation
calcinfo.remote_symlink_list = []
calcinfo.remote_copy_list = []
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):
"""
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
"""
settings = self.inputs.settings.get_dict(
) if 'settings' in self.inputs else {}
param_dict = self.inputs.parameters.get_dict()
# ---------------------------------------------------
# Write params.ini file
params_fn = folder.get_abs_path("params.ini")
with open(params_fn, 'w') as f:
for key, val in param_dict.items():
line = str(key) + " "
if isinstance(val, list):
line += " ".join(str(v) for v in val)
else:
line += str(val)
f.write(line + '\n')
# ---------------------------------------------------
# create code info
codeinfo = CodeInfo()
codeinfo.code_uuid = self.inputs.code.uuid
codeinfo.withmpi = False
# create calc info
calcinfo = CalcInfo()
calcinfo.uuid = self.uuid
calcinfo.codes_info = [codeinfo]
# file lists
calcinfo.remote_symlink_list = []
calcinfo.local_copy_list = [
(self.inputs.atomtypes.uuid, self.inputs.atomtypes.filename,
'atomtypes.ini')
]
calcinfo.remote_copy_list = []
calcinfo.retrieve_list = ["*/*/*.npy"]
# 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()
copy_info = (comp_uuid, remote_path, 'parent_calc_folder/')
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
# EOF
def prepare_for_submission(self, folder):
"""Create the input files from the input nodes passed to this instance of the `CalcJob`.
:param folder: an `aiida.common.folders.Folder` to temporarily write files on disk
:return: `aiida.common.datastructures.CalcInfo` instance
"""
self.logger.info("prepare_for_submission")
# These three lists are updated in self._create_additional_files(folder)
self._internal_retrieve_list = []
self._additional_cmd_params = []
self._calculation_cmd = []
self._create_additional_files(folder)
# ================= prepare the python input files =================
# BORN
if (not self.inputs.fc_only and 'nac_params' in self.inputs
and 'primitive' in self.inputs
and 'symmetry_tolerance' in self.inputs.settings.attributes):
born_txt = get_BORN_txt(self.inputs.nac_params,
self.inputs.primitive,
self.inputs.settings['symmetry_tolerance'])
with folder.open(self._INPUT_NAC, 'w', encoding='utf8') as handle:
handle.write(born_txt)
for params in self._additional_cmd_params:
params.append('--nac')
# ============================ calcinfo ===============================
local_copy_list = []
remote_copy_list = []
calcinfo = CalcInfo()
calcinfo.uuid = self.uuid
calcinfo.local_copy_list = local_copy_list
calcinfo.remote_copy_list = remote_copy_list
calcinfo.retrieve_list = self._internal_retrieve_list
calcinfo.codes_info = []
for i, (default_params, additional_params) in enumerate(
zip(self._calculation_cmd, self._additional_cmd_params)):
codeinfo = CodeInfo()
codeinfo.cmdline_params = default_params + additional_params
codeinfo.code_uuid = self.inputs.code.uuid
codeinfo.stdout_name = "%s%d" % (self.options.output_filename,
i + 1)
codeinfo.withmpi = False
calcinfo.codes_info.append(codeinfo)
return calcinfo
def prepare_for_submission(self, folder):
# create calculation info
calcinfo = CalcInfo()
calcinfo.uuid = self.uuid
calcinfo.codes_info = []
calcinfo.retrieve_list = []
for key, params in self.inputs.parameters.get_dict().items():
cube_name = key+".cube"
kind_str = params["kind"]
npts = params["npts"]
# create code info
codeinfo = CodeInfo()
codeinfo.cmdline_params = []
codeinfo.cmdline_params.append(str(self.inputs.metadata.options.resources['tot_num_mpiprocs']))
codeinfo.cmdline_params.append(kind_str)
codeinfo.cmdline_params.append(self._PARENT_FOLDER_NAME + "/" + self._DEFAULT_INPUT_FILE)
codeinfo.cmdline_params.append(cube_name)
codeinfo.cmdline_params.append(str(npts))
codeinfo.code_uuid = self.inputs.code.uuid
codeinfo.withmpi = self.inputs.metadata.options.withmpi
calcinfo.codes_info.append(codeinfo)
if self.inputs.retrieve_cubes.value:
calcinfo.retrieve_list.append(cube_name)
extra_prepend = "\nexport GAUSS_MEMDEF=%dMB\n" % self.inputs.gauss_memdef
if not hasattr(calcinfo, 'prepend_text') or not calcinfo.prepend_text:
calcinfo.prepend_text = extra_prepend
else:
calcinfo.prepend_text += extra_prepend
# symlink or copy to parent calculation
calcinfo.remote_symlink_list = []
calcinfo.remote_copy_list = []
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 input files.
:param folder: an `aiida.common.folders.Folder` to temporarily write files on disk
:return: `aiida.common.datastructures.CalcInfo` instance
"""
# Prepare CalcInfo to be returned to aiida
calcinfo = CalcInfo()
calcinfo.uuid = self.uuid
# network infers file format from file extension
structure = self.inputs.structure
structure_filename = self.inputs.parameters.get_structure_file_name(
structure)
calcinfo.local_copy_list = [(structure.uuid, structure.filename,
structure_filename)]
if 'atomic_radii' in self.inputs:
atomic_radii = self.inputs.atomic_radii
radii_file_name = atomic_radii.filename
calcinfo.local_copy_list.append(
(atomic_radii.uuid, atomic_radii.filename,
atomic_radii.filename))
else:
radii_file_name = None
calcinfo.remote_copy_list = []
calcinfo.retrieve_list = self.inputs.parameters.output_files
codeinfo = CodeInfo()
codeinfo.cmdline_params = self.inputs.parameters.cmdline_params(
structure_file_name=structure_filename,
radii_file_name=radii_file_name)
codeinfo.code_uuid = self.inputs.code.uuid
codeinfo.withmpi = False
calcinfo.codes_info = [codeinfo]
return calcinfo
def prepare_for_submission(self, folder):
"""
Create input files.
:param folder: aiida.common.folders.Folder subclass where
the plugin should put all its files.
"""
# create input files: d3
structure = self.inputs.get('structure', None)
try:
d3_content = D3(self.inputs.parameters.get_dict(), structure)
except (ValueError, NotImplementedError) as err:
raise InputValidationError(
"an input file could not be created from the parameters: {}".
format(err))
with folder.open(self._INPUT_FILE_NAME, "w") as f:
d3_content.write(f)
# create input files: fort.9
with self.inputs.wavefunction.open(mode="rb") as f:
folder.create_file_from_filelike(f,
self._WAVEFUNCTION_FILE_NAME,
mode="wb")
# Prepare CodeInfo object for aiida
codeinfo = CodeInfo()
codeinfo.code_uuid = self.inputs.code.uuid
codeinfo.stdin_name = self._INPUT_FILE_NAME
codeinfo.stdout_name = self._OUTPUT_FILE_NAME
codeinfo.withmpi = False
# Prepare CalcInfo object for aiida
calcinfo = CalcInfo()
calcinfo.uuid = self.uuid
calcinfo.codes_info = [codeinfo]
calcinfo.local_copy_list = []
calcinfo.remote_copy_list = []
calcinfo.retrieve_list = [self._PROPERTIES_FILE_NAME]
calcinfo.local_copy_list = []
return calcinfo
def prepare_for_submission(self, folder):
"""
The baseclass will only setup the basic calcinfo arguments but will
not write **any** files which has to be implemented in the subclassed
prepare_for_submission() method
"""
# if no custodian code is defined directly run the VASP calculation,
# i.e. initialize the CodeInfo for the passed VASP code
if not self.inputs.custodian.get('code', False):
codeinfo = CodeInfo()
codeinfo.code_uuid = self.inputs.code.uuid
codeinfo.stdout_name = self._default_output_file
codeinfo.stderr_name = self._default_error_file
# otherwise wrap in Custodian calculation and initialize CodeInfo for
# the passed Custodian code (This is sufficient as AiiDA will scan all
# Code-inputs to generate the required prepend / append lines)
else:
codeinfo = CodeInfo()
codeinfo.code_uuid = self.inputs.custodian.code.uuid
# define custodian-exe command line arguments
codeinfo.cmdline_params = ['run', PluginDefaults.CSTDN_SPEC_FNAME]
# never add the MPI command to custodian since it will call
# VASP using MPI itself
codeinfo.withmpi = False
calcinfo = CalcInfo()
calcinfo.uuid = self.uuid
calcinfo.codes_info = [codeinfo]
# those list are set defined in the inherited classes
calcinfo.local_copy_list = []
calcinfo.remote_copy_list = []
calcinfo.remote_symlink_list = []
# retrieve lists are defined on the base class
calcinfo.retrieve_temporary_list = self.retrieve_temporary_list()
calcinfo.retrieve_list = self.retrieve_permanent_list()
# need to set run mode since presubmit() takes all code inputs into
# account and would complain if both vasp and custodian codes are set
calcinfo.codes_run_mode = CodeRunMode.SERIAL
# finally write the neccessary calculation inputs to the calculation's
# input folder
calcinfo = self.create_calculation_inputs(folder, calcinfo)
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.CalcInfo` instance
"""
# assert that the potential and structure have the same kind elements
if self.inputs.potential.allowed_element_names is not None and not set(
k.symbol for k in self.inputs.structure.kinds
).issubset(self.inputs.potential.allowed_element_names):
raise ValidationError(
"the structure and potential are not compatible (different kind elements)"
)
# Setup structure
structure_txt, struct_transform = generate_lammps_structure(
self.inputs.structure, self.inputs.potential.atom_style
)
with open(
tempfolder.get_abs_path(self.options.cell_transform_filename), "w+b"
) as handle:
np.save(handle, struct_transform)
if "parameters" in self.inputs:
parameters = self.inputs.parameters
else:
parameters = Dict()
# Setup input parameters
input_txt = self.create_main_input_content(
parameter_data=parameters,
potential_data=self.inputs.potential,
kind_symbols=[kind.symbol for kind in self.inputs.structure.kinds],
structure_filename=self._INPUT_STRUCTURE,
trajectory_filename=self.options.trajectory_suffix,
system_filename=self.options.system_suffix,
restart_filename=self.options.restart_filename,
)
input_filename = tempfolder.get_abs_path(self._INPUT_FILE_NAME)
with open(input_filename, "w") as infile:
infile.write(input_txt)
self.validate_parameters(parameters, self.inputs.potential)
retrieve_list, retrieve_temporary_list = self.get_retrieve_lists()
retrieve_list.extend(
[self.options.output_filename, self.options.cell_transform_filename]
)
# prepare extra files if needed
self.prepare_extra_files(tempfolder, self.inputs.potential)
# =========================== dump to file =============================
structure_filename = tempfolder.get_abs_path(self._INPUT_STRUCTURE)
with open(structure_filename, "w") as infile:
infile.write(structure_txt)
for name, content in self.inputs.potential.get_external_files().items():
fpath = tempfolder.get_abs_path(name)
with open(fpath, "w") as infile:
infile.write(content)
# ============================ calcinfo ================================
codeinfo = CodeInfo()
codeinfo.cmdline_params = list(self._cmdline_params)
codeinfo.code_uuid = self.inputs.code.uuid
codeinfo.withmpi = self.metadata.options.withmpi
codeinfo.stdout_name = self._stdout_name
calcinfo = CalcInfo()
calcinfo.uuid = self.uuid
calcinfo.retrieve_list = retrieve_list
calcinfo.retrieve_temporary_list = retrieve_temporary_list
calcinfo.codes_info = [codeinfo]
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, folder):
"""Create the input files from the input nodes passed to this instance of the `CalcJob`.
:param folder: an `aiida.common.folders.Folder` to temporarily write files on disk
:return: `aiida.common.datastructures.CalcInfo` instance
"""
self.logger.info("prepare_for_submission")
self._internal_retrieve_list = []
self._additional_cmd_params = []
self._calculation_cmd = []
settings = self.inputs.settings
structure = self.inputs.structure
code = self.inputs.code
##############################
# END OF INITIAL INPUT CHECK #
##############################
# ================= prepare the python input files =================
self._create_additional_files(folder)
cell_txt = get_poscar_txt(structure)
input_txt = get_phonopy_conf_file_txt(settings)
input_filename = folder.get_abs_path(
self.inputs.metadata.options.input_filename)
with open(input_filename, 'w') as infile:
infile.write(input_txt)
cell_filename = folder.get_abs_path(self._INPUT_CELL)
with open(cell_filename, 'w') as infile:
infile.write(cell_txt)
if ('nac_params' in self.inputs and 'primitive' in self.inputs):
born_txt = get_BORN_txt(self.inputs.nac_params,
self.inputs.primitive,
settings['symmetry_tolerance'])
nac_filename = folder.get_abs_path(self._INPUT_NAC)
with open(nac_filename, 'w') as infile:
infile.write(born_txt)
for params in self._additional_cmd_params:
params.append('--nac')
# ============================ calcinfo ===============================
local_copy_list = []
remote_copy_list = []
calcinfo = CalcInfo()
calcinfo.uuid = self.uuid
# Empty command line by default
calcinfo.local_copy_list = local_copy_list
calcinfo.remote_copy_list = remote_copy_list
# Retrieve files
calcinfo.retrieve_list = self._internal_retrieve_list
calcinfo.codes_info = []
for default_params, additional_params in zip(
self._calculation_cmd, self._additional_cmd_params):
codeinfo = CodeInfo()
codeinfo.cmdline_params = ([
self.inputs.metadata.options.input_filename,
] + default_params + additional_params)
codeinfo.code_uuid = code.uuid
codeinfo.stdout_name = self.inputs.metadata.options.output_filename
codeinfo.withmpi = False
calcinfo.codes_info.append(codeinfo)
return calcinfo
def prepare_for_submission(self, folder):
# create calculation info
calcinfo = CalcInfo()
calcinfo.uuid = self.uuid
calcinfo.codes_info = []
calcinfo.retrieve_list = []
calcinfo.retrieve_temporary_list = []
calcinfo.prepend_text = "export GAUSS_MEMDEF=%dMB\n" % self.inputs.gauss_memdef
calcinfo.local_copy_list = []
if "stencil" in self.inputs:
calcinfo.local_copy_list.append(
(self.inputs.stencil.uuid, self.inputs.stencil.filename,
'stencil.txt'))
for key, params in self.inputs.parameters.get_dict().items():
cube_name = key + ".cube"
kind_str = params["kind"]
npts = params["npts"]
# create code info
codeinfo = CodeInfo()
codeinfo.cmdline_params = []
codeinfo.cmdline_params.append(
str(self.inputs.metadata.options.resources['tot_num_mpiprocs'])
)
codeinfo.cmdline_params.append(kind_str)
codeinfo.cmdline_params.append(self.PARENT_FOLDER_NAME + "/" +
self.DEFAULT_INPUT_FILE)
codeinfo.cmdline_params.append(cube_name)
if npts == -1:
if 'stencil' not in self.inputs:
self.report(
"Warning: npts: -1 set but no stencil provided, using -2"
)
codeinfo.cmdline_params.append("-2")
else:
codeinfo.cmdline_params.append(str(npts))
codeinfo.stdin_name = "stencil.txt"
else:
codeinfo.cmdline_params.append(str(npts))
codeinfo.code_uuid = self.inputs.code.uuid
codeinfo.withmpi = self.inputs.metadata.options.withmpi
calcinfo.codes_info.append(codeinfo)
if self.inputs.retrieve_cubes.value:
calcinfo.retrieve_list.append(cube_name)
else:
calcinfo.retrieve_temporary_list.append(cube_name)
# symlink or copy to parent calculation
calcinfo.remote_symlink_list = []
calcinfo.remote_copy_list = []
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
"""
# create json input file
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()
# replace all the random seed
input['model']['descriptor']['seed'] = np.random.randint(100000000)
input['model']['fitting_net']['seed'] = np.random.randint(100000000)
input['training']['seed'] = np.random.randint(100000000)
warn("All seeds in user input will be automatically replaced by numpy.")
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")
# Create the subfolder that will contain the train data
local_copy_list = []
for datadir in self.inputs.datadirs:
# change to absolute path
if not os.path.exists(datadir):
raise FileExistsError("This datadir dose not exist")
absdatadir = os.path.abspath(datadir)
# create subfolder
datadir_basename = os.path.basename(absdatadir)
datadir_in_workdir = os.path.join("./", datadir_basename)
folder.get_subfolder(datadir_in_workdir, create=True)
# this loop use to copy the training data under the datadir
for root, directories, files in os.walk(top=absdatadir, topdown=True):
relroot = os.path.relpath(root, absdatadir)
# create subtree folders
for name in directories:
folder.get_subfolder(
os.path.join(
datadir_basename,
relroot,
name),
create=True)
# give the singlefiledata to file
for name in files:
fobj = SinglefileData(
file=os.path.join(root, name)
)
# must save fobj otherwise the node is empty and can't be copied
fobj.store()
dst_path = os.path.join(
datadir_basename,
relroot,
name)
local_copy_list.append((fobj.uuid, fobj.filename, dst_path))
# settings = self.inputs.settings.get_dict() if 'settings' in self.inputs else {}
# set two code info here, once the training finished, the model will freeze then.
# create code info for training
codeinfotrain = CodeInfo()
codeinfotrain.cmdline_params = ["train", self._DEFAULT_INPUT_FILE]
#codeinfotrain.stdin_name = self._DEFAULT_INPUT_FILE
codeinfotrain.stdout_name = self._DEFAULT_TRAIN_OUTPUT_FILE
codeinfotrain.join_files = True
codeinfotrain.code_uuid = self.inputs.code.uuid
codeinfotrain.withmpi = self.inputs.metadata.options.withmpi
# create code info for freeze
codeinfofreeze = CodeInfo()
codeinfofreeze.cmdline_params = ["freeze", '-o', self._DEFAULT_FREEZE_OUTPUT_FILE]
#codeinfofreeze.stdout_name = self._DEFAULT_FREEZE_OUTPUT_FILE
codeinfofreeze.code_uuid = self.inputs.code.uuid
codeinfofreeze.withmpi = self.inputs.metadata.options.withmpi
# create calc info
calcinfo = CalcInfo()
calcinfo.uuid = self.uuid
calcinfo.local_copy_list = local_copy_list
calcinfo.codes_info = [codeinfotrain, codeinfofreeze]
calcinfo.retrieve_list = [
self._DEFAULT_TRAIN_OUTPUT_FILE,
self._DEFAULT_FREEZE_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.CalcInfo` instance
"""
# assert that the potential and structure have the same kind elements
if [k.symbol for k in self.inputs.structure.kinds] != self.inputs.potential.kind_elements:
raise ValidationError("the structure and potential are not compatible (different kind elements)")
# Setup potential
potential_txt = self.inputs.potential.get_potential_file()
# Setup structure
structure_txt, struct_transform = generate_lammps_structure(
self.inputs.structure, self.inputs.potential.atom_style)
with open(tempfolder.get_abs_path(self.options.cell_transform_filename), 'w+b') as handle:
np.save(handle, struct_transform)
if "parameters" in self.inputs:
parameters = self.inputs.parameters
else:
parameters = Dict()
pdict = parameters.get_dict()
# Check lammps version date in parameters
lammps_date = convert_date_string(
pdict.get("lammps_version", '11 Aug 2017'))
# Setup input parameters
input_txt = self._generate_input_function(
parameters=parameters,
potential_obj=self.inputs.potential,
structure_filename=self._INPUT_STRUCTURE,
trajectory_filename=self.options.trajectory_name,
info_filename=self.options.info_filename,
restart_filename=self.options.restart_filename,
add_thermo_keywords=pdict.get("thermo_keywords", []),
version_date=lammps_date)
input_filename = tempfolder.get_abs_path(self._INPUT_FILE_NAME)
with open(input_filename, 'w') as infile:
infile.write(input_txt)
self.validate_parameters(parameters, self.inputs.potential)
# prepare extra files if needed
self.prepare_extra_files(tempfolder, self.inputs.potential)
# =========================== dump to file =============================
structure_filename = tempfolder.get_abs_path(self._INPUT_STRUCTURE)
with open(structure_filename, 'w') as infile:
infile.write(structure_txt)
if potential_txt is not None:
potential_filename = tempfolder.get_abs_path(
self.inputs.potential.potential_filename)
with open(potential_filename, 'w') as infile:
infile.write(potential_txt)
# ============================ calcinfo ================================
codeinfo = CodeInfo()
codeinfo.cmdline_params = self._cmdline_params
codeinfo.code_uuid = self.inputs.code.uuid
codeinfo.withmpi = False # Set lammps openmpi environment properly
codeinfo.stdout_name = self._stdout_name
calcinfo = CalcInfo()
calcinfo.uuid = self.uuid
calcinfo.retrieve_list = self._retrieve_list + [
self.options.output_filename,
self.options.cell_transform_filename]
calcinfo.retrieve_temporary_list = self._retrieve_temporary_list
calcinfo.codes_info = [codeinfo]
return calcinfo