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, 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`.
"""
# 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, 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
def test_generate(db_test_app, get_structure_data, structure, file_regression):
structure = get_structure_data(structure)
text, transform = generate_lammps_structure(structure, round_dp=8)
file_regression.check(text)