本家チュートリアル1 〜其之弐〜で説明した,Cut3Dを用いた電荷密度ファイル変換操作例をひとまとめにして再掲します。緑色文字がユーザー入力部分,赤色文字がabinitからの質問です。
D:\abinit\L01>cut3d
.Version 7.4.3 of CUT3D
.(MPI version, prepared for a i686_cygwin_gnu4.7 computer)
.Copyright (C) 1998-2013 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.t
xt .
Please read ~abinit/doc/users/acknowledgments.html for suggested
acknowledgments of the ABINIT effort.
For more information, see http://www.abinit.org .
.Starting date : Mon 17 Nov 2014.
- ( at 02h08 )
What is the name of the 3D function (density, potential or wavef) file ?
tbase1_xo_DEN
=> Your 3D function file is : tbase1_xo_DEN
Does this file contain formatted 3D ASCII data (=0)
or unformatted binary header + 3D data (=1) ?
or ETSF binary (=2) ?
1
1 => Your file contains unformatted binary header + 3D data
The information it contains should be sufficient.
cut3d : read file tbase1_xo_DEN from unit number 19.
===============================================================================
ECHO of the ABINIT file header
First record :
.codvsn,headform,fform = 7.4.3 57 52
Second record :
bantot,intxc,ixc,natom = 2 0 1 2
ngfft(1:3),nkpt = 30 30 30 1
nspden,nspinor = 1 1
nsppol,nsym,npsp,ntypat = 1 16 1 1
occopt,pertcase,usepaw = 1 0 0
ecut,ecutdg,ecutsm = 1.0000000000E+01 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) = 1.0000000000E+01 0.0000000000E+00 0.0000000000E+00
rprimd(1:3,2) = 0.0000000000E+00 1.0000000000E+01 0.0000000000E+00
rprimd(1:3,3) = 0.0000000000E+00 0.0000000000E+00 1.0000000000E+01
stmbias,tphysel,tsmear = 0.0000000000E+00 0.0000000000E+00 4.0000000000E-02
Third record :
istwfk= 2
nband = 2
npwarr= 752
so_psp= 1
symafm=
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
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
type = 1 1
kptns = (max 50 k-points will be written)
0.000000E+00 0.000000E+00 0.000000E+00
wtk =
1.00
occ =
2.00 0.00
tnons =
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
znucl= 1.00
Pseudopotential info :
title=Goedecker-Teter-Hutter Wed May 8 14:27:44 EDT 1996
znuclpsp= 1.00, zionpsp= 1.00, pspso= 0, pspdat=960508, pspcod= 2, pspxc=
1
lmnmax = 1
Last record :
residm,etot,fermie= 5.807846E-12 -1.103722421314E+00 -3.652486E-01
xred =
-7.000000E-02 0.000000E+00 0.000000E+00
7.000000E-02 0.000000E+00 0.000000E+00
End the ECHO of the ABINIT file header
===============================================================================
===========================================================
ECHO important input variables ...
Dimensional primitive vectors (ABINIT equivalent : rprimd):
1.000000E+01 0.000000E+00 0.000000E+00
0.000000E+00 1.000000E+01 0.000000E+00
0.000000E+00 0.000000E+00 1.000000E+01
Grid density (ABINIT equivalent : ngfft): 30 30 30
Number of atoms : 2
Number of atomic types: 1
# Atomic positions (cartesian coordinates - Bohr)
1 -7.000000E-01 0.000000E+00 0.000000E+00
2 7.000000E-01 0.000000E+00 0.000000E+00
This file is a Density or Potential file
3D function was read. Ready for further treatment.
===========================================================
What is your choice ? Type:
0 => exit
1 => point (interpolation of data for a single point)
2 => line (interpolation of data along a line)
3 => plane (interpolation of data in a plane)
4 => volume (interpolation of data in a volume)
5 => 3D formatted data (output the bare 3D data - one column)
6 => 3D indexed data (bare 3D data, preceeded by 3D index)
7 => 3D Molekel formatted data
8 => 3D data with coordinates (tecplot ASCII format)
9 => output .xsf file for XCrysDen
10 => output .dx file for OpenDx
11 => compute atomic charge using the Hirshfeld method
12 => NetCDF file
14 => Gaussian/cube wavefunction module
9
Your choice is 9
Enter the name of an output file:
tbase1_1.xsf
The name of your file is : tbase1_1.xsf
Extremas (x,y,z) of the cube in which the molecule is placed, in Angstroms
0.00000 5.29177 0.00000 5.29177 0.00000 5.29177
Number of points per side: 31 31 31
Total number of points: 29791
znucl = 1.0000000000000000 type = 1 1 ntypat =
1
Do you want to shift the grid along the x,y or z axis (y/n)?
n
Task 9 has been done !
More analysis of the 3D file ? ( 0=no ; 1=default=yes ; 2= treat another file -
restricted usage)
0
Provide some global information about the density and/or potential file(s)
File number 1, with name "tbase1_xo_DEN"
Number of grid points = 27000 ; Volume of real space cell (Bohr^3)= 1.0
00000E+03
Spin-component number 1
Sum of values, mean, mean times cell volume= 5.400000E+01 2.000000E-
03 2.000000E+00
Provide some global joint information about the stored density and potential fi
le(s)
File numbers : 1 1
Spin-component number 1
Dot product of values, mean, mean times cell volume= 4.091044E+00 1.
515201E-04 1.515201E-01
-
- Proc. 0 individual time (sec): cpu= 1.0 wall= 237.2
Thank you for using me
D:\abinit\L01>
.Version 7.4.3 of CUT3D
.(MPI version, prepared for a i686_cygwin_gnu4.7 computer)
.Copyright (C) 1998-2013 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.t
xt .
Please read ~abinit/doc/users/acknowledgments.html for suggested
acknowledgments of the ABINIT effort.
For more information, see http://www.abinit.org .
.Starting date : Mon 17 Nov 2014.
- ( at 02h08 )
What is the name of the 3D function (density, potential or wavef) file ?
tbase1_xo_DEN
=> Your 3D function file is : tbase1_xo_DEN
Does this file contain formatted 3D ASCII data (=0)
or unformatted binary header + 3D data (=1) ?
or ETSF binary (=2) ?
1
1 => Your file contains unformatted binary header + 3D data
The information it contains should be sufficient.
cut3d : read file tbase1_xo_DEN from unit number 19.
===============================================================================
ECHO of the ABINIT file header
First record :
.codvsn,headform,fform = 7.4.3 57 52
Second record :
bantot,intxc,ixc,natom = 2 0 1 2
ngfft(1:3),nkpt = 30 30 30 1
nspden,nspinor = 1 1
nsppol,nsym,npsp,ntypat = 1 16 1 1
occopt,pertcase,usepaw = 1 0 0
ecut,ecutdg,ecutsm = 1.0000000000E+01 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) = 1.0000000000E+01 0.0000000000E+00 0.0000000000E+00
rprimd(1:3,2) = 0.0000000000E+00 1.0000000000E+01 0.0000000000E+00
rprimd(1:3,3) = 0.0000000000E+00 0.0000000000E+00 1.0000000000E+01
stmbias,tphysel,tsmear = 0.0000000000E+00 0.0000000000E+00 4.0000000000E-02
Third record :
istwfk= 2
nband = 2
npwarr= 752
so_psp= 1
symafm=
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
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
type = 1 1
kptns = (max 50 k-points will be written)
0.000000E+00 0.000000E+00 0.000000E+00
wtk =
1.00
occ =
2.00 0.00
tnons =
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
znucl= 1.00
Pseudopotential info :
title=Goedecker-Teter-Hutter Wed May 8 14:27:44 EDT 1996
znuclpsp= 1.00, zionpsp= 1.00, pspso= 0, pspdat=960508, pspcod= 2, pspxc=
1
lmnmax = 1
Last record :
residm,etot,fermie= 5.807846E-12 -1.103722421314E+00 -3.652486E-01
xred =
-7.000000E-02 0.000000E+00 0.000000E+00
7.000000E-02 0.000000E+00 0.000000E+00
End the ECHO of the ABINIT file header
===============================================================================
===========================================================
ECHO important input variables ...
Dimensional primitive vectors (ABINIT equivalent : rprimd):
1.000000E+01 0.000000E+00 0.000000E+00
0.000000E+00 1.000000E+01 0.000000E+00
0.000000E+00 0.000000E+00 1.000000E+01
Grid density (ABINIT equivalent : ngfft): 30 30 30
Number of atoms : 2
Number of atomic types: 1
# Atomic positions (cartesian coordinates - Bohr)
1 -7.000000E-01 0.000000E+00 0.000000E+00
2 7.000000E-01 0.000000E+00 0.000000E+00
This file is a Density or Potential file
3D function was read. Ready for further treatment.
===========================================================
What is your choice ? Type:
0 => exit
1 => point (interpolation of data for a single point)
2 => line (interpolation of data along a line)
3 => plane (interpolation of data in a plane)
4 => volume (interpolation of data in a volume)
5 => 3D formatted data (output the bare 3D data - one column)
6 => 3D indexed data (bare 3D data, preceeded by 3D index)
7 => 3D Molekel formatted data
8 => 3D data with coordinates (tecplot ASCII format)
9 => output .xsf file for XCrysDen
10 => output .dx file for OpenDx
11 => compute atomic charge using the Hirshfeld method
12 => NetCDF file
14 => Gaussian/cube wavefunction module
9
Your choice is 9
Enter the name of an output file:
tbase1_1.xsf
The name of your file is : tbase1_1.xsf
Extremas (x,y,z) of the cube in which the molecule is placed, in Angstroms
0.00000 5.29177 0.00000 5.29177 0.00000 5.29177
Number of points per side: 31 31 31
Total number of points: 29791
znucl = 1.0000000000000000 type = 1 1 ntypat =
1
Do you want to shift the grid along the x,y or z axis (y/n)?
n
Task 9 has been done !
More analysis of the 3D file ? ( 0=no ; 1=default=yes ; 2= treat another file -
restricted usage)
0
Provide some global information about the density and/or potential file(s)
File number 1, with name "tbase1_xo_DEN"
Number of grid points = 27000 ; Volume of real space cell (Bohr^3)= 1.0
00000E+03
Spin-component number 1
Sum of values, mean, mean times cell volume= 5.400000E+01 2.000000E-
03 2.000000E+00
Provide some global joint information about the stored density and potential fi
le(s)
File numbers : 1 1
Spin-component number 1
Dot product of values, mean, mean times cell volume= 4.091044E+00 1.
515201E-04 1.515201E-01
-
- Proc. 0 individual time (sec): cpu= 1.0 wall= 237.2
Thank you for using me
D:\abinit\L01>
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