mopac automation answers
Here's a summary of the answers I got to my MOPAC question. I've cut to
the chase and just put the 'meat' of the answers here. The one that worked
very well for my situation was the csh shell script given in the 1st and 3rd
answers. The names of those who gave the answers are given to give credit
where credit is due and also to direct those with questions to the source.
Andrew.
This is dependent on the type of system you're using, but if all
your input files are named according to some pattern, you can set
up a csh script such as
foreach inp (*.inp)
mopac $inp
end
and run this in batch or "nohupped". Is this what you're looking for?
--
David J. Heisterberg (djh ^at^ ccl.net) The value of philosopy is, in fact, to
be
The Ohio Supercomputer Center sought largely in its very uncertainty.
Columbus, Ohio -- Bertrand Russell
Mike Cooledge at the Seiler Research Lab at the USAF Academy
has written a set of very nice scripts for setting up a queue that
will run jobs one after the other. You can add jobs to the list or
remove them also.
The problem is that I have missplaced his e-mail address. You
should be able to get in touch with a (719) 472-2655.
KURTZH ^at^ MEMSTVX1.BITENT
Try the equivalent of the following UNIX C shell script:
#! /bin/csh
foreach f (*.dat)
mopac `basename $f .dat`
end
where the "basename" command removes the '.dat' file extension (our
version
of the MOPAC script wants just the root file name).
Mike.
system ^at^ alchemy.chem.utoronto.ca
In our UNIX (GENIX5.3) system all you have to do is to
invoke MOPAC filename1 filename 2 filename3 ... & <return>
On UNIX systems the & puts the jobs in the background where
they run merrily without anyone knowing about them.
When they are done the flassk MOPAC DONE will appear on the
screen. This does not amuse anyone who is doing something else
so we preface our MOPAC call with nohup. the messages from mopac
are then in a file called nohup.out.
The entire procedure looks like this on our AEON system
NOHUP MOPAC filenmae1 filename2 filename3... &
The.dat extenders are not needed.
K.R.Fountain/ sc18 ^at^ NEMOMUS
This may not help you but there is a great method of automating MOPAC (or any
other type of molecular modelling calculation or operation) in the CHEM-X
modelling package. You can set up the type of calculation required, run the
batch of molecules and even get CHEM-X to save the results you want into a
molecular spreadsheet ready to do statistics on. CHEM-X is relatively
inexpensive (compared with its competition) . You can contact Chemical Design
Ltd (Oxford) by fax on 44-861-250-270.
Dave
__________________________________________________________________________
Dr. David A. Winkler Voice: 61-3-542-2244
Principal Research Scientist Fax: 61-3-543-8160
CSIRO Division of Chemicals and Polymers
Private Bag 10
Clayton, Australia.
dave ^at^ carbon.chem.csiro.au
If I were running MOPAC on a Vax I would use the "SYNCHRONIZE" DCL
command.
Surely there is something similar in UNIX? SYNCHRONIZE lets you submit multiple
batch jobs that won't start until the previously "synchronized" one
completes.
This works great on a Vax, but I don't know if there is something similar under
UNIX.
Greg Durst
DowElanco
Indpls, IN
DURST_GREGORY_L ^at^ LILLY.COM
store all what you do usually to run mopac in a command file
for example :
cp toto1.dat FOR005
mopac
cp FOR006 toto1.results
rm FOR005
cp toto2.dat FOR005
mopac
cp FOR006 toto2.results
etc ....
you can run this file by the command batch or at if you work
on a unix work station
------
Francois BAYARD | e-mail bayard ^at^ chitheo1.univ-lyon1.fr
UNIVERSITE CLAUDE BERNARD LYON 1 | tel (+33) 72 44 82 79
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