def validate_and_prepare_pseudos_inputs(
structure: orm.StructureData,
pseudos: typ.Optional[typ.Dict[str, typ.Union[Psp8Data, JthXmlData]]] = None
) -> typ.Dict[str, Psp8Data]: # pylint: disable=invalid-name
"""Validate the given pseudos mapping with respect to the given structure.
The pseudos dictionary should now be a dictionary of Psp8Data nodes with the kind as linkname
As such, if there are multiple kinds with the same element, there will be duplicate Psp8Data nodes
but multiple links for the same input node are not allowed. Moreover, to couple the Psp8Data nodes
to the Calculation instance, we have to go through the use_pseudo method, which takes the kind
name as an additional parameter. When creating a Calculation through a Process instance, one
cannot call the use methods directly but rather should pass them as keyword arguments. However,
we can pass the additional parameters by using them as the keys of a dictionary
:param structure: StructureData node
:param pseudos: a dictionary where keys are the kind names and value are Psp8 nodes
:raises: ValueError if no Psp8 is found for every element in the structure
:returns: a dictionary of Psp8 nodes where the key is the kind name
"""
if isinstance(pseudos, (str, orm.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(f'no pseudo available for element {kind}')
elif not isinstance(pseudos[kind], (Psp8Data, JthXmlData)):
raise ValueError(
f'pseudo for element {kind} is not of type Psp8Data or JthXmlData')
return pseudos
def _generate_inputdata(self,
parameters: orm.Dict,
pseudos,
structure: orm.StructureData,
kpoints: orm.KpointsData) -> ty.Tuple[str, list]:
"""Generate the input file content and list of pseudopotential files to copy.
:param parameters: input parameters Dict
:param pseudos: pseudopotential input namespace
:param structure: input structure
:param kpoints: input kpoints
:returns: input file content, pseudopotential copy list
"""
local_copy_pseudo_list = []
# abipy has its own subclass of Pymatgen's `Structure`, so we use that
pmg_structure = structure.get_pymatgen()
abi_structure = AbiStructure.as_structure(pmg_structure)
abi_structure = abi_structure.abi_sanitize(primitive=True)
for kind in structure.get_kind_names():
pseudo = pseudos[kind]
local_copy_pseudo_list.append((pseudo.uuid, pseudo.filename, f'{self._PSEUDO_SUBFOLDER}{pseudo.filename}'))
# Pseudopotentials _must_ be listed in the same order as 'znucl' in the input file.
# So, we need to get 'znucl' as abipy will write it then construct the appropriate 'pseudos' string.
znucl = structure_to_abivars(abi_structure)['znucl']
ordered_pseudo_filenames = [pseudos[constants.elements[Z]['symbol']].filename for Z in znucl]
pseudo_parameters = {
'pseudos': '"' + ', '.join(ordered_pseudo_filenames) + '"',
'pp_dirpath': f'"{self._PSEUDO_SUBFOLDER}"'
}
input_parameters = parameters.get_dict()
# k-points are provided to abipy separately from the main input parameters, so we pop out
# parameters related to the k-points
shiftk = input_parameters.pop('shiftk', [0.0, 0.0, 0.0])
# NOTE: currently, only k-point mesh are supported, not k-point paths
kpoints_mesh = kpoints.get_kpoints_mesh()[0]
# use abipy to write the input file
input_parameters = {**input_parameters, **pseudo_parameters}
# give abipy the HGH_TABLE only so it won't error, but don't actually print these to file
abi_input = AbinitInput(
structure=abi_structure,
pseudos=HGH_TABLE,
abi_kwargs=input_parameters
)
abi_input.set_kmesh(
ngkpt=kpoints_mesh,
shiftk=shiftk
)
return abi_input.to_string(with_pseudos=False), local_copy_pseudo_list