C2x: A tool for visualisation and input preparation for CASTEP and other electronic structure codes
C2x: A tool for visualisation and input preparation for CASTEP and other electronic structure codes
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DOI：
10.1016/j.cpc.2017.12.008
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发表时间：
2018-04-01
影响因子：
6.3
通讯作者：
Rutter, M. J.
中科院分区：
文献类型：
--
作者：
Rutter, M. J.
C2x代码扮演着两个截然不同的角色。它的第一个角色是充当来自广泛使用的CASTEP[1]电子结构代码的二进制格式检查文件和各种可视化程序之间的转换器。它的第二个作用是处理和分析来自各种电子结构代码的输入和输出文件，包括CASTEP、ONETEP和VASP，以及广泛使用的‘GaussCube’文件格式。分析包括对称性分析和操纵任意单元格变换。它还在继续开发中，具有越来越多的功能，其编写形式将使其易于扩展到直接使用其他电子结构代码的文件。c2x能够从CASTEP的二进制检查点文件中提取的数据包括电荷密度、自旋密度、波函数、弛豫原子位置、力、费米能级、总能量和对称操作。它可以重现。来自检查点文件的单元格输入文件。体积数据可以以许多常见可视化程序使用的格式输出，而c2x本身将计算积分，将数据扩展到超级单元格，并通过傅里叶和三线性插值法的组合来内插数据。它可以沿着任意线(如原子之间的线)提取数据作为1D输出。C2x能够在几种常见的描述分子和晶体的格式之间转换，包括。CASTEP的单元格格式。它可以构造超单元格，将单元格简化为原始形式，并添加指定的k点网格。它使用spglib库[2]来报告对称信息，它可以添加到这些信息中。C2x是一个命令行实用程序，因此很容易包含在脚本中。它是在通用公共许可证下提供的，可以从http://www.c2x.org.uk.获得程序摘要程序标题：c2x程序文件DOI：http://dx.doi.org/10.17632/wj5hcj7x39.1Licensing条款：GPLv3编程语言：cn问题：c2x能够从CASTEP的[1]大型二进制格式输出文件中提取大量数据，以便于进一步的处理或可视化。这些二进制文件针对CASTEP的快速输入和输出进行了优化，但在没有详细了解其内部结构的情况下无法读取，其内部结构因CASTEP的不同版本而异。其中波函数以平面波系数的形式存储，因此需要对其进行傅里叶变换，然后才能在真实空间中可视化。C2x可以处理CASTEP的输入文件和其他常见的晶体格式，执行对设置计算有用的功能，如超级单元构造、格式转换和对称分析。不同的电子结构代码使用不同的文件格式来输出密度。C2x能够在一些主要格式之间进行转换，允许针对一个电子结构代码的可视化和后处理工具与其他电子结构代码一起使用。解决方法：C2x是一个用标准C编写的命令行实用程序。它能够有效地处理大型(多GB)二进制文件，提取更小的数据集。C2x对不同版本的CASTEP编写的检查点文件的结构有相当多的了解。波函数可以选择性地转换为密度，然后使用其自己的FFT例程转换到真实空间。可以累加来自多个波段的密度的加权和。C2x通过使用用户指定的三线性和傅立叶插值组合对体数据进行内插。对于对称性分析，它依赖于现有的spglib[2]库，CASTEP也使用该库。它支持单元格转换，新单元格的轴用绝对值或原始轴表示。它有自己的单位单元格及其内容的内部表示，并有几个用于将其转换为常见晶体文件格式的例程。C2x能够从CASTEP的二进制格式读取密度，并读取和写入CASTEP的格式化密度文件、VASP的格式化密度文件和。其他注释：分发和文档的主要站点：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 Prples Methods Using CASTEP，Z.Kristall。220(2005)567-570.[2]A.多哥，Spglib，一个寻找和处理晶体对称性的图书馆[引用2017-02-23]。Https://atztogo.githullioispglibi(C)2017年提交人。爱思唯尔出版公司(Elsevier B.V.)
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.githullioispglibi (C) 2017 The Author. Published by Elsevier B.V.