From skhademi@IREARN.bitnet Fri Feb 3 03:41:59 1995 Received: from AWIUNI11.EDVZ.UniVie.AC.AT for skhademi@IREARN.bitnet by www.ccl.net (8.6.9/930601.1506) id DAA27388; Fri, 3 Feb 1995 03:02:12 -0500 From: Received: from ROSE.IPM.AC.IR by AWIUNI11.EDVZ.UniVie.AC.AT (IBM VM SMTP V2R2) with TCP; Fri, 03 Feb 95 09:02:07 MEZ Received: by IREARN.BITNET (MX V4.1 VAX) id 838; Fri, 03 Feb 1995 11:31:34 +0330 Date: Fri, 03 Feb 1995 11:31:33 +0330 To: chemistry@ccl.net Message-ID: <0098B6E2.297F6A60.838@IREARN.BITNET> Subject: PLS Calculation Dear All, I am looking for a program to do simple Partial Least Square analysis. Can anyone tell me of useful programs to do this that exist in the public domain? Thanks S. Khademi From oesterei@hrz.ba-freiberg.de Fri Feb 3 09:42:11 1995 Received: from orion.hrz.ba-freiberg.de for oesterei@hrz.ba-freiberg.de by www.ccl.net (8.6.9/930601.1506) id JAA00171; Fri, 3 Feb 1995 09:00:58 -0500 Message-Id: <199502031400.JAA00171@www.ccl.net> Received: by orion.hrz.ba-freiberg.de (1.38.193.5/15.6) id AA11835; Fri, 3 Feb 1995 15:00:44 +0100 From: Ralf Oestereich Subject: >ghostview< for RS6000 / Where? To: chemistry@ccl.net (Computer Chemistry List) Date: Fri, 3 Feb 95 15:00:43 MEZ Mailer: Elm [revision: 70.85.2.1] Dear netters! I tried the archie service, but without any success: Where can I find a GHOSTVIEW version for a IBM RS6000, or a program to preview postscript files? Thanks in advance, R. Oestereich Institut fuer Anorganische Chemie Leipziger Strasse 09599 Freiberg GERMANY From WallyR@netcom.netcom.com Fri Feb 3 12:42:12 1995 Received: from netcomsv.netcom.com for WallyR@netcom.netcom.com by www.ccl.net (8.6.9/930601.1506) id LAA03756; Fri, 3 Feb 1995 11:44:40 -0500 Received: from DialupEudora by netcomsv.netcom.com with SMTP (8.6.9/SMI-4.1) id IAA24686; Fri, 3 Feb 1995 08:43:13 -0800 X-Sender: wallyr@localhost Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 3 Feb 1995 08:43:45 -0800 To: CHEMISTRY@ccl.net, Leif Laaksonen From: WallyR@netcom.netcom.com (Walter E. Reiher III) Subject: Re: CCL:Chemistry on PC:s >One further aspect is also the fact that we can also run Windows NT >on "real" graphics workstations today. However, I don't know about >any computational chemistry applications ported to the graphics >workstation/Windows NT platform. Would any of you want to change >the Unix on your graphics workstation into Windows NT? > >If you have any opinions/ideas about these things, please let me know. I've been using NT quite a bit recently. It stands head and shoulders above DOS/Windows: it's much more stable and is actually usable. Though NT has some strong points, I wouldn't want to give up my UNIX box yet: . NT does allow you to run commodity "general productivity" applications like Word, Excel, etc. and buy them at a reasonable price; can't do that with UNIX. . However, although MOST Windows apps run under NT (NOT ALL), I have seen very few applications which support advanced features in NT. The one that bugs me the most is that most apps don't support NT's long filenames (as opposed to DUMBNAME.DOS). Forget those handy Windows utilities programs under NT; most of them don't work. Hopefully this will get better when Windows95 finally arrives, since 95 compatibility means NT compatibility. . NT has multitasking and pipes, but they don't work the way I (as a UNIX person) expect them to. . From my limited experience, I don't find PC compilers to be very robust. The particular problem I've seen is that a highly-regarded compiler (Watcom) isn't able to produce a working MOPAC 93 executable. For those of us who would like to continue to use mature, portable codes like this, this is a big barrier. I'm sure things are quite different for new code written in C++ or Visual Basic. It will be interesting to see what kind of market arises to support OpenGL boards; unless it's also in Windows 95, I doubt it will happen soon. NT is still viewed as a specialist product, and doesn't enjoy wide support yet. From what I've read, all one can hope for with OpenGL under NT at present is static images--it's far too slow to support interactive graphics. Hope these $.02 contribute to the discussion... Wally ======================================================================== Walter E. Reiher III, Ph.D. WallyR@netcom.com Consultant in Computational Chemistry P.O. Box 61056 voice 408-720-0240 Sunnyvale, CA 94088 fax 408-720-0378 From hcj@mazda.wavefun.com Fri Feb 3 13:42:12 1995 Received: from volvo.wavefun.com for hcj@mazda.wavefun.com by www.ccl.net (8.6.9/930601.1506) id NAA05656; Fri, 3 Feb 1995 13:29:11 -0500 Received: from mazda.wavefun.com by volvo.wavefun.com via SMTP (931110.SGI/930416.SGI) for chemistry@ccl.net id AA01051; Fri, 3 Feb 95 10:29:11 -0800 Received: by mazda.wavefun.com (931110.SGI/930416.SGI) for @volvo.wavefun.com:chemistry@ccl.net id AA01040; Fri, 3 Feb 95 10:29:04 -0800 Date: Fri, 3 Feb 95 10:29:04 -0800 From: hcj@mazda.wavefun.com (Harry C. Johnson) Message-Id: <9502031829.AA01040@mazda.wavefun.com> To: oesterei@hrz.ba-freiberg.de Cc: chemistry@ccl.net In-Reply-To: <199502031400.JAA00171@www.ccl.net> (message from Ralf Oestereich on Fri, 3 Feb 95 15:00:43 MEZ) Subject: Re: CCL:>ghostview< for RS6000 / Where? Reply-To: hcj@wavefun.com >>>>> "Ralf" == Ralf Oestereich writes: Ralf> Where can I find a GHOSTVIEW version for a IBM RS6000, or a Ralf> program to preview postscript files? Ghostview is available from ftp://prep.ai.mit.edu/pub/gnu, but keep in mind that you also need ghostscript and the ghostscript fonts which are available from the same site. I am not aware of any sites with precompiled binaries. Hope this helps! -Harry +-----------------------+--------------------------------------------+ |Harry C. Johnson | /--- ----\ /---/ ---\ ----- /---/ /| / | |Computational Chemist | \ / / / / / / / / / / | / | |Wavefunction Inc. | \ /---/ /---/ /---/ / /---/ / | / | |E-mail: hcj@wavefun.com|---/ / / / / \ / / / / |/ | +-----------------------+--------------------------------------------+ From JOHNSONB@CPWSCA.PSC.EDU Fri Feb 3 15:42:10 1995 Received: from CPWSCA.PSC.EDU for JOHNSONB@CPWSCA.PSC.EDU by www.ccl.net (8.6.9/930601.1506) id PAA08146; Fri, 3 Feb 1995 15:20:48 -0500 Date: Fri, 3 Feb 1995 15:21:27 -0500 (EST) From: JOHNSONB@B.PSC.EDU To: chemistry@ccl.net Message-Id: <950203152127.20402070@B.PSC.EDU> Subject: Re: G92/DFT bug? H and LYP >I was using the DFT module of Gaussian 92 (HP-PARisc-HPUX-G92/DFT-RevF.4) >and came across something that looks like a bug to me: when I try to >calculate an one-electron system (like the H atom) and use the Lee-Yang-Parr >functional, my G92 version stops with an IEEE division by zero error. >I browsed through the code, and sure enough found in the LYP subroutine >a division by Rho(Beta), which is, in the case of one electron, equal zero. >I dont have access to the original paper right now, so could someone just >reassure me that this behavior is definitely an unexpected one, and that >it doesnt mean that the LYP functional is not valid in the limit of one >electron or if I only have electrons of one spin species (Gaussian shouldnt >abort that ungracefully, anyway...). This is definitely not the correct behavior -- it's a bug in the code I wrote for Gaussian. Not long after Gaussian obtained the code from me, I came across the bug and comunicated it to Gaussian, Inc. but apparently they have not done anything about it. >A related question is how to get in contact with these Gaussian guys...I >sent a message to help@gaussian.com some weeks ago, but havent heard from >them back. >And, could anybody who has access to a DFT implementation (maybe there is >even a G92 version out there that doesnt show this behavior) that >supports Becke 3 parameter XC in connection with the LYP C functional >calculate the energy for a H radical (with a 6-31G* basis) for me? Pointers >to papers where this has been done (maybe as a test case for the functional) >are, of course, also highly welcome. I could do the calculation for you using the Q-Chem program, which doesn't have this bug. You'd need to send me the parameters used in the Becke3LYP functional, though. There seems to be a lot of confusion in the literature over the definition of this method. To my knowledge, there has never been a paper published in which the definition of the Becke3LYP method in G92/DFT has actually been given, nor does there seem to be any systematic validation study thoroughly documenting its performance. I don't know if you're aware, but the method in G92/DFT is not a method of Becke's. I have talked with Becke about this, and he is quite skeptical about the validity of using the particular LYP functional with his half-and-half approach employing his exchange functional. So, you may want to reconsider whether this method is the one you actually want to use. Best regards, Benny Johnson Q-Chem, Inc. 317 Whipple St. Pittsburgh, PA 15218 From m10!trucks@uunet.uu.net Fri Feb 3 22:36:37 1995 Received: from relay3.UU.NET for m10!trucks@uunet.uu.net by www.ccl.net (8.6.9/930601.1506) id VAA01341; Fri, 3 Feb 1995 21:44:07 -0500 Received: from uucp2.UU.NET by relay3.UU.NET with SMTP id QQybok06294; Fri, 3 Feb 1995 21:44:18 -0500 Message-Id: Received: from m10.UUCP by uucp2.UU.NET with UUCP/RMAIL ; Fri, 3 Feb 1995 21:44:09 -0500 Received: by m10.gaussian.com; Fri, 3 Feb 95 20:53:57 EST Date: Fri, 3 Feb 95 20:53:57 EST From: m10!trucks@uunet.uu.net (Gary Trucks) To: CHEMISTRY@ccl.net Subject: CCL:G92/DFT bug? H and LYP -- Solution Thomas Fox wrote: >>I was using the DFT module of Gaussian 92 (HP-PARisc-HPUX-G92/DFT-RevF.4) >>and came across something that looks like a bug to me: when I try to >>calculate an one-electron system (like the H atom) and use the Lee-Yang-Parr >>functional, my G92 version stops with an IEEE division by zero error. This problem was fixed some time ago (G92/DFT Rev.G); it does not affect systems with more electrons. If you need this fix, contact Gaussian, Inc., and it will be sent to you at no charge. Benny Johnson responded: >There seems to be a lot of confusion in the literature over the definition >of this method. To my knowledge, there has never been a paper published in >which the definition of the Becke3LYP method in G92/DFT has actually been >given, nor does there seem to be any systematic validation study thoroughly >documenting its performance. This is not correct. Becke3LYP is specified completely and calibrated in numerous papers and presentations. Here are a few examples: P.J. Stephens, F.J. Devlin, M.J. Frisch and C.F. Chabalowski, "Ab Initio Calculations of Vibrational Absorption and Circular Dichroism Spectra Using SCF, MP2, and Density Functional Theory Force Fields," J. Phys. Chem. 98, 11623 (1994). Yue Qin and Ralph A. Wheeler, "Density-functional methods give accurate vibrational frequencies and spin densities for phenoxyl radical," J. Chem. Phys. 102, 1689 (1995). Cary Chabalowski, "Current trends in Computational Chemistry" Phil Stephens, "Faraday Discussions" P.J. Stephens, F.J. Devlin, C.S. Ashvar, C.F. Chabalowski and M.J. Frisch, "Theoretical Calculation of Vibrational Circular Dichroism Spectra," Faraday Discucc. 99 (1994) in press. (Phil's work was also discussed in C&E News, January 16 (1995) 27.) Johnson continues: >I don't know if you're aware, but the method in G92/DFT is not a method of >Becke's. I have talked with Becke about this, and he is quite skeptical >about the validity of using the particular LYP functional with his >half-and-half approach employing his exchange functional. So, you may want >to reconsider whether this method is the one you actually want to use. This confuses the Becke3LYP functional with Becke's half-and-half theory. Becke3LYP is based on the suggestion by Becke of exact (i.e., Hartree-Fock) exchange with local and gradient-corrected exchange and correlation terms (A.D. Becke, "Density-functional thermochemistry III. The role of exact exchange," J. Chem. Phys. 98, 5648 (1993)) and is *NOT* based on his half- and-half theory (A.D. Becke, "A new mixing of Hartree-Fock and local density- functional theories," J. Chem. Phys. 98, 1372 (1993)). Sincerely, Gary Trucks Gaussian, Inc.