def test_fleurinp_modifier2(create_fleurinp, inpxml_etree):
"""Tests if fleurinp_modifier with various other modifations methods,
the detailed tests for method functionality is tested elsewhere."""
from aiida_fleur.tools.xml_util import eval_xpath
fleurinp_tmp = create_fleurinp(inpxmlfilefolder)
etree = inpxml_etree(inpxmlfilefolder)
fm = FleurinpModifier(fleurinp_tmp)
actions = fm.get_avail_actions()
assert isinstance(actions, dict)
new_tag = eval_xpath(etree, '/fleurInput/calculationSetup/scfLoop')
fm.delete_tag('/fleurInput/calculationSetup/scfLoop')
fm.replace_tag('/fleurInput/calculationSetup/cutoffs', new_tag)
fm.delete_att('/fleurInput/calculationSetup/soc', 'theta')
fm.create_tag('/fleurInput/calculationSetup/soc', 'theta')
fm.xml_set_all_text('/fleurInput/cell/symmetryOperations/symOp/row-1', 'test text')
fm.xml_set_text_occ('/fleurInput/cell/symmetryOperations/symOp/row-1', 'test text')
fm.xml_set_text('/fleurInput/cell/symmetryOperations/symOp/row-1', 'test text')
fm.xml_set_all_attribv('/fleurInput/calculationSetup/soc', 'theta', 12)
fm.xml_set_first_attribv('/fleurInput/calculationSetup/soc', 'theta', 12)
fm.xml_set_attribv_occ('/fleurInput/calculationSetup/soc', 'theta', 12)
fm.set_species_label(' 222', {'mtSphere': {'radius': 3.333}})
fm.set_atomgr_att_label(attributedict={'force': [('relaxXYZ', 'FFF')]}, atom_label=' 222')
fm.set_atomgr_att(attributedict={'force': [('relaxXYZ', 'TFF')]}, species='Fe-1')
fm.set_nkpts(500, gamma='T')
fm.set_kpath({'gamma': (0, 0, 0), 'L': (0.1, 0.1, 0.1)}, 300)
fm.add_num_to_att('/fleurInput/calculationSetup/soc', 'theta', 4)
#fm.set_species1
fm.show()
def create_new_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 'fleurinp' not in self.inputs:
for i in self.inputs.remote.get_incoming():
if isinstance(i.node, CalcJobNode):
self.ctx.fleurinp_scf = load_node(i.node.pk).get_incoming().get_node_by_label('fleurinpdata')
else:
self.ctx.fleurinp_scf = self.inputs.fleurinp
# how can the user say he want to use the given kpoint mesh, ZZ nkpts : False/0
fleurmode = FleurinpModifier(self.ctx.fleurinp_scf)
nkpts = wf_dict.get('nkpts', 500)
sigma = wf_dict.get('sigma', 0.005)
emin = wf_dict.get('emin', -0.30)
emax = wf_dict.get('emax', 0.80)
if wf_dict.get('mode') == 'dos':
change_dict = {'dos': True, 'ndir': -1, 'minEnergy': emin, 'maxEnergy': emax, 'sigma': sigma}
else:
change_dict = {'band': True, 'ndir': 0, 'minEnergy': emin, 'maxEnergy': emax, 'sigma': sigma}
fleurmode.set_inpchanges(change_dict)
if wf_dict.get('kpath') != 'auto':
fleurmode.set_kpath(wf_dict.get('kpath'), nkpts)
# if nkpts:
# fleurmode.set_nkpts(count=nkpts)
#fleurinp_new.replace_tag()
fleurmode.show(validate=True, display=False) # needed?
fleurinp_new = fleurmode.freeze()
self.ctx.fleurinp_banddos = fleurinp_new
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