def __init__(
self,
structure,
pseudos,
pseudo_dir=None,
comment=None,
abi_args=None,
abi_kwargs=None,
):
"""
Args:
structure: Parameters defining the crystalline structure. Accepts |Structure| object
file with structure (CIF, netcdf file, ...) or dictionary with ABINIT geo variables.
pseudos: Pseudopotentials to be used for the calculation. Accepts: string or list of strings
with the name of the pseudopotential files, list of |Pseudo| objects
or |PseudoTable| object.
pseudo_dir: Name of the directory where the pseudopotential files are located.
ndtset: Number of datasets.
comment: Optional string with a comment that will be placed at the beginning of the file.
abi_args: list of tuples (key, value) with the initial set of variables. Default: Empty
abi_kwargs: Dictionary with the initial set of variables. Default: Empty
"""
# Internal dict with variables. we use an ordered dict so that
# variables will be likely grouped by `topics` when we fill the input.
abi_args = [] if abi_args is None else abi_args
for key, value in abi_args:
self._check_varname(key)
abi_kwargs = {} if abi_kwargs is None else abi_kwargs
for key in abi_kwargs:
self._check_varname(key)
args = list(abi_args)[:]
args.extend(list(abi_kwargs.items()))
self._vars = dict(args)
self.set_structure(structure)
if pseudo_dir is not None:
pseudo_dir = os.path.abspath(pseudo_dir)
if not os.path.exists(pseudo_dir):
raise self.Error(f"Directory {pseudo_dir} does not exist")
pseudos = [
os.path.join(pseudo_dir, p) for p in list_strings(pseudos)
]
try:
self._pseudos = PseudoTable.as_table(
pseudos).get_pseudos_for_structure(self.structure)
except ValueError as exc:
raise self.Error(str(exc))
if comment is not None:
self.set_comment(comment)
def num_valence_electrons(structure, pseudos):
"""
Returns the number of valence electrons.
Args:
pseudos: List of |Pseudo| objects or list of filenames.
"""
nval, table = 0, PseudoTable.as_table(pseudos)
for site in structure:
pseudo = table.pseudo_with_symbol(site.specie.symbol)
nval += pseudo.Z_val
return int(nval) if int(nval) == nval else nval
def num_valence_electrons(self, pseudos):
"""
Returns the number of valence electrons.
Args:
pseudos: List of :class:`Pseudo` objects or list of filenames.
"""
nval, table = 0, PseudoTable.as_table(pseudos)
for site in self:
pseudo = table.pseudo_with_symbol(site.species_string)
nval += pseudo.Z_val
return nval
