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FLEUR with AiiDA

MIT license GitHub release PyPI version Build develop Coveralls github branch Documentation Status Code quality pylint

This software contains a plugin that enables the usage of the all-electron DFT FLEUR code with the AiiDA framework. Further this package contains common workflows and some utility.

Developed at Forschungszentrum Jülich GmbH

Documentation

Hosted at http://aiida-fleur.readthedocs.io/en/develop/index.html. For other information checkout the AiiDA docs or http://www.flapw.de.

License:

MIT license. See license file.

Comments/Disclaimer:

The plug-in and the workflows will only work with a Fleur version using xml files as I/O. For example check out the Fleur version released withing MAX.

Notice: This is still under heavy development. For anything contact j.broeder@fz-juelich.de and feel free to write issues and contribute.

Contents

  1. Introduction
  2. Installation Instructions
  3. Code Dependencies
  4. Further Information

Introduction

This is a python package (AiiDA plugin plus workflows plus utility) to use the FLEUR-code with the AiiDA Framework. The FLEUR-code is an all-electron DFT code using the FLAPW method, and widely applied in the material science and physics community.

The plugin :

The Fleur plug-in consists of a datastructure called FleurinpData and two plug-ins, one for the Fleur inputgenerator (inpgen) and one for a Fleur calculation itself.

Every plug-in has an input part (defines the calculation) and an output parser, see the AiiDA documentation for general info.

Workflows in this package:

workflow name Description
scf SCF-cycle of Fleur. Converge the charge density and the Total energy with multiple FLEUR runs
eos Calculate and Equation of States (Lattice constant) with FLEUR
dos Calculate a Density of States (DOS) with FLEUR
bands Calculate a Band structure with FLEUR
relax Relaxation of a crystal structure with FLEUR

See the AiiDA documentation for general info about the AiiDA workflow system or how to write workflows.

Utility/tools:

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.
...

Installation Instructions

From the aiida-fleur folder (after downloading the code, recommended) use:

$ pip install .
# or which is very useful to keep track of the changes (developers)
$ pip install -e .

To uninstall use:

$ pip uninstall aiida-fleur

Or install lates release version from pypi:

$ pip install aiida-fleur

Test Installation

To test rather the installation was successful use:

$ verdi calculation plugins
   # example output:

   ## Pass as a further parameter one (or more) plugin names
   ## to get more details on a given plugin.
   * codtools.cifcellcontents
   * codtools.cifcodcheck
   * codtools.cifcodnumbers
   * codtools.ciffilter
   * codtools.cifsplitprimitive
   * quantumespresso.cp
   * quantumespresso.pw
   * quantumespresso.pwimmigrant
   * simpleplugins.templatereplace
   ...
   * fleur.fleur
   * fleur.inpgen

You should see 'fleur.*' in the list

The other entry points can be checked with the AiiDA Factories (Data, Workflow, Calculation, Parser). (this is done in test_entry_points.py)

We suggest to run all the (unit)tests in the aiida-fleur/aiida_fleur/tests/ folder.

$ bash run_all_cov.sh

Files/Contents

A short sum up of the most important classes and where to find them, how to import them.

Plugin files:

Data:

fleurinpData : aiida_fleur.data.fleurinp.py fleurinpModifier : aiida_fleur.data.fleurinpmodifier.py

Calculations:

FleurinputgenCalculation : aiida_fleur.calculation.fleurinputgen.py FleurCalculation : aiida_fleur.calculation.fleur.py

Parsers:

FleurinpgenParser: aiida_fleur.parsers.fleur_inputgen.py FleurParser: aiida_fleur.parsers.fleur.py

XML Schema Files:

in fleur_schema folder

The Fleur code needs a XMLSchema file, the plugin searches (walks) for them in this fleur_schema folder. If nothing works add a path to schemafile_index.py, or search_paths (fleurinp). Also if you want to use/need different schemas add them to this folder.

Workflows/workchains:

Class name file name
fleur_scf_wc aiida_fleur.workflows.scf.py
fleur_eos_wc aiida_fleur.workflows.eos.py
fleur_dos_wc aiida_fleur.workflows.dos.py
fleur_band_wc aiida_fleur.workflows.band.py
fleur_relax_wc aiida_fleur.workflows.relax.py
...

Utility under '/aiida_fleur/tools/':

Structure_util.py merge_parameter.py read_cif.py ...

Code Dependencies

Requirements are listed in 'setup_requirements.txt' and setup.json.

most important are:

  • aiida_core >= 0.9
  • lxml
  • ase ...

Mainly AiiDA:

  1. Download from [www.aiida.net/?page_id=264](www.aiida.net -> Download)
  2. install and setup -> [http://aiida-core.readthedocs.org/en/stable/](aiida's documentation)

For easy ploting we recommend installing 'plot_methods' (not yet integrated into this package): https://bitbucket.org/broeder-j/plot_methods

Further Information

The plug-in source code documentation is here. also some documentation of the plug-in, further things can be found at www.flapw.de. Usage examples are shown in 'examples'.