def setup_kpoints(self):
"""
Define the k-point mesh for the relax and scf calculations. Also get the k-point path for
the bands calculation for the initial input structure from SeeKpath
"""
kpoints_mesh = KpointsData()
kpoints_mesh.set_cell_from_structure(self.inputs.structure)
kpoints_mesh.set_kpoints_mesh_from_density(
distance=self.ctx.protocol['kpoints_mesh_density'],
offset=self.ctx.protocol['kpoints_mesh_offset'])
self.ctx.kpoints_mesh = kpoints_mesh
def setup_kpoints(self):
"""
Define the k-point mesh for the relax and scf calculations.
"""
kpoints_mesh = KpointsData()
kpoints_mesh.set_cell_from_structure(self.ctx.structure_initial_primitive)
kpoints_mesh.set_kpoints_mesh_from_density(
distance=self.ctx.protocol['kpoints_mesh_density'],
offset=self.ctx.protocol['kpoints_mesh_offset']
)
self.ctx.kpoints_mesh = kpoints_mesh
def create_kpoints_from_distance(structure, distance, force_parity):
"""
Generate a uniformly spaced kpoint mesh for a given structure where 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 aiida.orm.data.array.kpoints import KpointsData
kpoints = KpointsData()
kpoints.set_cell_from_structure(structure)
kpoints.set_kpoints_mesh_from_density(distance.value,
force_parity=force_parity.value)
return kpoints
def run_bands(self):
"""
Run the SiestaBaseWorkChain in scf+bands mode on the primitive cell of the relaxed input structure
"""
self.report('Running bands calculation')
try:
structure = self.ctx.workchain_relax.out.output_structure
except:
self.abort_nowait('failed to get the output structure from the relaxation run')
return
self.ctx.structure_relaxed_primitive = structure
inputs = dict(self.ctx.inputs)
kpoints_mesh = KpointsData()
kpoints_mesh.set_cell_from_structure(self.ctx.structure_relaxed_primitive)
kpoints_mesh.set_kpoints_mesh_from_density(
distance=self.ctx.protocol['kpoints_mesh_density'],
offset=self.ctx.protocol['kpoints_mesh_offset'])
bandskpoints = KpointsData()
bandskpoints.set_cell(structure.cell, structure.pbc)
bandskpoints.set_kpoints_path(kpoint_distance = 0.05)
self.ctx.kpoints_path = bandskpoints
# Final input preparation, wrapping dictionaries in ParameterData nodes
inputs['bandskpoints'] = self.ctx.kpoints_path
inputs['kpoints'] = kpoints_mesh
inputs['structure'] = self.ctx.structure_relaxed_primitive
inputs['parameters'] = ParameterData(dict=inputs['parameters'])
inputs['basis'] = ParameterData(dict=inputs['basis'])
inputs['settings'] = ParameterData(dict=inputs['settings'])
running = submit(SiestaBaseWorkChain, **inputs)
self.report('launching SiestaBaseWorkChain<{}> in scf+bands mode'.format(running.pid))
return ToContext(workchain_bands=running)
def run_seekpath(self):
"""
Run the relaxed structure through SeeKPath to get the new primitive structure, just in case
the symmetry of the cell changed in the cell relaxation step
"""
if 'workchain_relax' not in self.ctx:
structure = self.inputs.structure
else:
try:
structure = self.ctx.workchain_relax.out.output_structure
except:
self.abort_nowait(
'the relax workchain did not output an output_structure node'
)
return
seekpath_parameters = ParameterData(
dict={
'reference_distance': self.inputs.kpoints_distance_bands.value
})
result = seekpath_structure_analysis(structure, seekpath_parameters)
self.ctx.structure = result['primitive_structure']
# Construct a new kpoint mesh for the scf calculation on the current primitive structure
kpoints_mesh = KpointsData()
kpoints_mesh.set_cell_from_structure(self.ctx.structure)
kpoints_mesh.set_kpoints_mesh_from_density(
self.inputs.kpoints_distance.value)
# Save the kpoints objects for the scf and bands calculation in the context
self.ctx.kpoints_mesh = kpoints_mesh
self.ctx.kpoints_path = result['explicit_kpoints']
self.out('primitive_structure', result['primitive_structure'])
self.out('seekpath_parameters', result['parameters'])
