Development of STM workchain

aiida_kkr/calculations/kkr.py

@@ -25,7 +25,7 @@
                  'IAS-1/PGI-1, Germany. All rights reserved.')
 __license__ = 'MIT license, see LICENSE.txt file'
 
-__version__ = '0.13.1'
+__version__ = '0.13.2'
 
 __contributors__ = ('Jens Bröder', 'Philipp Rüßmann')
 
@@ -1063,8 +1063,8 @@
                         f'Error: theta value out of range (0..180): iatom={iatom}, theta={theta}'
                     )
                 # convert fix_dir to boolean if given as integer
-                if not isinstance(fix_dir, bool):
-                    fix_dir = (fix_dir == 1)
+                if not isinstance(fix_dir[iatom], bool):
+                    fix_dir[iatom] = (fix_dir[iatom] == 1)
                 # write line
                 noco_angle_file.write(f'   {theta}    {phi}    {fix_dir[iatom]}\n')
 

aiida_kkr/calculations/kkrimp.py

@@ -77,7 +77,9 @@
     _OUT_LMDOS_INTERPOL = u'out_lmdos.interpol.atom=*'
     _OUT_MAGNETICMOMENTS = u'out_magneticmoments'
     _OUT_ORBITALMOMENTS = u'out_orbitalmoments'
-    _LDAUPOT = 'ldaupot'
+    _LDAUPOT = u'ldaupot'
+
+    _TEST_RHO2NS = u'test_rho2ns'
 
     # template.product entry point defined in setup.json
     _default_parser = u'kkr.kkrimpparser'
@@ -787,6 +789,10 @@
         # take care of LLYsimple (i.e. Lloyd in host system)
         if 'LLOYD' in runopts:
             runflag = self._use_lloyd(runflag, GFhost_folder, tempfolder)
+        # alternative to Lloyd mode: renormalization factor of energy integration weights
+        if params_host.get_value('WFAC_RENORM') is not None:
+            if params_host.get_value('WFAC_RENORM'):
+                runflag = self._use_lloyd(runflag, GFhost_folder, tempfolder, True)
 
         # now set runflags
         params_kkrimp.set_value('RUNFLAG', runflag)
@@ -824,19 +830,33 @@
                 for socscl in socscale:
                     kkrflex_socfac.write(f' {socscl}\n')
 
-    def _use_lloyd(self, runflag, GFhost_folder, tempfolder):
+    def _use_lloyd(self, runflag, GFhost_folder, tempfolder, wfac_renorm=False):
         """Use the LLYsimple version of KKRimp code with the average renormalization factor from the host calculation"""
+
         # add runflag for imp code
         runflag.append('LLYsimple')
-        # also extract renormalization factor and create kkrflex_llyfac file (contains one value only)
-        with GFhost_folder.open('output.000.txt') as f:
-            txt = f.readlines()
+
+        # find renormalization factor
+        if wfac_renorm:
+            # option 1: found wfac_renorm in Kkrhost parent's input parameters
+            with GFhost_folder.open('inputcard') as f:
+                txt = f.readlines()
+            iline = search_string('WFAC_RENORM', txt)
+        else:
+            # option 2: host parent is a Lloyd calculation
+            # extract renormalization factor and create kkrflex_llyfac file (contains one value only)
+            with GFhost_folder.open('output.000.txt') as f:
+                txt = f.readlines()
             iline = search_string('RENORM_LLY: Renormalization factor of total charge', txt)
-            if iline >= 0:
-                llyfac = txt[iline].split()[-1]
-                # now write kkrflex_llyfac to tempfolder where later on config file is also written
-                with tempfolder.open(self._KKRFLEX_LLYFAC, 'w') as f2:
-                    f2.writelines([llyfac])
+
+        if iline >= 0:
+            llyfac = txt[iline].split()[-1]
+        else:
+            raise ValueError('Failed to extract llyfac in KkrimpCalculation')
+
+        # now write kkrflex_llyfac to tempfolder where later on config file is also written
+        with tempfolder.open(self._KKRFLEX_LLYFAC, 'w') as f2:
+            f2.writelines([llyfac])
         return runflag
 
     def _activate_jij_calc(self, runflag, params_kkrimp, GFhost_folder, tempfolder):

aiida_kkr/calculations/voro.py

@@ -14,7 +14,7 @@
 __copyright__ = (u'Copyright (c), 2017, Forschungszentrum Jülich GmbH, '
                  'IAS-1/PGI-1, Germany. All rights reserved.')
 __license__ = 'MIT license, see LICENSE.txt file'
-__version__ = '0.5.3'
+__version__ = '0.5.4'
 __contributors__ = ('Jens Broeder', 'Philipp Rüßmann')
 
 
@@ -182,7 +182,8 @@ def prepare_for_submission(self, tempfolder):
         # Decide what files to copy
         local_copy_list = []
         if overwrite_potential:
-            # copy the right files #TODO check first if file, exists and throw
+            # copy the right files
+            #TODO check first if file, exists and throw
             # warning, now this will throw an error
             if found_parent and self._is_KkrCalc(parent_calc):
                 outfolder = parent_calc.outputs.retrieved  # copy from remote folder
@@ -199,11 +200,11 @@ def prepare_for_submission(self, tempfolder):
                     filename = self._POTENTIAL_IN_OVERWRITE
                 local_copy_list.append((outfolder.uuid, file1, filename))  # pylint: disable=possibly-used-before-assignment
 
-            # add shapefun to overwrite
-            if 'shapefun_overwrite' in self.inputs:
-                shapefun_overwrite = self.inputs.shapefun_overwrite
-                filename = shapefun_overwrite.filename
-                local_copy_list.append((shapefun_overwrite.uuid, filename, 'shapefun_overwrite'))
+        # add shapefun to overwrite
+        if 'shapefun_overwrite' in self.inputs:
+            shapefun_overwrite = self.inputs.shapefun_overwrite
+            filename = shapefun_overwrite.filename
+            local_copy_list.append((shapefun_overwrite.uuid, filename, 'shapefun_overwrite'))
 
         # Prepare CalcInfo to be returned to aiida
         calcinfo = CalcInfo()

aiida_kkr/parsers/kkrimp.py

@@ -8,8 +8,8 @@
 import tarfile
 import os
 from aiida import __version__ as aiida_core_version
-from aiida.orm import Dict
-from aiida.common.exceptions import InputValidationError, NotExistent
+from aiida.orm import Dict, CalcJobNode
+from aiida.common.exceptions import InputValidationError, NotExistent, NotExistentAttributeError
 from aiida.parsers.parser import Parser
 from aiida_kkr.calculations.kkrimp import KkrimpCalculation
 from aiida_kkr.tools.context import open_files_in_context
@@ -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__ = '0.6.2'
+__contributors__ = (u'Philipp Rüßmann', u'Raffaele Aliberti')
 
 
 class KkrimpParser(Parser):
@@ -42,7 +42,7 @@
 
     # pylint: disable=protected-access
     # pylint: disable=unexpected-keyword-arg
-    def parse(self, debug=False, ignore_nan=True, **kwargs):
+    def parse(self, debug=False, ignore_nan=True, doscalc=None, **kwargs):
         """
         Parse output data folder, store results in database.
 
@@ -64,6 +64,19 @@
         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 (if not specified in the input already)
+        if doscalc is None:
+            parent_host_calc = calc.inputs.host_Greenfunction_folder.get_incoming(node_class=CalcJobNode).first().node
+            # This parameter discriminates if it is a DOS calc or not
+            npol = parent_host_calc.inputs.parameters.get_dict().get('NPOL', 1)
+            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 @@
 
             # 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/__init__.py

@@ -6,7 +6,7 @@
 from .common_workfunctions import (
     update_params_wf, prepare_VCA_structure_wf, prepare_2Dcalc_wf, test_and_get_codenode, get_inputs_kkr,
     get_inputs_kkrimporter, get_inputs_voronoi, get_inputs_kkrimp, get_parent_paranode,
-    generate_inputcard_from_structure, check_2Dinput_consistency, structure_from_params, vca_check
+    generate_inputcard_from_structure, check_2Dinput_consistency, structure_from_params, vca_check, truncate_string
 )
 from .find_cluster_radius import find_cluster_radius
 from .plot_kkr import plot_kkr

aiida_kkr/tools/combine_imps.py

@@ -32,10 +32,6 @@ def get_host_structure(impurity_workflow_or_calc):
     extract host structure from impurity
     """
     #TODO extract host parent no from input but take into account calculation of host GF from inside kkrimp full workflow
-    print(
-        f'This is line in the combine impurity tool files at:: /opt/aiida-kkr/aiida_kkr/tools for deburging the line',
-        end=' '
-    )
     print(f'impurity_workflow_or_calc: {impurity_workflow_or_calc}')
     if impurity_workflow_or_calc.process_class == KkrimpCalculation:
         host_parent = impurity_workflow_or_calc.inputs.host_Greenfunction_folder

aiida_kkr/tools/common_workfunctions.py

@@ -336,6 +336,16 @@
     return builder
 
 
+def truncate_string(string, max_length):
+    """
+    Truncate the length of a string to max_length-3 entries.
+    The last three characters '...' to indicate the truncation.
+    """
+    if len(string) > max_length:
+        string = string[:max_length - 3] + '...'
+    return string
+
+
 def get_inputs_common(
     calculation,
     code,
@@ -381,7 +391,8 @@
         inputs.metadata.description = ''
 
     if label:
-        inputs.metadata.label = label
+        # Attention: max label length is 255 characters
+        inputs.metadata.label = truncate_string(label, 255)
     else:
         inputs.metadata.label = ''
 

aiida_kkr/tools/imp_cluster_tools.py

@@ -45,15 +45,22 @@
     :return: scoef array (positions [x,y,z], layer index, distance to first position in imp cluster)
     :type: numpy.array
     """
-    impinfo = impinfo_node.get_dict()
-    Rcut = impinfo.get('Rcut', None)
-    hcut = impinfo.get('hcut', -1.)
-    cylinder_orient = impinfo.get('cylinder_orient', [0., 0., 1.])
-    ilayer_center = impinfo.get('ilayer_center', 0)
-
-    clust = create_scoef_array(host_structure, Rcut, hcut, cylinder_orient, ilayer_center)
-    # sort after distance
-    clust = clust[(clust[:, -1]).argsort()]
+    # check if we can read it from a node extra
+    if 'imp_cls' not in impinfo_node.extras:
+        impinfo = impinfo_node.get_dict()
+        Rcut = impinfo.get('Rcut', None)
+        hcut = impinfo.get('hcut', -1.)
+        cylinder_orient = impinfo.get('cylinder_orient', [0., 0., 1.])
+        ilayer_center = impinfo.get('ilayer_center', 0)
+
+        clust = create_scoef_array(host_structure, Rcut, hcut, cylinder_orient, ilayer_center)
+        # sort after distance
+        clust = clust[(clust[:, -1]).argsort()]
+
+        # save as extra for second run
+        impinfo_node.set_extra('imp_cls', clust)
+    else:
+        clust = np.array(impinfo_node.extras['imp_cls'])
 
     return clust