Merge branch 'develop'

.gitignore

@@ -1,5 +1,6 @@
 # Byte-compiled / optimized / DLL files
 __pycache__/
+.pytest_cache/
 *.py[cod]
 *$py.class
 
@@ -105,3 +106,10 @@ ENV/
 
 # mypy
 .mypy_cache/
+
+# mac stuff
+.DS_Store
+**/.DS_Store
+.AppleDouble
+.LSOverride
+

.travis.yml

@@ -10,6 +10,7 @@ notifications:
 
 services:
     - postgresql
+    - rabbitmq
 
 addons:
     postgresql: "9.5"
@@ -20,18 +21,24 @@ before_install:  # copied from pgtest's travis.yml
     - sudo apt-get install locate
     - sudo service postgresql stop
     - sudo apt-get remove postgresql
-    - sudo apt-get install postgresql
+    - sudo apt-get install postgresql-9.5
     - sudo updatedb
 
 install:
     - pip install -U pip wheel setuptools
     - pip install -e git+https://github.com/aiidateam/aiida_core@develop#egg=aiida-core[testing]
+    - pip install -e git+https://github.com/JuDFTteam/masci-tools@master#egg=masci-tools
     - pip install -e .
+    - pip install codecov
 
 env:
     - TEST_TYPE="unittests"
 
-script: cd ./aiida_kkr/tests/ && ./run_all.sh
+script: 
+    - cd ./aiida_kkr/tests/ && ./run_all.sh
+
+after_success:
+    - codecov
 
 git:
   depth: 3

README.md

@@ -1,12 +1,29 @@
+[![Documentation Status](https://readthedocs.org/projects/aiida-kkr/badge/?version=latest)](https://aiida-kkr.readthedocs.io/en/latest/?badge=latest)
+[![Build Status](https://travis-ci.org/JuDFTteam/aiida-kkr.svg?branch=master)](https://travis-ci.org/JuDFTteam/aiida-kkr)
+[![codecov](https://codecov.io/gh/JuDFTteam/aiida-kkr/branch/master/graph/badge.svg)](https://codecov.io/gh/JuDFTteam/aiida-kkr)
+[![MIT license](http://img.shields.io/badge/license-MIT-brightgreen.svg)](http://opensource.org/licenses/MIT)
+[![GitHub version](https://badge.fury.io/gh/JuDFTteam%2Faiida-kkr.svg)](https://badge.fury.io/gh/JuDFTteam%2Faiida-kkr)
+[![PyPI version](https://badge.fury.io/py/aiida-kkr.svg)](https://badge.fury.io/py/aiida-kkr)
+
+
 # aiida-kkr
 
 AiiDA plugin for the KKR codes plus workflows and utility.
 
+## Features
+
+* KKR calculations for bulk and interfaces
+* treatment of alloys using VCA or CPA
+* self-consistency, DOS and bandstructure calculations
+* extraction of magnetic exchange coupling parameters (*J_ij*, *D_ij*)
+* impurity embedding solving the Dyson equation
+* ~~import old calculations using the calculation importer~~ (only working with aiida-core<1.0, i.e. in aiida-kkr v0.1.2)
+
 
 # Installation
 
 ```shell
-$ git clone https://github.com/broeder-j/aiida-kkr
+$ git clone https://github.com/JuDFTteam/aiida-kkr
 
 $ cd aiida-kkr
 $ pip install -e .  # also installs aiida, if missing (but not postgres)

aiida_kkr/__init__.py

@@ -3,4 +3,4 @@
 
 """
 
-__version__ = "0.1.0"
+__version__ = "1.0.0"

aiida_kkr/calculations/kkr.py

@@ -16,9 +16,9 @@
 from aiida_kkr.tools.common_workfunctions import (generate_inputcard_from_structure,
                                                   check_2Dinput_consistency, update_params_wf,
                                                   vca_check)
-from aiida_kkr.tools.common_functions import get_alat_from_bravais, get_Ang2aBohr
+from masci_tools.io.common_functions import get_alat_from_bravais, get_Ang2aBohr
 from aiida_kkr.tools.tools_kkrimp import make_scoef 
-from aiida_kkr.tools.kkr_params import __kkr_default_params__
+from masci_tools.io.kkr_params import __kkr_default_params__
 
 #define aiida structures from DataFactory of aiida
 RemoteData = DataFactory('remote')

aiida_kkr/calculations/kkrimp.py

@@ -8,11 +8,11 @@
 from aiida.common.exceptions import (InputValidationError, ValidationError, UniquenessError)
 from aiida.common.datastructures import (CalcInfo, CodeInfo)
 from aiida.orm import DataFactory
-from aiida_kkr.tools.kkr_params import kkrparams
+from masci_tools.io.kkr_params import kkrparams
 from aiida_kkr.calculations.kkr import KkrCalculation
 from aiida_kkr.tools.tools_kkrimp import modify_potential
 from aiida_kkr.tools.tools_kkrimp import make_scoef
-from aiida_kkr.tools.common_functions import search_string
+from masci_tools.io.common_functions import search_string
 from aiida_kkr.calculations.voro import VoronoiCalculation
 import os
 from numpy import array, sqrt, sum, where
@@ -109,28 +109,38 @@ def _use_methods(cls):
                 'additional_parameter': None,
                 'linkname': 'parameters',
                 'docstring':
-                ("Use a node that specifies the input parameters (calculation settings)")
+                ("Use a node that specifies the input parameters (calculation settings).")
                 },
             "host_Greenfunction_folder": {
                 'valid_types': RemoteData,
                 'additional_parameter': None,
                 'linkname': 'GFhost_folder',
                 'docstring':
-                ("Use a node that specifies the host KKR calculation contaning the host Green function and tmatrix (KkrCalculation with impurity_info input)")
+                ("Use a node that specifies the host KKR calculation contaning "
+                 "the host Green function and tmatrix (KkrCalculation with "
+                 "impurity_info input).")
                 },
             "impurity_potential": {
                 'valid_types': SinglefileData,
                 'additional_parameter': None,
                 'linkname': 'potential',
                 'docstring':
-                ("Use a node contains the input potential")
+                ("Use a node contains the input potential.")
                 },
             "parent_calc_folder": {
                 'valid_types': RemoteData,
                 'additional_parameter': None,
                 'linkname': 'parent_calc_folder',
                 'docstring':
-                ("Use a node that specifies a parent KKRimp calculation")
+                ("Use a node that specifies a parent KKRimp calculation.")
+                },
+            "impurity_info": {
+                'valid_types': ParameterData,
+                'additional_parameter': None,
+                'linkname': 'impurity_info',
+                'docstring':
+                ("Use a Parameter node that specifies properties "
+                 "for a impurity calculation.")
                 }
             })
         return use_dict
@@ -210,6 +220,28 @@ def _prepare_for_submission(self, tempfolder, inputdict):
                     retrieve_list.append((self._OUT_LDOS_INTERPOL_BASE%(iatom, ispin)).replace(' ', '0'))
                     retrieve_list.append((self._OUT_LMDOS_BASE%(iatom, ispin)).replace(' ', '0'))
                     retrieve_list.append((self._OUT_LMDOS_INTERPOL_BASE%(iatom, ispin)).replace(' ', '0'))
+
+        file = open(tempfolder.get_abs_path(self._CONFIG))
+        config = file.readlines()
+        file.close()
+        itmp = search_string('NSPIN', config)
+        if itmp>=0:
+            nspin = int(config[itmp].split()[-1])
+        else:
+            raise ValueError("Could not extract NSPIN value from config.cfg")
+        if 'tmatnew' in allopts and nspin>1:
+            retrieve_list.append(self._OUT_MAGNETICMOMENTS) 
+            file = open(tempfolder.get_abs_path(self._CONFIG))
+            outorb = file.readlines()
+            file.close()
+            itmp = search_string('CALCORBITALMOMENT', outorb)
+            if itmp>=0:
+                calcorb = int(outorb[itmp].split()[-1])
+            else:
+                calcorb = 0
+            if calcorb==1:
+                retrieve_list.append(self._OUT_ORBITALMOMENTS)
+
 
         # Prepare CalcInfo to be returned to aiida (e.g. retreive_list etc.)
         calcinfo = CalcInfo()
@@ -267,10 +299,51 @@ def _get_and_verify_hostfiles(self, inputdict):
             parent_calc = parent_calcs[0]
 
         # extract impurity_info
-        imp_info = parent_calc.get_inputs_dict().get('impurity_info', None)
-        if imp_info is None:
-            raise InputValidationError("host_Greenfunction calculation does not have an input node impurity_info")
-
+        try:
+            imp_info_inputnode = inputdict.pop(self.get_linkname('impurity_info'))
+            if not isinstance(imp_info_inputnode, ParameterData):
+                raise InputValidationError("impurity_info not of type ParameterData")
+            imp_info = parent_calc.get_inputs_dict().get('impurity_info', None)
+            if imp_info is None:
+                raise InputValidationError("host_Greenfunction calculation does not have an input node impurity_info")
+            found_impurity_inputnode = True
+            found_impurity_parent = True
+        except KeyError:
+            imp_info = parent_calc.get_inputs_dict().get('impurity_info', None)
+            if imp_info is None:
+                raise InputValidationError("host_Greenfunction calculation does not have an input node impurity_info")
+            found_impurity_inputnode = False
+        # if impurity input is seperate input, check if it is the same as 
+        # the one from the parent calc (except for 'Zimp'). If that's not the 
+        # case, raise an error
+        if found_impurity_inputnode and found_impurity_parent:
+            if (imp_info_inputnode.get_attr('ilayer_center') == imp_info.get_attr('ilayer_center')
+                and imp_info_inputnode.get_attr('Rcut') == imp_info.get_attr('Rcut')):
+                check_consistency_imp_info = True
+                try:
+                    if (imp_info_inputnode.get_attr('hcut') == imp_info.get_attr('hcut')
+                        and imp_info_inputnode.get_attr('cylinder_orient') == imp_info.get_attr('cylinder_orient')
+                        and imp_info_inputnode.get_attr('Rimp_rel') == imp_info.get_attr('Rimp_rel')
+                        and imp_info_inputnode.get_attr('imp_cls') == imp_info.get_attr('imp_cls')):
+                        print('impurity_info node from input and from previous GF calculation are compatible')
+                        check_consistency_imp_info = True
+                    else:
+                        print('impurity_info node from input and from previous GF calculation are NOT compatible!. ' 
+                              'Please check your impurity_info nodes for consistency.')
+                        check_consistency_imp_info = False
+                except AttributeError:
+                    print("Non default values of the impurity_info node from input and from previous "
+                          "GF calculation are compatible. Default values haven't been checked")
+                    check_consistency_imp_info = True
+            else:
+                print('impurity_info node from input and from previous GF calculation are NOT compatible!. ' 
+                      'Please check your impurity_info nodes for consistency.')
+                check_consistency_imp_info = False           
+            if check_consistency_imp_info:
+                imp_info = imp_info_inputnode
+            else:
+                raise InputValidationError("impurity_info nodes (input and GF calc) are not compatible") 
+
         # check if host parent was KKRFLEX calculation
         hostfolderpath = parent_calc.out.retrieved.folder.abspath
         hostfolderpath = os.path.join(hostfolderpath, 'path')

aiida_kkr/calculations/kkrimporter.py

@@ -12,7 +12,7 @@
 from aiida.common.datastructures import calc_states
 from aiida.common.links import LinkType
 from aiida_kkr.calculations.kkr import KkrCalculation
-from aiida_kkr.tools.kkr_params import kkrparams
+from masci_tools.io.kkr_params import kkrparams
 from aiida_kkr.tools.common_workfunctions import structure_from_params
 
 
@@ -474,4 +474,4 @@ def _OUTPUT_FILE_NAMES(self):
     @_OUTPUT_FILE_NAMES.setter
     def _OUTPUT_FILE_NAMES(self, value):
         self._set_attr('output_file_names', value)
-
+

aiida_kkr/parsers/kkr.py

@@ -9,8 +9,8 @@
 from aiida.orm.data.parameter import ParameterData
 from aiida_kkr.calculations.kkr import KkrCalculation
 from aiida.common.exceptions import InputValidationError
-from aiida_kkr.tools.kkrparser_functions import parse_kkr_outputfile, check_error_category
-from aiida_kkr.tools.common_functions import search_string
+from masci_tools.io.parsers.kkrparser_functions import parse_kkr_outputfile, check_error_category
+from masci_tools.io.common_functions import search_string
 
 __copyright__ = (u"Copyright (c), 2017, Forschungszentrum Jülich GmbH, "
                  "IAS-1/PGI-1, Germany. All rights reserved.")

aiida_kkr/parsers/kkrimp.py

@@ -9,7 +9,7 @@
 from aiida.orm.data.parameter import ParameterData
 from aiida_kkr.calculations.kkrimp import KkrimpCalculation
 from aiida.common.exceptions import InputValidationError
-from aiida_kkr.tools.kkrparser_functions import check_error_category
+from masci_tools.io.parsers.kkrparser_functions import check_error_category
 from aiida_kkr.tools.tools_kkrimp import kkrimp_parser_functions
 
 
@@ -129,7 +129,7 @@ def parse_with_retrieved(self, retrieved):
             filepath = out_folder.get_abs_path(fname)
             files['kkrflex_llyfac'] = filepath
         except OSError:
-            file_errors.append((2, "Critical error! file '{}' not found ".format(fname)))
+            file_errors.append((2, "Warning! file '{}' not found ".format(fname)))
             files['kkrflex_llyfac'] = None
         try:
             fname = self._calc._KKRFLEX_ANGLE

aiida_kkr/parsers/voro.py

@@ -4,7 +4,7 @@
 from aiida.orm.data.parameter import ParameterData
 from aiida_kkr.calculations.voro import VoronoiCalculation
 from aiida.common.exceptions import InputValidationError
-from aiida_kkr.tools.voroparser_functions import parse_voronoi_output
+from masci_tools.io.parsers.voroparser_functions import parse_voronoi_output
 
 
 
@@ -125,4 +125,4 @@ def parse_with_retrieved(self, retrieved):
 
         return success, node_list
 
-
+

aiida_kkr/tests/codecov.yml

@@ -0,0 +1,27 @@
+codecov:
+  notify:
+    require_ci_to_pass: yes
+
+coverage:
+  precision: 2
+  round: down
+  range: "0...100"
+
+  status:
+    project: yes
+    patch: yes
+    changes: no
+
+parsers:
+  gcov:
+    branch_detection:
+      conditional: yes
+      loop: yes
+      method: no
+      macro: no
+
+comment:
+  layout: "header, diff"
+  behavior: default
+  require_changes: no
+

aiida_kkr/tests/config.yml

@@ -8,8 +8,13 @@ computers:
     queue_name: test_queue_name
 
 codes:
-  tinpgen:
-    description: test inpgen code object
-    default_plugin: fleur.inpgen
+  voronoi:
+    description: test voronoi calculation
+    default_plugin: kkr.voro
     remote_computer: localhost
-    remote_abspath: /Users/broeder/codes/fleur_git_v27/fleur/build/inpgen
+    remote_abspath: /Users/ruess/sourcecodes/voronoi/voronoi.exe
+  kkr:
+    description: test KKRhost calculation
+    default_plugin: kkr.kkr
+    remote_computer: localhost
+    remote_abspath: /Users/ruess/sourcecodes/KKRcode/kkr.x