Merge branch 'retrieve_Jij_files'

CHANGELOG.md

@@ -0,0 +1,41 @@
+# Changelog
+
+## Conventions used for this changelog
+
+ - keep it concise but human readable
+ - keep the *UNRELEASED* section up to date with the `develop` branch
+ - create a new subsection for each release version
+ - each version should have the following information:
+   - a release date in the format `YYYY-MM-DD`
+   - a list of added new feature
+   - a list of changed functionnality of existing features
+   - a list of deprecated features (features that will be deleted in a future release)
+   - a list of removed feature (previously marked deprecated)
+   - a list of bug fixes
+
+----
+
+## *UNRELEASED* (last updated: 2018-11-19)
+
+**Here we collect the list of *added*, *changed*, *deprecated*, *removed* and *fixed* features in preparation for the next release.**
+
+Start of large KKR repository holding *voronoi*, *KKRhost*, *KKRimp*, *KKRsusc*, and *PKKprime* with major refactoring of code structure.
+
+
+### Added
+- None
+
+### Changed
+- kkr calculation retrieves Jij files
+
+### Deprecated
+- KKRimporter calculation now also retrieves Jij files
+
+### Removed
+- None
+
+### Fixed
+- None
+
+----
+

aiida_kkr/calculations/kkr.py

@@ -30,7 +30,7 @@
 __copyright__ = (u"Copyright (c), 2017, Forschungszentrum Jülich GmbH, "
                  "IAS-1/PGI-1, Germany. All rights reserved.")
 __license__ = "MIT license, see LICENSE.txt file"
-__version__ = "0.6"
+__version__ = "0.7"
 __contributors__ = ("Jens Broeder", "Philipp Rüßmann")
 
 
@@ -93,6 +93,9 @@ def _init_internal_params(self):
         self._KKRFLEX_INTERCELL_REF = 'kkrflex_intercell_ref'
         self._KKRFLEX_INTERCELL_CMOMS = 'kkrflex_intercell_cmoms'
         self._ALL_KKRFLEX_FILES = [self._KKRFLEX_GREEN, self._KKRFLEX_TMAT, self._KKRFLEX_ATOMINFO, self._KKRFLEX_INTERCELL_REF, self._KKRFLEX_INTERCELL_CMOMS]
+        # Jij files
+        self._Jij_ATOM = 'Jij.atom%0.5i'
+        self._SHELLS_DAT = 'shells.dat'
 
         # template.product entry point defined in setup.json
         self._default_parser = 'kkr.kkrparser'
@@ -539,6 +542,18 @@ def _prepare_for_submission(self, tempfolder, inputdict):
                     add_files.append((self._QDOS_ATOM%(iatom+1, ispin+1)).replace(' ','0'))
             calcinfo.retrieve_list += add_files
 
+        # 4. Jij calculation
+        retrieve_Jij_files = False
+        if 'RUNOPT' in  parameters.get_dict().keys():
+            runopts = parameters.get_dict()['RUNOPT']
+            if runopts is not None :
+                stripped_run_opts = [i.strip() for i in runopts]
+                if 'XCPL' in stripped_run_opts:
+                    retrieve_Jij_files = True
+        if retrieve_Jij_files:
+            add_files = [self._SHELLS_DAT] + [self._Jij_ATOM%iatom for iatom in range(1,natom+1)]
+            print('adding files for Jij output', add_files)
+            calcinfo.retrieve_list += add_files
 
         codeinfo = CodeInfo()
         codeinfo.cmdline_params = []

aiida_kkr/calculations/kkrimporter.py

@@ -25,7 +25,7 @@
 __copyright__ = (u"Copyright (c), 2017, Forschungszentrum Jülich GmbH, "
                  "IAS-1/PGI-1, Germany. All rights reserved.")
 __license__ = "MIT license, see LICENSE.txt file"
-__version__ = "0.1"
+__version__ = "0.2"
 __contributors__ = ("Philipp Rüßmann")
 
 
@@ -215,12 +215,20 @@ def _prepare_for_retrieval(self, open_transport):
         # Manually set the files that will be copied to the repository and that
         # the parser will extract the results from. This would normally be
         # performed in self._prepare_for_submission prior to submission.
+
+        natom = 1000 # maximal number of atom-resolved files that are retrieved
+        # TODO take actual natom value (maybe extract from number of files that are there)
         self._set_attr('retrieve_list',
-                       [self._DEFAULT_OUTPUT_FILE, self._NONCO_ANGLES_OUT, 
-                        self._OUTPUT_0_INIT, self._OUTPUT_000, self._OUTPUT_2,
+                       [self._INPUT_FILE_NAME, # inputcard needed for parsing
+                        self._DEFAULT_OUTPUT_FILE, # out_kkr, std shell output
+                        self._NONCO_ANGLES_OUT, # nonco angles files
+                        self._OUTPUT_0_INIT, self._OUTPUT_000, self._OUTPUT_2, # output files in new(er) style
                         'output.0','output.1a','output.1b','output.1c','output.2', # try to import old style output
-                        self._OUT_TIMING_000,
-                        self._OUT_POTENTIAL, self._SHAPEFUN])  # make sure to retrieve potential and shapefun as well
+                        self._OUT_TIMING_000, # timing file
+                        self._OUT_POTENTIAL, self._SHAPEFUN  # make sure to retrieve potential and shapefun as well
+                        # add Jij files etc for other run options
+                        ] + [self._SHELLS_DAT] + [self._Jij_ATOM%iatom for iatom in range(1,natom+1)]
+                        )
         self._set_attr('retrieve_singlefile_list', [])
 
         # Make sure the calculation and input links are stored.

aiida_kkr/tools/common_workfunctions.py

@@ -577,11 +577,16 @@ def structure_from_params(parameters):
     """
     from aiida_kkr.tools.common_functions import get_aBohr2Ang
     from aiida.common.constants import elements as PeriodicTableElements
+    from aiida_kkr.tools.kkr_params import kkrparams
     from numpy import array
-    StructureData = DataFactory('structure')
 
-    is_complete = True 
+    #check input
+    if not isinstance(parameters, kkrparams):
+        raise InputValidationError('input parameters needs to be a "kkrparams" instance!') 
 
+    # initialize some stuff
+    StructureData = DataFactory('structure')
+    is_complete = True
     for icheck in ['<ZATOM>', '<RBASIS>', 'BRAVAIS', 'ALATBASIS']:
         if parameters.get_value(icheck) is None:
             is_complete = False
@@ -625,13 +630,22 @@ def structure_from_params(parameters):
     else:
         pos_all = pos_all * alat * get_aBohr2Ang() # now positions are in Ang. units
 
+    # extract atom numbers
     zatom_all = parameters.get_value('<ZATOM>')
+    # convert to list if input contains a single entry only
+    if type(zatom_all) != list:
+        zatom_all = [zatom_all]
+        pos_all = [pos_all]
+
+    #extract weights and sites for CPA calculations
     if natyp==naez:
         weights = [1. for i in range(natyp)]
         sites = range(1,natyp+1)
     else:
         weights = parameters.get_value('<CPA-CONC>')
         sites = parameters.get_value('<SITE>')
+
+    # fill structure from zatom, weights and sites information
     for isite in sites:
         pos = pos_all[sites.index(isite)]
         weight = weights[sites.index(isite)]

aiida_kkr/tools/kkr_params.py

@@ -16,7 +16,7 @@ def raw_input(msg):
 __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"
+__version__ = "0.6"
 __contributors__ = u"Philipp Rüßmann"
 
 # This defines the default parameters for KKR used in the aiida plugin:
@@ -425,7 +425,12 @@ def _create_keywords_dict(self, **kwargs):
                                 ('RUNOPT', [None, '%s%s%s%s%s%s%s%s', False, 'Running and test options: 8-character keywords in a row without spaces between them']),
                                 ('TESTOPT', [None, '%s%s%s%s%s%s%s%s\n%s%s%s%s%s%s%s%s', False, 'Running and test options: optional 8-character keywords in a row without spaces between them plus a secod row of the same.']),
                                 #file names
-                                ('FILES', [None, '%s', False, 'Name of potential and shapefun file (list of two strings, empty string will set back to default of the one file that is supposed to be changed)'])
+                                ('FILES', [None, '%s', False, 'Name of potential and shapefun file (list of two strings, empty string will set back to default of the one file that is supposed to be changed)']),
+                                # special options
+                                ('JIJRAD', [None, '%f', False, 'Radius in alat which defines the cutoff for calcultion of Jij pairs']),
+                                ('JIJRADXY', [None, '%f', False, 'use a cylindical cluster in which Jij pairs are searched for']),
+                                ('JIJSITEI', [None, '%i', False, 'allow for the selection of specific sites in i in the unit cell, which should be considered in the calculation (default: all sites)']),
+                                ('JIJSITEJ', [None, '%i', False, 'allow for the selection of specific sites in j in the unit cell, which should be considered in the calculation (default: all sites)'])
                                 ])
 
         for key in kwargs:

setup.json

@@ -14,7 +14,7 @@
         "Topic :: Scientific/Engineering :: Physics",
         "Natural Language :: English"      
     ],
-    "version": "0.1.0",
+    "version": "0.1.2",
     "setup_requires": ["reentry"],
     "reentry_register": true,
     "install_requires": [