forum@abinit.org
Subject: The ABINIT Users Mailing List ( CLOSED )
List archive
- From: "Amancherla, Sundar (CORP, GEITC)" <Sundar.Amancherla@geind.ge.com>
- To: <forum@abinit.org>
- Subject: Al2O3 and Cut3d
- Date: Fri, 26 Sep 2003 16:31:50 +0530
Dear All...
Here is an input file I used for Al2O3 as a start
=============================
#Al2O3 - yttria
ecut 10
prtden 1
# unit cell
acell 4.607 4.607 12.997 angstrom
angdeg 90.0 90.0 120.0
spgroup 167
spgaxor 1
spgorig 1
chkprim 0
brvlatt 0
kptopt 1
ngkpt 1 1 1
natom 30
# Atom types
ntypat 2
znucl 13.0 8.0
# Define atoms
natrd 2
typat 1 2
xred 0.0000 0.0000 0.3521
0.6944 0.0000 0.2500
# define SCF procediew
nstep 40
toldfe 1.0e-6
============================
I have the WFK and DEN files which I wanted to visualize using XCrysden.
I used cut3d on the WFK file. Here are my inputs to cut3d -
============================
$ cut3d
Version 4.1.3 of CUT3D
(sequential version, prepared for a sgi computer)
Copyright (C) 1998-2003 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/Infos/copyright 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/Infos/contributors.
Please read ~ABINIT/Infos/acknowledgments.htm for suggested
acknowledgments of the ABINIT effort.
For more information, see http://www.abinit.org .
Starting date : Fri 26 Sep 2003.
What is the name of the 3D function (density, potential or wavef) file
?
al2o3_kpt111o_WFK
=> Your 3D function file is : al2o3_kpt111o_WFK
Does this file contain formatted 3D ASCII data (=0)
or unformatted binary header + 3D data (=1) ?
1
1 => Your file contains unformatted binary header + 3D data
The information it contains should be sufficient.
cut3d : read file al2o3_kpt111o_WFK from unit number 19.
========================================================
ECHO of the ABINIT file header
First record :
codvsn,headform,fform = 4.1.3 41 2
Second record :
bantot,intxc,ixc,natom = 76 0 1 30
ngfft(1:3),nkpt = 27 27 72 1
nspden,nspinor = 1 1
nsppol,nsym,npsp,ntypat,occopt,pertcase= 1 36 2 2 1
0
ecut,ecutsm = 1.0000000000E+01 0.0000000000E+00
ecut_eff = 1.0000000000E+01
qptn(1:3) = 0.0000000000E+00 0.0000000000E+00
0.0000000000E+00
rprimd(1:3,1) = 8.7059682990E+00 0.0000000000E+00
0.0000000000E+00
rprimd(1:3,2) = -4.3529841495E+00 7.5395897115E+00
0.0000000000E+00
rprimd(1:3,3) = 1.5039134527E-15 2.6048545103E-15
2.4560770563E+01
tphysel,tsmear = 0.0000000000E+00 4.0000000000E-02
Third record :
istwfk= 9
nband = 76
npwarr= 1216
so_typat= 1 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
symrel=
1 0 0 0 1 0 0 0 1 -1 -1 0 1 0 0
0 0 1
0 -1 0 -1 0 0 0 0 1 0 1 0 -1 -1 0
0 0 1
-1 0 0 1 1 0 0 0 1 1 1 0 0 -1 0
0 0 1
-1 0 0 0 -1 0 0 0 -1 1 1 0 -1 0 0
0 0 -1
0 1 0 1 0 0 0 0 -1 0 -1 0 1 1 0
0 0 -1
1 0 0 -1 -1 0 0 0 -1 -1 -1 0 0 1 0
0 0 -1
1 0 0 0 1 0 0 0 1 -1 -1 0 1 0 0
0 0 1
0 -1 0 -1 0 0 0 0 1 0 1 0 -1 -1 0
0 0 1
-1 0 0 1 1 0 0 0 1 1 1 0 0 -1 0
0 0 1
-1 0 0 0 -1 0 0 0 -1 1 1 0 -1 0 0
0 0 -1
0 1 0 1 0 0 0 0 -1 0 -1 0 1 1 0
0 0 -1
1 0 0 -1 -1 0 0 0 -1 -1 -1 0 0 1 0
0 0 -1
1 0 0 0 1 0 0 0 1 -1 -1 0 1 0 0
0 0 1
0 -1 0 -1 0 0 0 0 1 0 1 0 -1 -1 0
0 0 1
-1 0 0 1 1 0 0 0 1 1 1 0 0 -1 0
0 0 1
-1 0 0 0 -1 0 0 0 -1 1 1 0 -1 0 0
0 0 -1
0 1 0 1 0 0 0 0 -1 0 -1 0 1 1 0
0 0 -1
1 0 0 -1 -1 0 0 0 -1 -1 -1 0 0 1 0
0 0 -1
type = 1 2 2 1 2 2 2 2 1 1 1 2
2 1 2 2 2 2 1 1 1 2 2 1
2 2 2 2 1 1
kptns = (max 50 k-points will be written)
5.000000E-01 5.000000E-01 5.000000E-01
occ =
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 0.00 0.00 0.00 0.00
tnons =
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.500000 0.000000 0.000000 0.000000
0.000000 0.000000 0.500000 0.000000 0.000000 0.500000
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.500000 0.000000 0.000000 0.000000
0.000000 0.000000 0.500000 0.000000 0.000000 0.500000
-0.333333 0.333333 0.333333 -0.333333 0.333333 0.333333
-0.333333 0.333333 -0.166667 -0.333333 0.333333 0.333333
-0.333333 0.333333 -0.166667 -0.333333 0.333333 -0.166667
-0.333333 0.333333 0.333333 -0.333333 0.333333 0.333333
-0.333333 0.333333 -0.166667 -0.333333 0.333333 0.333333
-0.333333 0.333333 -0.166667 -0.333333 0.333333 -0.166667
0.333333 -0.333333 -0.333333 0.333333 -0.333333 -0.333333
0.333333 -0.333333 0.166667 0.333333 -0.333333 -0.333333
0.333333 -0.333333 0.166667 0.333333 -0.333333 0.166667
0.333333 -0.333333 -0.333333 0.333333 -0.333333 -0.333333
0.333333 -0.333333 0.166667 0.333333 -0.333333 -0.333333
0.333333 -0.333333 0.166667 0.333333 -0.333333 0.166667
znucl= 13.00 8.00
Pseudopotential info :
title= Troullier-Martins psp for element Al Thu Oct 27 17:31:05
EDT 1994
znuclpsp= 13.00, zionpsp= 3.00, pspso= 1, pspdat=940714, pspcod= 1,
pspxc= 1
title= Troullier-Martins psp for element O Thu Oct 27 17:29:57
EDT 1994
znuclpsp= 8.00, zionpsp= 6.00, pspso= 1, pspdat=940714, pspcod= 1,
pspxc= 1
Last record :
residm,etot,fermie= 3.561236E-05 -3.137004725140E+02
0.000000E+00
xred =
-1.850372E-17 -1.850372E-17 3.521000E-01
6.944000E-01 -1.233581E-17 2.500000E-01
3.056000E-01 3.056000E-01 2.500000E-01
-1.850372E-17 -1.850372E-17 8.521000E-01
-1.850372E-17 3.056000E-01 7.500000E-01
-1.233581E-17 6.944000E-01 2.500000E-01
3.056000E-01 -1.850372E-17 7.500000E-01
6.944000E-01 6.944000E-01 7.500000E-01
-1.850372E-17 -1.850372E-17 6.479000E-01
-1.850372E-17 -1.850372E-17 1.479000E-01
6.666667E-01 3.333333E-01 6.854333E-01
3.610667E-01 3.333333E-01 5.833333E-01
9.722667E-01 6.389333E-01 5.833333E-01
6.666667E-01 3.333333E-01 1.854333E-01
6.666667E-01 6.389333E-01 8.333333E-02
6.666667E-01 2.773333E-02 5.833333E-01
9.722667E-01 3.333333E-01 8.333333E-02
3.610667E-01 2.773333E-02 8.333333E-02
6.666667E-01 3.333333E-01 9.812333E-01
6.666667E-01 3.333333E-01 4.812333E-01
3.333333E-01 6.666667E-01 1.876667E-02
2.773333E-02 6.666667E-01 9.166667E-01
6.389333E-01 9.722667E-01 9.166667E-01
3.333333E-01 6.666667E-01 5.187667E-01
3.333333E-01 9.722667E-01 4.166667E-01
3.333333E-01 3.610667E-01 9.166667E-01
6.389333E-01 6.666667E-01 4.166667E-01
2.773333E-02 3.610667E-01 4.166667E-01
3.333333E-01 6.666667E-01 3.145667E-01
3.333333E-01 6.666667E-01 8.145667E-01
End the ECHO of the ABINIT file header
===========================================================
===========================================================
ECHO important input variables ...
Dimensional primitive vectors (ABINIT equivalent : rprimd):
8.705968E+00 0.000000E+00 0.000000E+00
-4.352984E+00 7.539590E+00 0.000000E+00
1.503913E-15 2.604855E-15 2.456077E+01
Grid density (ABINIT equivalent : ngfft): 27 27 72
Number of atoms : 30
Number of atomic types: 2
# Atomic positions (cartesian coordinates - Bohr)
1 4.489815E-16 7.776588E-16 8.647847E+00
2 6.045424E+00 5.582067E-16 6.140193E+00
3 1.330272E+00 2.304099E+00 6.140193E+00
4 1.200938E-15 2.080086E-15 2.092823E+01
5 -1.330272E+00 2.304099E+00 1.842058E+01
6 -3.022712E+00 5.235491E+00 6.140193E+00
7 2.660544E+00 1.814130E-15 1.842058E+01
8 3.022712E+00 5.235491E+00 1.842058E+01
9 8.938391E-16 1.548175E-15 1.591292E+01
10 1.418824E-16 2.457475E-16 3.632538E+00
11 4.352984E+00 2.513197E+00 1.683477E+01
12 1.692440E+00 2.513197E+00 1.432712E+01
13 5.683256E+00 4.817295E+00 1.432712E+01
14 4.352984E+00 2.513197E+00 4.554386E+00
15 3.022712E+00 4.817295E+00 2.046731E+00
16 5.683256E+00 2.090980E-01 1.432712E+01
17 7.013528E+00 2.513197E+00 2.046731E+00
18 3.022712E+00 2.090980E-01 2.046731E+00
19 4.352984E+00 2.513197E+00 2.409985E+01
20 4.352984E+00 2.513197E+00 1.181946E+01
21 1.360491E-15 5.026393E+00 4.609238E-01
22 -2.660544E+00 5.026393E+00 2.251404E+01
23 1.330272E+00 7.330492E+00 2.251404E+01
24 2.112448E-15 5.026393E+00 1.274131E+01
25 -1.330272E+00 7.330492E+00 1.023365E+01
26 1.330272E+00 2.722295E+00 2.251404E+01
27 2.660544E+00 5.026393E+00 1.023365E+01
28 -1.330272E+00 2.722295E+00 1.023365E+01
29 1.805349E-15 5.026393E+00 7.726000E+00
30 2.557305E-15 5.026393E+00 2.000639E+01
This file is a WF file.
=> Your k-point is : 1
For which band ? (1 to 76)
1
=> Your band number is : 1
=> Your spin polarisation number is : 1
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
0
You entered ratsph= 0.00000000 Bohr
3D wave function was read. Ready for further treatment.
===========================================================
What is your choice ? Type:
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 and position files
12 => exit to k-point / band / spin-pol loop
11
Your choice is 11
Enter the root of an output file:
test
The root of your file is : test
The corresponding filename is : test_k1_b1_s1
Give 1 files of formatted data
The files are ready to be used with XCrysDen
Do you want to shift the grid along the x,y or z axis (y/n)?
n
The name of your data files is :
testy_k1_b1_s1 for the density (norm of the wfk),
==============================================
When I tried using the file with XCrysDen, this is what I have.....
==============================================
ERROR: Error reading DATAGRID_3D_ section, while reading
"/home/aman/tmp/xcrys_tmp/xc_15270/test_k1_b1_s1.raw"
ERROR: An Error occured, while reading XSF file
/home/aman/tmp/xcrys_tmp/xc_15270/test_k1_b1_s1.raw} error 0 OK
************************************************************************
Deleting directory /home/aman/tmp/xcrys_tmp/xc_15270 ; Please Wait !!!
************************************************************************
Failed to delete the directory !
=============================================
APOLOGIES FOR A LONG ONE.... I WANTED TO GIVE ALL THE INFO. PLEASE LET
ME KNOW ANY SUGGESTIONS
TIA
--
Aman
- Al2O3 and Cut3d, Amancherla, Sundar (CORP, GEITC), 09/26/2003
- Re: [abinit-forum] Al2O3 and Cut3d, verstraete, 09/26/2003
Archive powered by MHonArc 2.6.16.