wavefunctions from _WFK file

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wenfei
Posts: 1
Joined: Mon Feb 03, 2020 2:36 am

wavefunctions from _WFK file

Post by wenfei » Mon Feb 03, 2020 3:32 am

Hi,

I ran two test calculations on Be and Ne atoms, respectively, and used cut3d to export wavefunctions from the respective _WFK files into Gaussian Cube files.
What I found was that the files only contain the absolute values of wavefunctions, but not the sign. When I visualize the 2p orbital of Ne with Vesta, both lobes are positive. I also plotted the wavefunction of Be 2s orbital against the distance to the atom, and instead of a node where the radial part cross the axis, I got a kink.
The two pictures are:
https://drive.google.com/file/d/14ghR_k ... sp=sharing
https://drive.google.com/file/d/1eZUOb9 ... sp=sharing

Below I attach the output I got with cut3d for Be atom:

.Version 8.10.2 of CUT3D
.(sequential version, prepared for a x86_64_linux_gnu4.9 computer)

.Copyright (C) 1998-2018 ABINIT group .
CUT3D comes with ABSOLUTELY NO WARRANTY.
It is free software, and you are welcome to redistribute it
under certain conditions (GNU General Public License,
see ~abinit/COPYING or http://www.gnu.org/copyleft/gpl.txt).

ABINIT is a project of the Universite Catholique de Louvain,
Corning Inc. and other collaborators, see ~abinit/doc/developers/contributors.txt .
Please read https://docs.abinit.org/theory/acknowledgments for suggested
acknowledgments of the ABINIT effort.
For more information, see https://www.abinit.org .

.Starting date : Sun 2 Feb 2020.
- ( at 20h21 )


What is the name of the 3D function (density, potential or wavef) file ?
=> Your 3D function file is: tpaw1_1o_WFK

- Your file contains unformatted binary header + 3D data

===============================================================================
ECHO of the ABINIT file header

First record :
.codvsn,headform,fform = 8.10.2 80 2

Second record :
bantot,intxc,ixc,natom = 4 0 9 1
ngfft(1:3),nkpt = 48 48 48 1
nspden,nspinor = 1 1
nsppol,nsym,npsp,ntypat = 1 48 1 1
occopt,pertcase,usepaw = 1 0 1
ecut,ecutdg,ecutsm = 4.0000000000E+01 4.0000000000E+01 5.0000000000E-01
ecut_eff = 4.0000000000E+01
qptn(1:3) = 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
rprimd(1:3,1) = 8.0000000000E+00 0.0000000000E+00 0.0000000000E+00
rprimd(1:3,2) = 0.0000000000E+00 8.0000000000E+00 0.0000000000E+00
rprimd(1:3,3) = 0.0000000000E+00 0.0000000000E+00 8.0000000000E+00
stmbias,tphysel,tsmear = 0.0000000000E+00 0.0000000000E+00 1.0000000000E-02

Third record :
istwfk= 2
nband = 4
npwarr= 3094
so_psp= 1
symafm=
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
symrel=
1 0 0 0 1 0 0 0 1 -1 0 0 0 -1 0 0 0 -1
-1 0 0 0 1 0 0 0 -1 1 0 0 0 -1 0 0 0 1
-1 0 0 0 -1 0 0 0 1 1 0 0 0 1 0 0 0 -1
1 0 0 0 -1 0 0 0 -1 -1 0 0 0 1 0 0 0 1
0 1 0 1 0 0 0 0 1 0 -1 0 -1 0 0 0 0 -1
0 -1 0 1 0 0 0 0 -1 0 1 0 -1 0 0 0 0 1
0 -1 0 -1 0 0 0 0 1 0 1 0 1 0 0 0 0 -1
0 1 0 -1 0 0 0 0 -1 0 -1 0 1 0 0 0 0 1
0 0 1 1 0 0 0 1 0 0 0 -1 -1 0 0 0 -1 0
0 0 -1 1 0 0 0 -1 0 0 0 1 -1 0 0 0 1 0
0 0 -1 -1 0 0 0 1 0 0 0 1 1 0 0 0 -1 0
0 0 1 -1 0 0 0 -1 0 0 0 -1 1 0 0 0 1 0
1 0 0 0 0 1 0 1 0 -1 0 0 0 0 -1 0 -1 0
-1 0 0 0 0 1 0 -1 0 1 0 0 0 0 -1 0 1 0
-1 0 0 0 0 -1 0 1 0 1 0 0 0 0 1 0 -1 0
1 0 0 0 0 -1 0 -1 0 -1 0 0 0 0 1 0 1 0
0 1 0 0 0 1 1 0 0 0 -1 0 0 0 -1 -1 0 0
0 -1 0 0 0 1 -1 0 0 0 1 0 0 0 -1 1 0 0
0 -1 0 0 0 -1 1 0 0 0 1 0 0 0 1 -1 0 0
0 1 0 0 0 -1 -1 0 0 0 -1 0 0 0 1 1 0 0
0 0 1 0 1 0 1 0 0 0 0 -1 0 -1 0 -1 0 0
0 0 -1 0 1 0 -1 0 0 0 0 1 0 -1 0 1 0 0
0 0 -1 0 -1 0 1 0 0 0 0 1 0 1 0 -1 0 0
0 0 1 0 -1 0 -1 0 0 0 0 -1 0 1 0 1 0 0
type = 1
kptns = (max 50 k-points will be written)
0.000000E+00 0.000000E+00 0.000000E+00
wtk =
1.00
occ =
2.00 2.00 0.00 0.00
tnons =
0.000000 0.000000 0.000000 -0.025000 -0.025000 -0.025000
-0.025000 0.000000 -0.025000 0.000000 -0.025000 0.000000
-0.025000 -0.025000 0.000000 0.000000 0.000000 -0.025000
0.000000 -0.025000 -0.025000 -0.025000 0.000000 0.000000
0.000000 0.000000 0.000000 -0.025000 -0.025000 -0.025000
0.000000 -0.025000 -0.025000 -0.025000 0.000000 0.000000
-0.025000 -0.025000 0.000000 0.000000 0.000000 -0.025000
-0.025000 0.000000 -0.025000 0.000000 -0.025000 0.000000
0.000000 0.000000 0.000000 -0.025000 -0.025000 -0.025000
0.000000 -0.025000 -0.025000 -0.025000 0.000000 0.000000
-0.025000 0.000000 -0.025000 0.000000 -0.025000 0.000000
-0.025000 -0.025000 0.000000 0.000000 0.000000 -0.025000
0.000000 0.000000 0.000000 -0.025000 -0.025000 -0.025000
-0.025000 -0.025000 0.000000 0.000000 0.000000 -0.025000
-0.025000 0.000000 -0.025000 0.000000 -0.025000 0.000000
0.000000 -0.025000 -0.025000 -0.025000 0.000000 0.000000
0.000000 0.000000 0.000000 -0.025000 -0.025000 -0.025000
-0.025000 -0.025000 0.000000 0.000000 0.000000 -0.025000
0.000000 -0.025000 -0.025000 -0.025000 0.000000 0.000000
-0.025000 0.000000 -0.025000 0.000000 -0.025000 0.000000
0.000000 0.000000 0.000000 -0.025000 -0.025000 -0.025000
-0.025000 0.000000 -0.025000 0.000000 -0.025000 0.000000
0.000000 -0.025000 -0.025000 -0.025000 0.000000 0.000000
-0.025000 -0.025000 0.000000 0.000000 0.000000 -0.025000
znucl= 4.00

Pseudopotential info :
title=Be
znuclpsp= 4.00, zionpsp= 4.00, pspso= 0, pspdat=******, pspcod= 17, pspxc= 7
lmn_size= 8

Last record :
residm,etot,fermie= 9.278309E-14 -1.461514959254E+01 -2.270450E-01
xred =
4.875000E-01 4.875000E-01 4.875000E-01
rhoij( 1,1)= (max 12 non-zero components will be written)
1.99898 -0.01214 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
-0.01214 1.57156 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
End the ECHO of the ABINIT file header
===============================================================================

===========================================================

ECHO important input variables ...

Dimensional primitive vectors (ABINIT equivalent: rprimd):
8.000000E+00 0.000000E+00 0.000000E+00
0.000000E+00 8.000000E+00 0.000000E+00
0.000000E+00 0.000000E+00 8.000000E+00
Grid density (ABINIT equivalent: ngfft): 48 48 48
Number of atoms : 1
Number of atomic types: 1

# Atomic positions (cartesian coordinates - Bohr)
1 3.900000E+00 3.900000E+00 3.900000E+00

This file is a WF file.
=> Your k-point is : 1


For which band ? (1 to 4)
=> Your band number is : 1

=> Your spin polarisation number is : 1

Do you want to analyze a GW wavefunction? (1=yes,0=no)
=> Your choice is : 0

Do you want the atomic analysis for this state :
(kpt,band)= ( 1 1)?
If yes, enter the radius of the atomic spheres, in bohr
If no, enter 0
You entered ratsph= 0.00000000 Bohr

3D wave function was read. Ready for further treatment.

===========================================================

What is your choice ? Type:
0 => exit to k-point / band / spin-pol loop
1 => 3D formatted real and imaginary data
(output the bare 3D data - two column,R,I)
2 => 3D formatted real data
(output the bare 3D data - one column)
3 => 3D formatted imaginary data
(output the bare 3D data - one column)
4 => 3D indexed real and imaginary data
(3D data, preceeded by 3D index)
5 => 3D indexed real data
(bare 3D data, preceeded by 3D index)
6 => 3D indexed imaginary data
(bare 3D data, preceeded by 3D index)
7 => 3D Data Explorer formatted data
(Real file and Imaginary file)
8 => 3D Data Explorer formatted data
(Only the Real file)
9 => 3D Data Explorer formatted data
(Only the Imaginary file)
10 => 3D Data Explorer formatted data and position files
11 => XCrysden formatted data (norm of wf) and position files
12 => NetCDF data and position file
13 => XCrysden/VENUS wavefunction (real part of data)
14 => Gaussian/cube wavefunction module

Your choice is 14


Enter the root of an output file:
The root of your file is : orb
The corresponding filename is : orb_k1_b1

Output a cube file of 3D volumetric data

Task 14 has been done !

Run interpolation again? (1=default=yes,0=no)
=> Your k-point is : 1


For which band ? (1 to 4)
=> Your band number is : 2

=> Your spin polarisation number is : 1

Do you want to analyze a GW wavefunction? (1=yes,0=no)
=> Your choice is : 0

Do you want the atomic analysis for this state :
(kpt,band)= ( 1 2)?
If yes, enter the radius of the atomic spheres, in bohr
If no, enter 0
You entered ratsph= 0.00000000 Bohr

3D wave function was read. Ready for further treatment.

===========================================================

What is your choice ? Type:
0 => exit to k-point / band / spin-pol loop
1 => 3D formatted real and imaginary data
(output the bare 3D data - two column,R,I)
2 => 3D formatted real data
(output the bare 3D data - one column)
3 => 3D formatted imaginary data
(output the bare 3D data - one column)
4 => 3D indexed real and imaginary data
(3D data, preceeded by 3D index)
5 => 3D indexed real data
(bare 3D data, preceeded by 3D index)
6 => 3D indexed imaginary data
(bare 3D data, preceeded by 3D index)
7 => 3D Data Explorer formatted data
(Real file and Imaginary file)
8 => 3D Data Explorer formatted data
(Only the Real file)
9 => 3D Data Explorer formatted data
(Only the Imaginary file)
10 => 3D Data Explorer formatted data and position files
11 => XCrysden formatted data (norm of wf) and position files
12 => NetCDF data and position file
13 => XCrysden/VENUS wavefunction (real part of data)
14 => Gaussian/cube wavefunction module

Your choice is 14


Enter the root of an output file:
The root of your file is : orb
The corresponding filename is : orb_k1_b2

Output a cube file of 3D volumetric data

Task 14 has been done !

Run interpolation again? (1=default=yes,0=no)
=> Your k-point is : 1


For which band ? (1 to 4)
=> Your band number is : 3

=> Your spin polarisation number is : 1

Do you want to analyze a GW wavefunction? (1=yes,0=no)
=> Your choice is : 0

Do you want the atomic analysis for this state :
(kpt,band)= ( 1 3)?
If yes, enter the radius of the atomic spheres, in bohr
If no, enter 0
You entered ratsph= 0.00000000 Bohr

3D wave function was read. Ready for further treatment.

===========================================================

What is your choice ? Type:
0 => exit to k-point / band / spin-pol loop
1 => 3D formatted real and imaginary data
(output the bare 3D data - two column,R,I)
2 => 3D formatted real data
(output the bare 3D data - one column)
3 => 3D formatted imaginary data
(output the bare 3D data - one column)
4 => 3D indexed real and imaginary data
(3D data, preceeded by 3D index)
5 => 3D indexed real data
(bare 3D data, preceeded by 3D index)
6 => 3D indexed imaginary data
(bare 3D data, preceeded by 3D index)
7 => 3D Data Explorer formatted data
(Real file and Imaginary file)
8 => 3D Data Explorer formatted data
(Only the Real file)
9 => 3D Data Explorer formatted data
(Only the Imaginary file)
10 => 3D Data Explorer formatted data and position files
11 => XCrysden formatted data (norm of wf) and position files
12 => NetCDF data and position file
13 => XCrysden/VENUS wavefunction (real part of data)
14 => Gaussian/cube wavefunction module

Your choice is 14


Enter the root of an output file:
The root of your file is : orb
The corresponding filename is : orb_k1_b3

Output a cube file of 3D volumetric data

Task 14 has been done !

Run interpolation again? (1=default=yes,0=no)
=> Your k-point is : 1


For which band ? (1 to 4)
=> Your band number is : 4

=> Your spin polarisation number is : 1

Do you want to analyze a GW wavefunction? (1=yes,0=no)
=> Your choice is : 0

Do you want the atomic analysis for this state :
(kpt,band)= ( 1 4)?
If yes, enter the radius of the atomic spheres, in bohr
If no, enter 0
You entered ratsph= 0.00000000 Bohr

3D wave function was read. Ready for further treatment.

===========================================================

What is your choice ? Type:
0 => exit to k-point / band / spin-pol loop
1 => 3D formatted real and imaginary data
(output the bare 3D data - two column,R,I)
2 => 3D formatted real data
(output the bare 3D data - one column)
3 => 3D formatted imaginary data
(output the bare 3D data - one column)
4 => 3D indexed real and imaginary data
(3D data, preceeded by 3D index)
5 => 3D indexed real data
(bare 3D data, preceeded by 3D index)
6 => 3D indexed imaginary data
(bare 3D data, preceeded by 3D index)
7 => 3D Data Explorer formatted data
(Real file and Imaginary file)
8 => 3D Data Explorer formatted data
(Only the Real file)
9 => 3D Data Explorer formatted data
(Only the Imaginary file)
10 => 3D Data Explorer formatted data and position files
11 => XCrysden formatted data (norm of wf) and position files
12 => NetCDF data and position file
13 => XCrysden/VENUS wavefunction (real part of data)
14 => Gaussian/cube wavefunction module

Your choice is 14


Enter the root of an output file:
The root of your file is : orb
The corresponding filename is : orb_k1_b4

Output a cube file of 3D volumetric data

Task 14 has been done !

Run interpolation again? (1=default=yes,0=no)
-
- Proc. 0 individual time (sec): cpu= 0.8 wall= 0.8

Thank you for using me

Best,
Wenfei

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