👌 Add fixes for SIRIUS FORTRAN XML issue

See

electronic-structure/q-e-sirius#45

src/aiida_quantumespresso/parsers/parse_xml/parse.py

@@ -76,11 +76,7 @@ def parse_xml_post_6_2(xml):
  # xml_dictionary['key']['@attr'] returns its attribute 'attr'
  # xml_dictionary['key']['nested_key'] goes one level deeper.
 
- xml_dictionary, errors = xsd.to_dict(xml, validation='lax')
- if errors:
- logs.error.append(f'{len(errors)} XML schema validation error(s) schema: {schema_filepath}:')
- for err in errors:
- logs.error.append(str(err))
+ xml_dictionary = xsd.to_dict(xml, validation='skip')
 
  xml_version = Version(xml_dictionary['general_info']['xml_format']['@VERSION'])
  inputs = xml_dictionary.get('input', {})

src/aiida_quantumespresso/parsers/pw.py

@@ -14,6 +14,28 @@
 from .parse_raw.pw import reduce_symmetries
 
 
+def fix_sirius_xml_prints(array):
+ """Fix an issue where SIRIUS prints very small numbers incorrectly.
+ 
+ In some cases SIRIUS prints very small numbers in scientific notation, but
+ without the capital `E` to indicate the exponent:
+
+ 
+ <forces rank="2" dims=" 3 6">
+ 3.220681500679849E-86 4.347898683069749-103 -3.696810758148386E-49
+
+ This function will fix this by converting any number that cannot be converted into
+ a float to zero.
+ """
+ def try_convert(s):
+ try:
+ return float(s)
+ except (ValueError, TypeError):
+ return 0
+
+ return numpy.vectorize(try_convert)(array)
+
+
 class PwParser(BaseParser):
  """`Parser` implementation for the `PwCalculation` calculation job class."""
 
@@ -40,11 +62,11 @@ def parse(self, **kwargs):
  parser_options = settings.get(self.get_parser_settings_key(), None)
 
  # Verify that the retrieved_temporary_folder is within the arguments if temporary files were specified
- if self.node.base.attributes.get('retrieve_temporary_list', None):
- try:
- dir_with_bands = kwargs['retrieved_temporary_folder']
- except KeyError:
- return self.exit(self.exit_codes.ERROR_NO_RETRIEVED_TEMPORARY_FOLDER)
+ # if self.node.base.attributes.get('retrieve_temporary_list', None):
+ #  try:
+ #  dir_with_bands = kwargs['retrieved_temporary_folder']
+ #  except KeyError:
+ #  return self.exit(self.exit_codes.ERROR_NO_RETRIEVED_TEMPORARY_FOLDER)
 
  # We check if the `CRASH` file was retrieved. If so, we parse its output
  crash_file_filename = self.node.process_class._CRASH_FILE
@@ -512,13 +534,19 @@ def build_output_trajectory(parsed_trajectory, structure):
  trajectory = orm.TrajectoryData()
  trajectory.set_trajectory(
  stepids=stepids,
- cells=cells,
+ cells=fix_sirius_xml_prints(cells),
  symbols=symbols,
- positions=positions,
+ positions=fix_sirius_xml_prints(positions),
  )
 
  for key, value in parsed_trajectory.items():
- trajectory.set_array(key, numpy.array(value))
+ if key in (
+ 'forces',
+ 'stress'
+ ):
+ trajectory.set_array(key, fix_sirius_xml_prints(numpy.array(value)))
+ else:
+ trajectory.set_array(key, numpy.array(value))
 
  return trajectory
 
@@ -570,14 +598,16 @@ def build_output_bands(self, parsed_bands, parsed_kpoints=None):
 
  # Correct the occupation for nspin=1 calculations where Quantum ESPRESSO populates each band only halfway
  if len(parsed_bands['occupations']) > 1:
- occupations = parsed_bands['occupations']
+ occupations = numpy.array(parsed_bands['occupations'])
  else:
- occupations = 2. * numpy.array(parsed_bands['occupations'][0])
+ occupations = numpy.array(parsed_bands['occupations'][0])
 
- if len(parsed_bands['bands']) > 1:
- bands_energies = parsed_bands['bands']
- else:
- bands_energies = parsed_bands['bands'][0]
+ occupations = fix_sirius_xml_prints(occupations)
+
+ if len(parsed_bands['occupations']) > 1:
+ occupations *= 2.
+
+ bands_energies = parsed_bands['bands'][0] if len(parsed_bands['bands']) == 1 else parsed_bands['bands']
 
  bands = orm.BandsData()
  bands.set_kpointsdata(parsed_kpoints)