ssthurai / macrodensity

Analyse VASP density & potential grids using python

MacroDensity

A set of python scripts to read in a electrostatic potentials and electron densities from electronic structure calculations and plot in a number of ways, including:

• Planar average
• Spherical average
• Atom centred averages

Requirements

Python

Matplotlib (to plot results on the fly)

ASE (for atom centred functionality)

Installation

pip install git+git://github.com/WMD-group/MacroDensity.git

• You are now ready to run the examples listed below
• If you have modified the source code, please run the unit tests with python setup.py test.

PlanarAverage.py

This example is for plotting the planar average of a potential along a vector (here it is z). The only variables which need to be set are in the first three lines. Note LOCPOT.slab file is just a regular LOCPOT grid file.

input_file = 'LOCPOT.slab'
lattice_vector = 4.75
output_file = 'planar.dat'

The variable lattice vector refers to the lattice vector of the bulk crystal structure in the direction of the plotting. It is used to get the macroscopic average, as defined in Jackson's Electrodynamics. See the heterojunction tutorial for an interactive description of this.

For the best overview of what the lattice_parameter setting should be, and how macroscopic averaging in general works, this paper from Baldereschi and the crew can't be beaten. http://iopscience.iop.org/article/10.1088/0022-3727/31/11/002/meta

The code is executed as:

python PlanarAverage.py

This results in a plot of the planar average and an output of the potential called planar.dat.

SphericalAverage.py

This example is for plotting the average potential inside a sphere of given radius. It is the method used in our 2014 study of metal-organic frameworks in JACS.

The lines which need to be edited for this are given below. Note LOCPOT.MiL is just a regular LOCPOT file that has been renamed.

input_file = 'LOCPOT.MiL'
cube_size = [2,2,2]    # This size is in units of mesh points
## origin defines the bottom left point of the cube the "0,0,0" point in fractional coordinates
cube_origin = [0,0,0]

To run the code simply type:

python SphericalAverage.py

This results in an output of the average potential in the volume, and the variance of the potential. If the variance is too high it means that you are not sampling a plateau in the potential; typically values below 10e-4 are acceptable.

OnSitePotential.py

This example is for calculating the potential at the sites of a certain atomic nucleus, for example the O nuclei in an oxide. This on-site potential calculated this way is equivalent to a Madelung potential and can be useful for predicting electron energy levels (see http://pubs.acs.org/doi/abs/10.1021/ar400115x for details).

The input lines to edit are :

potential_file = 'LOCPOT' # The file with VASP output for potential
coordinate_file = 'POSCAR' # The coordinates file NOTE NOTE This must be in vasp 4 format 
species = "O"  # The species whose on-site potential you are interested in 
sample_cube = [5,5,5] # The size of the sampling cube in units of mesh points (NGX/Y/Z)

The cube parameter determines the size of the sample area, the units are mesh points, the magnitude of the mesh point is calculated by dividing the appropriate lattice vector by the number of points (NGX/Y/Z in OUTCAR).

To run the code simply type:

python OnSitePotentail.py

The result is a histogram plot using Matplotlib. If you prefer data ouput simply edit the final lines of the script.

PlaneField.py

This plots the countour lines of the iso-surface of an electric field in an arbitrary plane as defined in the preamble part of the file.

a_point = [0, 0, 0]
b_point = [1, 0, 1]
c_point = [0, 1, 0]

input_file = 'LOCPOT.slab'

The execution is simply:

python PlaneField.py

This creates a contour plot of the field lines.