From chemistry-request@ccl.net Mon Oct 14 10:18:47 1991 Date: Mon, 14 Oct 91 10:01:05 -0400 From: Iosif Vaisman To: chemistry@ccl.net, fisher@scripps.edu Subject: Re: Educational software for the Macintosh Status: R In article <9110120300.AA26536@crystal.Scripps.EDU> fisher@scripps.edu (Cindy Fisher) writes: >Does anyone out there know of any software or know where to get information >about software (preferably not too expensive) that teaches concepts related >to biology or biochemistry available for the Macintosh? Any clues would be >much appreciated. Some biology-related software for Macintosh available from MacSciTech archive via anonymous ftp ra.nrl.navy.mil (/MacSciTech/biology, there are also chemical programs in /MacSciTech/chem). Iosif Vaisman From chemistry-request@ccl.net Mon Oct 14 19:15:12 1991 Date: 14 Oct 91 19:06 EDT From: PCJ%PSUVM.BITNET@OHSTVMA.ACS.OHIO-STATE.EDU To: CHEMISTRY@ccl.net Subject: Sending you "CEAS NOTE A1" in this note Status: R ********** MEETING ANNOUNCEMENT ********** 4th Symposium on Computer-Enhanced Analytical Spectroscopy Snowbird, Salt Lake City, Utah June 17-19, 1992 Purpose: To bring together experts in analytical spectroscopy and chemometrics to exchange information and to stimulate discussion and cooperation. Topics of Interest: Optimization and exploratory data analysis Spectral interpretation and library searching Visualization of higher dimensional data and nonlinear mapping Clustering and classification analysis of multivariate data Numerical extraction of multicomponent data Optimization and process control using spectral data Numerical modeling of spectral information Automated spectral interpretation, expert systems Multicomponent analysis Spectral enhancement and deconvolution Factor and discriminant analysis This will be a small symposium of < 100 participants. It will run like a Gordon Conference. Posters will be accepted. Registration fee is $350 which includes all meals for three days plus the book to be published. Support is available for academic participants. To obtain more information, please write to: Dr. Charles L. Wilkins, CEAS-92, Department of Chemistry, University of California-Riverside, Riverside, CA 92521-0403. From chemistry-request@ccl.net Mon Oct 14 20:29:35 1991 Date: Mon, 14 Oct 91 17:22:08 PDT From: fisher@scripps.edu (Cindy Fisher) To: chemistry@ccl.net Subject: Macintosh educational software for the sciences Status: R Many thanks to the respondents to my earlier posting concerning Mac educational software. Here I present a summary of responses (if you need any more info than I have here, feel free to contact me, and I'll try and point you in the right direction): ----------------------- Terry Yeung at Cal-Animage Berkeley forwarded a message he received about PD_Science, Professor Thomas O'Haver's catalog of science/math/engineering public domain and shareware programs available from CompuServe, America Online, GEnie, and a number of Internet addresses. I looked through this, and it's a fairly hefty list. It can be obtained by anonymous FTP >from ra.nrl.navy.mil as MacSciTech/info/PD_Science.txt. If you don't have Internet, you can grab it from GEnie or America OnLine, too. For further info, contact: Prof. T. C. O'Haver Department of Chemistry and Biochemistry University of Maryland College Park, MD 20742 Internet: toh@umd2.umd.edu ----------------------- Al Lowrey mentioned a molecular structure visualization program called NANOVISION and pointed me toward the software office at ACS. ----------------------- Laura Walsh at the University of Illinois suggested two software packages, SimEarth and SimAnt as potentially useful. ----------------------- Dongchul Lim from Yale sent an extensive reply to Richard Swenson's query, which I believe we all received, that describes several modeling packages that are commercially available. ----------------------- Mingzuo Shen pointed me toward several anonymous ftp sources for software. In addition to the ra.nrl.navy.mil MacSciTech group's collection mentioned by Iosif Vaisman to the bulletin board, he referred me to ftp.bio.indiana.edu, which has many scientific programs, and specific directories for biology, chemistry, and molecular biology programs (I'm still digging in this wealth of info), and to wuarchive.wustl.edu, at Washington University, which is REALLY loaded, and is going to take many fun hours of digging through. ----------------------- Terry Stouch from Squibb and Jacquelyn Fetrow from SUNY-Albany mentioned Michael Levitt's program MacImadad as a useful molecular modeling program. Jacquelyn Fetrow also suggested Autodesk for this purpose. ----------------------- Greg Durst at Lilly gave addresses for two scientific software houses: BioSoft, PO Box 580, Milltown, NJ 08850 and Trinity Software, PO Box 960, Campton, NH 03223. They have programs on enzyme kinetics and statistics, among others. ----------------------- Ralph Merkle at Xerox suggested Chem 3D plus from Cambridge Scientific Computing (617-491-6862), which is a bit pricey, but is apparently a very good MM2 package. He also suggested looking into the QCPE Mac software (812-855-4784). Cindy Fisher Department of Molecular Biology The Research Institute of Scripps Clinic La Jolla, CA 92037 E-mail to: fisher@scripps.edu From chemistry-request@ccl.net Mon Oct 14 21:07:01 1991 Date: Mon, 14 Oct 91 20:03:14 CDT From: shepard@dirac.tcg.anl.gov (Ron Shepard) To: chemistry@ccl.net Subject: COLUMBUS BETA Release Status: R Since last Saturday, October 12, was Columbus Day, and today, Monday October 14, is the official holiday this year, it seems appropriate to announce at this time the availability of a BETA version of the COLUMBUS Program System for molecular electronic structure calculations. The following is a short description of the program system, with instructions on how to obtain a copy of the source code and documentation. The COLUMBUS Program System is a collection of Fortran programs for performing general ab initio Multireference Single- and Double-excitation Configuration Interaction (MR-SDCI) and related calculations, such as averaged coupled-pair functional (ACPF) and linearized coupled-cluster method (LCCM). Closed- and open-shell single-reference CI calculations are subsets of the more general expansion forms. The source code, documentation, sample calculations, and shell scripts are available in three forms via anonymous FTP: (1) individual files within the directory structure, (2) a "tar" file of the entire program system, and (3) a compressed form of the "tar" file. If you only want to examine the documentation files before downloading the entire system, the following is a sample ftp session: % cd where/ever/you/want/the/files/to/go/ % ftp -n ftp.tcg.anl.gov ftp> user anonymous local_user_name ftp> cd pub/columbus/doc/ ftp> prompt # turn off prompting. ftp> mget * # get everything in doc/. ftp> bye If you decide you want to get the compressed tar file, and install the existing directory structure, then do the following: % cd where/ever/you/want/the/files/to/go/ % ftp -n ftp.tcg.anl.gov ftp> user anonymous local_user_name ftp> cd pub/tars/ ftp> binary # enable binary transfers. ftp> dir # see what's there. ftp> get Columbus.07-oct-91.Z # get the latest version. ftp> bye % uncompress -c Columbus.07-oct-91.Z | tar -xvf - # restore everything ADDITIONAL COMMENTS: Please note that this is a BETA version of the program system. It is recommended that these codes be used with caution for "production" work, and even then only if the results can be verified independently for correctness. All of the programs are close to their research-level counterparts EXCEPT for the MCSCF program, which is currently being modified. The updated MCSCF program will be added to the distribution codes as soon as it is available, and this new version will replace the old version completely. The integrals through SCF programs (ARGOS, CNVRT, SCFPQ) can be run in parallel on distributed memory parallel computers, shared memory parallel computers, homogeneous workstation networks, and heterogeneous mixtures of all of the above. This version of these codes has been included primarily as a demonstration of how simple it can be to port production-level chemistry codes to a parallel environment. However, there is no dynamic load-balancing in these codes, so this is not intended to be the optimal parallel implementation of these job steps. The TCGMSG library, written by R. J. Harrison and also available from the above anonymous ftp site, is necessary to run these codes in parallel (TCGMSG is not required for the "normal" serial codes). The MCSCF and MRCI analytic gradient codes and the parallel version of the diagonalization program (CIUDG) are not yet included in the COLUMBUS distribution. These codes are now being modified in preparation for inclusion at a later time (probably next spring or early summer). Other additions and enhancements are also in the works. *************** * DISCLAIMERS * *************** The computer programs described here contain work performed partially by the Argonne National Laboratory Theoretical Chemistry Group under the auspices of the Office Of Basic Energy Sciences, Division Of Chemical Sciences, U.S. Department Of Energy, under contract w-31-109-eng-38. Additional work was performed at the Ohio State University, with partial support from Cray Research, Inc., at the University of Vienna, and at other sites. These programs may not be (re)distributed without the written consent of the Argonne Theoretical Chemistry Group or the other development sites. Since these programs are under development, correct results are not guaranteed. The Argonne National Laboratory Theoretical Chemistry Group and the COLUMBUS programmers at the Ohio State University, the University of Vienna, and other sites disclaim all warranties, either express or implied, including but not limited to implied warranties of fitness for a particular purpose, with respect to these computer programs. In no event shall the Argonne National Laboratory Theoretical Chemistry Group, the Ohio State University, the University of Vienna, or the COLUMBUS programmers be liable for any damages whatsoever arising out of the use or inability to use these programs. *************************************** * COLUMBUS PROGRAMMER EMAIL ADDRESSES * *************************************** The COLUMBUS Program System has been developed over the last 10-15 years with contributions from several research groups and from many students, postdocs, and other collaborators. The references cited in the various program listings indicate the extent of this development effort. The following is a list of email addresses for the current COLUMBUS programmers who are primarily responsible for the ongoing development of the codes. shepard@tcg.anl.gov # Ron Shepard (Argonne) shavitt@mps.ohio-state.edu # Isaiah Shavitt (Ohio State) pitzer@neon.mps.ohio-state.edu # Russell M. Pitzer (Ohio State) lischka@itc.univie.ac.at # Hans Lischka (Vienna) ############################################################################## From chemistry-request@ccl.net Mon Oct 14 21:09:39 1991 Date: Tue, 15 Oct 91 08:56:26 SST From: Heng Kek Subject: Estimation of INT and RWF file sizes for G86 (Summary) To: Computational Chem Grp at Ohio Supercom Ctr Status: R Hi all, A while ago, I posted the following question. Now here's the summary of all the responses I got: >* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 41 > >Question: Is there a way to calculate beforehand, the size of the > INTEGRAL and RWF files, given the input to the G86 program? > >* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 40 >From: >The maximum size of the files can be estimated exactly but is a little >dificult and experience plays an important role. >The easier to determine is integral file because the maximum >number of integrals is roughly (N**4)/8 where N is the number of basis >functions. Each integral will need from 10 to 16 bytes depending on the hardwar >used. I know nothing about the SX. The program will eliminate small integrals >so the total number of integrals reduces from 5 to 30%, Therefore >experience in your systems will tell you a good estimate but knowing >the maximum is a good start. Later versions of gaussian (89,90,91) have >a DIRECT option in which you do not need to storage integrals and >is even faster when the total number of basis functions is bigger than 100. >Normally the RWF do not require lot of space exept in postHF >calculations where the above number have to multiplied by the number >of atoms in same cases or the number of occupaid orbitals etc the >deatails must be in the manual. Again, for these calculations >this is not true in latest versions of Gaussian. I used G90 >which is more eficient managing disk space. You should get G90 or >at least G88. G86 was not a good version (has many bugs) >and not many people use it right now. There are many details involved >I guess if you mail me the input file, could be of more help. >Best regards >Dr. Jorge M. Seminario >bitnet%"jsmcm@uno" >University of New Orleans >Dept of Chemistry >From: > >The problem with the RWF file is that its content have changed with >different versions of Gaussian, you probably can see the exact content >in the manual. I do not have one right now. A 94 basis functions MP2 >calculation would require the following disk space: >---------------------------------from output file--------------------------- >0Normal termination of Gaussian 90. > STATUS OF FILES > RWF: /tmp/users/4/seminari/sco1/97269/g90-a97282.rwf 453120 words deleted > INT: /tmp/users/4/seminari/sco1/97269/g90-a97282.int 19326464 words deleted > D2E: /tmp/users/4/seminari/sco1/97269/g90-a97282.d2e 0 words deleted > CHK: sco1mp2.chk 130560 words saved > SCR: /tmp/users/4/seminari/sco1/97269/g90-a97282.scr 24668160 words deleted > -----------------------------------------------------------------------end >This can help you a little to have an idea (remember 1word=8bytes) >In MP2 calculations RWF (G86) it probably contains the transformed integrals >and some other stuff for the frequency so the g86 would >contains the RWF and the SCR files of G90 plus an small additional for the >numerical second derivatives. But a word of advice here, >MP2 FREQ in Gaussian are done numerically as opposed to analytically >which for your system could take many times less >CPU time! (12 atoms means 36 coordinates so 72+1 energy calculations will >be required numerically.) The program that can do that analytically is >called CADPAC (Cambridge Analytic Derivative PACkage) I never do MP2 FREQ >using Gaussian programs. > >* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * = >From: djh@ccl.net > >>The problem: G86 on the SX uses a tremendous amount of scratch filespace > >For SCF-only jobs (that is, no MP, CI, etc.) find out how many basis functions >there are. The easiest way to do this is start up the job for a minute or so >and look through the output. If N is the number of basis functions, estimate >N^4/4 words of storage needed for the integral file. I assume the SX is a >64 bit machine, so if there are 50 basis functions you'd need 12.5MB. > >If there is symmetry in the molecule you won't need as much space. If the >user is doing a correlated calculation, you may need several times this space. > >Often, many similar jobs are run, or a series of runs with larger basis sets is >made, so an aware user can make a good estimate of file space needed after the >first successful run. Unfortunately, experience is the only good teacher in >this problem! > >>Another question is: Is this sort of filesize for the integrals and >>readwrite file typical?? > >We routinely run jobs requiring 8GBytes total disk space. Quantum chemistry >does not scale well! You might want to look into getting G90 though, as it >has the so-called "direct SCF", which uses only minimal disk space at some >increase in CPU time. >-- >David J. Heisterberg (djh@ccl.net) "Dost thou use to write thy name? >The Ohio Supercomputer Center or hast thou a mark to thyself, >Columbus, Ohio like an honest plain-dealing man?" > >* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * = >From: > >I'm a bit surprised that the rwf file takes more space than the >integral file: whenever I've run G86 on a Cray, the reverse >was true. A pretty decent estimate for the integral file is >10*N*N*N*N/4 bytes, where N is the number of basis functions. >This number can be obtained from the molecular formula, and >knowledge of the basis set. Tim Clark, in his "Handbook of >Computational Chemistry" (Wiley, I think) has a nice chart of >the number of basis functions per atom for the common basis sets. >I hope this helps you. >Irene Newhouse > >* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * = >From: m10!frisch@uunet.UU.NET (Michael Frisch) > >It is common for ab initio calculations to use large amounts of disk space. >The current version of Gaussian can trade CPU time for disk space for the >most common types of calculation (Hartree-Fock and MP2), and is much, much >faster, but these capabilities were not present in Gaussian 86. > >The integral file size depends on the number of basis functions. It will be >roughly 1.5N^4 bytes or 2N^4 bytes long, depending on how the integral >labels are packed (whether they fill 32 or 64 bits). For open-shell >Hartree-Fock calculations, the size will be 2.5N^4 or 3N^4. > >The read-write file size depends on N^2 for Hartree-Fock calculations, and >on N^4 in a complicated way for post-SCF calculations. The easiest way to >estimate the size is to run a smaller job an scale the size by the ratio >of OV^3 for the jobs (O=number of electrons, V=N-O=number of virtuals). > >The limitation of not being able to extend these files is specific to the >NEC implementation of Gaussian and is not present on other versions. Contact >your NEC representative for an explanation. > >All this is for Gaussian 86, of course. For SCF and MP2 calculations in >Gaussian 90 the integral file isn't needed. For MP2, whatever disk is made >available for the read-write file is used, with quantities being recomputed >instead of trying to use more disk than there is. > >Michael Frisch >Gaussian, Inc. >------- Acknowledge-To: