From chemistry-request@ccl.net Thu Oct 21 07:34:38 2004 Received: from seas.marine.usf.edu (seas.marine.usf.edu [131.247.136.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i9LCYbwe005724 for ; Thu, 21 Oct 2004 07:34:37 -0500 Received: from yluo (ms136dhcp239.marine.usf.edu [131.247.136.239]) by seas.marine.usf.edu (8.13.1/8.13.1) with SMTP id i9LCa0Td004272 for ; Thu, 21 Oct 2004 08:36:04 -0400 (EDT) Message-ID: <000c01c4b76a$8764e7d0$ef88f783-.at.-marine.usf.edu> From: "luo" To: Subject: Question: theoretical calculations of thermochemistry Date: Thu, 21 Oct 2004 08:35:59 -0400 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0009_01C4B748.FDCB1650" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1437 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1441 X-USFCMS-MailScanner-Information: Please contact the postmaster-.at.-marine.usf.edu for more information X-USFCMS-MailScanner: Scanned X-MailScanner-From: luo-.at.-seas.marine.usf.edu X-Spam-Status: No, hits=1.0 required=7.5 tests=HTML_50_60,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_0009_01C4B748.FDCB1650 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear ALL: I am very interested in theoretical calculations of thermochemistry. I = want to find some websites about this topic. But I have known good = website of NIST only.=20 Who could help me to show more websites about theoretical calculations = of thermochemistry?=20 Many thanks to you in advance. Yu-Ran Luo, Ph.D. luo-.at.-marine.usf.edu ------=_NextPart_000_0009_01C4B748.FDCB1650 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Dear ALL:

I am very interested in theoretical = calculations of=20 thermochemistry. I want to find some websites about this topic. But I = have=20 known good website of NIST only.

Who could help me to show more websites = about=20 theoretical calculations of thermochemistry?

Many thanks to you in = advance.

Yu-Ran Luo, Ph.D.

luo-.at.-marine.usf.edu

------=_NextPart_000_0009_01C4B748.FDCB1650-- From chemistry-request@ccl.net Thu Oct 21 12:06:42 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 i9LH6fPq021348 for ; Thu, 21 Oct 2004 12:06:42 -0500 Received: from localhost (localhost [127.0.0.1]) by osgood.cc.nd.edu (Switch-3.1.7/Switch-3.1.7) with ESMTP id i9LHIvOm009989; Thu, 21 Oct 2004 12:18:57 -0500 (EST) Received: from laptop.ccl.net (laptop.ccl.net [129.74.52.62]) by webmail.nd.edu (IMP) with HTTP for ; Thu, 21 Oct 2004 12:18:57 -0500 Message-ID: <1098379137.4177ef8113982-.at.-webmail.nd.edu> Date: Thu, 21 Oct 2004 12:18:57 -0500 From: Jan K Labanowski To: chemistry-.at.-ccl.net Cc: rbross-.at.-mmm.com, jlabanow-.at.-nd.edu Subject: 2nd Industrial Fluid Properties Simulation Challenge MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-2 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.6 X-Originating-IP: 129.74.52.62 X-ND-MTA-Date: Thu, 21 Oct 2004 12:18:58 -0500 (EST) X-ND-Virus-Scan: engine v4.3.20; dat v4400 X-Spam-Status: No, hits=0.0 required=7.5 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 ----- Forwarded message from rbross-.at.-mmm.com ----- Date: Thu, 21 Oct 2004 08:26:51 -0500 From: rbross-.at.-mmm.com Reply-To: rbross-.at.-mmm.com Title: AIChE Austin Symposium on 2nd Industrial Fluid Properties Simulation Challenge Dear Colleague, You're invited to attend the Industrial Fluid Properties Simulation Challenge sessions at the AIChE annual meeting in Austin, TX, on Sunday, November 7. These sessions will include presentations by the individuals who entered the Challenge as well as the announcement of the Champions. There will also be a time of general discussion to allow the audience to provide feedback and suggestions regarding the Challenge. [604] - Physical Properties Fluid Simulation Challenge I 9 AM, Sunday, November 7, 2004 Meeting Room 402 - Hilton Hotel [605] - Physical Properties Fluid Simulation Challenge II 1:30 PM, Sunday, November 7, 2004 Meeting Room 402 - Hilton Hotel The three areas of competition were: Problem 1: Vapor Pressure and Heat of Vaporization of Liquids Problem 2: Henry's Law Constant Problem 3: Heat of Mixing Hope to see you there, The Organizing Committee http://www.cstl.nist.gov/FluidSimulationChallenge/ From chemistry-request@ccl.net Wed Oct 20 23:30:30 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 i9L4UTwe012328 for ; Wed, 20 Oct 2004 23:30:29 -0500 Received: from localhost (localhost [127.0.0.1]) by osgood.cc.nd.edu (Switch-3.1.7/Switch-3.1.7) with ESMTP id i9L4ggqr013555; Wed, 20 Oct 2004 23:42:42 -0500 (EST) Received: from laptop.ccl.net (laptop.ccl.net [129.74.52.62]) by webmail.nd.edu (IMP) with HTTP for ; Wed, 20 Oct 2004 23:42:42 -0500 Message-ID: <1098333762.41773e4235c2e-.at.-webmail.nd.edu> Date: Wed, 20 Oct 2004 23:42:42 -0500 From: Jan K Labanowski To: chemistry-.at.-ccl.net Cc: mooney-.at.-icdd.com Subject: Courses on X-Ray Diffraction sponsored by Int. Ctr. for Diffraction Data MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="-MOQ1098333761b0b7e533ffe0b12e04ba702d1888d93d" User-Agent: Internet Messaging Program (IMP) 3.2.6 X-Originating-IP: 129.74.52.62 X-ND-MTA-Date: Wed, 20 Oct 2004 23:42:43 -0500 (EST) X-ND-Virus-Scan: engine v4.3.20; dat v4400 X-Spam-Status: No, hits=2.3 required=7.5 tests=HTML_60_70,HTML_FONTCOLOR_RED, HTML_FONT_FACE_BAD,HTML_MESSAGE,IMPRONONCABLE_1 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 message is in MIME format. ---MOQ1098333761b0b7e533ffe0b12e04ba702d1888d93d Content-Type: text/plain; charset=ISO-8859-2 Content-Transfer-Encoding: 8bit ----- Forwarded message from Leah Mooney ----- Date: Wed, 20 Oct 2004 14:59:34 -0400 From: Leah Mooney Reply-To: mooney-.at.-icdd.com Practical X-ray Fluorescence 2-6 May 2005 Sponsored by the International Centre for Diffraction Data Tel: 610-325-9814 Fax: 610-325-9823 E-mail: clinics-.at.-icdd.com Web: http://www.icdd.com/education Fundamentals of X-ray Powder Diffraction 6-10 June 2005 Sponsored by the International Centre for Diffraction Data Tel: 610-325-9814 Fax: 610-325-9823 E-mail: clinics-.at.-icdd.com Web: http://www.icdd.com/education Advanced Methods in X-ray Powder Diffraction 13-17 June 2005 Sponsored by the International Centre for Diffraction Data Tel: 610-325-9814 Fax: 610-325-9823 E-mail: clinics-.at.-icdd.com Web: http://www.icdd.com/education ********************************* Leah Mooney Education Coordinator ICDD 12 Campus Boulevard Newtown Square, PA 19073 U.S.A. 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---MOQ1098333761b0b7e533ffe0b12e04ba702d1888d93d-- From chemistry-request@ccl.net Thu Oct 21 01:38:15 2004 Received: from ozone.cs.vu.nl (ozone.cs.vu.nl [130.37.20.6]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i9L6cEwe016238 for ; Thu, 21 Oct 2004 01:38:15 -0500 Received: from [130.37.144.92] (diborane.chem.vu.nl [130.37.144.92]) by ozone.cs.vu.nl with esmtp (Smail #97) id m1CKWlM-00004lC; Thu, 21 Oct 2004 08:49 +0200 In-Reply-To: <20041019193418.33073.qmail.-at-.web53910.mail.yahoo.com> References: <20041019193418.33073.qmail.-at-.web53910.mail.yahoo.com> Mime-Version: 1.0 (Apple Message framework v619) Content-Type: text/plain; charset=ISO-8859-1; format=flowed Message-Id: <34ABE99E-232C-11D9-B124-000A95CEC3BA.-at-.few.vu.nl> Cc: "Comp. Chem. List" From: Stan van Gisbergen Subject: Re: CCL:Slater Basis Set Date: Thu, 21 Oct 2004 08:41:15 +0200 To: "A. Boufarik" X-Mailer: Apple Mail (2.619) X-Spam-Status: No, hits=0.0 required=7.5 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 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i9L6cFwe016242 Dear Dr. Boufarik, The Amsterdam Density Functional program (ADF, www.scm.com) uses Slater orbitals. Over the years, we have received several comments from ADF users around the world claiming that Slaters indeed have important practical advantages over Gaussians in several situations, including: - smaller Basis Set Superposition Errors (BSSEs), perhaps due to the correct cusp behavior. - better description of weak interactions, due to the better description of the tails in the outer region. - there are fewer Atomic Orbitals that give a sizable contribution to a particular Molecular Orbital. This makes it much easier to qualitatively understand the nature of the MO. These are some of the reasons why the difference between Slaters and Gaussians can indeed be of chemical relevance. Of course, some of the problems with Gaussian basis sets can either be corrected for or be circumvented by choosing a (much) larger basis set, which obviously has other drawbacks. Best regards, Stan van Gisbergen PS. A side remark: If one constructs an xc potential that exactly reproduces a Gaussian CI density, this xc potential will contain spurious oscillations and incorrect asymptotic behavior, unless additional constraints are imposed. This is a direct negative effect of the shape of the Gaussian orbitals. P.R.T. Schipper, O.V. Gritsenko & E.J. Baerends Kohn-Sham potentials corresponding to Slater and Gaussian basis set densities Theor. Chem. Acc. 98 (1997) 16-24 On Oct 19, 2004, at 9:34 PM, A. Boufarik wrote: > Greetings all, > > In the past years, I have seen many people trying to use Slater > orbitals as a basis set in the molecular calculations. Two main > arguments have been put forward: > [1] Theoretical: Shrodinger equation has solutions that are closer to > Slater orbitals that Gaussians. As an example, hydrogen functions all > have an exponential terms exp(-x) rather than exp(-x*x) > > [2] Practical : It has been argued that for CI calculations, we better > have a small basis set so to allow scan larger configurations spaces. > > Two questions are in my mind : > > [1] Have any of the Gaussian experts met a problem for which the basis > was too large to be handled during CI. Something that may support > statement (2) > > [2] From a chemistry point of view, is there any benefit for using > Slater orbitals. I mean by this, will there be any new > physics/chemistry that can only be detected by a Slater basis. Or, is > this just another way to do the same old chemistry with an extra > 10^(-15) accuracy instead of 10^(-13) with gaussians. > > Thanks for your comments and ideas, > > Boufarik Dr. S.J.A. van Gisbergen Chief Executive Officer Scientific Computing & Modelling NV Theoretical Chemistry, Vrije Universiteit De Boelelaan 1083 1081 HV Amsterdam The Netherlands T: +31-20-4447626 F: +31-20-4447629 vangisbergen.-at-.scm.com http://www.scm.com From chemistry-request@ccl.net Thu Oct 21 01:39:00 2004 Received: from web53903.mail.yahoo.com (web53903.mail.yahoo.com [206.190.36.126]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i9L6cxwe016281 for ; Thu, 21 Oct 2004 01:38:59 -0500 Message-ID: <20041021065113.14807.qmail[at]web53903.mail.yahoo.com> Received: from [129.128.136.71] by web53903.mail.yahoo.com via HTTP; Thu, 21 Oct 2004 02:51:13 EDT Date: Thu, 21 Oct 2004 02:51:13 -0400 (EDT) From: "A. Boufarik" Subject: LARGE Gaussian Basis Set To: "Comp. Chem. List" MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-525494599-1098341473=:13803" X-Spam-Status: No, hits=1.8 required=7.5 tests=FROM_ENDS_IN_NUMS,HTML_MESSAGE, MK_BAD_HTML_04 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --0-525494599-1098341473=:13803 Content-Type: text/plain; charset=us-ascii Hi all, Can anybody point me to where can I find a large basis set with polarization orbitals for hysdrogen. I have used a Huzinaga \-like basis [6s3p/4s3p] but the computed polarization is still not satisfactory. I wonder if anybody can suggest a basis set including D orbitals. Thansk a lot, Boufarik --------------------------------- Post your free ad now! Yahoo! Canada Personals --0-525494599-1098341473=:13803 Content-Type: text/html; charset=us-ascii

Hi all,

Can anybody point me to where can I find a large basis set with polarization orbitals for hysdrogen. I have used a Huzinaga \-like basis

[6s3p/4s3p] but the computed polarization is still not satisfactory. I wonder if anybody can suggest a basis set including D orbitals.

Thansk a lot,

Boufarik

Post your free ad now! Yahoo! Canada Personals
--0-525494599-1098341473=:13803-- From chemistry-request@ccl.net Thu Oct 21 09:46:30 2004 Received: from smtp4.server.rpi.edu (smtp4.server.rpi.edu [128.113.2.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i9LEkTe6013575 for ; Thu, 21 Oct 2004 09:46:29 -0500 Received: from rpi.edu (gryffindor-23.dynamic2.rpi.edu [128.113.133.64]) by smtp4.server.rpi.edu (8.13.0/8.13.0) with ESMTP id i9LEwaRO028473; Thu, 21 Oct 2004 10:58:42 -0400 Message-ID: <4177CE95.8070909[at]rpi.edu> Date: Thu, 21 Oct 2004 10:58:29 -0400 From: Curt Breneman User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.4) Gecko/20030624 Netscape/7.1 (ax) X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry[at]ccl.net, qsar_society[at]accelrys.com Subject: Reminder: CCG Excellence Award Fellowship applications due tomorrow! Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-CanItPRO-Stream: default X-RPI-SA-Score: undef - spam-scanning disabled X-Scanned-By: CanIt (www . canit . ca) X-Spam-Status: No, hits=0.0 required=7.5 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 Computational Chemist and Cheminformaticians... Just a reminder about the CCG Excellence Awards that are being offered by the Division of Computers in Chemistry and the Chemical Computing Group. If you are a graduate student thinking about presenting a talk or poster within a COMP symposium (or even a symposium co-sponsored by COMP), please do your best to E-mail materials to me ASAP for your best chance of winning this "all expenses paid" (up to $1,150 anway) trip to the San Diego ACS meeting! Here's the text from our earlier message: ============ Dear Computational Chemistry and Cheminfo folks, The ACS Division of Computers in Chemistry and the Chemical Computing Group (CCG) is pleased to invite applications for a new round of ten CCG Excellence Awards that provide travel funds and networking opportunities for graduate students presenting in a COMP (or COMP co-organized) symposium at the 229th National ACS Meeting in San Diego, California on March 13-17, 2005. In order to beconsidered for a CCG Excellence Award, you must send in the following items (electronic format is preferred) to me on or before Friday, October 23, 2004: 1) An extended (2-page) abstract of your oral or poster presentation. 2) A personal statement about your graduate and post-graduate career goals. 3) A letter of support from your dissertation advisor (this may be sent separately by the advisor). To qualify for an award, you must also submit your work to the ACS program prior to the COMP OASys abstract deadline of November 5, 2004. Winners will be announced after the OASys deadline date. See you in San Diego! Curt Breneman Professor of Chemistry and Chemical Biology RPI 110 8th St. Troy, NY 12180 brenec[at]rpi.edu From chemistry-request@ccl.net Thu Oct 21 10:18:40 2004 Received: from reformers.mr.itd.umich.edu (reformers.mr.itd.umich.edu [141.211.93.147]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i9LFIee6015299 for ; Thu, 21 Oct 2004 10:18:40 -0500 Received: from Garfield (pcp04776476pcs.howard01.md.comcast.net [68.55.105.17]) by reformers.mr.itd.umich.edu (smtp) with ESMTP id i9LFUoe6021869 for ; Thu, 21 Oct 2004 11:30:56 -0400 From: "Joslyn Kravitz" To: Subject: electron density in gaussian calculations Date: Thu, 21 Oct 2004 11:30:58 -0400 Message-ID: <000001c4b782$f837bb50$6500a8c0@Garfield> MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2627 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1441 Importance: Normal In-Reply-To: <2892.12.221.67.240.1076374395.squirrel|at|www.scs.uiuc.edu> Hello, Based on the output from a Gaussian geometry optimization calculation, or any subsequent one that can be done, is there a way to quantify how much electron density is on each atom in the molecule? What exactly is being analyzed in the Mulliken population analysis and density calculations? Thank you, Joslyn Kravitz From chemistry-request@ccl.net Thu Oct 21 05:11:28 2004 Received: from maya.uab.es (maya.uab.es [158.109.0.6]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i9LABPwe030551 for ; Thu, 21 Oct 2004 05:11:25 -0500 Received: from CONVERSION-DAEMON.maya.uab.es by maya.uab.es (PMDF V6.2-X20 #30859) id <0I5X00E01I4Z6K|at|maya.uab.es> for chemistry|at|ccl.net; Thu, 21 Oct 2004 11:53:29 +0200 (MEST) Received: from klingon.uab.es (klingon.uab.es [158.109.14.5]) by maya.uab.es (PMDF V6.2-X20 #30859) with ESMTP id <0I5X00ACTI4FPL|at|maya.uab.es> for chemistry|at|ccl.net; Thu, 21 Oct 2004 11:53:03 +0200 (MEST) Received: from astult.qf.uab.es ([158.109.14.42] helo=klingon.uab.es) by klingon.uab.es with esmtp (Exim 4.30) id 1CKZIK-0000Ba-Nv for chemistry|at|ccl.net; Thu, 21 Oct 2004 11:31:40 +0200 Date: Tue, 12 Oct 2004 22:57:30 +0200 From: Marc Noguera Julian Subject: Gaussian03 Rev C.02 - 64 bits To: chemistry|at|ccl.net Message-id: <416C453A.5050404|at|klingon.uab.es> MIME-version: 1.0 Content-type: text/plain; format=flowed; charset=us-ascii Content-transfer-encoding: 7BIT X-Accept-Language: en-us, en User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.6) Gecko/20040113 X-Spam-Status: No, hits=1.2 required=7.5 tests=DATE_IN_PAST_96_XX 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, I am trying to compile Gaussian03 Rev C.02 on a Dual Opteron machine. I am using Portland compiler for 64-bit systems on a Fedora Core 2 system. Fedora installed perfectly and works very well, being able to run gaussian 32 bit binaries. I am trying to compile Gaussian with the 64-bit compiler following Gaussian instructions, but it doesn't work. Does anyone have any experience with this? Thanks in advance Marc From chemistry-request@ccl.net Thu Oct 21 12:36:12 2004 Received: from mtaout-c.tc.umn.edu (mtaout-c.tc.umn.edu [160.94.128.21]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i9LHaBPq023602 for ; Thu, 21 Oct 2004 12:36:11 -0500 Received: from firefox.software.umn.edu (firefox.software.umn.edu [128.101.65.49]) by mtaout-c.tc.umn.edu with ESMTP; Thu, 21 Oct 2004 12:48:17 -0500 (CDT) X-Umn-Remote-Mta: [N] firefox.software.umn.edu [128.101.65.49] #+LO Received: (from nobody@localhost) by firefox.software.umn.edu (8.12.11/8.12.8) id i9LHmHhV008927; Thu, 21 Oct 2004 12:48:17 -0500 Message-Id: <200410211748.i9LHmHhV008927)at(firefox.software.umn.edu> Date: Thu, 21 Oct 2004 12:48:17 CDT From: Yan Zhao Subject: Re: CCL:Question: theoretical calculations of thermochemistry To: luo , CHEMISTRY)at(ccl.net MIME-Version: 1.0 Content-Type: TEXT/plain; CHARSET=US-ASCII X-Tick-Nemesis: American Maid X-remote-user-ip: 160.94.96.142 X-Spam-Status: No, hits=0.0 required=7.5 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 http://comp.chem.umn.edu/database/ On 21 Oct 2004, luo wrote: > Dear ALL: > > I am very interested in theoretical calculations of thermochemistry. I = > want to find some websites about this topic. But I have known good = > website of NIST only.=20 > > Who could help me to show more websites about theoretical calculations = > of thermochemistry?=20 > > Many thanks to you in advance. > > Yu-Ran Luo, Ph.D. > luo)at(marine.usf.edu > > > *************************************** Yan Zhao yzhao)at(chem.umn.edu Smith Hall 232 (612)-625-5311 Department of Chemistry University of Minnesota 207 Pleasant St SE Minneapolis, MN 55455 *************************************** From chemistry-request@ccl.net Thu Oct 21 12:21:08 2004 Received: from marge.uochb.cas.cz (marge.uochb.cas.cz [147.231.129.3]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i9LHL7Pq022592 for ; Thu, 21 Oct 2004 12:21:07 -0500 Received: by marge.uochb.cas.cz (Postfix, from userid 33) id 34DEC7AC3; Thu, 21 Oct 2004 19:33:23 +0200 (CEST) Received: from 62.24.92.191 (SquirrelMail authenticated user svozil); by marge.uochb.cas.cz with HTTP; Thu, 21 Oct 2004 19:33:23 +0200 (CEST) Message-ID: <33166.62.24.92.191.1098380003.squirrel..at..marge.uochb.cas.cz> Date: Thu, 21 Oct 2004 19:33:23 +0200 (CEST) Subject: How do you organize your *.pdf files? From: "Daniel Svozil" To: chemistry..at..ccl.net Reply-To: "Hi" User-Agent: SquirrelMail/1.4.3a X-Mailer: SquirrelMail/1.4.3a MIME-Version: 1.0 Content-Type: text/plain;charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Priority: 3 (Normal) Importance: Normal X-Spam-Status: No, hits=0.0 required=7.5 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 Hi all, though my posting is not only computational chemistry related, I think the discussion may be of general interest. I would like to know, if there is any free linux solution that would help in organizing pdf files with the articles downloaded from the web. I was looking for some application/script, but I didn't find anything. My question is, if it is possible to build a database (e.g. BibTeX) of pdf files (articles) that would include information such as title, author, journal, abstract etc. + path to the pdf file taken automatically from *.pdf. It seems to me, that thi is may be even not possible, as pdf format is not a markup language (as XML) and is not suitable to such a task. Maybe the best way would be to convert pdf to text (pdftotext in Linux), and than to parse the text file for the information. But such a script would be very complicated, as format of text data differs journal from journal, and many possibilities would have to be taken into account. I found one free application that makes life with my pdf mess much easier, it is called Quaneko (http://quaneko.sourceforge.net/), and it is available both for Linux and Windows. What Quaneko does it takes pdf by pdf, converts them to text files, and than indexes those, so one can easily query information using keywords and logical expressions. The possibility to view a text preview or full pdf by acroread is also avilable. Quaneko proved to be very useful and I rely on it quite heavy. And what is the way you organize your pdf articles in computer? Thanks in advance Dan P.S.; Please, post your responses to the list, so the whole community can benefit from them. -- Daniel Svozil, PhD Institute of Organic Chemistry and Biochemistry and Center for Complex Molecular Systems and Biomolecules http://www.molecular.cz/ Czech Republic phone: +420-220 410 312 From chemistry-request@ccl.net Thu Oct 21 14:57:17 2004 Received: from sandmail01.sd.accelrys.com (fw1.sd.accelrys.com [209.120.169.30]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i9LJvGe6032509; Thu, 21 Oct 2004 14:57:16 -0500 In-Reply-To: <33166.62.24.92.191.1098380003.squirrel..at..marge.uochb.cas.cz> To: "Daniel Svozil" Cc: chemistry..at..ccl.net, "Computational Chemistry List" Subject: Re: CCL:How do you organize your *.pdf files? MIME-Version: 1.0 X-Mailer: Lotus Notes Release 6.5.1 January 21, 2004 Message-ID: From: Jeff Nauss Date: Thu, 21 Oct 2004 13:09:31 -0700 X-MIMETrack: Serialize by Router on sandmail01/Server/Accelrys(Release 6.5.2|June 01, 2004) at 10/21/2004 01:09:35 PM, Serialize complete at 10/21/2004 01:09:35 PM Content-Type: text/plain; charset="US-ASCII" X-Spam-Status: No, hits=0.0 required=7.5 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 "Computational Chemistry List" wrote on 10/21/2004 10:33:23 AM: > And what is the way you organize your pdf articles in computer? For almost 15 years now, I have used a reference manager program. The program indexes each document by a reference number and has associated with it information such as author, title, keywords, etc. I then file each document by the index number, whether hard copy or electronic PDF. In the reference manager, I can search by keyword, abstract, author, date, and so forth. I get the index number and find the document in my file. I first used Papyrus which was cheap, easy to use, and pretty good. But it was not maintained well enough with updates to be useful with later versions of MS Word. I switched to EndNote a few years ago and have been quite happy with it. With EndNote I can download PubMed entries directly into the database. You can also download information from quite a few other databases as well. I suppose you could do something similar with a LINUX based database manager if not a reference manager program. Jeff -- Jeffrey L. Nauss, Ph.D. Lead Training Scientist Accelrys 9685 Scranton Road San Diego, CA 92121-1761 Phone: 858-799-5555 Fax: 858-799-5100 E-mail: jnauss..at..accelrys.com http://www.accelrys.com/training From chemistry-request@ccl.net Thu Oct 21 14:05:47 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 i9LJ5iPq030030 for ; Thu, 21 Oct 2004 14:05:44 -0500 Received: from hultin (hultin.chem.umanitoba.ca [130.179.48.60]) by electra.cc.umanitoba.ca (8.13.0/8.13.0) with SMTP id i9LJHxvN029009 for ; Thu, 21 Oct 2004 14:18:00 -0500 (CDT) From: "Phil Hultin" To: "Computational Chemistry List" Subject: RE: How do you organize your *.pdf files? Date: Thu, 21 Oct 2004 14:18:00 -0500 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.6604 (9.0.2911.0) X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1441 In-Reply-To: <33166.62.24.92.191.1098380003.squirrel=at=marge.uochb.cas.cz> Importance: Normal X-Spam-Status: No, hits=0.0 required=7.5 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 Daniel: Acrobat already provides a tool to do exactly what you are talking about. Note that I am using Windows, but I think the Linux versions of Acrobat would do the same thing. On the Tools... menu, select "Catalog...". This will create an index of all the words in all the pdf files in any specified set of directories, and save it as a file that can be searched and which is hyperlinked to the source file. I have not used this function before, but I just ran the routine to create an index of a bunch of PDFs of journal articles in three subdirectories on my disk. It indexed 131 pages from 25 documents in about 15-20 seconds. You then use the "Search" command from the "Edit" menu to find files containing text from within your index. The list of "hits" is hyperlinked and on clicking opens the paper in question in Acrobat. Dr. Philip G. Hultin Associate Professor of Chemistry University of Manitoba Winnipeg, MB, Canada R3T 2N2 (vox) 204-474-9814 (fax) 204-474-7608 mailto:hultin=at=cc.umanitoba.ca http://www.umanitoba.ca/chemistry/ From chemistry-request@ccl.net Thu Oct 21 14:37:28 2004 Received: from postfix4-1.free.fr (postfix4-1.free.fr [213.228.0.62]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i9LJbSPq031510 for ; Thu, 21 Oct 2004 14:37:28 -0500 Received: from [82.66.102.10] (michelet-4-82-66-102-10.fbx.proxad.net [82.66.102.10]) by postfix4-1.free.fr (Postfix) with ESMTP id 606F41F3F78; Thu, 21 Oct 2004 21:49:44 +0200 (CEST) In-Reply-To: <33166.62.24.92.191.1098380003.squirrel=at=marge.uochb.cas.cz> References: <33166.62.24.92.191.1098380003.squirrel=at=marge.uochb.cas.cz> Mime-Version: 1.0 (Apple Message framework v619) Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Message-Id: <5874BAC8-239A-11D9-B372-000A95AB5F10=at=llb.saclay.cea.fr> Content-Transfer-Encoding: 7bit Cc: CCL computational chemistry list (E-mail) From: hinsen=at=llb.saclay.cea.fr Subject: Re: CCL:How do you organize your *.pdf files? Date: Thu, 21 Oct 2004 21:49:40 +0200 To: "Daniel Svozil" X-Mailer: Apple Mail (2.619) On 21.10.2004, at 19:33, Daniel Svozil wrote: > I would like to know, if there is any free linux solution that would > help > in organizing pdf files with the articles downloaded from the web. I > was > looking for some application/script, but I didn't find anything. I use Leo (http://webpages.charter.net/edreamleo/front.html) for maintaining my personal bibliography database, with the help of a couple of Leo scripts that I wrote myself but that I'd be happy to share. The scripts import bibliography information from either Pubmed XML files or from ISI-format files (which I get from the Web of Knowledge). I only keep references to the PDF files in the database, they are not parsed or searched in any way. Searching the abstracts has proven to be enough for my needs. Once I have located an article, the reference to the PDF file makes it simple to open it. The main reasons for using Leo were 1) I already use it for other tasks (programming, project management) 2) Its scripting facilities are very powerful 3) It doesn't enforce any particular data layout Leo certainly has a higher learning curve than specialized bibliography software, but I found it well worth the effort, in particular if you use it for other tasks as well. > and than to parse the text file for the information. But such a script > would be very complicated, as format of text data differs journal from > journal, and many possibilities would have to be taken into account. Exactly. -- ------------------------------------------------------------------------ ------- Konrad Hinsen Laboratoire Leon Brillouin, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France Tel.: +33-1 69 08 79 25 Fax: +33-1 69 08 82 61 E-Mail: hinsen=at=llb.saclay.cea.fr ------------------------------------------------------------------------ ------- From chemistry-request@ccl.net Thu Oct 21 14:22:52 2004 Received: from postoffice10.mail.cornell.edu (postoffice10.mail.cornell.edu [132.236.56.14]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i9LJMpPq030752 for ; Thu, 21 Oct 2004 14:22:52 -0500 Received: from [192.168.1.2] (cesium.med.cornell.edu [140.251.33.58]) by postoffice10.mail.cornell.edu (8.12.10/8.12.6) with ESMTP id i9LJZ7p5018685; Thu, 21 Oct 2004 15:35:07 -0400 (EDT) In-Reply-To: <33166.62.24.92.191.1098380003.squirrel|at|marge.uochb.cas.cz> References: <33166.62.24.92.191.1098380003.squirrel|at|marge.uochb.cas.cz> Mime-Version: 1.0 (Apple Message framework v618) Content-Type: text/plain; charset=ISO-8859-1; format=flowed Message-Id: Cc: chemistry|at|ccl.net From: Guillaume Lamoureux Subject: Re: CCL:How do you organize your *.pdf files? Date: Thu, 21 Oct 2004 15:31:37 -0400 To: "Daniel Svozil" X-Mailer: Apple Mail (2.618) X-Spam-Status: No, hits=1.5 required=7.5 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 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i9LJMqPq030757 > I would like to know, if there is any free linux solution that would > help > in organizing pdf files with the articles downloaded from the web. I > was > looking for some application/script, but I didn't find anything. It's neither free nor for Linux, but DEVONthink (http://www.devon-technologies.com/products/devonthink/overview.php) is a great tool for organizing PDFs. It indexes the full content of the PDF file, and allows for a quick search. You can also browse the database by analogy, since it can show you articles semantically related to the one you're currently looking at. It's excellent at retrieving that paper you remember nothing about, except that it had this little idea about something. Guillaume Lamoureux Dipartement de physique, Universiti de Montrial From chemistry-request@ccl.net Thu Oct 21 13:16:01 2004 Received: from vscano-a.ucl.ac.uk (vscano-a.ucl.ac.uk [144.82.100.152]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i9LIG0Pq026938 for ; Thu, 21 Oct 2004 13:16:00 -0500 Received: from socrates-a.ucl.ac.uk ([144.82.100.160]) by vscano-a.ucl.ac.uk with esmtp (Exim 4.34) id 1CKhfW-0006RU-4h for chemistry{at}ccl.net; Thu, 21 Oct 2004 19:28:10 +0100 Received: (from uccatvm@localhost) by socrates-a.ucl.ac.uk (8.11.7p1+Sun/8.9.3) id i9LIS9i01860 for chemistry{at}ccl.net; Thu, 21 Oct 2004 19:28:09 +0100 (BST) Message-Id: <200410211828.i9LIS9i01860{at}socrates-a.ucl.ac.uk> Subject: Re: CCL:LARGE Gaussian Basis Set To: chemistry{at}ccl.net (CCL) Date: Thu, 21 Oct 2004 19:28:09 +0100 (BST) In-Reply-To: <20041021065113.14807.qmail{at}web53903.mail.yahoo.com> from "A. Boufarik" at Oct 21, 2004 02:51:13 AM From: Tanja van Mourik X-Mailer: ELM [version 2.5 PL3] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-UCL-MailScanner-Information: Please contact the UCL Helpdesk, helpdesk{at}ucl.ac.uk for more information X-UCL-MailScanner: Found to be clean X-UCL-MailScanner-SpamCheck: X-MailScanner-From: uccatvm{at}ucl.ac.uk X-Spam-Status: No, hits=3.0 required=7.5 tests=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 Hi Boufarik, > > Can anybody point me to where can I find a large basis set with polarization orbitals for hysdrogen. I have used a Huzinaga \-like basis > [6s3p/4s3p] but the computed polarization is still not satisfactory. I wonder if anybody can suggest a basis set including D orbitals. Have you looked at the EMSL basi set library? See: http://www.emsl.pnl.gov/forms/basisform.html You could for example have a look at the correlation consistent basis sets, (aug)-cc-(wC)VnZ. From triple zeta (n=T) these contain d functions on hydrogens. Best wishes, Tanja -- ================================================================= Tanja van Mourik Royal Society University Research Fellow Chemistry Department University College London phone: +44 (0)20-7679-4663 20 Gordon Street e-mail: work: T.vanMourik{at}ucl.ac.uk London WC1H 0AJ, UK home: tanja{at}van-mourik.me.uk http://www.chem.ucl.ac.uk/people/vanmourik/index.html ================================================================= From chemistry-request@ccl.net Thu Oct 21 14:25:05 2004 Received: from smtp2.server.rpi.edu (smtp2.server.rpi.edu [128.113.2.2]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i9LJP4Pq030934 for ; Thu, 21 Oct 2004 14:25:04 -0500 Received: from GILGAMESH (allium.net.rpi.edu [128.113.26.234]) by smtp2.server.rpi.edu (8.13.0/8.13.0) with ESMTP id i9LJbKUL008124 for ; Thu, 21 Oct 2004 15:37:20 -0400 Message-Id: <200410211937.i9LJbKUL008124{at}smtp2.server.rpi.edu> From: "Matthew Sundling" To: Subject: RE: How do you organize your *.pdf files? Date: Thu, 21 Oct 2004 15:37:16 -0400 MIME-Version: 1.0 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: 7bit X-Mailer: Microsoft Office Outlook, Build 11.0.5510 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1441 In-Reply-To: <33166.62.24.92.191.1098380003.squirrel{at}marge.uochb.cas.cz> Thread-Index: AcS3pA8n8ZU0xsvaTOyL3Ig5aOAWUQAAFL5A X-CanItPRO-Stream: default X-RPI-SA-Score: undef - spam-scanning disabled X-Scanned-By: CanIt (www . canit . ca) Hello, A similar program to Quaneko is dtSearch. I've been using it for a year, and been happy. It also uses Adobe reader to view the files when 'clicked' on. My $0.02. Matt S. -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request{at}ccl.net] On Behalf Of Daniel Svozil Sent: Thursday, October 21, 2004 1:33 PM To: chemistry{at}ccl.net Subject: CCL:How do you organize your *.pdf files? Hi all, though my posting is not only computational chemistry related, I think the discussion may be of general interest. I would like to know, if there is any free linux solution that would help in organizing pdf files with the articles downloaded from the web. I was looking for some application/script, but I didn't find anything. My question is, if it is possible to build a database (e.g. BibTeX) of pdf files (articles) that would include information such as title, author, journal, abstract etc. + path to the pdf file taken automatically from *.pdf. It seems to me, that thi is may be even not possible, as pdf format is not a markup language (as XML) and is not suitable to such a task. Maybe the best way would be to convert pdf to text (pdftotext in Linux), and than to parse the text file for the information. But such a script would be very complicated, as format of text data differs journal from journal, and many possibilities would have to be taken into account. I found one free application that makes life with my pdf mess much easier, it is called Quaneko (http://quaneko.sourceforge.net/), and it is available both for Linux and Windows. What Quaneko does it takes pdf by pdf, converts them to text files, and than indexes those, so one can easily query information using keywords and logical expressions. The possibility to view a text preview or full pdf by acroread is also avilable. Quaneko proved to be very useful and I rely on it quite heavy. And what is the way you organize your pdf articles in computer? Thanks in advance Dan P.S.; Please, post your responses to the list, so the whole community can benefit from them. -- Daniel Svozil, PhD Institute of Organic Chemistry and Biochemistry and Center for Complex Molecular Systems and Biomolecules http://www.molecular.cz/ Czech Republic phone: +420-220 410 312 -= This is automatically added to each message by the mailing script =- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line and send your message to: CHEMISTRY{at}ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST{at}ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your mail is bouncing from CCL.NET domain send it to the maintainer: Jan Labanowski, jlabanow{at}nd.edu (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ --- Incoming mail is certified Virus Free. Checked by AVG anti-virus system (http://www.grisoft.com). Version: 6.0.775 / Virus Database: 522 - Release Date: 10/8/2004 --- Outgoing mail is certified Virus Free. Checked by AVG anti-virus system (http://www.grisoft.com). Version: 6.0.775 / Virus Database: 522 - Release Date: 10/8/2004 From chemistry-request@ccl.net Thu Oct 21 15:35:46 2004 Received: from smtp.ucla.edu (smtp.ucla.edu [169.232.46.136]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i9LKZie6001756 for ; Thu, 21 Oct 2004 15:35:45 -0500 Received: from mail.ucla.edu (mail.ucla.edu [169.232.46.135]) by smtp.ucla.edu (8.13.1/8.13.1) with ESMTP id i9LKm0AX006299; Thu, 21 Oct 2004 13:48:01 -0700 Received: from [192.168.1.121] (TriangleFraternity.demarc.cogentco.com [66.28.31.218] (may be forged)) (authenticated bits=0) by mail.ucla.edu (8.13.1/8.13.1) with ESMTP id i9LKlwJe000710; Thu, 21 Oct 2004 13:47:58 -0700 Message-ID: <4178205A.6070300_at_ucla.edu> Date: Thu, 21 Oct 2004 13:47:22 -0700 From: Douglas Sievers User-Agent: Mozilla Thunderbird 0.8 (X11/20040913) X-Accept-Language: en-us, en MIME-Version: 1.0 To: Daniel Svozil CC: chemistry_at_ccl.net Subject: Re: How do you organize your *.pdf files? References: <33166.62.24.92.191.1098380003.squirrel_at_marge.uochb.cas.cz> In-Reply-To: <33166.62.24.92.191.1098380003.squirrel_at_marge.uochb.cas.cz> Content-Type: text/plain; charset=iso-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Probable-Spam: no X-Spam-Hits: 0 X-Scanned-By: smtp.ucla.edu X-Spam-Status: No, hits=0.0 required=7.5 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 Hi Daniel, I think in theory you could use DOI's, short for Digital Object Identifier. At www.doi.org, there is a DOI resolver, that you can enter a DOI and it will direct you to that document. The pdf's could be saved with the DOI in the file name. Supposedly, you can do a "reverse DOI lookup" to obtain the metadata, which is in XML format, and that could be used to create a local database. Unfortunately, the only reverse lookup engine that I could find is at www.CrossRef.org, which appears to require a subscription. There may be alternatives... but I don't have the time right now to search. Just thought I would throw the idea out there no less. Doug Daniel Svozil wrote: >Hi all, > >though my posting is not only computational chemistry related, I think the >discussion may be of general interest. > >I would like to know, if there is any free linux solution that would help >in organizing pdf files with the articles downloaded from the web. I was >looking for some application/script, but I didn't find anything. > >My question is, if it is possible to build a database (e.g. BibTeX) of pdf >files (articles) that would include information such as title, author, >journal, abstract etc. + path to the pdf file taken automatically from >*.pdf. It seems to me, that thi is may be even not possible, as pdf format >is not a markup language (as XML) and is not suitable to such a task. >Maybe the best way would be to convert pdf to text (pdftotext in Linux), >and than to parse the text file for the information. But such a script >would be very complicated, as format of text data differs journal from >journal, and many possibilities would have to be taken into account. > >I found one free application that makes life with my pdf mess much easier, >it is called Quaneko (http://quaneko.sourceforge.net/), and it is >available both for Linux and Windows. What Quaneko does it takes pdf by >pdf, converts them to text files, and than indexes those, so one can >easily query information using keywords and logical expressions. The >possibility to view a text preview or full pdf by acroread is also >avilable. Quaneko proved to be very useful and I rely on it quite heavy. > >And what is the way you organize your pdf articles in computer? > >Thanks in advance > Dan > > P.S.; Please, post your responses to the list, so the whole community >can benefit from them. > > > >