Merge pull request #98 from JuDFTteam/develop

Merge develop into master for release v1.1.2

.ci/test_script.sh

@@ -18,5 +18,5 @@ case "$TEST_TYPE" in
     unittests)
         # make sure we have the correct pg_ctl in our path for pgtest, to prevent issue #1722
         # this must match the version request in travis.yml
-       cd ./aiida_fleur/tests/ && ./run_all_cov.sh
+       cd ./tests/ && ./run_all_cov.sh
 esac

.github/workflows/ci.yml

@@ -59,7 +59,8 @@ jobs:
 
     - name: Install python dependencies
       run:
-        pip install .[pre-commit]
+        pip install git+https://github.com/aiidateam/aiida-testing@export_cache
+        pip install .[pre-commit,testing]
         pip freeze
 
     - name: Run pre-commit
@@ -108,14 +109,14 @@ jobs:
         pip install PyCifRW~=4.4
         # install aiida-testing manually
         #pip install git+https://github.com/broeder-j/aiida-testing.git@fa44c3ba4e57192fdbdee1cf3581576acc93800c
-        #pip install git+https://github.com/aiidateam/aiida-testing.git@export_cache
+        pip install git+https://github.com/aiidateam/aiida-testing.git@export_cache
         pip install .[testing]
         reentry scan
 
     - name: Run pytest
       run: |
        # create fake codes for tests to work on ci
-       cd ./aiida_fleur/tests/
+       cd ./tests/
        touch local_exe/inpgen && chmod +x local_exe/inpgen
        touch local_exe/fleur && chmod +x local_exe/fleur 
        ./run_all_cov.sh

.travis.yml

@@ -28,7 +28,7 @@ cache: pip
 #  - sudo updatedb
 
 install:
-  - pip install -U pip==18.1 wheel setuptools
+  - pip install -U pip wheel setuptools
   - pip install -e git+https://github.com/aiidateam/aiida_core@develop#egg=aiida-core[testing,docs]
   - if [ "$TEST_TYPE" == "docs" ]; then pip install . && pip install -r docs/requirements_for_rtd.txt; else pip install .; fi
 env:

AUTHORS.txt

@@ -2,7 +2,8 @@ Current active developers:
 
 Jens Broeder ([email protected]) 2015-today
 Vasily Tseplyaev ([email protected]) 2018-today
-
+Anoop Chandran ([email protected]) 2019-today
+Henning Janssen ([email protected])  2020-today
 
 We would also like to thank the following people for their contibution:
 
@@ -12,4 +13,4 @@ We ackowledge discussions (non-code related) input from:
 
 Daniel Wortmann ([email protected])
 Gregor Michalicek ([email protected])
-The AiiDAteam
+The AiiDAteam and other aiida plugin developers

CHANGELOG.md

@@ -1,3 +1,16 @@
+
+## v1.1.2
+### release compatible with AiiDA-core 1.3.0
+- still support of Fleur MaX4 version (release branch) with inpgen
+- downdgraded aiida-core dependency, do release does not depend on aiida-testing
+- Added userfriendly LDA+U support
+- SCF workchain can generate kpoints from a given density
+- Base fleur has now time limit error handler
+- Relax workchain can now run a final scf
+- Update documentation for corehole, initial CLS and create magnetic workchains
+- Various bug fixes and robustness improvements of magnetic workchains
+- For devs: Enforced pre-commit, tests dir moved out of source
+
 ## v1.1.1
 ### release compatible with AiiDA-core 1.4.0
 - still support of Fleur MaX4 version (release branch) with inpgen

MANIFEST.in

@@ -1,8 +1,8 @@
 
 include aiida_fleur/tools/exp_bindingenergies.json
 include aiida_fleur/fleur_schema/input/*/*.xsd
-include aiida_fleur/tests/run*
-recursive-include aiida_fleur/tests/files/ *
+include ./tests/run*
+recursive-include ./tests/files/ *
 include setup.json
 include setup_requirements.txt
 include AUTHORS.txt

aiida_fleur/__init__.py

@@ -12,4 +12,4 @@
 '''
 AiiDA-FLEUR
 '''
-__version__ = '1.1.1'
+__version__ = '1.1.2'

aiida_fleur/calculation/fleur.py

@@ -97,6 +97,7 @@ class FleurCalculation(CalcJob):
 
     # files for lda+U
     _NMMPMAT_FILE_NAME = 'n_mmp_mat'
+    _NMMPMAT_HDF5_FILE_NAME = 'n_mmp_mat_out'
 
     # files for hybrid functionals
     _COULOMB1_FILE_NAME = 'coulomb1'
@@ -169,6 +170,11 @@ class FleurCalculation(CalcJob):
         _WKF2_FILE_NAME, _MIX_HISTORY_FILE_NAME, _OUT_FILE_NAME, _POT_FILE_NAME
     ]
 
+    _copy_scf_ldau_nohdf = [[_CDN1_FILE_NAME, _CDN1_FILE_NAME], [_INPXML_FILE_NAME, _INPXML_FILE_NAME],
+                            [_NMMPMAT_FILE_NAME, _NMMPMAT_FILE_NAME]]
+
+    _copy_scf_ldau_noinp_nohdf = [[_CDN1_FILE_NAME, _CDN1_FILE_NAME], [_NMMPMAT_FILE_NAME, _NMMPMAT_FILE_NAME]]
+
     # files need for rerun
     _copy_filelist_dos = [_INPXML_FILE_NAME, _CDN1_FILE_NAME]
 
@@ -183,7 +189,7 @@ class FleurCalculation(CalcJob):
         'remove_from_remotecopy_list', 'cmdline'
     ]
     # possible modes?
-    _fleur_modes = ['band', 'dos', 'forces', 'chargeDen', 'latticeCo', 'scf', 'force_theorem', 'gw']
+    _fleur_modes = ['band', 'dos', 'forces', 'chargeDen', 'latticeCo', 'scf', 'force_theorem', 'gw', 'ldau']
 
     @classmethod
     def define(cls, spec):
@@ -242,9 +248,13 @@ def define(cls, spec):
         spec.exit_code(312, 'ERROR_MT_RADII', message='FLEUR calculation failed due to MT overlap.')
         spec.exit_code(313, 'ERROR_MT_RADII_RELAX', message='Overlapping MT-spheres during relaxation.')
         spec.exit_code(314, 'ERROR_DROP_CDN', message='Problem with cdn is suspected. Consider removing cdn')
+        spec.exit_code(315,
+                       'ERROR_INVALID_ELEMENTS_MMPMAT',
+                       message='The LDA+U density matrix contains invalid elements.')
+        spec.exit_code(316, 'ERROR_TIME_LIMIT', message='Calculation failed due to time limits.')
 
     @classproperty
-    def _get_outut_folder(self):
+    def _get_output_folder(self):
         return './'
 
     def prepare_for_submission(self, folder):
@@ -392,7 +402,10 @@ def prepare_for_submission(self, folder):
                 # if l_f="T" retrieve relax.xml
                 mode_retrieved_filelist.append(self._RELAX_FILE_NAME)
             if modes['ldau']:
-                mode_retrieved_filelist.append(self._NMMPMAT_FILE_NAME)
+                if with_hdf5:
+                    mode_retrieved_filelist.append(self._NMMPMAT_HDF5_FILE_NAME)
+                else:
+                    mode_retrieved_filelist.append(self._NMMPMAT_FILE_NAME)
             if modes['force_theorem']:
                 if 'remove_from_retrieve_list' not in settings_dict:
                     settings_dict['remove_from_retrieve_list'] = []
@@ -411,13 +424,26 @@ def prepare_for_submission(self, folder):
             outfolder_uuid = parent_calc.outputs.retrieved.uuid
             self.logger.info('out folder path %s', outfolder_uuid)
 
+            outfolder_filenames = [x.name for x in parent_calc.outputs.retrieved.list_objects()]
+            has_nmmpmat_file = self._NMMPMAT_FILE_NAME in outfolder_filenames
+            if (self._NMMPMAT_FILE_NAME in outfolder_filenames or \
+                self._NMMPMAT_HDF5_FILE_NAME in outfolder_filenames):
+                if has_fleurinp:
+                    if 'n_mmp_mat' in fleurinp.files:
+                        self.logger.warning('Ingnoring n_mmp_mat from fleurinp. '
+                                            'There is already an n_mmp_mat file '
+                                            'for the parent calculation')
+                        local_copy_list.remove((fleurinp.uuid, 'n_mmp_mat', 'n_mmp_mat'))
+
             if fleurinpgen and (not has_fleurinp):
                 for file1 in self._copy_filelist_inpgen:
                     local_copy_list.append((outfolder_uuid, os.path.join(file1), os.path.join(file1)))
             elif not fleurinpgen and (not has_fleurinp):  # fleurCalc
                 # need to copy inp.xml from the parent calc
                 if with_hdf5:
                     copylist = self._copy_scf_hdf
+                elif has_nmmpmat_file:
+                    copylist = self._copy_scf_ldau_nohdf
                 else:
                     copylist = self._copy_scf
                 for file1 in copylist:
@@ -430,6 +456,8 @@ def prepare_for_submission(self, folder):
                 # inp.xml will be copied from fleurinp
                 if with_hdf5:
                     copylist = self._copy_scf_noinp_hdf
+                elif has_nmmpmat_file:
+                    copylist = self._copy_scf_ldau_noinp_nohdf
                 else:
                     copylist = self._copy_scf_noinp
                 for file1 in copylist:
@@ -458,7 +486,7 @@ def prepare_for_submission(self, folder):
                 for file1 in filelist_tocopy_remote:
                     remote_copy_list.append(
                         (parent_calc_folder.computer.uuid, os.path.join(parent_calc_folder.get_remote_path(),
-                                                                        file1), self._get_outut_folder))
+                                                                        file1), self._get_output_folder))
 
                 self.logger.info('remote copy file list %s', str(remote_copy_list))
 

aiida_fleur/calculation/fleurinputgen.py

@@ -37,7 +37,7 @@ class FleurinputgenCalculation(CalcJob):
     For more information about produced files and the FLEUR-code family, go to http://www.flapw.de/.
     """
 
-    __version__ = '1.2.0'
+    __version__ = '1.2.1'
 
     # Default input and output files
     _INPUT_FILE = 'aiida.in'  # will be shown with inputcat
@@ -161,7 +161,7 @@ def prepare_for_submission(self, folder):
         # convert these 'booleans' to the inpgen format.
         replacer_values_bool = [True, False, 'True', 'False', 't', 'T', 'F', 'f']
         # some keywords require a string " around them in the input file.
-        string_replace = ['econfig', 'lo', 'element', 'name']
+        string_replace = ['econfig', 'lo', 'element', 'name', 'xctyp']
 
         # of some keys only the values are written to the file, specify them here.
         val_only_namelist = ['soc', 'qss']
@@ -306,9 +306,8 @@ def prepare_for_submission(self, folder):
             cell = structure.cell
             for vector in cell:
                 scaled = [a * scaling_pos for a in vector]  # scaling_pos=1./bohr_to_ang
-                cell_parameters_card += ('{0:18.10f} {1:18.10f} {2:18.10f}'
-                                         '\n'.format(scaled[0], scaled[1], scaled[2]))
-            scaling_factor_card += ('{0:18.10f} {1:18.10f} {2:18.10f}'
+                cell_parameters_card += ('{0:18.9f} {1:18.9f} {2:18.9f}' '\n'.format(scaled[0], scaled[1], scaled[2]))
+            scaling_factor_card += ('{0:18.9f} {1:18.9f} {2:18.9f}'
                                     '\n'.format(scaling_factors[0], scaling_factors[1], scaling_factors[2]))
 
         #### ATOMIC_POSITIONS ####
@@ -350,13 +349,14 @@ def prepare_for_submission(self, folder):
                     vector_rel[2] = vector_rel[2] * scaling_pos
 
                 if site_symbol != kind_name:  # This is an important fact, if user renames it becomes a new specie!
-                    suc = True
                     try:
                         head = kind_name.rstrip('0123456789')
                         kind_namet = int(kind_name[len(head):])
+                        if int(kind_name[len(head)]) > 4:
+                            raise InputValidationError('New specie name/label should start with a digit smaller than 4')
                     except ValueError:
-                        suc = False
-                    if suc:
+                        pass
+                    else:
                         atomic_number_name = '{}.{}'.format(atomic_number, kind_namet)
                     # append a label to the detached atom
                     atomic_positions_card_listtmp.append('    {0:7} {1:18.10f} {2:18.10f} {3:18.10f} {4}'

aiida_fleur/common/workchain/base/restart.py

@@ -69,7 +69,10 @@ def load_instance_state(self, saved_state, load_context):
         self._load_error_handlers()
 
     def _load_error_handlers(self):
-        # If an error handler entry point is defined, load them. If the plugin cannot be loaded log it and pass
+        """
+        If an error handler entry point is defined, load them.
+        If the plugin cannot be loaded log it and pass
+        """
         if self._error_handler_entry_point is not None:
             for entry_point_name in get_entry_point_names(self._error_handler_entry_point):
                 try:

aiida_fleur/data/fleurinp.py

@@ -198,12 +198,11 @@ def open(self, path='inp.xml', mode='r', key=None):
         :param mode: the mode with which to open the file handle
         :returns: A file handle in read mode
          """
-        from aiida.orm.nodes.node import WarnWhenNotEntered  # deep import might change
 
         if key is not None:
             path = key
 
-        return WarnWhenNotEntered(self._repository.open(path, mode=mode), repr(self))
+        return self._repository.open(path, mode=mode)
 
     def get_content(self, filename='inp.xml'):
         """
@@ -530,8 +529,10 @@ def get_fleur_modes(self):
                 fleur_modes['gw'] = int(self.inp_dict['calculationSetup']['expertModes']['gw']) != 0
             except KeyError:
                 fleur_modes['gw'] = False
-            ldau = False  # TODO test if ldau in inp_dict....
             fleur_modes['ldau'] = False
+            for species in self.inp_dict['atomSpecies']['species']:
+                if 'ldaU' in species:
+                    fleur_modes['ldau'] = True
         return fleur_modes
 
     def get_structuredata_ncf(self):