From chemistry-request@ccl.net Thu Feb 19 14:25:39 2004 Received: from mail.chem.tamu.edu (mail.chem.tamu.edu [165.91.176.8]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1JJPcDf004213 for ; Thu, 19 Feb 2004 14:25:39 -0500 Received: from [165.91.178.2] (HELO yubopclab) by mail.chem.tamu.edu (CommuniGate Pro SMTP 4.1.8) with SMTP id 971578 for CHEMISTRY..at..ccl.net; Thu, 19 Feb 2004 13:26:24 -0600 Message-ID: <014f01c3f71e$353e22d0$02b25ba5@yubopclab> From: "Yubo Fan" To: Subject: Read g03 chk file on g98 Date: Thu, 19 Feb 2004 13:26:00 -0600 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_014C_01C3F6EB.EA78F950" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Spam-Status: No, hits=0.5 required=7.0 tests=HTML_40_50,HTML_MESSAGE autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. ------=_NextPart_000_014C_01C3F6EB.EA78F950 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi, everyone, Is there any way to convert g03 checkpoint file into the format that g98 = can read? By the way, is it possible to read the wavefunction saved in a .wfn = file? Thanks in advance. Yubo =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Dr. Yubo Fan Email: yubofan..at..mail.chem.tamu.edu Department of Chemistry Tel: 1-979-845-7222 Texas A&M University College Station, TX 77843 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D ------=_NextPart_000_014C_01C3F6EB.EA78F950 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Hi, everyone,

Is there any way to convert g03 = checkpoint file=20 into the format that g98 can read?

By the way, is it possible to read the = wavefunction=20 saved in a .wfn file?

Thanks in advance.

Yubo

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Dr. Yubo=20 Fan &nbs= p; =20 Email: yubofan..at..mail.chem.tamu.edu=
Department=20 of Chemistry Tel: 1-979-845-7222
Texas = A&M=20 University
College Station, TX=20 77843
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D

------=_NextPart_000_014C_01C3F6EB.EA78F950-- From chemistry-request@ccl.net Thu Feb 19 14:17:31 2004 Received: from electra.cc.umanitoba.ca (electra.cc.umanitoba.ca [130.179.16.23]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1JJHTDf004059 for >ccl.net>; Thu, 19 Feb 2004 14:17:29 -0500 Received: from capella.cc.umanitoba.ca (server<>capella.cc.umanitoba.ca [130.179.16.13]) by electra.cc.umanitoba.ca (8.12.10/8.12.10) with ESMTP id i1JJI3eH029070; Thu, 19 Feb 2004 13:18:04 -0600 (CST) Received: (from server@localhost) by capella.cc.umanitoba.ca (8.12.10+Sun/8.12.2) id i1JJI35s015991; Thu, 19 Feb 2004 13:18:03 -0600 (CST) Received: from net118.chem.umanitoba.ca ( [net118.chem.umanitoba.ca]) as user schrecke@localhost by webware.cc.umanitoba.ca with HTTP; Thu, 19 Feb 2004 13:18:03 -0600 Message-ID: <1077218283.40350bebb97de<>webware.cc.umanitoba.ca> Date: Thu, 19 Feb 2004 13:18:03 -0600 From: "H. Georg Schreckenbach" >cc.UManitoba.CA> To: chemistry<>ccl.net Cc: schrecke<>cc.UManitoba.CA Subject: periodic boundary conditions MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.1 X-Originating-IP: 130.179.49.38 X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCL, I am looking for recommendations regarding literature about band-structure calculations. Specifically, we are coming from the "molecular electronic structure" background, and we want to branch out into extending some of our methods, applications and ideas into extended structures that require periodic boundary conditions. For that, we are looking for introductory material that explains to us the basic concepts etc. To give an example, we are thinking about questions such as, what is the equivalent of the total energy expressions that are the basis for most molecular methods? I appreciate your help! Please reply directly to me because I am not currently subscribed to the list. I will definitely post a summary. Best regards, Georg Schreckenbach -- Dr. H. Georg Schreckenbach Department of Chemistry, University of Manitoba Winnipeg, MB, R3T 2N2, Canada phone: (+204) 474-6261 FAX: (+204) 474-7608 http://home.cc.umanitoba.ca/~schrecke/ ------------------------------------------------- This mail sent through IMP: http://horde.org/imp/ From chemistry-request@ccl.net Thu Feb 19 18:25:36 2004 Received: from osgood.cc.nd.edu (osgood.cc.nd.edu [129.74.250.227]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1JNPZDf009564 for ; Thu, 19 Feb 2004 18:25:35 -0500 Received: from localhost (localhost [127.0.0.1]) by osgood.cc.nd.edu (Switch-3.1.4/Switch-3.1.0) with ESMTP id i1JNQNOp012496; Thu, 19 Feb 2004 18:26:23 -0500 (EST) Received: from 129.74.52.62 ([129.74.52.62]) by webmail.nd.edu (IMP) with HTTP for ; Thu, 19 Feb 2004 18:26:23 -0500 Message-ID: <1077233183.4035461f16140|at|webmail.nd.edu> Date: Thu, 19 Feb 2004 18:26:23 -0500 From: Jan K Labanowski To: chemistry|at|ccl.net Cc: jlabanow|at|nd.edu Subject: Fwd: ACS Pubs ends publishing moratorium MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.2 X-Originating-IP: 129.74.52.62 X-ND-MTA-Date: Thu, 19 Feb 2004 18:26:24 -0500 (EST) X-ND-Virus-Scan: engine v4.2.40; dat v4326 X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Not that I want to have a discussion of this issue at CCL, but you should probably know about it. -- Jan K. Labanowski, Ph.D. Tel. (574) 631-4565 Science Computing Facility FAX (574) 631-9293 University of Notre Dame 225 Nieuwland Science Hall Notre Dame, IN 46556-5670 ----- Forwarded message from "Culp, F B." ----- Date: Thu, 19 Feb 2004 17:34:17 -0500 From: "Culp, F B." Reply-To: CHEMICAL INFORMATION SOURCES DISCUSSION LIST Subject: ACS Pubs ends publishing moratorium To: CHMINF-L|at|LISTSERV.INDIANA.EDU Greetings- I offer with absolutely no comment or unclean thought the following item > from today's Chronicle of Higher Education: "In apparent defiance of U.S. Treasury Department regulations, the American Chemical Society decided on Tuesday to end its own temporary moratorium on publishing papers by scientists in countries under trade embargoes, such as Cuba, Iran, Iraq, Libya, and Sudan." The full text of the article is available for a limited time on the CHE Website at: http://chronicle.com/prm/daily/2004/02/2004021902n.htm Bartow Culp Purdue Univeristy CHMINF-L Archives (also to join or leave CHMINF-L, etc.) http://listserv.indiana.edu/archives/chminf-l.html Search the CHMINF-L archives at: http://listserv.indiana.edu/cgi-bin/wa?S1=chminf-l Sponsors of CHMINF-L: http://www.indiana.edu/~cheminfo/chminf-l_support.html ----- End forwarded message ----- From chemistry-request@ccl.net Thu Feb 19 15:03:41 2004 Received: from webmail.mta.ca (postal.mta.ca [138.73.1.51]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1JK3cDf005128 for ; Thu, 19 Feb 2004 15:03:38 -0500 Received: from nobody by webmail.mta.ca with local (Exim 4.20) id 1AtuOA-0008Iv-TB for chemistry|at|ccl.net; Thu, 19 Feb 2004 16:03:14 -0400 Received: from 138.73.24.161 ( [138.73.24.161]) as user smlpnt|at|mailserv.mta.ca by webmail.mta.ca with HTTP; Thu, 19 Feb 2004 16:03:14 -0400 Message-ID: <1077220994.40351682d6e75|at|webmail.mta.ca> Date: Thu, 19 Feb 2004 16:03:14 -0400 From: smlpnt|at|mta.ca To: chemistry|at|ccl.net Subject: Optimization error MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Originating-IP: 138.73.24.161 X-Spam-Status: No, hits=0.3 required=7.0 tests=NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi, I get this error sometimes when trying to do an optimization. It runs for a while and does quite a few steps then it dies and I get the following error message. Does anyone know what it is? > Raffenetti 2 integral format. > Two-electron integral symmetry is turned on. > 335 basis functions 595 primitive gaussians > 66 alpha electrons 66 beta electrons > nuclear repulsion energy 1444.4246875757 Hartrees. > One-electron integrals computed using PRISM. > NBasis= 335 RedAO= T NBF= 335 > NBsUse= 335 1.00D-04 NBFU= 335 > Initial guess read from the read-write file: > Requested convergence on RMS density matrix=1.00D-08 within 64 cycles. > Requested convergence on MAX density matrix=1.00D-06. > Integral accuracy reduced to 1.0D-05 until final iterations. > Problem detected with inexpensive integrals. > Switching to full accuracy and repeating last cycle. > Warning! Spurious integrated density: > NE= 132 NElCor= 0 Integral= -0.04786 Tolerance=1.00D-03 > Consistency failure #2 in CalDSu. > Error termination via Lnk1e in /programs/g98/linda-exe/l502.exel. > Job cpu time: 0 days 0 hours 0 minutes 41.7 seconds. > File lengths (MBytes): RWF= 69 Int= 0 D2E= 0 Chk= 12 Scr= 1 Shenna From chemistry-request@ccl.net Thu Feb 19 18:03:57 2004 Received: from mxout4.cac.washington.edu (mxout4.cac.washington.edu [140.142.33.19]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1JN3uDf009128 for ; Thu, 19 Feb 2004 18:03:57 -0500 Received: from dante53.u.washington.edu (dante53.u.washington.edu [140.142.15.103]) by mxout4.cac.washington.edu (8.12.11+UW04.02/8.12.11+UW04.02) with ESMTP id i1JN4W0W024209 for ; Thu, 19 Feb 2004 15:04:37 -0800 Received: from localhost (jzheng73@localhost) by dante53.u.washington.edu (8.12.10+UW03.09/8.12.10+UW03.09) with ESMTP id i1JN4W1q024336 for ; Thu, 19 Feb 2004 15:04:32 -0800 Date: Thu, 19 Feb 2004 15:04:32 -0800 (PST) From: Jie Zheng To: chemistry{at}ccl.net Subject: basic questions in MD Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.9 required=7.0 tests=FROM_ENDS_IN_NUMS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi, CCLer: I have a few basic questions for molecular dynamics. 1) why the system has to be neutral in molecular dynamics? From the numerial point of views, it seems that to be neutral or not does not affect the numerial algorithm. We still can get results. I know there must have some physical meaning behind this, anybody can give a answer? 2) why the cutoff distance can not larger than the half-size of box? If we use the Ewald sum method to calculate nonbonded interactions, the system and its images have been extend to infinite. If we use the cutoff method, the system is confined to the finite size by using periodic boundary conditon. My question is that if we extend our simulation system to infinite as the Ewald sum does, the half-box cutoff is not required for the simluation systems. I will appreciate for your clarification. Jay From chemistry-request@ccl.net Thu Feb 19 19:04:33 2004 Received: from iris (iris.inc.bme.hu [152.66.63.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1K04VDf010314 for ; Thu, 19 Feb 2004 19:04:31 -0500 Received: from dino (helo=localhost) by iris with local-esmtp (Exim 3.36 #1 (Debian)) id 1Aty9n-0000mp-00; Fri, 20 Feb 2004 01:04:39 +0100 Date: Fri, 20 Feb 2004 01:04:39 +0100 (CET) From: Szieberth Denes To: smlpnt..at..mta.ca cc: chemistry..at..ccl.net Subject: Re: CCL:Optimization error In-Reply-To: <1077220994.40351682d6e75..at..webmail.mta.ca> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net > I get this error sometimes when trying to do an optimization. It runs for a > while and does quite a few steps then it dies and I get the following error > message. Does anyone know what it is? > > > Raffenetti 2 integral format. > > Two-electron integral symmetry is turned on. > > 335 basis functions 595 primitive gaussians > > 66 alpha electrons 66 beta electrons > > nuclear repulsion energy 1444.4246875757 Hartrees. > > One-electron integrals computed using PRISM. > > NBasis= 335 RedAO= T NBF= 335 > > NBsUse= 335 1.00D-04 NBFU= 335 > > Initial guess read from the read-write file: > > Requested convergence on RMS density matrix=1.00D-08 within 64 cycles. > > Requested convergence on MAX density matrix=1.00D-06. > > Integral accuracy reduced to 1.0D-05 until final iterations. > > Problem detected with inexpensive integrals. > > Switching to full accuracy and repeating last cycle. > > Warning! Spurious integrated density: > > NE= 132 NElCor= 0 Integral= -0.04786 Tolerance=1.00D-03 > > Consistency failure #2 in CalDSu. As far as I know it's a dft-related error. Gaussian checks the charge resulting from the integration of the density to the number of electrons, and in case of a large difference prints this eror message. Try a denser grid with the "integral" keyword. cheers dino From chemistry-request@ccl.net Thu Feb 19 19:08:45 2004 Received: from iris (iris.inc.bme.hu [152.66.63.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1K08iDf010462 for ; Thu, 19 Feb 2004 19:08:44 -0500 Received: from dino (helo=localhost) by iris with local-esmtp (Exim 3.36 #1 (Debian)) id 1AtyEN-0000nn-00; Fri, 20 Feb 2004 01:09:23 +0100 Date: Fri, 20 Feb 2004 01:09:23 +0100 (CET) From: Szieberth Denes To: "H. Georg Schreckenbach" cc: chemistry!at!ccl.net Subject: Re: CCL:periodic boundary conditions In-Reply-To: <1077218283.40350bebb97de!at!webware.cc.umanitoba.ca> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net > > I am looking for recommendations regarding literature about band-structure > calculations. Specifically, we are coming from the "molecular electronic > structure" background, and we want to branch out into extending some of our > methods, applications and ideas into extended structures that require periodic > boundary conditions. For that, we are looking for introductory material that > explains to us the basic concepts etc. Some papers I have found useful: a "for beginners" one: Gillan MJ The virtual matter laboratory CONTEMP PHYS 38 (2): 115-130 MAR-APR 1997 and two "serious" ones: Jones & Gunnarsson Rev Mod Phys 91 (1989) 689 M. Payne et al Rev Mod Phys 64 (1992) 1045 cheers dino