[Wien] wien2phon package
Dr. Sharat Chandra
sharat at igcar.ernet.in
Mon Sep 26 11:34:16 CEST 2005
Dear Georg
I have been able to make the makedisp.pl script work properly for Si test
case. I have used the 1x1x1 unit cell in primitive (P1) space group. The
INPHON, DISP, POSCAR and case.struct files are attached.
After going through the script, I found that on line 48 one exit command
was not commented out. The errors reported in my mail were due to the fact
that I had not copied the SPOSCAR file to the POSCAR before attempting to
run the makedisp.pl script. It wants the input to be in proper format,
which is available only in SPOSCAR file.
With these modifications, I was able to run the makedisp.pl script and
create the CASE_* directories with the relevent files. But while creating
the different case directories, makedisp.pl prints warnings like:
Use of uninitialized value in addition (+) at ./makedisp.pl line 51.
Use of uninitialized value in concatenation (.) or string at ./makedisp.pl line 56.
Use of uninitialized value in concatenation (.) or string at ./makedisp.pl line 56.
Use of uninitialized value in concatenation (.) or string at ./makedisp.pl line 56.
and more messages like:
Use of uninitialized value in addition (+) at ./makedisp.pl line 96, <STRUC> line 57.
for all the lines of case.struct file. But the runs on each subdirectories
are completed without any problems.
The problem now is in extract.pl script. When I run the command
'extract.pl <case> [start]' in the top level calculation directory after
the scf runs are completed, I get the readline error:
readline() on closed filehandle PIP at /usr/local/wien2k/extract.pl line 16.
0 displacements found in .indisp
It shows that a file ".indsp" should exist in the directory before
extract.pl is run , but does not exist. How this file is created? Here I
took the start option to be the start case directory (CASE_00) in one case
and start for another, but with the same error.
Any way, I made the FORCES file by hand as the format is simple. That file
is also attached with this mail. I want to ask you that in the script you
multiply the :FOR forces with mRy/a.u. multiplication factor, but the
forces in :FOR are already in mRy/a.u. units, so is it necessary?
But with all this I am able to get only the DOS* files and not the
dispersion files. What is the error in the INPHON file?
Thanks for all the trouble.
Regards
Sharat Chandra
On Mon, 26 Sep 2005 georg at chem.au.dk wrote:
> Dear Sharat
>
> please attach your INPHON, DISP and POSCAR files which are used by makedisp.pl
> and I'll try to have a look at it
>
> Best wishes Georg
>
> Quoting "Dr. Sharat Chandra" <sharat at igcar.ernet.in>:
>
> > Dear Dr. Madsen
> >
> > I am trying to use the wien2phon package to calculate the phonon modes for
> > the Zn(CN)2 compound. The struct file is attached with the mail.
> >
> > I have followed the instructions in the README file in wien2phon package
> > till point 4 (generated POSCAR file, generated DISP file using PHON,
> > generated SPOSCAR file (with LSUPER = .T.; NDIM = 1 1 1; DISP = 200), and
> > used the attached struct file, which is already a supercell (2x2x2) and
> > initialized the wien2k calculation). Now after that when I want to run the
> > makedisp.pl command, I get the following error:
> >
> > Math::MatrixReal::new_from_rows(): Column mismatch 3 != 6 at
> > /usr/local/wien2k/makedisp.pl line 37
> >
> > The command then exits with out any other output.
> >
> > I am using the perl-Math-MatrixReal-1.9-1.2.fc4.rf rpm from Dries RPM
> > Repository and perl-5.8.6-15 on a Fedora Core 4 system with ifort 8.1
> > compiler and mkl-7.2.1 libraries.
> >
> > Can you please help me to get to the origin of the error? Is it because of
> > some mismatch with the version of perl-Math-MatrixReal module or is it
> > because of some error in the procedure that I have followed?
-------------- next part --------------
" 1 0.01000000 0.00000000 0.00000000 " \
" 1 0.00000000 0.01000000 0.00000000 " \
" 1 0.00000000 0.00000000 0.01000000 " \
" 2 0.01000000 0.00000000 0.00000000 " \
" 2 0.00000000 0.01000000 0.00000000 " \
" 2 0.00000000 0.00000000 0.01000000 " \
" 3 0.01000000 0.00000000 0.00000000 " \
" 3 0.00000000 0.01000000 0.00000000 " \
" 3 0.00000000 0.00000000 0.01000000 " \
" 4 0.01000000 0.00000000 0.00000000 " \
" 4 0.00000000 0.01000000 0.00000000 " \
" 4 0.00000000 0.00000000 0.01000000 " \
" 5 0.01000000 0.00000000 0.00000000 " \
" 5 0.00000000 0.01000000 0.00000000 " \
" 5 0.00000000 0.00000000 0.01000000 " \
" 6 0.01000000 0.00000000 0.00000000 " \
" 6 0.00000000 0.01000000 0.00000000 " \
" 6 0.00000000 0.00000000 0.01000000 " \
" 7 0.01000000 0.00000000 0.00000000 " \
" 7 0.00000000 0.01000000 0.00000000 " \
" 7 0.00000000 0.00000000 0.01000000 " \
" 8 0.01000000 0.00000000 0.00000000 " \
" 8 0.00000000 0.01000000 0.00000000 " \
" 8 0.00000000 0.00000000 0.01000000 " \
-------------- next part --------------
# symmetryze force constant matrix
# LSYMM=.FALSE.
NTI = 1
# generate superlattice
LSUPER = .T.
NDIM = 1 1 1
# number of ions types and masses
NTYPES = 8
MASS = 28.0855 28.0855 28.0855 28.0855 28.0855 28.0855 28.0855 28.0855
USETHIS = .T. .T. .T. .T. .T. .T. .T. .T.
# free energy calculation
LFREE = .TRUE.
TEMPERATURE = 1000
# q points section
LRECIP = .T.
ND = 4; NPOINTS = 50
QI = 0.5 0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.5 0.0 0.5
QF = 0.0 0.0 0.0 0.5 0.0 0.0 0.5 0.0 0.5 0.0 0.0 0.0
# density of states
LGAMMA = .TRUE.
QA = 12; QB = 12; QC = 12
DOSIN = 0; DOSEND = 25; DOSSTEP = 0.1; DOSSMEAR = 0.4
# write force constant matrix
# LFORCEOUT = .T.
# verbosity
IPRINT = 2
-------------- next part --------------
super cell
1.8897264359
5.429358000000000 0.000000000000000 0.000000000000000
0.000000000000000 5.429358000000000 0.000000000000000
0.000000000000000 0.000000000000000 5.429358000000000
1 1 1 1 1 1 1 1
Direct
0.375000000000000 0.375000000000000 0.375000000000000
0.625000000000000 0.625000000000000 0.625000000000000
0.875000000000000 0.875000000000000 0.375000000000000
0.125000000000000 0.125000000000000 0.625000000000000
0.875000000000000 0.375000000000000 0.875000000000000
0.125000000000000 0.625000000000000 0.125000000000000
0.375000000000000 0.875000000000000 0.875000000000000
0.625000000000000 0.125000000000000 0.125000000000000
-------------- next part --------------
24
1 0.01000000 0.00000000 0.00000000
-5.739 0.000 0.000
1.694 0.639 0.638
0.176 0.000 0.000
1.680 0.614 -0.614
0.176 0.000 0.000
1.680 -0.614 0.614
-1.377 0.000 0.000
1.694 -0.639 -0.638
1 0.00000000 0.01000000 0.00000000
0.000 -5.738 0.000
0.638 1.694 0.638
0.000 0.176 0.000
0.614 1.680 -0.614
0.000 -1.376 0.000
-0.638 1.694 -0.638
0.000 0.176 0.000
-0.613 1.680 0.614
1 0.00000000 0.00000000 0.01000000
0.000 0.000 -5.739
0.638 0.639 1.694
0.000 0.000 -1.376
-0.639 -0.638 1.694
0.000 0.000 0.176
0.614 -0.614 1.680
0.000 0.000 0.176
-0.613 0.613 1.680
2 0.01000000 0.00000000 0.00000000
1.680 0.614 0.614
-5.739 0.000 0.000
1.694 0.639 -0.638
0.176 0.000 0.000
1.694 -0.639 0.638
0.176 0.000 0.000
1.680 -0.614 -0.614
-1.377 0.000 0.000
2 0.00000000 0.01000000 0.00000000
0.614 1.680 0.614
0.000 -5.738 0.000
0.638 1.694 -0.638
0.000 0.176 0.000
-0.613 1.680 -0.614
0.000 -1.376 0.000
-0.638 1.694 0.638
0.000 0.176 0.000
2 0.00000000 0.00000000 0.01000000
0.614 0.614 1.680
0.000 0.000 -5.739
-0.613 -0.613 1.680
0.000 0.000 -1.376
0.638 -0.639 1.694
0.000 0.000 0.176
-0.639 0.638 1.694
0.000 0.000 0.176
3 0.01000000 0.00000000 0.00000000
0.176 0.000 0.000
1.680 0.614 -0.614
-5.739 0.000 0.000
1.694 0.639 0.638
-1.377 0.000 0.000
1.694 -0.639 -0.638
0.176 0.000 0.000
1.680 -0.614 0.614
3 0.00000000 0.01000000 0.00000000
0.000 0.176 0.000
0.614 1.680 -0.614
0.000 -5.738 0.000
0.638 1.694 0.638
0.000 0.176 0.000
-0.613 1.680 0.614
0.000 -1.376 0.000
-0.638 1.694 -0.638
3 0.00000000 0.00000000 0.01000000
0.000 0.000 -1.376
-0.639 -0.638 1.694
0.000 0.000 -5.739
0.638 0.639 1.694
0.000 0.000 0.176
-0.613 0.613 1.680
0.000 0.000 0.176
0.614 -0.614 1.680
4 0.01000000 0.00000000 0.00000000
1.694 0.639 -0.638
0.176 0.000 0.000
1.680 0.614 0.614
-5.739 0.000 0.000
1.680 -0.614 -0.614
-1.377 0.000 0.000
1.694 -0.639 0.638
0.176 0.000 0.000
4 0.00000000 0.01000000 0.00000000
0.638 1.694 -0.638
0.000 0.176 0.000
0.614 1.680 0.614
0.000 -5.738 0.000
-0.638 1.694 0.638
0.000 0.176 0.000
-0.613 1.680 -0.614
0.000 -1.376 0.000
4 0.00000000 0.00000000 0.01000000
-0.613 -0.613 1.680
0.000 0.000 -1.376
0.614 0.614 1.680
0.000 0.000 -5.739
-0.639 0.638 1.694
0.000 0.000 0.176
0.638 -0.639 1.694
0.000 0.000 0.176
5 0.01000000 0.00000000 0.00000000
0.176 0.000 0.000
1.680 -0.614 0.614
-1.377 0.000 0.000
1.694 -0.639 -0.638
-5.739 0.000 0.000
1.694 0.639 0.638
0.176 0.000 0.000
1.680 0.614 -0.614
5 0.00000000 0.01000000 0.00000000
0.000 -1.376 0.000
-0.638 1.694 -0.638
0.000 0.176 0.000
-0.613 1.680 0.614
0.000 -5.738 0.000
0.638 1.694 0.638
0.000 0.176 0.000
0.614 1.680 -0.614
5 0.00000000 0.00000000 0.01000000
0.000 0.000 0.176
0.614 -0.614 1.680
0.000 0.000 0.176
-0.613 0.613 1.680
0.000 0.000 -5.739
0.638 0.639 1.694
0.000 0.000 -1.376
-0.639 -0.638 1.694
6 0.01000000 0.00000000 0.00000000
1.694 -0.639 0.638
0.176 0.000 0.000
1.680 -0.614 -0.614
-1.377 0.000 0.000
1.680 0.614 0.614
-5.739 0.000 0.000
1.694 0.639 -0.638
0.176 0.000 0.000
6 0.00000000 0.01000000 0.00000000
-0.613 1.680 -0.614
0.000 -1.376 0.000
-0.638 1.694 0.638
0.000 0.176 0.000
0.614 1.680 0.614
0.000 -5.738 0.000
0.638 1.694 -0.638
0.000 0.176 0.000
6 0.00000000 0.00000000 0.01000000
0.638 -0.639 1.694
0.000 0.000 0.176
-0.639 0.638 1.694
0.000 0.000 0.176
0.614 0.614 1.680
0.000 0.000 -5.739
-0.613 -0.613 1.680
0.000 0.000 -1.376
7 0.01000000 0.00000000 0.00000000
-1.377 0.000 0.000
1.694 -0.639 -0.638
0.176 0.000 0.000
1.680 -0.614 0.614
0.176 0.000 0.000
1.680 0.614 -0.614
-5.739 0.000 0.000
1.694 0.639 0.638
7 0.00000000 0.01000000 0.00000000
0.000 0.176 0.000
-0.613 1.680 0.614
0.000 -1.376 0.000
-0.638 1.694 -0.638
0.000 0.176 0.000
0.614 1.680 -0.614
0.000 -5.738 0.000
0.638 1.694 0.638
7 0.00000000 0.00000000 0.01000000
0.000 0.000 0.176
-0.613 0.613 1.680
0.000 0.000 0.176
0.614 -0.614 1.680
0.000 0.000 -1.376
-0.639 -0.638 1.694
0.000 0.000 -5.739
0.638 0.639 1.694
8 0.01000000 0.00000000 0.00000000
1.680 -0.614 -0.614
-1.377 0.000 0.000
1.694 -0.639 0.638
0.176 0.000 0.000
1.694 0.639 -0.638
0.176 0.000 0.000
1.680 0.614 0.614
-5.739 0.000 0.000
8 0.00000000 0.01000000 0.00000000
-0.638 1.694 0.638
0.000 0.176 0.000
-0.613 1.680 -0.614
0.000 -1.376 0.000
0.638 1.694 -0.638
0.000 0.176 0.000
0.614 1.680 0.614
0.000 -5.738 0.000
8 0.00000000 0.00000000 0.01000000
-0.639 0.638 1.694
0.000 0.000 0.176
0.638 -0.639 1.694
0.000 0.000 0.176
-0.613 -0.613 1.680
0.000 0.000 -1.376
0.614 0.614 1.680
0.000 0.000 -5.739
-------------- next part --------------
Silicon
P LATTICE,NONEQUIV.ATOMS: 8
MODE OF CALC=RELA unit=bohr
10.260000 10.260000 10.260000 90.000000 90.000000 90.000000
ATOM -1: X=0.37500000 Y=0.37500000 Z=0.37500000
MULT= 1 ISPLIT= 8
Si1 NPT= 781 R0=0.00010000 RMT= 2.2100 Z: 14.0
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
0.0000000 1.0000000 0.0000000
0.0000000 0.0000000 1.0000000
ATOM -2: X=0.62500000 Y=0.62500000 Z=0.62500000
MULT= 1 ISPLIT= 8
Si2 NPT= 781 R0=0.00010000 RMT= 2.2100 Z: 14.0
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
0.0000000 1.0000000 0.0000000
0.0000000 0.0000000 1.0000000
ATOM -3: X=0.87500000 Y=0.87500000 Z=0.37500000
MULT= 1 ISPLIT= 8
Si3 NPT= 781 R0=0.00010000 RMT= 2.2100 Z: 14.0
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
0.0000000 1.0000000 0.0000000
0.0000000 0.0000000 1.0000000
ATOM -4: X=0.12500000 Y=0.12500000 Z=0.62500000
MULT= 1 ISPLIT= 8
Si4 NPT= 781 R0=0.00010000 RMT= 2.2100 Z: 14.0
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
0.0000000 1.0000000 0.0000000
0.0000000 0.0000000 1.0000000
ATOM -5: X=0.87500000 Y=0.37500000 Z=0.87500000
MULT= 1 ISPLIT= 8
Si5 NPT= 781 R0=0.00010000 RMT= 2.2100 Z: 14.0
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
0.0000000 1.0000000 0.0000000
0.0000000 0.0000000 1.0000000
ATOM -6: X=0.12500000 Y=0.62500000 Z=0.12500000
MULT= 1 ISPLIT= 8
Si6 NPT= 781 R0=0.00010000 RMT= 2.2100 Z: 14.0
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
0.0000000 1.0000000 0.0000000
0.0000000 0.0000000 1.0000000
ATOM -7: X=0.37500000 Y=0.87500000 Z=0.87500000
MULT= 1 ISPLIT= 8
Si7 NPT= 781 R0=0.00010000 RMT= 2.2100 Z: 14.0
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
0.0000000 1.0000000 0.0000000
0.0000000 0.0000000 1.0000000
ATOM -8: X=0.62500000 Y=0.12500000 Z=0.12500000
MULT= 1 ISPLIT= 8
Si8 NPT= 781 R0=0.00010000 RMT= 2.2100 Z: 14.0
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
0.0000000 1.0000000 0.0000000
0.0000000 0.0000000 1.0000000
1 NUMBER OF SYMMETRY OPERATIONS
1 0 0 0.0000000
0 1 0 0.0000000
0 0 1 0.0000000
1
More information about the Wien
mailing list