From WILLIAMS@flint.bucknell.edu Tue Jan 12 06:33:27 1993 Date: 12 Jan 1993 11:33:27 EST From: Brian Williams Subject: COULOMB "CUT OFF" OR PSEDOPOTENTIALS To: CHEMISTRY@ccl.net Message-Id: <930112.11332696.012284@BUCKNELL.CP6> I WOULD APPRECIATE SOME HELP/ADVICE ON THE FOLLOWING. I HAVE FOUND WHAT I BELIEVE TO BE AN EXACT ANALYTICAL SOLUTION TO A TYPE OF GENERALIZED COULOMB POTENTIAL, WHERE THE DENOMINATOR OF THE COULOMB-LIKE TERM IN THE POTENTIAL CONSISTS OF A "R + TAU" TERM, WHERE TAU CAN BE VARIED. OTHER TERMS IN THIS SOLVABLE QM POTENTIAL INVOLVE REPULSIVE TERMS THAT ARE MORE OR LESS RELATED TO AN ANGULAR MOMENTUM LIKE TERM. AN EARLIER PAPER REFERS TO THIS TYPE OF POTENTIAL AS A "CUT OFF" COLOMB POTENTIAL, AND SOLVED A LESS GENERAL VERSION OF THE POTENTIAL THAN I THINK I HAVE SOLVED HERE. WHAT I WOULD LIKE TO KNOW IS WHETHER OR NOT A) THIS TYPE OF POTENTIAL IS OF USE OR HAS BEEN USED IN MODELING ANY ATOMIC OR MOLECULAR SYSTEMS, AND /OR B) WOULD THE WAVEFUNCTIONS SOLVING THIS POTENTIAL HAVE A POSSIBLE USE AS A BASIS SET FOR COMPUTATIONAL PROBLEMS. MY BACKGROUND IS NOT IN COMPUTATIONAL CHEMISTRY, ALTHOUGH WHAT LITTLE I REMEMBER FROM MY COURSES IN QM SUGGESTS TO ME THAT THIS SOLUTION MIGHT BE OF POSSIBLE USE IN MODELLING MULTI-ELECTRON ATOMS, WHERE THE VALENCE ELECTRONS ARE VIEWED AS BEING ATTRACTED AND REPELLED BY A SCREENED COLOMB-LIKE POTENTIAL. AM I TOTALLY OFF BASE HERE? THE MAIN REASON I AM ASKING THE NET FOR HELP IS THAT ALTHOUGH I AM MAINLY CONCERNED WITH JUST TRYING TO FIND EXACTLY SOLVABLE QM POTENTIALS, I WOULD LIKE TO FIND APPLICATIONS WHEREEVER POSSIBLE. THANKS IN ADVANCE FOR ANY HELP OF OR LEADING LITERATURE REFERENCES. BRIAN WILLIAMS, WILLIAMS@BUCKNELL.EDU BRIAN WILLIAMS, WILLIAMS@BUCKNELL.EDU From richard@TC.Cornell.EDU Tue Jan 12 07:34:14 1993 Date: Tue, 12 Jan 1993 12:34:14 -0500 From: Richard Gillilan Message-Id: <199301121734.AA03630@theory.TC.Cornell.EDU> To: chemistry@ccl.net Subject: Summary of data flow responses >>>>>> Summary of Responses to inquiry about data flow programs <<<<<<<< Thanks to all for your interest. There seem to be relatively few users of data-flow programs for molecular modeling at present, but I did get a few interesting responses. First a few comments of my own. Here at the CTC we use IBM Data Explorer (DX) heavily for general visualization purposes. We also have AVS and MSI chemistry view but I'm less experienced with those products. DX falls somewhere between a low-level programming language for graphics and a high-level application with pull-down menus and a command line. This type of product is best suited for research groups who do a lot of graphics, especially animation, and need real flexibility, control and variety. Data flow programs are a real time-saver over lower-level programming in C! I would not recommend them to casual graphics users who would be better served with a specific program like Insight or Quanta. High-level applications can be written with a data-flow program (like MSI Chemistry viewer), but MSI is the only one I know about. These kinds of programs have a bright future, but they're still too new. What is data-flow programming? Instead of writing a program as a text file which you then compile and run, data flow programming uses a Graphical User Interface (GUI) to visually construct a network of boxes (modules) connected by pipes. When the visual program is run, data starts at the top of the network (usually from a data-reading module of some kind) and flows downward through the pipes. Whenever a module is encountered, the data is modified. A standard set of modules for performing such tasks as isosurface construction, interpolation, mapping, coloring, annotation and other data and data structure manipulations is usually included with the GUI. At the bottom of a network, one usually combines all the data pipes together and passes them to an image display module. Advantages o Easier than low-level graphics programming in C o Trivial to modify and play what-if games (you just point, click on and move boxes) o Can link in your own programs as modules (with some restrictions) o Natural coarse-grain parallelism (if you have multiple processors) o Can combine and compare many different data sets in a greater variety of ways than application-specific programs o Can add control panels customized to your application o Works well for animation (In my experience with DX) o Anonymous ftp sites for free modules exist for both AVS and IBM Data explorer. Disadvantages o Gives new meaning to the expression "plumber's nightmare" As in any programming language, it's easy to make an uncommented, disorganized mess. Personally, however, I find a well-organized network easier to understand than a directory fill of C files. o Lower-level than application-specific programs You won't see the word chemistry unless you write it yourself. The MSI chem viewer, however, is a product specifically for chemistry that runs under AVS. As far a I know this is the only commercial data-flow application for chemistry. Others may follow soon. o At least in IBM Data Explorer, the strict adherence to "pure-function semantics" discourages iterative or recursive calculations. Modules must not have internal states that change from one call to the next. The output results must be purely a function of the input data. Potential function evaluation is ok but trajectory calculation is tricky. o I find these programs to be not quite as interactively responsive as a custom-written C application using hardware polygon rendering. ******** List of replies ********* >Is there anyone else out there using data-flow type programs >for molecular modeling? > > IBM Visualization Data Explorer > SGI explorer > AVS > >How do you like them? What are their strengths and weaknesses? ---------------- From: jas@medinah.atc.ucarb.com (Jack Smith) Subject: Re: Molecular modeling with data flow programs Status: RO Richard: We have just started looking at them. We currently have SGI's Explorer and downloaded the MOPAC Viewer. We also just got IBM's Data Explorer in for evaluation and plan to look at AVS ChemistryViewer (from MSI) relatively soon. I started using SGI Explorer to analyze MOPAC and DMol results for metal surface reactions. I am particularly intrigued with opaque renderings of electron density. I plan on making a QuickTime movie of the complete reaction. (I make QuickTime movies of reactions pretty regularly on a CAChe system.) The visual programming concept is quite appealing and has a bright future, but I don't think it's quite ready for the casual user yet, although close. The "scripting" language in SGI Explorer is definitely geared toward C programmers -- which pleases me, but not my strictly-FORTRAN or non-programmer friends. I had quite a bit of experience with LabVIEW on the Mac in years past (for doing data acquisition and control) and I found that data flow programming is quite powerful, but there are some subtleties that one has to become aware of. Things are done asynchronously and with more degree of autonomy than in conventional sequential programming -- it's not just visual programming! Things like global variables, for example, become more ambiguous (or ill-defined). On the other hand, I think it's ideally suited for exploiting parallelism, and would highly encourage experimenting with data-flow architectures (visual or not) as a way to recognize opportunities for course grain parallelism. BTW, it was at the Cornell Theory Center that I first got to experiment with IBM's Data Explorer. If you have never had a chance to experiment with LabVIEW on a Mac (also now available on the PC, and soon on SGIs), I encourage you to do so -- National Instruments has quite a headstart in visual data-flow programming and has quickly outgrown it's original domain of digital signal processing (DSP). -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JACK A. SMITH ...................................................................... Union Carbide Corp. || Phone: (304) 747-5797 Advanced Technical Computing || FAX: (304) 747-5448 P.O. Box 8361 || S. Charleston, WV 25303 || Internet: jas@medinah.atc.ucarb.com -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From: jle@world.std.com (Joe M Leonard) Message-Id: <199212072106.AA01159@world.std.com> To: richard@TC.Cornell.EDU Subject: Re: Molecular modeling with data flow programs Status: RO I'd love to learn whether you hear of folks using these codes. I was a Stardent when we did the Chemistry support for AVS, although I am only aware of 1 company using it commercially (MSI). Henry Rzepa's group in the UK seems to be using SGI's explorer, and Doug SMith's group at U Toledo's using AVS. I think only AVS has explicit Chemistry datatype support to date... Joe Leonard 714-955-2120 jle@world.std.com From: "Bill,Molecular & Math Sciences, 508-467-6538 08-Dec-1992 1248" To: richard@TC.Cornell.EDU, desimone@mr4dec.enet.dec.com, loh@mr4dec.enet.dec.com Apparently-To: richard@TC.Cornell.EDU Subject: AVS uses in modeling Status: R Richard, There are two places that I know of that are using AVS in conjunction with their modeling efforts: UCSF (Jim Caldwell) - AMBER related biomolecular work nm%decwrl::"caldwell@cgl.ucsf.edu" Scripps Angela, can you send Richard contacts for Scripps. Richard, you might also talk to Joe Leonard of Wavefunction, Inc. nm%decwrl::"jle@world.std.com" Bill DeSimone Molecular Sciences Applications Marketing DEC From: davem@hydra.convex.com (Dave Mullally) Message-Id: <9212141739.AA29220@hydra.convex.com> To: richard@TC.Cornell.EDU Subject: Re: Molecular modeling with data flow programs Status: R Hi Richard, I have written a number of AVS modules which are used by customers who have AVS on a Convex. The 'data flow' part of AVS is actually a problem in general. Unless one has to, one does not want to know the details of how data flows in the model. All that people really want to do is to see their own molecule and some limited number of properties. To get people to use this type of program, you have to get make the data flow invisible in the final interface. I hope that this helps. Dave Mullally Convex Computer Corp. Date: Tue, 8 Dec 92 14:35:22 EST To: richard@TC.Cornell.EDU Cc: desimone@mr4dec.enet.dec.com Apparently-To: richard@TC.Cornell.EDU Subject: AVS users in modeling Status: RO Hi Richard, Art Olson of SCripps is a heavy user of AVS for protein modeling. Art may be reached at "olson@scripps.edu". Also, Ethan Merritt of U Washington is a user of AVS - he has converted RASTER3D to run with it - "MERRITT@GOUDA.BCHEM.WASHINGTON.EDU" is his address. Regards, Angela From: cushing@smoked.cse.ogi.edu (Judy Bayard Cushing) To: richard@TC.Cornell.EDU Subject: Re: Molecular modeling with data flow programs Status: RO i would appreciate being sent a summary or compendium of responses to your request. also, can you tell me about ibm visualization data explorer? thanks! judy From: msdrl!andose@uunet.UU.NET (Joe Andose) Subject: Molecular modeling with data flow programs To: richard@TC.Cornell.EDU Date: Tue, 8 Dec 92 11:38:40 EDT X-Mailer: ELM [version 2.2 PL0] Status: RO Richard, I saw your query on the CompuChem Mail Exploder. We briefly looked at SGI Explorer for ad hoc data visualization in chemistry. However, Explorer has no pre-constructed data types useful for chemistry at this time. AVS on the other hand has an extensive data structure defined for chemistry, and one company (Molecular Simulations Inc.) even has a commercial molecular modeling product based upon AVS. At the moment, we are not using either program. However, I am personally interested in the use of SGI Explorer for this purpose, and so would appreciate your forwarding any information you may receive related to this as a result of your query. Thanks, Joseph -- Dr. Joseph D. Andose Merck Research Laboratories Bldg 50SW-100 126 E. Lincoln Avenue, P.O. Box 2000 Rahway, NJ 07065 (908) 594-4391 (908) 594-4224 (FAX) From tudor@wucmd.wustl.edu Tue Jan 12 10:23:36 1993 Date: Tue, 12 Jan 93 16:23:36 -0600 From: tudor@wucmd.wustl.edu (Tudor Oprea) Message-Id: <9301122223.AA08161@wucmd> To: CHEMISTRY@ccl.net Subject: Sybyl/Ampac interface Dear Netters, Does anyone have a Sybyl/Ampac (Amsol) interface written, so that I can read the AM1 // SM2 charges into Sybyl without disturbing the .mol2 geometry? Any piece of code would be interesting... Thank you, Tudor ================================================================================ = Tudor Ionel OPREA = Tel. (1-314) 935 4672 = = Research Associate = Fax. (1-314) 935 4979 = = Washington University Center for Molecular Design = Email: = = Lopata Hall, Box 1099, One Brookings Drive = tudor@wucmd.wustl.edu = = St.Louis MO 63130 = = ================================================================================ From rhn900@anusf.anu.edu.au Wed Jan 13 07:32:16 1993 From: Ross Nobes Message-Id: <199301130132.AA09188@anusf.anu.edu.au> Subject: Parallel eigenvalue solver To: chemistry@ccl.net Date: Wed, 13 Jan 93 12:32:16 EST Can anyone tell me where I can get my hands on a real symmetric eigenvalue/eigenvector solver for a massively parallel distributed memory machine? Thanks. -- * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Ross Nobes * * Academic Consultant * * Supercomputer Facility Phone: + 61 6 249 4154 / 4161 * * Australian National University Fax: + 61 6 247 3425 * * Canberra, ACT 0200 * * Australia E-mail: R.Nobes@anu.edu.au * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *