def _parse_stdout(self, out_folder):
"""CP2K output parser"""
from aiida.orm import BandsData, Dict
# pylint: disable=protected-access
fname = self.node.process_class._DEFAULT_OUTPUT_FILE
if fname not in out_folder._repository.list_object_names():
raise OutputParsingError("Cp2k output file not retrieved")
abs_fn = os.path.join(
out_folder._repository._get_base_folder().abspath, fname)
with io.open(abs_fn, mode="r", encoding="utf-8") as fobj:
result_dict = parse_cp2k_output(fobj)
if "nwarnings" not in result_dict:
raise OutputParsingError("CP2K did not finish properly.")
if "kpoint_data" in result_dict:
bnds = BandsData()
bnds.set_kpoints(result_dict["kpoint_data"]["kpoints"])
bnds.labels = result_dict["kpoint_data"]["labels"]
bnds.set_bands(
result_dict["kpoint_data"]["bands"],
units=result_dict["kpoint_data"]["bands_unit"],
)
self.out("output_bands", bnds)
del result_dict["kpoint_data"]
self.out("output_parameters", Dict(dict=result_dict))
def _parse_stdout(self):
"""Advanced CP2K output file parser."""
from aiida.orm import BandsData
from aiida_cp2k.utils import parse_cp2k_output_advanced
fname = self.node.process_class._DEFAULT_OUTPUT_FILE # pylint: disable=protected-access
if fname not in self.retrieved.list_object_names():
raise OutputParsingError("Cp2k output file not retrieved")
try:
output_string = self.retrieved.get_object_content(fname)
except IOError:
return self.exit_codes.ERROR_OUTPUT_STDOUT_READ
result_dict = parse_cp2k_output_advanced(output_string)
# nwarnings is the last thing to be printed in th eCP2K output file:
# if it is not there, CP2K didn't finish properly
if 'nwarnings' not in result_dict:
raise OutputParsingError("CP2K did not finish properly.")
if "aborted" in result_dict:
return self.exit_codes.ERROR_OUTPUT_CONTAINS_ABORT
# Compute the bandgap for Spin1 and Spin2 if eigen was parsed (works also with smearing!)
if 'eigen_spin1_au' in result_dict:
if result_dict['dft_type'] == "RKS":
result_dict['eigen_spin2_au'] = result_dict['eigen_spin1_au']
lumo_spin1_idx = result_dict['init_nel_spin1']
lumo_spin2_idx = result_dict['init_nel_spin2']
if (lumo_spin1_idx > len(result_dict['eigen_spin1_au'])-1) or \
(lumo_spin2_idx > len(result_dict['eigen_spin2_au'])-1):
#electrons jumped from spin1 to spin2 (or opposite): assume last eigen is lumo
lumo_spin1_idx = len(result_dict['eigen_spin1_au']) - 1
lumo_spin2_idx = len(result_dict['eigen_spin2_au']) - 1
homo_spin1 = result_dict['eigen_spin1_au'][lumo_spin1_idx - 1]
homo_spin2 = result_dict['eigen_spin2_au'][lumo_spin2_idx - 1]
lumo_spin1 = result_dict['eigen_spin1_au'][lumo_spin1_idx]
lumo_spin2 = result_dict['eigen_spin2_au'][lumo_spin2_idx]
result_dict['bandgap_spin1_au'] = lumo_spin1 - homo_spin1
result_dict['bandgap_spin2_au'] = lumo_spin2 - homo_spin2
if "kpoint_data" in result_dict:
bnds = BandsData()
bnds.set_kpoints(result_dict["kpoint_data"]["kpoints"])
bnds.labels = result_dict["kpoint_data"]["labels"]
bnds.set_bands(
result_dict["kpoint_data"]["bands"],
units=result_dict["kpoint_data"]["bands_unit"],
)
self.out("output_bands", bnds)
del result_dict["kpoint_data"]
self.out("output_parameters", Dict(dict=result_dict))
return None
def _parse_stdout(self, out_folder):
"""Advanced CP2K output file parser"""
from aiida.orm import BandsData
from .parser_functions import parse_cp2k_output_advanced
# pylint: disable=protected-access
fname = self.node.process_class._DEFAULT_OUTPUT_FILE
if fname not in out_folder._repository.list_object_names():
raise OutputParsingError("Cp2k output file not retrieved")
abs_fn = os.path.join(
out_folder._repository._get_base_folder().abspath, fname)
with io.open(abs_fn, mode="r", encoding="utf-8") as fobj:
result_dict = parse_cp2k_output_advanced(fobj)
# nwarnings is the last thing to be printed in th eCP2K output file:
# if it is not there, CP2K didn't finish properly
if 'nwarnings' not in result_dict:
raise OutputParsingError("CP2K did not finish properly.")
# Compute the bandgap for Spin1 and Spin2 if eigen was parsed (works also with smearing!)
if 'eigen_spin1_au' in result_dict:
if result_dict['dft_type'] == "RKS":
result_dict['eigen_spin2_au'] = result_dict['eigen_spin1_au']
lumo_spin1_idx = result_dict['init_nel_spin1']
lumo_spin2_idx = result_dict['init_nel_spin2']
if (lumo_spin1_idx > len(result_dict['eigen_spin1_au'])-1) or \
(lumo_spin2_idx > len(result_dict['eigen_spin2_au'])-1):
#electrons jumped from spin1 to spin2 (or opposite): assume last eigen is lumo
lumo_spin1_idx = len(result_dict['eigen_spin1_au']) - 1
lumo_spin2_idx = len(result_dict['eigen_spin2_au']) - 1
homo_spin1 = result_dict['eigen_spin1_au'][lumo_spin1_idx - 1]
homo_spin2 = result_dict['eigen_spin2_au'][lumo_spin2_idx - 1]
lumo_spin1 = result_dict['eigen_spin1_au'][lumo_spin1_idx]
lumo_spin2 = result_dict['eigen_spin2_au'][lumo_spin2_idx]
result_dict['bandgap_spin1_au'] = lumo_spin1 - homo_spin1
result_dict['bandgap_spin2_au'] = lumo_spin2 - homo_spin2
if "kpoint_data" in result_dict:
bnds = BandsData()
bnds.set_kpoints(result_dict["kpoint_data"]["kpoints"])
bnds.labels = result_dict["kpoint_data"]["labels"]
bnds.set_bands(
result_dict["kpoint_data"]["bands"],
units=result_dict["kpoint_data"]["bands_unit"],
)
self.out("output_bands", bnds)
del result_dict["kpoint_data"]
self.out("output_parameters", Dict(dict=result_dict))
def _get_output_nodes(self, output_path, messages_path, xml_path,
json_path, bands_path):
"""
Extracts output nodes from the standard output and standard error
files. (And XML and JSON files)
"""
from aiida.orm import TrajectoryData
import re
parser_version = '1.0.1'
parser_info = {}
parser_info['parser_info'] = 'AiiDA Siesta Parser V. {}'.format(
parser_version)
parser_info['parser_warnings'] = []
#No need for checks anymore
xmldoc = get_parsed_xml_doc(xml_path)
in_struc = self.node.inputs.structure
try:
in_settings = self.node.inputs.settings
except exceptions.NotExistent:
in_settings = None
result_dict = get_dict_from_xml_doc(xmldoc)
# Add timing information
#if json_path is None:
###TODO###
#Not sure how to implement what once was logger.info
#Also not sure I understood the purpose of this file
if json_path is not None:
from .json_time import get_timing_info
global_time, timing_decomp = get_timing_info(json_path)
if global_time is None:
raise OutputParsingError(
"Cannot fully parse the time.json file")
else:
result_dict["global_time"] = global_time
result_dict["timing_decomposition"] = timing_decomp
# Add warnings
if messages_path is None:
# Perhaps using an old version of Siesta
warnings_list = ['WARNING: No MESSAGES file...']
else:
successful, warnings_list = self.get_warnings_from_file(
messages_path)
###TODO### or maybe not
#How do we process this successfull booelan?
result_dict["warnings"] = warnings_list
# Add parser info dictionary
parsed_dict = dict(
list(result_dict.items()) + list(parser_info.items()))
output_data = Dict(dict=parsed_dict)
self.out('output_parameters', output_data)
# If the structure has changed, save it
if is_variable_geometry(xmldoc):
# Get the input structure to copy its site names,
# as the CML file traditionally contained only the
# atomic symbols.
#
struc = get_last_structure(xmldoc, in_struc)
# result_list.append((self.get_linkname_outstructure(),struc))
self.out(self.get_linkname_outstructure(), struc)
# Save forces and stress in an ArrayData object
forces, stress = get_final_forces_and_stress(xmldoc)
if forces is not None and stress is not None:
# from aiida.orm.nodes.array import ArrayData
from aiida.orm import ArrayData
arraydata = ArrayData()
arraydata.set_array('forces', np.array(forces))
arraydata.set_array('stress', np.array(stress))
# result_list.append((self.get_linkname_fs_and_stress(),arraydata))
self.out(self.get_linkname_fs_and_stress(), arraydata)
# Parse band-structure information if available
if bands_path is not None:
bands, coords = self.get_bands(bands_path)
from aiida.orm import BandsData
arraybands = BandsData()
f = self.node.inputs.bandskpoints #Temporary workaround due to a bug
#f._set_reciprocal_cell() #in KpointData (issue #2749)
arraybands.set_kpoints(f.get_kpoints(cartesian=True))
arraybands.labels = f.labels
arraybands.set_bands(bands, units="eV")
self.out(self.get_linkname_bands(), arraybands)
bandsparameters = Dict(dict={"kp_coordinates": coords})
self.out(self.get_linkname_bandsparameters(), bandsparameters)
return result_dict
def band_parser_legacy(band_dat, band_kpt, special_points, structure): # pylint: disable=too-many-locals
"""
Parsers the bands output data, along with the special points retrieved
from the input kpoints to construct a BandsData object which is then
returned. Cannot handle discontinuities in the kpath, if two points are
assigned to same spot only one will be passed. Used for wannier90 < 3.0
:param band_dat: list of str with each str stores one line of aiida_band.dat file
:param band_kpt: list of str with each str stores one line of aiida_band.kpt file
:param special_points: special points to add labels to the bands a dictionary in
the form expected in the input as described in the wannier90 documentation
:return: BandsData object constructed from the input params,
and a list contains warnings.
"""
import numpy as np
from aiida.orm import BandsData
from aiida.orm import KpointsData
warnings = []
warnings.append((
"Note: no file named SEEDNAME_band.labelinfo.dat found. "
"You are probably using a version of Wannier90 before 3.0. "
"There, the labels associated with each k-points were not printed in output "
"and there were also cases in which points were not calculated "
"(see issue #195 on the Wannier90 GitHub page). "
"I will anyway try to do my best to assign labels, "
"but the assignment might be wrong "
"(especially if there are path discontinuities)."))
# imports the data
out_kpt = np.genfromtxt(band_kpt, skip_header=1, usecols=(0, 1, 2))
out_dat = np.genfromtxt(band_dat, usecols=1)
# reshaps the output bands
out_dat = out_dat.reshape(len(out_kpt), (len(out_dat) // len(out_kpt)),
order="F")
# finds expected points of discontinuity
kpath = special_points['path']
cont_break = [(i, (kpath[i - 1][1], kpath[i][0]))
for i in range(1, len(kpath))
if kpath[i - 1][1] != kpath[i][0]]
# finds the special points
special_points_dict = special_points['point_coords']
# We set atol to 1e-5 because in the kpt file the coords are printed with fixed precision
labels = [
(i, k) for k in special_points_dict for i in range(len(out_kpt))
if all(
np.isclose(special_points_dict[k], out_kpt[i], rtol=0, atol=1.e-5))
]
labels.sort()
# Checks and appends labels if discontinuity
appends = []
for x in cont_break:
# two cases the break is before or the break is after
# if the break is before
if labels[x[0]][1] != x[1][0]:
# checks to see if the discontinuity was already there
if labels[x[0] - 1] == x[1][0]:
continue
insert_point = x[0]
new_label = x[1][0]
kpoint = labels[x[0]][0] - 1
appends += [[insert_point, new_label, kpoint]]
# if the break is after
if labels[x[0]][1] != x[1][1]:
# checks to see if the discontinuity was already there
if labels[x[0] + 1] == x[1][1]:
continue
insert_point = x[0] + 1
new_label = x[1][1]
kpoint = labels[x[0]][0] + 1
appends += [[insert_point, new_label, kpoint]]
appends.sort()
for i, append in enumerate(appends):
labels.insert(append[0] + i, (append[2], six.text_type(append[1])))
bands = BandsData()
k = KpointsData()
k.set_cell_from_structure(structure)
k.set_kpoints(out_kpt, cartesian=False)
bands.set_kpointsdata(k)
bands.set_bands(out_dat, units='eV')
bands.labels = labels
return bands, warnings
def band_parser(band_dat, band_kpt, band_labelinfo, structure): # pylint: disable=too-many-locals
"""
Parsers the bands output data to construct a BandsData object which is then
returned. Used for wannier90 >= 3.0
:param band_dat: list of str with each str stores one line of aiida_band.dat file
:param band_kpt: list of str with each str stores one line of aiida_band.kpt file
:param band_labelinfo: list of str with each str stores one line in aiida_band.labelinfo.dat file
:return: BandsData object constructed from the input params
"""
import numpy as np
from aiida.orm import BandsData
from aiida.orm import KpointsData
warnings = []
# imports the data
out_kpt = np.genfromtxt(band_kpt, skip_header=1, usecols=(0, 1, 2))
out_dat = np.genfromtxt(band_dat, usecols=1)
# reshaps the output bands
out_dat = out_dat.reshape(len(out_kpt), (len(out_dat) // len(out_kpt)),
order="F")
labels_dict = {}
for line_idx, line in enumerate(band_labelinfo, start=1):
if not line.strip():
continue
try:
# label, idx, xval, kx, ky, kz = line.split()
label, idx, _, _, _, _ = line.split()
except ValueError:
warnings.append(
('Wrong number of items in line {} of the labelinfo file - '
'I will not assign that label')).format(line_idx)
continue
try:
idx = int(idx)
except ValueError:
warnings.append((
"Invalid value for the index in line {} of the labelinfo file, "
"it's not an integer - I will not assign that label"
)).format(line_idx)
continue
# I use a dictionary because there are cases in which there are
# two lines for the same point (e.g. when I do a zero-length path,
# from a point to the same point, just to have that value)
# Note the -1 because in fortran indices are 1-based, in Python are
# 0-based
labels_dict[idx - 1] = label
labels = [(key, labels_dict[key]) for key in sorted(labels_dict)]
bands = BandsData()
k = KpointsData()
k.set_cell_from_structure(structure)
k.set_kpoints(out_kpt, cartesian=False)
bands.set_kpointsdata(k)
bands.set_bands(out_dat, units='eV')
bands.labels = labels
return bands, warnings