XspectraCalculation+XspectraParser: Added Various Extra Features

Adds the following features to the `XspectraCalculation` and
`XspectraParser` classes:
- A save file ('xanes.sav') is now reserved by default and is printed
at the end of each calculation run or after a designated time limit.
The file can then be used for re-starting halted calculations or
re-plotting spectra from previously-finished calculations.
- The `XspectraCalculation` class now copies the save file from a
parent calculation if the calculation type is itself an
XspectraCalculation, thus re-starts and re-plot runs are handled
automatically.
- An error code has been added (315) for calculations which safely exit
after reaching their time limit, thus enabiling a restart.
- Additional information is now included in the `output_parameters`
node (e.g. the polarisation vectors used and whether the calculation was
set to "xonly_plot").

src/aiida_quantumespresso/calculations/xspectra.py

@@ -1,6 +1,8 @@
 # -*- coding: utf-8 -*-
 """Classes and methods for running xspectra.x with AiiDA."""
 
+import os
+
 from aiida import orm
 from aiida.common import exceptions
 from aiida.orm import Dict, SinglefileData, XyData
@@ -16,10 +18,13 @@ class XspectraCalculation(NamelistsCalculation):
 
  _Plotcore_FILENAME = 'stdout'
  _Spectrum_FILENAME = 'xanes.dat'
+ _XSPECTRA_SAVE_FILE = 'xanes.sav'
+ _XSPECTRA_GAMMA_FILE = 'gamma.dat'
  _default_namelists = ['INPUT_XSPECTRA', 'PLOT', 'PSEUDOS', 'CUT_OCC']
  _blocked_keywords = [('INPUT_XSPECTRA', 'outdir', NamelistsCalculation._OUTPUT_SUBFOLDER),
  ('INPUT_XSPECTRA', 'prefix', NamelistsCalculation._PREFIX),
- ('PSEUDOS', 'filecore', _Plotcore_FILENAME)]
+ ('INPUT_XSPECTRA', 'x_save_file', _XSPECTRA_SAVE_FILE),
+ ('PLOT', 'gamma_file', _XSPECTRA_GAMMA_FILE), ('PSEUDOS', 'filecore', _Plotcore_FILENAME)]
  _internal_retrieve_list = [_Spectrum_FILENAME]
  _retrieve_singlefile_list = []
  _retrieve_temporary_list = []
@@ -31,7 +36,7 @@ def define(cls, spec):
 
  super().define(spec)
 
- spec.input('parent_folder', valid_type=(orm.RemoteData, orm.FolderData), required=True)
+ spec.input('parent_folder', valid_type=(orm.RemoteData), required=True)
  spec.input(
  'core_wfc_data',
  valid_type=SinglefileData,
@@ -44,6 +49,14 @@ def define(cls, spec):
  required=True,
  help='The K-point sampling to be used for the XSpectra calculation'
  )
+ spec.input(
+ 'gamma_file',
+ valid_type=SinglefileData,
+ required=False,
+ help='An optional file containing the data for the broadening function used when'
+ ' `gamma_mode=file`'
+ )
+
  spec.output('output_parameters', valid_type=Dict)
  spec.output('spectra', valid_type=XyData)
  spec.default_output_node = 'output_parameters'
@@ -65,6 +78,12 @@ def define(cls, spec):
  'ERROR_OUTPUT_ABSORBING_SPECIES_ZERO',
  message='xiabs was either set to 0 or less, or was greater than ntyp.'
  )
+ spec.exit_code(
+ 315,
+ 'ERROR_OUTPUT_TIME_LIMIT_EXCEEDED',
+ message='The time limit set for the calculation was exceeded, and the job wrote a save file '
+ 'before exiting.'
+ )
  spec.exit_code(
  330,
  'ERROR_READING_SPECTRUM_FILE',
@@ -108,4 +127,21 @@ def prepare_for_submission(self, folder):
  core_file_info = (core_file.uuid, core_file.filename, core_file.filename)
  calcinfo.local_copy_list.append(core_file_info)
 
+ # if included as an input, append the gamma file node to the copy list
+ if 'gamma_file' in self.inputs.keys():
+ gamma_file = self.inputs.gamma_file
+ gamma_file_info = (gamma_file.uuid, gamma_file.filename, gamma_file.filename)
+ calcinfo.local_copy_list.append(gamma_file_info)
+
+ # Check if the parent folder is an XspectraCalculation type, if so we then copy the
+ # save file to enable calculation restarts and re-plots.
+ parent_folder = self.inputs.parent_folder
+ parent_calcs = parent_folder.get_incoming(node_class=orm.CalcJobNode).all()
+ parent_calc = parent_calcs[0].node
+ restart_flag = parent_calc.process_type == 'aiida.calculations:quantumespresso.xspectra'
+ if restart_flag:
+ calcinfo.remote_copy_list.append((
+ parent_folder.computer.uuid, os.path.join(parent_folder.get_remote_path(),
+ self._XSPECTRA_SAVE_FILE), '.'
+ ))
  return calcinfo

src/aiida_quantumespresso/parsers/xspectra.py

@@ -30,6 +30,8 @@ def parse(self, **kwargs):
  return self.exit(self.exit_codes.ERROR_OUTPUT_ABSORBING_SPECIES_WRONG)
  if 'xiabs < 1 or xiabs > ntyp' in line:
  return self.exit(self.exit_codes.ERROR_OUTPUT_ABSORBING_SPECIES_ZERO)
+ if 'Calculation not finished' in line:
+ return self.exit(self.exit_codes.ERROR_OUTPUT_TIME_LIMIT_EXCEEDED)
  if 'END JOB' in line:
  job_done = True
  break
@@ -161,6 +163,16 @@ def parse_stdout_xspectra(filecontent, codename=None, message_map=None):
  # Parse the necessary information for data plotting: core level energy of the
  # absorbing atom and the energy zero of the spectrum (typically the Fermi level)
  for line in lines:
+ if 'xepsilon' in line:
+ eps_vector_string = line.split(':')[-1].strip()
+ eps_vector_list = [float(i) for i in eps_vector_string.split(' ')]
+ parsed_data['epsilon_vector'] = eps_vector_list
+ if 'xonly_plot:' in line:
+ is_only_plot_string = line.split(':')[-1].strip()
+ if is_only_plot_string == 'FALSE':
+ parsed_data['plot_only'] = False
+ elif is_only_plot_string == 'TRUE':
+ parsed_data['plot_only'] = True
  if 'From SCF save directory' in line:
  if '(spin polarized work)' in line:
  spin = True