From chpajt@bath.ac.uk Thu Mar 20 07:30:35 1997 Received: from goggins.bath.ac.uk for chpajt@bath.ac.uk by www.ccl.net (8.8.3/950822.1) id GAA17735; Thu, 20 Mar 1997 06:42:26 -0500 (EST) Received: from bath.ac.uk (actually host midge.bath.ac.uk) by goggins.bath.ac.uk with SMTP (PP); Thu, 20 Mar 1997 09:24:52 +0000 Date: Thu, 20 Mar 1997 09:24:34 +0000 (GMT) From: A J Turner To: youngd2@mail.auburn.edu cc: CHEMISTRY@www.ccl.net Subject: Re: CCL:G:Chem Topic: SCF Convergence and Chaos Theory In-Reply-To: <199703192148.PAA28427@wood.mail.auburn.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi! In chaotic systems the period always doubles in the real set due to the intersection of the Mandelbrot set with the real set. Best wishes Alex ------------------------------------------------------------------- |Alexander J Turner |A.J.Turner@bath.ac.uk | |Post Graduate |http://www.bath.ac.uk/~chpajt/home.html| |School of Chemistry |+144 1225 8262826 ext 5137 | |University of Bath | | |Bath, Avon, U.K. |Field: QM/MM modeling | ------------------------------------------------------------------- From mariano@zeus.uncor.edu Thu Mar 20 09:30:35 1997 Received: from zeus.uncor.edu for mariano@zeus.uncor.edu by www.ccl.net (8.8.3/950822.1) id JAA18950; Thu, 20 Mar 1997 09:26:18 -0500 (EST) Received: by zeus.uncor.edu; (5.65/1.1.8.2/26Feb97-0222PM) id AA06524; Thu, 20 Mar 1997 11:28:13 -0500 Date: Thu, 20 Mar 1997 11:28:12 -0500 (AST) From: "Lic. Domingo M. Vera" To: chemistry@www.ccl.net Subject: Brief summary of queue systems. Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers Last week, I have posted a question about queue systems for submitting heavy computational chemistry jobs. Many thanks to all who responded, specially to Dr. Rick Venable - I'm now installig his program batchq. I have summarised the replies and added some comments and also a pointer to another software. I acknowledge help in dealing with NQS from Dr. Michael Hartmann. ======================= MY ORIGINAL QUESTION ============================== Dear CCLers I have shipped an executable (no code available) version of a popular computational methods package for a Hewlett-Packard HP9000 735, with a rather small amount of physical memory. As you may guess ... now I need urgently a good queue system. I appologize if my limitation seems to be specific, but I think that the problem of finding an adequate queue manager should be very common for computational chemists. Does anybody know a queue system that can be installed on a HP-UX or any machine running gcc (GNU-C compiler)? Either binaries or source codes are welcome, but I'm specially interested in those programs which can run on a HP9000 box. I know that NQS is really excellent (we installed it on a DEC Alpha / OSF/1 running Gaussian) but its source-code distribution needs several optional C modules installed (for example, ANSI-C support); I was trying to make it with gcc without success. Condor is another option I know, but it needs to recompile the program with special linking (then it is not suitable without the complete source code). Thanks in advance. I'll sumarize the answers if you find it useful. ... ======================== THE ANSWERS ===================================== .......................................................................... # from Sean Fox. Software: built-in batch (most Unix platforms) You're probably already aware of this but (since you didn't mention it) there's always batch. It has almost no features and hardly deserves to be called a queueing system. But if all you want is something that'll let you line up jobs to be executed serially it does the trick. The best part is, of course, that it's already installed as part of HP-UX. Sean Fox Academic Computing Coordinator Carleton College sfox@carleton.edu # It's a good idea. But when a single job can be running for # several days, the checkpointing and interleaving between jobs (and user # interleaving) are required features. # NQS can do it. When the system have enough resources and it is # possible to get two or more queues running, batch can be the solution; # better, as you said, it's already installed. .......................................................................... # from Rick Venable. Software: batchq (most Unix machines) I wrote a generic Unix batch queue system, using - /bin/csh scripts - a Fortran program - the 'cron' facility It should work on just about any Unix system, although it was developed under HP-UX; it has the following features: - jobs for a specific userid run in the order they were submitted - user interleaving; the pending list is re-sorted to prevent a single user from monopolizing a given queue It is available (caveat emptor) at URL ftp://deimos.cber.nih.gov/pub (or ftp to deimos.cber.nih.gov and login as anonymous) The entire bundle is in batchq.tar.Z, and the subdir batchq has all of the individual components. It may require some minor changes to the csh scripts; for example, HP-UX uses 'remsh' for a remote shell, while other versions of Unix use 'rsh' instead. -- Rick Venable =====\ |=| "Eschew Obfuscation" FDA/CBER Biophysics Lab |____/ |=| Bethesda, MD U.S.A. | \ / |=| ( Not an official statement or rvenable@deimos.cber.nih.gov \/ |=| position of the FDA; for that, http://nmr1.cber.nih.gov/venable.html |=| see http://www.fda.gov ) ........................................................................ # from Bill Ross. Soft: PBS (ported for various platforms) See PBS - successor to NQS at the place that invented NQS: http://www.nas.nasa.gov Bill Ross ........................................................................ # from Jochen Kuepper. Soft: just the NQS (problems in HP-UX with standar C # compiler, ported for HP-UX, AIX, DEC Alpha, Linux, BSD, Solaris, SunOs, # Irix, MIPS, Ultrix, Unicos). Try NQS, it's the best queue system I know. The source code is freely distrubuted, find it via any search engine. The latest version I Know of is like 3.50. Jochen ----------------------------------------------------------------------- Jochen Kuepper Heinrich-Heine-Universitaet Duesseldorf jochen@uni-duesseldorf.de Institut fuer Physikalische Chemie I Universitaetsstrasse 1, Geb 26.43.02.19 phone ++49-211-8113681 40225 Duesseldorf fax ++49-211-8115195 Germany ----------------------------------------------------------------------- ........................................................................ # I also found a sophisticated network-oriented queue system called # Condor. It is already ported for HP-UX 9.05 and -if you are a HP-UX user- # you can just install the binaries. The file is: hpux/Distributed/condor-4.5/condor-4.5-sd-9.01.tar.gz at the ftp server hpux.ask.uni-karlsruhe.de and its mirrors # If you want Condor for another platform, you can download # the README file (I think it has the main ftp address) from # the same URL. # Note: you must have the sources and makefiles of the programs you want to # run under Condor. Thank you. Mariano. D. Mariano A. Vera Fac. de Cs. Quimicas. U.N.C. Cordoba, Argentina. 54-51-334170 mariano@zeus.uncor.edu From chihaia@honer.racai.ro Thu Mar 20 10:30:35 1997 Received: from honer.racai.ro for chihaia@honer.racai.ro by www.ccl.net (8.8.3/950822.1) id JAA19096; Thu, 20 Mar 1997 09:47:27 -0500 (EST) Received: from (chihaia@localhost) by honer.racai.ro (8.7.3/jtpda-5.2) id QAA09442 for chemistry@www.ccl.net; Thu, 20 Mar 1997 16:42:28 +0200 (EET) Date: Thu, 20 Mar 1997 16:42:28 +0200 (EET) From: chihaia@honer.racai.ro (Chihaia Viorel - Institutul de Chimie-Fizica al Academiei Romane) Message-Id: <199703201442.QAA09442@honer.racai.ro> To: chemistry@www.ccl.net Subject: Collisio, Adsorption, Catalysis - Molecular Modeling X-Sun-Charset: US-ASCII Hi CCL-mailers, I am working in the field of the Surface Science and Catalysis modeled with quantum chemistry methods. Because I am now in position to end my Ph.D. thesis and in Romania there are not available recent documentation sources in this field due to temporary ( I hope ! ) economical problems, I would appreciate to get bibliography items in this topics ( Collision of small molecules with the crystal surface, Adsorption and Catalysis ). With best regards, Sincerely yours, 0---------0 | _ | CHIHAIA VIOREL | O O | | - | Institute of Chemical Physiscs | /I\ | "I.G.Murgulescu" of Romanian Academy, | / \ | Surface chemistry and Catalysis Laboratory, | | Spl. Independentei 202, Bucharest, 77208 0---------0 Romania From qibvigap@lg.ehu.es Thu Mar 20 10:37:44 1997 Received: from lgsx01.lg.ehu.es for qibvigap@lg.ehu.es by www.ccl.net (8.8.3/950822.1) id JAA19027; Thu, 20 Mar 1997 09:40:27 -0500 (EST) Received: from lgdx02.lg.ehu.es by lgsx01.lg.ehu.es (4.1/4.7 ) id AA18561; Thu, 20 Mar 97 15:39:13 GMT Received: by lgdx02.lg.ehu.es (5.65/4.7) id AA13633; Thu, 20 Mar 1997 15:48:13 GMT Date: Thu, 20 Mar 1997 15:48:13 +0000 (WET) From: Pablo Vitoria Garcia X-Sender: qibvigap@lgdx02 To: ccl Subject: Slater type orbitals in GAMESS or G94 (II) Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, First of all, thanks a lot to Dr. Rudolf Herrmann and Dr. Bruno Manunza, who told me to introduce the exponents using the $DATA input card. But I was in a hurry when I wrote my previous message about STO basis sets, and I think I didn't explain myself clearly. Sorry about that. The STOs (both in GAMESS and G94) are represented as a (weighted) sum of gaussian functions. The exponents for this gaussians can be either input or used as given by the program. What I would like to know is: which gaussian exponents (and contraction coefficients) should I use to reproduce a Slater type orbital (STO) with a particular Slater exponent (the factor multiplying -1/r)? Are there any table available in the literature? Or is it possible to change the Slater exponents (not the Gaussian) within GAMESS or G94? Should I use other programs that do the calculations in a STO basis instead of a Gaussian basis (as GAMESS and G94)? Thanks a lot for your help Pablo -------------------------------------------------------------------------------- Pablo Vitoria Garcia Departamento de Quimica Inorganica, Facultad de Ciencias Universidad del Pais Vasco (UPV/EHU) Apartado 644, E-48080 Bilbao SPAIN e-mail: qibvigap@lgdx02.lg.ehu.es Phone: +34 4 4647700 Ext. 2450 -------------------------------------------------------------------------------- From rherrman@nucleus.org.chemie.tu-muenchen.de Thu Mar 20 13:30:38 1997 Received: from sunsrv5.lrz-muenchen.de for rherrman@nucleus.org.chemie.tu-muenchen.de by www.ccl.net (8.8.3/950822.1) id MAA20590; Thu, 20 Mar 1997 12:36:39 -0500 (EST) Received: from nucleus.org.chemie.tu-muenchen.de by sunsrv5.lrz-muenchen.de; Thu, 20 Mar 97 18:36:27 +0100 Received: from NUCLEUS/TEMPQ by nucleus.org.chemie.tu-muenchen.de (Mercury 1.1); Thu, 20 Mar 97 18:36:50 GMT From: "Dr. Rudolf Herrmann" Organization: OCI TU-Munich Germany To: CHEMISTRY@www.ccl.net Date: Thu, 20 Mar 1997 18:36:26 GMT MIME-Version: 1.0 Content-type: text/plain; charset=ISO-8859-1 Content-transfer-encoding: Quoted-printable Subject: CCL:Experience with Q-Chem? Return-receipt-to: "Dr. Rudolf Herrmann" Priority: normal X-mailer: Pegasus Mail for Windows (v2.42a) Message-Id: <3331759b1105002@sunsrv5.lrz-muenchen.de> Dear CCL-ers, I have seen the web page of Q-Chem which is a massive parallel quantum chemistry package. I=B4m thinking about the possibility to convince our centre of calculations to buy it, but there is not much information available, the web page doesn=B4nt even tell the price... So before I start to do something, I would like to know if someone has already gained experience with that program, in particular if it can treat somewhat more problematic molecules like ferrocene, and if the results are the same as those with Gaussian or Gamess. I will summarize to the list. Thank you very much in advance. R.Herrmann Dr. Rudolf Herrmann Institut f=FCr Organische Chemie und Biochemie der Technischen Universit=E4t M=FCnchen Lichtenbergstr. 4 D-85747 Garching Tel. + 49 - 89 - 28913325 Fax + 49 - 89 - 28912727 From guenther@shfj.cea.fr Thu Mar 20 14:30:38 1997 Received: from nenuphar.saclay.cea.fr for guenther@shfj.cea.fr by www.ccl.net (8.8.3/950822.1) id OAA21197; Thu, 20 Mar 1997 14:02:26 -0500 (EST) Received: from muguet.saclay.cea.fr by nenuphar.saclay.cea.fr (8.6.9/ CEANET-ROUTER-3.0) with ESMTP id UAA16545 for ; Thu, 20 Mar 1997 20:02:10 +0100 Received: from pendragon-int.shfj.cea.fr by muguet.saclay.cea.fr (8.6.9/ CEANET-ROUTER-3.0) with SMTP id UAA09754 for ; Thu, 20 Mar 1997 20:02:12 +0100 Received: by pendragon-int.shfj.cea.fr; id AA06117; Thu, 20 Mar 97 20:00:02 +0100 Received: from uriens.shfj.cea.fr(193.48.23.6) by pendragon-int.shfj.cea.fr via smap (3.2) id xma006115; Thu, 20 Mar 97 19:59:52 +0100 Received: from [193.48.23.123] by shfj.cea.fr (SMI-8.6/PROTO-CEANET-3.0) with ESMTP id TAA01254 for ; Thu, 20 Mar 1997 19:59:43 +0100 X-Sender: guenther@193.48.23.36 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 20 Mar 1997 20:07:51 +0100 To: chemistry@www.ccl.net From: Ilonka Guenther Subject: log P of FDOPA Dear Colleagues, I am looking for the logP value of FDOPA. Does anyone has calculated it once or know where to find this value either calculated or measured? Thanks for any help. Kind regards, Ilonka Guenther ============================= Dr. Ilonka Guenther Service Hospital Frederic Joliot 4 Place de General Leclerc F- 91406 Orsay phone: +(33) (1) 69 86 77 52 fax: +(33) (1) 69 86 77 68 e-mail: guenther@uriens.shfj.cea.fr ============================= From jlye@tx.ncsu.edu Thu Mar 20 15:31:03 1997 Received: from ds10.tx.ncsu.edu for jlye@tx.ncsu.edu by www.ccl.net (8.8.3/950822.1) id OAA21628; Thu, 20 Mar 1997 14:50:47 -0500 (EST) Received: by ds10.tx.ncsu.edu (5.65/Eos/C-U-09Sep93) id AA18819; Thu, 20 Mar 1997 14:50:32 -0500 From: "Jason Lye" Message-Id: <9703201450.ZM18817@unity.ncsu.edu> Date: Thu, 20 Mar 1997 14:50:19 -0500 X-Mailer: Z-Mail (3.2.1 15feb95) To: chemistry@www.ccl.net Subject: ZINDO Energy Units Cc: cache@pacificu.edu, jsokolow@tx.ncsu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear Modelers, Our group is interested in estimating the energy difference between singet and triplet and also doublet and quartet states of metal complexes using CAChe ZINDO. Could somebody please tell me what the units of energy from Zindo are, and how we can convert the energy differences into cm-1, or electron volts for instance. I will summarize any responses and post them to the list. Thanks, Jason -- _______________________________________________________________________________ Jason Lye, | Dye Synthesis Research Group, | College Of Textiles, Box 8301, | "Lifes' cheap, but North Carolina State University, | the accessories will kill you!" Raleigh, N.C. 27695 - 8301 | | Ph: (919) 515-6615 | jlye@tx.ncsu.edu | _______________________________________________________________________________ From boufer@cennas.nhmfl.gov Thu Mar 20 17:30:40 1997 Received: from cennas.nhmfl.gov for boufer@cennas.nhmfl.gov by www.ccl.net (8.8.3/950822.1) id QAA22596; Thu, 20 Mar 1997 16:40:49 -0500 (EST) Received: from localhost (boufer@localhost) by cennas.nhmfl.gov (8.8.5/8.8.5) with SMTP id QAA12715 for ; Thu, 20 Mar 1997 16:40:50 -0500 (EST) Date: Thu, 20 Mar 1997 16:40:50 -0500 (EST) From: Ahmed Bouferguene X-Sender: boufer@cennas To: CHEMISTRY@www.ccl.net Subject: Completeness !!! Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi netters, Does anybody knows a reference where the completeness (or incompleteness) of s-type Slater orbitals is shown. thanks in advance. From tse@ned1.sims.nrc.ca Thu Mar 20 18:02:07 1997 Received: from ned1.sims.nrc.ca for tse@ned1.sims.nrc.ca by www.ccl.net (8.8.3/950822.1) id RAA22704; Thu, 20 Mar 1997 17:01:40 -0500 (EST) Message-Id: <199703202201.WAA07083@ned1.sims.nrc.ca> From: "Dr. J. S. Tse" Subject: quaternion To: chemistry@www.ccl.net Date: Thu, 20 Mar 1997 17:01:41 -0500 (EST) X-Mailer: ELM [version 2.4ME+ PL27 (25)] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear CCL netters, I greatly appreciate if anybody knows a simple program for the convertion of the cartesian coordinates of a triatomic molecule into quaternion? Thanks John -- From momot@iris5.chem.Arizona.EDU Thu Mar 20 18:30:40 1997 Received: from Arizona.EDU for momot@iris5.chem.Arizona.EDU by www.ccl.net (8.8.3/950822.1) id QAA22635; Thu, 20 Mar 1997 16:49:30 -0500 (EST) Received: from iris5.chem.Arizona.EDU by Arizona.EDU (PMDF V5.0-5 #2381) id <01IGQ9KMRTWG94FQOS@Arizona.EDU> for CHEMISTRY@www.ccl.net; Thu, 20 Mar 1997 14:49:29 -0700 (MST) Received: by iris5.chem.Arizona.EDU (920330.SGI/911001.SGI) for @maggie.telcom.Arizona.EDU:CHEMISTRY@www.ccl.net id AA20435; Thu, 20 Mar 1997 14:53:41 -0700 Date: Thu, 20 Mar 1997 14:53:40 +42000 From: Konstantin Momot Subject: G: orbital energies in G94's ROHF ? To: Computational Chemistry List Message-id: MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=US-ASCII Content-transfer-encoding: 7BIT Dear list members, I have a couple of questions about the meaning of one-electron energies in the G94 implementation of ROHF. The questions are stated at the end and are preceded by the description of some unexpected (for me) results. First, a couple of examples of what I'm talking about: 1. H atom in 3-21G basis set: from UHF, E total = -.496198636018 E e-e = 0.000000000000D+00 (of course!) e(1s) = -.49620 from ROHF, E total = -.496198635984 E e-e = 0.000000000000D+00 e(1s) = -.11747 (exhibit 1 !!!) The ROHF convergence and -V/T are .3888D-05 and 1.9645, resp. Clearly, 1) the ROHF result is inconsistent with E tot = Sum of orbital energies - E e-e 2) the orbital energy of the occ. MO does not have the meaning of Koopmans' ionization energy. 2. Li atom in 3-21G: from UHF: E total = -7.38151 -V/T = 2.0015 E e-e = 2.28290 e(1sa)=-2.46051 e(2sa)=-0.19443 e(1sb)=-2.44387 Sum of MO e's - E(ee) = -7.38171 (same as E tot, within -V/T) from ROHF: E total = -7.38151 E e-e = 2.28269 e(1s) = -2.44947 e(2s) = -0.05262 Sum of MO e's - E(ee) = -7.23425 (exhibit 2 !) The last value's difference from E total is much greater than warranted by -V/T, and the 2s energy from ROHF is noticeably higher than that from UHF. So, my QUESTIONS are: 1) What is the ROHF method implemented in G94 ? 2) Does it have anything to do with the method of half-electrons ? 3) Do the orbital energies from G94's ROHF have the meaning of Koopmans energies for at least some orbitals ? 4) Those which do not have the Koopmans IP meaning - do they have any particular meaning in terms of E total, E e-e, J's, K's, etc. ? Thanks in advance for all answers, leads, and suggestions. I will summarize and post the replies. -- Konstantin Momot momot@iris5.chem.arizona.edu |"The best lack all conviction http://aruba.ccit.arizona.edu/ | and the worst are filled ~momot/research.html | with a passionate intensity" - Yates From d3g359@fido.pnl.gov Thu Mar 20 19:30:42 1997 Received: from pnl.gov for d3g359@fido.pnl.gov by www.ccl.net (8.8.3/950822.1) id TAA23328; Thu, 20 Mar 1997 19:06:40 -0500 (EST) Received: from fido.pnl.gov by pnl.gov (PMDF V4.3-13 #6012) id <01IGQCA4A9AO90PWMS@pnl.gov>; Thu, 20 Mar 1997 16:06:32 -0800 (PST) Received: by fido.pnl.gov (951211.SGI.8.6.12.PATCH1042/951211.SGI.AUTO) for CHEMISTRY@www.ccl.net id QAA09938; Thu, 20 Mar 1997 16:02:05 -0800 Date: Thu, 20 Mar 1997 16:02:05 -0800 From: d3g359@fido.pnl.gov (John Nicholas) Subject: igo basis sets To: CHEMISTRY@www.ccl.net Message-id: <199703210002.QAA09938@fido.pnl.gov> Content-transfer-encoding: 7BIT Does anyone have availble an electronic, ftp-able copy of the IGLO basis sets? John ------------------------------------------------------------------------------ John Nicholas Office: (509) 375-6559 Senior Research Scientist FAX: (509) 375-6631 Environmental Molecular Sciences Laboratory Pacific Northwest National Laboratory Mailstop K1-96 Richland, WA 99352 ------------------------------------------------------------------------------