Merge branch 'develop' into master

.github/workflows/ci.yml

@@ -74,7 +74,18 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.6, 3.7, 3.8, 3.9]
+        python-version: [3.7, 3.8, 3.9]
+        aiida-version: ['aiida-core']
+        aiida-name: ['stable']
+        allowed-to-fail: [false]
+        include:
+          - python-version: 3.8
+            aiida-version: 'git+https://github.com/aiidateam/aiida-core.git@develop'
+            aiida-name: 'develop'
+            allowed-to-fail: true
+
+    name: tests-python-${{ matrix.python-version }}-${{ matrix.aiida-name }}
+    continue-on-error: ${{ matrix.allowed-to-fail }}
 
     services:
       postgres:
@@ -98,9 +109,9 @@ jobs:
       uses: actions/cache@v1
       with:
         path: ~/.cache/pip
-        key: pip-${{ matrix.python-version }}-tests-${{ hashFiles('**/setup.json') }}
+        key: pip-${{ matrix.python-version }}-${{ matrix.aiida-name }}-tests-${{ hashFiles('**/setup.json') }}
         restore-keys: |
-          pip-${{ matrix.python-version }}-tests
+          pip-${{ matrix.python-version }}-${{ matrix.aiida-name }}-tests
 
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v2
@@ -115,7 +126,8 @@ jobs:
     - name: Install python dependencies
       run: |
         pip install --upgrade wheel setuptools
-        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 ${{ matrix.aiida-version }}
         pip install .[testing]
         reentry scan
 

.pylintrc

@@ -86,6 +86,7 @@ disable=too-few-public-methods,
     too-many-lines, # FIXME ?
     too-many-return-statements, # FIXME ?
     too-many-arguments, # FIXME
+    unspecified-encoding, # FIXME ?
     pointless-string-statement # Because of multi line comments, or outcommented code
 
 # Enable the message, report, category or checker with the given id(s). You can

.zenodo.json

@@ -0,0 +1,88 @@
+{
+    "upload_type": "software",
+    "language": "eng", 
+    "title": "JuDFTteam/aiida-fleur: AiiDA-FLEUR release v1.3.0", 
+    "license": {
+      "id": "MIT"
+    }, 
+    "access_right": "open", 
+    "communities": [
+      {
+        "id": "compmatsci"
+      }
+    ], 
+    "grants": [
+      {
+        "id": "824143" 
+      }, 
+      {
+        "id": "676598" 
+      }
+    ], 
+    "keywords": [
+      "physics", 
+      "materials-science", 
+      "electronic-structure", 
+      "python", 
+      "scientific-computing",
+      "workflow",
+      "DFT",
+      "aiida-framework",
+      "aiida-plugin",
+      "max-repo",
+      "FLEUR",
+      "FLAPW",
+      "JLVMD",
+      "JuDFT"
+    ], 
+    "creators": [
+      {
+        "orcid": "0000-0001-7939-226X", 
+        "affiliation": "Forschungszentrum J\u00fclich GmbH", 
+        "name": "Jens Br\u00f6der"
+      },
+      {
+        "orcid": "0000-0001-9130-0049", 
+        "affiliation": "Forschungszentrum J\u00fclich GmbH", 
+        "name": "Vasily Tseplyaev"
+      }, 
+      {
+        "orcid": "0000-0003-3558-9487", 
+        "affiliation": "Forschungszentrum J\u00fclich GmbH", 
+        "name": "Henning Janssen"
+      }, 
+      {
+        "orcid": "0000-0001-9078-0132", 
+        "affiliation": "Forschungszentrum J\u00fclich GmbH", 
+        "name": "Anoop Chandran"
+      }, 
+
+      {
+        "orcid": "0000-0002-2248-1904", 
+        "affiliation": "Forschungszentrum J\u00fclich GmbH", 
+        "name": "Daniel Wortmann"
+      }, 
+      {
+        "orcid": "0000-0001-9987-4733", 
+        "affiliation": "Forschungszentrum J\u00fclich GmbH", 
+        "name": "Stefan Bl\u00fcgel"
+      }
+    ], 
+    "subjects": [
+      {
+        "term": "electronic structure", 
+        "scheme": "url", 
+        "identifier": "https://www.wikidata.org/wiki/Q5358432"
+      }, 
+      {
+        "term": "materials informatics", 
+        "scheme": "url", 
+        "identifier": "https://www.wikidata.org/wiki/Q6786605"
+      }
+    ], 
+    "resource_type": {
+      "type": "software", 
+      "title": "Software" 
+    }, 
+    "description": "<p><strong> This software contains a plugin that enables the usage of the all-electron DFT FLEUR program with the AiiDA framework.</strong></p>\n\n<p>Feel free to contribute.</p>\n\nThe code is hosted on GitHub at: https://github.com/JuDFTteam/aiida-fleur</p>\n\n<p>The documentation is hosted on https://aiida-fleur.readthedocs.io.</p>\n\n<p>Most functionality and workflows was developed for the use with the DFT program FLEUR developed at the Forschungszentrum J&uuml;lich (see http://judft.de, https://flapw.de for further information on the codes) and in the context of the AiiDA framework (https://aiida.net).</p>\n\n<p><strong>Installation</strong></p>\n\n<blockquote>\n<p><br>\npip install aiida-core<br>\n&nbsp;</p>\n</blockquote>\n\n<p><strong>Dependencies</strong></p>\n\n<p>These python packages are needed:</p>\n\n<ul>\n\t<li>`aiida-core[atomic_tools]`</li>\n\t<li>`masci-tools`</li>\n\t<li>`lxml`</li>\n\t<li>`pyhull` &nbsp;</li>\n\t<li>`sympy`</li>\n\t<li>`numpy`</li>\n\t<li>`future`</li>\n\t<li>`pyhull`</li>\n\t<li>`sqlalchemy<1.4`</li>\n</ul>\n\n<p><strong>Layout of aiida-fleur</strong></p>\n\n<ul>\n\t<li>&nbsp;`calculation`: Contains AiiDA job calculation plugins for the inpgen code and the FLEUR code.\n\t<ul>\n\t<li>`cmdline`: Contains files for the commandline interface.</li>\n\t</ul>\n\t</li>\n\t<li>`tests`: auto tests of `aiida-fleur` functions</li>\n\t<li>`common`: Contains base classes and constants which are used throughout the package.</li>\n\t<li>`data`: Contains AiiDA data plugins specific to FLEUR.</li>\n\t<li>`parsers`: Contains parser AiiDA plugins for the job calculation plugins.</li>\n\t<li>`tools`: Contains basic utility and high level utility which is rather complete</li>\n\t<li>`workflows`: Contains a collection of AiiDA workchains (workflows) specific to FLEUR which have HPC and HTC capabilties with full provenance tracking. </li>\n</ul>\n\n<p><strong>License</strong>:<br>\naiida-fleur is distributed under the terms and conditions of the MIT license which is specified in the `LICENSE` file.</p>"
+}

CHANGELOG.md

@@ -1,9 +1,16 @@
+## v.1.2.1
+### release compatible with AiiDA-core 1.3.0+
+- General improvements for CreateMagnetic workchain and related methods
+- Added OrbControl workchain
+- FleurBandDosWorkchain provides AiiDA BandsData for bandstructure calculations and XyData for DOS calculations as outputs
+- General Improvements to plot_fleur function, e.g. can now visualize FleurBandDosWorkChain
+
 ## v.1.2.0
 ### release compatible with AiiDA-core 1.3.0+
 possibly ready for aiida-core 2.0.0
-- supports Fleur MaXR4 and MaXR5 versions with new inpgen 
+- supports Fleur MaXR4 and MaXR5 versions with new inpgen
 MaXR4 requires providing versions in the code nodes
-- Some features relying on the id in the inpgen files, 
+- Some features relying on the id in the inpgen files,
 may be broken by the new inpgen interface change when using MaXR5.1
 - Added support for GW calculations with Spex, and the Strain workchain
 - Major code refactoring, moving all xml tools to masci-tools (therefore requires masci-tools >=0.4.8)
@@ -28,7 +35,7 @@ may be broken by the new inpgen interface change when using MaXR5.1
 - Implemented feature in fleurinputCalculation to set significant figures
 - Implemented feature scf can now use default queues specified in code extras
 - First implementation of relax type None, which cases the relax workchain to skip the
-relaxation, becoming a usual scf wc,  which might make it easier to switch relaxation on 
+relaxation, becoming a usual scf wc,  which might make it easier to switch relaxation on
 and off in other workchains.
 - Fleur parser parses now the total magnetic moment of the cell
 - Introduced common constants, for bohr and htr, increased precision

aiida_fleur/__init__.py

@@ -12,4 +12,4 @@
 '''
 AiiDA-FLEUR
 '''
-__version__ = '1.2.0'
+__version__ = '1.2.1'

aiida_fleur/calculation/fleur.py

@@ -100,6 +100,9 @@ class FleurCalculation(CalcJob):
     _NMMPMAT_FILE_NAME = 'n_mmp_mat'
     _NMMPMAT_HDF5_FILE_NAME = 'n_mmp_mat_out'
 
+    #files for crystal field calculations
+    _CFDATA_HDF5_FILE_NAME = 'CFdata.hdf'
+
     #files for greensfunctions
     _GREENSF_HDF5_FILE_NAME = 'greensf.hdf'
 
@@ -415,7 +418,12 @@ def prepare_for_submission(self, folder):
             if modes['greensf']:
                 if with_hdf5:
                     mode_retrieved_filelist.append(self._GREENSF_HDF5_FILE_NAME)
-            if modes['force_theorem']:
+            if modes['cf_coeff']:
+                if with_hdf5:
+                    mode_retrieved_filelist.append(self._CFDATA_HDF5_FILE_NAME)
+                else:
+                    self.logger.warning('CF calculation without HDF5 not supported ' 'for automatic file retrieval.')
+            if modes['force_theorem'] or modes['cf_coeff']:
                 if 'remove_from_retrieve_list' not in settings_dict:
                     settings_dict['remove_from_retrieve_list'] = []
                 if with_hdf5:
@@ -439,7 +447,7 @@ def prepare_for_submission(self, folder):
                 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. '
+                        self.logger.warning('Ignoring 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'))
@@ -475,14 +483,7 @@ def prepare_for_submission(self, folder):
             # TODO: not on same computer -> copy needed files from repository
             # if they are not there throw an error
             if copy_remotely:  # on same computer.
-                # from fleurmodes
-                if modes['dos']:
-                    pass
-                elif modes['band']:
-                    pass
-                else:
-                    filelist_tocopy_remote = filelist_tocopy_remote + \
-                        self._copy_filelist_scf_remote
+                filelist_tocopy_remote = filelist_tocopy_remote + self._copy_filelist_scf_remote
                 # from settings, user specified
                 # TODO: check if list?
                 for file1 in settings_dict.get('additional_remotecopy_list', []):
@@ -500,7 +501,7 @@ def prepare_for_submission(self, folder):
                 self.logger.info('remote copy file list %s', str(remote_copy_list))
 
         # create a JUDFT_WARN_ONLY file in the calculation folder
-        with io.StringIO(u'/n') as handle:
+        with io.StringIO('/n') as handle:
             warn_only_filename = self._JUDFT_WARN_ONLY_INFO_FILE_NAME
             folder.create_file_from_filelike(handle, filename=warn_only_filename, mode='w')
 
@@ -584,7 +585,7 @@ def prepare_for_submission(self, folder):
         # + ["<", self._INPXML_FILE_NAME,
         # ">", self._SHELLOUTPUT_FILE_NAME, "2>&1"]
         codeinfo.code_uuid = code.uuid
-        codeinfo.withmpi = self.node.get_attribute('max_wallclock_seconds')
+        codeinfo.withmpi = self.node.get_attribute('withmpi')
         codeinfo.stdin_name = None  # self._INPUT_FILE_NAME
         codeinfo.stdout_name = self._SHELLOUTPUT_FILE_NAME
         #codeinfo.join_files = True