def parse_with_retrieved(self, retrieved):
"""
Receives in input a dictionary of retrieved nodes.
Does all the logic here.
"""
from aiida.common.exceptions import InvalidOperation
import os
import glob
successful = True
# check if I'm not to overwrite anything
#state = self._calc.get_state()
#if state != calc_states.PARSING:
# raise InvalidOperation("Calculation not in {} state"
# .format(calc_states.PARSING) )
# retrieve the input parameter
calc_input = self._calc.inp.parameters
# look for eventual flags of the parser
try:
parser_opts = self._calc.inp.settings.get_dict()[
self.get_parser_settings_key()]
except (AttributeError, KeyError):
parser_opts = {}
# load the input dictionary
# TODO: pass this input_dict to the parser. It might need it.
input_dict = self._calc.inp.parameters.get_dict()
# Check that the retrieved folder is there
try:
out_folder = retrieved[self._calc._get_linkname_retrieved()]
except KeyError:
self.logger.error("No retrieved folder found")
return False, ()
# check what is inside the folder
list_of_files = out_folder.get_folder_list()
# at least the stdout should exist
if not self._calc._OUTPUT_FILE_NAME in list_of_files:
self.logger.error("Standard output not found")
successful = False
return successful, ()
# if there is something more, I note it down, so to call the raw parser
# with the right options
# look for xml
has_xml = False
if self._calc._DATAFILE_XML_BASENAME in list_of_files:
has_xml = True
# look for bands
has_bands = False
if glob.glob(os.path.join(out_folder.get_abs_path('.'), 'K*[0-9]')):
# Note: assuming format of kpoints subfolder is K*[0-9]
has_bands = True
# TODO: maybe it can be more general than bands only?
out_file = os.path.join(out_folder.get_abs_path('.'),
self._calc._OUTPUT_FILE_NAME)
xml_file = os.path.join(out_folder.get_abs_path('.'),
self._calc._DATAFILE_XML_BASENAME)
dir_with_bands = out_folder.get_abs_path('.')
# call the raw parsing function
parsing_args = [out_file, input_dict, parser_opts]
if has_xml:
parsing_args.append(xml_file)
if has_bands:
if not has_xml:
self.logger.warning("Cannot parse bands if xml file not "
"found")
else:
parsing_args.append(dir_with_bands)
out_dict, trajectory_data, structure_data, raw_successful = parse_raw_output(
*parsing_args)
# if calculation was not considered failed already, use the new value
successful = raw_successful if successful else successful
new_nodes_list = []
# I eventually save the new structure. structure_data is unnecessary after this
in_struc = self._calc.get_inputs_dict()['structure']
type_calc = input_dict['CONTROL']['calculation']
struc = in_struc
if type_calc in ['relax', 'vc-relax', 'md', 'vc-md']:
if 'cell' in structure_data.keys():
struc = convert_qe2aiida_structure(structure_data,
input_structure=in_struc)
new_nodes_list.append(
(self.get_linkname_outstructure(), struc))
k_points_list = trajectory_data.pop('k_points', None)
k_points_weights_list = trajectory_data.pop('k_points_weights', None)
if k_points_list is not None:
# build the kpoints object
if out_dict['k_points_units'] not in ['2 pi / Angstrom']:
raise QEOutputParsingError(
'Error in kpoints units (should be cartesian)')
# converting bands into a BandsData object (including the kpoints)
kpoints_from_output = KpointsData()
kpoints_from_output.set_cell_from_structure(struc)
kpoints_from_output.set_kpoints(k_points_list,
cartesian=True,
weights=k_points_weights_list)
kpoints_from_input = self._calc.inp.kpoints
try:
kpoints_from_input.get_kpoints()
except AttributeError:
new_nodes_list += [(self.get_linkname_out_kpoints(),
kpoints_from_output)]
# convert the dictionary into an AiiDA object
output_params = ParameterData(dict=out_dict)
# return it to the execmanager
new_nodes_list.append((self.get_linkname_outparams(), output_params))
if trajectory_data:
import numpy
from aiida.orm.data.array.trajectory import TrajectoryData
from aiida.orm.data.array import ArrayData
try:
positions = numpy.array(
trajectory_data.pop('atomic_positions_relax'))
try:
cells = numpy.array(
trajectory_data.pop('lattice_vectors_relax'))
# if KeyError, the MD was at fixed cell
except KeyError:
cells = numpy.array([in_struc.cell] * len(positions))
symbols = numpy.array(
[str(i.kind_name) for i in in_struc.sites])
stepids = numpy.arange(
len(positions)) # a growing integer per step
# I will insert time parsing when they fix their issues about time
# printing (logic is broken if restart is on)
traj = TrajectoryData()
traj.set_trajectory(
stepids=stepids,
cells=cells,
symbols=symbols,
positions=positions,
)
for x in trajectory_data.iteritems():
traj.set_array(x[0], numpy.array(x[1]))
# return it to the execmanager
new_nodes_list.append(
(self.get_linkname_outtrajectory(), traj))
except KeyError: # forces in scf calculation (when outputed)
arraydata = ArrayData()
for x in trajectory_data.iteritems():
arraydata.set_array(x[0], numpy.array(x[1]))
# return it to the execmanager
new_nodes_list.append(
(self.get_linkname_outarray(), arraydata))
return successful, new_nodes_list
def parse_with_retrieved(self, retrieved):
"""
Parse the output nodes for a PwCalculations from a dictionary of retrieved nodes.
Two nodes that are expected are the default 'retrieved' FolderData node which will
store the retrieved files permanently in the repository. The second required node
is the unstored FolderData node with the temporary retrieved files, which should
be passed under the key 'retrieved_temporary_folder_key' of the Parser class.
:param retrieved: a dictionary of retrieved nodes
"""
import os
import numpy
successful = True
# Load the input dictionary
parameters = self._calc.inp.parameters.get_dict()
# Look for optional settings input node and potential 'parser_options' dictionary within it
try:
settings = self._calc.inp.settings.get_dict()
parser_opts = settings[self.get_parser_settings_key()]
except (AttributeError, KeyError):
settings = {}
parser_opts = {}
# Check that the retrieved folder is there
try:
out_folder = retrieved[self._calc._get_linkname_retrieved()]
except KeyError:
self.logger.error("No retrieved folder found")
return False, ()
# Verify that the retrieved_temporary_folder is within the arguments if temporary files were specified
if self._calc._get_retrieve_temporary_list():
try:
temporary_folder = retrieved[self.retrieved_temporary_folder_key]
dir_with_bands = temporary_folder.get_abs_path('.')
except KeyError:
self.logger.error('the {} was not passed as an argument'.format(self.retrieved_temporary_folder_key))
return False, ()
else:
dir_with_bands = None
list_of_files = out_folder.get_folder_list()
# The stdout is required for parsing
if not self._calc._OUTPUT_FILE_NAME in list_of_files:
self.logger.error("The standard output file '{}' was not found but is required".format(self._calc._OUTPUT_FILE_NAME))
return False, ()
# The xml file is required for parsing
if not self._calc._DATAFILE_XML_BASENAME in list_of_files:
self.logger.error("The xml output file '{}' was not found but is required".format(self._calc._DATAFILE_XML_BASENAME))
successful = False
xml_file = None
else:
xml_file = os.path.join(out_folder.get_abs_path('.'), self._calc._DATAFILE_XML_BASENAME)
out_file = os.path.join(out_folder.get_abs_path('.'), self._calc._OUTPUT_FILE_NAME)
# Call the raw parsing function
parsing_args = [out_file, parameters, parser_opts, xml_file, dir_with_bands]
out_dict, trajectory_data, structure_data, bands_data, raw_successful = parse_raw_output(*parsing_args)
# If calculation was not considered failed already, use the new value
successful = raw_successful if successful else successful
# The symmetry info has large arrays, that occupy most of the database.
# turns out most of this is due to 64 matrices that are repeated over and over again.
# therefore I map part of the results in a list of dictionaries wrote here once and for all
# if the parser_opts has a key all_symmetries set to True, I don't reduce it
all_symmetries = parser_opts.get('all_symmetries', False)
if not all_symmetries:
try:
if 'symmetries' in out_dict.keys():
old_symmetries = out_dict['symmetries']
new_symmetries = []
for this_sym in old_symmetries:
name = this_sym['name']
index = None
for i,this in enumerate(self._possible_symmetries):
if name in this['name']:
index = i
if index is None:
self.logger.error("Symmetry {} not found".format(name))
new_dict = {}
# note: here I lose the information about equivalent
# ions and fractional_translation.
# They will be present with all_symmetries=True
new_dict['t_rev'] = this_sym['t_rev']
new_dict['symmetry_number'] = index
new_symmetries.append(new_dict)
out_dict['symmetries'] = new_symmetries # and overwrite the old one
except KeyError: # no symmetries were parsed (failed case, likely)
self.logger.error("No symmetries were found in output")
new_nodes_list = []
# I eventually save the new structure. structure_data is unnecessary after this
in_struc = self._calc.get_inputs_dict()['structure']
type_calc = parameters['CONTROL']['calculation']
struc = in_struc
if type_calc in ['relax', 'vc-relax', 'md', 'vc-md']:
if 'cell' in structure_data.keys():
struc = convert_qe2aiida_structure(structure_data, input_structure=in_struc)
new_nodes_list.append((self.get_linkname_outstructure(), struc))
k_points_list = trajectory_data.pop('k_points', None)
k_points_weights_list = trajectory_data.pop('k_points_weights', None)
if k_points_list is not None:
# Build the kpoints object
if out_dict['k_points_units'] not in ['2 pi / Angstrom']:
raise QEOutputParsingError('Error in kpoints units (should be cartesian)')
kpoints_from_output = KpointsData()
kpoints_from_output.set_cell_from_structure(struc)
kpoints_from_output.set_kpoints(k_points_list, cartesian=True, weights=k_points_weights_list)
kpoints_from_input = self._calc.inp.kpoints
if not bands_data:
try:
kpoints_from_input.get_kpoints()
except AttributeError:
new_nodes_list += [(self.get_linkname_out_kpoints(), kpoints_from_output)]
# Converting bands into a BandsData object (including the kpoints)
if bands_data:
kpoints_for_bands = kpoints_from_output
try:
kpoints_from_input.get_kpoints()
kpoints_for_bands.labels = kpoints_from_input.labels
except (AttributeError, ValueError, TypeError):
# AttributeError: no list of kpoints in input
# ValueError: labels from input do not match the output
# list of kpoints (some kpoints are missing)
# TypeError: labels are not set, so kpoints_from_input.labels=None
pass
# Get the bands occupations and correct the occupations of QE:
# If it computes only one component, it occupies it with half number of electrons
try:
bands_data['occupations'][1]
the_occupations = bands_data['occupations']
except IndexError:
the_occupations = 2.*numpy.array(bands_data['occupations'][0])
try:
bands_data['bands'][1]
bands_energies = bands_data['bands']
except IndexError:
bands_energies = bands_data['bands'][0]
the_bands_data = BandsData()
the_bands_data.set_kpointsdata(kpoints_for_bands)
the_bands_data.set_bands(bands_energies,
units = bands_data['bands_units'],
occupations = the_occupations)
new_nodes_list += [('output_band', the_bands_data)]
out_dict['linknames_band'] = ['output_band']
# Separate the atomic_occupations dictionary in its own node if it is present
atomic_occupations = out_dict.get('atomic_occupations', {})
if atomic_occupations:
out_dict.pop('atomic_occupations')
atomic_occupations_node = ParameterData(dict=atomic_occupations)
new_nodes_list.append(('output_atomic_occupations', atomic_occupations_node))
output_params = ParameterData(dict=out_dict)
new_nodes_list.append((self.get_linkname_outparams(), output_params))
if trajectory_data:
from aiida.orm.data.array.trajectory import TrajectoryData
from aiida.orm.data.array import ArrayData
try:
positions = numpy.array( trajectory_data.pop('atomic_positions_relax'))
try:
cells = numpy.array( trajectory_data.pop('lattice_vectors_relax'))
# if KeyError, the MD was at fixed cell
except KeyError:
cells = numpy.array([in_struc.cell] * len(positions))
symbols = numpy.array([str(i.kind_name) for i in in_struc.sites])
stepids = numpy.arange(len(positions)) # a growing integer per step
# I will insert time parsing when they fix their issues about time
# printing (logic is broken if restart is on)
traj = TrajectoryData()
traj.set_trajectory(
stepids = stepids,
cells = cells,
symbols = symbols,
positions = positions,
)
for x in trajectory_data.iteritems():
traj.set_array(x[0],numpy.array(x[1]))
new_nodes_list.append((self.get_linkname_outtrajectory(),traj))
except KeyError:
# forces, atomic charges and atomic mag. moments, in scf calculation (when outputed)
arraydata = ArrayData()
for x in trajectory_data.iteritems():
arraydata.set_array(x[0],numpy.array(x[1]))
new_nodes_list.append((self.get_linkname_outarray(),arraydata))
return successful, new_nodes_list
def parse_with_retrieved(self, retrieved):
"""
Receives in input a dictionary of retrieved nodes.
Does all the logic here.
"""
from aiida.common.exceptions import InvalidOperation
import os
import glob
successful = True
# check if I'm not to overwrite anything
#state = self._calc.get_state()
#if state != calc_states.PARSING:
# raise InvalidOperation("Calculation not in {} state"
# .format(calc_states.PARSING) )
# look for eventual flags of the parser
try:
parser_opts = self._calc.inp.settings.get_dict()[
self.get_parser_settings_key()]
except (AttributeError, KeyError):
parser_opts = {}
# load the input dictionary
# TODO: pass this input_dict to the parser. It might need it.
input_dict = self._calc.inp.parameters.get_dict()
# Check that the retrieved folder is there
try:
out_folder = retrieved[self._calc._get_linkname_retrieved()]
except KeyError:
self.logger.error("No retrieved folder found")
return False, ()
# check what is inside the folder
list_of_files = out_folder.get_folder_list()
# at least the stdout should exist
if not self._calc._OUTPUT_FILE_NAME in list_of_files:
self.logger.error("Standard output not found")
successful = False
return successful, ()
# if there is something more, I note it down, so to call the raw parser
# with the right options
# look for xml
has_xml = False
if self._calc._DATAFILE_XML_BASENAME in list_of_files:
has_xml = True
# look for bands
has_bands = False
if glob.glob(os.path.join(out_folder.get_abs_path('.'), 'K*[0-9]')):
# Note: assuming format of kpoints subfolder is K*[0-9]
has_bands = True
# TODO: maybe it can be more general than bands only?
out_file = os.path.join(out_folder.get_abs_path('.'),
self._calc._OUTPUT_FILE_NAME)
xml_file = os.path.join(out_folder.get_abs_path('.'),
self._calc._DATAFILE_XML_BASENAME)
dir_with_bands = out_folder.get_abs_path('.')
# call the raw parsing function
parsing_args = [out_file, input_dict, parser_opts]
if has_xml:
parsing_args.append(xml_file)
if has_bands:
if not has_xml:
self.logger.warning("Cannot parse bands if xml file not "
"found")
else:
parsing_args.append(dir_with_bands)
out_dict, trajectory_data, structure_data, bands_data, raw_successful = parse_raw_output(
*parsing_args)
# if calculation was not considered failed already, use the new value
successful = raw_successful if successful else successful
# The symmetry info has large arrays, that occupy most of the database.
# turns out most of this is due to 64 matrices that are repeated over and over again.
# therefore I map part of the results in a list of dictionaries wrote here once and for all
# if the parser_opts has a key all_symmetries set to True, I don't reduce it
all_symmetries = parser_opts.get('all_symmetries', False)
if not all_symmetries:
try:
if 'symmetries' in out_dict.keys():
old_symmetries = out_dict['symmetries']
new_symmetries = []
for this_sym in old_symmetries:
name = this_sym['name']
index = None
for i, this in enumerate(self._possible_symmetries):
if name in this['name']:
index = i
if index is None:
self.logger.error(
"Symmetry {} not found".format(name))
new_dict = {}
# note: here I lose the information about equivalent
# ions and fractional_translation.
# They will be present with all_symmetries=True
new_dict['t_rev'] = this_sym['t_rev']
new_dict['symmetry_number'] = index
new_symmetries.append(new_dict)
out_dict[
'symmetries'] = new_symmetries # and overwrite the old one
except KeyError: # no symmetries were parsed (failed case, likely)
self.logger.error("No symmetries were found in output")
new_nodes_list = []
# I eventually save the new structure. structure_data is unnecessary after this
in_struc = self._calc.get_inputs_dict()['structure']
type_calc = input_dict['CONTROL']['calculation']
struc = in_struc
if type_calc in ['relax', 'vc-relax', 'md', 'vc-md']:
if 'cell' in structure_data.keys():
struc = convert_qe2aiida_structure(structure_data,
input_structure=in_struc)
new_nodes_list.append(
(self.get_linkname_outstructure(), struc))
k_points_list = trajectory_data.pop('k_points', None)
k_points_weights_list = trajectory_data.pop('k_points_weights', None)
if k_points_list is not None:
# build the kpoints object
if out_dict['k_points_units'] not in ['2 pi / Angstrom']:
raise QEOutputParsingError(
'Error in kpoints units (should be cartesian)')
# converting bands into a BandsData object (including the kpoints)
kpoints_from_output = KpointsData()
kpoints_from_output.set_cell_from_structure(struc)
kpoints_from_output.set_kpoints(k_points_list,
cartesian=True,
weights=k_points_weights_list)
kpoints_from_input = self._calc.inp.kpoints
if not bands_data:
try:
kpoints_from_input.get_kpoints()
except AttributeError:
new_nodes_list += [(self.get_linkname_out_kpoints(),
kpoints_from_output)]
if bands_data:
import numpy
# converting bands into a BandsData object (including the kpoints)
kpoints_for_bands = kpoints_from_output
try:
kpoints_from_input.get_kpoints()
kpoints_for_bands.labels = kpoints_from_input.labels
except (AttributeError, ValueError, TypeError):
# AttributeError: no list of kpoints in input
# ValueError: labels from input do not match the output
# list of kpoints (some kpoints are missing)
# TypeError: labels are not set, so kpoints_from_input.labels=None
pass
# get the bands occupations.
# correct the occupations of QE: if it computes only one component,
# it occupies it with half number of electrons
try:
bands_data['occupations'][1]
the_occupations = bands_data['occupations']
except IndexError:
the_occupations = 2. * numpy.array(
bands_data['occupations'][0])
try:
bands_data['bands'][1]
bands_energies = bands_data['bands']
except IndexError:
bands_energies = bands_data['bands'][0]
the_bands_data = BandsData()
the_bands_data.set_kpointsdata(kpoints_for_bands)
the_bands_data.set_bands(bands_energies,
units=bands_data['bands_units'],
occupations=the_occupations)
new_nodes_list += [('output_band', the_bands_data)]
out_dict['linknames_band'] = ['output_band']
# convert the dictionary into an AiiDA object
output_params = ParameterData(dict=out_dict)
# return it to the execmanager
new_nodes_list.append((self.get_linkname_outparams(), output_params))
if trajectory_data:
import numpy
from aiida.orm.data.array.trajectory import TrajectoryData
from aiida.orm.data.array import ArrayData
try:
positions = numpy.array(
trajectory_data.pop('atomic_positions_relax'))
try:
cells = numpy.array(
trajectory_data.pop('lattice_vectors_relax'))
# if KeyError, the MD was at fixed cell
except KeyError:
cells = numpy.array([in_struc.cell] * len(positions))
symbols = numpy.array(
[str(i.kind_name) for i in in_struc.sites])
stepids = numpy.arange(
len(positions)) # a growing integer per step
# I will insert time parsing when they fix their issues about time
# printing (logic is broken if restart is on)
traj = TrajectoryData()
traj.set_trajectory(
stepids=stepids,
cells=cells,
symbols=symbols,
positions=positions,
)
for x in trajectory_data.iteritems():
traj.set_array(x[0], numpy.array(x[1]))
# return it to the execmanager
new_nodes_list.append(
(self.get_linkname_outtrajectory(), traj))
except KeyError:
# forces, atomic charges and atomic mag. moments, in scf
# calculation (when outputed)
arraydata = ArrayData()
for x in trajectory_data.iteritems():
arraydata.set_array(x[0], numpy.array(x[1]))
# return it to the execmanager
new_nodes_list.append(
(self.get_linkname_outarray(), arraydata))
return successful, new_nodes_list
def parse_with_retrieved(self, retrieved):
"""
Parses the calculation-output datafolder, and stores
results.
:param retrieved: a dictionary of retrieved nodes, where the keys
are the link names of retrieved nodes, and the values are the
nodes.
"""
from aiida.common.exceptions import InvalidOperation
from aiida.orm.data.array.trajectory import TrajectoryData
from aiida.orm.data.array import ArrayData
import os
import numpy
import copy
successful = True
# check if I'm not to overwrite anything
#state = self._calc.get_state()
#if state != calc_states.PARSING:
# raise InvalidOperation("Calculation not in {} state"
# .format(calc_states.PARSING) )
# look for eventual flags of the parser
try:
parser_opts = self._calc.inp.settings.get_dict()[
self.get_parser_settings_key()]
except (AttributeError, KeyError):
parser_opts = {}
# load the pw input dictionary
pw_input_dict = self._calc.inp.pw_parameters.get_dict()
# load the pw input dictionary
neb_input_dict = self._calc.inp.neb_parameters.get_dict()
# Check that the retrieved folder is there
try:
out_folder = retrieved[self._calc._get_linkname_retrieved()]
except KeyError:
self.logger.error("No retrieved folder found")
successful = False
return successful, ()
# check what is inside the folder
list_of_files = out_folder.get_folder_list()
# at least the stdout should exist
if not self._calc._OUTPUT_FILE_NAME in list_of_files:
self.logger.error("Standard output not found")
successful = False
return successful, ()
out_file = os.path.join(out_folder.get_abs_path('.'),
self._calc._OUTPUT_FILE_NAME)
# First parse the Neb output
neb_out_dict, iteration_data, raw_successful = parse_raw_output_neb(
out_file, neb_input_dict)
# if calculation was not considered failed already, use the new value
successful = raw_successful if successful else successful
# Retrieve the number of images
try:
num_images = neb_input_dict['num_of_images']
except KeyError:
try:
num_images = neb_out_dict['num_of_images']
except KeyError:
self.logger.error(
"Impossible to understand the number of images")
successful = False
return successful, ()
# Now parse the information from the single pw calculations for the different images
image_data = {}
positions = []
cells = []
for i in range(num_images):
# look for xml and parse
xml_file = os.path.join(out_folder.get_abs_path('.'),
self._calc._PREFIX + '_{}'.format(i + 1),
self._calc._PREFIX + '.save',
self._calc._DATAFILE_XML_BASENAME)
try:
with open(xml_file, 'r') as f:
xml_lines = f.read() # Note: read() and not readlines()
except IOError:
self.logger.error(
"No xml file found for image {} at {}".format(
i + 1, xml_file))
successful = False
return successful, ()
xml_data, structure_dict, bands_data = parse_pw_xml_output(
xml_lines)
# convert the dictionary obtained from parsing the xml to an AiiDA StructureData
structure_data = convert_qe2aiida_structure(structure_dict)
# look for pw output and parse it
pw_out_file = os.path.join(
out_folder.get_abs_path('.'),
self._calc._PREFIX + '_{}'.format(i + 1), 'PW.out')
try:
with open(pw_out_file, 'r') as f:
pw_out_lines = f.read() # Note: read() and not readlines()
except IOError:
self.logger.error(
"No pw output file found for image {}".format(i + 1))
successful = False
return successful, ()
pw_out_data, trajectory_data, critical_messages = parse_pw_text_output(
pw_out_lines, xml_data, structure_dict, pw_input_dict)
# I add in the out_data all the last elements of trajectory_data values.
# Safe for some large arrays, that I will likely never query.
skip_keys = [
'forces', 'atomic_magnetic_moments', 'atomic_charges',
'lattice_vectors_relax', 'atomic_positions_relax',
'atomic_species_name'
]
tmp_trajectory_data = copy.copy(trajectory_data)
for x in tmp_trajectory_data.iteritems():
if x[0] in skip_keys:
continue
pw_out_data[x[0]] = x[1][-1]
if len(x[1]) == 1: # delete eventual keys that are not arrays
trajectory_data.pop(x[0])
# As the k points are an array that is rather large, and again it's not something I'm going to parse likely
# since it's an info mainly contained in the input file, I move it to the trajectory data
for key in ['k_points', 'k_points_weights']:
try:
trajectory_data[key] = xml_data.pop(key)
except KeyError:
pass
key = 'pw_output_image_{}'.format(i + 1)
image_data[key] = dict(pw_out_data.items() + xml_data.items())
positions.append([site.position for site in structure_data.sites])
cells.append(structure_data.cell)
# If a warning was already present in the NEB, add also PW warnings to the neb output data,
# avoiding repetitions.
if neb_out_dict['warnings']:
for warning in pw_out_data['warnings']:
if warning not in neb_out_dict['warnings']:
neb_out_dict['warnings'].append(warning)
# Symbols can be obtained simply from the last image
symbols = [str(site.kind_name) for site in structure_data.sites]
new_nodes_list = []
# convert the dictionary into an AiiDA object
output_params = ParameterData(dict=dict(neb_out_dict.items() +
image_data.items()))
# return it to the execmanager
new_nodes_list.append((self.get_linkname_outparams(), output_params))
# convert data on structure of images into a TrajectoryData
traj = TrajectoryData()
traj.set_trajectory(
stepids=numpy.arange(1, num_images + 1),
cells=numpy.array(cells),
symbols=numpy.array(symbols),
positions=numpy.array(positions),
)
# return it to the execmanager
new_nodes_list.append((self.get_linkname_outtrajectory(), traj))
if parser_opts.get('all_iterations', False):
if iteration_data:
from aiida.orm.data.array import ArrayData
arraydata = ArrayData()
for x in iteration_data.iteritems():
arraydata.set_array(x[0], numpy.array(x[1]))
new_nodes_list.append(
(self.get_linkname_iterationarray(), arraydata))
# Load the original and interpolated energy profile along the minimum-energy path (mep)
try:
mep_file = os.path.join(out_folder.get_abs_path('.'),
self._calc._PREFIX + '.dat')
mep = numpy.loadtxt(mep_file)
except Exception:
self.logger.warning(
"Impossible to find the file with image energies "
"versus reaction coordinate.")
mep = numpy.array([[]])
try:
interp_mep_file = os.path.join(out_folder.get_abs_path('.'),
self._calc._PREFIX + '.int')
interp_mep = numpy.loadtxt(interp_mep_file)
except Exception:
self.logger.warning(
"Impossible to find the file with the interpolation "
"of image energies versus reaction coordinate.")
interp_mep = numpy.array([[]])
# Create an ArrayData with the energy profiles
mep_arraydata = ArrayData()
mep_arraydata.set_array('mep', mep)
mep_arraydata.set_array('interpolated_mep', interp_mep)
new_nodes_list.append((self.get_linkname_meparray(), mep_arraydata))
return successful, new_nodes_list
def parse(self, **kwargs):
"""Parse the retrieved files of a completed `NebCalculation` into output nodes.
Two nodes that are expected are the default 'retrieved' `FolderData` node which will store the retrieved files
permanently in the repository. The second required node is a filepath under the key `retrieved_temporary_files`
which should contain the temporary retrieved files.
"""
from aiida.orm import TrajectoryData, ArrayData
import os
import numpy
PREFIX = self.node.process_class._PREFIX
# Check that the retrieved folder is there
try:
out_folder = self.retrieved
except NotExistent:
return self.exit_codes.ERROR_NO_RETRIEVED_FOLDER
list_of_files = out_folder.list_object_names(
) # Note: this includes folders, but not the files they contain.
# The stdout is required for parsing
filename_stdout = self.node.get_attribute('output_filename')
if filename_stdout not in list_of_files:
self.logger.error(
"The standard output file '{}' was not found but is required".
format(filename_stdout))
return self.exit_codes.ERROR_READING_OUTPUT_FILE
# Look for optional settings input node and potential 'parser_options' dictionary within it
# Note that we look for both NEB and PW parser options under "inputs.settings.parser_options";
# we don't even have a namespace "inputs.pw.settings".
try:
settings = self.node.inputs.settings.get_dict()
parser_options = settings[self.get_parser_settings_key()]
except (AttributeError, KeyError, NotExistent):
settings = {}
parser_options = {}
try:
include_deprecated_v2_keys = parser_options[
'include_deprecated_v2_keys']
except (TypeError, KeyError):
include_deprecated_v2_keys = False
# load the pw input parameters dictionary
pw_input_dict = self.node.inputs.pw__parameters.get_dict()
# load the neb input parameters dictionary
neb_input_dict = self.node.inputs.parameters.get_dict()
stdout_abspath = os.path.join(
out_folder._repository._get_base_folder().abspath, filename_stdout)
# First parse the Neb output
try:
neb_out_dict, iteration_data, raw_successful = parse_raw_output_neb(
stdout_abspath, neb_input_dict)
# TODO: why do we ignore raw_successful ?
except QEOutputParsingError as exc:
self.logger.error(
'QEOutputParsingError in parse_raw_output_neb: {}'.format(exc))
return self.exit_codes.ERROR_READING_OUTPUT_FILE
for warn_type in ['warnings', 'parser_warnings']:
for message in neb_out_dict[warn_type]:
self.logger.warning('parsing NEB output: {}'.format(message))
if 'QE neb run did not reach the end of the execution.' in neb_out_dict[
'parser_warnings']:
return self.exit_codes.ERROR_OUTPUT_STDOUT_INCOMPLETE
# Retrieve the number of images
try:
num_images = neb_input_dict['num_of_images']
except KeyError:
try:
num_images = neb_out_dict['num_of_images']
except KeyError:
self.logger.error(
'Impossible to understand the number of images')
return self.exit_codes.ERROR_INVALID_OUTPUT
if num_images < 2:
self.logger.error('Too few images: {}'.format(num_images))
return self.exit_codes.ERROR_INVALID_OUTPUT
# Now parse the information from the individual pw calculations for the different images
image_data = {}
positions = []
cells = []
# for each image...
for i in range(num_images):
# check if any of the known XML output file names are present, and parse the first that we find
relative_output_folder = os.path.join(
'{}_{}'.format(PREFIX, i + 1), '{}.save'.format(PREFIX))
retrieved_files = self.retrieved.list_object_names(
relative_output_folder)
for xml_filename in PwCalculation.xml_filenames:
if xml_filename in retrieved_files:
xml_file_path = os.path.join(relative_output_folder,
xml_filename)
try:
with out_folder.open(xml_file_path) as xml_file:
parsed_data_xml, logs_xml = parse_pw_xml(
xml_file, None, include_deprecated_v2_keys)
except IOError:
return self.exit_codes.ERROR_OUTPUT_XML_READ
except XMLParseError:
return self.exit_codes.ERROR_OUTPUT_XML_PARSE
except XMLUnsupportedFormatError:
return self.exit_codes.ERROR_OUTPUT_XML_FORMAT
except Exception:
import traceback
traceback.print_exc()
return self.exit_codes.ERROR_UNEXPECTED_PARSER_EXCEPTION
# this image is dealt with, so break the inner loop and go to the next image
break
# otherwise, if none of the filenames we tried exists, exit with an error
else:
self.logger.error(
'No xml output file found for image {}'.format(i + 1))
return self.exit_codes.ERROR_MISSING_XML_FILE
# look for pw output and parse it
pw_out_file = os.path.join('{}_{}'.format(PREFIX, i + 1), 'PW.out')
try:
with out_folder.open(pw_out_file, 'r') as f:
pw_out_text = f.read() # Note: read() and not readlines()
except IOError:
self.logger.error(
'No pw output file found for image {}'.format(i + 1))
return self.exit_codes.ERROR_READING_OUTPUT_FILE
try:
parsed_data_stdout, logs_stdout = parse_pw_stdout(
pw_out_text, pw_input_dict, parser_options,
parsed_data_xml)
except Exception:
import traceback
traceback.print_exc()
return self.exit_codes.ERROR_UNEXPECTED_PARSER_EXCEPTION
parsed_structure = parsed_data_stdout.pop('structure', {})
parsed_trajectory = parsed_data_stdout.pop('trajectory', {})
parsed_parameters = PwParser.build_output_parameters(
parsed_data_xml, parsed_data_stdout)
# Explicit information about k-points does not need to be queryable so we remove it from the parameters
parsed_parameters.pop('k_points', None)
parsed_parameters.pop('k_points_units', None)
parsed_parameters.pop('k_points_weights', None)
# Delete bands # TODO: this is just to make pytest happy; do we want to keep them instead?
parsed_parameters.pop('bands', None)
# Append the last frame of some of the smaller trajectory arrays to the parameters for easy querying
PwParser.final_trajectory_frame_to_parameters(
parsed_parameters, parsed_trajectory)
# If the parser option 'all_symmetries' is False, we reduce the raw parsed symmetries to save space
all_symmetries = False if parser_options is None else parser_options.get(
'all_symmetries', False)
if not all_symmetries and 'cell' in parsed_structure:
reduce_symmetries(parsed_parameters, parsed_structure,
self.logger)
structure_data = convert_qe2aiida_structure(parsed_structure)
key = 'pw_output_image_{}'.format(i + 1)
image_data[key] = parsed_parameters
positions.append([site.position for site in structure_data.sites])
cells.append(structure_data.cell)
# Add also PW warnings and errors to the neb output data, avoiding repetitions.
for log_type in ['warning', 'error']:
for message in logs_stdout[log_type]:
formatted_message = '{}: {}'.format(log_type, message)
if formatted_message not in neb_out_dict['warnings']:
neb_out_dict['warnings'].append(formatted_message)
# Symbols can be obtained simply from the last image
symbols = [str(site.kind_name) for site in structure_data.sites]
output_params = Dict(
dict=dict(list(neb_out_dict.items()) + list(image_data.items())))
self.out('output_parameters', output_params)
trajectory = TrajectoryData()
trajectory.set_trajectory(
stepids=numpy.arange(1, num_images + 1),
cells=numpy.array(cells),
symbols=symbols,
positions=numpy.array(positions),
)
self.out('output_trajectory', trajectory)
if parser_options is not None and parser_options.get(
'all_iterations', False):
if iteration_data:
arraydata = ArrayData()
for k, v in six.iteritems(iteration_data):
arraydata.set_array(k, numpy.array(v))
self.out('iteration_array', arraydata)
# Load the original and interpolated energy profile along the minimum-energy path (mep)
try:
filename = PREFIX + '.dat'
with out_folder.open(filename, 'r') as handle:
mep = numpy.loadtxt(handle)
except Exception:
self.logger.warning(
'could not open expected output file `{}`.'.format(filename))
mep = numpy.array([[]])
try:
filename = PREFIX + '.int'
with out_folder.open(filename, 'r') as handle:
interp_mep = numpy.loadtxt(handle)
except Exception:
self.logger.warning(
'could not open expected output file `{}`.'.format(filename))
interp_mep = numpy.array([[]])
# Create an ArrayData with the energy profiles
mep_arraydata = ArrayData()
mep_arraydata.set_array('mep', mep)
mep_arraydata.set_array('interpolated_mep', interp_mep)
self.out('output_mep', mep_arraydata)
return
def parse_with_retrieved(self, retrieved):
"""
Parse the output nodes for a PwCalculations from a dictionary of retrieved nodes.
Two nodes that are expected are the default 'retrieved' FolderData node which will
store the retrieved files permanently in the repository. The second required node
is the unstored FolderData node with the temporary retrieved files, which should
be passed under the key 'retrieved_temporary_folder_key' of the Parser class.
:param retrieved: a dictionary of retrieved nodes
"""
import os
successful = True
# Load the input dictionary
parameters = self._calc.inp.parameters.get_dict()
# Look for optional settings input node and potential 'parser_options' dictionary within it
try:
settings = self._calc.inp.settings.get_dict()
parser_opts = settings[self.get_parser_settings_key()]
except (AttributeError, KeyError):
settings = {}
parser_opts = {}
# Check that the retrieved folder is there
try:
out_folder = retrieved[self._calc._get_linkname_retrieved()]
except KeyError:
self.logger.error("No retrieved folder found")
return False, ()
# Verify that the retrieved_temporary_folder is within the arguments if temporary files were specified
if self._calc._get_retrieve_temporary_list():
try:
temporary_folder = retrieved[
self.retrieved_temporary_folder_key]
dir_with_bands = temporary_folder.get_abs_path('.')
except KeyError:
self.logger.error(
'the {} was not passed as an argument'.format(
self.retrieved_temporary_folder_key))
return False, ()
else:
dir_with_bands = None
list_of_files = out_folder.get_folder_list()
# The stdout is required for parsing
if self._calc._OUTPUT_FILE_NAME not in list_of_files:
self.logger.error(
"The standard output file '{}' was not found but is required".
format(self._calc._OUTPUT_FILE_NAME))
return False, ()
# The xml file is required for parsing
if self._calc._DATAFILE_XML_BASENAME not in list_of_files:
self.logger.error(
"The xml output file '{}' was not found but is required".
format(self._calc._DATAFILE_XML_BASENAME))
successful = False
xml_file = None
else:
xml_file = os.path.join(out_folder.get_abs_path('.'),
self._calc._DATAFILE_XML_BASENAME)
out_file = os.path.join(out_folder.get_abs_path('.'),
self._calc._OUTPUT_FILE_NAME)
# Call the raw parsing function
parsing_args = [
out_file, parameters, parser_opts, xml_file, dir_with_bands
]
out_dict, trajectory_data, structure_data, bands_data, raw_successful = parse_raw_output(
*parsing_args)
# If calculation was not considered failed already, use the new value
successful = raw_successful if successful else successful
# If the parser option 'all_symmetries' is not set to True, we reduce the raw parsed symmetries to safe space
all_symmetries = parser_opts.get('all_symmetries', False)
if not all_symmetries:
# In the standard output, each symmetry operation print two rotation matrices:
#
# * S_cryst^T: matrix in crystal coordinates, transposed
# * S_cart: matrix in cartesian coordinates,
#
# The XML files only print one matrix:
#
# * S_cryst: matrix in crystal coordinates
#
# The raw parsed symmetry information from the XML is large and will load the database heavily if stored as
# is for each calculation. Instead, we will map these dictionaries onto a static dictionary of rotation
# matrices generated by the _get_qe_symmetry_list static method. This dictionary will return the rotation
# matrices in cartesian coordinates, i.e. S_cart. In order to compare the raw matrices from the XML to these
# static matrices we have to convert S_cryst into S_cart. We derive here how that is done:
#
# S_cryst * v_cryst = v_cryst'
#
# where v_cryst' is the rotated vector v_cryst under S_cryst
# We define `cell` where cell vectors are rows. Converting a vector from crystal to cartesian
# coordinates is defined as:
#
# cell^T * v_cryst = v_cart
#
# The inverse of this operation is defined as
#
# v_cryst = cell^Tinv * v_cart
#
# Replacing the last equation into the first we find:
#
# S_cryst * cell^Tinv * v_cart = cell^Tinv * v_cart'
#
# Multiply on the left with cell^T gives:
#
# cell^T * S_cryst * cell^Tinv * v_cart = v_cart'
#
# which can be rewritten as:
#
# S_cart * v_cart = v_cart'
#
# where:
#
# S_cart = cell^T * S_cryst * cell^Tinv
#
# We compute here the transpose and its inverse of the structure cell basis, which is needed to transform
# the parsed rotation matrices, which are in crystal coordinates, to cartesian coordinates, which are the
# matrices that are returned by the _get_qe_symmetry_list staticmethod
cell = structure_data['cell']['lattice_vectors']
cell_T = numpy.transpose(cell)
cell_Tinv = numpy.linalg.inv(cell_T)
try:
if 'symmetries' in out_dict.keys():
old_symmetries = out_dict['symmetries']
new_symmetries = []
for this_sym in old_symmetries:
name = this_sym['name'].strip()
for i, this in enumerate(self._possible_symmetries):
# Since we do an exact comparison we strip the string name from whitespace
# and as soon as it is matched, we break to prevent it from matching another
if name == this['name'].strip():
index = i
break
else:
index = None
self.logger.error(
'Symmetry {} not found'.format(name))
new_dict = {}
if index is not None:
# The raw parsed rotation matrix is in crystal coordinates, whereas the mapped rotation
# in self._possible_symmetries is in cartesian coordinates. To allow them to be compared
# to make sure we matched the correct rotation symmetry, we first convert the parsed matrix
# to cartesian coordinates. For explanation of the method, see comment above.
rotation_cryst = this_sym['rotation']
rotation_cart_new = self._possible_symmetries[
index]['matrix']
rotation_cart_old = numpy.dot(
cell_T, numpy.dot(rotation_cryst, cell_Tinv))
inversion = self._possible_symmetries[index][
'inversion']
if not are_matrices_equal(
rotation_cart_old,
rotation_cart_new,
swap_sign_matrix_b=inversion):
self.logger.error(
'Mapped rotation matrix {} does not match the original rotation {}'
.format(rotation_cart_new,
rotation_cart_old))
new_dict['all_symmetries'] = this_sym
else:
# Note: here I lose the information about equivalent ions and fractional_translation.
new_dict['t_rev'] = this_sym['t_rev']
new_dict['symmetry_number'] = index
else:
new_dict['all_symmetries'] = this_sym
new_symmetries.append(new_dict)
out_dict[
'symmetries'] = new_symmetries # and overwrite the old one
except KeyError: # no symmetries were parsed (failed case, likely)
self.logger.error("No symmetries were found in output")
new_nodes_list = []
# I eventually save the new structure. structure_data is unnecessary after this
in_struc = self._calc.get_inputs_dict()['structure']
type_calc = parameters['CONTROL']['calculation']
struc = in_struc
if type_calc in ['relax', 'vc-relax', 'md', 'vc-md']:
if 'cell' in structure_data.keys():
struc = convert_qe2aiida_structure(structure_data,
input_structure=in_struc)
new_nodes_list.append(
(self.get_linkname_outstructure(), struc))
k_points_list = trajectory_data.pop('k_points', None)
k_points_weights_list = trajectory_data.pop('k_points_weights', None)
if k_points_list is not None:
# Build the kpoints object
if out_dict['k_points_units'] not in ['2 pi / Angstrom']:
raise QEOutputParsingError(
'Error in kpoints units (should be cartesian)')
kpoints_from_output = KpointsData()
kpoints_from_output.set_cell_from_structure(struc)
kpoints_from_output.set_kpoints(k_points_list,
cartesian=True,
weights=k_points_weights_list)
kpoints_from_input = self._calc.inp.kpoints
if not bands_data:
try:
kpoints_from_input.get_kpoints()
except AttributeError:
new_nodes_list += [(self.get_linkname_out_kpoints(),
kpoints_from_output)]
# Converting bands into a BandsData object (including the kpoints)
if bands_data:
kpoints_for_bands = kpoints_from_output
try:
kpoints_from_input.get_kpoints()
kpoints_for_bands.labels = kpoints_from_input.labels
except (AttributeError, ValueError, TypeError):
# AttributeError: no list of kpoints in input
# ValueError: labels from input do not match the output
# list of kpoints (some kpoints are missing)
# TypeError: labels are not set, so kpoints_from_input.labels=None
pass
# Get the bands occupations and correct the occupations of QE:
# If it computes only one component, it occupies it with half number of electrons
try:
bands_data['occupations'][1]
the_occupations = bands_data['occupations']
except IndexError:
the_occupations = 2. * numpy.array(
bands_data['occupations'][0])
try:
bands_data['bands'][1]
bands_energies = bands_data['bands']
except IndexError:
bands_energies = bands_data['bands'][0]
the_bands_data = BandsData()
the_bands_data.set_kpointsdata(kpoints_for_bands)
the_bands_data.set_bands(bands_energies,
units=bands_data['bands_units'],
occupations=the_occupations)
new_nodes_list += [('output_band', the_bands_data)]
out_dict['linknames_band'] = ['output_band']
# Separate the atomic_occupations dictionary in its own node if it is present
atomic_occupations = out_dict.get('atomic_occupations', {})
if atomic_occupations:
out_dict.pop('atomic_occupations')
atomic_occupations_node = ParameterData(dict=atomic_occupations)
new_nodes_list.append(
('output_atomic_occupations', atomic_occupations_node))
output_params = ParameterData(dict=out_dict)
new_nodes_list.append((self.get_linkname_outparams(), output_params))
if trajectory_data:
from aiida.orm.data.array.trajectory import TrajectoryData
from aiida.orm.data.array import ArrayData
try:
positions = numpy.array(
trajectory_data.pop('atomic_positions_relax'))
try:
cells = numpy.array(
trajectory_data.pop('lattice_vectors_relax'))
# if KeyError, the MD was at fixed cell
except KeyError:
cells = numpy.array([in_struc.cell] * len(positions))
symbols = numpy.array(
[str(i.kind_name) for i in in_struc.sites])
stepids = numpy.arange(
len(positions)) # a growing integer per step
# I will insert time parsing when they fix their issues about time
# printing (logic is broken if restart is on)
traj = TrajectoryData()
traj.set_trajectory(
stepids=stepids,
cells=cells,
symbols=symbols,
positions=positions,
)
for x in trajectory_data.iteritems():
traj.set_array(x[0], numpy.array(x[1]))
new_nodes_list.append(
(self.get_linkname_outtrajectory(), traj))
except KeyError:
# forces, atomic charges and atomic mag. moments, in scf calculation (when outputed)
arraydata = ArrayData()
for x in trajectory_data.iteritems():
arraydata.set_array(x[0], numpy.array(x[1]))
new_nodes_list.append(
(self.get_linkname_outarray(), arraydata))
return successful, new_nodes_list
