A set of scripts to pre/post-process data for/from FHI-aims/GULP/KLMC simulations.

Python v.2.7.x (x => 9)

Matplotlib v.1.x (x => 5.0)

numpy v.1.x (x => 10.1)

ADUL v.2.0 (For DM_Surface_Energy)

Calculates a thermally averaged statistical value of a property.

Usage:

DA_Thermally_Averaged_Statistics.py [options] input_file

Options: -h, --help show this help message and exit -t TEMPS List of temperatures, separated by a comma (default t=293) -u A flag to say whether the input file contains only unique values. Default = False

Summary:

Reads in a text file in csv format, where the first column is the energy and the second column is the property value that will be statistically averaged. If the parameter -u is set, then it is assumed that the file contains only unique energies and property values and a third column having values of occurrences is expected.

Formula:

Finds unique structures by examining the working directory (recursively) and reading in systems with the predefined extension. Then examines them using the hashkey and creates a directory with all the unique systems and a statistics file.

Usage: DA_Unique_Structures.py extension

Options: -h, --help show this help message and exit

Calculates cluster's surface energy.

Reads in a structure from an xyz file, estimates the area of a cluster using a predefined radius and calculates cluster's surface energy using a provided bulk energy of one atom.

Plots the energy evolution graph of the n lowest energy structures during a KLMC GA simulation.

Plots energy distribution histogram from the last iteration of a KLMC GA simulation.

Finds parents, grandparents, etc for a specific GA iteration.

Finds the GA iteration number on which the GM has been found.

Plots DOS (and integrated DOS) graphs [Based on the David Mora Fonz's (UCL) implementation].

Analyses FHI-aims simulations in terms of runtime, systems' energies etc.

Prepares and executes FHIaims spin polarized simulations.

Reads in structures in xyz format, prepares geometry.in and control.in files by varying the default_initial_moment keyword. The script can also run the prepared simulations one by one.

Plots radial distribution function.

(Being developed) Analyses the change in a system by comparing two xyz files: initial and final configurations.

(Being developed) Analyses a geometry with FHIaims - pushes a system in the direction of a chosen eigenvector and performs FHIaims single point evaluation.

(Being developed) Compares structures in terms of their energy ranking between different levels of theory (IPs (GULP) and DFT (FHIaims))

Converts files from one format to another. Works with the most popular formats, such us XYZ, CAR, and GIN.

Analyses systems (xyz format) in terms of avg. bond distance and coordination.