PyVaspwfc
This is a python class for dealing with VASP
pseudowavefunction file WAVECAR
.
It can be used to extract the planewave coefficients of any single KohnSham (KS)
orbital from the file. In addition, by padding the planewave coefficients to a
3D grid and performing 3D Fourier Transform, the pseudowavefunction in real
space can also be obtained and saved to file that can be viewed with VESTA
.
Transition dipole moment
With the knowledge of the planewave coefficients of the
pseudowavefunction,
transition dipole moment between
any two KS states can also be calculated.
Inverse Participation Ratio
IPR is a measure of the localization of KohnSham states. For a particular KS
state \phi_j, it is defined as
\sum_n \phi_j(n)^4
IPR(\phi_j) = 
\sum_n \phi_j(n)^2^2
where n iters over the number of grid points.
Electron Localization Function
(Still need to be tested!)
In quantum chemistry, the electron localization function (ELF) is a measure of
the likelihood of finding an electron in the neighborhood space of a reference
electron located at a given point and with the same spin. Physically, this
measures the extent of spatial localization of the reference electron and
provides a method for the mapping of electron pair probability in
multielectronic systems. (from wiki)
 Nature, 371, 683686 (1994)
 Becke and Edgecombe, J. Chem. Phys., 92, 5397(1990)
 M. Kohout and A. Savin, Int. J. Quantum Chem., 60, 875882(1996)
 http://www2.cpfs.mpg.de/ELF/index.php?content=06interpr.txt
NOTE that if you are using VESTA to view the resulting ELF file, please rename
the output file as “ELFCAR”, otherwise there will be some error in the
isosurface plot! When VESTA read in CHG*/PARCHG/*.vasp to visualize isosurfaces
and sections, data values are divided by volume in the unit of bohr^3. The unit
of charge densities input by VESTA is, therefore, bohr^−3. For LOCPOT/ELFCAR
files, volume data are kept intact.
Band unfolding
Using the pseudowavefunction from supercell calculation, it is possible to
perform electronic band structure unfolding to obtain the effective band
structure. For more information, please refer to the following article and the
GPAW website.
V. Popescu and A. Zunger Extracting E versus k effective band structure
from supercell calculations on alloys and impurities Phys. Rev. B 85, 085201
(2012)
Installation

Manual Installation
Put
vasp_constant.py
andvaspwfc.py
in any directory you like and add the
path of the directory toPYTHONPATH
export PYTHONPATH=/the/path/of/your/dir:${PYTHONPATH}
requirements
 numpy
 scipy
 matplotlib

Using Pip
pip install git+https://github.com/QijingZheng/VaspBandUnfolding
Examples
Pseudowavefunction in real space
 Write a simple script and choose whichever state you like.
from vaspwfc import vaspwfc
wav = vaspwfc('./examples/wfc_r/WAVECAR')
# KS orbital in real space, double the size of the FT grid
phi = wav.wfc_r(ikpt=2, iband=27, ngrid=wav._ngrid * 2)
# Save the orbital into files. Since the wavefunction consist of complex
# numbers, the real and imaginary part are saved separately.
wav.save2vesta(phi, poscar='./examples/wfc_r/POSCAR')
# for WAVECAR from a noncollinear run, the wavefunction at each kpiont/band is
# a two component spinor. Turn on the lsorbit flag when reading WAVECAr.
xx = vaspwfc('examples/wfc_r/wavecar_mose2wse2', lsorbit=True)
phi_spinor = xx.wfc_r(1, 1, 36, ngrid=xx._ngrid*2)
for ii in range(2):
phi = phi_spinor[ii]
prefix = 'spinor_{:02d}'.format(ii)
xx.save2vesta(phi, prefix=prefix,
poscar='examples/wfc_r/poscar_mose2wse2')
Below are the real (left) and imaginary (right) part of the selected KS orbital:
 Or you can also use the script
wfcplot
in thescripts
folder
$ wfcplot w WAVECAR p POSCAR s spin_index k kpoint_index n band_index # for normal WAVECAR
$ wfcplot w WAVECAR p POSCAR s spin_index k kpoint_index n band_index lgamma # for gammaonly WAVECAR
$ wfcplot w WAVECAR p POSCAR s spin_index k kpoint_index n band_index lgamma # for noncollinear WAVECAR
Please refer to wfcplot h
for more information of the usage.
Electron Localization Function
import numpy as np
from vaspwfc import vaspwfc, save2vesta
kptw = [1, 6, 6, 6, 6, 6, 6, 12, 12, 12, 6, 6, 12, 12, 6, 6]
wfc = vaspwfc('./WAVECAR')
# chi = wfc.elf(kptw=kptw, ngrid=wfc._ngrid * 2)
chi = wfc.elf(kptw=kptw, ngrid=[20, 20, 150])
save2vesta(chi[0], lreal=True, poscar='POSCAR', prefix='elf')
Remember to rename the output file “elf_r.vasp” as “ELFCAR”!
Band unfolding
Here, we use MoS2 as an example to illustrate the procedures of band unfolding.
Below is the band structure of MoS2 using a primitive cell. The calculation was
performed with VASP
and the input files can be found in the
examples/unfold/primitive

Create the supercell from the primitive cell, in my case, the supercell is of
the size 3x3x1, which means that the transformation matrix between supercell
and primitive cell is# The tranformation matrix between supercell and primitive cell. M = [[3.0, 0.0, 0.0], [0.0, 3.0, 0.0], [0.0, 0.0, 1.0]]

In the second step, generate band path in the primitive Brillouin Zone (PBZ)
and find the correspondig K points of the supercell BZ (SBZ) onto which they
fold.from unfold import make_kpath, removeDuplicateKpoints, find_K_from_k # highsymmetry point of a Hexagonal BZ in fractional coordinate kpts = [[0.0, 0.5, 0.0], # M [0.0, 0.0, 0.0], # G [1./3, 1./3, 0.0], # K [0.0, 0.5, 0.0]] # M # create band path from the highsymmetry points, 30 points inbetween each pair # of highsymmetry points kpath = make_kpath(kpts, nseg=30) K_in_sup = [] for kk in kpath: kg, g = find_K_from_k(kk, M) K_in_sup.append(kg) # remove the duplicate Kpoints reducedK, kid = removeDuplicateKpoints(K_in_sup, return_map=True) # save to VASP KPOINTS save2VaspKPOINTS(reducedK)

Do one nonSCF calculation of the supercell using the folded Kpoints and
obtain the corresponding pseudowavefunction. The input files are in
examples/unfold/sup_3x3x1/
. The effective band structure (EBS) and
then be obtained by processing the WAVECAR file.from unfold import unfold # basis vector of the primitive cell cell = [[ 3.1850, 0.0000000000000000, 0.0], [1.5925, 2.7582909110534373, 0.0], [ 0.0000, 0.0000000000000000, 35.0]] WaveSuper = unfold(M=M, wavecar='WAVECAR') from unfold import EBS_scatter sw = WaveSuper.spectral_weight(kpath) # show the effective band structure with scatter EBS_scatter(kpath, cell, sw, nseg=30, eref=4.01, ylim=(3, 4), factor=5) from unfold import EBS_cmaps e0, sf = WaveSuper.spectral_function(nedos=4000) # or show the effective band structure with colormap EBS_cmaps(kpath, cell, e0, sf, nseg=30, eref=4.01, show=False, ylim=(3, 4))
The EBS from a 3x3x1 supercell calculation are shown below:
Another example of EBS from a 3x3x1 supercell calculation, where we introduce a
S
vacancy in the structure.Yet another band unfolding example from a tetragonal 3x3x1 supercell
calculation, where the transformation matrix isM = [[3.0, 0.0, 0.0], [3.0, 6.0, 0.0], [0.0, 0.0, 1.0]]
Compared to the band structure of the primitive cell, there are some empty
states at the top of figure. This is due to a too small value ofNBANDS
in
supercell nonscf calculation, and thus those states are not included.
Band unfolding wth atomic contributions
After band unfolding, we can also superimpose the atomic contribution of each KS
states on the spectral weight. Below is the resulting unfolded band structure of
Cedoped bilayerMoS2. Refer to
./examples/unfold/[email protected]_3x3x1/plt_unf.py
for the entire code.
Band reordering
Band reordering is possible by maximizing the overlap between nerghbouring
kpoints. The overlap is defined as the inner product of the periodic part of
the Bloch wavefunctions.
`< u(n, k)  u(m, k1) >`
Note, however, the WAVECAR
only contains the pseudowavefunction, and thus the
pseudo u(n,k)
are used in this function. Moreover, since the number of
planewaves for each kpoints are different, the inner product is performed in
real space.
The overlap maximalization procedure is as follows:
 Pick out those bands with large overlap (> olap_cut).
 Assign those unpicked bands by maximizing the overlap.
An example band structure reordering is performed in MoS2. The result is shown
in the following image, where the left/right panel shows the
unordered/reordered band structure.