[Jmol-users] WebMO and Jmol Application

[Kubasik, Matthew A.]

Bob and list,

Like many others, I’ve been using WebMO to facilitate student access to 
computational engines on a server.  Unfortunately, WebMO (on a desktop browser) 
still uses Java.  

Fortunately, WebMO easily facilitates running input files uploaded from a 
desktop.  

So, the plan is, create g09 input files using Jmol Application>Tool>Gaussian, 
then upload and submit jobs to the computational server using WebMO.  

Here’s the hitch, I think:  Gaussian input file needs to terminate in an 
“empty” line.  When I upload the file, the “empty line” that I put in seems to 
get stripped, and the job fails.

Here are my questions:  Can the Gaussian tool be configured, by default, to add 
an empty line?  What is the best way to do this?  

I have found that terminating the file created by the Jmol app with:

[blank line]
! 

creates a g09 input files that run to completion.  ! is a comment, of course, 
and text in [blank line ] should be empty.

I’m interested in hearing other strategies, of course.  “Why aren’t you using 
X?” is welcome.  (E.g., why aren’t you using the iOS version of WebMO?)  For 
the time being, though, I like the WebMO interface for keeping track of 
jobs/job failures of newbie quantum chemists!   (We of course could add the 
[blank line] \r ! to each file, but it’d be nice to have something that’s 
automatic.)

Matt Kubasik
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Re: [Jmol-users] WebMO and Jmol Application

[Robert Hanson]

It was a missing character at the end of the line just as the file was
saved. Very easy fix.

http://chemapps.stolaf.edu/jmol/zip/Jmol.jar

fixes that.

Question: Could you just use JSmol and a bit of extra interface to do this
on the web? Obviously there's a lot more to WebMO than that -- scheduling
and monitoring jobs, for instance. But still...

Bob


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Re: [Jmol-users] WebMO and Jmol Application

[Kubasik, Matthew A.]

Thank you, Bob, for your rapid fix.

As to your question:  yes, I am learning that there is almost nothing that Jmol 
cannot do!

I’m not exactly sure what WebMO is doing, as installed on a computational 
server, so that it can receive/upload gaussian input files and run gaussian 
computations.  If you are suggesting that there has to be something that could 
be installed on a server/web page, serving up the Jmol applet, that could 
execute gaussian jobs, I am certain that you are right.  It’s what WebMO does, 
right?

For anyone who wants to check out WebMO, which supports Gaussian, GAMESS, and 
eight(!) other computational engines, visit the demo server at 
http://www.webmo.net/demo/index.html.

So, I agree that the “bit of extra interface” you mention is certainly do-able, 
but I’m not really sure how it’s done!

Matt


On Aug 31, 2015, at 8:06 PM, Robert Hanson 
> wrote:

It was a missing character at the end of the line just as the file was saved. 
Very easy fix.

http://chemapps.stolaf.edu/jmol/zip/Jmol.jar

fixes that.

Question: Could you just use JSmol and a bit of extra interface to do this on 
the web? Obviously there's a lot more to WebMO than that -- scheduling and 
monitoring jobs, for instance. But still...

Bob


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