I am wondering why I got the following message from the data file
commit. Did I do something wrong? This is the first time I tried
committing things with SVN (and Eclipse):
Your mail to 'Jmol-commits' with the subject
SF.net SVN: jmol: [4622] trunk/Jmol-datafiles/spartan
Is being held until the list moderator can review it for approval.
The reason it is being held:
Message body is too big: 242501 bytes but there's a limit of 60 KB
Either the message will get posted to the list, or you will receive
notification of the moderator's decision.
René
On Mar 15, 2006, at 4:25 PM, SourceForge.net wrote:
Bugs item #1255787, was opened at 2005-08-10 08:08
Message generated for change (Comment added) made by rkanters
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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: Rene Kanters (rkanters)
Date: 2006-03-15 16:25
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I just uploaded to Jmol-datafiles some spartan smol files generated
on Mac
Spartan 02 using some different methods and types of calculations.
I think the minimum information we want to capture is the GEOMETRY (or
GEOMETRY2) section in the BEGINARCHIVE...ENDARCHIVE section.
The vibrational information is stored in the BEGINPROPARC/ENDPROPARC
section's subsection of VIBFREQ...END. The IR intensities are
listed earlier in
the PROPARC section under PROP VALUE IR_INTENS #ofvibs# BEGIN ...
END.
It would be nice to have the setAtomSetName set the IR frequency and
symmetry as the name and for a regular structure to have ENERGY (as
found
in the main BEGINARCHIVE...ENDARCHIVE section.
Note that there are all kinds of other properties one could assign
to the
structure based on what is in the PROPARC section, which the
AtomSetChooser could display (similar to what the nwchem and gaussian
readers do).
I hope this helps.
----------------------------------------------------------------------
Comment By: Bob Hanson (hansonr)
Date: 2006-03-15 16:22
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Spartan SMOL file atoms are now read from the
BEGINARCHIVE
GEOMETRY
section
see the prototype at
http://www.stolaf.edu/people/hansonr/jmol/test/json/spin.htm
load SF6.smol
load CH4.smol
load CH3F.smol
Bob Hanson
----------------------------------------------------------------------
Comment By: Bob Hanson (hansonr)
Date: 2006-03-15 15:36
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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 13:04
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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 12:12
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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
----------------------------------------------------------------------
Comment By: Rene Kanters (rkanters)
Date: 2006-03-15 11:13
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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
----------------------------------------------------------------------
Comment By: Einar Coutin (einarc)
Date: 2006-03-15 10:35
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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 07:32
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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 23:26
Message:
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Darn jmol doesnt even opens the file CH3F.smol which you
attached. wth?
----------------------------------------------------------------------
Comment By: Nobody/Anonymous (nobody)
Date: 2006-03-14 23:15
Message:
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In my case jmol doesnt even reads an spartan file.
----------------------------------------------------------------------
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