Implemented support for elasticity calculion in matdyn

aiida_quantumespresso/calculations/matdyn.py

@@ -1,7 +1,6 @@
 # -*- coding: utf-8 -*-
 """`CalcJob` implementation for the matdyn.x code of Quantum ESPRESSO."""
 from aiida import orm
-
 from aiida_quantumespresso.calculations.namelists import NamelistsCalculation
 from aiida_quantumespresso.data.force_constants import ForceConstantsData
 
@@ -12,16 +11,18 @@ class MatdynCalculation(NamelistsCalculation):
     _PHONON_FREQUENCIES_NAME = 'phonon_frequencies.dat'
     _PHONON_MODES_NAME = 'phonon_displacements.dat'
     _PHONON_DOS_NAME = 'phonon_dos.dat'
+    _PHONON_ELASTICITY_NAME = 'phonon_elasticity.yaml'
 
     _default_namelists = ['INPUT']
     _blocked_keywords = [
         ('INPUT', 'flfrq', _PHONON_FREQUENCIES_NAME),  # output frequencies
         ('INPUT', 'flvec', _PHONON_MODES_NAME),  # output displacements
         ('INPUT', 'fldos', _PHONON_DOS_NAME),  # output density of states
+        ('INPUT', 'flelc', _PHONON_ELASTICITY_NAME),  # output elastic properties
         ('INPUT', 'q_in_cryst_coord', True),  # kpoints always in crystal coordinates
     ]
 
-    _internal_retrieve_list = [_PHONON_FREQUENCIES_NAME, _PHONON_DOS_NAME]
+    _internal_retrieve_list = [_PHONON_FREQUENCIES_NAME, _PHONON_DOS_NAME, _PHONON_ELASTICITY_NAME]
     _default_parser = 'quantumespresso.matdyn'
 
     @classmethod
@@ -34,13 +35,16 @@ def define(cls, spec):
         spec.inputs.pop('parent_folder')
         spec.output('output_parameters', valid_type=orm.Dict)
         spec.output('output_phonon_bands', valid_type=orm.BandsData)
+        spec.output('output_elasticity', valid_type=orm.Dict)
         spec.default_output_node = 'output_parameters'
         spec.exit_code(310, 'ERROR_OUTPUT_STDOUT_READ',
             message='The stdout output file could not be read.')
         spec.exit_code(312, 'ERROR_OUTPUT_STDOUT_INCOMPLETE',
             message='The stdout output file was incomplete probably because the calculation got interrupted.')
         spec.exit_code(330, 'ERROR_OUTPUT_FREQUENCIES',
             message='The output frequencies file could not be read from the retrieved folder.')
+        spec.exit_code(340, 'ERROR_OUTPUT_ELASTICITY',
+            message='The output elasticity file could not be read from the retrieved folder.')
         spec.exit_code(410, 'ERROR_OUTPUT_KPOINTS_MISSING',
             message='Number of kpoints not found in the output data')
         spec.exit_code(411, 'ERROR_OUTPUT_KPOINTS_INCOMMENSURATE',
@@ -56,7 +60,7 @@ def _get_following_text(self):
 
         kpoints_string = [f'{len(kpoints)}']
         for kpoint in kpoints:
-            kpoints_string.append('{:18.10f} {:18.10f} {:18.10f}'.format(*kpoint))  # pylint: disable=consider-using-f-string
+            kpoints_string.append('{:18.10f} {:18.10f} {:18.10f}'.format(*kpoint))
 
         return '\n'.join(kpoints_string) + '\n'
 
@@ -71,7 +75,9 @@ def prepare_for_submission(self, folder):
         :return: :py:`~aiida.common.datastructures.CalcInfo` instance.
         """
         force_constants = self.inputs.force_constants
-        self._blocked_keywords.append(('INPUT', 'flfrc', force_constants.filename))
+        flfrc_tuple = ('INPUT', 'flfrc', force_constants.filename)
+        if flfrc_tuple not in self._blocked_keywords:
+            self._blocked_keywords.append(flfrc_tuple)
 
         calcinfo = super().prepare_for_submission(folder)
         calcinfo.local_copy_list.append((force_constants.uuid, force_constants.filename, force_constants.filename))

aiida_quantumespresso/parsers/matdyn.py

@@ -3,7 +3,6 @@
 from qe_tools import CONSTANTS
 
 from aiida_quantumespresso.calculations.matdyn import MatdynCalculation
-
 from .base import Parser
 
 
@@ -15,6 +14,7 @@ def parse(self, **kwargs):
         retrieved = self.retrieved
         filename_stdout = self.node.get_option('output_filename')
         filename_frequencies = MatdynCalculation._PHONON_FREQUENCIES_NAME
+        filename_elasticity = MatdynCalculation._PHONON_ELASTICITY_NAME
 
         if filename_stdout not in retrieved.list_object_names():
             return self.exit(self.exit_codes.ERROR_OUTPUT_STDOUT_READ)
@@ -48,6 +48,12 @@ def parse(self, **kwargs):
         output_bands.set_kpointsdata(kpoints_for_bands)
         output_bands.set_bands(parsed_data.pop('phonon_bands'), units='THz')
 
+        if filename_elasticity in retrieved.list_object_names():
+            output_elasticity = parse_elasticity_file(retrieved.get_object_content(filename_elasticity))
+            self.out('output_elasticity', orm.Dict(dict=output_elasticity))
+        else:
+            return self.exit(self.exit_codes.ERROR_OUTPUT_ELASTICITY)
+
         for message in parsed_data['warnings']:
             self.logger.error(message)
 
@@ -67,9 +73,8 @@ def parse_raw_matdyn_phonon_file(phonon_frequencies):
          * num_kpoints: number of kpoints read from the file
          * phonon_bands: BandsData object with the bands for each kpoint
     """
-    import re
-
     import numpy
+    import re
 
     parsed_data = {}
     parsed_data['warnings'] = []
@@ -99,7 +104,7 @@ def parse_raw_matdyn_phonon_file(phonon_frequencies):
             # case in which there are two frequencies attached like -1204.1234-1020.536
             if '-' in b:
                 c = re.split('(-)', b)
-                d = [i for i in c if i != '']
+                d = [i for i in c if i is not '']
                 for i in range(0, len(d), 2):  # d should have an even number of elements
                     corrected_data.append(float(d[i] + d[i + 1]))
             else:
@@ -123,3 +128,19 @@ def parse_raw_matdyn_phonon_file(phonon_frequencies):
     parsed_data['phonon_bands'] = freq_matrix
 
     return parsed_data
+
+
+def parse_elasticity_file(elasticity_file):
+    """Parses the elastic properties file.
+
+    :param elasticity_file: elasticity file from the matdyn calculation
+
+    :return dict parsed_data:
+        A dictionary of elastic properties, see example output yaml file
+        of elasticity about the supported keys.
+    """
+    import yaml
+
+    parsed_data = yaml.full_load(elasticity_file)
+
+    return parsed_data