Discussion:
[Pw_forum] Error with gnuplot
Roberto G. A. Veiga
2005-01-12 19:40:31 UTC
Permalink
When I try to view a plot using gnuplot, I see:

gnuplot> 25 25 1 0.41666666666667E-01 0.41666666666667E-01
^
"plots/charge.plot", line 1: invalid command

Why?

[]s,

Roberto



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Eyvaz Isaev
2005-01-12 21:55:25 UTC
Permalink
Hi,

Probably, you try to run a command "gnuplot file.dat".

If so, it is not correct. First you should enter
"gnuplot" and then "plot file.dat".
If you try to visualize a 3D object, say charge
density, "splot" command should be used and this case
requires some additional keys.
If you like to see a charge density mapped on a plane,
I remember, a PS-file should be produced by program.
In this case Gnuplot is not required. Just enter "gv
file.ps" (or ggv instead gv).

If the aforementioned cases are not your case, please
provide more information.

Bests,
Eyvaz.
Post by Roberto G. A. Veiga
gnuplot> 25 25 1 0.41666666666667E-01
0.41666666666667E-01
^
"plots/charge.plot", line 1: invalid
command
Why?
[]s,
Roberto
---------------------------------
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http://democracialiberal.blogspot.com.
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Roberto G. A. Veiga
2005-01-13 16:02:00 UTC
Permalink
Ok, now it works. Thank you, Eyvaz.

By the way, which format should I use to save STM images?I've tried gOpenMol, but gOpenMol says there are problems with the [Atoms] tag.

[]s,

Roberto

Eyvaz Isaev <eyvaz_isaev at yahoo.com> wrote:
Hi,

Probably, you try to run a command "gnuplot file.dat".

If so, it is not correct. First you should enter
"gnuplot" and then "plot file.dat".
If you try to visualize a 3D object, say charge
density, "splot" command should be used and this case
requires some additional keys.
If you like to see a charge density mapped on a plane,
I remember, a PS-file should be produced by program.
In this case Gnuplot is not required. Just enter "gv
file.ps" (or ggv instead gv).

If the aforementioned cases are not your case, please
provide more information.

Bests,
Eyvaz.
gnuplot> 25 25 1 0.41666666666667E-01
0.41666666666667E-01
^
"plots/charge.plot", line 1: invalid
command
Why?
[]s,
Roberto
---------------------------------
Blogs: http://robertoveiga.blogspot.com e
http://democracialiberal.blogspot.com.
---------------------------------
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Yahoo!




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Paolo Giannozzi
2005-01-15 21:54:07 UTC
Permalink
Post by Roberto G. A. Veiga
By the way, which format should I use to save STM images?
I've tried gOpenMol, but gOpenMol says there are problems
with the [Atoms] tag.
example 16 deals with STM images. The gOpenMol format is
implemented only for 3d plot, I think. All valid 2d formats
(documented in INPUT_CHDENS) should work.

Paolo
Paolo Giannozzi
2005-01-15 21:54:07 UTC
Permalink
Post by Roberto G. A. Veiga
By the way, which format should I use to save STM images?
I've tried gOpenMol, but gOpenMol says there are problems
with the [Atoms] tag.
example 16 deals with STM images. The gOpenMol format is
implemented only for 3d plot, I think. All valid 2d formats
(documented in INPUT_CHDENS) should work.

Paolo
aaron
2005-01-17 14:24:50 UTC
Permalink
Hi All,

I'm trying to view my charge density output. I succeed to write an xsf
file but I do not have a viewer (vmd 1.8.3 is failing on my platform(s)).
I'd like to write a cube file, but the chdens.x complains when I set my
output_format=6. The error is "Atom C not found". How can I alleviate
this error? I'd like to note that I'm trying to generate a cube file
from densities of a complete system and taking the difference between
that and it's constituents (illustrated below). Could this be the
problem? Has anyone experience with converting a .xsf to .cube format?
I'm appending my input file for chdens.x to the end of this message.

Thanks for your kind and helpful suggestions,

Aaron

&input
nfile = 3,
filepp(1) = '../C32form.bs/C32formbscharge',
filepp(2) = '../C32.bs/C32bscharge',
filepp(3) = '../form.bs/${JOB}charge',
weight(1) =-1.0,
weight(2) = 1.0,
weight(3) = 1.0,
iflag = 3,
plot_out = 1,
output_format = 5, !! 6 for cube file
fileout = '${JOB}rho.dat',
nx=10, ny=10, nz=10
/
EOF
${CD} < ${JOB}.chdens.in > ${JOB}.chdens.out
Paolo Giannozzi
2005-01-18 11:21:15 UTC
Permalink
Post by aaron
I'd like to write a cube file, but the chdens.x complains when I set my
output_format=6. The error is "Atom C not found".
it comes from flib/atomic_number.f90, called by PP/cube.f90 . Verify
that it is not something trivial. Which version of the code are you
using? There was some problem in version 2.1 with one-letter atoms.
There is a new version on the web site, by the way, that fixes several
bugs.

Paolo
Paolo Giannozzi
2005-01-18 11:21:15 UTC
Permalink
Post by aaron
I'd like to write a cube file, but the chdens.x complains when I set my
output_format=6. The error is "Atom C not found".
it comes from flib/atomic_number.f90, called by PP/cube.f90 . Verify
that it is not something trivial. Which version of the code are you
using? There was some problem in version 2.1 with one-letter atoms.
There is a new version on the web site, by the way, that fixes several
bugs.

Paolo
aaron
2005-01-18 09:09:35 UTC
Permalink
Thanks for advice. I will get the new code. I am now creating some nice
postscript slices with plotrho.

Thanks again

Aaron
Post by Paolo Giannozzi
Post by aaron
I'd like to write a cube file, but the chdens.x complains when I set my
output_format=6. The error is "Atom C not found".
it comes from flib/atomic_number.f90, called by PP/cube.f90 . Verify
that it is not something trivial. Which version of the code are you
using? There was some problem in version 2.1 with one-letter atoms.
There is a new version on the web site, by the way, that fixes several
bugs.
Paolo
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Roberto G. A. Veiga
2005-01-12 19:40:31 UTC
Permalink
When I try to view a plot using gnuplot, I see:

gnuplot> 25 25 1 0.41666666666667E-01 0.41666666666667E-01
^
"plots/charge.plot", line 1: invalid command

Why?

[]s,

Roberto



---------------------------------

Blogs: http://robertoveiga.blogspot.com e http://democracialiberal.blogspot.com.




---------------------------------
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Eyvaz Isaev
2005-01-12 21:55:25 UTC
Permalink
Hi,

Probably, you try to run a command "gnuplot file.dat".

If so, it is not correct. First you should enter
"gnuplot" and then "plot file.dat".
If you try to visualize a 3D object, say charge
density, "splot" command should be used and this case
requires some additional keys.
If you like to see a charge density mapped on a plane,
I remember, a PS-file should be produced by program.
In this case Gnuplot is not required. Just enter "gv
file.ps" (or ggv instead gv).

If the aforementioned cases are not your case, please
provide more information.

Bests,
Eyvaz.
Post by Roberto G. A. Veiga
gnuplot> 25 25 1 0.41666666666667E-01
0.41666666666667E-01
^
"plots/charge.plot", line 1: invalid
command
Why?
[]s,
Roberto
---------------------------------
Blogs: http://robertoveiga.blogspot.com e
http://democracialiberal.blogspot.com.
---------------------------------
Do you Yahoo!?
All your favorites on one personal page ? Try My
Yahoo!




__________________________________
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Roberto G. A. Veiga
2005-01-13 16:02:00 UTC
Permalink
Ok, now it works. Thank you, Eyvaz.

By the way, which format should I use to save STM images?I've tried gOpenMol, but gOpenMol says there are problems with the [Atoms] tag.

[]s,

Roberto

Eyvaz Isaev <eyvaz_isaev at yahoo.com> wrote:
Hi,

Probably, you try to run a command "gnuplot file.dat".

If so, it is not correct. First you should enter
"gnuplot" and then "plot file.dat".
If you try to visualize a 3D object, say charge
density, "splot" command should be used and this case
requires some additional keys.
If you like to see a charge density mapped on a plane,
I remember, a PS-file should be produced by program.
In this case Gnuplot is not required. Just enter "gv
file.ps" (or ggv instead gv).

If the aforementioned cases are not your case, please
provide more information.

Bests,
Eyvaz.
gnuplot> 25 25 1 0.41666666666667E-01
0.41666666666667E-01
^
"plots/charge.plot", line 1: invalid
command
Why?
[]s,
Roberto
---------------------------------
Blogs: http://robertoveiga.blogspot.com e
http://democracialiberal.blogspot.com.
---------------------------------
Do you Yahoo!?
All your favorites on one personal page ? Try My
Yahoo!




__________________________________
Do you Yahoo!?
Yahoo! Mail - now with 250MB free storage. Learn more.
http://info.mail.yahoo.com/mail_250
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
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---------------------------------

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---------------------------------
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aaron
2005-01-17 14:24:50 UTC
Permalink
Hi All,

I'm trying to view my charge density output. I succeed to write an xsf
file but I do not have a viewer (vmd 1.8.3 is failing on my platform(s)).
I'd like to write a cube file, but the chdens.x complains when I set my
output_format=6. The error is "Atom C not found". How can I alleviate
this error? I'd like to note that I'm trying to generate a cube file
from densities of a complete system and taking the difference between
that and it's constituents (illustrated below). Could this be the
problem? Has anyone experience with converting a .xsf to .cube format?
I'm appending my input file for chdens.x to the end of this message.

Thanks for your kind and helpful suggestions,

Aaron

&input
nfile = 3,
filepp(1) = '../C32form.bs/C32formbscharge',
filepp(2) = '../C32.bs/C32bscharge',
filepp(3) = '../form.bs/${JOB}charge',
weight(1) =-1.0,
weight(2) = 1.0,
weight(3) = 1.0,
iflag = 3,
plot_out = 1,
output_format = 5, !! 6 for cube file
fileout = '${JOB}rho.dat',
nx=10, ny=10, nz=10
/
EOF
${CD} < ${JOB}.chdens.in > ${JOB}.chdens.out
aaron
2005-01-18 09:09:35 UTC
Permalink
Thanks for advice. I will get the new code. I am now creating some nice
postscript slices with plotrho.

Thanks again

Aaron
Post by Paolo Giannozzi
Post by aaron
I'd like to write a cube file, but the chdens.x complains when I set my
output_format=6. The error is "Atom C not found".
it comes from flib/atomic_number.f90, called by PP/cube.f90 . Verify
that it is not something trivial. Which version of the code are you
using? There was some problem in version 2.1 with one-letter atoms.
There is a new version on the web site, by the way, that fixes several
bugs.
Paolo
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum
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