Subject: Re: CCL:XML as program output?

From: "David E. Bernholdt" <[email-masked]>
Date: Tue, 18 May 1999 15:30:30 -0400

On Tue, 18 May 1999 12:56:10 -0400 I wrote:
< I'm curious what people think about using XML for the output of
< chemistry programs?  I'd appreciate your response to the scenarios I
< present below.

I realize that I should clarify a little what I meant by XML markup of
output. My purpose here is not simply to pretty-print program output --
I envision marking up the actual information content so that it can be
unambiguously identified, extracted, and otherwise processed.

For example, energies might be marked up as:
<energy type="nuclear repulsion" units="Hartrees">101.8303753234</energy>
<energy type="uhf" units="Hartrees">-190.784836075</energy>

MO vectors might be marked up like this:
<orbital id="1" type="canonical mo" occupation="1.0">
<energy type="orbital" units="Hartrees">-20.65958</energy>
<array>...</array><!-- holds MO coefficients -->
</orbital>

Molecular structures might be reported using CML's (Chemical Markup
Language) <MOL> construct, dipole moments could be marked up as an
array of values.  

I don't claim that the actual product would look anything like my off
the cuff examples here, but the main point is that the markup is not
"make this boldface and blue, and that in italics", it actually
describes the information content of the document for us.

With an appropriate stylesheet, one could arrange that XML-based
output look "pretty" in the browser, invoke a 3d viewer for molecular
structures, MOs, etc.  But more importantly, in my opinion, it now
becomes possible to use standard tools for manipulating XML documents
to access the information stored within the output file.  

Right now, this kind of thing can only be done by if you know the
output format of a program intimately, and can depend on it not to
change with a new release, or on another platform, etc.
--
David E. Bernholdt                      | Email:  [email-masked]
Northeast Parallel Architectures Center | Phone:  +1 315 443 3857
111 College Place, Syracuse University  | Fax:    +1 315 443 1973
Syracuse, NY 13244-4100                 | URL:    http://www.npac.syr.edu

---

From: "Jim Kress" <[email-masked]>
Date: Tue, 18 May 1999 16:47:03 -0400

1)  Having an XML POSTprocessor would be great.  Modifying the QC or SM (or
whatever) code would be a real pain.

2) If Gaussian put surround sound into their product  a) You'd probably only
get sound out of 1.5 speakers and b) They'd still have a manual that claimed
full feature content but software that did not live up to the manual's
claims.

Jim

Check out my web site http://www.kressworks.com/
It'll blow your mind (politically), stimulate your senses (artistically)
and provide scientific insights that boggle the mind!!

-----Original Message-----
From: Dmitry Khoroshun <[email-masked]>
To: Richard Wood <[email-masked]>
Cc: David van der Spoel <[email-masked]>; David E. Bernholdt
<[email-masked]>; [email-masked] <[email-masked]>
Date: Tuesday, May 18, 1999 4:29 PM
Subject: CCL:XML as program output?

>According to Richard Wood:
>>
>> But rasmol reads a "text" file format!  Why change it and other programs
>> that already read text files?  That doesn't make any sense to me.
>
>This indeed makes not much sense. What use is of introducing a "type"
>of the energy, like "nuclear repulsion"? You still have to read and
>understand it, not just click on it with a mouse. Unix scripting
>possibilities allow for many many things like sorting or similar. And of
course
>programs such as molden have no problems with reading text files.
>
>I guess the next step would be implementing surrounding sound into
Gaussian.
>
>Sincerely,
>Dmitry Khoroshun
>[email-masked]
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