Merge pull request #126 from JuDFTteam/develop

Merge develop into master for new release 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 MaXR4 requires providing versions in the code nodes - 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) - Also all file parsers are overworked and moved to masci-tools - Work over of the BanddosWorkChain. - FleurinpData now consistently supports more included xml files (kpts.xml, sym.xml, ...) - Added new modification functions to the FleurinpModifier for kpoint manipulation for Max5
JuDFTteam · Jun 7, 2021 · 652570a · 652570a
2 parents 8ef56cb + 37bae04
commit 652570a
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -11,10 +11,10 @@ jobs:
     steps:
     - uses: actions/checkout@v2
 
-    - name: Set up Python 3.7
+    - name: Set up Python 3.8
       uses: actions/setup-python@v2
       with:
-        python-version: 3.7
+        python-version: 3.8
 
     - name: Cache python dependencies
       id: cache-pip
@@ -26,13 +26,14 @@ jobs:
           pip-docs-
 
     - name: Install python dependencies
-      run:
+      run: |
         pip install -e .[docs]
+        reentry scan
 
     - name: Build documentation
       env:
         READTHEDOCS: 'True'
-      run:
+      run: |
         SPHINXOPTS='-nW' make -C docs html
 
   pre-commit:
@@ -63,7 +64,7 @@ jobs:
         pip freeze
 
     - name: Run pre-commit
-      run:
+      run: |
         pre-commit run --all-files || (git status --short; git diff ; exit 1)
 
   tests:

diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -0,0 +1,20 @@
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   builder: html
+   configuration: docs/source/conf.py
+
+# Optionally build your docs in additional formats such as PDF
+formats:
+   - pdf
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+   version: 3.8
+   install:
+     - requirements: docs/requirements_for_rtd.txt
+     - method: pip
+       path: .
+   system_packages: true
diff --git a/AUTHORS.txt b/AUTHORS.txt
@@ -5,7 +5,7 @@ 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:
+We would also like to thank the following people for their contribution:
 
 ...
 

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,7 +1,22 @@
+## 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 
+MaXR4 requires providing versions in the code nodes
+- 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)
+- Also all file parsers are overworked and moved to masci-tools
+- Work over of the BanddosWorkChain.
+- FleurinpData now consistently supports more included xml files (kpts.xml, sym.xml, ...)
+- Added new modification functions to the FleurinpModifier for kpoint manipulation for Max5
+
+
 ## v.1.1.4
 ### release compatible with AiiDA-core 1.3.0
-### still support of Fleur MaXR4 version with inpgen
-### Does not support yet Fleur MaXR5 and new inpgen
+- still support of Fleur MaXR4 version with inpgen
+- Does not support yet Fleur MaXR5 and new inpgen
 - Fixed numpy dependency issue with aiida-common-workflows and quantum mobile
 
 ## v1.1.3

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,8 +1,6 @@
 
 include aiida_fleur/tools/exp_bindingenergies.json
 include aiida_fleur/fleur_schema/input/*/*.xsd
-include ./tests/run*
-recursive-include ./tests/files/ *
 include setup.json
 include setup_requirements.txt
 include AUTHORS.txt

diff --git a/README.md b/README.md
@@ -21,11 +21,15 @@ Developed at [Forschungszentrum Jülich GmbH](http://www.fz-juelich.de/pgi/pgi-1
 | `v1.0.0 < v2.0.0` | <img class="svg-badge" title="Compatible with aiida-core >=1.3.0,<2.0.0" src="https://img.shields.io/badge/AiiDA->=1.3.0,<2.0.0-007ec6.svg?logo=data%3Aimage%2Fpng%3Bbase64%2CiVBORw0KGgoAAAANSUhEUgAAACMAAAAhCAYAAABTERJSAAAABHNCSVQICAgIfAhkiAAAAAlwSFlzAAAFhgAABYYBG6Yz4AAAABl0RVh0U29mdHdhcmUAd3d3Lmlua3NjYXBlLm9yZ5vuPBoAAAUbSURBVFiFzZhrbFRVEMd%2Fc%2B5uu6UUbIFC%2FUAUVEQCLbQJBIiBDyiImJiIhmohYNCkqJAQxASLF8tDgYRHBLXRhIcKNtFEhVDgAxBJqgmVh4JEKg3EIn2QYqBlt917xg%2BFss%2ByaDHOtzsz5z%2B%2FuZl7ztmF%2F5HJvxVQN6cPYX8%2FPLnOmsvNAvqfwuib%2FbNIk9cQeQnLcKRL5xLIV%2Fic9eJeunjPYbRs4FjQSpTB3aS1IpRKeeOOewajy%2FKKEO8Q0DuVdKy8IqsbPulxGHUfCBBu%2BwUYGuFuBTK7wQnht6PEbf4tlRomVRjCbXNjQEB0AyrFQOL5ENIJm7dTLZE6DPJCnEtFZVXDLny%2B4Sjv0PmmYu1ZdUek9RiMgoDmJ8V0L7XJqsZ3UW8YsBOwEeHeeFce7jEYXBy0m9m4BbXqSj2%2Bxnkg26MCVrN6DEZcwggtd8pTFx%2Fh3B9B50YLaFOPwXQKUt0tBLegtSomfBlfY13PwijbEnhztGzgJsK5h9W9qeWwBqjvyhB2iBs1Qz0AU974DciRGO8CVN8AJhAeMAdA3KbrKEtvxhsI%2B9emWiJlGBEU680Cfk%2BSsVqXZvcFYGXjF8ABVJ%2BTNfVXehyms1zzn1gmIOxLEB6E31%2FWBe5rnCarmo7elf7dJEeaLh80GasliI5F6Q9cAz1GY1OJVNDxTzQTw7iY%2FHEZRQY7xqJ9RU2LFe%2FYqakdP911ha0XhjjiTVAkDwgatWfCGeYocx8M3glG8g8EXhSrLrHnEFJ5Ymow%2FkhIYv6ttYUW1iFmEqqxdVoUs9FmsDYSqmtmJh3Cl1%2BVtl2s7owDUdocR5bceiyoSivGTT5vzpbzL1uoBpmcAAQgW7ArnKD9ng9rc%2BNgrobSNwpSkkhcRN%2BvmXLjIsDovYHHEfmsYFygPAnIDEQrQPzJYCOaLHLUfIt7Oq0LJn9fxkSgNCb1qEIQ5UKgT%2Fs6gJmVOOroJhQBXVqw118QtWLdyUxEP45sUpSzqP7RDdFYMyB9UReMiF1MzPwoUqHt8hjGFFeP5wZAbZ%2F0%2BcAtAAcji6LeSq%2FMYiAvSsdw3GtrfVSVFUBbIhwRWYR7yOcr%2FBi%2FB1MSJZ16JlgH1AGM3EO2QnmMyrSbTSiACgFBv4yCUapZkt9qwWVL7aeOyHvArJjm8%2Fz9BhdI4XcZgz2%2FvRALosjsk1ODOyMcJn9%2FYI6IrkS5vxMGdUwou2YKfyVqJpn5t9aNs3gbQMbdbkxnGdsr4bTHm2AxWo9yNZK4PXR3uzhAh%2BM0AZejnCrGdy0UvJxl0oMKgWSLR%2B1LH2aE9ViejiFs%2BXn6bTjng3MlIhJ1I1TkuLdg6OcAbD7Xx%2Bc3y9TrWAiSHqVkbZ2v9ilCo6s4AjwZCzFyD9mOL305nV9aonvsQeT2L0gVk4OwOJqXXVRW7naaxswDKVdlYLyMXAnntteYmws2xcVVZzq%2BtHPAooQggmJkc6TLSusOiL4RKgwzzYU1iFQgiUBA1H7E8yPau%2BZl9P7AblVNebtHqTgxLfRqrNvZWjsHZFuqMqKcDWdlFjF7UGvX8Jn24DyEAykJwNcdg0OvJ4p5pQ9tV6SMlP4A0PNh8aYze1ArROyUNTNouy8tNF3Rt0CSXb6bRFl4%2FIfQzNMjaE9WwpYOWQnOdEF%2BTdJNO0iFh7%2BI0kfORzQZb6P2kymS9oTxzBiM9rUqLWr1WE5G6ODhycQd%2FUnNVeMbcH68hYkGycNoUNWc8fxaxfwhDbHpfwM5oeTY7rUX8QAAAABJRU5ErkJggg%3D%3D"> |  [![PyPI pyversions](https://img.shields.io/pypi/pyversions/aiida-fleur.svg)](https://pypi.org/project/aiida-fleur.svg) | MaXR1 < MaXR5 (v0.29)|
 | `< v0.6.3` | <img class="svg-badge" title="Compatible with aiida-core >=0.12,<1.0.0" src="https://img.shields.io/badge/AiiDA->=0.12,<1.0.0-007ec6.svg?logo=data%3Aimage%2Fpng%3Bbase64%2CiVBORw0KGgoAAAANSUhEUgAAACMAAAAhCAYAAABTERJSAAAABHNCSVQICAgIfAhkiAAAAAlwSFlzAAAFhgAABYYBG6Yz4AAAABl0RVh0U29mdHdhcmUAd3d3Lmlua3NjYXBlLm9yZ5vuPBoAAAUbSURBVFiFzZhrbFRVEMd%2Fc%2B5uu6UUbIFC%2FUAUVEQCLbQJBIiBDyiImJiIhmohYNCkqJAQxASLF8tDgYRHBLXRhIcKNtFEhVDgAxBJqgmVh4JEKg3EIn2QYqBlt917xg%2BFss%2ByaDHOtzsz5z%2B%2FuZl7ztmF%2F5HJvxVQN6cPYX8%2FPLnOmsvNAvqfwuib%2FbNIk9cQeQnLcKRL5xLIV%2Fic9eJeunjPYbRs4FjQSpTB3aS1IpRKeeOOewajy%2FKKEO8Q0DuVdKy8IqsbPulxGHUfCBBu%2BwUYGuFuBTK7wQnht6PEbf4tlRomVRjCbXNjQEB0AyrFQOL5ENIJm7dTLZE6DPJCnEtFZVXDLny%2B4Sjv0PmmYu1ZdUek9RiMgoDmJ8V0L7XJqsZ3UW8YsBOwEeHeeFce7jEYXBy0m9m4BbXqSj2%2Bxnkg26MCVrN6DEZcwggtd8pTFx%2Fh3B9B50YLaFOPwXQKUt0tBLegtSomfBlfY13PwijbEnhztGzgJsK5h9W9qeWwBqjvyhB2iBs1Qz0AU974DciRGO8CVN8AJhAeMAdA3KbrKEtvxhsI%2B9emWiJlGBEU680Cfk%2BSsVqXZvcFYGXjF8ABVJ%2BTNfVXehyms1zzn1gmIOxLEB6E31%2FWBe5rnCarmo7elf7dJEeaLh80GasliI5F6Q9cAz1GY1OJVNDxTzQTw7iY%2FHEZRQY7xqJ9RU2LFe%2FYqakdP911ha0XhjjiTVAkDwgatWfCGeYocx8M3glG8g8EXhSrLrHnEFJ5Ymow%2FkhIYv6ttYUW1iFmEqqxdVoUs9FmsDYSqmtmJh3Cl1%2BVtl2s7owDUdocR5bceiyoSivGTT5vzpbzL1uoBpmcAAQgW7ArnKD9ng9rc%2BNgrobSNwpSkkhcRN%2BvmXLjIsDovYHHEfmsYFygPAnIDEQrQPzJYCOaLHLUfIt7Oq0LJn9fxkSgNCb1qEIQ5UKgT%2Fs6gJmVOOroJhQBXVqw118QtWLdyUxEP45sUpSzqP7RDdFYMyB9UReMiF1MzPwoUqHt8hjGFFeP5wZAbZ%2F0%2BcAtAAcji6LeSq%2FMYiAvSsdw3GtrfVSVFUBbIhwRWYR7yOcr%2FBi%2FB1MSJZ16JlgH1AGM3EO2QnmMyrSbTSiACgFBv4yCUapZkt9qwWVL7aeOyHvArJjm8%2Fz9BhdI4XcZgz2%2FvRALosjsk1ODOyMcJn9%2FYI6IrkS5vxMGdUwou2YKfyVqJpn5t9aNs3gbQMbdbkxnGdsr4bTHm2AxWo9yNZK4PXR3uzhAh%2BM0AZejnCrGdy0UvJxl0oMKgWSLR%2B1LH2aE9ViejiFs%2BXn6bTjng3MlIhJ1I1TkuLdg6OcAbD7Xx%2Bc3y9TrWAiSHqVkbZ2v9ilCo6s4AjwZCzFyD9mOL305nV9aonvsQeT2L0gVk4OwOJqXXVRW7naaxswDKVdlYLyMXAnntteYmws2xcVVZzq%2BtHPAooQggmJkc6TLSusOiL4RKgwzzYU1iFQgiUBA1H7E8yPau%2BZl9P7AblVNebtHqTgxLfRqrNvZWjsHZFuqMqKcDWdlFjF7UGvX8Jn24DyEAykJwNcdg0OvJ4p5pQ9tV6SMlP4A0PNh8aYze1ArROyUNTNouy8tNF3Rt0CSXb6bRFl4%2FIfQzNMjaE9WwpYOWQnOdEF%2BTdJNO0iFh7%2BI0kfORzQZb6P2kymS9oTxzBiM9rUqLWr1WE5G6ODhycQd%2FUnNVeMbcH68hYkGycNoUNWc8fxaxfwhDbHpfwM5oeTY7rUX8QAAAABJRU5ErkJggg%3D%3D"> |  [![PyPI pyversions](https://img.shields.io/pypi/pyversions/aiida-fleur/0.6.svg)](https://pypi.python.org/pypi/aiida-fleur/0.6.3/) | MaXR1 < MaXR3 (v0.28)|
 
-### Documentation
+### Documentation and User Support
 
 Hosted at http://aiida-fleur.readthedocs.io/en/develop/index.html.
 For other information see the AiiDA-core docs or http://www.flapw.de.
 
+Users can post any questions in the Fleur user [forum](http://fleur.xobor.de/)
+
+For bugs, feature requests and further issues please use the issue tracker on github of the aiida-fleur repository.
+
 ### License:
 
 MIT license.
@@ -94,7 +98,6 @@ filename | Description
 ---------|------------
 Structure_util.py | Constains some methods to handle AiiDA structures (some of them might now be methods of the AiiDA structureData, if so use them from there!)
 merge_parameter.py | Methods to handle parameterData nodes, i.e merge them. Which is very useful for all-electron codes, because instead of pseudo potentialsfamilies you can create now families of parameter nodes for the periodic table.
-xml_util.py | All xml functions that are used, by parsers and other tools are in here. Some are 'general' some a very specific to Fleur.
 read_cif.py | This can be used as stand-alone to create StructureData nodes from .cif files from an directory tree.
 
 Utility and tools, which are independend of AiiDA are moved to the [masci-tools](https://github.com/JuDFTteam/masci-tools) (material science tools) repository,
@@ -214,11 +217,10 @@ Usage examples are shown in 'examples'.
 
 ## Acknowledgements
 
-Besides the Forschungszentrum Juelich, this work is supported by the [MaX
-European Centre of Excellence](<http://www.max-centre.eu/>) funded by the Horizon 2020 EINFRA-5 program,
-Grant No. 676598.
+Besides the Forschungszentrum Juelich, this work is supported by the European MaX Centre of Excellence 'Materials design at the Exascale' [MaX](<http://www.max-centre.eu/>) funded by the Horizon 2020 EINFRA-5 program, Grant No. 676598 and under grant agreement No. 824143. This work is further supported by the Joint Lab Virtual Materials Design (JLVMD) of the Forschungszentrum Jülich.
 
 For this work essential is AiiDA, which itself is supported by the [MARVEL National Centre for Competency in Research](<http://nccr-marvel.ch>) funded by the [Swiss National Science Foundation](<http://www.snf.ch/en>).
 
 
-![MaX](docs/source/images/MaX.png)
+<img src="docs/source/images/MAX-orizz.png" alt="MaX" width="200"/>
+<img src="docs/source/images/Logo-JLVMD.png" alt="JLVMD" width="200"/>
diff --git a/aiida_fleur/__init__.py b/aiida_fleur/__init__.py
@@ -12,4 +12,4 @@
 '''
 AiiDA-FLEUR
 '''
-__version__ = '1.1.4'
+__version__ = '1.2.0'
diff --git a/aiida_fleur/calculation/fleur.py b/aiida_fleur/calculation/fleur.py
@@ -78,6 +78,7 @@ class FleurCalculation(CalcJob):
     _DOSINP_FILE_NAME = 'dosinp'
     _BAND_GNU_FILE_NAME = 'band.gnu'
     _BAND_FILE_NAME = 'bands.*'
+    _BANDDOS_FILE_NAME = 'banddos.hdf'
 
     # helper files
     _FLEUR_WARN_ONLY_INFO_FILE_NAME = 'FLEUR_WARN_ONLY'
@@ -99,6 +100,9 @@ class FleurCalculation(CalcJob):
     _NMMPMAT_FILE_NAME = 'n_mmp_mat'
     _NMMPMAT_HDF5_FILE_NAME = 'n_mmp_mat_out'
 
+    #files for greensfunctions
+    _GREENSF_HDF5_FILE_NAME = 'greensf.hdf'
+
     # files for hybrid functionals
     _COULOMB1_FILE_NAME = 'coulomb1'
     _MIXBAS_FILE_NAME = 'mixbas'
@@ -188,8 +192,6 @@ class FleurCalculation(CalcJob):
         'additional_retrieve_list', 'remove_from_retrieve_list', 'additional_remotecopy_list',
         'remove_from_remotecopy_list', 'cmdline'
     ]
-    # possible modes?
-    _fleur_modes = ['band', 'dos', 'forces', 'chargeDen', 'latticeCo', 'scf', 'force_theorem', 'gw', 'ldau']
 
     @classmethod
     def define(cls, spec):
@@ -396,16 +398,23 @@ def prepare_for_submission(self, folder):
             if modes['band']:
                 mode_retrieved_filelist.append(self._BAND_FILE_NAME)
                 mode_retrieved_filelist.append(self._BAND_GNU_FILE_NAME)
+                if with_hdf5:
+                    mode_retrieved_filelist.append(self._BANDDOS_FILE_NAME)
             if modes['dos']:
                 mode_retrieved_filelist.append(self._DOS_FILE_NAME)
-            if modes['forces']:
+                if with_hdf5:
+                    mode_retrieved_filelist.append(self._BANDDOS_FILE_NAME)
+            if modes['relax']:
                 # if l_f="T" retrieve relax.xml
                 mode_retrieved_filelist.append(self._RELAX_FILE_NAME)
             if modes['ldau']:
                 if with_hdf5:
                     mode_retrieved_filelist.append(self._NMMPMAT_HDF5_FILE_NAME)
                 else:
                     mode_retrieved_filelist.append(self._NMMPMAT_FILE_NAME)
+            if modes['greensf']:
+                if with_hdf5:
+                    mode_retrieved_filelist.append(self._GREENSF_HDF5_FILE_NAME)
             if modes['force_theorem']:
                 if 'remove_from_retrieve_list' not in settings_dict:
                     settings_dict['remove_from_retrieve_list'] = []
@@ -514,7 +523,13 @@ def prepare_for_submission(self, folder):
         # Retrieve by default the output file and the xml file
         retrieve_list = []
         retrieve_list.append(self._OUTXML_FILE_NAME)
-        retrieve_list.append(self._INPXML_FILE_NAME)
+        if has_fleurinp:
+            allfiles = fleurinp.files
+            for file1 in allfiles:
+                if file1.endswith('.xml'):
+                    retrieve_list.append(file1)
+        else:
+            retrieve_list.append(self._INPXML_FILE_NAME)
         retrieve_list.append(self._SHELLOUTPUT_FILE_NAME)
         retrieve_list.append(self._ERROR_FILE_NAME)
         retrieve_list.append(self._USAGE_FILE_NAME)
@@ -526,7 +541,8 @@ def prepare_for_submission(self, folder):
             retrieve_list.append(self._CDN1_FILE_NAME)
 
         for mode_file in mode_retrieved_filelist:
-            retrieve_list.append(mode_file)
+            if mode_file not in retrieve_list:
+                retrieve_list.append(mode_file)
         self.logger.info('retrieve_list: %s', str(retrieve_list))
 
         # user specific retrieve

diff --git a/aiida_fleur/calculation/fleurinputgen.py b/aiida_fleur/calculation/fleurinputgen.py
@@ -27,9 +27,11 @@
 
 from aiida_fleur.data.fleurinp import FleurinpData
 from aiida_fleur.tools.StructureData_util import abs_to_rel_f, abs_to_rel
-from aiida_fleur.tools.xml_util import convert_to_fortran_bool, convert_to_fortran_string
 from aiida_fleur.common.constants import BOHR_A
 
+from masci_tools.util.xml.converters import convert_to_fortran_bool
+from masci_tools.io.common_functions import convert_to_fortran_string
+
 
 class FleurinputgenCalculation(CalcJob):
     """
@@ -137,8 +139,7 @@ def define(cls, spec):
         spec.exit_code(307, 'ERROR_MISSING_RETRIEVED_FILES', message='Some required files were not retrieved.')
         spec.exit_code(308,
                        'ERROR_FLEURINPDATA_INPUT_NOT_VALID',
-                       message=('During parsing: FleurinpData could not be initialized, see log. '
-                                'Maybe no Schemafile was found or the Fleurinput is not valid.'))
+                       message=('During parsing: FleurinpData could not be initialized, see log. '))
         spec.exit_code(309, 'ERROR_FLEURINPDATA_NOT_VALID', message='During parsing: FleurinpData failed validation.')
 
     def prepare_for_submission(self, folder):
@@ -346,6 +347,9 @@ def prepare_for_submission(self, folder):
                 site_symbol = kind.symbols[0]
                 atomic_number = _atomic_numbers[site_symbol]
                 atomic_number_name = atomic_number
+                if atomic_number == 0:  # 'X' element for vacancies
+                    natoms = natoms - 1
+                    continue
 
                 # per default we use relative coordinates in Fleur
                 # we have to scale back to atomic units from angstrom
@@ -484,8 +488,15 @@ def prepare_for_submission(self, folder):
 
         codeinfo = CodeInfo()
         # , "-electronConfig"] # TODO? let the user decide -electronconfig?
-        #cmdline_params = ['-explicit', '-inc', '+all', '-f', '{}'.format(self._INPUT_FILE_NAME)]
-        cmdline_params = ['-explicit']
+
+        # We support different inpgen and fleur version via reading the version from the code node extras
+        code_extras = code.extras
+        code_version = code_extras.get('version', 32)
+        if int(code_version) < 32:
+            # run old inpgen
+            cmdline_params = ['-explicit']
+        else:
+            cmdline_params = ['-explicit', '-inc', '+all', '-f', '{}'.format(self._INPUT_FILE_NAME)]
 
         # user specific commandline_options
         for command in settings_dict.get('cmdline', []):
@@ -618,3 +629,27 @@ def _lowercase_dict(dic, dict_name):
         return new_dict
     else:
         raise TypeError('_lowercase_dict accepts only dictionaries as argument')
+
+
+def write_inpgen_file_aiida_struct(structure, path, input_params=None, settings=None):
+    """Wraps around masci_tools write inpgen_file, unpacks aiida structure"""
+    from masci_tools.io.io_fleur_inpgen import write_inpgen_file  # pylint: disable=import-error,no-name-in-module
+
+    atoms_dict_list = []
+    kind_list = []
+
+    for kind in structure.kinds:
+        kind_list.append(kind.get_raw())
+
+    for site in structure.sites:
+        atoms_dict_list.append(site.get_raw())
+
+    report = write_inpgen_file(structure.cell,
+                               atoms_dict_list,
+                               kind_list,
+                               path=path,
+                               pbc=structure.pbc,
+                               input_params=input_params,
+                               settings=settings)
+
+    return report
diff --git a/aiida_fleur/cmdline/__init__.py b/aiida_fleur/cmdline/__init__.py
@@ -14,12 +14,15 @@
 '''
 import click
 import click_completion
+import difflib
 
+from aiida_fleur import __version__
 from aiida.cmdline.params import options, types
 from .launch import cmd_launch
 from .data import cmd_data
 from .workflows import cmd_workflow
 from .visualization import cmd_plot
+from .util import options as options_af
 
 # Activate the completion of parameter types provided by the click_completion package
 # for bash: eval "$(_AIIDA_FLEUR_COMPLETE=source aiida-fleur)"
@@ -30,14 +33,54 @@
 # less material science specific
 
 
+class MostSimilarCommandGroup(click.Group):
+    """
+    Overloads the get_command to display a list of possible command
+    candidates if the command could not be found with an exact match.
+    """
+
+    def get_command(self, ctx, cmd_name):
+        """
+        Override the default click.Group get_command with one giving the user
+        a selection of possible commands if the exact command name could not be found.
+        """
+        cmd = click.Group.get_command(self, ctx, cmd_name)
+
+        # return the exact match
+        if cmd is not None:
+            return cmd
+
+        matches = difflib.get_close_matches(cmd_name, self.list_commands(ctx), cutoff=0.5)
+
+        if not matches:
+            # single letters are sometimes not matched, try with a simple startswith
+            matches = [c for c in sorted(self.list_commands(ctx)) if c.startswith(cmd_name)][:3]
+
+        if matches:
+            ctx.fail("'{cmd}' is not a aiida-fleur command.\n\n"
+                     'The most similar commands are: \n'
+                     '{matches}'.format(cmd=cmd_name, matches='\n'.join('\t{}'.format(m) for m in sorted(matches))))
+        else:
+            ctx.fail(f"'{cmd_name}' is not a aiida-fleur command.\n\nNo similar commands found.")
+
+        return None
+
+
+# Uncomment this for now, has problems with sphinx-click
+#@click.command('aiida-fleur', cls=MostSimilarCommandGroup, context_settings={'help_option_names': ['-h', '--help']})
 @click.group('aiida-fleur', context_settings={'help_option_names': ['-h', '--help']})
 @options.PROFILE(type=types.ProfileParamType(load_profile=True))
+# Note, __version__ should always be passed explicitly here,
+# because click does not retrieve a dynamic version when installed in editable mode
+@click.version_option(__version__, '-v', '--version', message='AiiDA-FLEUR version %(version)s')
 def cmd_root(profile):  # pylint: disable=unused-argument
     """CLI for the `aiida-fleur` plugin."""
 
 
 # To avoid circular imports all commands are not yet connected to the root
-# but they have to be here because of bash completion
+# but they have to be here because of bash completion on the other hand, this
+# makes them not work with the difflib...
+# see how aiida-core does it.
 
 cmd_root.add_command(cmd_launch)
 cmd_root.add_command(cmd_data)