应《网络安全法》要求，自2017年10月1日起，未进行实名认证将不得使用互联网跟帖服务。为保障您的帐号能够正常使用，请尽快对帐号进行手机号验证，感谢您的理解与支持！

24小时热门版块排行榜    

小木虫论坛-学术科研互动平台 » 计算模拟区 » 第一性原理 » Vasp&MedeA » 推荐几个vasp处理计算结果的python脚本
671/2返回列表12下一页
查看: 8975  |  回复: 66
只看楼主@他人 存档 新回复提醒 (忽略) 收藏    在APP中查看
【奖励】 本帖被评价59次，作者mywai520增加金币 47.2 个

mywai520

铁杆木虫 (著名写手)

[资源] 推荐几个vasp处理计算结果的python脚本

python在处理二维图形还是有很多优势的，在这里推荐几个python脚本。附件中是个人已经下载的相关python脚本。
其中第一个提供的脚本只适应vasp.5.3.3, 第二个提供的脚本需要用到ase，所有需要自己先行安装ase。
1:    VASP Tools  下载地址：http://www.nsc.liu.se/~pla/vasptools/
Peter’s collection of small, but useful, VASP scripts. Some of these may be found on NSC’s computers by loading the “vasptools” module.

vaspcheck

The “vaspcheck” script scans your input files and looks for common errors such as: forgetting to copy CONTCAR to POSCAR, misspelled INCAR tags, and various inconsistent configurations such as having N atoms but only N-x magnetic moments specified. If you supply it with information about the intended number of cpu cores and nodes that you will run on, it will also check the NPAR and KPAR values and warn if they are unreasonable.

An alpha version is available in the “vasptools” module on Triolith, and once the script has become more robust, I will make a version available for download here. The idea is to integrate it with the queue system in the future, so that your VASP jobs will be automatically checked when running the “sbatch” command.

Install: Click here to download to the Python script. Install it by putting it in a folder in your $PATH (such as~/bin) and then do:

mv vaspcheck-standalone.py vaspcheck
chmod u+x vaspcheck
This should allow you to write “vaspcheck” in any job folder.

grad2

The gradient program is used to quickly get an overview of VASP geometry optimization runs. It also works for molecular dynamics. It parses the OUTCAR file and writes a one-line summary per ionic step, including average forces and run-time per step. The output looks like this:

$ grad2 OUTCAR
Step   1  Energy: -42.794090  Log|dE|: +1.631  Avg|F|: 1.720176  Max|F|: 2.710237  SCF:  15  Time: 0.52m
Step   2  Energy: -43.336931  Log|dE|: -0.265  Avg|F|: 0.513256  Max|F|: 0.696803  SCF:   9  Time: 0.32m
Step   3  Energy: -43.384337  Log|dE|: -1.324  Avg|F|: 0.095940  Max|F|: 0.178813  SCF:   7  Time: 0.24m
Step   4  Energy: -43.387267  Log|dE|: -2.533  Avg|F|: 0.050399  Max|F|: 0.071963  SCF:   6  Time: 0.20m
Step   5  Energy: -43.388250  Log|dE|: -3.007  Avg|F|: 0.043184  Max|F|: 0.061866  SCF:   4  Time: 0.13m
Step   6  Energy: -43.390384  Log|dE|: -2.671  Avg|F|: 0.030630  Max|F|: 0.047413  SCF:   5  Time: 0.18m
Step   7  Energy: -43.392498  Log|dE|: -2.675  Avg|F|: 0.003760  Max|F|: 0.005849  SCF:   6  Time: 0.20m
Step   8  Energy: -43.392509  Log|dE|: -4.959  Avg|F|: 0.001285  Max|F|: 0.001861  SCF:   3  Time: 0.09m
The Log\|dE\| is the base-10 logarithm of the absolute value of the energy difference between steps, essentially the number of “stable” decimals in the total energy, i.e. for a VASP run with EDIFF=1.0E-5, Log\|dE\| should approach -5 for convergence.

If your terminal has colors, each line will be color-coded with red color signalling convergence problems, and green color corresponding to energy convergence having been reached (as judged by the EDIFF tag in the INCAR file.)

Install: Click here to download to the Python script (version 2012-01-07). Install it by putting it in a folder in your $PATH (such as~/bin) and then do:

mv grad2.py grad2
chmod u+x grad2
This should allow you to write “grad2 OUTCAR” in any job folder.

vasp2cif

The vasp2cif program creates a CIF-file from a POSCAR/CONTCAR file, which can be used for visualization in graphical applications, such as VESTA. Note that it will not preserve symmetries from VASP – the output CIF is always in P1 symmetry. If there is no POTCAR file available, the script has a flag (“–elements”) whereby you can specify the atomic species.

Install: Click here to download to the Python script (version 2012-12-15). Install it by putting it in a folder in your $PATH (such as~/bin) and then do:

mv vasp2cif.py vasp2cif
chmod u+x vasp2cif
This should allow you to write e.g. “vasp2cif CONTCAR” in any job folder.

cif2vasp

For CIF to VASP input conversion, a recommend a program by Torbjörn Björkman called cif2cell, which can generate input from CIF files for many ab initio programs, including VASP.

If anyone is interested in doing high-performance CIF to VASP conversion with optimized C code, I can provide source code to a CIF lexer written with the Ragel state machine compiler and CIF parser written with Lemon. Unfortunately, the tool I built to do CIF to VASP with this framework does not compile correctly anymore on recent platforms, so I cannot put up any binaries for download. You can email me at pla@nsc.liu.se if you want to give it a try.

supersize

Yet another script to make supercells out of VASP’s POSCAR/CONTCAR files. It is basically a wrapper around the corresponding feature in ASE.

It works like this:

$ supersize POSCAR 4x4x4
And you get a new POSCAR file called “POSCAR.4x4x4” containing the supercell repeated 4 times in a,b,c directions. You can achieve the same effect with three lines of Python code in ASE:

import ase.io.vasp
cell = ase.io.vasp.read_vasp("POSCAR"
ase.io.vasp.write_vasp("POSCAR.4x4x4",cell*(4,4,4), label='444supercell',direct=True,sort=True)
The script is a little bit more elaborate, however, since it includes error checks.

2.   Scripts  下载地址：http://gvallver.perso.univ-pau.fr/vasptools/
The followings scripts are short programs which use the vasptools module. In the terminal if you give the option -h to the script a short help will be printed.

chgsplit
chgsplit [CHGCAR]
Split charge density into spin up and spin down charge density and write them into files.

Parameters:        CHGCAR (file) – name of a CHGCAR file (default is CHGCAR).
Default file name for the CHGCAR file is CHGCAR. In output the spin up charge density is written in file CHGCAR_up and the spin down charge density is written in file CHGCAR_down.

Examples

chgsplit

chgsplit CHGCAR
chgsum
chgsum CHGCAR1 CHGCAR2 fact1 fact2
Do simple linear operations on charge densities from two CHGCAR file.

Parameters:       
CHGCAR1 (file) – name of the first CHGCAR file
CHGCAR2 (file) – name of the second CHGCAR file
fact1 (float) – scaling factor for CHGCAR1 (default 1.0)
fact2 (float) – scaling factor for CHGCAR2 (default 1.0)
On output the file CHGCAR_sum contains the density computed by the following expression

fact1 * CHGCAR1 + fact2 * CHGCAR2
Examples

chgsum AECAR0 AECAR2

chgsum AECAR0 CHGCAR 1.8 0.2
cvgVASP
convVASP [OPTIONS] ... [FILES]
convVASP read convergence data on the OUTCAR file and either write them into files in order to plot them with your favorite soft or plot them directly using matplotlib. The last argument has to be an OUTCAR file, if absent, ‘./OUTCAR’ will be used.

Parameters:       
-h – print help and exit
-t – instead of plot convergence data, they are printed into files.
Examples

cvgVASP

cvgVASP ../OUTCAR
getBands
getBands [OPTIONS] ... [FILE]
Read energy bands on vasprun.xml file and either extract them into files or plot them directly. The last argument has to be the xml file, if absent ‘./vasprun.xml’ will be used.

Parameters:       
–help (-h) – print this help
–tofiles (-t) – Print energy bands into files.
–directions (-d) – One file is created for each line of the reciprocal space along which energy bands were computed. This option is relevant only when you want to print energy bands into file, -t option, and if the k-point grid was generated automatically.
–quiet (-q) – Remove output
Examples

getBands

getBands -t
getDeplacement
getDeplacement [FILE1] [FILE2]
Read first and last structures in a vasprun.xml file and, for each atom, compute the distance between the initial position and the last position. You can also give two POSCAR files (or CONTCAR). The first one will be use as the initial position and the second will be use as the final position.

By default, the file ‘./vasprun.xml’ is read. You can give an other file in the command line.

Examples

getDeplacement my_calculation.xml
getDeplacement POSCAR CONTCAR
getDOS
getDOS [OPTIONS] ... [FILE]
Read density of states data on vasprun.xml files and either extract them into files or plot them directly. The last argument has to be the xml file, if absent ‘./vasprun.xml’ will be used.

Parameters:       
–help (-h) – Print this help
–tofiles (-t) – Print total DOS into files. Projected DOS are printed if you add -p option.
–projected (-p) – Print projected DOS into files.
–quiet (-q) – Low verbosity
Examples

getDOS
getDOS -t
getDOS -t -p
getDOS -p
postDOS
postDOS()
Read density of states data on vasprun.xml files and do some post treatments :

Compute the sum of all projected DOS
Compute the contribution to the total DOS of each atom type or the contribution of one specific atom if -iat option is specified.
Parameters:       
–help (-h) – Print help and exit
–help – Print help and exit
-iat N (int) – Output the contribution of atom N to the total DOS
getMaille
getMaille [POSCAR]
Read the lattice vectors in a POSCAR or CONTCAR file and print the lattice parameters. If you do not give a file name getMaille will print suggestions.

getCharges
getCharges()
Compute atomic charges from a Bader caclculations done with the bader program of the University of Texas at Austin : bader.

Parameters:        –help (-h) – Print help and exit
Run the script in the same directory where you did the bader calculation. Requirements :

a ACF.dat file (bader program output).
a vasprun.xml file or a POSCAR/CONTCAR file in order to read atom namess.
visVMD
I wrote this script before I found VESTA and today I do not use it anymore. But it could be useful in order to do nice crystal pictures such as the one in the sidebar.

visVMD [OPTIONS]
visVMD read output files of VASP and write a VMD script in order to visualize VASP structures with VMD. visVMD can read either POSCAR and CONTCAR files or directly vasprun.xml files. The xml file is the best choice because it contains atom names. If you read a POSCAR or a CONTCAR file of a 4.X version of VASP, visVMD will ask you the name of each atom.

Parameters:       
–help (-h) – print this help
-p –prefix prefix (string) – visVMD use [prefix] in order to name output files (default is ‘vis’).
-f –file file (string) – file is an output file of VASP containing structure data. It is either the xml file or a POSCAR or CONTCAR (default ‘vasprun.xml’).
–poscar – say that the file is either a POSCAR or a CONTCAR
–unitcell (-u) – add all images of the atoms of the unit cell which are into the unit cell.
–final (-e) – read the last structure of the xml file (default if [file] is an xml file).
–initial (-i) – read the first structure of the xml file.
-n –supercell N1xN2xN3 (int*int*int) – make a supercell N1 times N2 times N3. Do not set spaces in the expression.
–liaisons (-l) – make connectivity between atoms.
Examples

visVMD -u -l
visVMD -u -l --poscar -f POSCAR
visVMD -u -l -n 2x2x2
回复此楼

» 本帖附件资源列表

  • 欢迎监督和反馈：小木虫仅提供交流平台，不对该内容负责。
    本内容由用户自主发布，如果其内容涉及到知识产权问题，其责任在于用户本人，如对版权有异议，请联系邮箱：libolin3@tal.com
  • 附件 1 : VASP_Tools_python.zip
    • 2014-04-03 22:51:37, 3.86 M

» 收录本帖的淘贴专辑推荐

VASP 第一性原理计算-tg VASP软件从入门到高深 表界面计算
计算模拟-MS-CASTEP vasp 晶型研究 VASP资料
VASP 值得收藏 第一性 科研
第一性原理计算

» 本帖已获得的红花（最新10朵）

前田庆次

» 猜你喜欢

» 本主题相关价值贴推荐，对您同样有帮助:
1楼2014-04-03 22:52:08
已阅   回复此楼   关注TA 给TA发消息 送TA红花 TA的回帖
回帖支持 ( 显示支持度最高的前 50 名 )

mywai520

铁杆木虫 (著名写手)
下面是本人用上面一些脚本做的图，大家可以参考一下：
推荐几个vasp处理计算结果的python脚本
QQ图片20140403225756.jpg


推荐几个vasp处理计算结果的python脚本-1
QQ图片20140403230111.jpg


推荐几个vasp处理计算结果的python脚本-2
QQ图片20140403230147.jpg
赞一下(2人) 回复此楼
2楼2014-04-03 23:02:22
 已阅   回复此楼   关注TA 给TA发消息 送TA红花 TA的回帖

lidanyt

新虫 (初入文坛)

★★★★★ 五星级,优秀推荐

非常好，顶一下，感谢分享！
回复此楼
5楼2014-05-05 13:42:05
 已阅   回复此楼   关注TA 给TA发消息 送TA红花 TA的回帖

甲斐之虎

银虫 (正式写手)

★★★★★ 五星级,优秀推荐

受益良多！谢谢！
回复此楼
7楼2014-05-10 09:20:18
 已阅   回复此楼   关注TA 给TA发消息 送TA红花 TA的回帖

前田庆次

木虫 (著名写手)
送红花一朵
相当棒，其中的一个工具，解决了贫僧一个大难题
感谢楼主分享！
赞一下 回复此楼
8楼2014-05-19 16:14:08
 已阅   回复此楼   关注TA 给TA发消息 送TA红花 TA的回帖

轻轻飘过之

金虫 (正式写手)

★★★★★ 五星级,优秀推荐

很感谢楼主给我们提供这么好的资源！最近我想画自旋电荷密度图，想用chgsplit来处理CHGCAR，但是运行这个小程序读取vasptools.utils时出现了错误，报错是找不到vasptools.utils文件。不知道这是为什么？
我是在你给的链接上找到vasptools.utils的code，然后将code复制黏贴到一个文件中，将这个文件和chgsplit放到同一个目录下运行的，不知道这样做对不对？
对python完全陌生，不知是否要先对这些程序进行编译然后再运行？怎样编译呢？希望楼主能够给一些解答，我自己也在继续摸索中，如果有进展，及时向大家汇报！
谢谢！
赞一下 回复此楼
13楼2014-07-03 05:00:55
 已阅   回复此楼   关注TA 给TA发消息 送TA红花 TA的回帖

tonglijia

木虫 (正式写手)
引用回帖:
13楼: Originally posted by 轻轻飘过之 at 2014-07-03 05:00:55
很感谢楼主给我们提供这么好的资源！最近我想画自旋电荷密度图，想用chgsplit来处理CHGCAR，但是运行这个小程序读取vasptools.utils时出现了错误，报错是找不到vasptools.utils文件。不知道这是为什么？
我是在你给 ...

您好！我也遇到这个问题了　　请问您解决了吗？
赞一下 回复此楼
32楼2015-05-22 14:13:56
 已阅   回复此楼   关注TA 给TA发消息 送TA红花 TA的回帖

scuedu2

金虫 (小有名气)
感谢

发自小木虫Android客户端
回复此楼
44楼2016-01-25 13:20:28
 已阅   回复此楼   关注TA 给TA发消息 送TA红花 TA的回帖
简单回复
stoneyww3楼
2014-04-04 08:24   回复  
五星好评  顶一下，感谢分享！
2853520654楼
2014-04-04 11:07   回复  
五星好评  顶一下，感谢分享！
chao_xuan6楼
2014-05-06 13:47   回复  
五星好评  顶一下，感谢分享！
wangzg92929楼
2014-06-19 08:37   回复  
五星好评  顶一下，感谢分享！
lwk20510楼
2014-06-26 08:45   回复  
五星好评  顶一下，感谢分享！
流年水11楼
2014-06-27 12:12   回复  
五星好评  顶一下，感谢分享！
2008089012楼
2014-07-02 19:34   回复  
五星好评  顶一下，感谢分享！
huichli14楼
2014-07-15 00:07   回复  
五星好评  顶一下，感谢分享！
zhaostao15楼
2014-07-26 22:06   回复  
五星好评  顶一下，感谢分享！
hnuliquan16楼
2014-07-31 09:38   回复  
五星好评  顶一下，感谢分享！
yh316617楼
2014-08-01 10:45   回复  
五星好评  顶一下，感谢分享！
佳佳98818楼
2014-09-16 00:52   回复  
五星好评  顶一下，感谢分享！
Tius19楼
2014-09-24 22:04   回复  
五星好评  顶一下，感谢分享！
fuyuhaoy20楼
2014-10-15 10:56   回复  
五星好评  顶一下，感谢分享！
ridge888821楼
2014-11-22 21:36   回复  
五星好评  顶一下，感谢分享！
leozpj22楼
2014-12-26 20:54   回复  
五星好评  顶一下，感谢分享！
MikeMatt23楼
2015-01-10 15:38   回复  
五星好评  顶一下，感谢分享！
韩璐1949100124楼
2015-01-26 11:01   回复  
五星好评  顶一下，感谢分享！
不做伸手党25楼
2015-01-28 16:48   回复  
五星好评  顶一下，感谢分享！
nanost26楼
2015-02-06 12:07   回复  
五星好评  顶一下，感谢分享！
1xiaohua127楼
2015-03-29 15:48   回复  
五星好评  顶一下，感谢分享！
wangjb40128楼
2015-04-08 14:55   回复  
五星好评  顶一下，感谢分享！
gn0253064029楼
2015-04-08 21:21   回复  
五星好评  顶一下，感谢分享！
geqone30楼
2015-05-20 11:08   回复  
五星好评  顶一下，感谢分享！
tonglijia31楼
2015-05-22 14:04   回复  
五星好评  顶一下，感谢分享！
shadowlisong33楼
2015-05-28 12:55   回复  
五星好评  顶一下，感谢分享！
凉风送爽34楼
2015-06-26 14:48   回复  
五星好评  顶一下，感谢分享！
凉风送爽35楼
2015-06-26 14:49   回复  
感谢分享
li63413970536楼
2015-07-17 14:00   回复  
五星好评  顶一下，感谢分享！
txwang37楼
2015-09-19 18:10   回复  
五星好评  顶一下，感谢分享！
jackjiejl38楼
2015-10-31 19:16   回复  
五星好评  顶一下，感谢分享！
Hysen39楼
2015-11-10 20:25   回复  
五星好评  顶一下，感谢分享！
wenshow1140楼
2015-12-30 10:08   回复  
五星好评  顶一下，感谢分享！
zbai41楼
2016-01-21 13:34   回复  
五星好评  顶一下，感谢分享！
solarman42楼
2016-01-23 10:03   回复  
五星好评  顶一下，感谢分享！
yymmwl43楼
2016-01-25 10:57   回复  
五星好评  顶一下，感谢分享！
wlyht45楼
2016-03-10 14:26   回复  
五星好评  顶一下，感谢分享！
biancheng15946楼
2016-03-19 16:01   回复  
五星好评  顶一下，感谢分享！
灵魂双舞47楼
2016-03-28 15:06   回复  
五星好评  顶一下，感谢分享！
txwang48楼
2016-04-30 11:15   回复  
顶一下，感谢分享！
jylaugh49楼
2016-05-03 21:11   回复  
五星好评  顶一下，感谢分享！
sbingyi50楼
2016-06-27 19:38   回复  
五星好评  顶一下，感谢分享！
相关版块跳转 我要订阅楼主 mywai520 的主题更新
671/2返回列表12下一页
☆ 无星级 ★ 一星级 ★★★ 三星级 ★★★★★ 五星级
普通表情 龙 兔 虎 猫 高级回复(可上传附件) 论文翻译-EnPapers美助理教授团队-SCI英文润色
最具人气热帖推荐 [查看全部] 作者 回/看 最后发表
[基金申请] 最新消息：2024国自然下载文件名变了 +9 dream200606 2024-06-16 12/600 2024-06-17 00:34 by kobe0107
[硕博家园] 博士毕业高校和就业的相关问题 +5 SCITOPPP 2024-06-14 8/400 2024-06-16 21:33 by kingkongking
[基金申请] 2024国社科通讯评审 +9 qsd10086 2024-06-13 17/850 2024-06-16 19:14 by onroad24
[基金申请] Nature 11日发文，中国著名学者们称造假迫不得已 +6 babu2015 2024-06-14 6/300 2024-06-16 18:37 by 喜欢和一氧化二�
[教师之家] 请问事业编制和年薪制冲突吗？ +8 ZHONGWU_U 2024-06-14 8/400 2024-06-16 17:37 by spj860iuy
[找工作] 初始合伙人来啦！（生物试剂耗材标准品） +8 欢快的小科研人 2024-06-15 14/700 2024-06-16 16:00 by 欢快的小科研人
[基金申请] 面青地会评时间 +6 tanjydd 2024-06-15 6/300 2024-06-16 15:42 by 我是王小帅
[教师之家] 每次骚扰女学生的都是院系领导，而不是普通教师，小编们要注意措辞正确 +9 zju2000 2024-06-15 11/550 2024-06-16 14:49 by appleapple2
[基金申请] 希望今年自己国自然面上项目和老婆青年项目能中！ +7 恐龙爸爸 2024-06-14 7/350 2024-06-16 14:48 by redfish105
[基金申请] 博士后创新人才支持计划公示 +9 aishida144 2024-06-14 15/750 2024-06-16 09:52 by msjy
[文学芳草园] 累并快乐着 +13 MYHLD521 2024-06-14 13/650 2024-06-15 22:59 by zeolitess
[论文投稿] 投稿时忘记修改一作 +7 gll123456 2024-06-13 11/550 2024-06-15 11:49 by gll123456
[论文投稿] 投稿kbs被拒后，系统提供的推荐的其他期刊有用吗？ +3 chenrui2015 2024-06-10 3/150 2024-06-14 10:30 by Tr.sjx1997
[论文投稿] 最近写了一篇控制优化领域的文章，可以投哪里啊？有没有水一些的期刊推荐 +7 香瓜木香 2024-06-12 13/650 2024-06-14 07:05 by 香瓜木香
[考博] 博导选择 +3 bing85977 2024-06-12 3/150 2024-06-13 15:34 by 我是邱尧
[硕博家园] 考博应该从哪里开始准备 +6 亮姐2019 2024-06-11 8/400 2024-06-13 12:53 by 帕秋莉GO
[论文投稿] with editor日期变更 +3 慎独的小花卷 2024-06-12 8/400 2024-06-13 11:00 by 慎独的小花卷
[论文投稿] 摩擦磨损论文投稿 +3 jmysan 2024-06-12 3/150 2024-06-13 08:36 by 莱茵润色
[基金申请] 博后特助这周出结果吗？往年都是啥时候啊？ +13 jsqy 2024-06-12 17/850 2024-06-12 19:55 by Lynn212
[论文投稿] water research状态咨询 5+3 Flyyawa 2024-06-10 6/300 2024-06-11 09:45 by bobvan
信息提示
关闭
请填处理意见
关闭