def test_fleurinp_modifier_set_kpointsdata(create_fleurinp):
"""Test if setting a kpoints list to a fleurinp data node works"""
from aiida.orm import KpointsData
fleurinp_tmp = create_fleurinp(inpxmlfilefolder)
fleurinp_tmp.store() # needed?
struc = fleurinp_tmp.get_structuredata_ncf()
kps = KpointsData()
kps.set_cell(struc.cell)
kps.pbc = struc.pbc
kpoints_pos = [[0.0, 0.0, 0.0], [0.0, 0.5, 0.0], [0.5, 0.0, 0.0], [0.5, 0.0, 0.5], [0.5, 0.5, 0.5], [1.0, 1.0, 1.0]]
kpoints_weight = [1.0, 1.0, 1.0, 1.0, 1.0, 1.0]
# Fleur renormalizes
kps.set_kpoints(kpoints_pos, cartesian=False, weights=kpoints_weight)
kps.store() # needed, because node has to be loaded...
#print(fleurinp_tmp)
fm = FleurinpModifier(fleurinp_tmp)
fm.set_kpointsdata(kps)
fm.show(validate=True, display=False)
fm.freeze()
# check if kpoint node is input into modification
# uuid of node show also work
fm = FleurinpModifier(fleurinp_tmp)
fm.set_kpointsdata(kps.uuid)
fm.freeze()
def test_get_kpoints(self):
"""Test the `get_kpoints` method."""
kpt = KpointsData()
kpt.set_cell_from_structure(self.structure)
kpoints = [
[0., 0., 0.],
[0.5, 0.5, 0.5],
]
cartesian_kpoints = [
[0., 0., 0.],
[np.pi / self.alat, np.pi / self.alat, np.pi / self.alat],
]
kpt.set_kpoints(kpoints)
self.assertEqual(
np.abs(kpt.get_kpoints() - np.array(kpoints)).sum(), 0.)
self.assertEqual(
np.abs(
kpt.get_kpoints(cartesian=True) -
np.array(cartesian_kpoints)).sum(), 0.)
# Check also after storing
kpt.store()
kpt2 = load_node(kpt.pk)
self.assertEqual(
np.abs(kpt2.get_kpoints() - np.array(kpoints)).sum(), 0.)
self.assertEqual(
np.abs(
kpt2.get_kpoints(cartesian=True) -
np.array(cartesian_kpoints)).sum(), 0.)
def test_reciprocal_cell(self):
"""
Test the `reciprocal_cell` method.
This is a regression test for #2749.
"""
kpt = KpointsData()
kpt.set_cell_from_structure(self.structure)
self.assertEqual(np.abs(kpt.reciprocal_cell - self.expected_reciprocal_cell).sum(), 0.)
# Check also after storing
kpt.store()
kpt2 = load_node(kpt.pk)
self.assertEqual(np.abs(kpt2.reciprocal_cell - self.expected_reciprocal_cell).sum(), 0.)
def change_fleurinp(self):
"""
create a new fleurinp from the old with certain parameters
"""
# TODO allow change of kpoint mesh?, tria?
wf_dict = self.ctx.wf_dict
if self.ctx.scf_needed:
try:
fleurin = self.ctx.scf.outputs.fleurinp
except NotExistent:
error = 'Fleurinp generated in the SCF calculation is not found.'
self.control_end_wc(error)
return self.exit_codes.ERROR_SCF_CALCULATION_FAILED
else:
if 'fleurinp' not in self.inputs:
fleurin = get_fleurinp_from_remote_data(self.inputs.remote)
else:
fleurin = self.inputs.fleurinp
# how can the user say he want to use the given kpoint mesh, ZZ nkpts : False/0
fleurmode = FleurinpModifier(fleurin)
fchanges = wf_dict.get('inpxml_changes', [])
# apply further user dependend changes
if fchanges:
try:
fleurmode.add_task_list(fchanges)
except (ValueError, TypeError) as exc:
error = (
'ERROR: Changing the inp.xml file failed. Tried to apply inpxml_changes'
f', which failed with {exc}. I abort, good luck next time!'
)
self.control_end_wc(error)
return self.exit_codes.ERROR_CHANGING_FLEURINPUT_FAILED
kpath = wf_dict['kpath']
explicit = wf_dict['kpoints_explicit']
distance = wf_dict['kpoints_distance']
nkpts = wf_dict['kpoints_number']
listname = wf_dict['klistname']
if explicit is not None:
try:
fleurmode.set_kpointlist(**explicit)
except (ValueError, TypeError) as exc:
error = (
'ERROR: Changing the inp.xml file failed. Tried to apply kpoints_explicit'
f', which failed with {exc}. I abort, good luck next time!'
)
self.control_end_wc(error)
return self.exit_codes.ERROR_CHANGING_FLEURINPUT_FAILED
if listname is None:
if wf_dict.get('mode') == 'band':
listname = 'path-2'
if nkpts is None and distance is None:
nkpts = 500
if 'kpoints' in self.inputs:
fleurmode.set_kpointsdata(self.inputs.kpoints, switch=True)
if kpath == 'auto':
if fleurin.inp_version >= '0.32' and listname is not None:
fleurmode.switch_kpointset(listname)
elif isinstance(kpath, dict):
if fleurin.inp_version < '0.32':
if distance is not None:
raise ValueError(
'set_kpath only supports specifying the number of points for the kpoints'
)
fleurmode.set_kpath(kpath, nkpts)
else:
raise ValueError(
'set_kpath is only supported for inputs up to Max4')
elif kpath == 'seek':
#Use aiida functionality
struc = fleurin.get_structuredata()
if distance is not None:
output = get_explicit_kpoints_path(struc,
reference_distance=distance)
else:
output = get_explicit_kpoints_path(struc)
primitive_struc = output['primitive_structure']
#check if primitive_structure and input structure are identical:
maxdiff_cell = sum(
abs(np.array(primitive_struc.cell) -
np.array(struc.cell))).max()
if maxdiff_cell > 3e-9:
self.report(f'Error in cell : {maxdiff_cell}')
self.report(
'WARNING: The structure data from the fleurinp is not the primitive structure type, which is mandatory in some cases'
)
output['explicit_kpoints'].store()
fleurmode.set_kpointsdata(output['explicit_kpoints'], switch=True)
elif kpath == 'skip':
return
else:
#Use ase
struc = fleurin.get_structuredata()
path = bandpath(kpath,
cell=struc.cell,
npoints=nkpts,
density=distance)
special_points = path.special_points
labels = []
for label, special_kpoint in special_points.items():
for index, kpoint in enumerate(path.kpts):
if sum(abs(np.array(special_kpoint) -
np.array(kpoint))).max() < 1e-12:
labels.append((index, label))
labels = sorted(labels, key=lambda x: x[0])
kpts = KpointsData()
kpts.set_cell(struc.cell)
kpts.pbc = struc.pbc
weights = np.ones(len(path.kpts)) / len(path.kpts)
kpts.set_kpoints(kpoints=path.kpts,
cartesian=False,
weights=weights,
labels=labels)
kpts.store()
fleurmode.set_kpointsdata(kpts, switch=True)
sigma = wf_dict['sigma']
emin = wf_dict['emin']
emax = wf_dict['emax']
if fleurin.inp_version < '0.32':
if wf_dict.get('mode') == 'dos':
fleurmode.set_inpchanges({'ndir': -1})
if wf_dict.get('mode') == 'dos':
change_dict = {
'dos': True,
'minEnergy': emin,
'maxEnergy': emax,
'sigma': sigma
}
else:
change_dict = {
'band': True,
'minEnergy': emin,
'maxEnergy': emax,
'sigma': sigma
}
fleurmode.set_inpchanges(change_dict)
try:
fleurmode.show(display=False, validate=True)
except etree.DocumentInvalid:
error = (
'ERROR: input, user wanted inp.xml changes did not validate')
self.control_end_wc(error)
return self.exit_codes.ERROR_INVALID_INPUT_FILE
except ValueError as exc:
error = (
'ERROR: input, user wanted inp.xml changes could not be applied.'
f'The following error was raised {exc}')
self.control_end_wc(error)
return self.exit_codes.ERROR_CHANGING_FLEURINPUT_FAILED
fleurinp_new = fleurmode.freeze()
self.ctx.fleurinp_banddos = fleurinp_new
