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_fleurxml_modifier_modify_xmlfile_simple():
"""Tests if fleurinp_modifier with various modifations on species"""
from masci_tools.io.fleurxmlmodifier import FleurXMLModifier, ModifierTask
fm = FleurXMLModifier()
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.xml_set_attrib_value_no_create('/fleurInput/calculationSetup/cutoffs',
'Gmax', '14.0')
assert fm.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'}),
ModifierTask(name='set_species',
args=('all', {
'mtSphere': {
'radius': 3.333
}
}),
kwargs={}),
ModifierTask(name='xml_set_attrib_value_no_create',
args=(
'/fleurInput/calculationSetup/cutoffs',
'Gmax',
'14.0',
),
kwargs={})
]
#The underlying methods are tested in the specific tests for the setters
#We only want to ensure that the procedure finishes without error
xmltree = fm.modify_xmlfile(TEST_INPXML_PATH)
assert xmltree is not None
def set_file(self, filename, dst_filename=None, node=None):
"""
Appends a :py:func:`~aiida_fleur.data.fleurinp.FleurinpData.set_file()` to
the list of tasks that will be done on the FleurinpData instance.
:param filename: absolute path to the file or a filename of node is specified
:param dst_filename: str of the filename, which should be used instead of the real filename
to store it
:param node: a :class:`~aiida.orm.FolderData` node containing the file
"""
from aiida.orm import FolderData, load_node
node_uuid = None
if node is not None:
if isinstance(node, FolderData):
node_uuid = node.uuid
num_nodes = sum('folder' in label
for label in self._other_nodes) + 1
node_label = f'folder_{num_nodes}'
# Be more careful? Needs to be stored, otherwise we cannot load it
self._other_nodes[node_label] = load_node(node_uuid)
self._tasks.append(
ModifierTask('set_file',
args=(filename, ),
kwargs={
'dst_filename': dst_filename,
'node': node_uuid
}))
def del_file(self, filename):
"""
Appends a :py:func:`~aiida_fleur.data.fleurinp.FleurinpData.del_file()` to
the list of tasks that will be done on the FleurinpData instance.
:param filename: name of the file to be removed from FleurinpData instance
"""
self._tasks.append(
ModifierTask('del_file', args=(filename, ), kwargs={}))
def set_kpointsdata(self, kpointsdata_uuid, name=None, switch=False):
"""
Appends a :py:func:`~aiida_fleur.tools.xml_aiida_modifiers.set_kpointsdata_f()` to
the list of tasks that will be done on the FleurinpData.
:param kpointsdata_uuid: an :class:`aiida.orm.KpointsData` or node uuid, since the node is self cannot be be serialized in tasks.
"""
from aiida.orm import KpointsData, load_node
if isinstance(kpointsdata_uuid, KpointsData):
kpointsdata_uuid = kpointsdata_uuid.uuid
# Be more careful? Needs to be stored, otherwise we cannot load it
num_nodes = sum('kpoints' in label for label in self._other_nodes) + 1
node_label = f'kpoints_{num_nodes}'
self._other_nodes[node_label] = load_node(kpointsdata_uuid)
self._tasks.append(
ModifierTask('set_kpointsdata',
args=(kpointsdata_uuid, ),
kwargs={
'name': name,
'switch': switch
}))
def modify_fleurinpdata(original, modifications, **kwargs):
"""
A CalcFunction that performs the modification of the given FleurinpData and stores
the result in a database.
:param original: a FleurinpData to be modified
:param modifications: a python dictionary of modifications in the form of {'task': ...}
:param kwargs: dict of other aiida nodes to be linked to the modifications
:returns new_fleurinp: a modified FleurinpData that is stored in a database
"""
# copy
# get schema
# read in inp.xml
# add modifications
# validate
# save inp.xml
# store new fleurinp (copy)
import tempfile
from masci_tools.util.xml.common_functions import reverse_xinclude
new_fleurinp = original.clone()
modification_tasks = modifications.get_dict()['tasks']
#We need to rebuild the namedtuples since the serialization for the calcufunction inputs
#converts the namedtuples into lists
modification_tasks = [ModifierTask(*task) for task in modification_tasks]
FleurinpModifier.apply_fleurinp_modifications(new_fleurinp,
modification_tasks)
xmltree, schema_dict, included_tags = new_fleurinp.load_inpxml(
remove_blank_text=True, return_included_tags=True)
try:
with new_fleurinp.open(path='n_mmp_mat', mode='r') as n_mmp_file:
nmmplines = n_mmp_file.read().split('\n')
except FileNotFoundError:
nmmplines = None
new_fleurtree, new_nmmplines = FleurinpModifier.apply_modifications(xmltree=xmltree,\
nmmp_lines=nmmplines,\
modification_tasks=modification_tasks,
validate_changes=False)
# To include object store storage this prob has to be done differently
inpxmltree, includedtrees = reverse_xinclude(new_fleurtree, schema_dict,
included_tags)
new_fleurinp.del_file('inp.xml')
with tempfile.TemporaryDirectory() as td:
inpxml_path = os.path.join(td, 'inp.xml')
inpxmltree.write(inpxml_path, encoding='utf-8', pretty_print=True)
new_fleurinp.set_file(inpxml_path, 'inp.xml')
for file_name, tree in includedtrees.items():
file_path = os.path.join(td, file_name)
tree.write(file_path, encoding='utf-8', pretty_print=True)
new_fleurinp.set_file(file_path, file_name)
if new_nmmplines is not None:
n_mmp_path = os.path.join(td, 'n_mmp_mat')
with open(n_mmp_path, 'w') as n_mmp_file:
n_mmp_file.write('\n'.join(new_nmmplines))
new_fleurinp.set_file(n_mmp_path, 'n_mmp_mat')
# default label and description
new_fleurinp.label = 'mod_fleurinp'
new_fleurinp.description = 'Fleurinpdata with modifications (see inputs of modify_fleurinpdata)'
return new_fleurinp
def test_fleurxml_modifier_from_list():
"""Tests if fleurinp_modifier with various modifations on species"""
from masci_tools.io.fleurxmlmodifier import FleurXMLModifier, ModifierTask
fm = FleurXMLModifier.fromList([('set_inpchanges', {
'change_dict': {
'dos': True,
'Kmax': 3.9
}
}), ('shift_value', {
'change_dict': {
'Kmax': 0.1
},
'mode': 'rel'
}),
('shift_value_species_label', {
'atom_label': ' 222',
'attributename': 'radius',
'value_given': 3,
'mode': 'abs'
}),
('set_kpointlist', {
'kpoints': [[0, 0, 0]],
'weights': [1]
}),
('set_species', {
'species_name': 'all',
'attributedict': {
'mtSphere': {
'radius': 3.333
}
}
})])
assert fm.changes() == [
ModifierTask(name='set_inpchanges',
args=(),
kwargs={'change_dict': {
'dos': True,
'Kmax': 3.9
}}),
ModifierTask(name='shift_value',
args=(),
kwargs={
'change_dict': {
'Kmax': 0.1
},
'mode': 'rel'
}),
ModifierTask(name='shift_value_species_label',
args=(),
kwargs={
'atom_label': ' 222',
'attributename': 'radius',
'value_given': 3,
'mode': 'abs'
}),
ModifierTask(name='set_kpointlist',
args=(),
kwargs={
'kpoints': [[0, 0, 0]],
'weights': [1]
}),
ModifierTask(name='set_species',
args=(),
kwargs={
'species_name': 'all',
'attributedict': {
'mtSphere': {
'radius': 3.333
}
}
})
]
#The underlying methods are tested in the specific tests for the setters
#We only want to ensure that the procedure finishes without error
xmltree = fm.modify_xmlfile(TEST_INPXML_PATH)
assert xmltree is not None