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Useful tools for VASP users

已有 7867 次阅读 2013-10-26 03:10 |个人分类:图形化处理|系统分类:科研笔记

关注:

1) VASP tools不仅仅是tools;它是建立在开发者对理论知识的很深的理解基础上;

2) 了解vasp tools的工作流程,及操作原理。

3) 小工具要做到普适其实并不容易。虽然很多课题组都有自己开发的小工具;但并不能普及,不能被VASP收录,一部分原因是这些课题组不愿意,当然很大一部分原因,是这些小脚本的普适性太差。

4)  很欣赏calypso和multiwfn的做法,他们当属中国学者的骄傲。


以下摘录自:

http://tfy.tkk.fi/~job/



Here are links to some tools which I hope VASP users will find useful.


VaspviewThis program can be used to visualize the calculated charge density (CHGCAR). This is an updated version of the original program, made by yours truly, solving the performance issues in the original program.


Transition State Tools for VASPA site with tools e.g. for NEB calculations. Formerly known as the Jónsson group vasp page, now apparently done in collaboration with another group. Especially their Script collection contains a lot of useful small scripts.


VASP freewareSome VASP utilities by Dr. Jürgen Furthmüller, one of the VASP developers. Contains source for some extra stuff, e.g. for calculating optical properties.


LEV00 & TETR manualManual of the lev00 and tetr utilities. These utilities are very useful, although somewhat cumbersome to use. You can use this matlab script to plot the charge density generated with lev00. Note that this matlab script works correctly only when the size of the plot in the x and y directions are equal; the vasputil_chgplaneplot script, part of vasputil (see below) does not have this restriction. Update 2008-02-21:lev00 has been converted to Fortran 95 and now uses dynamic memory allocation, so you no longer need to recompile it again and again and again for every system, making it no-longer-cumbersome!


OpenDXSomewhat gigantic, complicated and slow. It is however very useful. With the help of lev00, opendx and for example this net file (i.e. script for opendx) you can create nice charge density pictures.


Charge density in OpenDXA C program and some net files that can be used to plot charge density with OpenDX.


v2xsfA tool to convert VASP files to XCrysDen format.


PythonPython is an awesome very high level programming language. Together with the IPython enhanced interactive prompt and the matplotlib plotting library, Python provides an interactive scientific analysis environment like R or MATLAB, except with a nice general purpose programming language and open source.


RA very good open source statistics program with plotting capabilities. It is a clone of the popular S and S-plus statistics programs.GraceA plotting program with a GUI. Successor to the famous xmgr program.


jmol  A simple molecule viewer. There are zillions of molecule viewers around, and I haven't tested all of them.


VMDA molecular visualization program. Like jmol, but much more advanced. Newer versions have direct support for some VASP file formats, including POSCAR and CHGCAR.


p4vaspA graphical VASP utility program.


My own VASP utility

Vasputil (older website here), a VASP utility package. Vasputil contains a Python library that can be used to create your own analysis utilities or to analyze stuff interactively, and a set of command line utilities. These can be used to measure and manipulate various stuff in POSCAR files, do simple arithmetic on charge density files, in conjunction with lev00 plot charge density in a plane, and so forth.


As of vasputil 5.0, vasputil is now a 100 % pure Python package. This should make it easier to install and develop (contributions welcome!). For information on the older vasputil 4.x, that contained some utilities not available in vasputil 5.0, see the README-4.3. You can download all available version from the link above.

Other stuffsyshwinfo


syshwinfo is a collection of tools to gather system information (CPU, memory, HD, OS version, etc.) from Linux systems. It contains a simple command-line tool, and a set of CGI scripts and an agent program that can be used to gather information about a number of computers and store them centrally in a database.
Download it
here.

VASP benchmarks on kvartsi

I have made some notes and benchmarks about running VASP on the Linux/dual Opteron/GbEth/pgf90 cluster "kvartsi". See here.




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