From chemistry-request@ccl.net Mon Mar 16 10:28:59 1992 Date: Mon, 16 Mar 92 09:02:05 EST From: Evelyn Goldfield Subject: Density Functional Theory Workshop To: chemistry@ccl.net Status: R Cornell Theory Center / Cornell National Supercomputer Facility Density Functional Theory: Hands-on Workshop September 8 - 12, 1992 The Cornell Theory Center will conduct a one-week hands-on workshop on density functional theory and methods from Tuesday September 8 through Saturday, September 12, 1992. The workshop, which will be geared toward computational physicists, chemists, and scientists in related fields, will focus on the electronic structure of both molecules and extended systems such as solids. Three density functional packages will be featured. This workshop will make density functional methods available to a larger range of scientists. Quantum chemistry packages, such as GAUSSIAN and HONDO, are widely used by researchers who are not experts in quantum chemistry methods. These packages served to make the methods of quantum chemistry accessible to experimentalists and theorists working in other fields. As Density Functional Theory (DFT) packages become available, the use of DFT methods is expected to increase, particularly by scientists studying large systems. There will be four components to the workshop: o Introductory Lectures-- These will introduce participants to the basic ideas of the density functional method, its range of applicability, and its strengths and limitations. o Method-Specific Lectures-- Lectures that describe the capabilities and the computational methods used in the following three programs: a) Car-Parinello, b) CORNING and c) DMOL. The first two treat extended systems, although they can also be used for molecules. DMOL is designed for the study of molecular systems. To the extent possible, these will be taught by the authors of the programs. o Research seminars-- The wide range of applications of DFT, as well as recent methodological developments, will be the focus of an entire day of research talks given by some of the foremost authorities in the field, including: Dr. Michael Schluter (Bell Laboratories); Professor Karin Rabe (Yale University); Dr. Detlef Hohl (NCSA); Dr. Bernard Delley (Paul Scherrer Institut, Zurich); Dr. Douglas Allan (Corning Inc.); and Professor Michael Teter (Cornell University). These seminars are open to the public. o Hands-On Sessions-- Most of the afternoons will be devoted to hands- on sessions on IBM RISC System/6000 workstations. The workshop will provide exercises that illustrate the most important features of each of the programs, and also provide assistance to participants in implementing their own research projects. The final day of the workshop, Saturday September 12, is an optional day with consulting expertise available for continued work with the packages. This workshop will be limited to 20 participants and will be held in the training facility of the Engineering and Theory Center building. The workshop is aimed primarily at graduate students, post-doctoral fellows and other researchers who are not experts in density functional methods, but whose research may profit from the ability to perform density functional calculations. It will also be of interest to corporate participants and computer support personnel interested in providing their users with a similar capability for performing density functional computations. To Apply Registration fees are outlined in the form below. Contingent upon availability of funds, support may be available to help meet participant housing and travel expenses. If you require further information on any aspect of the workshop, please contact Donna Smith (address below). To apply, please return the completed registration form along with the appropriate registration fee (checks payable to Cornell University) postmarked by August 3, 1992. Applications will be accepted after this date if openings remain. Cornell applicants may charge their registration fees to the appropriate Cornell University account number. Applications which do not include payment cannot be accepted. Applicants will receive notification of their participation by August 17, 1992. Attendees are responsible for their own travel, meals, and lodging arrangements. Paid parking is available one block from the training facility. Blocks of rooms have been reserved for this workshop at the Collegetown Motor Lodge, located three blocks from the training facility, at 312 College Avenue, Ithaca, NY, 14850, 607-273-3542, $56-$75 per night. The rooms will be held until August 7, 1992. Please mention this workshop when making your reservation. Commercial airport limousine service is also available. Send registration form and fee to: Donna Smith Conference Coordinator Cornell Theory Center 422 Engineering and Theory Center Building Ithaca, New York 14853-3801 (607) 254-8614 phone (607) 254-8888 fax donna@theory.tc.cornell.edu ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Registration Form Density Functional Theory Workshop September 8 - 12, 1992 Name: Institution: Address: Telephone: Preferred Electronic Address: CNSF userid (if any): Academic Discipline: Any special needs? (diet, mobility impaired) Status (check one): __Undergraduate Student __Graduate Student __Faculty __Research Staff __Other Staff __Corporate __Other (explain) How much experience do you have with UNIX? ___none ___a little ___some ___fair amount ___much What are your present research interests? How will attending this workshop help you in your work? Workshop Registration Fees: University: $100 __________ CRI Member: $250 __________ Corporate: $400 __________ Check for _____ (payable to Cornell University) is attached - or - Charge to Cornell account number ____________ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From jkl@ccl.net Mon Mar 16 11:15:27 1992 Date: Mon, 16 Mar 1992 11:15:24 -0500 From: jkl@ccl.net To: chemistry@ccl.net Subject: Good Color Postscript Printers? Status: R Forwarding to the list. ---------- Begin Forwarded Message ---------- --Date: Mon, 16 Mar 92 07:46:31 EST --From: Mark Murcko --To: chemistry-request@ccl.net -- --To: chemistry-request@ccl.net Hello. We are thinking about color postscript printers. We have lots of information from MacWorld and similar sources, but it would be better to know what kinds of experiences people have using such devices for the complex images we often generate in computational chemistry, NMR, and X-ray applications. Can anyone comment on whether they (a) have used a particular brand of printer, (b) how reliable it is, (c) how fast it is, and most importantly, (d) how good was the image? Direct experiences are best, but rumors, anecdotal information, and second-hand experiences are also appreicated. It would be especially useful to hear from the software companies on this topic (Polygen, Biosym, Tripos, BioCAD, Cambridge Scientific ... are you out there?). As this is likely to be a topic of some general interest, I would be happy to summarize the results for the group. Thanks for your help. / Mark Mark A. Murcko (markm@vpharm.com) Vertex Pharmaceuticals ----------- End Forwarded Message ----------- From chemistry-request@ccl.net Mon Mar 16 15:01:46 1992 Date: Mon, 16 Mar 92 13:55:00 EST From: shenkin@avogadro.barnard.columbia.EDU (Peter S. Shenkin) Subject: Color PostScript Printers To: chemistry@ccl.net Status: R jkl suggested that I post the following summary to the list. The original just went to jkl, who was the original poster of Mark Murcko's query. I did a personal survey of this subject through comp.sys.sgi about six months ago. Answer: for native color PostScript printers, people like the Tektronix offerings, which are also supported by SGI (obviously not relevant unless you use SGI! ) A path that is cheaper by a factor of ten is to buy an HP PaintJet (not a color DeskJet!) and attach it to a serial port. Then by putting up GhostScript (GNU PostScript) you can print a PostScript file to it. Or you can buy a commercial package that does the same thing, called Freedom of the Press. FOP is available for micros and for UNIX platforms. Then there are a variety of routes for turning other formats into PostScript; public domain routes include (1) pbmplus, (2) a graphics suite from the San Diego Supercomputer Center, (3) for SGI, a variety of conversion programs that can be obtained by anonymous ftp from sgi.com, and (4) I hear there's a new suite of conversion routines from the Princeton Univ. Interactive Computer Graphics Lab. (5) Finally, xpr -- if you use x-windows -- supports the PaintJet directly. The HP Paintjet does not give output quite as nice as the ~$10,000 (list) Tektronics machines, but it lists for about $900, and I got mine for under $600. The Tektronics output is certainly not ten times nicer. Mack Price at NASA, who has both printers, was kind enough to send me sample output >from both, and there are even specific cases where the PaintJet output looks better to me. I have a student working on setting our PaintJet up right now, so I can't say I've gotten everything to work. But others have, and I've seen the output, so I'm reasonably confident we'll succeed, too. It's just that my student hasn't been able to devote the necessary time to the task so far. -P. ************************f*u*cn*rd*ths*u*cn*gt*a*gd*jb************************* Peter S. Shenkin, Department of Chemistry, Barnard College, New York, NY 10027 (212)854-1418 shenkin@avogadro.barnard.columbia.edu shenkin@cunixf.BITNET ********** "I've got algorithm -- who could ask for anything more?" ********** From chemistry-request@ccl.net Mon Mar 16 17:05:16 1992 Date: Mon, 16 Mar 92 21:45:46 +0100 From: martin@link.sunet.SE (Martin Norin, Dept. Biochem., Royal Inst. Technol., Subject: POSTSCRIPT. To: "chemistry@ccl.net"@kth.sunet.SE Status: R Netters, About color postscript: At our department we make our color postscript images of pictures from the modelling package in the following way: 1) Generate a postscript file of the picture from the molecular modelling package ( Sybyl) on our UNIX machine (ESV). 2) Transfer of the file to our VAX. 3) Print the file using the PSPRINT program on a LJ250 companion color printer (a sixel graphics printer from Digital). It sounds a little complicated but it is a very inexpensive way of making colored "pseudo postscript images". Also it is quite easy to make a script which do all this. The key is the PSPRINT program, which is a part of the DEC-print utility (Digital). This program converts postscript files to sixel graphics. I do not have the exact price of the LJ250 printer but it is far lot cheaper than a postscript color printer. The resulting pictures are also very nice. In fact it is hard to tell the difference between our PSPRINT pictures and a postscript one. Greetings /martin ************************************************************************ Martin Norin tel: +46-8-790 7512 Dept. Biochem fax: +46-8-723 1890 KTH e-mail: martin@physchem.kth.se 100 44 Stockholm Sweden ************************************************************************ From chemistry-request@ccl.net Mon Mar 16 17:07:27 1992 Date: Mon, 16 Mar 92 15:30:46 EST From: m10!trucks@uunet.UU.NET (Gary Trucks) To: chemistry@ccl.net Status: R >>On Mar 14 3:11am, Ole Swang wrote: >> in most cases a CC treatment is a factor 3 or 6 or something more >> expensive than a CI treatment. (there shouldn't be an exponential >> differennce betweeen the two). David Bernholdt responded: >This is a fairly common misconception. For a CC calculation and a CI >calculation with the same excitation operators included and the same >underlying formalism, the cost is essentially the same. A difference >you will see is that most CI codes are completely spin adapted, while >most CC codes are written in a spin-orbital framework. >The differences between a CC and CI implementation, then, depend on >whether the spin-orbital CC has been implemented to also take >advantage of the spin adaption when possible (for a closed shell >reference). For an open-shell molecule, there are effectively several >CC equations being solved simultaneously, to it's going to take longer >than a spin-adapted CI code. This deserves some clarification. Formally, CC is more expensive per iteration than CI for a given level of excitation. For example, Scuseria, et al., J. Chem. Phys. 89 (1988) 7382 show closed-shell CCSD costs within a factor of 2 of CISD. Their formalism is spin adapted, although, they correctly point out that spin adaptation is not essential for efficient formulation of the CC/CI equations. Further, given an efficient implementation for open-shell systems, the ratio of CCSD/CISD is also within a factor of 2. >On the other hand, CC methods are size-extensive (important for >treating larger systems), and recover more of the correlation energy >for a fixed amount of computational resources than CI. The benefits of CC theory certainly overshadow the modest cost increase over CI. -- Gary Trucks Lorentzian, Inc. trucks@lorentzian.com From chemistry-request@ccl.net Mon Mar 16 20:03:53 1992 Date: Mon, 16 Mar 92 18:11:15 CST From: shepard@dirac.tcg.anl.GOV (Ron Shepard) Subject: More on CC and CI To: chemistry@ccl.net Status: R Regarding CI and CC wave functions, here is an EXCELLENT review article: "Error analysis and improvements of coupled-cluster theory", W. Kutzelnigg, Theor. Chim. Acta 80, 349-386 (1991) It should also be mentioned that in addition to the energy being more expensive with CC than with CI (usually by a factor of 3 or so as implemented), the analytic energy gradient of a nonvariational wave function such as CC is at least an order of magnitude more expensive than that of a variational wave function such as CI. This is because computation of a CI density matrix is noniterative, whereas computation of the analogous array for a nonvariational wave function is an iterative process, roughly comparable in effort to computation of the wave function itself (10-15 iterations). In fact, for a large-scale CI wave function (large enough so that the wave function optimization dominates the integral derivative time), the energy gradient evaluation requires only a small fraction of the effort required for the energy. At present, due to the above argument, it appears that for a nonvariational wave function such as traditional CC, the gradient will always cost MORE THAN the energy! See JCP 96, 2085 (1992) for further discussions of this point. This brings us to the possibility of variational CC methods. Ideally these would possess correct size-extensivity and due to their variational nature still allow cheap calculation of response properties (such as analytic energy gradients). Several such methods which satisfy these requirements to some degree of approximation, including the multireference ACPF method which is included in the COLUMBUS Program System, are discussed in the above review article. Finally, in the article "A comparison of variational and non-variational internally contracted multiconfiguration-reference configuration interaction calculations", H.-J. Werner and P. J. Knowles, Theor. Chim. Acta 78, 175-187 (1990) the authors show that "In most cases the variational CMRCI wavefunctions yield more accurate spectroscopic constants than any of the employed non-variational methods". [Note that they call ACPF nonvariational, whereas I am calling it variational. We're chemists, so we can do this. -rls] -ron shepard, acting gadfly (:-) shepard@tcg.anl.gov From hughc@extro.ucc.su.OZ.AU Mon Mar 16 20:05:22 1992 Date: Tue, 17 Mar 1992 01:06:14 GMT From: hughc@extro.ucc.su.OZ.AU (Hugh Capper) To: chemistry@ccl.net, jkl@ccl.net Subject: Re: Good Color Postscript Printers? Status: R Dear Netters, We access CHEM-X on a Vax through a terminal emulation program on a IBM PC clone 386/33 micro. Whenever we wish to print a colour image we simply capture the image using the Windows 3.0 image grabber transfer to the paint program where we can add text. This is then sent to any colour printer that is available on the university net.Printers that are available include QMS-100 colour, Apple colour laser and HP pPaintjet. As you can see, there are few problems involved and the cost is minimal in time and money, but the quality is as good as the monitor. Hugh Capper From chemistry-request@ccl.net Mon Mar 16 23:56:46 1992 Date: Mon, 16 Mar 1992 23:02:42 EST From: Bill Winter To: chemistry@ccl.net Status: R An organic chemistry colleague inquired about software for a PC (DOS flavor preferably) to draw 3-dimensional images (wire frame possibly) of molecular orbitals. As a modeler of fibrous biopolymers, I had to confess my ignorance and so I seek you assistance in locating such programs. Please reply to address in signature below. Thanks for your help. ============================================================================ William T. Winter, Polymer Structure and Dynamics Group 315 Baker Lab, SUNY-ESF, Syracuse, NY 13210-2786, USA Internet: wtwinter@suvm.acs.syr.edu or wtwinter@mailbox.syr.edu Phone: (315)470-6876; FAX: (315)470-6512