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.inputs.wf_parameters.get_dict()
nkpts = wf_dict.get('nkpts', 500)
# how can the user say he want to use the given kpoint mesh, ZZ nkpts : False/0
sigma = wf_dict.get('sigma', 0.005)
emin = wf_dict.get('emin', -0.30)
emax = wf_dict.get('emax', 0.80)
fleurmode = FleurinpModifier(self.inputs.fleurinp)
#change_dict = {'band': True, 'ndir' : -1, 'minEnergy' : self.inputs.wf_parameters.get_dict().get('minEnergy', -0.30000000),
#'maxEnergy' : self.inputs.wf_parameters.get_dict().get('manEnergy','0.80000000'),
#'sigma' : self.inputs.wf_parameters.get_dict().get('sigma', '0.00500000')}
change_dict = {'band': True, 'ndir' : 0, 'minEnergy' : emin,
'maxEnergy' : emax, 'sigma' : sigma} #'ndir' : 1, 'pot8' : True
fleurmode.set_inpchanges(change_dict)
if nkpts:
fleurmode.set_nkpts(count=nkpts)
#fleurinp_new.replace_tag()
fleurmode.show(validate=True, display=False) # needed?
fleurinp_new = fleurmode.freeze()
self.ctx.fleurinp1 = fleurinp_new
def test_fleurinp_modifier_instance_modifications(create_fleurinp):
"""Tests if set_nmmpmat works on fleurinp modifier works, with right interface"""
fleurinp_tmp = create_fleurinp(inpxmlfilefolder2)
n_mmp_mat_file = os.path.dirname(os.path.abspath(__file__))
n_mmp_mat_file = os.path.abspath(os.path.join(n_mmp_mat_file, '../files/n_mmp_mat/n_mmp_mat_GaAsMultiForceXML'))
fm = FleurinpModifier(fleurinp_tmp)
fm.set_file(n_mmp_mat_file, dst_filename='n_mmp_mat')
new_fleurinp = fm.freeze()
assert 'n_mmp_mat' in new_fleurinp.files
fm = FleurinpModifier(new_fleurinp)
fm.del_file('n_mmp_mat')
new_fleurinp = fm.freeze()
assert 'n_mmp_mat' not in new_fleurinp.files
def test_fleurinp_modifier_set_nmmpmat(create_fleurinp):
"""Tests if set_nmmpmat works on fleurinp modifier works, with right interface"""
fleurinp_tmp = create_fleurinp(inpxmlfilefolder2)
fm = FleurinpModifier(fleurinp_tmp)
fm.set_nmmpmat('Ga-1', orbital=2, spin=1, occStates=[1, 2, 3, 4, 5])
fm.set_nmmpmat('As-2', orbital=1, spin=1, denmat=[[1, -2, 3], [4, -5, 6], [7, -8, 9]])
# Does not validate
# Found invalid diagonal element for species Ga-1, spin 1 and l=2
with pytest.raises(ValueError):
fm.show(validate=True, display=False)
new_fleurinp = fm.freeze()
assert 'n_mmp_mat' in new_fleurinp.files
def test_fleurinp_modifier_instance_modifications_node(create_fleurinp):
"""Tests if set_nmmpmat works on fleurinp modifier works, with right interface"""
from aiida.orm import FolderData
fleurinp_tmp = create_fleurinp(inpxmlfilefolder2)
n_mmp_mat_folder = os.path.dirname(os.path.abspath(__file__))
n_mmp_mat_folder = os.path.abspath(os.path.join(n_mmp_mat_folder, '../files/n_mmp_mat'))
n_mmp_mat_folder = FolderData(tree=n_mmp_mat_folder)
n_mmp_mat_folder.store()
fm = FleurinpModifier(fleurinp_tmp)
fm.set_file('n_mmp_mat_GaAsMultiForceXML', dst_filename='n_mmp_mat', node=n_mmp_mat_folder)
new_fleurinp = fm.freeze()
assert 'n_mmp_mat' in new_fleurinp.files
fm = FleurinpModifier(new_fleurinp)
fm.del_file('n_mmp_mat')
new_fleurinp = fm.freeze()
assert 'n_mmp_mat' not in new_fleurinp.files
def test_fleurinpmodifier_error_messages(create_fleurinp):
"""Test error interface of fleurinpmodifier"""
fleurinp_tmp = create_fleurinp(inpxmlfilefolder)
fm = FleurinpModifier(fleurinp_tmp)
fm._tasks.append(('not_existent', 1, 2, 3)) # task does not exists.
with pytest.raises(ValueError):
fm.freeze()
fm = FleurinpModifier(fleurinp_tmp)
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 test_fleurinp_single_value_modification(create_fleurinp, inpxmlfilepath):
"""
set kmax, itmax, minDistance in inp.xml input file of fleurinpdata to
10.2, 99, 0.000001, then check if it everything set
"""
from aiida_fleur.data.fleurinpmodifier import FleurinpModifier
fleurinp_tmp = create_fleurinp(inpxmlfilepath)
fleurinpmode = FleurinpModifier(fleurinp_tmp)
fleurinpmode.set_inpchanges({
'itmax': 99,
'minDistance': 0.01,
'Kmax': 10.2
})
fleurinpmode.show(display=False, validate=True)
out = fleurinpmode.freeze()
assert isinstance(out, type(fleurinp_tmp))
def change_fleurinp(self):
"""
This routine sets somethings in the fleurinp file before running a fleur
calculation.
"""
self.report('INFO: run change_fleurinp')
if self.ctx.scf_needed: # use fleurinp from scf wc
try:
fleurin = self.ctx.reference.outputs.fleurinp
except NotExistent:
error = 'Fleurinp generated in the reference calculation is not found.'
self.control_end_wc(error)
return self.exit_codes.ERROR_REFERENCE_CALCULATION_FAILED
else:
if 'fleurinp' in self.inputs: # use the given fleurinp
fleurin = self.inputs.fleurinp
else: # or generate a new one from inp.xml located in the remote folder
remote_node = self.inputs.remote
for link in remote_node.get_incoming().all():
if isinstance(link.node, CalcJobNode):
parent_calc_node = link.node
retrieved_node = parent_calc_node.get_outgoing().get_node_by_label('retrieved')
fleurin = FleurinpData(files=['inp.xml'], node=retrieved_node)
# copy inpchanges from wf parameters
fchanges = self.ctx.wf_dict.get('inpxml_changes', [])
# create forceTheorem tags
fchanges.extend([('create_tag', {
'xpath': '/fleurInput',
'newelement': 'forceTheorem'
}), ('create_tag', {
'xpath': '/fleurInput/forceTheorem',
'newelement': 'spinSpiralDispersion'
})])
for i, vectors in enumerate(self.ctx.wf_dict['q_vectors']):
fchanges.append(('create_tag', {
'xpath': '/fleurInput/forceTheorem/spinSpiralDispersion',
'newelement': 'q'
}))
fchanges.append(('xml_set_text_occ', {
'xpathn': '/fleurInput/forceTheorem/spinSpiralDispersion/q',
'text': ' '.join(six.moves.map(str, vectors)),
'create': False,
'occ': i
}))
changes_dict = {'itmax': 1, 'l_noco': True, 'ctail': False, 'l_ss': True}
fchanges.append(('set_inpchanges', {'change_dict': changes_dict}))
# change beta parameter
for key, val in six.iteritems(self.ctx.wf_dict.get('beta')):
fchanges.append(('set_atomgr_att_label', {
'attributedict': {
'nocoParams': [('beta', val)]
},
'atom_label': key
}))
if fchanges: # change inp.xml file
fleurmode = FleurinpModifier(fleurin)
avail_ac_dict = fleurmode.get_avail_actions()
# apply further user dependend changes
for change in fchanges:
function = change[0]
para = change[1]
method = avail_ac_dict.get(function, None)
if not method:
error = ("ERROR: Input 'inpxml_changes', function {} "
'is not known to fleurinpmodifier class, '
'please check/test your input. I abort...'
''.format(function))
self.control_end_wc(error)
return self.exit_codes.ERROR_CHANGING_FLEURINPUT_FAILED
else: # apply change
method(**para)
# validate
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
# apply
out = fleurmode.freeze()
self.ctx.fleurinp = out
return
else: # otherwise do not change the inp.xml
self.ctx.fleurinp = fleurin
return
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_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 change_fleurinp(self):
"""
This routine sets somethings in the fleurinp file before running a fleur
calculation.
"""
self.report('INFO: run change_fleurinp')
if self.ctx.scf_needed:
try:
fleurin = self.ctx.reference.outputs.fleurinp
except NotExistent:
error = 'Fleurinp generated in the reference calculation is not found.'
self.control_end_wc(error)
return self.exit_codes.ERROR_REFERENCE_CALCULATION_FAILED
else:
if 'fleurinp' in self.inputs:
fleurin = self.inputs.fleurinp
else:
# In this case only remote is given
# fleurinp data has to be generated from the remote inp.xml file
fleurin = get_fleurinp_from_remote_data(self.inputs.remote)
# copy inpchanges from wf parameters
fchanges = self.ctx.wf_dict.get('inpxml_changes', [])
# create forceTheorem tags
fchanges.extend([
('create_tag', {
'xpath': '/fleurInput',
'newelement': 'forceTheorem'
}),
('create_tag', {
'xpath': '/fleurInput/forceTheorem',
'newelement': 'DMI'
}),
('create_tag', {
'xpath': '/fleurInput/forceTheorem/DMI',
'newelement': 'qVectors'
}),
('xml_set_attribv_occ', {
'xpathn':
'/fleurInput/forceTheorem/DMI',
'attributename':
'theta',
'attribv':
' '.join(six.moves.map(str,
self.ctx.wf_dict.get('sqas_theta')))
}),
('xml_set_attribv_occ', {
'xpathn':
'/fleurInput/forceTheorem/DMI',
'attributename':
'phi',
'attribv':
' '.join(six.moves.map(str, self.ctx.wf_dict.get('sqas_phi')))
})
])
for i, vectors in enumerate(self.ctx.wf_dict['q_vectors']):
fchanges.append(('create_tag', {
'xpath': '/fleurInput/forceTheorem/DMI/qVectors',
'newelement': 'q'
}))
fchanges.append(('xml_set_text_occ', {
'xpathn': '/fleurInput/forceTheorem/DMI/qVectors/q',
'text': ' '.join(six.moves.map(str, vectors)),
'create': False,
'occ': i
}))
changes_dict = {
'itmax': 1,
'l_noco': True,
'ctail': False,
'spav': True,
# 'l_soc': True,
'l_ss': True
}
fchanges.append(('set_inpchanges', {'change_dict': changes_dict}))
# change beta parameter
for key, val in six.iteritems(self.ctx.wf_dict.get('beta')):
fchanges.append(('set_atomgr_att_label', {
'attributedict': {
'nocoParams': {
'beta': val
}
},
'atom_label': key
}))
# switch off SOC on an atom specie
for atom_label in self.ctx.wf_dict['soc_off']:
fchanges.append(('set_species_label', {
'at_label': atom_label,
'attributedict': {
'special': {
'socscale': 0.0
}
},
'create': True
}))
if fchanges: # change inp.xml file
fleurmode = FleurinpModifier(fleurin)
avail_ac_dict = fleurmode.get_avail_actions()
# apply further user dependend changes
for change in fchanges:
function = change[0]
para = change[1]
method = avail_ac_dict.get(function, None)
if not method:
error = ("ERROR: Input 'inpxml_changes', function {} "
'is not known to fleurinpmodifier class, '
'please check/test your input. I abort...'
''.format(function))
self.control_end_wc(error)
return self.exit_codes.ERROR_CHANGING_FLEURINPUT_FAILED
else: # apply change
method(**para)
# validate?
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
# apply
out = fleurmode.freeze()
self.ctx.fleurinp = out
return
else: # otherwise do not change the inp.xml
self.ctx.fleurinp = fleurin
return
def change_fleurinp(self):
"""
This routine sets somethings in the fleurinp file before running a fleur
calculation.
"""
self.report('INFO: run change_fleurinp')
inputs = self.inputs
# Has to never crash because corresponding check was done in validate function
if self.ctx.fleurinp: # something was already changed
return
elif 'fleurinp' in inputs:
fleurin = self.inputs.fleurinp
elif 'structure' in inputs:
if not self.ctx['inpgen'].is_finished_ok:
error = 'Inpgen calculation failed'
self.control_end_wc(error)
return self.exit_codes.ERROR_INPGEN_CALCULATION_FAILED
fleurin = self.ctx['inpgen'].outputs.fleurinpData
elif 'remote_data' in inputs:
# In this case only remote_data for input structure is given
# fleurinp data has to be generated from the remote inp.xml file to use change_fleurinp
remote_node = self.inputs.remote_data
for link in remote_node.get_incoming().all():
if isinstance(link.node, CalcJobNode):
parent_calc_node = link.node
retrieved_node = parent_calc_node.get_outgoing().get_node_by_label('retrieved')
try:
if self.ctx.wf_dict['use_relax_xml']:
fleurin = FleurinpData(files=['inp.xml', 'relax.xml'], node=retrieved_node)
self.report('INFO: generated FleurinpData from inp.xml and relax.xml')
else:
raise ValueError
except ValueError:
fleurin = FleurinpData(files=['inp.xml'], node=retrieved_node)
self.report('INFO: generated FleurinpData from inp.xml')
fleurin.store()
wf_dict = self.ctx.wf_dict
force_dict = wf_dict.get('force_dict')
converge_mode = wf_dict.get('mode')
fchanges = wf_dict.get('inpxml_changes', [])
fleurmode = FleurinpModifier(fleurin)
# set proper convergence parameters in inp.xml
if converge_mode == 'density':
dist = wf_dict.get('density_converged')
fleurmode.set_inpchanges({'itmax': self.ctx.default_itmax, 'minDistance': dist})
elif converge_mode == 'force':
force_converged = wf_dict.get('force_converged')
dist = wf_dict.get('density_converged')
fleurmode.set_inpchanges({
'itmax': self.ctx.default_itmax,
'minDistance': dist,
'force_converged': force_converged,
'l_f': True,
'qfix': force_dict.get('qfix'),
'forcealpha': force_dict.get('forcealpha'),
'forcemix': force_dict.get('forcemix')
})
elif converge_mode == 'energy':
dist = 0.0
fleurmode.set_inpchanges({'itmax': self.ctx.default_itmax, 'minDistance': dist})
avail_ac_dict = fleurmode.get_avail_actions()
# apply further user dependend changes
if fchanges:
for change in fchanges:
function = change[0]
para = change[1]
method = avail_ac_dict.get(function, None)
if not method:
error = ("ERROR: Input 'inpxml_changes', function {} "
'is not known to fleurinpmodifier class, '
'please check/test your input. I abort...'
''.format(function))
self.control_end_wc(error)
return self.exit_codes.ERROR_CHANGING_FLEURINPUT_FAILED
else: # apply change
try:
method(**para)
except ValueError as vale:
error = ('ERROR: Changing the inp.xml file failed. Tried to apply {}'
', which failed with {}. I abort, good luck next time!'
''.format(change, vale))
self.control_end_wc(error)
return self.exit_codes.ERROR_CHANGING_FLEURINPUT_FAILED
# validate?
try:
fleurmode.show(display=False, validate=True)
except etree.DocumentInvalid:
error = ('ERROR: input, user wanted inp.xml changes did not validate')
self.report(error)
return self.exit_codes.ERROR_INVALID_INPUT_FILE
# apply
out = fleurmode.freeze()
self.ctx.fleurinp = out
return
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 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
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 change_fleurinp(self):
"""
This routine sets somethings in the fleurinp file before running a fleur
calculation.
"""
# TODO recongize inpgen fail, then no fleurin exists...
if self.ctx.fleurinp: #something was already changed
#print('Fleurinp already exists')
return
elif 'fleurinp' in self.inputs:
fleurin = self.inputs.fleurinp
else:
try:
fleurin = self.ctx['inpgen'].out.fleurinpData
except AttributeError:
error = 'No fleurinpData found, inpgen failed'
self.control_end_wc(error)
wf_dict = self.inputs.wf_parameters.get_dict()
converge_te = wf_dict.get('converge_energy', False)
fchanges = wf_dict.get('inpxml_changes', [])
if not converge_te or fchanges: # change inp.xml file
fleurmode = FleurinpModifier(fleurin)
if not converge_te:
dist = wf_dict.get('density_criterion', 0.00002)
fleurmode.set_inpchanges({'itmax': 30, 'minDistance': dist})
avail_ac_dict = fleurmode.get_avail_actions()
# apply further user dependend changes
if fchanges:
for change in fchanges:
function = change[0]
para = change[1]
method = avail_ac_dict.get(function, None)
if not method:
error = ("ERROR: Input 'inpxml_changes', function {} "
"is not known to fleurinpmodifier class, "
"plaese check/test your input. I abort..."
"".format(method))
self.control_end_wc(error)
else: # apply change
method(**para)
# validate?
apply_c = True
try:
fleurmode.show(display=False, validate=True)
except XMLSyntaxError:
error = (
'ERROR: input, user wanted inp.xml changes did not validate'
)
#fleurmode.show(display=True)#, validate=True)
self.control_end_wc(error)
apply_c = False
# apply
if apply_c:
out = fleurmode.freeze()
self.ctx.fleurinp = out
return
else: # otherwise do not change the inp.xml
self.ctx.fleurinp = fleurin
return
def change_fleurinp(self):
"""
This routine sets somethings in the fleurinp file before running a fleur
calculation.
"""
if self.ctx.scf_needed:
try:
fleurin = self.ctx.reference.outputs.fleurinp
except NotExistent:
error = 'Fleurinp generated in the reference calculation is not found.'
self.control_end_wc(error)
return self.exit_codes.ERROR_REFERENCE_CALCULATION_FAILED
else:
if 'fleurinp' in self.inputs:
fleurin = self.inputs.fleurinp
else:
# In this case only remote is given
# fleurinp data has to be generated from the remote inp.xml file
fleurin = get_fleurinp_from_remote_data(self.inputs.remote)
# copy default changes
fchanges = self.ctx.wf_dict.get('inpxml_changes', [])
# add forceTheorem tag into inp.xml
fchanges.extend([
('create_tag', {
'xpath': '/fleurInput',
'newelement': 'forceTheorem'
}),
('create_tag', {
'xpath': '/fleurInput/forceTheorem',
'newelement': 'MAE'
}),
('xml_set_attribv_occ', {
'xpathn':
'/fleurInput/forceTheorem/MAE',
'attributename':
'theta',
'attribv':
' '.join(six.moves.map(str,
self.ctx.wf_dict.get('sqas_theta')))
}),
('xml_set_attribv_occ', {
'xpathn':
'/fleurInput/forceTheorem/MAE',
'attributename':
'phi',
'attribv':
' '.join(six.moves.map(str, self.ctx.wf_dict.get('sqas_phi')))
}),
('set_inpchanges', {
'change_dict': {
'itmax': 1,
'l_soc': True
}
}),
])
if fchanges: # change inp.xml file
fleurmode = FleurinpModifier(fleurin)
avail_ac_dict = fleurmode.get_avail_actions()
# apply further user dependend changes
for change in fchanges:
function = change[0]
para = change[1]
method = avail_ac_dict.get(function, None)
if not method:
error = ("ERROR: Input 'inpxml_changes', function {} "
'is not known to fleurinpmodifier class, '
'please check/test your input. I abort...'
''.format(function))
self.control_end_wc(error)
return self.exit_codes.ERROR_CHANGING_FLEURINPUT_FAILED
else: # apply change
method(**para)
# validate?
try:
fleurmode.show(display=False, validate=True)
except etree.DocumentInvalid:
error = (
'ERROR: input, user wanted inp.xml changes did not validate'
)
self.report(error)
return self.exit_codes.ERROR_INVALID_INPUT_FILE
# apply
out = fleurmode.freeze()
self.ctx.fleurinp = out
return
else: # otherwise do not change the inp.xml
self.ctx.fleurinp = fleurin
return
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
def test_fleurinp_modifier_included_files(create_fleurinp, inpxml_etree, file_regression):
"""Tests if fleurinp_modifier with various other modifations methods,
the detailed tests for method functionality is tested elsewhere."""
TEST_FOLDER = os.path.dirname(os.path.abspath(__file__))
TEST_FOLDER = os.path.abspath(os.path.join(TEST_FOLDER, '../files/included_xml_files'))
INPXML_FILE = os.path.join(TEST_FOLDER, 'inp.xml')
KPTSXML_FILE = os.path.join(TEST_FOLDER, 'kpts.xml')
SYMXML_FILE = os.path.join(TEST_FOLDER, 'sym.xml')
fleurinp_tmp = create_fleurinp(INPXML_FILE, additional_files=[KPTSXML_FILE, SYMXML_FILE])
fm = FleurinpModifier(fleurinp_tmp)
#Modify main inp.xml file
fm.set_inpchanges({'dos': True, 'Kmax': 3.9})
fm.shift_value({'Kmax': 0.1}, 'rel')
#Modify included xml files
fm.delete_tag('symmetryOperations')
fm.create_tag('symmetryOperations')
fm.create_tag('kPointList')
fm.create_tag('kPoint', occurrences=0)
fm.set_attrib_value('name', 'TEST', contains='kPointList', occurrences=0)
fm.set_text('kPoint', [0.0, 0.0, 0.0],
complex_xpath="/fleurInput/cell/bzIntegration/kPointLists/kPointList[@name='TEST']/kPoint")
fm.show()
new_fleurinp = fm.freeze()
assert new_fleurinp.files == ['kpts.xml', 'sym.xml', 'inp.xml']
file_content = [
new_fleurinp.get_content('inp.xml'),
new_fleurinp.get_content('kpts.xml'),
new_fleurinp.get_content('sym.xml')
]
file_regression.check('\n'.join(file_content), extension='.xml')
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 change_fleurinp(self):
"""
This routine sets somethings in the fleurinp file before running a fleur
calculation.
"""
self.report('INFO: run change_fleurinp')
inputs = self.inputs
# Has to never crash because corresponding check was done in validate function
if self.ctx.fleurinp: # something was already changed
return
elif 'fleurinp' in inputs:
fleurin = self.inputs.fleurinp
elif 'structure' in inputs:
if not self.ctx['inpgen'].is_finished_ok:
error = 'Inpgen calculation failed'
self.control_end_wc(error)
return self.exit_codes.ERROR_INPGEN_CALCULATION_FAILED
fleurin = self.ctx['inpgen'].outputs.fleurinpData
elif 'remote_data' in inputs:
# In this case only remote_data for input structure is given
# fleurinp data has to be generated from the remote inp.xml file to use change_fleurinp
fleurin = get_fleurinp_from_remote_data(self.inputs.remote_data,
store=True)
self.report(f'INFO: generated FleurinpData from files {fleurin}')
wf_dict = self.ctx.wf_dict
force_dict = wf_dict.get('force_dict')
converge_mode = wf_dict.get('mode')
fchanges = wf_dict.get('inpxml_changes', [])
fleurmode = FleurinpModifier(fleurin)
# set proper convergence parameters in inp.xml
if converge_mode == 'density':
dist = wf_dict.get('density_converged')
fleurmode.set_inpchanges({
'itmax': self.ctx.default_itmax,
'minDistance': dist
})
elif converge_mode == 'force':
force_converged = wf_dict.get('force_converged')
dist = wf_dict.get('density_converged')
fleurmode.set_inpchanges({
'itmax': self.ctx.default_itmax,
'minDistance': dist,
'force_converged': force_converged,
'l_f': True,
'qfix': force_dict.get('qfix'),
'forcealpha': force_dict.get('forcealpha'),
'forcemix': force_dict.get('forcemix')
})
elif converge_mode == 'energy':
dist = 0.0
fleurmode.set_inpchanges({
'itmax': self.ctx.default_itmax,
'minDistance': dist
})
elif converge_mode == 'gw':
dist = 0.0
fleurmode.set_inpchanges({
'itmax': self.ctx.default_itmax,
'minDistance': dist,
'gw': 1
})
if 'settings' in self.inputs:
self.inputs.settings.append({
'additional_retrieve_list':
['basis.hdf', 'pot.hdf', 'ecore']
})
self.inputs.settings.append({
'additional_remotecopy_list':
['basis.hdf', 'pot.hdf', 'ecore']
})
else:
self.inputs.settings = {
'additional_retrieve_list':
['basis.hdf', 'pot.hdf', 'ecore'],
'additional_remotecopy_list':
['basis.hdf', 'pot.hdf', 'ecore']
}
# 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
# validate?
try:
fleurmode.show(display=False, validate=True)
except etree.DocumentInvalid:
error = (
'ERROR: input, user wanted inp.xml changes did not validate')
self.report(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
# apply
out = fleurmode.freeze()
self.ctx.fleurinp = out
return
#schemanameQq
path = os.getcwd()#path.realpath(__file__)
print path
filepath = path + '/inp.xml'
#'/Users/broeder/aiida/scratch/broeder/aiida_run2/ff/4c/c14d-8a1b-40b3-af95-400e23002bcb/inp.xml'
new_fleurinpData = FleurInpData(files= [filepath])
print new_fleurinpData.get_file_abs_path('inp.xml')
#new_fleurinpData.store()
#new_fleurinpData= load_node(6)
fleurmode = FleurinpModifier(new_fleurinpData)
#fleurmode.set_switch({'dos': True})
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'}