Fixed parser for impurity calculations in dos mode

aiida_kkr/parsers/kkrimp.py

@@ -8,7 +8,7 @@
 import tarfile
 import os
 from aiida import __version__ as aiida_core_version
-from aiida.orm import Dict
+from aiida.orm import Dict, CalcJobNode
 from aiida.common.exceptions import InputValidationError, NotExistent
 from aiida.parsers.parser import Parser
 from aiida_kkr.calculations.kkrimp import KkrimpCalculation
@@ -21,8 +21,8 @@
 __copyright__ = (u'Copyright (c), 2018, Forschungszentrum Jülich GmbH, '
                  'IAS-1/PGI-1, Germany. All rights reserved.')
 __license__ = 'MIT license, see LICENSE.txt file'
-__version__ = '0.6.0'
-__contributors__ = ('Philipp Rüßmann')
+__version__ = '0.6.1'
+__contributors__ = (u'Philipp Rüßmann', u'Raffaele Aliberti')
 
 
 class KkrimpParser(Parser):
@@ -64,6 +64,19 @@ def parse(self, debug=False, ignore_nan=True, **kwargs):
         file_errors = []
         files = {}
 
+        # Get the node of the parent calculation (useful for the imp calculations)
+        calc = out_folder.get_incoming(node_class=CalcJobNode).first().node
+
+        # figure out if this is a DOS calculation
+        parent_host_calc = calc.inputs.host_Greenfunction_folder.get_incoming(node_class=CalcJobNode).first().node
+        npol = parent_host_calc.inputs.parameters.get_dict().get(
+            'NPOL', 1
+        )  # This parameter discriminates if it is a DOS calc or not
+        doscalc = (npol == 0)
+
+        if debug:
+            print('doscalc = ', doscalc)
+
         # Parse output files of KKRimp calculation
 
         # first get path to files and catch errors if files are not present
@@ -113,7 +126,7 @@ def parse(self, debug=False, ignore_nan=True, **kwargs):
 
             # now we can parse the output files
             success, msg_list, out_dict = KkrimpParserFunctions().parse_kkrimp_outputfile(
-                out_dict, named_file_handles, debug=debug, ignore_nan=ignore_nan
+                out_dict, named_file_handles, debug=debug, ignore_nan=ignore_nan, doscalc=doscalc
             )
 
         out_dict['parser_errors'] = msg_list

aiida_kkr/tools/tools_STM_scan.py

@@ -132,7 +132,9 @@ def get_imp_info_add_position(add_position, host_structure, imp_info):
     # combine cluster information
     pos_exists_in_imp1, _ = pos_exists_already(clust1, clust2)
     if pos_exists_in_imp1:
-        raise ValueError('Additional position exists already in impurity cluster.')
+        # If the position exists already we simply skip the addition of the new scanning position
+        return None
+        #raise ValueError('Additional position exists already in impurity cluster.')
     cluster_combined, rimp_rel_combined, _, _ = combine_clusters(clust1, clust2_offset, False, debug=False)
     # combine the zimp arrays
     zimp_combined = imp_info['Zimp'] + imp_info2['Zimp']

aiida_kkr/workflows/kkr_STM.py

@@ -195,18 +195,21 @@ def combine_potentials(self, host_structure, impurity_to_combine, da, db):
         """
         Here we want to combine the impurity information and the host information
         """
-        tip_position = {}
+        tip_position = {
+        }  # Since the objects in AiiDA are immutable we have to create a new dictionary and then convert
+        # it to the right AiiDA type
 
         tip_position['ilayer'] = self.inputs.tip_position['ilayer']
         tip_position['da'] = da
         tip_position['db'] = db
         imp_info = self.inputs.imp_info  #(impurity to combine)
 
         combined_imp_info = get_imp_info_add_position(Dict(tip_position), host_structure, imp_info)
-        # Since the objects in AiiDA are immutable we have to create a new dictionary and then convert
-        # it to the right AiiDA type
 
-        #new_combined_imp_info = {}
+        # If the position already exists we simply return the old dictionary
+        if combined_imp_info is None:
+            return impurity_to_combine
+
         # Add check to see if imp_cls is there
         if 'imp_cls' in impurity_to_combine: