def test_fleurinp_modifier1(create_fleurinp):
"""Tests if fleurinp_modifier with various modifations on species"""
fleurinp_tmp = create_fleurinp(inpxmlfilefolder)
fm = FleurinpModifier(fleurinp_tmp)
fm.set_inpchanges({'dos': True, 'Kmax': 3.9})
fm.shift_value({'Kmax': 0.1}, 'rel')
fm.shift_value_species_label(' 222', 'radius', 3, mode='abs')
fm.set_species('all', {'mtSphere': {'radius': 3.333}})
fm.undo()
changes = fm.changes()
assert changes == [('set_inpchanges', {
'Kmax': 3.9,
'dos': True
}), ('shift_value', {
'Kmax': 0.1
}, 'rel'), ('shift_value_species_label', ' 222', 'radius', 3, 'abs')]
fm.show(validate=True)
fm.freeze()
fm = FleurinpModifier(fleurinp_tmp)
fm.set_inpchanges({'dos': True, 'Kmax': 3.9})
fm.undo(revert_all=True)
changes = fm.changes()
assert changes == []
def test_fleurinp_modifier1(create_fleurinp):
"""Tests if fleurinp_modifier with various modifations on species"""
from masci_tools.io.fleurxmlmodifier import ModifierTask
fleurinp_tmp = create_fleurinp(inpxmlfilefolder)
fm = FleurinpModifier(fleurinp_tmp)
fm.set_inpchanges({'dos': True, 'Kmax': 3.9})
fm.shift_value({'Kmax': 0.1}, 'rel')
fm.shift_value_species_label(' 222', 'radius', 3, mode='abs')
fm.set_species('all', {'mtSphere': {'radius': 3.333}})
fm.undo()
changes = fm.changes()
assert changes == [
ModifierTask(name='set_inpchanges', args=({
'dos': True,
'Kmax': 3.9
},), kwargs={}),
ModifierTask(name='shift_value', args=({
'Kmax': 0.1
}, 'rel'), kwargs={}),
ModifierTask(name='shift_value_species_label',
args=(' 222', 'radius', 3),
kwargs={'mode': 'abs'})
]
fm.show(validate=True)
fm.freeze()
fm = FleurinpModifier(fleurinp_tmp)
fm.set_inpchanges({'dos': True, 'Kmax': 3.9})
fm.undo(revert_all=True)
changes = fm.changes()
assert changes == []
def test_fleurinp_modifier_regression(create_fleurinp, inpxml_etree, file_regression):
"""Tests if fleurinp_modifier with various other modifations methods,
the detailed tests for method functionality is tested elsewhere."""
fleurinp_tmp = create_fleurinp(inpxmlfilefolder)
fm = FleurinpModifier(fleurinp_tmp)
fm.set_inpchanges({'dos': True, 'Kmax': 3.9})
fm.shift_value({'Kmax': 0.1}, 'rel')
fm.shift_value_species_label(' 222', 'radius', 3, mode='abs')
fm.set_species('all', {'mtSphere': {'radius': 3.333}})
#fm.set_nkpts(500, gamma='T')
#fm.set_kpath({'gamma': (0, 0, 0), 'L': (0.1, 0.1, 0.1)}, 300)
with pytest.deprecated_call():
fm.add_num_to_att('/fleurInput/calculationSetup/scfLoop', 'minDistance', 4)
#fm.set_species1
fm.show()
new_fleurinp = fm.freeze()
file_regression.check(new_fleurinp.get_content('inp.xml'), extension='.xml')
def get_inputs_fixed_configurations(self, index, config):
"""
Sets up the input for the fixed density matrix calculation.
"""
remote_data = None
if self.ctx.scf_no_ldau_needed:
try:
fleurinp = self.ctx.scf_no_ldau.outputs.fleurinp
remote_data = load_node(
self.ctx.scf_no_ldau.outputs.output_scf_wc_para['last_calc_uuid']).outputs.remote_folder
except NotExistent:
error = 'Fleurinp generated in the SCF calculation is not found.'
self.control_end_wc(error)
return {}, self.exit_codes.ERROR_SCF_NOLDAU_FAILED
else:
remote_data = self.inputs.remote
if 'fleurinp' not in self.inputs:
fleurinp = get_fleurinp_from_remote_data(remote_data, store=True)
self.report(f'INFO: generated FleurinpData from {fleurinp.files}')
else:
fleurinp = self.inputs.fleurinp
inputs = self.inputs
label = f'Fixed_{index}'
description = f'LDA+U with fixed nmmpmat for config {index}'
if 'settings' not in inputs:
settings = {}
else:
settings = inputs.settings.get_dict()
if 'remove_from_remotecopy_list' not in settings:
settings['remove_from_remotecopy_list'] = []
settings['remove_from_remotecopy_list'].append('mixing_history*')
self.report(f'INFO: create fleurinp for config {index}')
fm = FleurinpModifier(fleurinp)
fm.set_inpchanges({'itmax': self.ctx.wf_dict['iterations_fixed'], 'l_linMix': True, 'mixParam': 0.0})
for atom_species, ldau_dict in self.ctx.wf_dict['ldau_dict'].items():
fm.set_species(species_name=atom_species, attributedict={'ldaU': ldau_dict})
for config_index, config_species in config.items():
orbital = config_index.split('-')[-1]
atom_species = '-'.join(config_index.split('-')[:-1])
for spin, config_spin in enumerate(config_species):
if self.ctx.wf_dict['use_orbital_occupation']:
fm.set_nmmpmat(species_name=atom_species,
orbital=int(orbital),
spin=spin + 1,
orbital_occupations=config_spin)
else:
fm.set_nmmpmat(species_name=atom_species,
orbital=int(orbital),
spin=spin + 1,
state_occupations=config_spin)
try:
fm.show(display=False, validate=True)
except etree.DocumentInvalid:
error = ('ERROR: input, 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, 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_fixed = fm.freeze()
input_fixed = get_inputs_fleur(inputs.fleur,
remote_data,
fleurinp_fixed,
self.ctx.options,
label,
description,
settings=settings)
return input_fixed, None
fleurmode.set_inpchanges({})
fleurmode.set_inpchanges({'dos': True})
tria = True
nkpts = 800
change_dict = {'dos': True, 'ndir' : -1, 'minEnergy' : -0.8,
'maxEnergy' : 0.8, 'sigma' : 0.005}
fleurmode.set_inpchanges(change_dict)
if tria:
change_dict = {'mode': 'tria'}
fleurmode.set_inpchanges(change_dict)
if nkpts:
fleurmode.set_nkpts(count=nkpts)
'''
fleurmode.set_species('W-1', {'radius' : 3.5})
fleurmode.change_atom('forces', True, position=(0.0, 0.0, 0.0))
fleurmode.set_xpath('/fleurinput/@dos', True)
'''
'''
name = 'Na-1'
xpathn = '/fleurInput/atomSpecies/species[@name = "{}"]/mtSphere'.format(name)# 'radius':
attributename = 'radius'
attribv = 0.0000
fleurmode.xml_set_all_attribv(xpathn, attributename, attribv)
xpathn = '/fleurInput/atomSpecies/species/mtSphere'
xpathn = '/fleurInput'
#attribv = [0.0000, '1.2', 3.4]
#fleurmode.xml_set_all_attribv(xpathn, attributename, attribv)