C2x: A tool for visualisation and input preparation for Castep and other electronic structure codes

Abstract

The c2x code fills two distinct roles. Its first role is in acting as a converter between the binary format .check files from the widely-used Castep [1] electronic structure code and various visualisation programs. Its second role is to manipulate and analyse the input and output files from a variety of electronic structure codes, including Castep, Onetep and Vasp, as well as the widely-used ‘Gaussian cube’ file format. Analysis includes symmetry analysis, and manipulation arbitrary cell transformations. It continues to be under development, with growing functionality, and is written in a form which would make it easy to extend it to working directly with files from other electronic structure codes.Data which c2x is capable of extracting from Castep’s binary checkpoint files include charge densities, spin densities, wavefunctions, relaxed atomic positions, forces, the Fermi level, the total energy, and symmetry operations. It can recreate .cell input files from checkpoint files. Volumetric data can be output in formats useable by many common visualisation programs, and c2x will itself calculate integrals, expand data into supercells, and interpolate data via combinations of Fourier and trilinear interpolation. It can extract data along arbitrary lines (such as lines between atoms) as 1D output.C2x is able to convert between several common formats for describing molecules and crystals, including the .cell format of Castep. It can construct supercells, reduce cells to their primitive form, and add specified k-point meshes. It uses the spglib library [2] to report symmetry information, which it can add to .cell files.C2x is a command-line utility, so is readily included in scripts. It is available under the GPL and can be obtained from http://www.c2x.org.uk. It is believed to be the only open-source code which can read Castep’s .check files, so it will have utility in other projects. Program summaryProgram Title: c2xProgram Files doi:http://dx.doi.org/10.17632/wj5hcj7x39.1Licensing provisions: GPLv3Programming language: CNature of problem: C2x is able to extract a large variety of data from Castep’s [1] large, binary-format, output files to facilitate further processing or visualisation. These binary files are optimised for rapid input and output by Castep, but are impossible to read without detailed knowledge of their internal structure, which varies between different versions of Castep. In them wavefunctions are stored as plane wave coefficients, so need to be Fourier transformed before they can be visualised in real space. C2x can manipulate the input files of Castep, and other common crystallographic formats, performing functions useful for setting up calculations, such as supercell construction, format conversions, and symmetry analysis.Different electronic structure codes use different file formats for outputting densities. C2x is able to convert between some of the major formats, allowing visualisation and post-processing tools targeted at one electronic structure code to be used with others.Solution method: C2x is a command-line utility written in standard C. It is able to process large (multi-GB) binary files efficiently, extracting much smaller datasets. C2x has considerable knowledge of the structure of the checkpoint files as written by various versions of Castep. Wavefunctions are optionally converted to densities, and then transformed to real space using its own FFT routine. Weighted sums of densities from multiple bands can be accumulated. C2x interpolates volumetric data by using user-specified combinations of trilinear and Fourier interpolation. For symmetry analysis it relies on the existing spglib [2] library, which is also used by Castep. It supports cell transformations with the axes of the new cell expressed in absolute terms, or in terms of the original axes. It has its own internal representation of the unit cell and its contents, and has several routines for converting this to and from common crystallographic file formats.C2x is able to read densities from Castep’s binary formats, and both read and write Castep’s formatted density files, Vasp’s formatted density files, and the .cube files used by Gaussian and Onetep.Additional comments: Primary site for distribution and documentation: www.c2x.org.uk[1] S. J. Clark, M. D. Segall, C. J. Pickard, P. J. Hasnip, M. J. Probert, K. Refson, M. Payne, First principles methods using CASTEP, Z. Kristall. 220 (2005) 567–570.[2] A. Togo, Spglib, a library for finding and handling crystal symmetries [cited 2017-02-23].https://atztogo.github.io/spglib/