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Fix: trajectories from SIRIUS stdout #7

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Fix: trajectories from SIRIUS stdout #7

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19 changes: 14 additions & 5 deletions src/aiida_quantumespresso/parsers/parse_raw/pw.py
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Original file line number Diff line number Diff line change
Expand Up @@ -328,6 +328,9 @@ def parse_stdout(stdout, input_parameters, parser_options=None, parsed_xml=None,
# Determine whether the input switched on an electric field
lelfield = input_parameters.get('CONTROL', {}).get('lelfield', False)

# Determine whether SIRIUS is used
uses_sirius = 'SIRIUS' in ' '.join(data_lines[:50])

# Find some useful quantities.
if not parsed_xml.get('number_of_bands', None):
try:
Expand Down Expand Up @@ -513,11 +516,14 @@ def parse_stdout(stdout, input_parameters, parser_options=None, parsed_xml=None,
# (cell, initial positions, kpoints, ...) and I skip them.
# In case, parse for them before this point.
# Put everything in a trajectory_data dictionary
relax_steps = stdout.split('Self-consistent Calculation')[1:]
if uses_sirius:
relax_steps = stdout.split('* running SCF ground state *')[1:]
else:
relax_steps = stdout.split('Self-consistent Calculation')[1:]

relax_steps = [i.split('\n') for i in relax_steps]

# now I create a bunch of arrays for every step.

for data_step in relax_steps:
trajectory_frame = {}

Expand Down Expand Up @@ -677,9 +683,8 @@ def parse_stdout(stdout, input_parameters, parser_options=None, parsed_xml=None,
pass

# grep energy and possibly, magnetization
elif '!' in line:
elif re.search(r'^\s*!\s+total energy\s*', line, re.IGNORECASE):
try:

En = float(line.split('=')[1].split('Ry')[0]) * CONSTANTS.ry_to_ev

# Up till v6.5, the line after total energy would be the Harris-Foulkes estimate, followed by the
Expand Down Expand Up @@ -876,7 +881,11 @@ def parse_stdout(stdout, input_parameters, parser_options=None, parsed_xml=None,
trajectory_data.setdefault('ionic_dipole_cartesian_axes', []).append(id_axes)

# check consistency of scf_accuracy and scf_iterations
if 'scf_accuracy' in trajectory_data:

# we skip the skip is SIRIUS is used, as SIRIUS does not print the scf_accuracy
# for all scf steps per default, only at the end of each ionic step. Therefore,
# the lenghts will typically not match
if 'scf_accuracy' in trajectory_data and not uses_sirius:
if 'scf_iterations' in trajectory_data:
if len(trajectory_data['scf_accuracy']) != sum(trajectory_data['scf_iterations']):
logs.warning.append(
Expand Down
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