def get_kpointsdata_ncf(self, name=None, index=None, only_used=False):
"""
This routine returns an AiiDA :class:`~aiida.orm.KpointsData` type produced from the
``inp.xml`` file. This only works if the kpoints are listed in the in inpxml.
This is NOT a calcfunction and does not keep the provenance!
:param name: str, optional, if given only the kpoint set with the given name
is returned
:param index: int, optional, if given only the kpoint set with the given index
is returned
:returns: :class:`~aiida.orm.KpointsData` node
"""
from aiida.orm import KpointsData
from masci_tools.util.xml.xml_getters import get_kpoints_data
# HINT, TODO:? in this routine, the 'cell' you might get in an other way
# exp: StructureData.cell, but for this you have to make a structureData Node,
# which might take more time for structures with lots of atoms.
# then just parsing the cell from the inp.xml
# as in the routine get_structureData
xmltree, schema_dict = self.load_inpxml()
if name is None and index is None:
kpoints, weights, cell, pbc = get_kpoints_data(xmltree,
schema_dict,
only_used=only_used)
else:
kpoints, weights, cell, pbc = get_kpoints_data(xmltree,
schema_dict,
name=name,
index=index,
only_used=only_used)
if isinstance(kpoints, dict):
kpoints_data = {}
for (label,
kpoints_set), weights_set in zip(kpoints.items(),
weights.values()):
kps = KpointsData()
kps.set_cell(cell)
kps.pbc = pbc
kps.set_kpoints(kpoints_set,
cartesian=False,
weights=weights_set)
#kpoints_data.add_link_from(self, label='fleurinp.kpts', link_type=LinkType.CREATE)
kps.label = 'fleurinp.kpts'
kpoints_data[label] = kps
else:
kpoints_data = KpointsData()
kpoints_data.set_cell(cell)
kpoints_data.pbc = pbc
kpoints_data.set_kpoints(kpoints, cartesian=False, weights=weights)
#kpoints_data.add_link_from(self, label='fleurinp.kpts', link_type=LinkType.CREATE)
kpoints_data.label = 'fleurinp.kpts'
return kpoints_data
def get_kpointsdata_ncf(self):
"""
This routine returns an AiiDA :class:`~aiida.orm.KpointsData` type produced from the
``inp.xml`` file. This only works if the kpoints are listed in the in inpxml.
This is NOT a calcfunction and does not keep the provenance!
:returns: :class:`~aiida.orm.KpointsData` node
"""
from aiida.orm import KpointsData
# HINT, TODO:? in this routine, the 'cell' you might get in an other way
# exp: StructureData.cell, but for this you have to make a structureData Node,
# which might take more time for structures with lots of atoms.
# then just parsing the cell from the inp.xml
# as in the routine get_structureData
# Disclaimer: this routine needs some xpath expressions.
# these are hardcoded here, therefore maintainance might be needed,
# if you want to circumvent this, you have
# to get all the paths from somewhere.
#######
# all hardcoded xpaths used and attributes names:
bravaismatrix_bulk_xpath = '/fleurInput/cell/bulkLattice/bravaisMatrix/'
bravaismatrix_film_xpath = '/fleurInput/cell/filmLattice/bravaisMatrix/'
kpointlist_xpath = '/fleurInput/calculationSetup/bzIntegration/kPointList/'
kpoint_tag = 'kPoint'
kpointlist_attrib_posscale = 'posScale'
kpointlist_attrib_weightscale = 'weightScale'
#kpointlist_attrib_count = 'count'
kpoint_attrib_weight = 'weight'
row1_tag_name = 'row-1'
row2_tag_name = 'row-2'
row3_tag_name = 'row-3'
########
if 'inp.xml' not in self.files:
print(
'cannot get a KpointsData because fleurinpdata has no inp.xml file yet'
)
# TODO what to do in this case?
return False
# else read in inpxml
if self._schema_file_path: # Schema there, parse with schema
xmlschema_doc = etree.parse(self._schema_file_path)
xmlschema = etree.XMLSchema(xmlschema_doc)
parser = etree.XMLParser(attribute_defaults=True, encoding='utf-8')
with self.open(path='inp.xml', mode='r') as inpxmlfile:
tree = etree.parse(inpxmlfile, parser)
tree.xinclude()
# remove comments from inp.xml
comments = tree.xpath('//comment()')
for c in comments:
p = c.getparent()
p.remove(c)
if not xmlschema.validate(tree):
raise ValueError(
'Input file is not validated against the schema.')
else: # schema not there, parse without
print('parsing inp.xml without XMLSchema')
with self.open(path='inp.xml', mode='r') as inpxmlfile:
tree = etree.parse(inpxmlfile)
tree.xinclude()
# remove comments from inp.xml
comments = tree.xpath('//comment()')
for c in comments:
p = c.getparent()
p.remove(c)
root = tree.getroot()
# get cell matrix from inp.xml
cell = None
row1 = root.xpath(bravaismatrix_bulk_xpath +
row1_tag_name) # [0].text.split()
if row1: # bulk calculation
row1 = row1[0].text.split()
row2 = root.xpath(bravaismatrix_bulk_xpath +
row2_tag_name)[0].text.split()
row3 = root.xpath(bravaismatrix_bulk_xpath +
row3_tag_name)[0].text.split()
# TODO? allow math?
for i, cor in enumerate(row1):
row1[i] = float(cor) * BOHR_A
for i, cor in enumerate(row2):
row2[i] = float(cor) * BOHR_A
for i, cor in enumerate(row3):
row3[i] = float(cor) * BOHR_A
cell = [row1, row2, row3]
# set boundary conditions
pbc1 = [True, True, True]
elif root.xpath(bravaismatrix_film_xpath + row1_tag_name):
# film calculation
row1 = root.xpath(bravaismatrix_film_xpath +
row1_tag_name)[0].text.split()
row2 = root.xpath(bravaismatrix_film_xpath +
row2_tag_name)[0].text.split()
row3 = root.xpath(bravaismatrix_film_xpath +
row3_tag_name)[0].text.split()
for i, cor in enumerate(row1):
row1[i] = float(cor) * BOHR_A
for i, cor in enumerate(row2):
row2[i] = float(cor) * BOHR_A
for i, cor in enumerate(row3):
row3[i] = float(cor) * BOHR_A
# row3 = [0, 0, 0]#? TODO:what has it to be in this case?
cell = [row1, row2, row3]
pbc1 = [True, True, False]
if cell is None:
print('Could not extract Bravias matrix out of inp.xml. Is the '
'Bravias matrix explicitly given? i.e Latnam definition '
'not supported.')
return None
# get kpoints only works if kpointlist in inp.xml
kpoints = root.xpath(kpointlist_xpath + kpoint_tag)
if kpoints:
posscale = root.xpath(kpointlist_xpath + '@' +
kpointlist_attrib_posscale)
weightscale = root.xpath(kpointlist_xpath + '@' +
kpointlist_attrib_weightscale)
#count = root.xpath(kpointlist_xpath + '@' + kpointlist_attrib_count)
kpoints_pos = []
kpoints_weight = []
for kpoint in kpoints:
kpoint_pos = kpoint.text.split()
for i, kval in enumerate(kpoint_pos):
kpoint_pos[i] = float(kval) / float(posscale[0])
kpoint_weight = float(
kpoint.get(kpoint_attrib_weight)) / float(
weightscale[0])
kpoints_pos.append(kpoint_pos)
kpoints_weight.append(kpoint_weight)
totalw = 0
for weight in kpoints_weight:
totalw = totalw + weight
kps = KpointsData()
kps.set_cell(cell)
kps.pbc = pbc1
kps.set_kpoints(kpoints_pos,
cartesian=False,
weights=kpoints_weight)
#kps.add_link_from(self, label='fleurinp.kpts', link_type=LinkType.CREATE)
kps.label = 'fleurinp.kpts'
# return {label: kps}
return kps
else: # TODO parser other kpoints formats, if they fit in an AiiDA node
print('No kpoint list in inp.xml')
return None
