https://github.com/asaboor-gh/pivotpy
Python Processing Tool for Vasp Ipnut/Output
https://github.com/asaboor-gh/pivotpy
bandstructure dft dos interpolate matplotlib plotly powershell python spin-polarized vasprun
Last synced: 3 months ago
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Python Processing Tool for Vasp Ipnut/Output
- Host: GitHub
- URL: https://github.com/asaboor-gh/pivotpy
- Owner: asaboor-gh
- License: apache-2.0
- Created: 2020-04-11T22:01:15.000Z (almost 6 years ago)
- Default Branch: master
- Last Pushed: 2023-07-06T21:36:36.000Z (over 2 years ago)
- Last Synced: 2025-09-06T11:28:22.410Z (5 months ago)
- Topics: bandstructure, dft, dos, interpolate, matplotlib, plotly, powershell, python, spin-polarized, vasprun
- Language: Jupyter Notebook
- Homepage: https://massgh.github.io/pivotpy/
- Size: 340 MB
- Stars: 13
- Watchers: 2
- Forks: 6
- Open Issues: 5
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
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README
# PivotPy
> A Python Processing Tool for Vasp Input/Output. A CLI is available in Powershell, see Vasp2Visual.
[](https://testazurenotebooks-massaz.notebooks.azure.com/j/notebooks/test.ipynb)
[](https://colab.research.google.com/github/massgh/pivotpy/blob/master/test.ipynb)
a{text-decoration: none !important;color:lightkblue;font-weight:bold;}
a:focus,a:active,a:hover{color:hotpink !important;}
> [ `▶` Index● ](https://massgh.github.io/pivotpy/)
> [ `▶` Example ](https://massgh.github.io/pivotpy/Example)
> [ `▶` StaticPlots ](https://massgh.github.io/pivotpy/StaticPlots)
> [ `▶` InteractivePlots ](https://massgh.github.io/pivotpy/InteractivePlots)
> [ `▶` SpinProjectedSurfaces ](https://massgh.github.io/pivotpy/SpinProjectedSurfaces)
> [ `▶` StructureIO ](https://massgh.github.io/pivotpy/StructureIO)
> [ `▶` Widgets ](https://massgh.github.io/pivotpy/Widgets)
> [ `▶` MainAPI ](https://massgh.github.io/pivotpy/MainAPI)
## Install
`pip install pivotpy`
To install as developer and make changes (Recommended), do the following:
```shell
git clone https://github.com/massgh/pivotpy.git
cd pivotpy
pip install -r requirements.txt
pip install -e .
```
## How to use
- Use commnad `pivotpy` in regular terminal to quickly launch documentation any time.
- See [Full Documentation](https://massgh.github.io/pivotpy/).
- See a [Calculation Example](https://massgh.github.io/pivotpy/Example.html)
- For CLI, use [Vasp2Visual](https://github.com/massgh/Vasp2Visual).
- See [PDF Slides](https://github.com/massgh/InteractiveHTMLs/tree/master/docs/IPySlides.pdf) for detailed introduction.
## CLI commnds
- Use `pivotpy` in system terminal to launch DOCS.
- Use `pivotpy_get_poscar` to download POSCAR.
- Use `pivotpy_get_kpath` to create fine controlled KPATH.
## Plot in Terminal without GUI
Use `pp.plt2text(colorful=True/False)` after matplotlib's code and your figure will appear in terminal. You need to zoom out alot to get a good view like below.
Tip: Use file [matplotlib2terminal.py](https://gist.github.com/massgh/d5cc44ad32510d3ff58cfefd75c6884e) on github independent of this package to plot in terminal.
# Ipywidgets-based GUI
See GIF here:
# Live Slides in Jupyter Notebook
Navigate to [ipyslides](https://github.com/massgh/ipyslides) or do `pip install ipyslides` to create beautiful data driven presentation in Jupyter Notebook.
```python
import os, pivotpy as pp
with pp.set_dir('E:/Research/graphene_example/ISPIN_1/bands'):
vr = pp.Vasprun(elim=[-5,5])
print('Try Follwing Methods:')
for v in dir(vr):
if not v.startswith('_'):
print('vr.'+v)
```
Try Follwing Methods:
vr.Fermi
vr.data
vr.elim
vr.fermi
vr.get_band_info
vr.get_en_diff
vr.get_fermi
vr.iplot_dos_lines
vr.iplot_rgb_lines
vr.kticks
vr.poscar
vr.select
vr.splot_bands
vr.splot_color_lines
vr.splot_dos_lines
vr.splot_en_diff
vr.splot_rgb_lines
vr.to_json
vr.to_pickle
```python
import matplotlib.pyplot as plt
ax1,ax2 = pp.get_axes((6,3),ncols=2)
ax1.plot(vr.data.scsteps['e_fr_energy'],lw=3, label = 'e_fr_energy',color='k')
ax1.plot(vr.data.scsteps['e_0_energy'],lw=0.7,ls='dashed',label='e_0_energy',color='skyblue')
ax1.set_ylabel('Energy (eV)')
ax1.set_xlabel('Iteration Number')
ax1.legend()
vr.poscar.splot_lat(ax=ax2,plane='xy')
X, Y, Z = vr.data.poscar.coords.T
q = ax2.quiver(X,Y,*vr.data.force[:,:2].T,scale=25,color='r')
ax2.quiverkey(q, 0.7, 1, 7, 'Force (arb. units)')
ax2.add_legend()
```
## Matplotlib's static plots
- Add anything from legend,colorbar, colorwheel. In below figure, all three are shown.
- Use aliases such as sbands, sdos,srgb,irgb,scolor,idos for plotting.
```python
#collapse_input
import pivotpy as pp, numpy as np
import matplotlib.pyplot as plt
vr1=pp.Vasprun('E:/Research/graphene_example/ISPIN_2/bands/vasprun.xml')
vr2=pp.Vasprun('E:/Research/graphene_example/ISPIN_2/dos/vasprun.xml')
axs = pp.get_axes(ncols=3,widths=[2,1,2.2],sharey=True,wspace=0.05,figsize=(8,2.6))
elements=[0,[0],[0,1]]
orbs=[[0],[2],[1,3]]
labels=['s','$p_z$','$(p_x+p_y)$']
ti_cks=dict(ktick_inds=[0,30,60,-1],ktick_vals=['Γ','M','K','Γ'])
args_dict=dict(elements=elements,orbs=orbs,labels=labels,elim=[-20,15],colormap='viridis',)
vr1.splot_bands(ax=axs[0],**ti_cks,elim=[-20,15])
vr1.splot_rgb_lines(ax=axs[2],**args_dict,**ti_cks,colorbar=False)
vr2.splot_dos_lines(ax=axs[1],vertical=True,spin='both',include_dos='pdos',**args_dict,legend_kwargs={'ncol': 3})
axs[2].color_cube(loc=(0.7,0.25),size=0.35)
pp._show()
```
[0;92m Given 0 at position 1 of sequence => 'C': range(0, 2). To just pick one ion, write it as [0].[00m
## Interactive plots using plotly
```python
args_dict['labels'] = ['s','p_z','p_x+p_y']
args_dict.pop('colormap')
fig1 = vr1.iplot_rgb_lines(**args_dict)
#pp.iplot2html(fig1) #Do inside Google Colab, fig1 inside Jupyter
from IPython.display import Markdown
Markdown("[See Interactive Plot](https://massgh.github.io/InteractiveHTMLs/iGraphene.html)")
```
[See Interactive Plot](https://massgh.github.io/InteractiveHTMLs/iGraphene.html)
## Brillouin Zone (BZ) Processing
- Look in `pivotpy.sio` module or `pivotpy.api.POSCAR` class for details on generating mesh and path of KPOINTS as well as using Materials Projects' API to get POSCAR right in the working folder. Below is a screenshot of interactive BZ plot. You can `double click` on blue points and hit `Ctrl + C` to copy the high symmetry points relative to reciprocal lattice basis vectors.
- Same color points lie on a sphere, with radius decreasing as red to blue and gamma point in gold color. These color help distinguishing points but the points not always be equivalent, for example in FCC, there are two points on mid of edges connecting square-hexagon and hexagon-hexagon at equal distance from center but not the same points.
- Any colored point's hover text is in gold background.
#### Look the output of `pivotpy.sio.splot_bz`.
[See Interactive BZ Plot](https://massgh.github.io/InteractiveHTMLs/BZ.html)
## Interpolation
Amost every bandstructure and DOS plot function has an argument `interp_nk` which is a dictionary with keys `n` (Number of additional points between adjacent points) and `k` (order of interpolation 0-3). `n > k` must hold.
```python
#collapse_input
import pivotpy as pp, matplotlib.pyplot as plt
plt.style.use('ggplot')
k = vr1.data.kpath
ef = vr1.data.bands.Fermi
evals = vr1.data.bands.evals.SpinUp - ef
#Let's interpolate our graph to see effect. It is useful for colored graphs.
knew,enew=pp.interpolate_data(x=k,y=evals,n=10,k=3)
plot = plt.plot(k,evals,'m',lw=5,label='real data')
plot = plt.plot(k,evals,'w',lw=1,label='interpolated',ls='dashed')
pp.splots.add_text(ax=plt.gca(),txts='Graphene')
```
## LOCPOT,CHG Visualization
check out the class `pivotpy.LOCPOT` to visulize local potential/charge and magnetization in a given direction.
## Running powershell commands from python.
Some tasks are very tideious in python while just a click way in powershell. See below, and try to list processes in python yourself to see the difference!
```python
pp.utils.ps2std(ps_command='(Get-Process)[0..4]')
```
[32;1m NPM(K) PM(M) WS(M) CPU(s) Id SI ProcessName[0m
[32;1m ------ ----- ----- ------ -- -- -----------[0m
22 6.92 8.27 0.33 14100 1 AcrobatNot…
6 1.29 5.68 0.00 7724 0 Aggregator…
19 7.22 20.85 0.00 5608 0 AppHelperC…
26 39.25 57.59 0.48 2064 1 Applicatio…
9 1.67 6.88 0.00 5264 0 armsvc
## Advancaed: Poweshell Cell/Line Magic `%%ps/%ps`
- You can create a IPython cell magic to run powershell commands directly in IPython Shell/Notebook (Powershell core installation required).
- Cell magic can be assigned to a variable `foo` by `%%ps --out foo`
- Line magic can be assigned to a variable by `foo = %ps powershell_command`
Put below code in ipython profile's startup file (create one) "~/.ipython/profile_default/startup/powershell_magic.py"
```python
from IPython.core.magic import register_line_cell_magic
from IPython import get_ipython
@register_line_cell_magic
def ps(line, cell=None):
if cell:
return get_ipython().run_cell_magic('powershell',line,cell)
else:
get_ipython().run_cell_magic('powershell','--out posh_output',line)
return posh_output.splitlines()
```
Additionally you need to add following lines in "~/.ipython/profile_default/ipython_config.py" file to make above magic work.
```python
from traitlets.config.application import get_config
c = get_config()
c.ScriptMagics.script_magics = ['powershell']
c.ScriptMagics.script_paths = {
'powershell' : 'powershell.exe -noprofile -command -',
'pwsh': 'pwsh.exe -noprofile -command -'
}
```
```python
%%ps
Get-ChildItem 'E:\Research\graphene_example\'
```
Directory: E:\Research\graphene_example
Mode LastWriteTime Length Name
---- ------------- ------ ----
da---- 6/9/2022 10:33 AM ISPIN_1
da---- 5/9/2020 1:05 PM ISPIN_2
-a---- 5/9/2020 1:01 PM 75331 OUTCAR
-a---- 5/9/2020 1:01 PM 240755 vasprun.xml
```python
x = %ps (Get-ChildItem 'E:\Research\graphene_example\').Name
x
```
['ISPIN_1', 'ISPIN_2', 'OUTCAR', 'vasprun.xml']
[Functions Reference](functions.md)
a{text-decoration: none !important;color:lightkblue;font-weight:bold;}
a:focus,a:active,a:hover{color:hotpink !important;}
> [ `▶` Index● ](https://massgh.github.io/pivotpy/)
> [ `▶` Example ](https://massgh.github.io/pivotpy/Example)
> [ `▶` StaticPlots ](https://massgh.github.io/pivotpy/StaticPlots)
> [ `▶` InteractivePlots ](https://massgh.github.io/pivotpy/InteractivePlots)
> [ `▶` SpinProjectedSurfaces ](https://massgh.github.io/pivotpy/SpinProjectedSurfaces)
> [ `▶` StructureIO ](https://massgh.github.io/pivotpy/StructureIO)
> [ `▶` Widgets ](https://massgh.github.io/pivotpy/Widgets)
> [ `▶` MainAPI ](https://massgh.github.io/pivotpy/MainAPI)