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Manipulating VASP files with Python.

Home Page: https://pypi.python.org/pypi/vaspy/

License: MIT License

Python 99.54% Shell 0.46%

vasp data-processing data-visualization chemistry catalysis-informatics computational-chemistry

vaspy's Introduction

VASPy

Introduction

VASPy is a pure Python library designed to make it easy and quick to manipulate VASP files.

You can use VASPy to manipulate VASP files in command lins or write your own python scripts to process VASP files and visualize VASP data.

In /scripts , there are some scripts written by me for daily use.

More interfaces examples in Jupyter Notebook format are in /examples. Any contribution is welcomed!

Installation

Via pip(recommend):
```
pip install vaspy
```
Via easy_install:
```
easy_install vaspy
```
From source:
```
python setup.py install
```

If you want to use mayavi to visualize VASP data, it is recommened to install Canopy environment on your device instead of installing it manually.

After installing canopy, you can set corresponding aliases, for example:

alias canopy='/Users/<yourname>/Library/Enthought/Canopy/edm/envs/User/bin/python'
alias canopy-pip='/Users/<yourname>/Library/Enthought/Canopy/edm/envs/User/bin/pip'
alias canopy-ipython='/Users/<yourname>/Library/Enthought/Canopy/edm/envs/User/bin/ipython'
alias canopy-jupyter='/Users/<yourname>/Library/Enthought/Canopy/edm/envs/User/bin/jupyter'

Then you can install VASPy to canopy:

canopy-pip install vaspy

Examples

manipulate splited DOS file in command-line

# Manipulate splited DOS files.
>>> from vaspy.electro import DosX
>>> a = DosX('DOS1')
>>> b = DosX('DOS8')

# Merge DOS data.
>>> c = a
>>> c.reset_data()              # Initialize DOS data
>>> for i in range(1, 10):
>>>    c += DosX('DOS'+str(i))  # Merge DOS data.
>>> ...
>>> c.data                      # Get data(numpy array/matrix)
>>> c.tofile()                  # Get new DOS file with merged data

# Plot.
>>> c.plotsum(0, (5, 10))

Output

Visualize ELFCAR

>>> from vaspy.electro import ElfCar
>>> a = ElfCar()
>>> a.plot_contour()   # Plot coutour
>>> a.plot_mcontour()  # Plot coutour using mlab(with Mayavi installed)
>>> a.plot_contour3d() # Plot 3D coutour
>>> a.plot_field()     # Plot scalar field

Output

3D contour

Scalar field

Charge difference (Use ChgCar class)

Manipulate XDATCAR:

>>> from vaspy.atomco import XdatCar
>>> xdatcar = XdatCar()
>>> # Get Cartisan coordinates and step number in XDATCAR.
>>> for item in xdatcar:
>>>     print(item.step)
>>>     print(xdatcar.dir2cart(xdatcar.bases, item.coordinates))

>>> python xdatcar_to_arc.py

animation

Process animation file:

Now VASPy can manipulate animation files to get more realistice results like atom trajectories or 2D/3D probability distribution.

You can write your OWN script to process VASP files

From the author

Welcome to use VASPy (●'◡'●)ﾉ♥

If you find any bug, please report it to me by opening a issue.
VASPy needs to be improved, your contribution will be welcomed.

Important update log

Date	Version	Description
2016-08-08	0.7.0	Enhance universality
2016-07-15	0.6.0	Compatible with python 3
2015-08-04	0.1.0	Initial version

vaspy's People

Contributors

Stargazers

Watchers

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odconfront avrise songsr lemon5847 li-kezhi dyaopf kcantosh hsulab captaindasheng triphysics paperdock rebortboss yabeiwu amani739861 zqhuang2014 jtsun ndari hungpham2017 litao1991 nicolaschotard zhenyuanwei syllzp wwjcmp nickirk kaswat liming-liu choudarykvsp chrinide aoowweenn jchxu antimo24 foresighter007 jochym rlpaul zjyx147 yangkf1985 373kice realac qiyeqiao ljzhou86 lijielife chenminacm supersonic594 tamaswells finthon 2013311026 qiwen77 gvenus yanhuanjin hnwglsh ramanavais chang-renlab huazhz lxf-gzu wasxiyabbi joshua-sexton quantummisaka agrh fuzhuliu xinyud01 alvinxds hitliaomq jhkim96 cjbartel yunyeongchoi cooperhp wangvei zhucongx qlyang94 flash-jaehyun yinxx sailfish009 kittiphong-am computational-chemistry-research songsiwei computational-nanoscience-group-usf martely xmcao-ccc sangicook cdk6182chr 540340079 zwj2 skyirm huzhyn chandan2710 zshtju pshatom xiaoxl-tu raolixiang-up iq-scm nikyadav002 qingshanbao zzzmx-josh

vaspy's Issues

vaspy路径错误

在cannopy环境中，C:\Users\y7216\Downloads\VASPy-master\scripts\md_viz\map.py路径下运行vasp包中的map程序发生报错：

C:\Users\y7216\AppData\Local\Enthought\Canopy\edm\envs\User\lib\site-packages\matplotlib\pyplot.py:524: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_open_warning`).
  max_open_warning, RuntimeWarning)
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
C:\Users\y7216\Downloads\VASPy-master\scripts\md_viz\map.py in <module>()
     29     # Merge all positions.
     30 
---> 31     trajs = get_trajectories()
     32     positions = np.concatenate(trajs)
     33 
C:\Users\y7216\Downloads\VASPy-master\scripts\md_viz\traj.py in get_trajectories()
     12 
     13 def get_trajectories():
---> 14     xdatcar = XdatCar()
     15     ani = AniFile()
     16 
C:\Users\y7216\AppData\Local\Enthought\Canopy\edm\envs\User\lib\site-packages\vaspy\atomco.py in __init__(self, filename)
    488           ============  =======================================================
    489         """
--> 490         AtomCo.__init__(self, filename)
    491         self.info_nline = 7  # line numbers of lattice info
    492         self.load()
C:\Users\y7216\AppData\Local\Enthought\Canopy\edm\envs\User\lib\site-packages\vaspy\atomco.py in __init__(self, filename)
     24     "Base class to be inherited by atomco classes."
     25     def __init__(self, filename):
---> 26         VasPy.__init__(self, filename)
     27 
     28     def verify(self):
C:\Users\y7216\AppData\Local\Enthought\Canopy\edm\envs\User\lib\site-packages\vaspy\__init__.py in __init__(self, filename)
     30         # Check filename validity.
     31 
---> 32         if not os.path.exists(filename):
     33             raise ValueError("{} not exist!!!".format(filename')+'!)
     34 
ValueError: XDATCAR not exist.

在map代码报错位置前一行添加： print(os.path)语句后，结果中增加了一行：
%run "C:/Users/y7216/Downloads/VASPy-master/scripts/md_viz/map.py" C:\Users\y7216\AppData\Local\Enthought\Canopy\edm\envs\User\lib\site-packages\matplotlib\pyplot.py:524: RuntimeWarning: More than 20 figures have been opened.
同样的问题也存在test系列程序中

Traceback (most recent call last):
  File "C:\Users\y7216\Downloads\VASPy-master\tests\incar_test.py", line 23, in test_rdata
    incar = InCar(filename)
  File "C:\Users\y7216\AppData\Local\Enthought\Canopy\edm\envs\User\lib\site-packages\vaspy\incar.py", line 32, in __init__
    super(self.__class__, self).__init__(filename)
  File "C:\Users\y7216\AppData\Local\Enthought\Canopy\edm\envs\User\lib\site-packages\vaspy\__init__.py", line 32, in __init__
    if not os.path.exists(filename):
ValueError: ./testdata/INCAR not exist.

----------------------------------------------------------------------
Ran 9 tests in 0.016s

FAILED (errors=8)

Error in Reading ELFCAR

Hi,
I am facing issues with reading the ELFCAR file with VASPy.
Do you think if its a python issue or something else?

map_mayavi 需要的 PySide、PyQt4 不能适配现在的python版本

这两个库已经停止更新，对于最新的cannopy环境中自带的python3.5没有可用的PySide、PyQt4库

How to do a contour_3d plot of an ELFCAR for a hexagonal cell?

It is easy to do a contour_3d plot of an ELFCAR plot for orthogonal cell. But for the hexagonal cell, it will be wrongly reshaped to orthogonal cell. Now, for a hexagonal cell, what should I do to get a right visualization?

CHGCAR plot error

I get the following error

Traceback (most recent call last):
  File "test.py", line 9, in <module>
    a = ChgCar()
  File "/home/gallo/software/VASPy/vaspy/electro.py", line 549, in __init__
    ElfCar.__init__(self, filename)
  File "/home/gallo/software/VASPy/vaspy/electro.py", line 268, in __init__
    super(ElfCar, self).__init__(filename)
  File "/home/gallo/software/VASPy/vaspy/atomco.py", line 357, in __init__
    self.load()
  File "/home/gallo/software/VASPy/vaspy/electro.py", line 289, in load
    datalist = line2list(line)
  File "/home/gallo/software/VASPy/vaspy/functions.py", line 20, in line2list
    datalist = [dtype(i) for i in strlist if i != '']
  File "/home/gallo/software/VASPy/vaspy/functions.py", line 20, in <listcomp>
    datalist = [dtype(i) for i in strlist if i != '']
ValueError: could not convert string to float: 'augmentation'

witht the following script

import vaspy

from vaspy.electro import ChgCar

a = ChgCar()

a.plot_contour3d()

调用XsdFile创建POSCAR的问题

您好！这几天在学习VASP，看到您提供的代码，觉得挺好的，想试用一下。但是发现按照您的scripts里边的例子，调用XsdFile类创建POSCAR时候，出现了两个问题。

您的这个代码不能识别P1群之外的其他空间群吗？我发现如果我用Materials Studio 7.0创建的.xsd文件，如果不是P1群，生成的POSCAR就缺对称原子。
创建的POSCAR总是缺第一个原子。比如我用了一个Na8Cl8的.xsd晶胞做测试，发现得到的POSCAR漏掉了原点处的那个Na原子。

我用的Python是2.7版本，MS是7.0版本，用的操作系统是Win10 (32-bit)。因为您提供的.xsd测试文件是8.0版本，我的MS打不开，所以没法测试。附件是MS7.0生成的NaCl文件，我改写的Windows版本的POSCAR生成的Python脚本以及生成的POSCAR，可以看见POSCAR里边缺了原点处的Na原子。想请教一下是哪里出了问题？十分感谢！

test.zip

求助DOS绘制和计算相关内容

您好开发者，
非常感谢您能开发这款方便的工具，有一个疑问就是如何快速分别地计算带有自旋极化的态密度积分数值（如下图，分别计算up和down的积分），并且计算出他们的d-band center，另外如何进行一个选定区域的积分态密度计算（如-1～0eV区域）。
是否需要重新编写脚本呢，还是可以在vaspy自带功能框架下实现？谢谢！！

canopy install error

Hi there,
I got stuck in the installation through canopy. The canopy env is all set, while

weiweis@cori07:~/vaspy-0.8.6> canopy-pip install vaspy
-bash: /global/homes/w/weiweis/Canopy/appdata/canopy-2.1.6.3665.rh6-x86_64/bin/pip: /home/vagrant/workspace/Canopy-Installers/ARCH/64bit/LABEL/rh6/build_scripts/: bad interpreter: No such file or directory

I was trying to find it in setup.py to change /home/vagrant/workspace/Canopy-Installers/ARCH/64bit/LABEL/rh6/build_scripts/, but unfortunately, it's not there.

Could you figure out the error?

Thanks
Bests,
Weiwei