def parse_ph_tensor(data):
"""
Parse the xml tensor file of QE v5.0.3
data must be read from the file with the .read() function (avoid readlines)
"""
from xml.dom.minidom import parseString
dom = parseString(data)
parsed_data = {}
# card EF_TENSORS
cardname = 'EF_TENSORS'
target_tags = read_xml_card(dom, cardname)
tagname = 'DONE_ELECTRIC_FIELD'
parsed_data[tagname.lower()] = parse_xml_child_bool(tagname, target_tags)
if parsed_data[tagname.lower()]:
try:
second_tagname = 'DIELECTRIC_CONSTANT'
parsed_data[second_tagname.lower()] = parse_xml_matrices(
second_tagname, target_tags)
except:
raise QEOutputParsingError('Failed to parse Dielectric constant')
tagname = 'DONE_EFFECTIVE_CHARGE_EU'
parsed_data[tagname.lower()] = parse_xml_child_bool(tagname, target_tags)
if parsed_data[tagname.lower()]:
try:
second_tagname = 'EFFECTIVE_CHARGES_EU'
dumb_matrix = parse_xml_matrices(second_tagname, target_tags)
# separate the elements of the messy matrix, with a matrix 3x3 for each element
new_matrix = []
this_at = []
for i in dumb_matrix:
this_at.append(i)
if len(this_at) == 3:
new_matrix.append(this_at)
this_at = []
parsed_data[second_tagname.lower()] = new_matrix
except:
raise QEOutputParsingError('Failed to parse effective charges eu')
return parsed_data
def parse_cp_xml_output(data):
"""Parse xml data data must be a single string, as returned by file.read() (notice the difference with
parse_text_output!) On output, a dictionary with parsed values.
Democratically, we have decided to use picoseconds as units of time, eV for energies, Angstrom for lengths.
"""
import copy
dom = parseString(data)
parsed_data = {}
#CARD HEADER
parsed_data = copy.deepcopy(xml_card_header(parsed_data, dom))
# CARD CONTROL
cardname = 'CONTROL'
target_tags = read_xml_card(dom, cardname)
tagname = 'PP_CHECK_FLAG'
parsed_data[tagname.lower()] = parse_xml_child_bool(tagname, target_tags)
# CARD STATUS
cardname = 'STATUS'
target_tags = read_xml_card(dom, cardname)
tagname = 'STEP'
attrname = 'ITERATION'
parsed_data[(tagname + '_' + attrname).lower()] = int(
parse_xml_child_attribute_str(tagname, attrname, target_tags))
tagname = 'TIME'
attrname = 'UNITS'
value = parse_xml_child_float(tagname, target_tags)
units = parse_xml_child_attribute_str(tagname, attrname, target_tags)
if units not in ['pico-seconds']:
raise QEOutputParsingError(
'Units {} are not supported by parser'.format(units))
parsed_data[tagname.lower()] = value
tagname = 'TITLE'
parsed_data[tagname.lower()] = parse_xml_child_str(tagname, target_tags)
# CARD CELL
parsed_data, lattice_vectors, volume = copy.deepcopy(
xml_card_cell(parsed_data, dom))
# CARD IONS
parsed_data = copy.deepcopy(
xml_card_ions(parsed_data, dom, lattice_vectors, volume))
# CARD PLANE WAVES
parsed_data = copy.deepcopy(xml_card_planewaves(parsed_data, dom, 'cp'))
# CARD SPIN
parsed_data = copy.deepcopy(xml_card_spin(parsed_data, dom))
# CARD EXCHANGE_CORRELATION
parsed_data = copy.deepcopy(xml_card_exchangecorrelation(parsed_data, dom))
# TODO CARD OCCUPATIONS
# CARD BRILLOUIN ZONE
# TODO: k points are saved for CP... Why?
cardname = 'BRILLOUIN_ZONE'
target_tags = read_xml_card(dom, cardname)
tagname = 'NUMBER_OF_K-POINTS'
parsed_data[tagname.replace('-', '_').lower()] = parse_xml_child_integer(
tagname, target_tags)
tagname = 'UNITS_FOR_K-POINTS'
attrname = 'UNITS'
metric = parse_xml_child_attribute_str(tagname, attrname, target_tags)
if metric not in ['2 pi / a']:
raise QEOutputParsingError(
'Error parsing attribute %s, tag %s inside %s, units unknown' %
(attrname, tagname, target_tags.tagName))
parsed_data[tagname.replace('-', '_').lower()] = metric
# TODO: check what happens if one does not use the monkhorst pack in the code
tagname = 'MONKHORST_PACK_GRID'
try:
a = target_tags.getElementsByTagName(tagname)[0]
value = [int(a.getAttribute('nk' + str(i + 1))) for i in range(3)]
parsed_data[tagname.replace('-', '_').lower()] = value
except:
raise QEOutputParsingError('Error parsing tag %s inside %s.' %
(tagname, target_tags.tagName))
tagname = 'MONKHORST_PACK_OFFSET'
try:
a = target_tags.getElementsByTagName(tagname)[0]
value = [int(a.getAttribute('k' + str(i + 1))) for i in range(3)]
parsed_data[tagname.replace('-', '_').lower()] = value
except:
raise QEOutputParsingError('Error parsing tag %s inside %s.' %
(tagname, target_tags.tagName))
try:
kpoints = []
for i in range(parsed_data['number_of_k_points']):
tagname = 'K-POINT.' + str(i + 1)
a = target_tags.getElementsByTagName(tagname)[0]
b = a.getAttribute('XYZ').replace('\n', '').rsplit()
value = [float(s) for s in b]
metric = parsed_data['units_for_k_points']
if metric == '2 pi / a':
value = [
float(s) / parsed_data['lattice_parameter'] for s in value
]
weight = float(a.getAttribute('WEIGHT'))
kpoints.append([value, weight])
parsed_data['k_point'] = kpoints
except:
raise QEOutputParsingError('Error parsing tag K-POINT.# inside %s.' %
(target_tags.tagName))
tagname = 'NORM-OF-Q'
# TODO decide if save this parameter
parsed_data[tagname.replace('-', '_').lower()] = parse_xml_child_float(
tagname, target_tags)
# CARD PARALLELISM
# can be optional
try:
cardname = 'PARALLELISM'
target_tags = read_xml_card(dom, cardname)
tagname = 'GRANULARITY_OF_K-POINTS_DISTRIBUTION'
parsed_data[tagname.lower().replace('-',
'_')] = parse_xml_child_integer(
tagname, target_tags)
tagname = 'NUMBER_OF_PROCESSORS'
parsed_data[tagname.lower().replace('-',
'_')] = parse_xml_child_integer(
tagname, target_tags)
tagname = 'NUMBER_OF_PROCESSORS_PER_POOL'
parsed_data[tagname.lower().replace('-',
'_')] = parse_xml_child_integer(
tagname, target_tags)
tagname = 'NUMBER_OF_PROCESSORS_PER_IMAGE'
parsed_data[tagname.lower().replace('-',
'_')] = parse_xml_child_integer(
tagname, target_tags)
tagname = 'NUMBER_OF_PROCESSORS_PER_TASKGROUP'
parsed_data[tagname.lower().replace('-',
'_')] = parse_xml_child_integer(
tagname, target_tags)
tagname = 'NUMBER_OF_PROCESSORS_PER_POT'
parsed_data[tagname.lower().replace('-',
'_')] = parse_xml_child_integer(
tagname, target_tags)
tagname = 'NUMBER_OF_PROCESSORS_PER_BAND_GROUP'
parsed_data[tagname.lower().replace('-',
'_')] = parse_xml_child_integer(
tagname, target_tags)
tagname = 'NUMBER_OF_PROCESSORS_PER_DIAGONALIZATION'
parsed_data[tagname.lower().replace('-',
'_')] = parse_xml_child_integer(
tagname, target_tags)
except:
pass
# CARD TIMESTEPS
cardname = 'TIMESTEPS'
target_tags = read_xml_card(dom, cardname)
for tagname in ['STEP0', 'STEPM']:
try:
tag = target_tags.getElementsByTagName(tagname)[0]
try:
second_tagname = 'ACCUMULATORS'
second_tag = tag.getElementsByTagName(second_tagname)[0]
data = second_tag.childNodes[0].data.rstrip().split(
) # list of floats
parsed_data[second_tagname.replace(
'-', '_').lower()] = [float(i) for i in data]
except:
pass
second_tagname = 'IONS_POSITIONS'
second_tag = tag.getElementsByTagName(second_tagname)[0]
third_tagname = 'stau'
third_tag = second_tag.getElementsByTagName(third_tagname)[0]
list_data = third_tag.childNodes[0].data.rstrip().split()
list_data = [float(i) for i in list_data]
# convert to matrix
val = []
mat = []
for i, data in enumerate(list_data):
val.append(data)
if (i + 1) % 3 == 0:
mat.append(val)
val = []
parsed_data[(second_tagname + '_' + third_tagname).replace(
'-', '_').lower()] = mat
third_tagname = 'svel'
third_tag = second_tag.getElementsByTagName(third_tagname)[0]
list_data = third_tag.childNodes[0].data.rstrip().split()
list_data = [float(i) for i in list_data]
# convert to matrix
val = []
mat = []
for i, data in enumerate(list_data):
val.append(data)
if (i + 1) % 3 == 0:
mat.append(val)
val = []
parsed_data[(second_tagname + '_' + third_tagname).replace(
'-', '_').lower()] = mat
try:
third_tagname = 'taui'
third_tag = second_tag.getElementsByTagName(third_tagname)[0]
list_data = third_tag.childNodes[0].data.rstrip().split()
list_data = [float(i) for i in list_data]
# convert to matrix
val = []
mat = []
for i, data in enumerate(list_data):
val.append(data)
if (i + 1) % 3 == 0:
mat.append(val)
val = []
parsed_data[(second_tagname + '_' + third_tagname).replace(
'-', '_').lower()] = mat
except:
pass
try:
third_tagname = 'cdmi'
third_tag = second_tag.getElementsByTagName(third_tagname)[0]
list_data = third_tag.childNodes[0].data.rstrip().split()
parsed_data[(second_tagname + '_' + third_tagname).replace(
'-', '_').lower()] = [float(i) for i in list_data]
except:
pass
try:
third_tagname = 'force'
third_tag = second_tag.getElementsByTagName(third_tagname)[0]
list_data = third_tag.childNodes[0].data.rstrip().split()
list_data = [float(i) for i in list_data]
# convert to matrix
val = []
mat = []
for i, data in enumerate(list_data):
val.append(data)
if (i + 1) % 3 == 0:
mat.append(val)
val = []
parsed_data[(second_tagname + '_' + third_tagname).replace(
'-', '_').lower()] = mat
except:
pass
second_tagname = 'IONS_NOSE'
second_tag = tag.getElementsByTagName(second_tagname)[0]
third_tagname = 'nhpcl'
third_tag = second_tag.getElementsByTagName(third_tagname)[0]
parsed_data[(second_tagname + '_' + third_tagname).replace(
'-', '_').lower()] = float(third_tag.childNodes[0].data)
third_tagname = 'nhpdim'
third_tag = second_tag.getElementsByTagName(third_tagname)[0]
parsed_data[(second_tagname + '_' + third_tagname).replace(
'-', '_').lower()] = float(third_tag.childNodes[0].data)
third_tagname = 'xnhp'
third_tag = second_tag.getElementsByTagName(third_tagname)[0]
parsed_data[(second_tagname + '_' + third_tagname).replace(
'-', '_').lower()] = float(third_tag.childNodes[0].data)
try:
third_tagname = 'vnhp'
third_tag = second_tag.getElementsByTagName(third_tagname)[0]
parsed_data[(second_tagname + '_' + third_tagname).replace(
'-', '_').lower()] = float(third_tag.childNodes[0].data)
except:
pass
try:
second_tagname = 'ekincm'
second_tag = tag.getElementsByTagName(second_tagname)[0]
parsed_data[second_tagname.replace('-', '_').lower()] = float(
second_tag.childNodes[0].data)
except:
pass
second_tagname = 'ELECTRONS_NOSE'
second_tag = tag.getElementsByTagName(second_tagname)[0]
try:
third_tagname = 'xnhe'
third_tag = second_tag.getElementsByTagName(third_tagname)[0]
parsed_data[(second_tagname + '_' + third_tagname).replace(
'-', '_').lower()] = float(third_tag.childNodes[0].data)
except:
pass
try:
third_tagname = 'vnhe'
third_tag = second_tag.getElementsByTagName(third_tagname)[0]
parsed_data[(second_tagname + '_' + third_tagname).replace(
'-', '_').lower()] = float(third_tag.childNodes[0].data)
except:
pass
second_tagname = 'CELL_PARAMETERS'
second_tag = tag.getElementsByTagName(second_tagname)[0]
try:
third_tagname = 'ht'
third_tag = second_tag.getElementsByTagName(third_tagname)[0]
list_data = third_tag.childNodes[0].data.rstrip().split()
list_data = [float(i) for i in list_data]
# convert to matrix
val = []
mat = []
for i, data in enumerate(list_data):
val.append(data)
if (i + 1) % 3 == 0:
mat.append(val)
val = []
parsed_data[(second_tagname + '_' + third_tagname).replace(
'-', '_').lower()] = mat
except:
pass
try:
third_tagname = 'htvel'
third_tag = second_tag.getElementsByTagName(third_tagname)[0]
list_data = third_tag.childNodes[0].data.rstrip().split()
list_data = [float(i) for i in list_data]
# convert to matrix
val = []
mat = []
for i, data in enumerate(list_data):
val.append(data)
if (i + 1) % 3 == 0:
mat.append(val)
val = []
parsed_data[(second_tagname + '_' + third_tagname).replace(
'-', '_').lower()] = mat
except:
pass
try:
third_tagname = 'gvel'
third_tag = second_tag.getElementsByTagName(third_tagname)[0]
list_data = third_tag.childNodes[0].data.rstrip().split()
list_data = [float(i) for i in list_data]
# convert to matrix
val = []
mat = []
for i, data in enumerate(list_data):
val.append(data)
if (i + 1) % 3 == 0:
mat.append(val)
val = []
parsed_data[(second_tagname + '_' + third_tagname).replace(
'-', '_').lower()] = mat
except:
pass
second_tagname = 'CELL_NOSE'
second_tag = tag.getElementsByTagName(second_tagname)[0]
try:
third_tagname = 'xnhh'
third_tag = second_tag.getElementsByTagName(third_tagname)[0]
list_data = third_tag.childNodes[0].data.rstrip().split()
list_data = [float(i) for i in list_data]
# convert to matrix
val = []
mat = []
for i, data in enumerate(list_data):
val.append(data)
if (i + 1) % 3 == 0:
mat.append(val)
val = []
parsed_data[(second_tagname + '_' + third_tagname).replace(
'-', '_').lower()] = mat
except:
pass
try:
third_tagname = 'vnhh'
third_tag = second_tag.getElementsByTagName(third_tagname)[0]
list_data = third_tag.childNodes[0].data.rstrip().split()
list_data = [float(i) for i in list_data]
# convert to matrix
val = []
mat = []
for i, data in enumerate(list_data):
val.append(data)
if (i + 1) % 3 == 0:
mat.append(val)
val = []
parsed_data[(second_tagname + '_' + third_tagname).replace(
'-', '_').lower()] = mat
except:
pass
except:
raise QEOutputParsingError(
'Error parsing CARD {}'.format(cardname))
# CARD BAND_STRUCTURE_INFO
cardname = 'BAND_STRUCTURE_INFO'
target_tags = read_xml_card(dom, cardname)
tagname = 'NUMBER_OF_ATOMIC_WFC'
parsed_data[tagname.lower().replace('-', '_')] = parse_xml_child_integer(
tagname, target_tags)
tagname = 'NUMBER_OF_ELECTRONS'
parsed_data[tagname.lower().replace('-', '_')] = int(
parse_xml_child_float(tagname, target_tags))
tagname = 'NUMBER_OF_BANDS'
parsed_data[tagname.lower().replace('-', '_')] = parse_xml_child_integer(
tagname, target_tags)
tagname = 'NUMBER_OF_SPIN_COMPONENTS'
parsed_data[tagname.lower().replace('-', '_')] = parse_xml_child_integer(
tagname, target_tags)
# TODO
# - EIGENVALUES (that actually just contains occupations)
# Why should I be interested in that, if CP works for insulators only?
# - EIGENVECTORS
# - others TODO are written in the function
return parsed_data