I presume we want Jmol to read the OUTPUT, not the INPUT coordinates,
right? Currently it is reading the INPUT coordinates and ignoring the
results of calculation.
SourceForge.net wrote:
Bugs item #1255787, was opened at 2005-08-10 08:08
Message generated for change (Comment added) made by hansonr
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Category: File Input/Output
Group: None
Status: Open
Resolution: None
Priority: 5
Submitted By: Rene Kanters (rkanters)
Assigned to: Miguel (migueljmol)
Summary: Spartan reader
Initial Comment:
I tried reading an smol file from Spartan 02 (Mac), and got the
message that no atoms were present.
It seems that depending on how you set up the calculation the
"Standard Nuclear Orientation" part may not be present. (before or
after the BEGINOUTPUT section).
For instance, I did a geometry optimization of a small molecule: 'No
atoms in file'.
I did a transition state calculation, followed (separately) by a
frequency calculation: I do have atoms..
It seems that it may be safer to use the geometry information in the
ARCHIVE section since that section is always present.
While the following section BEGINPROPARC, contains vibrational
information, (PROP VALUE IR_INTENS), and frequencies and
symmetries of the frequencies, followed by the displacement
vectors, which need to be multiplied by -1.6804058339 to get the
values that are reported in the BEGINVOUTPUT section, which is
currently parsed.
René
----------------------------------------------------------------------
Comment By: Bob Hanson (hansonr)
Date: 2006-03-15 14:36
Message:
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I have a bit of time today; I'll get the Spartan reader to
read that file, but we need a long-term plan. Can someone
(einarc?, rkanters?) collect for us a set of files
representative of what we want to support? I'd really like
to get the vibration info out of a Spartan file, for example.
Bob
----------------------------------------------------------------------
Comment By: Einar Coutin (einarc)
Date: 2006-03-15 12:04
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Last Minute:
Just tried the spartan files included in the repository you
mentioned. The Jmol application doesnt loads them either.
Unrecognized file format error again.
----------------------------------------------------------------------
Comment By: Einar Coutin (einarc)
Date: 2006-03-15 11:12
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I've tried a file summited to me by René which he says it
works with jmol... I tried, a coworker tried opening it,
both with the applet and the independent application... Same
Error.
I still have to try the jmol default data files
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Comment By: Rene Kanters (rkanters)
Date: 2006-03-15 10:13
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I think that *.spartan files are generated by older SGI versions of Spartan, but I
am not sure.
You can check out all the data files through svn:
svn co https://svn.sourceforge.net/svnroot/jmol/trunk/Jmol-datafiles jmol-
datafiles
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Comment By: Einar Coutin (einarc)
Date: 2006-03-15 09:35
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And what about *.spartan files. And where can I find the
J-mol data files?
Thanks...
----------------------------------------------------------------------
Comment By: Rene Kanters (rkanters)
Date: 2006-03-15 06:32
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The CH3F.smol file was an example of a case where the Spartan smol reader
fails. The sample spartan files in the Jmol-datafiles of the project load
properly.
This reader looks for the text "BEGINOUTPUT" followed by "Standard Nuclear
Orientation (Ang", which is not always present in the smol file. Their presence
is dependent on what type of calculation is done. I just did a few quick tests
on H2 geometry optimizations:
PM3 no IR (frequency analysis) : fails to load
PM3 with freq: fails to load
RHF no IR: fails to load
RHF with IR: loads
My message, which started this, pointed out that it may be safer to look for
the 'archive' type information in the .smol file as opposed to the captured text
log generated by the modules in spartan itself.
----------------------------------------------------------------------
Comment By: Einar Coutin (einarc)
Date: 2006-03-14 22:26
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Darn jmol doesnt even opens the file CH3F.smol which you
attached. wth?
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Comment By: Nobody/Anonymous (nobody)
Date: 2006-03-14 22:15
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In my case jmol doesnt even reads an spartan file.
----------------------------------------------------------------------
You can respond by visiting:
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--
Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107
Professor of Chemistry, St. Olaf College
1520 St. Olaf Ave., Northfield, MN 55057
mailto:[EMAIL PROTECTED]
http://www.stolaf.edu/people/hansonr
"Imagination is more important than knowledge." - Albert Einstein
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