PwCalculation: remove deprecated key functionality (#495)

The added maintenance cost of this functionality is not worth the added
benefit. The keys made little sense anyway and besides these are not the
only backward incompatible changes between v2 and v3 of the plugin.

aiida_quantumespresso/parsers/neb.py

@@ -59,11 +59,6 @@ def parse(self, **kwargs):
  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()
 
@@ -111,7 +106,7 @@ def parse(self, **kwargs):
  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)
+ parsed_data_xml, logs_xml = parse_pw_xml(xml_file, None)
  except IOError:
  return self.exit(self.exit_codes.ERROR_OUTPUT_XML_READ)
  except XMLParseError:

aiida_quantumespresso/parsers/parse_xml/pw/legacy.py

@@ -18,12 +18,11 @@
 default_length_units = 'Angstrom'
 
 
-def parse_pw_xml_pre_6_2(xml_file, dir_with_bands, include_deprecated_keys=False):
+def parse_pw_xml_pre_6_2(xml_file, dir_with_bands):
  """Parse the content of XML output file written by `pw.x` with the old schema-less XML format.
 
  :param xml_file: filelike object to the XML output file
  :param dir_with_bands: absolute filepath to directory containing k-point XML files
- :param include_deprecated_v2_keys: boolean, if True, includes deprecated keys from old parser v2
  :returns: tuple of two dictionaries, with the parsed data and log messages, respectively
  """
  import copy
@@ -260,9 +259,10 @@ def parse_pw_xml_pre_6_2(xml_file, dir_with_bands, include_deprecated_keys=False
  parsed_data['occupations'] = 'tetrahedra' # TODO: might also be tetrahedra_lin or tetrahedra_opt: check input?
  elif parsed_data['fixed_occupations']:
  parsed_data['occupations'] = 'fixed'
- if not include_deprecated_keys:
- for tagname in ['SMEARING_METHOD','TETRAHEDRON_METHOD','FIXED_OCCUPATIONS']:
- parsed_data.pop(tagname.lower())
+
+ # Remove the following deprecated keys
+ for tagname in ['SMEARING_METHOD','TETRAHEDRON_METHOD','FIXED_OCCUPATIONS']:
+ parsed_data.pop(tagname.lower())
 
  #CARD CHARGE-DENSITY
  cardname='CHARGE-DENSITY'

aiida_quantumespresso/parsers/parse_xml/pw/parse.py

@@ -43,7 +43,7 @@ def cell_volume(a1, a2, a3):
  return abs(float(a1[0] * a_mid_0 + a1[1] * a_mid_1 + a1[2] * a_mid_2))
 
 
-def parse_xml(xml_file, dir_with_bands=None, include_deprecated_v2_keys=False):
+def parse_xml(xml_file, dir_with_bands=None):
  try:
  xml_parsed = ElementTree.parse(xml_file)
  except ElementTree.ParseError:
@@ -52,19 +52,18 @@ def parse_xml(xml_file, dir_with_bands=None, include_deprecated_v2_keys=False):
  xml_file_version = get_xml_file_version(xml_parsed)
 
  if xml_file_version == QeXmlVersion.POST_6_2:
- parsed_data, logs = parse_pw_xml_post_6_2(xml_parsed, include_deprecated_v2_keys)
+ parsed_data, logs = parse_pw_xml_post_6_2(xml_parsed)
  elif xml_file_version == QeXmlVersion.PRE_6_2:
  xml_file.seek(0)
- parsed_data, logs = parse_pw_xml_pre_6_2(xml_file, dir_with_bands, include_deprecated_v2_keys)
+ parsed_data, logs = parse_pw_xml_pre_6_2(xml_file, dir_with_bands)
 
  return parsed_data, logs
 
 
-def parse_pw_xml_post_6_2(xml, include_deprecated_v2_keys=False):
+def parse_pw_xml_post_6_2(xml):
  """Parse the content of XML output file written by `pw.x` with the new schema-based XML format.
 
  :param xml: parsed XML
- :param include_deprecated_v2_keys: boolean, if True, includes deprecated keys from old parser v2
  :returns: tuple of two dictionaries, with the parsed data and log messages, respectively
  """
  e_bohr2_to_coulomb_m2 = 57.214766 # e/a0^2 to C/m^2 (electric polarization) from Wolfram Alpha
@@ -123,35 +122,6 @@ def parse_pw_xml_post_6_2(xml, include_deprecated_v2_keys=False):
  else:
  occupations = None
 
- if include_deprecated_v2_keys:
-
- # NOTE: these flags are not super clear
- # TODO: remove them and just use 'occupations' as a string, with possible values "smearing","tetrahedra", ...
-
- if occupations == 'from_input': # False for 'fixed' # TODO: does this make sense?
- fixed_occupations = True
- else:
- fixed_occupations = False
-
- if occupations and 'tetrahedra' in occupations:
- tetrahedron_method = True
- else:
- tetrahedron_method = False
-
- if occupations == 'from_input':
- smearing_method = False
- else:
- smearing_method = True
-
- if smearing_method:
- if 'smearing' not in (list(outputs['band_structure'].keys()) + list(inputs.keys())):
- logs.error.append("occupations is '{}' but key 'smearing' is not present under input/bands "
- 'nor under output/band_structure'.format(occupations))
- # TODO: this error is triggered if no smearing is specified in input. But this is a valid input, so we should't throw an error.
- # Should we ask QE to print something nonetheless?
- # Also happens if occupations='fixed'.
- # (Example: occupations is 'fixed' but key 'smearing' is not present under input/bands nor output/band_structure. See calculation 4940, versus 4981.)
-
  starting_magnetization = []
  magnetization_angle1 = []
  magnetization_angle2 = []
@@ -468,11 +438,6 @@ def parse_pw_xml_post_6_2(xml, include_deprecated_v2_keys=False):
  # 3 = ionic convergence failed
  # These might be changed in the future. Also see PW/src/run_pwscf.f90
 
- if include_deprecated_v2_keys:
- xml_data['fixed_occupations'] = fixed_occupations
- xml_data['tetrahedron_method'] = tetrahedron_method
- xml_data['smearing_method'] = smearing_method
-
  try:
  berry_phase = outputs['electric_field']['BerryPhase']
  except KeyError:

aiida_quantumespresso/parsers/pw.py

@@ -274,14 +274,9 @@ def parse_xml(self, dir_with_bands=None, parser_options=None):
  self.exit_code_xml = self.exit_codes.ERROR_OUTPUT_XML_MULTIPLE
  return parsed_data, logs
 
- try:
- include_deprecated_keys = parser_options['include_deprecated_v2_keys']
- except (TypeError, KeyError):
- include_deprecated_keys = False
-
  try:
  with self.retrieved.open(xml_files[0]) as xml_file:
- parsed_data, logs = parse_xml(xml_file, dir_with_bands, include_deprecated_keys)
+ parsed_data, logs = parse_xml(xml_file, dir_with_bands)
  except IOError:
  self.exit_code_xml = self.exit_codes.ERROR_OUTPUT_XML_READ
  except XMLParseError:

docs/source/user_guide/calculation_plugins/pw.rst

@@ -381,17 +381,3 @@ occupations::
 
 Note that for ``pw.x`` to print the required information, the flag ``lda_plus_u`` has to be
 set to ``True`` in the ``SYSTEM`` card of the input ``parameters`` node.
-
-Include deprecated output keys
-..........................
-In version 3 of the plugin, some keys have been deprecated and removed by default
-from the ``output_parameters`` node, often replaced by more appropriate keys.
-To also include the deprecated keys, add ``include_deprecated_v2_keys: True``
-to the ``parser_options`` element of the settings dictionary.
-The default value of this options is ``False``. Example::
-
- settings_dict = {
- 'parser_options': {
- 'include_deprecated_v2_keys': True,
- }
- }

tests/parsers/test_neb.py

@@ -105,29 +105,3 @@ def test_neb_all_iterations(
 
  data = build_num_regression_dictionary([results['iteration_array']], [results['iteration_array'].get_arraynames()])
  num_regression.check(data, default_tolerance=dict(atol=0, rtol=1e-18))
-
-
-def test_neb_deprecated_keys(aiida_profile, fixture_localhost, generate_calc_job_node, generate_parser):
- """Test a NEB calculation with the parser option `include_deprecated_v2_keys=True`."""
- name = 'default'
- entry_point_calc_job = 'quantumespresso.neb'
- entry_point_parser = 'quantumespresso.neb'
-
- inputs = generate_inputs(parser_options={'include_deprecated_v2_keys': True})
- node = generate_calc_job_node(entry_point_calc_job, fixture_localhost, name, inputs)
- parser = generate_parser(entry_point_parser)
- results, calcfunction = parser.parse_from_node(node, store_provenance=False)
-
- assert calcfunction.is_finished, calcfunction.exception
- assert calcfunction.is_finished_ok, calcfunction.exit_message
- assert not orm.Log.objects.get_logs_for(node)
- assert 'output_parameters' in results
- assert 'output_mep' in results
- assert 'output_trajectory' in results
- assert 'iteration_array' not in results
-
- for key, dictionary in results['output_parameters'].get_dict().items():
- if key.startswith('pw_output_image'):
- assert dictionary['fixed_occupations'] is False
- assert dictionary['smearing_method'] is True
- assert dictionary['tetrahedron_method'] is False