Subject: Summary: Visualisation program suggestion

From: Wai-To Chan <[email-masked]>
Date: Fri, 12 Mar 1999 19:26:38 -0500 (EST)

Dear CCLers,
             More than a month ago I asked for suggestion
of visualization software and got plenty of responses. 
I've delayed posting this summary partly because I 
thought I though I could also provide some of my own comments on 
my final choices. 
However I still have not decided on what program 
to use to this day so I better have all the 
responses posted. Note that I might have
skipped a few replies which suggested the same
program. But I do appreciate each and every response. Thanks.

Wai-To Chan
Department of Chemistry
York University
Toronto, Ontario
Canada

My original question:

 ...........................................
Dear colleagues,

		 I am writing this note to solicit your comments on 
any appropriate visualization package for developing molecular
graphics applications on a SGI workstation. I am looking for 
a program that can extract from a cubic grid of 
various electron density properties (computed from Gaussian 
using the cube option) these features:

2D and 3D contour plots
3D multi-isovalued surfaces
gradient vectors (in 2D and 3D space)  
Locations of maxima and minima 

   Specifically the program must enable me to produce
an isovalued electron-density surface.
The program also must put out the cartesian coordinates 
of this surface which I will need for subsequent evaluation 
of other quantities on this surface.

  At present I have in my mind either AVS 
(advanced visualization system) or Iris explorer. 
Can someone comment on these two programs particularly?
My primiary considerations are prices, user-friendliness, 
flexiblity and popularity among computational chemists. 

   Any suggestion of freeware would be very useful 
although I've not been able to find one free program 
that meets all my needs.  Other than modular
graphics package an easy-to-program graphics subroutine 
library (compatible with C if not FORTRAN) 
would also be helpful. Thanks.

 ............................................

Summary of answers:

*****************************************
> From: "Fred P. Arnold" <[email-masked]>

gOpenMol is a good choice, though due to the Tk/Tcl interface, it's slower
than death and tends to crash under Linux.

Molden can calculate the properties, but you'll have to reformat them for
it to read cubes generated externally.

SciAn (www.scri.fsu.edu) can read generic data, and a program by Laurent
Joubert (spelling?) converts gaussian cube files to SciAn native files.

In a similar vein (now we're talking commercial, expensive, but powerful
software) IBM DataExplorer (www.almaden.ibm.com/dx) or NAG Explorer
(www.nag.com) are capable of reading and visualizing general cube data, as
well as transformations and other features.

Personally, I'd probably use SciAn as a first choice, and proceed from
there.  If you have the budget DataExplorer (IBM) is a wonderful program,
though with a steep learning curve)

							-fred

                                        Frederick P. Arnold, Jr.  
 "...But if you give theorists enough   Advanced Research Systems     
  time, they can predict anything."     5640 S. Ellis Ave             
        Dr. M. S. Turner, U. Chicago.   Chicago, IL 60637             

****************************************

> From: Ken Flurchick <[email-masked]>

Wai-To
I am Ken Flurchick and I have written modules
 to process Gaussian Cube files, and extract freq from
a chkpnt file plur display structure
Look at http://www.ccl.net/~kenf
	go to Visualization then Software for a discussion
	of the software.

If you go with AVS this may be of help
I recommend AVS, greater flexibility
kenf

> From [email-masked] Fri Jan 29 00:40 EST 1999

Hi,

I can't promise you everything but please have a look at gOpenMol
at

http://laaksonen.csc.fi/gopenmol/

Regards,

-leif laaksonen

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> From [email-masked] Fri Jan 29 03:03 EST 1999

Hi,

I suggest you take a look at my old homepage :

http://134.157.11.11/Pages/LECA/GP/Laurent/soft.html

During my PhD thesis, I used the freeware SciAn to visualize
some molecular properties.
SciAn is a really impressive program if you have a good graphic card
on your SGI.

I wrote small programs as an interface between SciAn and Gaussian.

I think you will be able to modify these programs in order to display
supplementary data such as gradients.

Sincerely,

Laurent

> From [email-masked] Fri Jan 29 04:20 EST 1999
You may try a nice program called VU available from
ftp://ftp.cerca.umontreal.ca/VU/bin/. 
Infos from http://www;cerca.umontreal.ca/VU

Free software and lots of documentation including a tutorial.

If you have enough money, you may also look to IRIS EXPLORER.

Good luck

Dr Marc G. De Backer 
Lasir - HEI - CNRS UMR 8516
13, rue de Toul 
59046 LILLE (FRANCE) 
[email-masked] (home) 

Tel : (33) 3 28 38 48 58 
Fax : (33) 3 28 38 48 04  
--=====================_84563564==_.ALT

> From [email-masked] Fri Jan 29 05:22 EST 1999

Wai-to,
	not sure if this is going to be available to you, but it may
be worth a try. MAVIS is and AVS based package developed in manchester
a few years ago. It will produce some density plots and contours. The
current web-page :

(http://www.man.ac.uk/MVC/research/MAVIS/) 

has a link describing the license, it says that it is available for a
nominal fee (1 pound) to all UK HEI's. 
So I'm not sure if they'd let you have it, get in touch with Matt
Cooper and I'm sure he'd let you know.

noj

-- 
Dr. Noj Malcolm			
Theory Group,			
Dept. of Chemistry,		
University of Manchester,	
Oxford Road,			
Manchester.			
M13 9PL

e-mail [email-masked]                  

> From [email-masked] Fri Jan 29 05:22 EST 1999

Whilst I was at Imperial College, London, I wrote, together with Omer
Casher, a number of modules for Iris Explorer to work with Gaussian cube
files, and found it to be extraordinarily powerful.  Using these modules
in conjunction with the standard library, it is possible to create 2D and
3D contour plots and 3D multi-isovalued surfaces.  Outputting the
Cartesian coordinates and interpolating other data to them is also facile:
one of our interests was in projecting MEPs onto either isodensity
surfaces or Connolly surfaces.  I haven't tried to do gradient vectors,
but believe that there is a module in the standard library for extracting
these.  Similarly there is bound to be one for extracting maximum and
minimum values and their coordinates (and if there isn't, it would be
trivial to write one).

The 3D graphical output is Open Inventor.   It is fully optimised for
SGI/OpenGL, and, to be honest, I have yet to see anything that beats it
either for performance or quality.   Conversion to VRML can be performed
using standard scripts.

The main reservation I have with recommending Explorer is that, to use it
effectively, there is quite a steep learning curve, and, in particular, if
a module doesn't exist to do what you want, you have to be prepared to
write it yourself.  That said, if you are interested, I can make the cube
file reader available to you, and various other utilities I have written,
so hopefully this situation won't arise immediately. 

A demo version of Explorer can be arranged by contacting Jeremy Walton at
NAG ([email-masked]).

I have no experience of AVS, but Ian Hillier's group in Manchester, UK,
has written a number of chemistry-specific extensions, under the name of
"Mavis".  Perhaps you can contact [email-masked] for details. 

If I can be of any further help, please let me know.

regards,

Chris Page
__________

Departamento de Quimica Fisica                   Tel: +34 630 604 375
Universidad de Valencia
Dr. Moliner 50
Burjassot
E-46100 Valencia

> From [email-masked] Fri Jan 29 09:42 EST 1999
I have used IBM's Data Explorer for many years now and find it 
very appealing, although it is not free. It is supported on
all major platforms including NT and can take advantage of 
OpenGl hardware. One can also build applications directly calling
the C module library. Although the user interface is not as snappy as 
I would like, the underlying structure of the system, including it's
sophisticated user-definable data model is very nice. As with AVS,
this is a general viz package with little built-in chemistry specifics,
however, my chemistry module add-ons are freely available source and
all,
just ask.

There is also considerable interest here in VTK: one member of our
center
is very enthusiastic about a Python scripting interface to VTK. 

Personally, I see little point in scripting interfaces, especially
unusual ones.
The small set of users who are likely to take the time to learn a new
language,
even a simple one, will already know C or C++. Why not just compile and
get 
the better (superior) performance? 

Richard Gillilan
Cornell Theory Center

> From [email-masked] Mon Feb  1 08:43 EST 1999

Dear Wai-To, 

I read your message on CCL. My favourite is "Vis5d", free, available both
in source and precompiled. It comes from weather-forecasting and is the
fastest I've seen running on my laptop under Linux. Only problem: I
haven't found a way yet (and not been trying hard) to get also balls and
sticks for the atoms + bonds. 

Other suggestions: 

- gopenmol (from Finland)

- vu       (from Quebec)

Good luck 

Fred A. Hamprecht                          

 Institute of Physical Chemistry | Institute of Organic Chemistry  
 ETH Zentrum                     |          University of Zuerich
 Tel: +41-1-632 6841             |           Tel:  +41-1-635 6119
 CH-8092 Zuerich     [email-masked]    CH-8057 Zuerich

> From [email-masked] Wed Feb  3 15:21 EST 1999

Hi there -

You can do these things with the Cerius2 developers kit from MSI. It is available for free.
Look at http://www.msi.com/support/sdk/ for details on how to get a license. Also have
a look at the iso surface application in the examples sections. This is similar to what
you want to do.

Regards - Ton