From S.M.Todd@chem.hull.ac.uk Tue Oct 28 07:33:36 1997 Received: from lehar.ucc.hull.ac.uk for S.M.Todd@chem.hull.ac.uk by www.ccl.net (8.8.3/950822.1) id GAA00848; Tue, 28 Oct 1997 06:33:38 -0500 (EST) Received: from humus1.ucc.hull.ac.uk by lehar.ucc.hull.ac.uk; Tue, 28 Oct 1997 11:32:34 +0000 Received: from chpsmt by humus1.ucc.hull.ac.uk with local (Exim 1.60 #1) id 0xQ9sw-0001Qg-00; Tue, 28 Oct 1997 11:32:34 +0000 Date: Tue, 28 Oct 1997 11:32:34 +0000 (GMT) From: Vagster X-Sender: chpsmt@humus1 Reply-To: S.M.Todd@chem.hull.ac.uk To: chemistry@www.ccl.net Subject: MOPAC/Dipole Moment calculations In-Reply-To: <199710272050.PAA04094@krakow.ccl.net> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi there I am currently using Cerius2 V3 and MOPAC to calculate dipole moments for single molecules. However, I now wish to rotate one particular bond by say 5 degrees and calculate the dipole moment and repeat this for the whole 360 degrees thus giving me a view of how the dipoles change with single bond rotations. Can this be done using Cerius2 and MOPAC ? or can it be done using just MOPAC ? If not, can anybody recommend a piece of software which can do this ? I have access to Pentiums, SGI or Sun workstations but the software must be freely available. Cheers for any advice Steve Todd ".... for a country is considered the more civilized the more the wisdom and efficiency of it's laws hinder a weak man from becoming too weak or a powerful one becoming too powerful." If This Is a Man - Primo Levi mail to : S.M.Todd@chem.hull.ac.uk web-site: http://www.hull.ac.uk/php/chpsmt/ From ENZO@CHEMNA.DICHI.UNINA.IT Tue Oct 28 08:33:38 1997 Received: from CHEMNA.DICHI.UNINA.IT for ENZO@CHEMNA.DICHI.UNINA.IT by www.ccl.net (8.8.3/950822.1) id IAA01329; Tue, 28 Oct 1997 08:29:06 -0500 (EST) From: Received: from CHEMNA.DICHI.UNINA.IT by CHEMNA.DICHI.UNINA.IT (PMDF V5.1-7 #23999) id <01IPCDIUSX5S00005C@CHEMNA.DICHI.UNINA.IT> for CHEMISTRY@www.ccl.net; Tue, 28 Oct 1997 14:28:24 CET Date: Tue, 28 Oct 1997 14:28:23 +0100 (CET) Subject: Gaussian & PCM To: CHEMISTRY@www.ccl.net Message-id: <01IPCDIUYA2A00005C@CHEMNA.DICHI.UNINA.IT> X-VMS-To: IN%"CHEMISTRY@www.ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Recently there have been some inquiries about different PCM models available in the Gaussian package and, in particular, dr.Norrby has given some incomplete information about the new version developed in Italy (the so-called PCM/DIR). Actually this version is being developed by our group at the University of Naples, in collaboration with Jacopo Tomasi's group at the University of Pisa. A fully integrated version will be available in the next release of the Gaussian package (hopefully at the beginning of the new year). A part of the code has been implemented also in Gaussian 94 (version D.4): this implementation, which has been distributed to some researchers that had requested it, allows PCM and COSMO computations of energies and analytical gradients at the HF and DFT levels and of energies also at post-HF levels. Several solvents can be used changing a single keyword and a particularly effective cavity model (UAHF) has been also implemented. This version is being used by more than two years and a number of papers (see below) are already available, which document its development and validation. If someone is interested in the version running on Gaussian 94 (recalling that it is not the complete version that is going to appear in the next Gaussian), he can contact us at the addresses below. STRUCTURE AND MOLECULAR DYNAMICS GROUP (University of Naples, Italy) Professor Vincenzo Barone Dr. Maurizio Cossi Dr. Carlo Adamo Dr. Andrea Di Matteo Dr. Nadia Rega ****************** References of PCM ************************** M.Cossi,V.Barone,R.Cammi,J.Tomasi, Chem.Phys.Lett. 255,327-335 (1996). V.Barone, Chem.Phys.Lett. 262,201-206 (1996). C.Adamo,V.Dillet,V.Barone, Chem.Phys.Lett. 263,113-118 (1996). N.Rega,M.Cossi,V.Barone, J.Chem.Phys. 105,11060-11067 (1996). V.Barone,M.Cossi,J.Tomasi, J.Chem.Phys. 107,3210-3221 (1997). V.Barone,M.Cossi, J.Phys.Chem. in press V.Barone,M.Cossi,J.Tomasi,J.Comput.Chem., in press. N.Rega,M.Cossi,V.Barone, J.Am.Chem.Soc. in press V.Barone,A.Bencini,A.Di Matteo, J.Am.Chem.Soc., in press. ------------------------------------------------------------------------------- prof. Vincenzo Barone | Dipartimento di Chimica | tel. +39-81-5476503 Universita' Federico II | fax +39-81-5527771 via Mezzocannone 4 | e-mail ENZO@CHEMNA.DICHI.UNINA.IT I-80134 Napoli | Italy | ------------------------------------------------------------------------------- Dr. Maurizio Cossi | Dipartimento di Chimica | tel. +39-81-5476504 Universita' Federico II | fax +39-81-5527771 via Mezzocannone 4 | e-mail cossi@risc55.dichi.unina.it I-80134 Napoli | Italy | ________________________________________________________________________________ From tamasgunda@tigris.klte.hu Tue Oct 28 08:40:27 1997 Received: from tigris.klte.hu for tamasgunda@tigris.klte.hu by www.ccl.net (8.8.3/950822.1) id IAA01194; Tue, 28 Oct 1997 08:04:01 -0500 (EST) Message-Id: <199710281304.IAA01194@www.ccl.net> Received: from anti02 (anti02.chem.klte.hu) by tigris.klte.hu (MX V4.1 VAX) with SMTP; Tue, 28 Oct 1997 09:41:22 +0100 Comments: Authenticated sender is From: "Tamas Gunda" To: chemistry@www.ccl.net Date: Tue, 28 Oct 1997 09:46:21 +1 MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7BIT Subject: Re: CCL: language Priority: normal X-mailer: Pegasus Mail for Windows (v2.42a) Didier MATHIEU wrote: > For me I have to choose a programming langage. Indeed, facing a serious > need for a broad range of specific programs for molecular engineering of > energetic materials (implementing simple and efficient empirical models > based on molecular mechanics, groups increments, QSPR relationships...) > we have these programs written by students who remain in the team for > short training periods (few months). > In this context of fairly long-term projects with high turnover and poor > communication between succesive programmers, pieces of code written by > some people must be used easily by others, hence codes must be at least > modular. Experience with Fortran has shown us that training students, > because of the limited time allocated, are in a hurry to implement as > much as possible, and resulting code is not well structured. On the > other hand, since they are mostly students in physics or chemistry, most > of them do not master C or C++ , although all of them have some > programming experience, for instance with Pascal or Basic. > > According to me, none of those free langages, C, C++ and Fortran, is a > good choice and I am looking for a SIMPLE langage supporting REUSABILITY > and QUICK DEVELOPMENT. > It is difficult to suggest, as the demands are contraversial: you need a structured, modular, but simple language for students with little practice. The most simple is classical Basic. Frankly speaking, I would suggest C, but not classical Pascal, Fortran is a language of the past (even if some does not agree). The only advantage of the latter that quite a lot of scientific algorithms, procedures can be found in libraries - but these can be easily converted to another environment. Anyway, you have to consider the demands. Programming under Windows or DOS or UNIX etc? Only small scientific applications will be done or something bigger is in mind? What kind of previous practice your students have? Is everybody on the same level? etc etc. DOS based applications can be done even today, especially for in-house scientific calculations, without the many bells-and-whistles of Windows of course (but this may be an advantage too...) The languages under Windows are not immediately straightforward, even Visual Basic: it is quite far from the classical DOS-based Basic and needs some excercising before something serious can be done. In Basic one can write structured and modular code, but it needs very careful planning in advance - of course, its modularity will never be on same high level as in C. Borland's Delphi is growing to more popular recently. The next is C or C++, which is the most sympathic for me, and the latest is JAVA (but I have no practice with it, so I cannot say any pro or con). Tamas E. Gunda ************************************************************************ Dr Tamas E. Gunda phone: (+36-52) 316666 ext 2479 Research Group of Antibiotics fax : (+36-52) 310936 L. Kossuth University e-mail: tamasgunda@tigris.klte.hu POBox 36 H-4010 Debrecen Hungary ************************************************************************ From mnolan@nmrc.ucc.ie Tue Oct 28 09:33:38 1997 Received: from bastion.nmrc.ucc.ie for mnolan@nmrc.ucc.ie by www.ccl.net (8.8.3/950822.1) id IAA01357; Tue, 28 Oct 1997 08:34:38 -0500 (EST) Received: by nmrc.ucc.ie (8.6.12/8.6.6) with ESMTP id NAA19043 for ; Tue, 28 Oct 1997 13:36:30 GMT From: mnolan@nmrc.ucc.ie (Michael Nolan) Message-Id: <199710281329.NAA02423@malaga.nmrc.ucc.ie> Subject: dft software..summary To: chemistry@www.ccl.net Date: Tue, 28 Oct 1997 13:29:02 +0000 (GMT) X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear CCLers, Many thanks to you all for the replies about DFT software I was already aware of the usual packages (ADF,G94, GAMESS-UK, DMol, DGauss, DeMon etc..), but at the moment we can't afford any of them (our msi software costs a fortune). We are now in the process of checking everything out. Michael *************************************************************************** Michael Nolan Wenn ich Daimler fahren will, Materials Group rufe ich ein Taxi an National Microelectronics Research Centre (German humor) Lee Maltings Prospect Row Cork IRELAND mnolan@nmrc.ucc.ie **************************************************************************** ***************************************************************************************** 1: From choic@gusun.georgetown.edu Mon Oct 20 19:58:17 1997 Hi Michael, There is a free DFT software (called DeFT) in the CCL ftp site. In order to run it, you need a fortran compiler to compile it. G94w (Gaussian94 for Windows95/NT) can to DFT calculations, it is not free though. Check their web page at www.gaussian.com. Spartan (PC version) can, I think , do DFT. I forget their web page. But you can easily locate their web page with yahoo. I hope It helps. Cheol-Ho Choi Georgetown Univ. ***************************************************************************************** 2: From gene@q-chem.com Mon Oct 20 22:49:08 1997 Return-Path: gene@q-chem.com Dear Michael, We don't have Q-Chem running under Windows (NT) yet, but we do run on a wide variety of UNIX workstations. The price might be a lot lower than you think. Please take a look at our website: http://www.q-chem.com and you will find feature, platform, and pricing information. Of course, the bottom line is that we have an excellent DFT package that includes several different treatments of correlation and exchange. Q-Chem also includes Hartree-Fock and Hybrid HF-DFT methods as well as pure DFT. Sincerely, Eugene Fleischmann +--------------------------------------------------------------------+ | Eugene D. Fleischmann, Ph.D. http://www.q-chem.com | | Director of Sales | | Q-Chem, Inc. voice: (609) 896-3942 | | 317 Whipple St. FAX: (609) 896-1244 | | Pittsburgh, PA 15218 email: gene@q-chem.com | +--------------------------------------------------------------------+ ********************************************************************************************** 3: From gmercier@mail.med.upenn.edu Tue Oct 21 00:39:02 1997 Return-Path: gmercier@mail.med.upenn.edu Hi! In the ccl archives you may find DeFT, a cousin of turbomole (I believe.). I came across another software package, JEEP. This is apparently an "easy to use" DFT program based on Car-Parrinello ab initio MD with plane wave basis sets and ECP's. I've never used it, but you can try to do molecules using the "isolated particle model" -- nothing fancy but a periodic system with a large square box that contains your molecule. The box is large enough that the molecules "don't interact" with each other in the periodic system. This is a convenient construct to perform computations on molecules using software designed for periodic systems. I understand JEEP is free(?!) There are other packages like ADF, DGauss, DMOL, etc, but these are not free. Good luck! -- ("`-/")_.-'"``-._ Gustavo A. Mercier,Jr.,MD,PhD (. . `) -._ )-;-,_() Division of Nuclear Medicine (v_,)' _ )`-.\ ``- Dept. of Radiology _;- _,-_/ / ((,' University of Pennsylvania ((,.-' ((,/ 3400 Spruce St. gmercier@mail.med.upenn.edu Philadelphia, PA 19104 215-662-3069/3091 fax: 215-349-5843 **************************************************************************************************** 4: From paschedag@fhi-berlin.mpg.de Tue Oct 21 07:59:17 1997 Return-Path: paschedag@fhi-berlin.mpg.de Hi, I guess your success will to some extent depend on the type of calculations you want to perform. >From your signature I deduce that plane wave calculations with periodic boundary conditions may be what you're looking for. If that is so try our fhi96md program. It's free and comes with source. It's mostly for UNIX but we've had recent reports that it can be ported to Win95 (try NT if you can, it's faster) with minimal effort. http://www.fhi-berlin.mpg.de/th/fhi96md/code.html Best regards, N. Paschedag Dr. Norbert Paschedag ___ /__ / / Fritz-Haber-Institut der Max-Planck-Gesellschaft __/ ___ / / Faradayweg 4-6, D-14195 Berlin-Dahlem, Germany __/ __/ __/__/ tel +49 30 8413 4822 / fax +49 30 8413 4909 paschedag@fhi-berlin.mpg.de ******************************************************************************************************** 5: From <@ICINECA.CINECA.IT,@cinymp.cineca.it:bruno@antas.agraria.uniss.it> Tue Oct 21 08:32:45 1997 Return-Path: <@ICINECA.CINECA.IT,@cinymp.cineca.it:bruno@antas.agraria.uniss.it> Dear Michael, you may found useful the DeFT program, free after signing a licence see: http://hackberry.chem.niu.edu/ChemistrySoftware/DensityFunctionalPrograms/DeFT also have a look to our links to DFT codes at: http://antas.agraria.uniss.it/software.html hope it helps regards Bruno Dr Bruno Manunza DISAABA (Dept. of Agricultural Environm. Sci) University of Sassari V.le Italia 39 07100 Sassari, ITALY phone: 39 79 229215 fax: 39 79 229276 e-mail: bruno@antas.agraria.uniss.it e-mail: bruno@tharros.dipchim.uniss.it e-mail: gx6bot81@cray.cineca.it web: http://antas.agraria.uniss.it From mnolan@nmrc.ucc.ie Tue Oct 28 09:41:58 1997 Received: from bastion.nmrc.ucc.ie for mnolan@nmrc.ucc.ie by www.ccl.net (8.8.3/950822.1) id IAA01435; Tue, 28 Oct 1997 08:46:12 -0500 (EST) Received: by nmrc.ucc.ie (8.6.12/8.6.6) with ESMTP id NAA19119 for ; Tue, 28 Oct 1997 13:48:04 GMT From: mnolan@nmrc.ucc.ie (Michael Nolan) Message-Id: <199710281340.NAA02432@malaga.nmrc.ucc.ie> Subject: Another DFT question.....summary To: chemistry@www.ccl.net Date: Tue, 28 Oct 1997 13:40:36 +0000 (GMT) X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Once more I greet the great and helpful CCLers, See my question below as regards "systematic studies" using B3-LYP and B3-PW91 in particular. The replies were excellent and I have tracked down most of the articles referenced. My main problem is that here in the wilds of southern ireland we do not have JCC, or J. Mol. Struct., which is inconvenient to say the least (we actually got electricity last summer). What I have found interesting is (1) the dearth of studies using B3-PW91, as everyone seems to go for LYP instead. This makes my comparison quite difficult (2) that B3 implemented in G94 is different to the original B3 from Becke and in Turbomole (I hope to look into this) (3) overall though this functional performs very well, but improvements are necessary. An interesting article from GRant Merill and Kass in JPC early this year showed some weaknesses in B3, and the need for exact exchange. Again, thank you all very much Michael *************************************************************************** Michael Nolan Wenn ich Daimler fahren will, Materials Group rufe ich ein Taxi an National Microelectronics Research Centre (German humor) Lee Maltings Prospect Row Cork IRELAND mnolan@nmrc.ucc.ie **************************************************************************** The original question: Hello to CCL again.... I have another question on DFT for you all. I'm trying to track down any systematic studies carried out using DFT, IN THE LAST 3 or 4 YEARS. These would especially include harmonic frequencies and (or) comparisons with HF and highly correlated methods. I have some such studies up to about 1993, therefore these deal mostly with B88-LYP or B88 in combination with Perdew's correlation functionals (also Xalfa, VWN etc..). What I am most interested in is the following: systematic tests on B3-LYP AND B3-PW91 (see above), as it seems that PW91 may perform better than LYP. Basis sets would be regular basis sets such as 6-31G* or DZP (due to computational pressure). Important are the strengths and weaknesses of the functionals (and a reason, if known) [I have looked in Chem. Abstr. but there is rather a lot under the heading of DFT, and we do NOT have it on CD-ROM; as my Masters exams are due soon, I do not have time to go looking in JCP, JPC, JACS etc] Many thanks for any helpful replies I recieve *************************************************************************************** 1: From prs@organik.uni-erlangen.de Tue Oct 21 19:13:01 1997 Return-Path: prs@organik.uni-erlangen.de Check Radom 1996 or 1997 JPC; Wong, same years, JPC or CPL. It's all there. -- //// ___|--00___________________________________________________________________ C ^ Dr. Peter R. Schreiner \ ~/ Institut fuer Organische Chemie <><> Georg-August Universitaet Goettingen Tammannstr. 2 Phone: +49-(0)551-393287 D-37077 Goettingen, Germany FAX: +49-(0)551-399475 http://www.gwdg.de/~pschrei ___________________________________________________________________________ **************************************************************************************** 2: From peon@medchem.dfh.dk Wed Oct 22 01:18:44 1997 Return-Path: peon@medchem.dfh.dk Hi, > systematic tests on B3-LYP AND B3-PW91 (see above), as it seems that PW= 91 >may perform better than LYP. Basis sets would be regular basis sets such >as 6-31G* or DZP (due to computational pressure). Important are the >strengths and weaknesses of the functionals (and a reason, if known) I have one that seems tailor made for you: J.Phys.Chem, 1996, 100, 16502-16513. I think you should take the time to look through J.Comp.Chem., the last two years I think I've seen something like what you need in many issues. A few more relevant refs.: Singleton, D. A.; Merrigan, S. R.; Liu, J.; Houk, K. N. J. Am. Chem. Soc. 1997, 119, 3385-3386. Lundell, J.; Latajka, Z. J. Phys. Chem., 1997, 101, 5004-5009 Foresman, J. B.; Frisch, =C6. Exploring Chemistry with Electronic Structu= re Methods, 2nd Ed., Gaussian, Inc., Pittsburgh, 1996. (comes with Gaussian= 94) Regards, Per-Ola Norrby ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ * Per-Ola Norrby, Associate Professor * The Royal Danish School of Pharmacy, Dept. of Med. Chem. * Universitetsparken 2, DK 2100 Copenhagen, Denmark * tel. +45-35376777-506, +45-35370850 fax +45-35372209 * Internet: peon@medchem.dfh.dk, http://compchem.dfh.dk/ ********************************************************************************** 3: From chem8@york.ac.uk Tue Oct 21 21:11:54 1997 Return-Path: chem8@york.ac.uk Hi Michael, For DFT calculations, basis sets optimised for these type of calculations are far superior, both in Energy values and convergence properties, than HF optimised ones. I suggest you pull from CCL's FTP anonymous account, under pub/chemistry the UniChem.basis filel this is also available from Oxford Molecular. Cheers, John Dr. John Waite, e-mail: chem8@york.ac.uk * or The National Hellenic Research Foundation,* john@john1.eie.gr Organic and Pharaceutical Chemistry Institute, phone: ++30-1-7238958 (direct) Vas. Konstantinou 48, phone: ++30-1-7247913(secrtry. Mary) Athens 116-35, fax: ++30-1-7247913 Greece or NCRS "Democritos", phone: ++30-1-6513112-5 X219 * c/o Dr. G.Kordas, e-mail john@john.nrcps.ariadne-t.gr Material Science Institute, Aghia Paraskevi, Attikis, Athens 153-10, Greece ************************************************************************************** 4: From elazhary@theochem.uni-stuttgart.de Wed Oct 22 08:17:46 1997 Return-Path: elazhary@theochem.uni-stuttgart.de Dear Michael: Look at JPC, 1996, 100, 15056 and referencies theirin. In addition I hope the following list of references is also good enough. Good luck. Best regards, Adel El-Azhary ============================================================================ \bibitem{b3lyp} Stephens, P. J.; Devlin, F. J.; Chabalowski, C. F.; Frisch; M. J. {\em J. Phys. Chem.} {\bf 1994}, {\em 98}, 11623. \bibitem{adel8} El--Azhary, A. A; Suter, H. U. {\em J. Phys. Chem.} {\bf 1996}, {\em 100}, 15056; El--Azhary, A. A {\em Spectrochim. Acta}; in press. \bibitem{steph} Finaly, J. W.; Stephens, P. J. {\em THEOCHEM} {\bf 1995}, {\em 357}, 225. \bibitem{steph1} Ashvar, C. S.; Devlin, F. J.; Bak, K. L.; Taylor, P. R.; Stephens, P. J. {\em J. Phys. Chem.} {\bf 1996}, {\em 100}, 9262. \bibitem{pople} Johnson, B. G.; Gill, P. M. W.; Pople, J. A. {\em J. Chem. Phys.} {\bf{1993}}, {\em 98}, 5612. \bibitem{amos} Murray, C. W.; Laming, G. J.; Handy, N. C.; Amos, R. D. {\em Chem. Phys. Lett.} {\bf 1992}, {\em 199}, 551; Handy, N. C.; Murray, C. W.; Amos, R. D. {\em J. Phys. Chem.} {\bf 1993}, {\em 97}, 4392. \bibitem{mart} Martin, J. M. L.; El-Yazal, J.; Francois, J.-P. {\em Mol. Phys.} {\bf 1995}, {\em 86}, 1437. \bibitem{pulay} Rauhut, G; Pulay, P. {\em J. Phys. Chem.} {\bf 1995}, {\em 99}, 3093. \bibitem{scot} Scott, A. P.; Radom, L. {\em J. Phys. Chem.} {\bf 1996}, {\em 100}, 16502; \bibitem{wong} Wong, M. W. {\em Chem. Phys. Lett.} {\bf 1996}, {\em 256}, 391. \bibitem{vib} Bour, P.; Tam, C. N.; Shaharuzzaman, M. ; Chickos, J. S.; Keiderling, T. A. {\em J. Phys. Chem.} {\bf 1996}, {\em 100}, 15041; Qin, Y; Wheeler, R. A. {\em J. Phys. Chem.} {\bf 1996}, {\em 100}, 10554; Nonella, M; Tavan, P. {\em Chem. Phys.} {\bf 1995}, {\em 199}, 19; Martin, J. M. L.; El-Yazal, J.; Francois, J.-P. {\em Chem. Phys. Lett.} {\bf 1996}, {\em 252}, 9; Muir, M; Baker, J. {\em Mol. Phys.} {\bf 1996}, {\em 89}, 211; Miaskiewicz, K.; Smith, D. A. {\em Chem. Phys. Lett.} {\bf 1997}, {\em 270}, 376. \bibitem{appl} See for example: Bauschlicher Jr., C. W. {\em Chem. Phys. Lett.} {\bf 1995}, {\em 246}, 40; Chaquin, P.; Bahou, M.; Schriver, A.; Schriver, L. {\em Chem. Phys. Lett.} {\bf 1996}, {\em 256}, 609; Jursic, B. S. {\em Chem. Phys. Lett.} {\bf 1996}, {\em 256}, 603; Durant, J. L.; Cheeseman, J. R.; Trucks, G. W.; Keith, T. A; Frisch, M. J. {\em J. Chem. Phys.} {\bf 1996}, {\em 104}, 5497; King, R. A.; Galbraith, J. M.; Schaefer III, H. F. {\em J. Phys. Chem.} {\bf 1996}, {\em 100}, 6061. ======================================================================== 5: From schiffer@h1tw0036.hoechst.com Wed Oct 22 08:27:05 1997 Return-Path: schiffer@h1tw0036.hoechst.com Hi Michael, here are two references which may be of interest for you: Jan M. L. Martin, Jamal El-Yazal, Jean-Pierre Francois Basis set convergence and performance of density functional theory including exact exchange contributions for geometries and harmonic frequencies Mol. Phys. 86(6) (1995) 1437-1450 Andrew C. Scheiner, Jon Baker, Jan W. Andzelm Molecular Energies and Properties from Density Functional Theory: Exploring Basis Set Dependence of Kohn-Sham Equation Using Several Density Functionals J. Comput. Chem. 18(6) (1997) 775-795 Both papers report studies for many molecules with different functionals (including B3 etc.) and compare also with traditional methods like MP2 and CCSD(T). Ciao, Heinz -- Dr. Heinz Schiffer Phone ++49-69-305-2330 Hoechst Research & Technology Fax ++49-69-305-81162 Scientific Computing, G864 Email schiffer@h1tw0036.hoechst.com 65926 Frankfurt am Main Schiffer@CRT.hoechst.com ************************************************************************************** 6: From paul@bellatrix.pcl.ox.ac.uk Wed Oct 22 08:48:31 1997 Return-Path: paul@bellatrix.pcl.ox.ac.uk St.-Amant, Kollmand and others wrote a DFT paper that essentially wasa test case paper for DeFT (their new program). It was published in J Comp Chem in 1995 (late) or early 1996. I think it may be of interest to you. All the best Paul --------------------------------------------------------------------------- Dr. Paul D. Lyne Department of Chemistry New Chemistry Laboratory Office: +44 1865 275932 South Parks Road Lab: +44 1865 275933 Oxford, OX1 3QT Main: +44 1865 275990 United Kingdom Fax: +44 1865 275905 --------------------------------------------------------------------------- *(*************************************************************************************** 7: From ugliengo@ch.unito.it Wed Oct 22 09:38:15 1997 Return-Path: ugliengo@ch.unito.it Dear Michael, we have done some work in the arena of H-bonding and DFT. Our papers are in press so I can give you the title and the place where they should appear very soon (a month or so): Density functional study of hydrogen-bonded systems: from gas-phase adducts to catalytically relevan systems P. Ugliengo, B. Civalleri and E. Garrone Il Nuovo Cimento (D) Vol. 19 Pag. ??? 1997 Density functional study of hydrogen-bonded systems: Energetic and vibrational features of some gas-phase adducts of hydrogen fluoride B. Civalleri, E. Garrone and P. Ugliengo J. Molecular Structure (Theochem) ?? (1997) ??? As soon as they will appear I will let you know Sincerely yours P. Ugliengo Piero Ugliengo Dip. Chimica IFM Via P. Giuria, 7 I-10125 Torino ITALY Voice: +39-11-6707845 FAX: +39-11-6707855 E-mail: ugliengo@ch.unito.it Web: http://www.ch.unito.it/ch/DipIFM MOLDRAW at: http://www.ch.unito.it/ch/DipIFM/Software/MOLDRAW/moldraw.html ************************************************************************************** 8: From miquel@stark.udg.es Wed Oct 22 10:36:55 1997 Return-Path: miquel@stark.udg.es Dear Michael, A couple of references that you can find interesting from our=20 group are: M. Sol=E0, J. Mestres, R. Carb=F3, M. Duran=20 "A Comparative Analysis by means of Quantum Molecular Similarity Measures of Density Distributions derived from Conventional ab initio and Density Functional Methods"=20 Journal of Chemical Physics 1996, 104, 636-647=20 M. Torrent, M. Duran, M. Sol=E0=20 "An Assessment of Density Functional Theory on Evaluating Activation Barriers for Small Organic Gas-Phase Rearrangement Reactions"=20 Theochem-Journal of Molecular Structure 1996, 362, 163-173=20 M. Torrent, P. Gili, M. Duran, M. Sol=E0=20 "Exploring Chromium (VI) Dioxodihalides Chemistry. Is Density Functional Theory the Most Suitable Tool?"=20 Journal of Chemical Physics 1996, 104, 9499-9510=20 -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*= - Dr. Miquel Sola =20 Institut de Quimica Computacional =20 Universitat de Girona =20 Campus Montilivi 17071 Girona, CATALONIA (Spain) =20 Voice +34.72.41.83.62 FAX +34.72.41.83.56 =20 World Wide Web: http://stark.udg.es/~miquel/mike.html =20 e-mail: miquel@stark.udg.es =20 -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*= - ************************************************************************************ 9: From jmartell@lyon.edu Wed Oct 22 15:36:32 1997 Return-Path: jmartell@lyon.edu Michael I have done some work in this field. See J. Phys. Chem. A, 1997, 101, 1927-1934. It has the functionals and basis sets you want, unfortunately not frequencies. It deals with energetics and was intended as the first in a series. Geometries and frequencies were to be part 2, but I never got around to it before moving to a second postdoc. There may be at least some useful references in there. Best wishes Jaime Jaime Martell, Ph.D. P.O. Box 2317 Camille and Henry Dreyfus Fellow Batesville, AR 72503-2317 Biology and Chemistry Division Phone: 870-698-4688 Lyon College Fax: 870-698-4622 ************************************************************************************* From jpdognon@concerto.valrho.cea.fr Tue Oct 28 10:33:39 1997 Received: from nenuphar.saclay.cea.fr for jpdognon@concerto.valrho.cea.fr by www.ccl.net (8.8.3/950822.1) id JAA01804; Tue, 28 Oct 1997 09:48:19 -0500 (EST) Received: from muguet.saclay.cea.fr (muguet.saclay.cea.fr [132.166.192.6]) by nenuphar.saclay.cea.fr (8.8.5/ CEANET-ROUTER-3.0) with ESMTP id PAA29768 for ; Tue, 28 Oct 1997 15:48:15 +0100 (MET) Received: from concerto.valrho.cea.fr (concerto.valrho.cea.fr [193.48.15.49]) by muguet.saclay.cea.fr (8.8.5/ CEANET-ROUTER-3.0) with SMTP id PAA04690 for ; Tue, 28 Oct 1997 15:48:14 +0100 (MET) Received: from [194.57.214.81] by concerto.valrho.cea.fr (SMI-8.6/CEANET.2.0.1) id PAA11259; Tue, 28 Oct 1997 15:53:30 +0100 Message-Id: <199710281453.PAA11259@concerto.valrho.cea.fr> Subject: bsse Date: Mar, 28 Oct 97 15:49:11 +0100 x-mailer: Claris Emailer 1.1 From: dognon To: "CCL" Mime-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Dear CCL readers, I search some references of publications on : - BSSE - dynamical and nondynamical correlation and there effects on atomic and molecular properties (charges, energies, ...).I assume there is a lot but is it possible to found some reviews ? Thanks Jean-Pierre Dognon Jean-Pierre DOGNON CEA/Valrho (Marcoule) DCC/DRRV/SEMP/LCTS Bat. 166 B.P. 171 30207 Bagnols-sur-Ceze Cedex FRANCE Phone: 33 (0) 4 66 79 61 52 Fax: 33 (0) 4 66 79 16 30 email: jpdognon@concerto.valrho.cea.fr From M.E.Parker@surrey.ac.uk Tue Oct 28 10:39:21 1997 Received: from mailc.surrey.ac.uk for M.E.Parker@surrey.ac.uk by www.ccl.net (8.8.3/950822.1) id KAA01908; Tue, 28 Oct 1997 10:04:16 -0500 (EST) Message-Id: <199710281504.KAA01908@www.ccl.net> Received: from surrey.ac.uk by mailc.surrey.ac.uk id <00070-0@mailc.surrey.ac.uk>; Tue, 28 Oct 1997 15:03:56 +0000 Subject: dl-poly Makefile To: chemistry@www.ccl.net Date: Tue, 28 Oct 1997 15:03:55 +0000 (GMT) X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit From: Dr Malcolm E Parker Sender: M.E.Parker@surrey.ac.uk Dear all I have recently aquired the source code for dl-poly. I have successfully compiled this up on an SG. I now wish to compile it on a dec alpha (OSF) now. Unfortunately this is not an option with the Makefile supplied. I know it *is* possible to run this program on an alpha. Can anybody e-mail me (or the list) either a suitable Makefile or the f90 options that are required? Thanks in advance. Mal -- Dr Malcolm Parker | email: m.e.parker@surrey.ac.uk Department of Chemistry, | www: http://www.chem.surrey.ac.uk/~chs1mp University of Surrey, | Guildford, Surrey. GU2 5XH. UK. | Tel: (01483) 300800x2580 Fax: (01483) 259514 |(International calls replace 01483 by +44 1483) From MARIE-JOSE.CAZAUX@TLS1.elfsanofi.fr Tue Oct 28 11:33:48 1997 Received: from xn1-gw.atlas.fr for MARIE-JOSE.CAZAUX@TLS1.elfsanofi.fr by www.ccl.net (8.8.3/950822.1) id LAA02284; Tue, 28 Oct 1997 11:20:37 -0500 (EST) X400-Received: by /PRMD=INTERNET/ADMD=ATLAS/C=FR/; Relayed; Tue, 28 Oct 1997 17:16:36 +0100 X400-Received: by mta xn1-gw.atlas.fr in /PRMD=INTERNET/ADMD=ATLAS/C=FR/; Relayed; Tue, 28 Oct 1997 17:16:36 +0100 X400-Received: by /ADMD=ATLAS/C=FR/; Relayed; Tue, 28 Oct 1997 17:14:09 +0100 X400-Received: by /PRMD=ELF02/ADMD=ATLAS/C=FR/; Relayed; Tue, 28 Oct 1997 09:08:07 +0100 Date: Tue, 28 Oct 1997 09:08:07 +0100 X400-Originator: MARIE-JOSE.CAZAUX@TLS1.elfsanofi.fr X400-Recipients: CHEMISTRY@www.ccl.net X400-MTS-Identifier: [/PRMD=ELF02/ADMD=ATLAS/C=FR/;87808368745580000cazaux] X400-Content-Type: P2-1984 (2) Content-Identifier: UCOMX Alternate-Recipient: Allowed From: CAZAUX MARIE-JOSE Message-ID: <87808368745580000cazaux*/G=MARIE-JOSE/S=CAZAUX/OU=TLS1/O=ELFSANOFI/PRMD=ELF02/ADMD=ATLAS/C=FR/@MHS> To: CHEMISTRY (Receipt Notification Requested) (Reply Requested) Subject: SEA Please, can you send us a free demo version of SEA (Sophisticated Elemental Analysis) software, running on Windows 95. Thank you Regards. Mohamed MAFTOUH SANOFI RECHERCHE 195 Route d'Espagne 31036 Toulouse cedex - France Tel : (33) 05.61.16.22.92 Fax : (33) 05.62.11.92.37 E-mail : mohamed.maftouh@tls1.elfsanofi.fr From hinsen@lmspc1.ibs.fr Tue Oct 28 12:33:50 1997 Received: from ibs.ibs.fr for hinsen@lmspc1.ibs.fr by www.ccl.net (8.8.3/950822.1) id LAA02473; Tue, 28 Oct 1997 11:36:57 -0500 (EST) Received: from lmspc1.ibs.fr (hinsen@lmspc1.ibs.fr [192.134.36.141]) by ibs.ibs.fr (8.6.12/8.6.12) with ESMTP id RAA16140; Tue, 28 Oct 1997 17:35:47 +0100 Received: (from hinsen@localhost) by lmspc1.ibs.fr (8.8.5/8.8.5) id RAA22490; Tue, 28 Oct 1997 17:34:14 +0100 Date: Tue, 28 Oct 1997 17:34:14 +0100 Message-Id: <199710281634.RAA22490@lmspc1.ibs.fr> From: Konrad Hinsen To: mathieu@ripault.cea.fr CC: chemistry@www.ccl.net In-reply-to: <344EFAA0.24E258B8@ripault.cea.fr> (message from Didier MATHIEU on Thu, 23 Oct 1997 09:20:00 +0200) Subject: Re: CCL:langage > In this context of fairly long-term projects with high turnover and poor > communication between succesive programmers, pieces of code written by > some people must be used easily by others, hence codes must be at least > modular. Experience with Fortran has shown us that training students, > because of the limited time allocated, are in a hurry to implement as > much as possible, and resulting code is not well structured. On the > other hand, since they are mostly students in physics or chemistry, most > of them do not master C or C++ , although all of them have some > programming experience, for instance with Pascal or Basic. > > According to me, none of those free langages, C, C++ and Fortran, is a > good choice and I am looking for a SIMPLE langage supporting REUSABILITY > and QUICK DEVELOPMENT. You don't list all of your requirements, and their relative importance, so it is difficult to make precise suggestions. If simplicity and rapid development of reusable code is your top priority, you should be looking at object-oriented high-level (generally interpreted) languages. You do pay in execution speed, however, although the penalty factor depends very much on your problem (and it can in practice even be to your advantage in some cases). In this language category, my recommendation for scientific use is Python. It is an exceptionally clear language (no weird symbols with special meanings), and there is already a useful collection of modules for scientific use. Moreover, Python allows integration of C code in an almost trivial way, so you can always write the time-critical parts of your code in C. More information on Python is at http://www.python.org, and on scientific applications in Python at http://starship.skyport.net/crew/hinsen/. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@ibs.ibs.fr Laboratoire de Dynamique Moleculaire | Tel.: +33-4.76.88.99.28 Institut de Biologie Structurale | Fax: +33-4.76.88.54.94 41, av. des Martyrs | Deutsch/Esperanto/English/ 38027 Grenoble Cedex 1, France | Nederlands/Francais ------------------------------------------------------------------------------- From herbert.homeier@na-net.ornl.gov Tue Oct 28 15:33:41 1997 Received: from rrzs2.rz.uni-regensburg.de for herbert.homeier@na-net.ornl.gov by www.ccl.net (8.8.3/950822.1) id PAA03666; Tue, 28 Oct 1997 15:06:42 -0500 (EST) Received: from rchs4.chemie.uni-regensburg.de (rchs4.chemie.uni-regensburg.de [132.199.48.4]) by rrzs2.rz.uni-regensburg.de (8.8.5/8.8.5) with SMTP id VAA13701; Tue, 28 Oct 1997 21:06:13 +0100 (MET) Sender: Herbert.Homeier@rchs4.chemie.uni-regensburg.de Message-Id: <345645C8.36DC@na-net.ornl.gov> Date: Tue, 28 Oct 1997 21:06:32 +0100 From: Herbert Homeier Organization: Theoretical Chemistry, U Regensburg, Germany X-Mailer: Mozilla 3.0Gold (X11; I; SunOS 5.5.1 sun4u) Mime-Version: 1.0 To: chemistry@www.ccl.net Cc: spectroscopy-group@mailbase.ac.uk, molecular-dynamics-news@mailbase.ac.uk, ELETQM-L@PITANGA.UFU.BR, na.digest@na-net.ornl.gov Subject: Scientific Questions and Answers Database Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Apologies for any cross-postings. Dear colleagues, a data base to read and to enter and answer questions of scientific interest has been created Oct 28, 1997 in the WWW. This data base is working only via the internet. There is normally no other expert than some friendly human being in the internet that happens to be willing to share his or her insight with you. So please do not blame anybody if there is a huge delay until an answer to a question is to be found in the data base. Additional data can be entered via a form. The URL is http://www.chemie.uni-regensburg.de/QA Enjoy -- Priv.-Doz. Dr. Herbert H. H. Homeier Institut fuer Physikalische und Theoretische Chemie Universitaet Regensburg, D-93040 Regensburg, Germany Phone: +49-941-943 4720 FAX: +49-941-943 4719/+49-941-943 2305 email: herbert.homeier@na-net.ornl.gov WWW: http://www.chemie.uni-regensburg.de/~hoh05008 From richmc@entropy.ucsc.edu Tue Oct 28 15:40:48 1997 Received: from entropy.ucsc.edu for richmc@entropy.ucsc.edu by www.ccl.net (8.8.3/950822.1) id PAA03703; Tue, 28 Oct 1997 15:10:51 -0500 (EST) Received: (qmail 11551 invoked by uid 500); 28 Oct 1997 20:10:52 -0000 From: "Rich McClellan" Message-Id: <9710281210.ZM11549@entropy.ucsc.edu> Date: Tue, 28 Oct 1997 12:10:51 -0800 In-Reply-To: Taisung Lee "CCL:Re: CCL:PCI vs. SCSI and Linux" (Sep 27, 21:55) References: X-Mailer: Z-Mail (3.2.1 24feb96 Caldera) To: Taisung Lee Subject: Re: CCL:Re: CCL:PCI vs. SCSI and Linux Cc: CHEMISTRY@www.ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii I apologize for replying to this email so long after it was originally posted, but I have conducted some benchmarks on my system that you people may find interesting. My system: o PPRO 180 MHz (256 kb cache) o Buslogic BT-948 SCSI controller (fast, scsi-ii) o Conner fast, scsi ii disk (model no. elludes me, but it has a 256kb cache and spindle rotation rate of 7200 rpm) o Triton chipset for EIDE controller o Seagate EIDE model no. ST3780A (256 kb cache, 4500 rpm) o Running the Linux OS of course :-) Two factors that influenced my decision to install a SCSI controller and disk were the perceived higher I/O of the SCSI disks and the smaller fraction of CPU used during reads/writes. Results: The SCSI disk has throughput consistently higher than the EIDE disk (probably due to the higher rpm) BUT when the EIDE disk is tune with the hdparm utility to enable bus mastering and mulitple sector I/O, the throughout of the EIDE drive increases but more notable the CPU usage GOES DOWN DRASTICALLY. Have a look at the benchmark results. My conclusions: Go with SCSI (preferably fast, wide), but EIDE properly tuned is a cheap alternative. ***************************BENCHMARK RESULTS********************************* (Note that sda is the scsi disk and hda is the eide disk) On sda: -------Sequential Output-------- ---Sequential Input-- --Random-- -Per Char- --Block--- -Rewrite-- -Per Char- --Block--- --Seeks--- Machine MB K/sec %CPU K/sec %CPU K/sec %CPU K/sec %CPU K/sec %CPU /sec %CPU entropy 100 4021 65.0 3848 21.9 1631 17.8 4758 57.0 4483 19.4 53.8 3.2 on hda: Note: drive NOT tuned with hdparm utility -------Sequential Output-------- ---Sequential Input-- --Random-- -Per Char- --Block--- -Rewrite-- -Per Char- --Block--- --Seeks--- Machine MB K/sec %CPU K/sec %CPU K/sec %CPU K/sec %CPU K/sec %CPU /sec %CPU entropy 100 2642 82.4 2783 27.5 1140 37.7 2071 69.7 2589 59.7 32.3 4.7 on hda: Note: Drive tuned with hdparm utilities (-d1 -X34 -m32) -------Sequential Output-------- ---Sequential Input-- --Random-- -Per Char- --Block--- -Rewrite-- -Per Char- --Block--- --Seeks--- Machine MB K/sec %CPU K/sec %CPU K/sec %CPU K/sec %CPU K/sec %CPU /sec %CPU entropy 100 3115 50.1 2750 12.4 1228 12.6 2557 29.0 2871 10.1 32.7 1.6 #################################### 150 Mb cache ############# SCSI drive -------Sequential Output-------- ---Sequential Input-- --Random-- -Per Char- --Block--- -Rewrite-- -Per Char- --Block--- --Seeks--- Machine MB K/sec %CPU K/sec %CPU K/sec %CPU K/sec %CPU K/sec %CPU /sec %CPU entropy 150 4237 70.6 4241 22.7 1543 16.2 3167 37.3 4058 16.4 53.2 3.2 EIDE drive, hdparm on -------Sequential Output-------- ---Sequential Input-- --Random-- -Per Char- --Block--- -Rewrite-- -Per Char- --Block--- --Seeks--- Machine MB K/sec %CPU K/sec %CPU K/sec %CPU K/sec %CPU K/sec %CPU /sec %CPU entropy 150 2794 44.2 2569 12.7 1179 11.9 2468 27.2 2758 10.1 28.0 1.3 ******************************************************************************* The benchmarks are called "bonnie". You can get them from any Linux mirror like Sunsite. I hope these are helpful, Rich -- Molecular Engineering Laboratory Department of Chemistry and Biochemistry University of California, Santa Cruz From katz@indigo.ucdavis.edu Tue Oct 28 19:33:43 1997 Received: from indigo.ucdavis.edu for katz@indigo.ucdavis.edu by www.ccl.net (8.8.3/950822.1) id TAA08555; Tue, 28 Oct 1997 19:16:31 -0500 (EST) Received: from indigo.ucdavis.edu by indigo.ucdavis.edu via SMTP (940816.SGI.8.6.9/940406.SGI.AUTO) for id QAA14014; Tue, 28 Oct 1997 16:18:18 -0800 Date: Tue, 28 Oct 1997 16:18:18 -0800 (PST) From: Daniel Katz To: chemistry@www.ccl.net Subject: SUMMARY for: where are Alvarez's parameters? In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 14 Oct 1997, I wrote: > > I have been told that the program ehmacc (a program for extended Huckel > molecular orbital calculations) uses parameters from Alvarez. Is there a > published reference in which one can find Alvarez's parameters? > > Thanks. > > Daniel J. Katz > UC Davis > katz@indigo.ucdavis.edu > > In response to this, someone put Alvarez himself in touch with me. If anybody really needs to contact Alvarez, I suppose they should do as I did. His list of parameters for extended Huckel calculations has been circulated about the community. Daniel J. Katz From nakiya@engin.umich.edu Tue Oct 28 20:33:54 1997 Received: from phoenix.engin.umich.edu for nakiya@engin.umich.edu by www.ccl.net (8.8.3/950822.1) id SAA08526; Tue, 28 Oct 1997 18:53:00 -0500 (EST) Received: from localhost (nakiya@localhost [127.0.0.1]) by phoenix.engin.umich.edu (8.8.7/8.8.7) with SMTP id RAA12139 for ; Tue, 28 Oct 1997 17:34:39 -0500 (EST) Date: Tue, 28 Oct 1997 17:34:38 -0500 (EST) From: Naoko Akiya To: chemistry@www.ccl.net Subject: CCL:G: open shell calculation with DFT In-Reply-To: <199710281329.NAA02423@malaga.nmrc.ucc.ie> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear All, I have a question regarding the open shell calculation with DFT. I am trying to calculate the energy of a transition state structure. Although the structure is designated as a singlet in the input, it is "partially" open shell. How can I account for this in the calculation using DFT methods? I realize that this is probably a really basic question, and I apologize. I have already sent an email to gaussian.com, but I need this information rather soon. Thank you very much. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Naoko Akiya nakiya@engin.umich.edu University of Michigan Dept. of Chemical Engineering phone (313) 764-7121 Ann Arbor, MI 48109-2136 fax (313) 763-0459 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From richmc@entropy.ucsc.edu Tue Oct 28 21:33:45 1997 Received: from entropy.ucsc.edu for richmc@entropy.ucsc.edu by www.ccl.net (8.8.3/950822.1) id UAA08707; Tue, 28 Oct 1997 20:35:15 -0500 (EST) Received: (qmail 16516 invoked by uid 500); 29 Oct 1997 01:35:04 -0000 From: "Rich McClellan" Message-Id: <9710281735.ZM16514@entropy.ucsc.edu> Date: Tue, 28 Oct 1997 17:35:04 -0800 In-Reply-To: Jochen Kuepper "CCL:G:Model Builders for LINUX" (Oct 27, 10:14) References: <9710270914.AA20464@bacchus.pc1.uni-duesseldorf.de> X-Mailer: Z-Mail (3.2.1 24feb96 Caldera) To: Jochen Kuepper , CHEMISTRY@www.ccl.net, chburger@aci.unizh.ch Subject: Re: CCL:G:Model Builders for LINUX Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii On Oct 27, 10:14, Jochen Kuepper wrote: > Subject: CCL:G:Model Builders for LINUX > > :> some time ago an inquiry about molecular model builders > :> for LINUX was posted to this list. Unfortunately, > :> I have not seen any replies to this question besides > :> the suggestion to use Molden, which is > :> however, mostly a tool to analyze G94 and > :> Gamess data and _not_ a model builder (correct > :> me if I am wrong here). > > Yes, but not exactly. > Molden does have an zmat editor, which let's you build up structures > interactively - it's not exactly like Spartan, but still you might > wanna look at it. > > Be sureto grb the latest version (3.2 - IIRC). > > Jochen > [-----------snip-------------] You should also have a look at the CACTVS applications, in particular csed, which despite an inability to save files in most all of the formats it advertises, can save files in MDL Mol format. You can then convert between file formats with Babel. The FTP site at schiele.organik.uni-erlangen.de should have CACTVS. good luck, Rich From katz@indigo.ucdavis.edu Tue Oct 28 22:33:45 1997 Received: from indigo.ucdavis.edu for katz@indigo.ucdavis.edu by www.ccl.net (8.8.3/950822.1) id TAA08567; Tue, 28 Oct 1997 19:24:53 -0500 (EST) Received: from indigo.ucdavis.edu by indigo.ucdavis.edu via SMTP (940816.SGI.8.6.9/940406.SGI.AUTO) for id QAA14555; Tue, 28 Oct 1997 16:26:40 -0800 Date: Tue, 28 Oct 1997 16:26:39 -0800 (PST) From: Daniel Katz To: chemistry@www.ccl.net Subject: SUMMARY for: Code for overlapping STOs In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 16 Oct 1997, I wrote: > > IS there a free and non obscure piece of code (preferably C) for > calculating the overlap integrals between two Slater-Type-Orbitals (single > zeta, radial part, angular parts are real spherical harmonics for s,p, and > d)? I have the MOPAC FORTRAN routines, but they are not clear to me. > > Thanks in advance. > > Daniel J. Katz > UC Davis, Dept. of Chemistry > katz@indigo.ucdavis.edu > I got two replies, one from Ernst-Udo Wallenborn and one from Frederic A. Van-Catledge. Both sent code, for which I am very grateful. In addition Frederic wrote on the general method: 1. The key to getting good STO overlaps is having good routines/functions for calculating the A & B auxiliary integrals,... *especially* the B's. ... [my elipsis here] If one has that, the problem reduces to recasting the formal integral from local cartesian coordinates into confocla elliptical coordinates, i.e., I(Xa, Ya, Za, Xb, Yb, Zb) --> I(mu, nu, phi) The rest, as they say, is a simple mater of algebra. Daniel J. Katz University of California at Davis katz@indigo.ucdavis.edu From richmc@entropy.ucsc.edu Tue Oct 28 23:33:43 1997 Received: from entropy.ucsc.edu for richmc@entropy.ucsc.edu by www.ccl.net (8.8.3/950822.1) id VAA08848; Tue, 28 Oct 1997 21:03:33 -0500 (EST) Received: (qmail 16730 invoked by uid 500); 29 Oct 1997 02:03:23 -0000 From: "Rich McClellan" Message-Id: <9710281803.ZM16728@entropy.ucsc.edu> Date: Tue, 28 Oct 1997 18:03:22 -0800 In-Reply-To: "Dr. Peter Burger" "CCL:G:Model Builders for LINUX" (Oct 25, 19:46) References: X-Mailer: Z-Mail (3.2.1 24feb96 Caldera) To: "Dr. Peter Burger" , CHEMISTRY@www.ccl.net Subject: Re: CCL:G:Model Builders for LINUX Cc: jefff@caldera.com, anna@redhat.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii On Oct 25, 19:46, Dr. Peter Burger wrote: > Subject: CCL:G:Model Builders for LINUX > > Dear CCL fellows, > > some time ago an inquiry about molecular model builders > for LINUX was posted to this list. Unfortunately, > I have not seen any replies to this question besides > the suggestion to use Molden, which is > however, mostly a tool to analyze G94 and > Gamess data and _not_ a model builder (correct > me if I am wrong here). > > My question now is: > > Is there such a program available either > in public domain or as commercial product? Something > like Spartan (perhaps the ultimate) or PCMODEL > would be just great (since both companies are also > concerned about inorganic chemists like me). > > Perhaps, one could convince people from Wavefunction > and other companies that the LINUX/Intel platform is definitely a > market for computational chemistry software, examples include > already Gaussian94, Gamess, Turbomole, Jaguar etc. > I've talked with people at Wavefunction (at ACS conferences, not exactly Prof. Hehre himself... actually, yeah, I did ask him about porting to Linux in the summer of 96 when he was speaking at CSU Fullerton and he just chuckled) and they say that the reason they don't want to support Linux is becuase they would have to put together their own distribution of Linux in order to provide any type of support. Further, they conveyed the general attitude that Linux development moves too quickly for them to take a chance and port to Linux (I volunteered to type 'xmkmf' for them). The people that bring you PCMODEL are aware of Linux and have (I *think*) an alpha version that runs on Linux, but no word on plans to sell it. I've successfully used a program called Chem Site which is an editor, viewer, simulation program for Windows under Wabi. Perhaps the freeware analog of Wabi, Wine, will do the same? AS my previous post stated the CACTVS (schiele.organik.uni-erlangen.de) tools include a molecule editor. While buggy and not like the Spartan builder, they will give you the freedom to not run Windows. There is a complete periodic table, too, although I wasn't (in a few minutes) able to construct ferrocene. I've CC'd this to the folks at Red Hat and Caldera. While we're not a huge market, perhaps they can lobby for more commercial grade scientific sofware for Linux. (I'm still willing to type 'xmkmf' for the folks at Wavefunction :-) Employees of various companies (including Interactive Simulations, Inc. who make SCULPT which reportedly runs on Linux) that are reading this email should have a look at http://www.redhat.com/news/news-details.phtml?id=26 cheers, Rich Molecular Engineering Laboratory Department of Chemistry University of California, Santa Cruz -------------------------------------------------- Contact info: Wavefunction, Inc. 18401 Von Karman Ave. Suite 370 Irvine, CA 92612 Web site http://www.wavefun.com Interactive Simulations, Inc. 5330 Carroll Canyon Rd. San Diego, CA 92121 Web site http://www.intsim.com Not sure about PCMODEL... > Care to comment? Any programs around there to be used? > Switching back and forward to WINNT/WIN95 is not really > too convenient. > > Peter > > P.S. Don't get me wrong - I am referring to molecular model > builders not just _viewers_ as for example Rasmol. > > ------------------------------- > Peter Burger > Anorg.-Chem. Institut > University of Zuerich > chburger@aci.unizh.ch > ~ > > >