Merge develop into master for release v1.1.3

Merge pull request #103 from JuDFTteam/develop From CHANGELOG.md ## v1.1.3 ### release compatible with AiiDA-core 1.3.0 - still support of Fleur MaXR4 version with inpgen - Does not support yet for Fleur MaXR5 and new inpgen - Set_kpoints was moved from fleurinp to fleurinpmodifier - Break_symmetry of a structure was refactored - 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 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 - Command line interface (CLI) `aiida-fleur` with various functionalities exposed - For devs: Increased test coverage, codecov is now added to CI and linked to badge removed some older outdated code
JuDFTteam · Dec 15, 2020 · df33e9a · df33e9a
2 parents 786f067 + f6716ac
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -6,7 +6,7 @@ jobs:
 
   docs:
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-18.04
 
     steps:
     - uses: actions/checkout@v1
@@ -37,7 +37,7 @@ jobs:
 
   pre-commit:
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-18.04
     timeout-minutes: 30
 
     steps:
@@ -69,7 +69,7 @@ jobs:
 
   tests:
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-18.04
     timeout-minutes: 30
 
     strategy:
@@ -120,3 +120,9 @@ jobs:
        touch local_exe/inpgen && chmod +x local_exe/inpgen
        touch local_exe/fleur && chmod +x local_exe/fleur 
        ./run_all_cov.sh
+    
+    - name: Upload report to Codecov
+      uses: codecov/codecov-action@v1
+      with:
+        file: ./tests/coverage.xml
+        fail_ci_if_error: False
diff --git a/.gitignore b/.gitignore
@@ -1,6 +1,7 @@
 
 # Created by https://www.gitignore.io/api/python,linux,macos
-
+#
+.aiida/
 submit_test/
 
 ### Python ###

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,3 +1,19 @@
+## v1.1.3
+### release compatible with AiiDA-core 1.3.0
+- still support of Fleur MaXR4 version with inpgen
+- Does not support yet for Fleur MaXR5 and new inpgen
+- Set_kpoints was moved from fleurinp to fleurinpmodifier
+- Break_symmetry of a structure was refactored
+- 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 
+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
+- Command line interface (CLI) `aiida-fleur` with various functionalities exposed
+- For devs: Increased test coverage, codecov is now added to CI and linked to badge
+removed some older outdated code
 
 ## v1.1.2
 ### release compatible with AiiDA-core 1.3.0

diff --git a/README.md b/README.md
@@ -3,17 +3,23 @@
 [![MIT license](https://img.shields.io/badge/license-MIT-blue.svg)](LICENSE)
 [![GitHub release](https://img.shields.io/github/release/JuDFTteam/aiida-fleur.svg)](https://github.com/JuDFTteam/aiida-fleur/releases)
 [![PyPI version](https://badge.fury.io/py/aiida-fleur.svg)](https://badge.fury.io/py/aiida-fleur)
-[![Build develop](https://travis-ci.org/JuDFTteam/aiida-fleur.svg?branch=master)](https://travis-ci.org/JuDFTteam/aiida-fleur)
-[![Coveralls github branch](https://github.com/JuDFTteam/aiida-fleur/blob/develop/aiida_fleur/tests/coverage.svg)](https://github.com/JuDFTteam/aiida-fleur/tree/develop)
-[![Code quality pylint](https://github.com/JuDFTteam/aiida-fleur/blob/develop/aiida_fleur/tests/pylint.svg)](https://github.com/JuDFTteam/aiida-fleur/tree/develop)
+[![PyPI pyversions](https://img.shields.io/pypi/pyversions/aiida-fleur.svg)](https://pypi.python.org/pypi/aiida-fleur)
+[![Build status](https://github.com/JuDFTteam/aiida-fleur/workflows/aiida-fleur/badge.svg?branch=develop&event=push)](https://github.com/JuDFTteam/aiida-fleur/actions)
 [![Documentation Status](https://readthedocs.org/projects/aiida-fleur/badge/?version=develop)](https://aiida-fleur.readthedocs.io/en/develop/?badge=develop)
+[![codecov](https://codecov.io/gh/JuDFTteam/aiida-fleur/branch/develop/graph/badge.svg)](https://codecov.io/gh/JuDFTteam/aiida-fleur)
 
 
 This software contains a plugin that enables the usage of the all-electron
 DFT [FLEUR code](http://www.flapw.de) with the [AiiDA framework](http://www.aiida.net).
 
 Developed at [Forschungszentrum Jülich GmbH](http://www.fz-juelich.de/pgi/pgi-1/DE/Home/home_node.html)
 
+## Compatibility matrix
+
+| FLEUR Plugin | AiiDA CORE | Python | FLEUR |
+|-|-|-|-|
+| `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
 
@@ -37,7 +43,7 @@ In Extreme Data Workshop 2018 Proceedings, 2019, vol 40, p 43-48
 
 ### Comments/Disclaimer:
 
-The plug-in and the workflows will only work with a Fleur version using xml files as I/O.
+The plug-in and the workflows will only work with a Fleur version using xml files as I/O, i.e >v0.27.
 
 
 ### Contents
@@ -94,6 +100,49 @@ read_cif.py | This can be used as stand-alone to create StructureData nodes from
 Utility and tools, which are independend of AiiDA are moved to the [masci-tools](https://github.com/JuDFTteam/masci-tools) (material science tools) repository,
 which is a dependency of aiida-fleur.
 
+
+### Command line interface (CLI)
+
+Besides the python API, aiida-fleur comes with a builtin CLI: `aiida-fleur`. 
+This interface is built using the click library and supports tab-completion. 
+
+To enable tab-completion, add the following to your shell loading script, e.g. the .bashrc or virtual environment activate script:
+
+    eval "$(_AIIDA_FLEUR_COMPLETE=source aiida-fleur)"
+
+the main subcommands include:
+
+    data: Commands to create and inspect data nodes
+        fleurinp   Commands to handle `FleurinpData` nodes.
+        parameter  Commands to create and inspect `Dict` nodes containing FLAPW parameters
+        structure  Commands to create and inspect `StructureData` nodes.
+    launch: Commands to launch workflows and calcjobs of aiida-fleur
+
+        banddos          Launch a banddos workchain
+        corehole         Launch a corehole workchain
+        create_magnetic  Launch a create_magnetic workchain
+        dmi              Launch a dmi workchain
+        eos              Launch a eos workchain
+        fleur            Launch a base_fleur workchain.
+        init_cls         Launch an init_cls workchain
+        inpgen           Launch an inpgen calcjob on given input If no    code is...
+        mae              Launch a mae workchain
+        relax            Launch a base relax workchain # TODO final scf    input
+        scf              Launch a scf workchain
+        ssdisp           Launch a ssdisp workchain
+
+    plot: Invoke the plot_fleur command on given nodes
+
+    workflow: Commands to inspect aiida-fleur workchains and prepare inputs
+
+for example to launch an scf workchain on a given structure execute:
+
+    $ aiida-fleur launch scf -i <inpgenpk> -f <fleurpk> -S <structurepk>
+
+the command can also process structures in any format `ase` can handle, this includes `Cif`, `xsf` and `poscar` files. In such a case simply parse the path to the file:
+
+    $ aiida-fleur launch scf -i <inpgenpk> -f <fleurpk> -S ./structure/Cu.cif
+
 ## Installation Instructions <a name="Installation"></a>
 
 From the aiida-fleur folder (after downloading the code, recommended) use:
@@ -154,7 +203,7 @@ Mainly AiiDA:
 Easy plotting and other useful routines that do not depend on aiida_core are part of
 the [masci-tools](https://github.com/JuDFTteam/masci-tools) (material science tools) repository.
 
-For easy ploting we recommend using 'plot_methods' from masci-tools, which are also deployed by the 'plot_fleur(<node(s)>)' function.
+For easy plotting we recommend using 'plot_methods' from masci-tools, which are also deployed by the 'plot_fleur(<node(s)>)' function.
 
 ## Further Information <a name="FurtherInfo"></a>
 

diff --git a/aiida_fleur/__init__.py b/aiida_fleur/__init__.py
@@ -12,4 +12,4 @@
 '''
 AiiDA-FLEUR
 '''
-__version__ = '1.1.2'
+__version__ = '1.1.3'
diff --git a/aiida_fleur/calculation/fleur.py b/aiida_fleur/calculation/fleur.py
@@ -193,7 +193,7 @@ class FleurCalculation(CalcJob):
 
     @classmethod
     def define(cls, spec):
-        super(FleurCalculation, cls).define(spec)
+        super().define(spec)
 
         # spec.input('metadata.options.input_filename', valid_type=six.string_types,
         #            default=cls._INPXML_FILE_NAME)

diff --git a/aiida_fleur/calculation/fleurinputgen.py b/aiida_fleur/calculation/fleurinputgen.py
@@ -28,7 +28,7 @@
 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 aiida_fleur.common.constants import BOHR_A
 
 
 class FleurinputgenCalculation(CalcJob):
@@ -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__ = '1.2.1'
+    __version__ = '1.2.2'
 
     # Default input and output files
     _INPUT_FILE = 'aiida.in'  # will be shown with inputcat
@@ -51,7 +51,10 @@ class FleurinputgenCalculation(CalcJob):
     _ERROR_FILE_NAME = 'out.error'
     _STRUCT_FILE_NAME = 'struct.xsf'
 
-    _settings_keys = ['additional_retrieve_list', 'remove_from_retrieve_list', 'cmdline']
+    _settings_keys = [
+        'additional_retrieve_list', 'remove_from_retrieve_list', 'cmdline', 'significant_figures_cell',
+        'significant_figures_positions'
+    ]
     # TODO switch all these to init_internal_params?
     _OUTPUT_SUBFOLDER = './fleur_inp_out/'
     _PREFIX = 'aiida'
@@ -97,7 +100,7 @@ class FleurinputgenCalculation(CalcJob):
 
     @classmethod
     def define(cls, spec):
-        super(FleurinputgenCalculation, cls).define(spec)
+        super().define(spec)
 
         spec.input('metadata.options.input_filename', valid_type=six.string_types, default=cls._INPUT_FILE)
         spec.input('metadata.options.output_filename', valid_type=six.string_types, default=cls._INPXML_FILE_NAME)
@@ -136,7 +139,7 @@ def define(cls, spec):
                        '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.'))
-        spec.exit_code(309, 'ERROR_FLEURINPDATE_NOT_VALID', message='During parsing: FleurinpData failed validation.')
+        spec.exit_code(309, 'ERROR_FLEURINPDATA_NOT_VALID', message='During parsing: FleurinpData failed validation.')
 
     def prepare_for_submission(self, folder):
         """
@@ -170,7 +173,7 @@ def prepare_for_submission(self, folder):
         # but we have to convert from Angstrom to a.u (bohr radii)
         scaling_factors = [1.0, 1.0, 1.0]
         scaling_lat = 1.  # /bohr_to_ang = 0.52917720859
-        scaling_pos = 1. / bohr_a  # Angstrom to atomic
+        scaling_pos = 1. / BOHR_A  # Angstrom to atomic
         own_lattice = False  # not self._use_aiida_structure
 
         ##########################################
@@ -258,7 +261,8 @@ def prepare_for_submission(self, folder):
                     if self._use_aiida_structure:
                         input_params.pop('lattice', {})
                         own_lattice = False
-
+        #TODO check if input parameter dict is consistent to given structure.
+        # if not issue warnings.
         # TODO allow only usual kpt meshes and use therefore Aiida kpointData
         # if self._use_kpoints:
         #     try:
@@ -301,14 +305,18 @@ def prepare_for_submission(self, folder):
 
         scaling_factor_card = ''
         cell_parameters_card = ''
-
+        # We allow to set the significant figures format, because sometimes
+        # inpgen has numerical problems which are not there with less precise formatting
+        sf_c = str(settings_dict.get('significant_figures_cell', 9))
+        sf_p = str(settings_dict.get('significant_figure_positions', 10))
         if not own_lattice:
             cell = structure.cell
             for vector in cell:
                 scaled = [a * scaling_pos for a in vector]  # scaling_pos=1./bohr_to_ang
-                cell_parameters_card += ('{0:18.9f} {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]))
+                reg_string = '{0:18.' + sf_c + 'f} {1:18.' + sf_c + 'f} {2:18.' + sf_c + 'f}\n'
+                cell_parameters_card += (reg_string.format(scaled[0], scaled[1], scaled[2]))
+            reg_string = '{0:18.' + sf_c + 'f} {1:18.' + sf_c + 'f} {2:18.' + sf_c + 'f}\n'
+            scaling_factor_card += (reg_string.format(scaling_factors[0], scaling_factors[1], scaling_factors[2]))
 
         #### ATOMIC_POSITIONS ####
 
@@ -348,24 +356,27 @@ def prepare_for_submission(self, folder):
                     vector_rel = abs_to_rel_f(pos, cell, structure.pbc)
                     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!
+                if site_symbol != kind_name:  # This is an important fact, if user renames it becomes a new atomtype or species!
                     try:
+                        # Kind names can be more then numbers now, this might need to be reworked
                         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')
+                        #if int(kind_name[len(head)]) > 4:
+                        #    raise InputValidationError('New specie name/label should start with a digit smaller than 4')
                     except ValueError:
-                        pass
+                        self.report(
+                            'Warning: Kind name {} will be ignored by the FleurinputgenCalculation and not set a charge number.'
+                            .format(kind_name))
                     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}'
-                                                         '\n'.format(atomic_number_name, vector_rel[0], vector_rel[1],
-                                                                     vector_rel[2], kind_namet))
+                    reg_string = '    {0:7} {1:18.' + sf_p + 'f} {2:18.' + sf_p + 'f} {3:18.' + sf_p + 'f} {4}\n'
+                    atomic_positions_card_listtmp.append(
+                        reg_string.format(atomic_number_name, vector_rel[0], vector_rel[1], vector_rel[2], kind_namet))
                 else:
-                    atomic_positions_card_listtmp.append('    {0:7} {1:18.10f} {2:18.10f} {3:18.10f}'
-                                                         '\n'.format(atomic_number_name, vector_rel[0], vector_rel[1],
-                                                                     vector_rel[2]))
+                    reg_string = '    {0:7} {1:18.' + sf_p + 'f} {2:18.' + sf_p + 'f} {3:18.' + sf_p + 'f}\n'
+                    atomic_positions_card_listtmp.append(
+                        reg_string.format(atomic_number_name, vector_rel[0], vector_rel[1], vector_rel[2]))
             # TODO check format
             # we write it later, since we do not know what natoms is before the loop...
             atomic_positions_card_list.append('    {0:3}\n'.format(natoms))
@@ -557,8 +568,8 @@ def get_input_data_text(key, val, value_only, mapping=None):
         for elemk, itemval in six.iteritems(val):
             try:
                 idx = mapping[elemk]
-            except KeyError:
-                raise ValueError("Unable to find the key '{}' in the mapping " 'dictionary'.format(elemk))
+            except KeyError as exc:
+                raise ValueError("Unable to find the key '{}' in the mapping " 'dictionary'.format(elemk)) from exc
 
             list_of_strings.append((idx, '  {0}({2})={1} '.format(key, conv_to_fortran(itemval), idx)))
             # changed {0}({2}) = {1}\n".format