XspectraParser: Fix bugs in parsing vector/coord system

Adds information on the coordinate system used in the XSpectra
calculation (either crystallographic or Cartesian). Also addresses a bug
spotted in the stdout of XSpectra itself, where the epsilon/k-vector is
reported by the code during the `read_save_file` subroutine as being in
`[Cartesian frame]` regardless of the coordinate system used by the
parent XSpectra calculation. Because of this, calculations where
`xonly_plot=.true.` cannot meaningfully have metadata for the coordinate
system used by the calculation recorded in the `output_parameters`
dictionary by the parser.

This fix also addresses the fact that the epsilon/k-vector is
essentially reported twice in the event of a calculation restart: once
when the input file is read and a second time when the save file is
read.

src/aiida_quantumespresso/parsers/xspectra.py

@@ -157,22 +157,38 @@ def parse_stdout_xspectra(filecontent, codename=None, message_map=None):
 
  logs = get_logging_container()
  parsed_data = {}
+ # We need to assign this before the loop over each line due to a bug spotted in the code
+ # when `only_plot=True`. Since the epsilon vector is reported before the value of
+ # `xonly_plot`, we need a starting value before the loop begins.
+ parsed_data['plot_only'] = False
 
  lines = filecontent if isinstance(filecontent, list) else filecontent.split('\n')
 
  # 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':
+ if is_only_plot_string == 'TRUE':
  parsed_data['plot_only'] = True
+ if 'xepsilon [crystallographic coordinates]' 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
+ parsed_data['eps_k_vector_coords'] = 'crystal'
+ elif 'xepsilon [cartesian coordinates]' 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
+ parsed_data['eps_k_vector_coords'] = 'cartesian'
+ # There is an oversight in the XSpectra code where the value of xepsilon is reported
+ # as being in "Cartesian frame" when read from the save file regardless of the
+ # coordinate set in the parent calculation, thus we don't report the coordinate system
+ # used in the case of an "only_plot" run.
+ if 'xepsilon [Cartesian frame]' in line and parsed_data['plot_only']:
+ 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 'From SCF save directory' in line:
  if '(spin polarized work)' in line:
  spin = True
@@ -204,7 +220,7 @@ def parse_stdout_xspectra(filecontent, codename=None, message_map=None):
  parsed_data['fermi_energy'] = ef_energy
  parsed_data['fermi_energy_units'] = ef_energy_units
 
- # parse dynamical RAM estimates
+ # parse per-process dynamical RAM estimates
  if 'Estimated max dynamical RAM per process' in line:
  value = line.split('>')[-1]
  match = re.match(r'\s+([+-]?\d+(\.\d*)?|\.\d+([eE][+-]?\d+)?)\s*(Mb|MB|GB)', value)
@@ -215,7 +231,7 @@ def parse_stdout_xspectra(filecontent, codename=None, message_map=None):
  except (IndexError, ValueError):
  pass
 
- # parse dynamical RAM estimates
+ # parse total dynamical RAM estimates
  if 'Estimated total dynamical RAM' in line:
  value = line.split('>')[-1]
  match = re.match(r'\s+([+-]?\d+(\.\d*)?|\.\d+([eE][+-]?\d+)?)\s*(Mb|MB|GB)', value)

tests/parsers/test_xspectra/test_xspectra_default.yml

@@ -4,6 +4,7 @@ parameters:
  core_level_energy_units: eV
  energy_zero: '4.1718'
  energy_zero_units: eV
+ eps_k_vector_coords: crystal
  epsilon_vector:
  - 1.0
  - 0.0

tests/parsers/test_xspectra/test_xspectra_spin.yml

@@ -4,6 +4,7 @@ parameters:
  core_level_energy_units: eV
  energy_zero: '6.8316'
  energy_zero_units: eV
+ eps_k_vector_coords: crystal
  epsilon_vector:
  - 1.0
  - 0.0