From chemistry-request@server.ccl.net Fri Nov 12 06:11:51 1999 Received: from mail.rwth-aachen.de (mail.RWTH-Aachen.DE [137.226.144.9]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA03124 for ; Fri, 12 Nov 1999 06:11:50 -0500 Received: from ac.rwth-aachen.de (pae102.ac.RWTH-Aachen.DE) by mail.rwth-aachen.de (PMDF V5.1-12 #D3869) with ESMTP id <01JI8ZNGDOMO0005AC@mail.rwth-aachen.de> for CHEMISTRY@ccl.net; Fri, 12 Nov 1999 12:05:38 +0200 Date: Fri, 12 Nov 1999 13:04:35 +0100 From: Krzysztof Radacki Subject: Re: CCL:Chkpt File Sender: krzys@mail.rwth-aachen.de To: CCL Message-id: <382C0253.6F096B7B@ac.rwth-aachen.de> Organization: Inst. Inorg. Chem., RWTH Aachen, Germany MIME-version: 1.0 X-Mailer: Mozilla 4.7 [en] (X11; I; Linux 2.2.12-20 i586) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en References: <3.0.6.32.19991111162611.009257e0@chem.boisestate.edu> Benny Moritz wrote: > > Dear Netters, > > How do I read a checkpoint file? I have been unable to read my checkpoint > files in GaussView (G98). I have been using an FTP program (CuteFTP) and > all my gaussian jobs are stored in one directory, so I decided to make > sub-directories to sort out all my jobs. I transferred the files from the > FTP to my personal computer and then back into their appropriate > sub-directories using ASCII mode for both transfers. But when I go into > GaussView to view my checkpoint file an error message comes up saying > unable to read checkpoint file. Is there anyway to fix my problem, or am I > screwed? > > Thank You, > > Ben Moritz I think that you can forget all your chk-files. They are binary so you shoul copy them not as asci- but as bin-transfer. Krzys Radacki _________________------------------------------------------------ ----------------- e-mail: Krys.Radacki@ac.RWTH-Aachen.DE --- ----------------------------------------------------------------- From chemistry-request@server.ccl.net Fri Nov 12 11:14:34 1999 Received: from icp.ac.ru (icp.ac.ru [193.233.43.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA05066 for ; Fri, 12 Nov 1999 11:14:21 -0500 Received: from phot2.pc.icp.ac.ru (phot2.pc.icp.ac.ru [192.168.1.93]) by icp.ac.ru (8.9.1/8.9.1) with SMTP id TAA28887 for ; Fri, 12 Nov 1999 19:04:31 +0300 (MSK) Message-ID: <382CD49E.AA4@icp.ac.ru> Date: Fri, 12 Nov 1999 19:01:50 -0800 From: "Mikhayl F.Budyka" Reply-To: budyka@icp.ac.ru Organization: Institute of Problems of Chemical Physics X-Mailer: Mozilla 3.0Gold (Win95; I; 16bit) MIME-Version: 1.0 To: chemistry@ccl.net Subject: DOS under UNIX Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 7bit Dear CCL'ers, I have very small (17 kB) but very useful (for me) homemade DOS-program (written in turbo-pascal). Whether it is possible to run it under UNIX, just as I do this under W95 in DOS-window? Are there programs that can "imitate" DOS under UNIX? Thanks in advance. M.Budyka budyka@icp.ac.ru From chemistry-request@server.ccl.net Wed Nov 10 23:15:59 1999 Received: from yakko.cimav.edu.mx ([207.248.161.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id XAA27762 for ; Wed, 10 Nov 1999 23:15:58 -0500 Received: from glossman ([207.248.161.148]) by yakko.cimav.edu.mx (8.8.7/8.8.7) with SMTP id WAA13014 for ; Wed, 10 Nov 1999 22:05:36 -0600 Message-ID: <000c01bf2c03$45152180$94a1f8cf@cimav.edu.mx> From: "Dr. Daniel Glossman" To: "Computational Chemistry List" Subject: bond orders in G94W Date: Wed, 10 Nov 1999 21:11:53 -0800 Dear netters: Can somebody explain me how to get Wiberg atom-atom bond orders from a = Gaussian 94W output run? Thanks in advance Dr. Daniel Glossman ************************************************************************* Dr. Daniel Glossman Centro de Investigaci=F3n en Materiales Avanzados (CIMAV) Divisi=F3n de Pol=EDmeros Phone: (52) 1 4391151 Miguel de Cervantes 120 FAX: (52) 1 4391112 Complejo Industrial Chihuahua E-mail: glossman@mail.cimav.edu.mx Chihuahua, Chih. 31109 glossman@hotmail.com Mexico *************************************************************************= From chemistry-request@server.ccl.net Thu Nov 11 09:55:57 1999 Received: from kasei.materials.ox.ac.uk (kasei.materials.ox.ac.uk [163.1.64.46]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA31314 for ; Thu, 11 Nov 1999 09:55:56 -0500 Received: from localhost (hfield@localhost) by kasei.materials.ox.ac.uk (8.9.3/8.9.3) with ESMTP id OAA30304 for ; Thu, 11 Nov 1999 14:47:57 GMT X-Authentication-Warning: kasei.materials.ox.ac.uk: hfield owned process doing -bs Date: Thu, 11 Nov 1999 14:47:57 +0000 (GMT) From: Andrew Horsfield X-Sender: hfield@kasei.materials.ox.ac.uk Reply-To: Andrew Horsfield To: Computational Chemistry List Subject: Problem with LCAO for solids Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I have had a problem with applying an LCAO-DFT (using numerical orbitals) method to solids. When I expand the basis set from sdps*p* to sdps*p*d* (i.e. I add an extra set of d orbitals), I suddenly get ghost states (eigenvalues with very low energies - one or two orders of magnitude too big). I originally thought this was due to the ill conditioning of the overlap matrix. But on inspection I find that its smallest eigenvalues are about 0.0005, which does not seem all that small. I have tried shifting the small eigenvalues up in value, but this makes no difference at all. Can anyone suggest another possible cause for this problem? Cheers, Andrew +----------------------------------------------------+ Andrew Horsfield e-mail: horsfield@fecit.co.uk FECIT, 2 Longwalk Road, Stockley Park, Uxbridge, Middlesex UB11 1AB, United Kingdom. phone: +44-(0)181-606-4653 FAX: +44-(0)181-606-4422 +----------------------------------------------------+ From chemistry-request@server.ccl.net Fri Nov 12 15:07:08 1999 Received: from castor.rice.edu (castor.rice.edu [128.42.81.29]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA06178 for ; Fri, 12 Nov 1999 15:07:07 -0500 Received: from localhost (knk@localhost) by castor.rice.edu (AIX4.3/8.9.3/8.9.3) with ESMTP id NAA11990; Fri, 12 Nov 1999 13:59:29 -0600 Date: Fri, 12 Nov 1999 13:59:28 -0600 (CST) From: "Konstantin N. Kudin" To: Andrew Horsfield cc: Computational Chemistry List Subject: Re: CCL:Problem with LCAO for solids In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 11 Nov 1999, Andrew Horsfield wrote: > Hi, > > I have had a problem with applying an LCAO-DFT (using numerical orbitals) > method to solids. When I expand the basis set from sdps*p* to sdps*p*d* > (i.e. I add an extra set of d orbitals), I suddenly get ghost states > (eigenvalues with very low energies - one or two orders of magnitude too > big). I originally thought this was due to the ill conditioning of the > overlap matrix. But on inspection I find that its smallest eigenvalues are > about 0.0005, which does not seem all that small. I have tried shifting > the small eigenvalues up in value, but this makes no difference at all. > Can anyone suggest another possible cause for this problem? > > Cheers, > > Andrew What you have there is called linear dependencies (LD). The problem will go away after you eliminate few smallest eigenvalues/eigenvectors from the overlap matrix. The relation between the magnitude of smallest overlap eigenvalue and LD is not very straightforward, and 0.0005 value can certainly lead to LD in some occasions. You can also try to overcome the problem by increasing the accuracy of the Kohn-Sham matrix evaluation or doubling the unit cell size. The following reference contains a discussion of LD for GTO basis sets, however, the stuff is actually more general and can apply to your case as well: Choosing GTO basis sets for periodic HF calculations A. Gruneich, B. A. Heb, Theor. Chem. Acc., 100, 253 (1998). Regards, Konstantin Kudin From chemistry-request@server.ccl.net Fri Nov 12 16:42:03 1999 Received: from sunu450.rz.ruhr-uni-bochum.de (sunu450.rz.ruhr-uni-bochum.de [134.147.222.33]) by server.ccl.net (8.8.7/8.8.7) with SMTP id QAA06530 for ; Fri, 12 Nov 1999 16:42:02 -0500 From: Christoph.van.Wuellen@ruhr-uni-bochum.de Received: (qmail 20139 invoked from network); 12 Nov 1999 21:34:08 -0000 Received: from sgi249.rz.ruhr-uni-bochum.de (134.147.64.2) by mailhost.rz.ruhr-uni-bochum.de with SMTP; 12 Nov 1999 21:34:08 -0000 Received: (qmail 26287 invoked by uid 10283); 12 Nov 1999 21:33:40 -0000 Message-ID: <19991112213340.26286.qmail@sgi249.rz.ruhr-uni-bochum.de> Subject: Re: CCL:Chkpt File To: bmoritz@chem10.idbsu.edu (Benny Moritz) Date: Fri, 12 Nov 1999 22:33:40 +0100 (MET) Cc: chemistry@ccl.net In-Reply-To: <3.0.6.32.19991111162611.009257e0@chem.boisestate.edu> from "Benny Moritz" at Nov 11, 99 04:26:11 pm X-Mailer: ELM [version 2.4 PL24] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit ... checkpoint files are binary, so binary transfer is required. However, unformatted (i.e. binary) files are not necessarily transportable across platforms. I cannot use gv (which runs under AIX) to read a chkpnt file created under LINUX. It might be possible to convert the checkpoint file to a formatted file (formchk) on the "Calculator" and do the reverse on the "Viewer", i have not tried it. ---------------------------+------------------------------------------------ Christoph van Wullen | Fon (University): +49 234 32 26485 Theoretical Chemistry | Fax (University): +49 234 32 14109 Ruhr-Universitaet | Fon/Fax (private): +49 234 33 22 75 D-44780 Bochum, Germany | eMail: Christoph.van.Wuellen@Ruhr-Uni-Bochum.de ---------------------------+------------------------------------------------ From chemistry-request@server.ccl.net Fri Nov 12 18:06:51 1999 Received: from prserv.net (out1.prserv.net [165.87.194.252]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA06881 for ; Fri, 12 Nov 1999 18:06:51 -0500 From: jmmckel@attglobal.net Received: from schutz ([32.100.233.190]) by prserv.net (out1) with SMTP id <1999111222585525201fo4fce>; Fri, 12 Nov 1999 22:58:56 +0000 Message-ID: <382DA935.4475@attglobal.net> Date: Sat, 13 Nov 1999 18:08:53 +0000 Reply-To: jmmckel@attglobal.net X-Mailer: Mozilla 3.04 (WinNT; I) MIME-Version: 1.0 To: Christoph.van.Wuellen@ruhr-uni-bochum.de CC: Benny Moritz , chemistry@ccl.net Subject: Re: CCL:Chkpt File References: <19991112213340.26286.qmail@sgi249.rz.ruhr-uni-bochum.de> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Christoph.van.Wuellen@ruhr-uni-bochum.de wrote: > > >... checkpoint files are binary, so binary transfer is required. However, > unformatted (i.e. binary) files are not necessarily transportable across > platforms. I cannot use gv (which runs under AIX) to read a chkpnt file > created under LINUX. It might be possible to convert the checkpoint > file to a formatted file (formchk) on the "Calculator" and do the reverse > on the "Viewer", i have not tried it. > ---------------------------+------------------------------------------------ > Christoph van Wullen | Fon (University): +49 234 32 26485 > Theoretical Chemistry | Fax (University): +49 234 32 14109 > Ruhr-Universitaet | Fon/Fax (private): +49 234 33 22 75 > D-44780 Bochum, Germany | eMail: Christoph.van.Wuellen@Ruhr-Uni-Bochum.de > ---------------------------+------------------------------------------------ > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net Convert checkpoint file to ASCii.. move.. convert back to binary.... John McKelvey From chemistry-request@server.ccl.net Fri Nov 12 13:41:26 1999 Received: from bacchus.pc1.uni-duesseldorf.de (root@bacchus.pc1.uni-duesseldorf.de [134.99.152.11]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA05769 for ; Fri, 12 Nov 1999 13:41:26 -0500 Received: from bacchus.pc1.uni-duesseldorf.de (jochen@localhost [127.0.0.1]) by bacchus.pc1.uni-duesseldorf.de (8.8.7/8.8.7) with SMTP id TAA05404; Fri, 12 Nov 1999 19:32:44 +0100 From: Jochen Reply-To: jochen@pc1.uni-duesseldorf.de Organization: Heinrich-Heine-Universität To: "Mikhayl F.Budyka" , chemistry@ccl.net Subject: Re: CCL:DOS under UNIX Date: Fri, 12 Nov 1999 19:32:02 +0100 X-Mailer: KMail [version 1.0.28] Content-Type: text/plain References: <382CD49E.AA4@icp.ac.ru> In-Reply-To: <382CD49E.AA4@icp.ac.ru> MIME-Version: 1.0 Message-Id: <99111219324405.01208@bacchus.pc1.uni-duesseldorf.de> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id NAA05770 On Sam, 13 Nov 1999 Mikhayl F.Budyka wrote: >I have very small (17 kB) but very useful (for me) homemade DOS-program >(written in turbo-pascal). >Whether it is possible to run it under UNIX, If you are on an x86 machine, use dosemu. If not, you could try boochs. -- Jochen Heinrich-Heine-Universität, Institut für Physikalische Chemie I Universitätsstr. 1, Geb. 26.43.02.29, 40225 Düsseldorf, Germany phone 02118113681 fax 02118115195 -- www-public.rz.uni-duesseldorf.de/~jochen Jochen@Uni-Duesseldorf.de -- Jochen.Kuepper@FernUni-Hagen.de -- Kuepper@ACM.org From chemistry-request@server.ccl.net Fri Nov 12 16:58:46 1999 Received: from darkwing.uoregon.edu (genghis@darkwing.uoregon.edu [128.223.142.13]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA06625 for ; Fri, 12 Nov 1999 16:58:46 -0500 Received: from localhost (genghis@localhost) by darkwing.uoregon.edu (8.9.3/8.9.3) with SMTP id NAA16093 for ; Fri, 12 Nov 1999 13:50:51 -0800 (PST) Date: Fri, 12 Nov 1999 13:50:51 -0800 (PST) From: "Dale A. Braden" To: Computational Chemistry List Subject: Re: CCL:bond orders in G94W In-Reply-To: <000c01bf2c03$45152180$94a1f8cf@cimav.edu.mx> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dr. Glossman, The following example input file will generate the kind of thing you want: # hf/sto-3g pop=nboread water 0 1 O H1 O 0.96 H2 O 0.96 H1 107. $nbo bndidx $end Best wishes, Dale Braden Department of Chemistry University of Oregon Eugene, OR 97403-1253 genghis@darkwing.uoregon.edu On Wed, 10 Nov 1999, Dr. Daniel Glossman wrote: > Dear netters: > > Can somebody explain me how to get Wiberg atom-atom bond orders from a = > Gaussian 94W > output run? > > Thanks in advance > > > Dr. Daniel Glossman > > ************************************************************************* > Dr. Daniel Glossman > Centro de Investigaci=F3n en Materiales Avanzados (CIMAV) > Divisi=F3n de Pol=EDmeros Phone: (52) 1 4391151 > Miguel de Cervantes 120 FAX: (52) 1 4391112 > Complejo Industrial Chihuahua E-mail: glossman@mail.cimav.edu.mx > Chihuahua, Chih. 31109 glossman@hotmail.com > Mexico > *************************************************************************= > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Fri Nov 12 18:04:41 1999 Received: from prserv.net (out1.prserv.net [165.87.194.252]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA06861 for ; Fri, 12 Nov 1999 18:04:41 -0500 From: jmmckel@attglobal.net Received: from schutz ([32.100.233.190]) by prserv.net (out1) with SMTP id <19991112225645252011gilde>; Fri, 12 Nov 1999 22:56:45 +0000 Message-ID: <382DA8B0.6FD5@attglobal.net> Date: Sat, 13 Nov 1999 18:06:40 +0000 Reply-To: jmmckel@attglobal.net X-Mailer: Mozilla 3.04 (WinNT; I) MIME-Version: 1.0 To: "Dr. Daniel Glossman" CC: Computational Chemistry List Subject: Re: CCL:bond orders in G94W References: <000c01bf2c03$45152180$94a1f8cf@cimav.edu.mx> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dr. Daniel Glossman wrote: > > Dear netters: > > Can somebody explain me how to get Wiberg atom-atom bond orders from a = > Gaussian 94W > output run? > > Thanks in advance > > Dr. Daniel Glossman > > ************************************************************************* > Dr. Daniel Glossman > Centro de Investigaci=F3n en Materiales Avanzados (CIMAV) > Divisi=F3n de Pol=EDmeros Phone: (52) 1 4391151 > Miguel de Cervantes 120 FAX: (52) 1 4391112 > Complejo Industrial Chihuahua E-mail: glossman@mail.cimav.edu.mx > Chihuahua, Chih. 31109 glossman@hotmail.com > Mexico > *************************************************************************= > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net Here's how... Convert the checkpoint file to ASCII... Extract the density matrix and overlap matrix. Create S**(+1/2) P'=get S**(1/2)*P*S**(1/2) Get Sums Of Squares of off diagonal elements of P' between atoms.. That's it. John McKelvey From chemistry-request@server.ccl.net Fri Nov 12 19:24:38 1999 Received: from mailhost.lanl.gov (mailhost.lanl.gov [128.165.3.12]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA07313 for ; Fri, 12 Nov 1999 19:24:38 -0500 Received: from [128.165.22.209] (machgs.lanl.gov [128.165.22.209]) by mailhost.lanl.gov (8.9.3/8.9.3/(cic-5, 2/8/99)) with SMTP id RAA18588 for ; Fri, 12 Nov 1999 17:16:41 -0700 X-Sender: schrecke@t12mail.lanl.gov Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 12 Nov 1999 17:18:34 -0600 To: CHEMISTRY@ccl.net (CCL) From: schrecke@t12.lanl.gov (Georg Schreckenbach) Subject: IOp(11) in l601 of Gaussian Dear all: looking thru' the comment section of l601 of the Gaussian program, G94 or G98, I find that, supposedly, IOp(11) regulates Mulliken output of "gross orbital type charges". However, turning it on or off has no influence whatsoever on my output. Further, scanning the l6*.F source files for the string "IOp(11)" doesn't turn up anything but the mentioned comments. Is this a dead IOp? And how do I get those charges per orbital type, e.g., s or p charge on atom N? (Well, I can, of course, add the Mulliken charges per basis function as desired, but this is rather tedious for a large basis set.) Thanx! I'll summarize as usual if there is any interest. Best regards, Georg P.S. I have send the very same question to Gaussian also. -- ============================================================== Dr. Georg Schreckenbach Tel: (USA)-505-667 7605 Theoretical Chemistry T-12 FAX: (USA)-505-665 3909 M.S. B268, Los Alamos National E-mail: schrecke@t12.lanl.gov Laboratory, Los Alamos, New Mexico, 87545, USA Internet: http://www.t12.lanl.gov/home/schrecke/ ============================================================== From chemistry-request@server.ccl.net Fri Nov 12 21:49:55 1999 Received: from panix3.panix.com (tfr+V3ZXgmeoqoztj0uZm0SK5p1FVPjx@panix3.panix.com [166.84.0.228]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id VAA08015 for ; Fri, 12 Nov 1999 21:49:55 -0500 From: kynn@panix.com Received: (from kynn@localhost) by panix3.panix.com (8.8.5/8.8.8/PanixU1.4) id UAA04340; Fri, 12 Nov 1999 20:35:39 -0500 (EST) Date: Fri, 12 Nov 1999 20:35:39 -0500 (EST) Message-Id: <199911130135.UAA04340@panix3.panix.com> To: To:, CHEMISTRY@ccl.net Subject: [Q] Multiple histogram method Several works (e.g. [1, 2]) reporting multiple histogram techniques to construct a free-energy surface, use a formulas containing a factor g, which equals (1 + 2*tau), where \tau is referred to as the "integrated correlation time". The exact definition of tau is given in pp. 33-34 of [3], and amounts to the integral with respect to t from 0 to infinity of - ^2 divided by the variance of A, where A is some quantity of interest. I have tried to obtain numerically the tau used in the multiple histogram techniques, but no matter how much data I amass, I still end up with something that doesn't come even close to converging (i.e. the integral above fluctuates widely throughout as one lets the upper limit of integration grow to infinity). Does anybody know where I can find more info on how to compute this tau? Thanks! KJ [1] Ferrenberg, A. M. and Swendsen, R. H. "Optimized Monte Carlo Data Analysis", 1989, Phys. Rev. Lett. 63(12) 1195-1198. [2] Kumar, S., et al. "The Weighted Histogram Analysis Method for Free-Energy Calculations on Biomolecules. I. The Method", 1992, J. Comp. Chem., 13(8) 1011-1021. [3] Binder, K. and Heermann, D. W. "Monte Carlo Simulation in Statistical Physics", 2nd Corr. Ed., 1992, pp. 33-34.