def validate_inputs(value, _):
"""
Validate the entire input namespace. It takes care to ckeck the consistency
and compatibility of the inputed basis, pseudos, pseudofamilies and ions.
Also calls the `bandskpoints_warnings` that issues warning about bandskpoints selection.
It is similar to the `validate_inputs` of SiestaCalculation but with the additional complexity
due to the presence of 'pseudo_family' input.
"""
import warnings
bandskpoints_warnings(value)
if 'basis' in value:
structure = internal_structure(value["structure"],
value["basis"].get_dict())
if structure is None:
return "Not possibe to specify `floating_sites` (ghosts) with the same name of a structure kind."
else:
structure = value["structure"]
#Check each kind in the structure (including freshly added ghosts) have a corresponding pseudo or ion
kinds = [kind.name for kind in structure.kinds]
if 'ions' in value:
quantity = 'ions'
if 'pseudos' in value or 'pseudo_family' in value:
warnings.warn(
"At least one ion file in input, all the pseudos or pseudo_family will be ignored"
)
else:
quantity = 'pseudos'
if 'pseudos' not in value and 'pseudo_family' not in value:
return "No `pseudos`, nor `ions`, nor `pseudo_family` specified in input"
if 'pseudos' in value and 'pseudo_family' in value:
return "You cannot specify both `pseudos` and `pseudo_family`"
if 'pseudo_family' in value:
group = orm.Group.get(label=value['pseudo_family'].value)
# To be removed in v2.0
if "data" in group.type_string:
from aiida_siesta.data.common import get_pseudos_from_structure
try:
get_pseudos_from_structure(structure,
value['pseudo_family'].value)
except NotExistent:
return "The pseudo family does not incude all the required pseudos"
else:
try:
group.get_pseudos(structure=structure)
except ValueError:
return "The pseudo family does not incude all the required pseudos"
else:
if set(kinds) != set(value[quantity].keys()):
ps_io = ', '.join(list(value[quantity].keys()))
kin = ', '.join(list(kinds))
string_out = (
'mismatch between defined pseudos/ions and the list of kinds of the structure\n'
+ f' pseudos/ions: {ps_io} \n kinds(including ghosts): {kin}')
return string_out
def prepare_pseudo_inputs(self,
structure,
pseudos=None,
pseudo_family=None):
from aiida.orm import Str
if pseudos and pseudo_family:
raise ValueError(
'you cannot specify both "pseudos" and "pseudo_family"')
elif pseudos is None and pseudo_family is None:
raise ValueError(
'neither an explicit pseudos dictionary nor a pseudo_family was specified'
)
elif pseudo_family:
# This will already raise some exceptions, potentially, like the ones below
pseudos = get_pseudos_from_structure(structure,
pseudo_family.value)
elif isinstance(pseudos, (six.string_types, Str)):
raise TypeError(
'you passed "pseudos" as a string - maybe you wanted to pass it as "pseudo_family" instead?'
)
for kind in structure.get_kind_names():
if kind not in pseudos:
raise ValueError(
'no pseudo available for element {}'.format(kind))
return pseudos
def _get_pseudos(self, key, structure):
family = self._protocols[key]["pseudo_family"]
group = Group.get(label=family)
# To be removed in v2.0
if "data" in group.type_string:
from aiida_siesta.data.common import get_pseudos_from_structure
pseudos = get_pseudos_from_structure(structure, family)
return pseudos
pseudos = group.get_pseudos(structure=structure)
return pseudos
def prepare_inputs(self):
"""
Initialize context variables. Note that in context we must include
exactly the same data nodes obtained in input (except the parameters
where we add `max-walltime`)
On the contrary, useless nodes would be created.
"""
self.report("Preparing inputs of the SiestaBaseWorkChain")
structure = self.inputs.structure
self.ctx.inputs = {
'code': self.inputs.code,
'parameters': self.inputs.parameters,
'structure': structure,
'metadata': {
'options': self.inputs.options.get_dict(),
}
}
# Ions or pseudos
if 'ions' in self.inputs:
self.ctx.inputs['ions'] = self.inputs.ions
else:
if "pseudo_family" in self.inputs:
fam_name = self.inputs.pseudo_family.value
group = orm.Group.get(label=fam_name)
if 'basis' in self.inputs:
temp_structure = internal_structure(
structure, self.inputs.basis.get_dict())
# To be removed in v2.0
if "data" in group.type_string:
from aiida_siesta.data.common import get_pseudos_from_structure
self.ctx.inputs[
'pseudos'] = get_pseudos_from_structure(
temp_structure, fam_name)
else:
self.ctx.inputs['pseudos'] = group.get_pseudos(
structure=temp_structure)
else:
# To be removed in v2.0
if "data" in group.type_string:
from aiida_siesta.data.common import get_pseudos_from_structure
self.ctx.inputs[
'pseudos'] = get_pseudos_from_structure(
structure, fam_name)
else:
self.ctx.inputs['pseudos'] = group.get_pseudos(
structure=structure)
else:
self.ctx.inputs['pseudos'] = self.inputs.pseudos
# Now the optional inputs
if 'basis' in self.inputs:
self.ctx.inputs['basis'] = self.inputs.basis
if 'kpoints' in self.inputs:
self.ctx.inputs['kpoints'] = self.inputs.kpoints
if 'settings' in self.inputs:
self.ctx.inputs['settings'] = self.inputs.settings
if 'bandskpoints' in self.inputs:
self.ctx.want_band_structure = True
self.ctx.inputs['bandskpoints'] = self.inputs.bandskpoints
if 'parent_calc_folder' in self.inputs:
self.ctx.inputs[
'parent_calc_folder'] = self.inputs.parent_calc_folder