Programs¶

es_fitting.py¶

Calculates the Wigner-Seitz projection of cube file data of periodic data.

es_fitting.main(parser)[source]¶

Main routine wrapper.

Parameters:	parser (argparse.ArgumentParser) – Argument parser

Command Line Interface¶

filename¶: The cubefile to read from. Both Bohr and Angstrom units are supported.

--periodic¶: Whether to treat input file in periodic boundary conditions. In the current implementation, this requires copying all atom positions for the 26 direct neighbouring cubes and therefore carries substantial cost in terms of memory requirements. The runtime scales O(log n) with the number of atoms.

--leafsize¶: Number of points at which brute-force nearest neighbour search is employed. Increasing this number introduces higher memory requirements, but may speed up processing. Default: 5000.

Implementation¶

es_fitting.main(parser)[source]

Main routine wrapper.

Parameters:	parser (argparse.ArgumentParser) – Argument parser

es_cp2kpretty.py¶

Reads a CP2K input file and reformats it such that

Every section is properly indented.
Every section is terminated with a &END line that includes the name of the section.
Sections are enclosed in blank lines.

Command Line Interface¶

input¶: CP2K input filename.

output¶: CP2K output filename.

Implementation¶

es_cp2kpretty.main(parser)[source]¶

Main routine wrapper.

Parameters:	parser (argparse.ArgumentParser) – Argument parser

es_cp2k2xyz.py¶

Extracts coordinates from CP2K input format into XYZ files.

Supports scaled CP2K coordinates and scaled XYZ output.

Command Line Interface¶

input¶: CP2K input filename.

output¶: XYZ output filename.

--scaled¶: Whether the output should be in fractions of the box.

Implementation¶

es_cp2k2xyz.main(parser)[source]¶

Main routine wrapper.

Parameters:	parser (argparse.ArgumentParser) – Argument parser

es_cellmultiply.py¶

Multiplies a cell along the lattice vectors.

Comes with support for scaled input and output, h matrices and arbitrary cell shapes. Works only on XYZ files.

Command Line Interface¶

input¶: XYZ input filename.

output¶: XYZ output filename.

--X¶: X repeat count. Default: 1. Only positive integers supported.

--Y¶: Y repeat count. Default: 1. Only positive integers supported.

--Z¶: Z repeat count. Default: 1. Only positive integers supported.

--sc_in¶: Whether the input file contains scaled coordinates.

--sc_out¶: Whether the out file contains scaled coordinates.

--hmat¶: H matrix (cell vectors in columns). Comma-separated in row-first notation without spaces.

--abc¶: a, b, c, alpha, beta, gamma. Comma-separated without spaces.

--radians¶: Whether angles in `–abc are given in radians.

Implementation¶

es_cellmultiply.main(parser)[source]¶

Main routine wrapper.

Parameters:	parser (argparse.ArgumentParser) – Argument parser