pyFDMNES

Python interface to fdmnes simulations. Simplifies and automates data input/output.

• load cif files
• Read/Modify/Write FDMNES input files
• easily perform repeated Convolution on existing DOS calculation
• flexibly extract DAFS/XANES curves from existing calculation

A new FDMNES simulation is represented by the fdmnes object which can be created by loading an existing (manually created) FDMNES input file, a .cif file of by defining space-group or metric and subsequently fill the unit cell with atoms.

After loading an existing input file, one can for example change some parameters in the fdmnes.P Parameter instance and save/create new input files with WriteInputFile. One can add the saved file to the job queue which can be executed using sim.Run().

Furthermore, the fdmnes.P Parameters Object similar to a python dict but does some consistency check of all given parameters, to a certain extent. Basically it checks if the given parameter has the proper shape (2d, 1d, 0d, or bool, etc..). How the definitions are stored, can be seen in the settings file: fdmnes/settings.py The idea is also to identify parameters which are crucial for the computation of the matrix elements and others which are used for post-processing (e.g. Convolution). This would allow to let pyFDMNES decide when a new computation of the matrix elements or electron density is necessary.

Certainly, FDMNES evolved and not all parameters are correctly represented in the settings file. Therefore it is not complete yet and updates are needed.

Requirements:

• python 2.7 or 3
• numpy
• PyCifRW
• fdmnes (version > March 28th 2014) from e.g. https://fdmnes.neel.cnrs.fr/

Installation

Change dir to the downloaded repository (where the setup.py is found) and modify the setup.cfg.

using pip (recommended)

pip install . [--user]

using setup script

python setup.py install [--user]

Usage

See examples folder.

You may set the FDMNES environment variable to specify the FDMNES executable command, for instance when using MPI:

FDMNES='mpirun fdmnes'
FDMNES='/path/to/fdmnes_linux_serial'
FDMNES='/path/to/fdmnes_linux_parallel'

For instance you may start:

cd examples/BaTiO3
FDMNES="mpirun fdmnes_parallel" python3 BaTiO3_cif_open.py

The default is to use the executable defined in the setup.cfg file of the pyFDMNES package.

You may as well set the FDMNES_SPACEGROUP environment variable to specify the spacegroup.txt file which defines the space-group operators. The default is to use the file provided by the pyFDMNES package.