Subject: Re: CCL:CCL:Re: High Cost of Comp. Chem.

From: [email-masked]
Date: Wed, 9 Feb 1994 09:44:25 +0200

We computational chemists (before we used to be quantum chemists) we used
to be in the forefront of computational science. Usually this job involved
the task of finding a solution to a diff. equation or a solution to some
other equation. During the last 30 years we have developed huge program
packages to tackle this problem. However, as I see it, computational
sciences (and computational chemistry) is much more that that. Today we also
have to use other tools like visualisation tools (molecular graphics),
databases, information servers (Mosaic or Gopher). Traditional
computational
chemists have not contributed too much in these fields. In fact quite much
of this has been developed by the Biology community. And surprising much of
this is available free of charge (at least so far). Only time shows if
the software from the Biology community also will be commercialised.

>
>>As the object orientation becomes stronger,
>>so maintenance might just become less of a problem.
>
>Heh, Heh...  ;-)
>

This is really a long time dream of mine. Just imagine if there would be
more object oriented classes in computational chemistry code. You could
just plug in and use a class for PM3, MP2, Leap-Frog algorithm and so on.
All code would be easier reused. Today too much code is still developed
for one particular approximation or application.

It does not really bother me a bit if I have to learn a new operating
system or programming language to solve a new scientific problem.
The problem is the old code. The computational biochemists have been
in a very lucky position because when they started hardly nobody wanted
to program in FORTRAN (no war, please) and they could use all the nice 
networking tools available in Unix. I believe this is something we 
quantum chemists have in front of us very soon. The whole consept
has to be redefined. Perhaps this will never happen because there is
so much "old" code available which will never be rewritten. But for
the sake of science I wish this will happen. After all as Ron Shepard
said we all appreciate more the kind of knowledge that remains useful
for decades rather than months or years.

My $.02

-leif laaksonen

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 Leif Laaksonen                     |
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              New opinions are always suspected, and
              usually opposed, without any other 
              reason but because they are not already
              common.

                                   John Locke
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From: [email-masked] (Jack Martin Miller)
Date: Wed, 9 Feb 94 10:50:39 -0500

>>so maintenance might just become less of a problem.

Agreed
>
> In order to use new RISC workstations, you have to
>learn unix and give up VMS.  In order to use PHIGS, you have to give up
>fortran and learn C.

And now PHIGS may be replace by SGI's open 3D libraries and X or Motif are
the standard.

>
>I have noticed however that this doesn't bother people in computing as
>much as it does people in science.  I think this is related to the
>maturity of the different disciplines.  It could be that our training in
>science allows us to appreciate more the kind of knowledge that remains
>useful for decades (or centuries) rather than months or years.
>
As a former chair of a Computer Science department let me say that there
are two attitiudes --- "lets not change --- the VAX is the best invention
since white bread" to "its new therefore we must have it  --- even if it
doesn't work, won't work and can't work"

The experimental chemist is more likely tochange than the theoretician
since no software for use with insttrumentation is currently being written
in Fortran and most old fortran based stuff has been replaced with C. If
your mass spec or nmr is driven from a UNIX workstation you have no choice
but to mighrate to the new technology and deal with windows, C and UNIX -
and if you want your data moved to your desktop Mac or PC you have to get
involved in networking and networking standards. The theoretician is still
likely to submit batch jobs and get out a single number or a little table
after a day of number crunching --- there is no incentive to change from
the Fortran they cut their teeth on --- and anyway Fortran code usually
runs faster than C.

Jack Martin Miller
Professor of Chemistry
Adjunct Professor of Computer Science
Brock University,
St. Catharines, Ontario, Canada, L2S 3A1.

Phone (905) 688 5550, ext 3402
FAX   (905) 682 9020
e-mail [email-masked]