Subject: programming language

From: "Douglas Smith`" <[email-masked]>
Date: Thu, 01 Feb 2001 00:53:28 -0500

I am somewhat surprised to see how many people are suggesting FORTRAN.

Perhaps this is due to the bias of this list, which is primarily focused on 
molecular modeling, theoretical chemistry, and high end number crunching.

Perhaps it is due to the fact that so many of us have been around so long 
and historically, FORTRAN is where we came from and our first love.  (In the 
same vein, Mark Zottola says almost 100% of the supercomputer codes at 
Alabama are FORTRAN... is this possibly historical?  What about codes that 
have originated within the past few years rather than those that have been 
around for so long, like GAMESS, AMBER, etc.)

Jan:  what is the percentage makeup of codes at the Ohio Supercomputer 
Center?  And, since OSC is still involved (I believe) with the computational 
chemistry codes at the DOD Major Shared Resource Centers, what is the makeup 
there?  That would be of interest, since so many of those codes had to be 
rewritten (or newly developed) for the highly parallel machines at those 
centers?

At the same time, I notice that we have not yet heard from commercial 
software developers, such as Gaussian Inc., Schrodinger, Tripos, or MSI.  I 
believe that MSI is the largest "group" of PhD computational chemists in the 
world, and many of them read this list.  What is the language used for 
commercial codes?  Feel free to break down your analysis to discuss front 
ends separate from servers, and to even tell us the answer based on the type 
of codes.

Now, what about all those other types of "computational chemistry" 
activities, such as cheminformatics?  I know that RS3, Oxford Molecular's 
database/registration code, is written in C.  What about other informatics 
codes?

Also conspicuously absent so far is Henry Rzepa.  Henry, if you are 
listening, I know you have an opinion.  You have done some wonderful work on 
graphics and browser-based chemistry, what do you think?

And yes, what about a language for those chemistry students that will not 
become computational or theoretical chemists?  Isn't JAVA, or C++ or Visual 
Basic important to them, so that they can work with information exchange, 
build little applets and servlets that will ease their workflow in the labs? 
  For that matter, what about LabView, Mathmatica, or other languages for 
interfacing equipment to computers, creating forms and documents and 
reports, and more?

In the broader scheme of things, the best answer to the original question is 
that the language of most utility will depend on the student, their projects 
and type of work they do.  Later in their professional lives, the same 
question would be answered by stating that it depends on their workflow and 
corporate environment.

> From a pedagogical point of view (and I am not a programmer nor a computer 
scientist) what ever course can teach them strongly in the fundamentals of 
good code design and programming practices, starting from the proper time 
and effort spent on functional and engineering specifications, including key 
points such as the need for documenting code, good QA/QC, and even perhaps 
an introduction to the CMM levels would be good.  If we teach fundamentals 
and good practices, careful thought and execution, any programming language 
should be useful.

These opinions and comments are my own, not my company's... otherwise I 
would use their email system.  :>)

Doug Smith

Product Manager, ADME/Tox software
Oxford Molecular Group (a wholly owned subsidiary of Pharmacopeia)
_________________________________________________________________
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From: "Dr. Richard Wood" <[email-masked]>
Date: Thu, 01 Feb 2001 13:41:04 -0500

Dr. Smith-

Two comments:

First of all, she stated that the students didn't think Java was useful to
them.
So shouldn't Java be out of the mix of our disscussions?

Secondly, I wonder why a lot of MD codes are/were written in Fortran and not
C++?   When i was a Ph. D. student, there was an attempt in our group to
convert
our Fortran based MD program into a C++ based one.  However, it soon hit us
that there were things that one could not do with C++ that one could do with
the
Fortran code.  Bear in mind, this was less than 2 years ago.

Richard

--
Richard L. Wood, Ph. D.
Physical/Computational Chemist
Post-doctoral Associate
Cornell University, Ithaca, NY 14853

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From: "Jochen Küpper" <[email-masked]>
Date: 01 Feb 2001 18:20:32 -0500

>>>>> Richard Wood wrote on Thu, 01 Feb 2001 13:41:04 -0500:

Richard> When i was a Ph. D. student, there was an attempt in our
Richard> group to convert our Fortran based MD program into a C++
Richard> based one.  However, it soon hit us that there were things
Richard> that one could not do with C++ that one could do with the
Richard> Fortran code.  

I think with this statement you should tell us what can be in Fortran
and not in C++? Or probably you need to clarify tour statement a bit
further.

Greetings,
Jochen
-- 
University of North Carolina                          phone: 919-962-1579
Department of Chemistry                                 fax: 919-843-6041
Venable Hall CB#3290
Chapel Hill, NC 26599, USA