singroup / dft_grid

Contains tools for post processing and visualizing grid based data from DFT calculations (charge density, electric potential) using Python.

DFT grid atomic geo post proc

Description

Contains tools for post processing and visualizing grid based data from DFT calculations (charge density, electric potential) using Python. Data on a non-orthogonal grid can be efficiently interpolated into a regular orthogonal grid and the grid points can be translated inside the periodic cell. Contains many functions for plotting slices of different kinds of data represented on the grid. Functions for plotting projections of the atomic geometry are also included. Uses a separate `PyDFTFileIO <>`_ package to read the DFT output files containing the data grids.

Requirements

• Python 2.7
• Cython (http://cython.org/)
• NumPy (version >= 1.9)
• SciPy (version >= 0.14)
• matplotlib
• `PyDFTFileIO <>`_

For plot_atoms: - Atomic Simulation Environment (ASE), https://wiki.fysik.dtu.dk/ase/

Installation

Put this directory containing the Python and Cython (.pyx) modules to your PYTHONPATH environment variable. The Cython modules should be compiled automatically at runtime as long as the Python scripts using them have the line import pyximport; pyximport.install() and you have Cython installed. See http://docs.cython.org/en/latest/src/tutorial/cython_tutorial.html for more information.

Usage

nonorthogonal_to_orthogonal_grid_interpolation:

Can be used to interpolate data on a non-orthogonal grid into a regular orthogonal grid for plotting purposes. The interpolation functions are computationally heavy and thus this module is written with Cython. See plot_locpot_efield_z and scripts/nonorthogonal_to_orthogonal_cube for example use cases.

plot_atoms:

Can be used to plot projection of an atomic geometry into a plane spanned by two Cartersian coordinate axes. plot_atoms different kinds of atoms with different colors and sizes. Supports projection to any Cartesian plane. plot_atoms_height_xy represents the height of the atoms with respect to the plane (hard coded to xy) by mapping the height to a color.

plot_atoms_mechafm:

The plot_atoms_pbc function is a more complicated version of the plot_atoms_height_xy supporting repetition of the atomic configuration accross periodic boundary conditions. It can plot atoms to any area by repeating the unit cell. Works well for plotting atom overlay to MechAFM (https://github.com/SINGROUP/MechAFM) images, thus the name of the module. Should be combined with plot_atoms module.

plot_dft_grid_data:

Can be used to plot different kinds of data on grids that can be obtained as an output from DFT codes. Currently supports plotting of charge density, electric potential and electric field (calculated by taking numerical gradient of the potential). One can plot either a slice of the 3D grid or values along a line parallel to one of the coordinate axes. See the plot_epot_cube and plot_locpot_efield_z modules and the scripts in examples and scripts folders for usage examples.

Author

Juha Ritala (2016) [email protected]