From chemistry-request@server.ccl.net Mon Mar 13 17:06:03 2000 Received: from dfw7-1.relay.mail.uu.net (dfw7-1.relay.mail.uu.net [199.171.54.106]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA16181 for ; Mon, 13 Mar 2000 17:06:02 -0500 Received: from wodc7-1.uucp-gw.mail.uu.net by dfw7sosrv11.alter.net with ESMTP (peer crosschecked as: wodc7-1.uucp-gw.mail.uu.net [199.171.54.178]) id QQigjw13882 for ; Mon, 13 Mar 2000 22:06:01 GMT Received: from wodc7uc0.ffx.ops.us.uu.net by wodc7ug0.ffx.ops.us.uu.net with SMTP (peer crosschecked as: wodc7-2.uucp.uu.net [199.171.54.180]) id QQigjw28457 for ; Mon, 13 Mar 2000 22:06:01 GMT Message-Id: Received: from m10.UUCP by wodc7uc0.ffx.ops.us.uu.net with UUCP/RMAIL ; Mon, 13 Mar 2000 22:06:01 +0000 Received: by m10.gaussian.com; Mon, 13 Mar 2000 16:37:32 -0500 Received: by mousse.gaussian.com; Mon, 13 Mar 2000 15:22:59 -0500 From: gaussian.com!moses@gaussian.com (David Moses) Subject: Gaussian Workshops To: chemistry@ccl.net Date: Mon, 13 Mar 2000 15:22:59 -0500 (EST) X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Gaussian, Inc. is pleased to announce two upcoming workshops: INTRODUCTION TO GAUSSIAN: THEORY AND PRACTICE SPAIN, in conjunction with CESCA. Date: September 12-15, 2000 Location: CESCA- Centre de Supercomputacia Barcelona Edifici Nexus Gran Capita, 2-4 Barcelona, SPAIN JAPAN, in conjunction with COMPAQ Date: October 3-6, 2000 Location: Compaq JAPAN Headquarters Tennonz Higashi Shinagwa, Shinagawa-ku Tokyo JAPAN "Introduction to Gaussian: Theory and Practice." will be presented by representatives of Gaussian, Inc. The workshops will cover the full range of methods available in the Gaussian 98 package with emphasis on new methods and features which make Gaussian 98 applicable to an ever widening spectrum of research applications. The workshop is structured to provide an introduction to electronic structure theory as well as a hands-on review for researchers active in the field. The workshop is open to researchers at all levels of academic, government and industrial research. Preliminary Topic List: Independent Particle Methods Model Chemistries: A Framework for Understanding Electronic Structure Theory Results Using ONIOM MCSCF Methods and Applications Geometry Optimization Techniques Electron Correlation Methods Density Functional Theory Methods Methods for Excited Electronic States Interpretation of Gaussian Results Prediction of Molecular Properties Solvent Effects via Electronic Structure Methods Estimating Resource Requirements There will be hands-on sessions each day between the morning and afternoon lectures. Additional hands-on sessions will be available until the building closes. Workshop participants will be provided with use of a workstations to complete exercises, experiment and/or conduct short research topics. The GaussView user interface will be used to perform visualization of results and to facilitate calculation setup. Each workshop participant will also be provided a copy of the lecture notes, a copy of Exploring Chemistry with Electronic Structure Methods, 2nd Edition, and a Gaussian 98 User's Reference. For an Application please contact (Please specify which workshop): Workshop Coordinator Gaussian, Inc. Carnegie Office Park, Bldg. 6 Pittsburgh, PA 15106 Additional information can be obtained from: Telephone: 412 279 6700 Fax: 412 279 2118 email: info@gaussian.com COST: $350.00 per person. Attendees will be responsible for meals and lodging. Hotel Accommodations: A list of hotel accommodations in the vicinity of the the workshop location will be made available to all registrants. Hotel accommodations will be the responsibility of each participant. Meals: Meals will be the responsibility of each participant. DEADLINES: Receipt of Registration Materials along with the registration fee must be received by: September 1, 2000 for the SPAIN Workshop and September 15, 200 for the JAPAN workshop. **************************************************************************** This notice is sent without warranty of any kind, expressed or implied by Gaussian Inc., CESCA or COMPAQ. Gaussian is a registered trademark of Gaussian, Inc. *------------------------*------------------------*-----------------------* | David J. Moses, Ph.D. | Carnegie Office Park | info@gaussian.com | | Vice President, C.O.O. | Building Six | 412-279-6700 (Voice) | | Gaussian, Inc. | Pittsburgh, PA 15106 | 412-279-2118 (FAX) | *------------------------*------------------------*-----------------------* | Be sure to visit our Website at http://www.gaussian.com | *------------------------*------------------------*-----------------------* From chemistry-request@server.ccl.net Mon Mar 13 17:28:40 2000 Received: from lrz.uni-muenchen.de (lsanca1-ar99-078-106.biz.dsl.gtei.net [4.3.78.106]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA16275 for ; Mon, 13 Mar 2000 17:28:40 -0500 Received: (from eugene.leitl@localhost) by lrz.uni-muenchen.de (8.8.8/8.8.8) id OAA21937 for ; Mon, 13 Mar 2000 14:26:36 -0800 Resent-From: Eugene Leitl Resent-Message-ID: <14541.27410.249338.737794@lrz.uni-muenchen.de> Resent-Date: Mon, 13 Mar 2000 14:26:26 -0800 (PST) Resent-To: Message-Id: X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 8bit Precedence: bulk From: To: Subject: >2 GByte patch for ext2 (fwd) Date: Mon, 13 Mar 100 21:44:05 +0300 (MSK) From: Mikhail Kuzminsky To: beowulf@beowulf.gsfc.nasa.gov According to Eugene Leitl > From owner-beowulf@beowulf.org Fri Mar 10 04:49:08 2000 > From: Eugene Leitl > Date: Thu, 9 Mar 2000 14:14:23 -0800 (PST) > To: > Subject: >2 GByte patch for ext2 > Sender: owner-beowulf@beowulf.org > > Sorry for such a banal question, but I've tried to find the ext2 patch > which allows >2 GByte files, so far in vain. (It is a big problem in > computational chemistry with QM packages like Gaussian and GAMESS). I > thought there was a search engine for the Beowulf list, but I wasn't > able to find it, either (it isn't linked from the Beowulf site?). > I think that ext2 patch isn't enough for work w/large files "from" G98 or GAMESS. The reason is that you need to use in the program the new system calls suppoted by patch instead of usual. But in the case of GAMESS you have Fortran I/O which runtime library don't use new system calls. In the case of G98 you will need to change NTRAN routines source to use new system calls. I may be wrong because I'm not using this patch really (the reason is practically - that I said above), but I'll be happy if I'm incorrect :-) ! PS. May be you may try to split files in G98 (%RWF etc) between different filesystems ? Mikhail Kuzminsky Zelinsky Institute of Organic Chemistrty Moscow ------------------------------------------------------------------- To unsubscribe send a message body containing "unsubscribe" to beowulf-request@beowulf.org From chemistry-request@server.ccl.net Mon Mar 13 20:20:45 2000 Received: from lrz.uni-muenchen.de (lsanca1-ar99-078-106.biz.dsl.gtei.net [4.3.78.106]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA16967 for ; Mon, 13 Mar 2000 20:20:45 -0500 Received: (from eugene.leitl@localhost) by lrz.uni-muenchen.de (8.8.8/8.8.8) id RAA22939 for ; Mon, 13 Mar 2000 17:18:39 -0800 Resent-From: Eugene Leitl Resent-Message-ID: <14541.37742.561095.20765@lrz.uni-muenchen.de> Resent-Date: Mon, 13 Mar 2000 17:18:38 -0800 (PST) Resent-To: Reply-To: 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 8.5, Build 4.71.2173.0 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Precedence: bulk From: To: Subject: FW: >2 GByte patch for ext2 (fwd) Date: Mon, 13 Mar 2000 16:30:33 -0500 From: "Greg Lindahl" To: > I think that ext2 patch isn't enough for work w/large files > "from" G98 or GAMESS. The reason is that you need to use in the > program the new system calls suppoted by patch instead of usual. Um, I guess you're assuming that you're using x86? As mentioned before a few times, 64-bit Linux ports run these programs fine, once you work around the 32-bitisms in GAMESS. Actually, the new linker supports -taso, which is about all you need. > But in the case of GAMESS you have Fortran I/O which runtime library > don't use new system calls. So if you're using an x86, it shouldn't be that hard to build a Fortran I/O library that always uses the other calls, but then you still have to convince the library that the record sizes should be 8 bytes, not 4. That's a #define somewhere. -- g ------------------------------------------------------------------- To unsubscribe send a message body containing "unsubscribe" to beowulf-request@beowulf.org From chemistry-request@server.ccl.net Tue Mar 14 02:51:46 2000 Received: from www0c.netaddress.usa.net (www0c.netaddress.usa.net [204.68.24.32]) by server.ccl.net (8.8.7/8.8.7) with SMTP id CAA18607 for ; Tue, 14 Mar 2000 02:51:46 -0500 Received: (qmail 28906 invoked by uid 60001); 14 Mar 2000 07:48:05 -0000 Message-ID: <20000314074805.28905.qmail@www0c.netaddress.usa.net> Received: from 204.68.24.32 by www0c for [196.1.114.10] via web-mailer(M3.3.1.96) on Tue Mar 14 07:48:05 GMT 2000 Date: 13 Mar 00 23:48:05 PST From: abcdefg hijklm To: CHEMISTRY@server.ccl.net Subject: A small request. Read-Receipt: femtohertz@netscape.net Disposition-Notification-To: femtohertz@netscape.net X-Mailer: USANET web-mailer (M3.3.1.96) Mime-Version: 1.0 Content-Type: text/html; charset=us-ascii; charset=US-ASCII Content-Transfer-Encoding: quoted-printable Sir, we are a group of students studying at the Dept. of chemistry,Pune University ; India. We want to run a PPP PUBLIC DOMAIN PROGRAM for the following systems :ethylene,benzene & butadiene. We hereby request you to mail the program (or some relevant information regarding the same) to us at the following address...... femtohertz@netscape.net Thanking you. Yours sincerely, Nikhil A. Gokhale. (India)

Get your own FREE, personal Netscape WebMail account today at http://webmail.netscape.com. From chemistry-request@server.ccl.net Tue Mar 14 03:57:13 2000 Received: from classic.chem.msu.su (classic.chem.msu.su [158.250.32.143]) by server.ccl.net (8.8.7/8.8.7) with SMTP id DAA18896 for ; Tue, 14 Mar 2000 03:57:08 -0500 From: gran@classic.chem.msu.su Received: from localhost ( [127.0.0.1] ) by classic.chem.msu.su (Hethmon Brothers Smtpd) ; Tue, 14 Mar 2000 11:50:09 MSK-3MSD-4,3,5,0,7200,10,5,0,10800 Message-Id: <200002141150.0925886.7@classic.chem.msu.su> Date: Tue, 14 Mar 2000 11:47:41 +0300 To: chemistry@ccl.net In-Reply-To: Subject: Re: CCL:>2 GByte patch for ext2 X-Mailer: MR/2 Internet Cruiser Edition for OS/2 v1.60 b60 (Unregistered) The PC GAMESS v. 5.5 (and newer) is capable to support large files on ext2 volumes via transparent splitting of large files. Best regards, Alex Granovsky >According to Eugene Leitl >> From owner-beowulf@beowulf.org Fri Mar 10 04:49:08 2000 >> From: Eugene Leitl >> Date: Thu, 9 Mar 2000 14:14:23 -0800 (PST) >> To: >> Subject: >2 GByte patch for ext2 >> Sender: owner-beowulf@beowulf.org >> >> Sorry for such a banal question, but I've tried to find the ext2 patch >> which allows >2 GByte files, so far in vain. (It is a big problem in >> computational chemistry with QM packages like Gaussian and GAMESS). I >> thought there was a search engine for the Beowulf list, but I wasn't >> able to find it, either (it isn't linked from the Beowulf site?). >> > I think that ext2 patch isn't enough for work w/large files >"from" G98 or GAMESS. The reason is that you need to use in the >program the new system calls suppoted by patch instead of usual. >But in the case of GAMESS you have Fortran I/O which runtime library don't use >new system calls. In the case of G98 you will need >to change NTRAN routines source to use new system calls. > I may be wrong because I'm not using this patch really >(the reason is practically - that I said above), but I'll >be happy if I'm incorrect :-) ! >PS. May be you may try to split files in G98 (%RWF etc) between >different filesystems ? >Mikhail Kuzminsky >Zelinsky Institute of Organic Chemistrty >Moscow From chemistry-request@server.ccl.net Tue Mar 14 04:27:05 2000 Received: from analyt471-2.chem.msu.ru (analyt471-2.chem.msu.ru [195.208.209.169] (may be forged)) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA19214 for ; Tue, 14 Mar 2000 04:27:02 -0500 Received: from localhost (michael@localhost) by analyt471-2.chem.msu.ru (8.9.3/8.8.7) with ESMTP id NAA00782 for ; Tue, 14 Mar 2000 13:24:50 +0300 Date: Tue, 14 Mar 2000 13:24:50 +0300 (MSK) From: "Michael G. Razumov" To: CCL Subject: MM parameters for phosphorus(V) halides Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, everybody! Does anybody know where to take from MM parameters for calculating P(V) halides (with mixed P(V) surrounding, e.g. PF3Cl2) and, if possible, the (ED, IR or MW) structures of these molecules. Thanks in advance. ------------------------------------------------------------- Michael G. Razumov, Postgraduate Student of Kurnakov Institute of General and Inorganic Chemistry and Lomonosov Moscow State University E-Mail: michraz@analyt.chem.msu.ru michael@analyt.chem.msu.su ICQ UIN: 25169010 From chemistry-request@server.ccl.net Tue Mar 14 11:15:12 2000 Received: from kdmail.netcologne.de (kdmail.netcologne.de [194.8.194.80]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA21751 for ; Tue, 14 Mar 2000 11:15:11 -0500 Received: from mail.icd-gmbh.de ([194.8.221.108]) by kdmail.netcologne.de (Post.Office MTA v3.5.3 release 223 ID# 127-61375U6500L550S0V35) with SMTP id de for ; Tue, 14 Mar 2000 17:14:54 +0100 Received: from Unknown Host [192.6.2.62] by benjamin-gw.icd-gmbh.de at 14.03.00 17:13:51 (MET) Message-ID: <004e01bf8dd0$8c8b5a00$3e0206c0@pc62> From: "Ansgar Schuffenhauer" To: Subject: converting of chemical structures into graphical images Date: Tue, 14 Mar 2000 17:15:40 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 I am looking for tools to convert chemical structure files (preferably MDL molfiles or Chemical markup Language) into graphic files. As an output format I am considering a) vector graphics [Windows Metafile (WMF) or perhaps the new Stylable Vector Graphics format (SVG)] b) bitmaps (e.g JPEG) I am aware that chemical structure drawing programmes like ISIS/Draw are able to do this interactively, but I would rather prefer having a tool which can be started from the command line or within a script. It would also be nice having the source code available. The aim is not to generate rendered images, but simple structure drawings. Any information on such conversion tools would be appreciated. I'll summarise the answers Thanks Ansgar ------------------------------- Ansgar Schuffenhauer aschuffenhauer@icd-gmbh.de ------------------------------- From chemistry-request@server.ccl.net Tue Mar 14 11:36:25 2000 Received: from wn1.sci.kun.nl (wn1.sci.kun.nl [131.174.8.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA21882 for ; Tue, 14 Mar 2000 11:36:24 -0500 Received: from studs3.sci.kun.nl by wn1.sci.kun.nl via studs3.sci.kun.nl [131.174.124.4] with ESMTP for id RAA16693 (8.8.8/3.29); Tue, 14 Mar 2000 17:36:11 +0100 (MET) From: "E.L. Willighagen" Received: by studs3.sci.kun.nl via egonw@localhost for CHEMISTRY@ccl.net id RAA07229 (8.8.8/3.1); Tue, 14 Mar 2000 17:36:10 +0100 (MET) Date: Tue, 14 Mar 2000 17:36:10 +0100 (MET) Message-Id: <200003141636.RAA07229@studs3.sci.kun.nl> To: CHEMISTRY@ccl.net Subject: re: converting of chemical structures into graphical images > I am looking for tools to convert chemical structure files (preferably MDL > molfiles or Chemical markup Language) into graphic files. As an output format: > SVG, bitmap (JPEG) > It would also be nice havingthe source code available. If you are willing to do some programming: have a look at these two programs: JMol (3D) or JChemPaint (2D). Both are opensource, written in Java, and have CML import filter (one has MDL as well i think) and can export bitmaps... Just pick the appropriate classes and glue them together... the addresses are: http://www.openscience.org/jmol/ and http://www.ice.mpg.de/~stein/projects/JChemPaint/ Egon From chemistry-request@server.ccl.net Tue Mar 14 13:47:54 2000 Received: from shiva.hunter.cuny.edu (shiva.hunter.cuny.edu [146.95.128.96]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA22494 for ; Tue, 14 Mar 2000 13:47:54 -0500 Received: from shiva (shiva [146.95.128.96]) by shiva.hunter.cuny.edu (8.9.3/8.9.3) with ESMTP id NAA19932; Tue, 14 Mar 2000 13:54:01 -0500 (EST) Date: Tue, 14 Mar 2000 13:54:00 -0500 (EST) From: AM To: J.Baell@bioresi.com.au cc: chemistry@ccl.net Subject: RE: minimization of a crystal structure Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Jonathan, If you optimize starting form experimental structure, almost any force field will work. Even solid spheres. If you search for the lowest among many local minima, it's another story. For an example, see the recent paper from Sheraga's group (JACS, 2000, 122, p.907). They found AMBER FF to work a little better then DREIDING. I see no reason to introduce dielectric constant in description where all molecules are treated explicitly (like crystal). If you have any arguments in favor of it, I'd be happy to learn. Use of the distance-dependent dielectric constant may be appropriate to describe two solute molecules if the solvent between them is more structured, than in the bulk (like water). But there is no disordered water in crystals of small molecules! Regards, Artem Masunov Jonathan Baell wrote: > Does anyone one have any references on the use of MMF94 ( with modified > amide parameters for static minimizations, a la MMF94s as implemented in > sybyl 6.5) for minimization of a crystal structure of a small molecule > such as, for example, a substituted benzanilide? > This is especially in regard to choice of dielectric function (e.g. > distance-dependent with base diel. of 4?) to best approximate the > solid-state electrostatic environment. The latest review on crystal structure minimization can be found in the long introduction to the paper from From chemistry-request@server.ccl.net Tue Mar 14 14:21:55 2000 Received: from ns.mnc.md (root@[212.0.192.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA22696 for ; Tue, 14 Mar 2000 14:21:40 -0500 Received: from 212.0.193.107 ([212.0.193.107]) by ns.mnc.md (8.8.7/8.8.7) with ESMTP id VAA02387 for ; Tue, 14 Mar 2000 21:21:29 +0200 Date: Tue, 14 Mar 2000 21:25:25 +0200 From: Mike Peleah X-Mailer: The Bat! (v1.41) Reply-To: Mike Peleah X-Priority: 3 (Normal) Message-ID: <2892.000314@mnc.md> To: chemistry@ccl.net Subject: rootines to translate/rotate/... Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit +======================---------------- --- -- - - - - . | Dear chemistry, : . I need source codes of routines (C/C++ is preferable) for rotation / translation / mirroring molecules. Could anybody know where could I download it? Best regards, Mike mailto:mike@mnc.md . : | . - - - - -- --- ----------------======================+ From chemistry-request@server.ccl.net Tue Mar 14 14:16:12 2000 Received: from ntsvexch.albmolecular.com (mail.albmolecular.com [205.247.153.6]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA22667 for ; Tue, 14 Mar 2000 14:16:12 -0500 Received: by Ntsvexch with Internet Mail Service (5.5.2650.21) id ; Tue, 14 Mar 2000 14:14:58 -0500 Message-ID: <80F79FF3ECD6D1119D9000805FCC602A82CD17@Ntsvexch> From: "Andruski, Stephen W." To: "'CCL'" Subject: Re:converting of chemical structures Date: Tue, 14 Mar 2000 14:14:57 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain Ansgar Schuffenhauer wrote: ******************************* I am looking for tools to convert chemical structure files (preferably MDL molfiles or Chemical markup Language) into graphic files. As an output format..... ****************************** Answer: There was a product called Consystant that ran on the Windows platform put out by a company called ExoGraphics. I believe it could take MDL mol files and turn them into .wmf files. It could also do batch conversions. A quick Web search turned up several things. First it appears that Consystant was included with ISIS 2.0 from MDL. Also the scientific software developer list at: http://www.sisweb.com/software/softdlnk.htm has this entry for ExoGraphics. ExoGraphics (973) 728-0188 exographics@compuserve.com and the site: http://www.sgi.com/Products/appsdirectory.dir/SolutionIXComputational_Chemis try.html has this listing: ConSystant ConSystant is a utility that allows the user to interconvert chemical structure files. ConSystant allows users of software packages that manipulate chemical structures (such as molecular modeling software, chemical databases, and 2-D structure drawing) to exchange data. The current version 3.0 supports many different chemical data interchange file formats as well as several simple graphical outputs. Carol Gallmann President ExoGraphics 144 Pinecliff Lake Drive West Milford, NJ 07480 USA 201-728-0188 201-728-0735 (fax) exographics@compuserve.com Hope that this program is still available and is of some help with your problem. Steve Andruski > *********************************** > Dr. Stephen W. Andruski > Senior Research Chemist II > Albany Molecular Research, Inc. > 21 Corporate Circle > Albany, New York 12203 USA > Tel. (518) 464-0279, Ext. 2414 > Fax (518) 464-0289 > E-mail: stephena@albmolecular.com > http://www.albmolecular.com > ************************************ > > From chemistry-request@server.ccl.net Tue Mar 14 17:00:23 2000 Received: from mail.chem.tamu.edu (mail.chem.tamu.edu [165.91.176.8]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA23545 for ; Tue, 14 Mar 2000 17:00:23 -0500 Received: from mail.chem.tamu.edu ([165.91.176.197]) by mail.chem.tamu.edu (Post.Office MTA v3.5.3 release 223 ID# 0-64333U1000L100S0V35) with ESMTP id edu for ; Tue, 14 Mar 2000 16:08:46 -0600 Sender: fan@mail.chem.tamu.edu (Huajun Fan) Message-ID: <38CEB5F3.EBB975B5@mail.chem.tamu.edu> Date: Tue, 14 Mar 2000 15:58:11 -0600 From: Huajun Fan X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP28) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: call in Fortran code Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers I wonder if the fortran code can call a excutable file, instead of a source code. If so, how can I do it? Any advice will be highly appreciated. Thanks in advance. huajun From chemistry-request@server.ccl.net Tue Mar 14 18:10:48 2000 Received: from ice.lanl.gov (ice.lanl.gov [128.165.22.6]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA23887 for ; Tue, 14 Mar 2000 18:10:47 -0500 Received: from localhost (localhost [[UNIX: localhost]]) by ice.lanl.gov (8.9.3/8.9.3) id QAA15427; Tue, 14 Mar 2000 16:10:43 -0700 From: Matt Challacombe Reply-To: MChalla@T12.LANL.Gov Organization: Group T-12, Theoretical Chemistry and Molecular Physics To: Huajun Fan , CHEMISTRY@ccl.net Subject: Re: CCL:call in Fortran code Date: Tue, 14 Mar 2000 16:10:28 -0700 X-Mailer: KMail [version 1.0.28] Content-Type: text/plain References: <38CEB5F3.EBB975B5@mail.chem.tamu.edu> In-Reply-To: <38CEB5F3.EBB975B5@mail.chem.tamu.edu> MIME-Version: 1.0 Message-Id: <00031416104300.15422@ice> Content-Transfer-Encoding: 8bit Dear Huajun, The easiest way to do this is to use the SYSTEM intrinsic: CALL SYSTEM('/usr/bin/joe_exec') but this is not entirely satisfactory since you don't have return control, and you can get rogue processes. A better way is to fork a process and use execvp to spawn a child, but this requires some c programming. Cheers, Matt On Tue, 14 Mar 2000, Huajun Fan wrote: > Dear CCLers > > I wonder if the fortran code can call a excutable file, instead of a > source code. If so, how can I do it? Any advice will be highly > appreciated. > > Thanks in advance. > > huajun > > > -= 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 -- +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ + Matt Challacombe, Ph.D. http://www.t12.lanl.gov/~mchalla/ + + Los Alamos National Laboratory email: mchalla@t12.lanl.gov + + Theoretical Division vmail: (505) 698-4112 + + Group T-12, Mail Stop B268 phone: (505) 665-5905 + + Los Alamos, New Mexico 87545 fax: (505) 665-3909 + + + + "The secret to mountain biking is pretty simple. The slower you go + + the more likely it is you'll crash." -- Julie Furtado + +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@server.ccl.net Tue Mar 14 20:03:44 2000 Received: from sungod.ccs.yorku.ca (lhtDvaG1ahnBmWJSgWmkWtdn1Ai3wiRo@sungod.ccs.yorku.ca [130.63.236.104]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA24360 for ; Tue, 14 Mar 2000 20:03:44 -0500 Received: from sunburn.ccs.yorku.ca (sunburn.ccs.yorku.ca [130.63.236.110]) by sungod.ccs.yorku.ca (8.9.3/8.9.3) with ESMTP id UAA21520 for ; Tue, 14 Mar 2000 20:03:39 -0500 (EST) Received: from localhost (serge@localhost) by sunburn.ccs.yorku.ca (8.9.3/8.9.3) with ESMTP id UAA29792 for ; Tue, 14 Mar 2000 20:03:36 -0500 (EST) X-Authentication-Warning: sunburn.ccs.yorku.ca: serge owned process doing -bs Date: Tue, 14 Mar 2000 20:03:33 -0500 (EST) From: Sergey Gorelsky X-Sender: serge@sunburn.ccs.yorku.ca To: chemistry@ccl.net Subject: DFT and spin states Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Recently we started to study some open shell transition metal complexes where the electronic states can be spin doublets and spin quartets. We are interested to estimate the energy difference between spin doublet and spin quartet states. I wonder how well different DFT functionals perform for open shell systems? Do LSDA and GGA functionals "favour" low-spin or high-spin states? How well hydrid functionals (like B3LYP) work for a prediction of relative energy of different spin states? I will summarize the replies if this question is of interest to CCL. ________________________________________________________________ Sergey Gorelsky, M. Sc. Department of Chemistry, York University 4700 Keele St., Toronto, Ontario M3J 1P3, Canada tel.(416) 736-2100 ext#77720 and ext#70131 fax:(416) 736-5936 http://www.chem.yorku.ca/ ________________________________________________________________ From chemistry-request@server.ccl.net Tue Mar 14 22:29:10 2000 Received: from gw5smtp.um.edu.my ([202.185.112.1]) by server.ccl.net (8.8.7/8.8.7) with SMTP id WAA24979 for ; Tue, 14 Mar 2000 22:29:05 -0500 Received: from Gwdom1-Message_Server by gw5smtp.um.edu.my with Novell_GroupWise; Wed, 15 Mar 2000 11:29:06 +0800 Message-Id: X-Mailer: Novell GroupWise 5.5 Date: Wed, 15 Mar 2000 11:28:44 +0800 From: "Liew Fui fah" To: Subject: Molecular Modeling - expert opinion needed Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id WAA24980 Dear CCLers, Nowadays, Internet has become a tool for scientists in order to perform their work efficiently. Almost every one of us relies on the Internet to have discussion, looking for information and communicating with others. Indeed, through Internet we are effectively engaged with research, publications and information sharing that need collaboration with geographically dispersed colleagues. With a thought of fully utilizing the strength of Internet, I foresee there is a possibility to develop a web based molecular modeling station/portal, that would allow chemists to carry out experiment work, share information and modeling results with just a simple login to the server through an Internet browser. The molecular modeling engine, computing facilities and the working space are provided by the station. In order to carry out an analysis on this idea, I need expert opinion from fellow CCLers as to inspect the need and how should such a web based molecular modeling station perform. Please kindly give your opinions from a user or developer*s perspective with respect to the following aspects. (These are some basic guidelines for the survey, you are most welcome to add additional comments) A. Interface - What are the interface features that you would like to see and use when manipulating your structure? Beside the common editing and browsing tools, you are welcome to suggest new feature the meet your requirements. - Would you like to have an interface setting that match the way you want to work? - How do you like the information of transition states, molecular properties, orbitals, vibration, electronic spectrum, etc to be displayed? - Which molecular modeling package(s) that has the user interface that you like most. B. Modeling Methods - What are the general features / methods that are a *must* for a molecular modeling package? - What modeling methods are you using? - What are the advance characteristics of a molecular modeling package that will meet you requirements? - Please suggest the molecular modeling package(s) that you like to use most in terms of it accuracy and ease to use. C. Platform - Since it will be a web based molecular modeling station, it is ideal to have access from multi-platform machine. As a reference, please suggest the platforms that most of the chemists engage with while they carry out their work. - Would you like to have a direct access to the web based station at your current working platform? - What platform do you think that is most capable to operate as a server which can handle large amount of job load and provide enough storage? D. Technologies - Do you think that Java will meet most of the web based application requirements while incorporating various plug-ins and formats (e.g. XML, SVG). What is your comment on this particular technology? - Please suggest other technologies that you think is powerful in developing a web based chemical application. (if any) E. Database - What are the existing databases that you would like to use in your searches? Please provide references. F. General - What do you think about a web based molecular modeling station/portal? - Will it be convenient to do molecular modeling job in a remote machine through Internet? Your opinions and comments are very useful to my research, please kindly reply to fuifah@um.edu.my Thanks. Regards, Liew Fui Fah, University Malaya, Malaysia. fuifah@um.edu.my