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Fix matdyn parser column offset and ph.py parameter handling #1233

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Fix matdyn parser column offset and ph.py parameter handling #1233

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12 changes: 6 additions & 6 deletions src/aiida_quantumespresso/calculations/ph.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,10 +8,9 @@
from aiida.common import datastructures, exceptions
from aiida.common.warnings import AiidaDeprecationWarning

from aiida_quantumespresso.calculations import _uppercase_dict
from aiida_quantumespresso.calculations import _lowercase_dict, _uppercase_dict
from aiida_quantumespresso.calculations.pw import PwCalculation
from aiida_quantumespresso.utils.convert import convert_input_to_namelist_entry
from aiida_quantumespresso.utils.validation.parameters import validate_parameters

from .base import CalcJob

Expand Down Expand Up @@ -64,7 +63,7 @@ def define(cls, spec):
spec.input('metadata.options.parser_name', valid_type=str, default='quantumespresso.ph')
spec.input('metadata.options.withmpi', valid_type=bool, default=True)
spec.input('qpoints', valid_type=orm.KpointsData, help='qpoint mesh')
spec.input('parameters', valid_type=orm.Dict, help='', validator=validate_parameters)
spec.input('parameters', valid_type=orm.Dict, help='')
spec.input('settings', valid_type=orm.Dict, required=False, help='')
spec.input('parent_folder', valid_type=orm.RemoteData, help='the folder of a completed `PwCalculation`')
spec.output('output_parameters', valid_type=orm.Dict)
Expand Down Expand Up @@ -169,7 +168,8 @@ def prepare_for_submission(self, folder):
raise exceptions.InputValidationError(msg) from exception
parent_calc_out_subfolder = settings.pop('PARENT_CALC_OUT_SUBFOLDER', default_parent_output_folder)

parameters = self.inputs.parameters.get_dict()
parameters = _uppercase_dict(self.inputs.parameters.get_dict(), dict_name='parameters')
parameters = {k: _lowercase_dict(v, dict_name=k) for k, v in parameters.items()}

prepare_for_d3 = settings.pop('PREPARE_FOR_D3', False)
if prepare_for_d3:
Expand Down Expand Up @@ -337,7 +337,7 @@ def prepare_for_submission(self, folder):
self._FOLDER_DYNAMICAL_MATRIX,
)
)
if parameters['INPUTPH'].get('electron_phonon', None) is not None:
if parameters.get('INPUTPH', {}).get('electron_phonon', None) is not None:
remote_symlink_list.append(
(
parent_folder.computer.uuid,
Expand All @@ -361,7 +361,7 @@ def prepare_for_submission(self, folder):
'.',
)
)
if parameters['INPUTPH'].get('electron_phonon', None) is not None:
if parameters.get('INPUTPH', {}).get('electron_phonon', None) is not None:
remote_copy_list.append(
(
parent_folder.computer.uuid,
Expand Down
4 changes: 2 additions & 2 deletions src/aiida_quantumespresso/parsers/matdyn.py
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Original file line number Diff line number Diff line change
Expand Up @@ -137,7 +137,7 @@ def parse_raw_matdyn_phonon_file(phonon_frequencies):
parsed_data['warnings'].append('Bad formatting of frequencies')
return parsed_data

counter = 3
counter = 4
for i in range(num_kpoints):
for j in range(num_bands):
try:
Expand All @@ -148,7 +148,7 @@ def parse_raw_matdyn_phonon_file(phonon_frequencies):
parsed_data['warnings'].append('Error while parsing the frequencies, dimension exceeded')
return parsed_data
counter += 1
counter += 3 # move past the kpoint coordinates
counter += 4

parsed_data['phonon_bands'] = freq_matrix

Expand Down