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.
"""
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 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 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 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.
"""
# 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