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 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):
"""
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): # noqa: MC0001 - is mccabe too complex funct -
"""
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
"""
code = self.inputs.code
ldos_folder = self.inputs.ldos_folder
value = self.inputs.value
spin_option = self.inputs.spin_option
mode = self.inputs.mode
# As internal convention, the keys of the settings dict are uppercase
if 'settings' in self.inputs:
settings = self.inputs.settings.get_dict()
settings_dict = {str(k).upper(): v for (k, v) in settings.items()}
else:
settings_dict = {}
# List of files for restart
remote_copy_list = []
# ======================== Creation of input file =========================
# Input file is only necessary for the old versions of plstm.
# For the new versions, all is done through command line (next section).
# To have easy access to inputs metadata options
metadataoption = self.inputs.metadata.options
# input_filename access
input_filename = folder.get_abs_path(metadataoption.input_filename)
# Getting the prefix from ldos_folder
if "prefix" in ldos_folder.creator.attributes:
prefix = str(ldos_folder.creator.get_attribute("prefix"))
else:
self.report(
"No prefix detected from the remote folder, set 'aiida' as prefix"
)
prefix = "aiida"
ldosfile = prefix + ".LDOS"
# Convert height to bohr...
if mode.value == "constant-height":
vvalue = value.value / 0.529177
else:
vvalue = value.value
with open(input_filename, 'w') as infile:
infile.write(f"{prefix}\n")
infile.write("ldos\n")
infile.write(f"{mode.value}\n")
infile.write(f"{vvalue:.5f}\n")
infile.write("unformatted\n")
# ============================== Code and Calc info ===============================
# Code information object is used to set up the the bash line that launches siesta
# (CMDLINE and input output files).
# Calc information object is to set up thee list of files to retrieve.
# The presence of a 'ldos_folder' is mandatory, to get the LDOS file as indicated in
# the self._restart_copy_from attribute. (this is not technically a restart, though)
# It will be copied to the current calculation's working folder.
remote_copy_list.append(
(ldos_folder.computer.uuid,
os.path.join(ldos_folder.get_remote_path(),
self._restart_copy_from), self._restart_copy_to))
# Empty command line by default. Why use 'pop' ?
cmdline_params = settings_dict.pop('CMDLINE', [])
# Code information object. Sets the command line
codeinfo = CodeInfo()
if mode.value == "constant-height":
cmdline_params = (list(cmdline_params) +
['-z', '{0:.5f}'.format(vvalue)])
else:
cmdline_params = (list(cmdline_params) +
['-i', '{0:.5f}'.format(vvalue)])
if spin_option.value != "q":
cmdline_params = (list(cmdline_params) +
['-s', str(spin_option.value), ldosfile])
else:
cmdline_params = (list(cmdline_params) + [ldosfile])
codeinfo.cmdline_params = list(cmdline_params)
codeinfo.stdin_name = metadataoption.input_filename
codeinfo.stdout_name = metadataoption.output_filename
codeinfo.code_uuid = code.uuid
# Calc information object. Important for files to copy, retrieve, etc
calcinfo = CalcInfo()
calcinfo.uuid = str(self.uuid)
calcinfo.local_copy_list = [
] #No local files to copy (no pseudo for instance)
calcinfo.remote_copy_list = remote_copy_list
calcinfo.codes_info = [codeinfo]
# Retrieve by default: the output file and the plot file. Some logic to understand which
# is the plot file will be in parser, here we put to retrieve every file ending in *.STM
calcinfo.retrieve_list = []
calcinfo.retrieve_list.append(metadataoption.output_filename)
calcinfo.retrieve_list.append("*.STM")
# 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
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, 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
def prepare_for_submission(
self, folder): # noqa: MC0001 - is mccabe too complex funct -
"""
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
"""
# ============================ Initializations =============================
# All input ports are validated, here asses their presence in case optional.
code = self.inputs.code
# self.initialize preprocess structure and basis. Decides whether use ions or pseudos
structure, basis_dict, floating_species_names, ion_or_pseudo_str = self.initialize(
)
ion_or_pseudo = self.inputs[ion_or_pseudo_str]
parameters = self.inputs.parameters
if 'kpoints' in self.inputs:
kpoints = self.inputs.kpoints
else:
kpoints = None
# As internal convention, the keys of the settings dict are uppercase
if 'settings' in self.inputs:
settings = self.inputs.settings.get_dict()
settings_dict = {str(k).upper(): v for (k, v) in settings.items()}
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
lua_inputs = self.inputs.lua
if 'script' in lua_inputs:
lua_script = lua_inputs.script
else:
lua_script = None
if 'parameters' in lua_inputs:
lua_parameters = lua_inputs.parameters
else:
lua_parameters = None
if 'input_files' in lua_inputs:
lua_input_files = lua_inputs.input_files
else:
lua_input_files = None
if 'retrieve_list' in lua_inputs:
lua_retrieve_list = lua_inputs.retrieve_list
else:
lua_retrieve_list = None
# List of files to copy in the folder where the calculation runs, e.g. pseudo files
local_copy_list = []
# List of files for restart
remote_copy_list = []
# ================ Preprocess of input parameters =================
input_params = FDFDict(parameters.get_dict())
input_params.update(
{'system-name': self.inputs.metadata.options.prefix})
input_params.update(
{'system-label': self.inputs.metadata.options.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)})
input_params.update({'geometry-must-converge': 'T'})
input_params.update({'lattice-constant': '1.0 Ang'})
input_params.update({'atomic-coordinates-format': 'Ang'})
if lua_script is not None:
input_params.update({'md-type-of-run': 'Lua'})
input_params.update({'lua-script': lua_script.filename})
local_copy_list.append(
(lua_script.uuid, lua_script.filename, lua_script.filename))
if lua_input_files is not None:
# Copy the whole contents of the FolderData object
for file in lua_input_files.list_object_names():
local_copy_list.append((lua_input_files.uuid, file, file))
if ion_or_pseudo_str == "ions":
input_params.update({'user-basis': 'T'})
# NOTES:
# 1) The lattice-constant parameter must be 1.0 Ang to impose the units and consider
# that the dimenstions of the lattice vectors are already correct with no need of alat.
# This breaks the band-k-points "pi/a" option. The use of this option is banned.
# 2) The implicit coordinate convention of the StructureData class corresponds to the "Ang"
# convention in Siesta. That is why "atomic-coordinates-format" is blocked and reset.
# 3) The Siesta code doesn't raise any warining if the geometry is not converged, unless
# the keyword geometry-must-converge is set. That's why it is always added.
# ============================ 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/IONS-------------------------------
atomic_species_card_list = []
# Dictionary to get the atomic number of a given element
datmn = {v['symbol']: k for k, v in elements.items()}
spind = {}
spcount = 0
for kind in structure.kinds:
spcount += 1 # species count
spind[kind.name] = spcount
atomic_number = datmn[kind.symbol]
# Siesta expects negative atomic numbers for floating species
if kind.name in floating_species_names:
atomic_number = -atomic_number
#Create the core of the chemicalspecieslabel block
atomic_species_card_list.append("{0:5} {1:5} {2:5}\n".format(
spind[kind.name], atomic_number, kind.name.rjust(6)))
psp_or_ion = ion_or_pseudo[kind.name]
# Add pseudo (ion) file to the list of files to copy (create), 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 copy the file ('C.psf') twice, once as 'C.psf',
# and once as 'C_surf.psf'. This is required by Siesta.
# It is passed as list of tuples with format ('node_uuid', 'filename', 'relativedestpath').
# Since no subfolder is present in Siesta for pseudos, filename == relativedestpath.
if isinstance(psp_or_ion, IonData):
file_name = kind.name + ".ion"
with folder.open(file_name, 'w', encoding='utf8') as handle:
handle.write(psp_or_ion.get_content_ascii_format())
if isinstance(psp_or_ion, (PsfData, DeprecatedPsfData)):
local_copy_list.append(
(psp_or_ion.uuid, psp_or_ion.filename, kind.name + ".psf"))
if isinstance(psp_or_ion, (PsmlData, DeprecatedPsmlData)):
local_copy_list.append((psp_or_ion.uuid, psp_or_ion.filename,
kind.name + ".psml"))
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 (default of siesta)
if kpoints is not None:
mesh, offset = kpoints.get_kpoints_mesh()
kpoints_card_list = ["%block kgrid_monkhorst_pack\n"]
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.
# 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 not supported because a=1 always. BandLinesScale ReciprocalLatticeVectors
# always set.
if bandskpoints is not None:
#the band line scale
bandskpoints_card_list = [
"BandLinesScale ReciprocalLatticeVectors\n"
]
#set the BandPoints
if bandskpoints.labels is None:
bandskpoints_card_list.append("%block BandPoints\n")
for kpo in bandskpoints.get_kpoints():
bandskpoints_card_list.append(
"{0:8.3f} {1:8.3f} {2:8.3f} \n".format(
kpo[0], kpo[1], kpo[2]))
fbkpoints_card = "".join(bandskpoints_card_list)
fbkpoints_card += "%endblock BandPoints\n"
#set the BandLines
else:
bandskpoints_card_list.append("%block BandLines\n")
savindx = []
listforbands = bandskpoints.get_kpoints()
for indx, label in bandskpoints.labels:
savindx.append(indx)
rawindex = 0
for indx, label in bandskpoints.labels:
rawindex = rawindex + 1
x, y, z = listforbands[indx]
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, label))
else:
bandskpoints_card_list.append(
"{0:3} {1:8.3f} {2:8.3f} {3:8.3f} {4:1} \n".format(
indx - savindx[rawindex - 2], x, y, z, label))
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, just the density-matrix file is copied
# to the current calculation's working folder.
# ISSUE: Is this mechanism flexible enough? An alternative would be to
# 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 = folder.get_abs_path(metadataoption.input_filename)
# Print to file
with open(input_filename, 'w') as infile:
# Parameters
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.
if basis_dict: #It migh also be empty dict. In such case we do not write.
infile.write("#\n# -- Basis Set Info follows\n#\n")
for k, v in basis_dict.items():
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
# This should prevent SiestaCalculation from being terminated by scheduler, however the
# strategy is not 100% effective since SIESTA checks the simulation time versus max-walltime
# only at the end of each SCF and geometry step. The scheduler might kill the process in between.
infile.write("#\n# -- Max wall-clock time block\n#\n")
infile.write(
f"maxwalltime {metadataoption.max_wallclock_seconds}\n")
# ================================== Lua parameters file ===================================
if lua_parameters is not None:
lua_config_filename = folder.get_abs_path("config.lua")
# Generate a 'config.lua' file with Lua syntax
with open(lua_config_filename, 'w') as f_lua:
f_lua.write("--- Lua script parameters \n")
for k, v in lua_parameters.get_dict().items():
if isinstance(v, str):
f_lua.write('%s = "%s"\n' % (k, v))
else:
f_lua.write("%s = %s\n" % (k, v))
# ============================= 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)
calcinfo.local_copy_list = local_copy_list
calcinfo.remote_copy_list = remote_copy_list
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 = []
xml_file = str(metadataoption.prefix) + ".xml"
bands_file = str(metadataoption.prefix) + ".bands"
calcinfo.retrieve_list.append(metadataoption.output_filename)
calcinfo.retrieve_list.append(xml_file)
calcinfo.retrieve_list.append(self._JSON_FILE)
calcinfo.retrieve_list.append(self._MESSAGES_FILE)
calcinfo.retrieve_list.append(self._BASIS_ENTHALPY_FILE)
calcinfo.retrieve_list.append("*.ion.xml")
if bandskpoints is not None:
calcinfo.retrieve_list.append(bands_file)
if lua_retrieve_list is not None:
calcinfo.retrieve_list += lua_retrieve_list.get_list()
# If we ever want to avoid having the config.lua file in the repository,
# since the information is already in the lua_parameters dictionary:
# if lua_parameters is not None:
# calcinfo.provenance_exclude_list = ['config.lua']
# 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
def _prepare_codeinfo(self):
# Prepare CodeInfo object for aiida
codeinfo = CodeInfo()
codeinfo.code_uuid = self.inputs.code.uuid
codeinfo.stdin_name = self.inputs.metadata.options.input_filename
return codeinfo