PwParser: add smearing_type and smearing from new XML output (#445

)

These keys were not yet being parsed from the output file with the new
XML schema. In addition, if an exception is thrown by the raw XML or
stdout parser, it is now caught and added as a critical warning. Finally
the test input generator for `PwParser` is simplified and only a single
generator is used for both scf and relax tests.

Note that the units of the `degauss` depends on the version of the XML
output. It should always be in Hartree, but up until 6.5, it was
erroneously being written in Rydberg. This was corrected  in commit
`a9698a6971e4ad975ce89a15bc9b74294799ef3f`.

aiida_quantumespresso/parsers/parse_xml/pw/parse.py

@@ -2,13 +2,14 @@
 from __future__ import absolute_import
 from __future__ import print_function
 
+from distutils.version import StrictVersion
 import numpy as np
 from xmlschema import XMLSchema
 from xmlschema.etree import ElementTree
 from xmlschema.exceptions import URLError
 
 from aiida_quantumespresso.utils.mapping import get_logging_container
-from qe_tools.constants import hartree_to_ev, bohr_to_ang
+from qe_tools.constants import hartree_to_ev, bohr_to_ang, ry_to_ev
 
 from .exceptions import XMLParseError
 from .legacy import parse_pw_xml_pre_6_2
@@ -50,17 +51,11 @@ def parse_xml(xml_file, dir_with_bands=None, include_deprecated_v2_keys=False):
 
  xml_file_version = get_xml_file_version(xml_parsed)
 
- try:
- if xml_file_version == QeXmlVersion.POST_6_2:
- parsed_data, logs = parse_pw_xml_post_6_2(xml_parsed, include_deprecated_v2_keys)
- 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)
- except Exception:
- import traceback
- logs = get_logging_container()
- logs.critical.append(traceback.format_exc())
- parsed_data = {}
+ if xml_file_version == QeXmlVersion.POST_6_2:
+ parsed_data, logs = parse_pw_xml_post_6_2(xml_parsed, include_deprecated_v2_keys)
+ 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)
 
  return parsed_data, logs
 
@@ -107,6 +102,7 @@ def parse_pw_xml_post_6_2(xml, include_deprecated_v2_keys=False):
  for err in errors:
  logs.error.append(str(err))
 
+ xml_version = StrictVersion(xml_dictionary['general_info']['xml_format']['@VERSION'])
  inputs = xml_dictionary['input']
  outputs = xml_dictionary['output']
 
@@ -156,35 +152,6 @@ def parse_pw_xml_post_6_2(xml, include_deprecated_v2_keys=False):
  # 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.)
 
- # TODO/NOTE: Not including smearing type and width for now.
- # In the old XML format they are under OCCUPATIONS as SMEARING_TYPE and SMEARING_PARAMETER,
- # but watch out: the value in the old format is half of that in the new format
- # (the code divides it by e2=2.0, see PW/src/pw_restart.f90:446)
- '''
- if 'smearing' in outputs['band_structure']:
- smearing_xml = outputs['band_structure']['smearing']
- elif 'smearing' in inputs:
- smearing_xml = inputs['smearing']
- try:
- smearing_type = smearing_xml['$']
- smearing_degauss = smearing_xml['@degauss']
- except NameError:
- pass
- '''
-
- # Here are some notes from the QE code for reference.
- # SMEARING_METHOD = lgauss
- # lgauss, &! if .TRUE.: use gaussian broadening
- # ltetra, &! if .TRUE.: use tetrahedra
- # SMEARING_TYPE = ngauss (see Modules/qexml.f90:1530)
- # ngauss ! type of smearing technique
- # From dos.x input description:
- # Type of gaussian broadening:
- # = 0 Simple Gaussian (default)
- # = 1 Methfessel-Paxton of order 1
- # = -1 Marzari-Vanderbilt "cold smearing"
- # =-99 Fermi-Dirac function
-
  starting_magnetization = []
  magnetization_angle1 = []
  magnetization_angle2 = []
@@ -340,6 +307,26 @@ def parse_pw_xml_post_6_2(xml, include_deprecated_v2_keys=False):
  # Band structure
  if 'band_structure' in outputs:
  band_structure = outputs['band_structure']
+
+ smearing_xml = None
+
+ if 'smearing' in outputs['band_structure']:
+ smearing_xml = outputs['band_structure']['smearing']
+ elif 'smearing' in inputs:
+ smearing_xml = inputs['smearing']
+
+ if smearing_xml:
+ degauss = smearing_xml['@degauss']
+
+ # Versions below 19.03.04 (Quantum ESPRESSO<=6.4.1) incorrectly print degauss in Ry instead of Hartree
+ if xml_version < StrictVersion('19.03.04'):
+ degauss *= ry_to_ev
+ else:
+ degauss *= hartree_to_ev
+
+ xml_data['degauss'] = degauss
+ xml_data['smearing_type'] = smearing_xml['$']
+
  num_k_points = band_structure['nks']
  num_electrons = band_structure['nelec']
  num_atomic_wfc = band_structure['num_of_atomic_wfc']

aiida_quantumespresso/parsers/pw.py

@@ -2,6 +2,8 @@
 """`Parser` implementation for the `PwCalculation` calculation job class."""
 from __future__ import absolute_import
 
+import traceback
+
 import numpy
 
 from aiida import orm
@@ -285,8 +287,7 @@ def parse_xml(self, dir_with_bands=None, parser_options=None):
  except XMLUnsupportedFormatError:
  self.exit_code_xml = self.exit_codes.ERROR_OUTPUT_XML_FORMAT
  except Exception:
- import traceback
- traceback.print_exc()
+ logs.critical.append(traceback.format_exc())
  self.exit_code_xml = self.exit_codes.ERROR_UNEXPECTED_PARSER_EXCEPTION
 
  return parsed_data, logs
@@ -319,8 +320,7 @@ def parse_stdout(self, parameters, parser_options=None, parsed_xml=None):
  try:
  parsed_data, logs = parse_stdout(stdout, parameters, parser_options, parsed_xml)
  except Exception:
- import traceback
- traceback.print_exc()
+ logs.critical.append(traceback.format_exc())
  self.exit_code_stdout = self.exit_codes.ERROR_UNEXPECTED_PARSER_EXCEPTION
 
  # If the stdout was incomplete, most likely the job was interrupted before it could cleanly finish, so the

tests/parsers/test_neb/test_neb_default.yml

@@ -70,6 +70,7 @@ parameters:
  scf_error: 2.251833940343682e-10
  creator_name: pwscf
  creator_version: 6.4.1
+ degauss: 0.0408170751759
  dft_exchange_correlation: PBE
  do_magnetization: false
  do_not_use_time_reversal: false
@@ -137,6 +138,7 @@ parameters:
  q_real_space: false
  rho_cutoff: 1360.56917253
  rho_cutoff_units: eV
+ smearing_type: gaussian
  smooth_fft_grid:
  - 36
  - 15
@@ -183,6 +185,7 @@ parameters:
  scf_error: 2.987478357372217e-09
  creator_name: pwscf
  creator_version: 6.4.1
+ degauss: 0.0408170751759
  dft_exchange_correlation: PBE
  do_magnetization: false
  do_not_use_time_reversal: false
@@ -234,6 +237,7 @@ parameters:
  q_real_space: false
  rho_cutoff: 1360.56917253
  rho_cutoff_units: eV
+ smearing_type: gaussian
  smooth_fft_grid:
  - 36
  - 15
@@ -296,6 +300,7 @@ parameters:
  scf_error: 2.80245941733356e-10
  creator_name: pwscf
  creator_version: 6.4.1
+ degauss: 0.0408170751759
  dft_exchange_correlation: PBE
  do_magnetization: false
  do_not_use_time_reversal: false
@@ -363,6 +368,7 @@ parameters:
  q_real_space: false
  rho_cutoff: 1360.56917253
  rho_cutoff_units: eV
+ smearing_type: gaussian
  smooth_fft_grid:
  - 36
  - 15