Hi,
I *think* I *may* have some time to look at this over the weekend,
but I am a bit rusty with Java coding. I did consider doing this
earlier (when I wrote the initially bug report) but since it was not
code that I had started I did not want to 'take it over'.
Also the flurry of emails about formatting has me now a bit worried :-).
René
On Mar 15, 2006, at 11:55 AM, Bob Hanson wrote:
who wants to do this? Egon? Obviously we need this fixed. Spartan's
important.
Bob
SourceForge.net wrote:
Bugs item #1255787, was opened at 2005-08-10 08:08
Message generated for change (Comment added) made by rkanters
You can respond by visiting: https://sourceforge.net/tracker/?
func=detail&atid=379133&aid=1255787&group_id=23629
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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 11:13
Message:
Logged In: YES user_id=905185
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
Message:
Logged In: YES user_id=1475990
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
Message:
Logged In: YES user_id=905185
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.
---------------------------------------------------------------------
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Comment By: Einar Coutin (einarc)
Date: 2006-03-14 23:26
Message:
Logged In: YES user_id=1475990
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 23:15
Message:
Logged In: NO In my case jmol doesnt even reads an spartan file.
---------------------------------------------------------------------
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