From chemistry-request@ccl.net Thu Apr 15 01:24:07 2004 Received: from oceanite.ens-lyon.fr (oceanite.ens-lyon.fr [140.77.1.22]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i3F6O5uR016040 for ; Thu, 15 Apr 2004 01:24:05 -0500 Received: from localhost (oceanite.ens-lyon.fr [127.0.0.1]) by oceanite.ens-lyon.fr (Postfix) with ESMTP id 5A47A320532 for ; Thu, 15 Apr 2004 08:24:21 +0200 (CEST) Received: from oceanite.ens-lyon.fr ([127.0.0.1]) by localhost (oceanite [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 08122-10 for ; Thu, 15 Apr 2004 08:24:21 +0200 (CEST) Received: from ens-lyon.fr (unknown [140.77.2.15]) by oceanite.ens-lyon.fr (Postfix) with ESMTP id 29034320535 for ; Thu, 15 Apr 2004 08:24:21 +0200 (CEST) Message-ID: <407E478A.80702^at^ens-lyon.fr> Date: Thu, 15 Apr 2004 08:27:54 +0000 From: Paul Fleurat-Lessard Reply-To: Paul.Fleurat-Lessard^at^ens-lyon.fr User-Agent: Mozilla/5.0 (X11; U; Linux i686; fr; rv:1.3.1) Gecko/20030428 X-Accept-Language: fr-fr, en-us, en MIME-Version: 1.0 Cc: chemistry^at^ccl.net Subject: Compiling g03 with ifc (bis) References: <407D3B2E.5050309^at^ens-lyon.fr> In-Reply-To: <407D3B2E.5050309^at^ens-lyon.fr> Content-Type: text/plain; charset=ISO-8859-1; format=flowed X-Virus-Scanned: by amavisd-new-20030616-p7 (Debian) at ens-lyon.fr X-Spam-Status: No, hits=2.7 required=7.5 tests=NO_RDNS,NO_RDNS2,RM_tl_ToNone autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i3F6O7uR016044 Dear CCLers, I just asked: > We have bought Gaussian 2003 some time ago, and we discovered that we > cannot compile it with the version of pgf we have. Has any of you tried > to compile g03 with ifc ? Some details about our configuration: we are using Athlon and PentiumIV processors, our system is Mandrake 9.0 (almost equivalent to RedHat 9.0) and we have ifc 7.1 and 8.0 with MKL 6.1 Regards, Paul. -- Fleurat-Lessard Paul, Lecturer e-mail: Paul.Fleurat-Lessard^at^ens-lyon.fr Laboratoire de Chimie Ecole Normale Supirieure de Lyon Tel: + 33 (0)4 72 72 81 54 46, Allie d'Italie Fax: + 33 (0)4 72 72 84 83 69364 Lyon Cedex 07 From chemistry-request@ccl.net Thu Apr 15 11:56:00 2004 Received: from shiva.jussieu.fr (shiva.jussieu.fr [134.157.0.129]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i3FGtxuR016376 for ; Thu, 15 Apr 2004 11:55:59 -0500 Received: from webmail.ccr.jussieu.fr (webmail.ccr.jussieu.fr [134.157.1.31]) by shiva.jussieu.fr (8.12.11/jtpda-5.4) with ESMTP id i3FGuDkU024852 for ; Thu, 15 Apr 2004 18:56:13 +0200 (CEST) X-Ids: 164 Received: from webmail.ccr.jussieu.fr (localhost.localdomain [127.0.0.1]) by webmail.ccr.jussieu.fr (8.12.8/jtpda-5.4) with ESMTP id i3FGuXg7010248 for ; Thu, 15 Apr 2004 18:56:33 +0200 Received: (from apache@localhost) by webmail.ccr.jussieu.fr (8.12.8/8.12.8/Submit) id i3FGuXDP010246 for CHEMISTRY^at^ccl.net; Thu, 15 Apr 2004 18:56:33 +0200 Received: from m96.net81-65-68.noos.fr (m96.net81-65-68.noos.fr [81.65.68.96]) by webmail.ccr.jussieu.fr (IMP) with HTTP for ; Thu, 15 Apr 2004 18:56:33 +0200 Message-ID: <1082048193.407ebec1b61e8^at^webmail.ccr.jussieu.fr> Date: Thu, 15 Apr 2004 18:56:33 +0200 From: hocquet^at^ccr.jussieu.fr To: CHEMISTRY^at^ccl.net Subject: CCL : wavefunction files and 100 MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.1 X-Miltered: at shiva.jussieu.fr with ID 407EBEAD.000 by Joe's j-chkmail (http://j-chkmail.ensmp.fr)! X-Antivirus: scanned by sophie at shiva.jussieu.fr X-Spam-Status: No, hits=3.2 required=7.5 tests=NO_REAL_NAME,RCVD_IN_DYNABLOCK, RCVD_IN_RFCI,RCVD_IN_SORBS 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 CCLers, I have been unsuccessfully trying to read with an AIM analysis program (AIM2000) various wavefunction .wfn files. After examination of the text .wfn files, it appears that when the calculated structure has more than a hundred atoms, a space between digits is missing in the "centre assignments" columns (counting from centre number 100) , thus making the whole file unreadable. After editing the .wfn file, the program can read it....but fails to converge while searching for critical points. So my question is : are the two events linked or is it that my particular molecule density has some strange spatial configuration, or is it that AIM2000 fails to cope with such big files or both ? Thanks in advance, *********************************************** Alexandre Hocquet Recherche : Laboratoire de Chimie-Physique Macromoleculaire UMR CNRS-INPL 7568 BP 451 54001 Nancy cedex fax : 33.3.83.37.99.77 Alexandre.Hocquet^at^ensic.inpl-nancy.fr http://www.ensic.inpl-nancy.fr/ENSIC/LCPM/ Enseignement : Ecole Europienne d'Inginieurs en Ginie des Matiriaux 6, rue Bastien Lepage 54010 Nancy Cedex Alexandre.Hocquet^at^eeigm.inpl-nancy.fr http://www.eeigm.inpl-nancy.fr/ Soutenez le mouvement SAUVONS LA RECHERCHE : http://recherche-en-danger.apinc.org/ *********************************************** From chemistry-request@ccl.net Thu Apr 15 11:46:27 2004 Received: from yakko.cimav.edu.mx (yakko.cimav.ecustomer.mx [148.223.46.2] (may be forged)) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i3FGkPuR016226 for ; Thu, 15 Apr 2004 11:46:26 -0500 Received: from yakko (localhost [127.0.0.1]) by localhost.cimav.edu.mx (Postfix) with ESMTP id 668791B8013 for ; Thu, 15 Apr 2004 10:46:54 -0600 (MDT) Received: from localhost ([127.0.0.1]) by yakko.cimav.edu.mx (MailMonitor for SMTP v1.2.2 ) ; Thu, 15 Apr 2004 10:46:54 -0600 (MDT) Received: from laquicom05 (byron.cimav.edu.mx [148.223.46.1]) by yakko.cimav.edu.mx (Postfix) with SMTP id E81661B8013 for ; Thu, 15 Apr 2004 10:46:53 -0600 (MDT) Message-ID: <003c01c42311$9feecca0$df01000a@laquicom05> From: "Dr. Daniel Glossman-Mitnik" To: Subject: CCL: links between computational chemistry and molecular nanotechnology Date: Thu, 15 Apr 2004 10:46:47 -0700 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0039_01C422D6.F3885380" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1409 Disposition-Notification-To: "Dr. Daniel Glossman-Mitnik" X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 X-Spam-Status: No, hits=2.2 required=7.5 tests=COMBINED_FROM,HTML_50_60, HTML_MESSAGE,NO_RDNS2 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_0039_01C422D6.F3885380 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear netters: Can somebody give me some pointers (published papers, books, URLs, etc) about links or relationships between computational chemistry and = molecular nanotechnology? Thanks in advance Dr. Daniel = Glossman-Mitnik E-mail : daniel.glossman)at(cimav.edu.mx dglossman)at(prodigy.net.mx ------=_NextPart_000_0039_01C422D6.F3885380 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
 

Dear netters:
 
Can somebody give me some pointers = (published=20 papers, books, URLs, etc)
about links or relationships between = computational=20 chemistry and molecular
nanotechnology?
 
Thanks in advance
 
          &nbs= p;            = ;            =              = Dr. Daniel Glossman-Mitnik
 
E-mail :  daniel.glossman)at(cimav.edu.mx=
          &nbs= p;  dglossman)at(prodigy.net.mx
 
------=_NextPart_000_0039_01C422D6.F3885380-- From chemistry-request@ccl.net Thu Apr 15 16:18:53 2004 Received: from f23.mail.ru (f23.mail.ru [194.67.57.149]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i3FLIpuR029885 for >ccl.net>; Thu, 15 Apr 2004 16:18:52 -0500 Received: from mail by f23.mail.ru with local id 1BEEGc-00076L-00; Fri, 16 Apr 2004 01:19:26 +0400 Received: from [62.221.42.113] by msg.mail.ru with HTTP; Fri, 16 Apr 2004 01:19:26 +0400 From: =?koi8-r?Q?=22=E1=CC=C5=CB=D3=C1=CE=C4=D2=20=E7=CC=D5=DB=CB=CF=D7=22=20?=>inbox.ru> To: "=?koi8-r?Q?=22?=Dr. Daniel Glossman-Mitnik=?koi8-r?Q?=22=20?=">cimav.edu.mx> Cc: CHEMISTRY<>ccl.net Disposition-Notification-To: =?koi8-r?Q?=22=E1=CC=C5=CB=D3=C1=CE=C4=D2=20=E7=CC=D5=DB=CB=CF=D7=22=20?=>inbox.ru> Subject: Re: CCL:links between computational chemistry and molecular nanotechnology Mime-Version: 1.0 X-Mailer: mPOP Web-Mail 2.19 X-Originating-IP: [62.221.42.113] Date: Fri, 16 Apr 2004 01:19:26 +0400 In-Reply-To: <003c01c42311$9feecca0$df01000a@laquicom05> Reply-To: =?koi8-r?Q?=22=E1=CC=C5=CB=D3=C1=CE=C4=D2=20=E7=CC=D5=DB=CB=CF=D7=22=20?=>inbox.ru> Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 8bit Message-Id: >f23.mail.ru> X-Spam-Status: No, hits=0.9 required=7.5 tests=MY_BAD_DOT autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net See, e.g. book by T.A.Romanova, P.O.Krasnov et al. Theory and Practice of Computer Modelling of Nanoobjects, Krasnoyarsk, 2002, 223 pp. URL Link to this book can be found at page http://physics-of-molecules.odessit.org/frame.php?name=library/software/hyperchem/index&title=HyperChem Romanova's book is in Russian. -----Original Message----- From: "Dr. Daniel Glossman-Mitnik" >cimav.edu.mx> To: >ccl.net> Date: Thu, 15 Apr 2004 10:46:47 -0700 Subject: CCL:links between computational chemistry and molecular nanotechnology > > > > Dear netters: > > Can somebody give me some pointers (published papers, books, URLs, etc) > about links or relationships between computational chemistry and molecular > nanotechnology? > > Thanks in advance > > Dr. Daniel Glossman-Mitnik > > E-mail : daniel.glossman<>cimav.edu.mx > dglossman<>prodigy.net.mx > > From chemistry-request@ccl.net Thu Apr 15 17:28:20 2004 Received: from freyr.chem.washington.edu (freyr.chem.washington.edu [128.95.128.138]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i3FMSJuR000566 for ; Thu, 15 Apr 2004 17:28:19 -0500 Received: from freyr.chem.washington.edu (localhost [127.0.0.1]) by freyr.chem.washington.edu (8.12.8/8.12.8) with ESMTP id i3FMLr3E009022 for ; Thu, 15 Apr 2004 15:21:53 -0700 Received: from localhost (fer@localhost) by freyr.chem.washington.edu (8.12.8/8.12.8/Submit) with ESMTP id i3FMLpXh009018 for ; Thu, 15 Apr 2004 15:21:53 -0700 Date: Thu, 15 Apr 2004 15:21:50 -0700 (PDT) From: "Fernando D. Vila" To: Computational Chemistry List Subject: Finite Fields in Gaussian Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=-0.5 required=7.5 tests=SMILEY autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hello everybody.. I have pretty much exhausted all other alternatives, so here I'm asking the CCL community... I have been using the Field keyword in Gaussian for many years, mostly to calculate multipole moments and dipole and quadrupole polarizabilities. Now I wanted to calculate some hyperpolarizabilities using the following formulas: E = E0 - mu0_i F_i - 1/2 alp_ij F_i F_j - 1/6 bet_ijk F_i F_j F_k mu_i = m0_i + alp_ij F_j + 1/2 bet_ijk F_j F_k where F_i is the perturbing electric field in the i direction, E is the total energy including the perturbation, E0 is the energy without the perturbation, mu, alp and bet are the dipole, polarizability and hyperpolarizability. The summation over the i, j, k indices is implied. To verify that the finite differences were giving me a small error I decided to check by calculating NH3 at HF level (Gaussian produces analytic values at this level). Here are the results: Dipole=0.,0.,-0.7000795 Polar=9.4875931,0.,9.4875931,0.,0.,9.799189 HyperPolar=0.,-14.2904879,0.,14.2904879,-3.6541021,0.,-3.6541021,0.,0.,-19.6122974 If I now apply a finite electric field along the z axis and fit the results to a polymomial I get: For the energy: -56.200911807600 -0.700079533332 * F -4.899299996216 * F^2 3.333331240659 * F^3 -400.002401571933 * F^4 For the dipole moment: -0.700079500000 -9.799183333333 * F 9.783333333291 * F^2 -466.666666569064 * F^3 66666.666631576154 * F^4 If you compare the coefficients of this polymomials with the coefficients in the formulas above you will see that there are many sign differences with respect to the analytic results I showed above. This problem is not new to me and the Gaussian manual very helpfully :-P informs us that "the coefficients are those of the Cartesian operator matrices; be careful of the choice of sign convention when interpreting the results". Before I had always assumed that although Gaussian says that is adding an electric field, what is actually doing is adding a potential gradient ( dV/di = V_i = -F_i ). This assumption always gave me correct results, but now it is totally irreconciliable with the sign I get for the hyperpolarizability. So finally, my question: what is the CORRECT FORM of the perturbation introduced by the Gaussian keyword Field. Cheers and I will really appreciate any comments (Doug Fox, are you there?? :-) Fer. "The biggest cause of trouble in the world today is that the stupid people are so sure about things and the intelligent folks are so full of doubts." Bertrand Russell ******************************************************************************* Fernando D. Vila Voice (206)616-3207 Department of Chemistry Fax (206)685-8665 University of Washington E-mail fdv(at)u.washington.edu Seattle, WA 98195, USA WWW http://faculty.washington.edu/fdv *******************************************************************************