def get_distance_from_kmesh(calc):
mesh = calc.inputs.kpoints.get_kpoints_mesh()[0]
k = KpointsData()
k.set_cell_from_structure(
calc.inputs.structure
) #these take trace of PBC...if set in the inputs.!!
for i in range(4, 400):
k.set_kpoints_mesh_from_density(1 / (i * 0.25))
if k.get_kpoints_mesh()[0] == mesh:
print('ok, {} is the density'.format(i * 0.25))
print(k.get_kpoints_mesh()[0], mesh)
return i * 0.25
def create_kpoints_from_distance(structure, distance, force_parity):
"""Generate a uniformly spaced kpoint mesh for a given structure.
The spacing between kpoints in reciprocal space is guaranteed to be at least the defined distance.
:param structure: the StructureData to which the mesh should apply
:param distance: a Float with the desired distance between kpoints in reciprocal space
:param force_parity: a Bool to specify whether the generated mesh should maintain parity
:returns: a KpointsData with the generated mesh
"""
from numpy import linalg
from aiida.orm import KpointsData
epsilon = 1E-5
kpoints = KpointsData()
kpoints.set_cell_from_structure(structure)
kpoints.set_kpoints_mesh_from_density(distance.value, force_parity=force_parity.value)
lengths_vector = [linalg.norm(vector) for vector in structure.cell]
lengths_kpoint = kpoints.get_kpoints_mesh()[0]
is_symmetric_cell = all(abs(length - lengths_vector[0]) < epsilon for length in lengths_vector)
is_symmetric_mesh = all(length == lengths_kpoint[0] for length in lengths_kpoint)
# If the vectors of the cell all have the same length, the kpoint mesh should be isotropic as well
if is_symmetric_cell and not is_symmetric_mesh:
nkpoints = max(lengths_kpoint)
kpoints.set_kpoints_mesh([nkpoints, nkpoints, nkpoints])
return kpoints
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
def kpt_crop(kpoints: orm.KpointsData, centers: orm.ArrayData,
radii: orm.ArrayData, anticrop: orm.Bool) -> orm.KpointsData:
kpt_cryst = kpoints.get_kpoints_mesh(print_list=True)
cell = kpoints.cell
recipr = recipr_base(cell)
centers = centers.get_array('centers')
centers = centers.dot(recipr)
radii = radii.get_array('radii')
kpt, wgt = _kpt_crop(kpt_cryst,
recipr,
centers=centers,
radii=radii,
anticrop=anticrop.value)
res = orm.KpointsData()
res.set_cell(cell)
res.set_kpoints(kpt, cartesian=True, weights=wgt)
return res
