Merge pull request #136 from JuDFTteam/fix_rotations

Rotations in KKRimp code

aiida_kkr/calculations/kkrimp.py

@@ -22,7 +22,7 @@
 __copyright__ = (u'Copyright (c), 2018, Forschungszentrum Jülich GmbH, '
                  'IAS-1/PGI-1, Germany. All rights reserved.')
 __license__ = 'MIT license, see LICENSE.txt file'
-__version__ = '0.8.2'
+__version__ = '0.9.0'
 __contributors__ = (u'Philipp Rüßmann', u'Fabian Bertoldo')
 
 #TODO: implement 'ilayer_center' consistency check
@@ -171,13 +171,6 @@ def define(cls, spec):
     Note: The length of the theta, phi and fix_dir lists have to be equal to the number of atoms in the impurity cluster.
 """
         )
-        spec.input(
-            'cleanup_outfiles',
-            valid_type=Bool,
-            required=False,
-            default=lambda: Bool(False),
-            help='Cleanup and compress output (works only in aiida-core<2.0 and breaks caching ability).'
-        )
 
         # define outputs
         spec.output('output_parameters', valid_type=Dict, required=True, help='results of the KKRimp calculation')

aiida_kkr/parsers/kkr.py

@@ -18,7 +18,7 @@
 __copyright__ = (u'Copyright (c), 2017, Forschungszentrum Jülich GmbH, '
                  'IAS-1/PGI-1, Germany. All rights reserved.')
 __license__ = 'MIT license, see LICENSE.txt file'
-__version__ = '0.7.0'
+__version__ = '0.8.0'
 __contributors__ = ('Jens Broeder', u'Philipp Rüßmann')
 
 
@@ -229,21 +229,3 @@ def parse(self, debug=False, **kwargs):
 
         if not success:
             return self.exit_codes.ERROR_KKR_PARSING_FAILED
-        else:  # cleanup after parsing (only if parsing was successful)
-            # cleanup only works below aiida-core v2.0
-            if int(aiida_core_version.split('.')[0]) < 2:
-                # delete completely parsed output files
-                self.remove_unnecessary_files()
-                # then (maybe) tar the output to save space
-                # TODO needs implementing (see kkrimp parser)
-
-    def remove_unnecessary_files(self):
-        """
-        Remove files that are not needed anymore after parsing
-        The information is completely parsed (i.e. in outdict of calculation)
-        and keeping the file would just be a duplication.
-        """
-        files_to_delete = [KkrCalculation._POTENTIAL, KkrCalculation._SHAPEFUN]
-        for fileid in files_to_delete:
-            if fileid in self.retrieved.list_object_names():
-                self.retrieved.delete_object(fileid, force=True)

aiida_kkr/parsers/kkrimp.py

@@ -21,7 +21,7 @@
 __copyright__ = (u'Copyright (c), 2018, Forschungszentrum Jülich GmbH, '
                  'IAS-1/PGI-1, Germany. All rights reserved.')
 __license__ = 'MIT license, see LICENSE.txt file'
-__version__ = '0.5.0'
+__version__ = '0.6.0'
 __contributors__ = ('Philipp Rüßmann')
 
 
@@ -42,7 +42,7 @@ def __init__(self, calc):
 
     # pylint: disable=protected-access
 
-    def parse(self, debug=False, **kwargs):
+    def parse(self, debug=False, ignore_nan=True, **kwargs):  # pylint: disable=unexpected-keyword-arg
         """
         Parse output data folder, store results in database.
 
@@ -113,7 +113,7 @@ def parse(self, debug=False, **kwargs):
 
             # now we can parse the output files
             success, msg_list, out_dict = KkrimpParserFunctions().parse_kkrimp_outputfile(
-                out_dict, named_file_handles, debug=debug
+                out_dict, named_file_handles, debug=debug, ignore_nan=ignore_nan
             )
 
         out_dict['parser_errors'] = msg_list
@@ -132,22 +132,7 @@ def parse(self, debug=False, **kwargs):
         # create output node and link
         self.out('output_parameters', Dict(dict=out_dict))
 
-        # cleanup after parsing (only if parsing was successful), only works below aiida-core v2.0
-        if success:
-            if int(aiida_core_version.split('.')[0]) < 2:
-                # check if we should do the cleanup or not
-                cleanup_outfiles = False
-                if 'cleanup_outfiles' in self.node.inputs:
-                    cleanup_outfiles = self.node.inputs.cleanup_outfiles.value
-                if cleanup_outfiles:
-                    # reduce size of timing file
-                    self.cleanup_outfiles(files['out_timing'], ['Iteration number', 'time until scf starts'])
-                    # reduce size of out_log file
-                    self.cleanup_outfiles(files['out_log'], ['Iteration Number'])
-                    # delete completely parsed output files and create a tar ball to reduce size
-                    self.remove_unnecessary_files()
-                    self.final_cleanup()
-        else:
+        if not success:
             return self.exit_codes.ERROR_PARSING_KKRIMPCALC
 
     def _check_file_existance(self, files, keyname, fname, icrit, file_errors):
@@ -168,71 +153,3 @@ def _check_file_existance(self, files, keyname, fname, icrit, file_errors):
                 raise ValueError('icrit should be either 1 or 2')
             file_errors.append((icrit, crit_level + f" File '{fname}' not found."))
             files[keyname] = None
-
-    def cleanup_outfiles(self, fileidentifier, keyslist):
-        """open file and remove unneeded output"""
-        if fileidentifier is not None:
-            lineids = []
-            with self.retrieved.open(fileidentifier) as tfile:
-                txt = tfile.readlines()
-                for iline in range(len(txt)):
-                    for key in keyslist:  # go through all keys
-                        if key in txt[iline]:  # add line id to list if key has been found
-                            lineids.append(iline)
-            # rewrite file deleting the middle part
-            if len(lineids) > 1:  # cut only if more than one iteration was found
-                txt = txt[:lineids[0]] + \
-                    ['# ... [removed output except for last iteration] ...\n'] + \
-                    txt[lineids[-1]:]
-                with self.retrieved.open(fileidentifier, 'w') as tfilenew:
-                    tfilenew.writelines(txt)
-
-    def remove_unnecessary_files(self):
-        """
-        Remove files that are not needed anymore after parsing
-        The information is completely parsed (i.e. in outdict of calculation)
-        and keeping the file would just be a duplication.
-        """
-        # first delete unused files (completely in parsed output)
-        files_to_delete = [
-            KkrimpCalculation._OUT_ENERGYSP_PER_ATOM, KkrimpCalculation._OUT_ENERGYTOT_PER_ATOM,
-            KkrimpCalculation._SHAPEFUN
-        ]
-        for fileid in files_to_delete:
-            if fileid in self.retrieved.list_object_names():
-                self.retrieved.delete_object(fileid, force=True)
-
-    def final_cleanup(self):
-        """Create a tarball of the rest."""
-
-        # short name for retrieved folder
-        ret = self.retrieved
-
-        # Now create tarball of output
-        #
-        # check if output has been packed to tarfile already
-        # only if tarfile is not there we create the output tar file
-        if KkrimpCalculation._FILENAME_TAR not in ret.list_object_names():
-            # first create dummy file which is used to extract the full path that is given to tarfile.open
-            with ret.open(KkrimpCalculation._FILENAME_TAR, 'w') as f:
-                filepath_tar = f.name
-
-            # now create tarfile and loop over content of retrieved directory
-            to_delete = []
-            with tarfile.open(filepath_tar, 'w:gz') as tf:
-                for f in ret.list_object_names():
-                    with ret.open(f) as ftest:
-                        filesize = os.stat(ftest.name).st_size
-                        ffull = ftest.name
-                    if (
-                        f != KkrimpCalculation._FILENAME_TAR  # ignore tar file
-                        and filesize > 0  # ignore empty files
-                        # ignore files starting with '.' like '.nfs...'
-                        and f[0] != '.'
-                    ):
-                        tf.add(ffull, arcname=os.path.basename(ffull))
-                        to_delete.append(f)
-
-            # finally delete files that have been added to tarfile
-            for f in to_delete:
-                ret.delete_object(f, force=True)

aiida_kkr/workflows/imp_BdG.py

@@ -144,7 +144,7 @@ def define(cls, spec):
         spec.expose_inputs(
             kkr_imp_wc,
             namespace='imp_scf',
-            include=('startpot', 'wf_parameters', 'gf_writeout', 'scf.params_overwrite')
+            include=('startpot', 'wf_parameters', 'gf_writeout', 'scf.params_overwrite', 'scf.initial_noco_angles')
         )
         spec.inputs['imp_scf']['gf_writeout']['kkr'].required = False
         spec.input('imp_scf.options', required=False, help='computer options for impurity scf step')
@@ -157,7 +157,11 @@ def define(cls, spec):
         )
 
         # inputs for impurity BdG scf
-        spec.expose_inputs(kkr_imp_wc, namespace='BdG_scf', include=('startpot', 'remote_data_gf', 'gf_writeout'))
+        spec.expose_inputs(
+            kkr_imp_wc,
+            namespace='BdG_scf',
+            include=('startpot', 'remote_data_gf', 'gf_writeout', 'scf.initial_noco_angles')
+        )
         spec.inputs['BdG_scf']['gf_writeout']['kkr'].required = False
         spec.input('BdG_scf.options', required=False, help='computer options for BdG impurity scf step')
 
@@ -166,7 +170,11 @@ def define(cls, spec):
         )
 
         # inputs for impurity dos
-        spec.expose_inputs(kkr_imp_dos_wc, namespace='dos', include=('wf_parameters', 'gf_dos_remote', 'gf_writeout'))
+        spec.expose_inputs(
+            kkr_imp_dos_wc,
+            namespace='dos',
+            include=('wf_parameters', 'gf_dos_remote', 'gf_writeout', 'initial_noco_angles')
+        )
 
         spec.input(
             'dos.gf_writeout.host_remote',
@@ -275,6 +283,8 @@ def imp_pot_calc(self):
             builder.options = self.inputs.imp_scf.options
         else:
             builder.options = self.inputs.options
+        if 'initial_noco_angles' in self.inputs.imp_scf:
+            builder.scf.initial_noco_angles = self.inputs.imp_scf.initial_noco_angles  # pylint: disable=no-member
 
         if 'gf_writeout' in self.inputs.imp_scf:
             if 'options' in self.inputs.imp_scf.gf_writeout:
@@ -319,6 +329,8 @@ def imp_BdG_calc(self):
                 builder.params_kkr_overwrite = self.inputs.BdG_scf.gf_writeout.params_kkr_overwrite
         if 'kkr' in self.inputs:
             builder.gf_writeout.kkr = builder.kkr  # pylint: disable=no-member
+        if 'initial_noco_angles' in self.inputs.BdG_scf:
+            builder.scf.initial_noco_angles = self.inputs.BdG_scf.initial_noco_angles  # pylint: disable=no-member
 
         builder.remote_data_host = self.inputs.BdG_scf.remote_data_host
 
@@ -384,6 +396,10 @@ def DOS_calc(self):
                 else:
                     builder.options = self.inputs.options
 
+        # set nonco angles
+        if 'initial_noco_angles' in self.inputs.dos:
+            builder.initial_noco_angles = self.inputs.dos.initial_noco_angles
+
         # skip BdG step and just use the starting potential instead?
         # faster and same accuracy?!
         if 'startpot' in self.inputs.BdG_scf:

aiida_kkr/workflows/kkr_imp.py

@@ -13,7 +13,7 @@
 from aiida_kkr.tools import test_and_get_codenode, neworder_potential_wf, update_params_wf
 from aiida_kkr.workflows.gf_writeout import kkr_flex_wc
 from aiida_kkr.workflows.voro_start import kkr_startpot_wc
-from aiida_kkr.workflows.kkr_imp_sub import kkr_imp_sub_wc, clean_sfd
+from aiida_kkr.workflows.kkr_imp_sub import kkr_imp_sub_wc
 import numpy as np
 from aiida_kkr.tools.save_output_nodes import create_out_dict_node
 
@@ -101,7 +101,8 @@ def define(cls, spec):
                 # 'kkrimp',
                 'options',
                 # 'wf_parameters',
-                'params_overwrite'
+                'params_overwrite',
+                'initial_noco_angles'
             )
         )
 
@@ -338,7 +339,6 @@ def start(self):
         self.ctx.hfield = wf_dict.get('hfield', self._wf_default['hfield'])
         self.ctx.init_pos = wf_dict.get('init_pos', self._wf_default['init_pos'])
         self.ctx.accuracy_params = wf_dict.get('accuracy_params', self._wf_default['accuracy_params'])
-        self.ctx.do_final_cleanup = wf_dict.get('do_final_cleanup', self._wf_default['do_final_cleanup'])
         # set up new parameter dict to pass to kkrimp subworkflow later
         self.ctx.kkrimp_params_dict = Dict({
             'nsteps': self.ctx.nsteps,
@@ -354,15 +354,11 @@ def start(self):
             'hfield': self.ctx.hfield,
             'init_pos': self.ctx.init_pos,
             'accuracy_params': self.ctx.accuracy_params,
-            'do_final_cleanup': self.ctx.do_final_cleanup
         })
 
         # retrieve option for kkrlfex files
         self.ctx.retrieve_kkrflex = wf_dict.get('retrieve_kkrflex', self._wf_default['retrieve_kkrflex'])
 
-        # list of things that are cleaned if everything ran through
-        self.ctx.sfd_final_cleanup = []
-
         # report the chosen parameters to the user
         self.report(
             'INFO: use the following parameter:\n'
@@ -738,8 +734,6 @@ def construct_startpot(self):
 
         # add starting potential for kkrimp calculation to context
         self.ctx.startpot_kkrimp = startpot_kkrimp
-        # add to list for final cleanup
-        self.ctx.sfd_final_cleanup.append(startpot_kkrimp)
 
         self.report(
             'INFO: created startpotential (pid: {}) for the impurity calculation '
@@ -793,6 +787,8 @@ def run_kkrimp_scf(self):
                 builder.params_overwrite = self.inputs.scf.params_overwrite
             if 'options' in self.inputs.scf:
                 builder.options = self.inputs.scf.options
+            if 'initial_noco_angles' in self.inputs.scf:
+                builder.initial_noco_angles = self.inputs.scf.initial_noco_angles
         builder.wf_parameters = kkrimp_params
         future = self.submit(builder)
 
@@ -853,10 +849,6 @@ def return_results(self):
             self.out('converged_potential', self.ctx.kkrimp_scf_sub.outputs.host_imp_pot)
             self.out('remote_data_gf', self.ctx.gf_remote)
 
-            # cleanup things that are not needed anymore
-            if self.ctx.do_final_cleanup:
-                self.final_cleanup()
-
             # print final message before exiting
             self.report('INFO: created 3 output nodes for the KKR impurity workflow.')
             self.report(
@@ -869,23 +861,6 @@ def return_results(self):
             self.report(self.exit_codes.ERROR_KKRIMP_SUB_WORKFLOW_FAILURE)  # pylint: disable=no-member
             return self.exit_codes.ERROR_KKRIMP_SUB_WORKFLOW_FAILURE  # pylint: disable=no-member
 
-    def final_cleanup(self):
-        """
-        Remove unneeded files to save space
-        """
-        for sfd in self.ctx.sfd_final_cleanup:
-            clean_sfd(sfd)
-        if self.ctx.create_startpot:
-            kkr_startpot = self.ctx.last_voro_calc
-            vorocalc = kkr_startpot.outputs.last_voronoi_remote.get_incoming(link_label_filter=u'remote_folder'
-                                                                             ).first().node
-            ret = vorocalc.outputs.retrieved
-            for fname in ret.list_object_names():
-                if fname not in [VoronoiCalculation._OUTPUT_FILE_NAME, VoronoiCalculation._OUT_POTENTIAL_voronoi]:
-                    # delete all except vor default output file
-                    with ret.open(fname) as f:
-                        ret.delete_object(fname, force=True)
-
     def error_handler(self):
         """Capture errors raised in validate_input"""
         if self.ctx.exit_code is not None: