From chemistry-request@ccl.net Fri Jun 4 06:42:57 2004 Received: from TheWorld.com (pcls2.std.com [192.74.137.142]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i54BgtLg024292 for ; Fri, 4 Jun 2004 06:42:55 -0500 Received: from shell.TheWorld.com (shell04.theworld.com [192.74.137.74]) by TheWorld.com (8.12.8p1/8.12.8) with ESMTP id i54BkXul001769 for ; Fri, 4 Jun 2004 07:46:33 -0400 Received: (from websrvr@localhost) by shell.TheWorld.com (8.9.3/8.9.3) id HAA1329696; Fri, 4 Jun 2004 07:46:17 -0400 (EDT) From: jle$at$TheWorld.com X-Authentication-Warning: shell04.TheWorld.com: websrvr set sender to jle$at$TheWorld.com using -f Received: from 130.36.62.126 (proxying for unknown) (SquirrelMail authenticated user jle) by www.TheWorld.com with HTTP; Fri, 4 Jun 2004 07:46:17 -0400 (EDT) Message-ID: <43165.130.36.62.126.1086349577.squirrel$at$www.TheWorld.com> Date: Fri, 4 Jun 2004 07:46:17 -0400 (EDT) Subject: Why program in Java? To: chemistry$at$ccl.net User-Agent: SquirrelMail/1.4.2 MIME-Version: 1.0 Content-Type: text/plain;charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Priority: 3 Importance: Normal X-Complaints-To: The World : www.TheWorld.com X-Spam-Status: No, hits=1.5 required=7.5 tests=NO_REAL_NAME,PRIORITY_NO_NAME, 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 Folks, I would appreciate pointers to any article/book discussing the pros and cons of programming in Java. Either with regards to other interpreted languages such as Python/Perl, or with regards to compiled languages such as C/C++. Truly comparative articles would be best, although evangelical texts would suffice (i.e. I've read some of the XP literature :-). Thanks in advance! Joe From chemistry-request@ccl.net Fri Jun 4 10:19:36 2004 Received: from smtp1.utdallas.edu (smtp1.utdallas.edu [129.110.10.12]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i54FJaLg011163 for ; Fri, 4 Jun 2004 10:19:36 -0500 Received: from utdallas.edu (pascal.utdallas.edu [10.110.62.70]) by smtp1.utdallas.edu (Postfix) with ESMTP id B5C63388E71 for ; Fri, 4 Jun 2004 10:23:13 -0500 (CDT) Sender: wfisher(at)utdallas.edu Message-ID: <40C09355.314B368C(at)utdallas.edu> Date: Fri, 04 Jun 2004 10:20:53 -0500 From: Wayne Fisher X-Mailer: Mozilla 4.79 [en] (X11; U; HP-UX B.11.11 9000/785) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry(at)ccl.net" Subject: CCL: Gaussian 03 Output Interpretation Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Ladies and Gentlemen, Below is a portion of the output from a Gaussian 03 DFT optimization calculation on a molecule in a solvent using the pcm method. What is the "Total free energy in solution: with all non electrostatic terms"? I can see that this is the sum of the electronic energy E(RB+HF-LYP) and the cavitation, dispersion, and repulsion energies, but why is this labeled a free energy? At this point in the job no frequency calculation has yet been done and no entropy calculated as far as I can tell. Can anyone explain or point me to documentation that explains this output? ********** Error on total polarization charges = 0.02091 SCF Done: E(RB+HF-LYP) = -613.441845676 A.U. after 10 cycles Convg = 0.2485D-08 -V/T = 2.0048 S**2 = 0.0000 KE= 6.105335890138D+02 PE=-1.734494797920D+03 EE= 3.688267374326D+02 -------------------------------------------------------------------- Variational PCM results ======================= (a.u.) = -613.431671 (a.u.) = -613.441846 Total free energy in solution: with all non electrostatic terms (a.u.) = -613.439088 -------------------------------------------------------------------- (Polarized solute)-Solvent (kcal/mol) = -6.38 -------------------------------------------------------------------- Cavitation energy (kcal/mol) = 8.63 Dispersion energy (kcal/mol) = -7.56 Repulsion energy (kcal/mol) = 0.66 Total non electrostatic (kcal/mol) = 1.73 -------------------------------------------------------------------- ********* Thanks, Wayne Fisher wfisher-at-utdallas.edu The University of Texas at Dallas From chemistry-request@ccl.net Fri Jun 4 10:56:37 2004 Received: from sccrmhc12.comcast.net (sccrmhc12.comcast.net [204.127.202.56]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i54FuaNh015170 for ; Fri, 4 Jun 2004 10:56:36 -0500 Received: from planaria (c-24-18-55-222.client.comcast.net[24.18.55.222]) by comcast.net (sccrmhc12) with SMTP id <20040604160013012001plbke>; Fri, 4 Jun 2004 16:00:14 +0000 Reply-To: From: "Mark Thompson" To: , Subject: RE: Why program in Java? Date: Fri, 4 Jun 2004 09:00:08 -0700 Message-ID: <000001c44a4d$026a61c0$0200a8c0@planaria> 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) Importance: Normal In-Reply-To: <43165.130.36.62.126.1086349577.squirrel:at:www.TheWorld.com> X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 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 One major drawback to scientific programing in Java, at the present time, is good 3D graphics. Currently, JOGL (Java bindings to OpenGL) is pretty much the best you can do, and it's quite good with one big caveat. JOGL supports hardware accelerated graphics, but only through using a heavyweight JOGL component. This means if you write a Swing-based application, you must use the lightweight Swing-compatible JOGL component (which does not support hardware acceleration). I've done extensive business and scienfitic SW development in Java for ~10 years and I still prefer C++ for scientific apps. I have found that Java is very good for writing stable (even high performance) server-side applications, but that it really lacks polish for GUIs in stand-alone apps. In defense of Java, the JOGL development team claims that there will be openGl bindings in Java 1.5 and I suspect 3D graphics in Java will only get better over time. C++ using Qt for the GUI is hard to beat in my personal opinion. Mark *************************** Mark Thompson ArgusLab PO Box 55207 Seattle, WA 98155 voice: 206.240.4769 FAX: 206.440.3305 mark:at:arguslab.com http://www.arguslab.com *************************** -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request:at:ccl.net]On Behalf Of jle:at:TheWorld.com Sent: Friday, June 04, 2004 4:46 AM To: chemistry:at:ccl.net Subject: CCL:Why program in Java? Folks, I would appreciate pointers to any article/book discussing the pros and cons of programming in Java. Either with regards to other interpreted languages such as Python/Perl, or with regards to compiled languages such as C/C++. Truly comparative articles would be best, although evangelical texts would suffice (i.e. I've read some of the XP literature :-). Thanks in advance! Joe -= 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) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Fri Jun 4 10:30:34 2004 Received: from mx5.informatik.uni-tuebingen.de (mx5.Informatik.Uni-Tuebingen.De [134.2.12.32]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i54FUWNh012492 for ; Fri, 4 Jun 2004 10:30:33 -0500 Received: from localhost (loopback [127.0.0.1]) by mx5.informatik.uni-tuebingen.de (Postfix) with ESMTP id 7A23910D; Fri, 4 Jun 2004 17:34:11 +0200 (MST) Received: from mx3.informatik.uni-tuebingen.de ([134.2.12.26]) by localhost (mx5 [134.2.12.32]) (amavisd-new, port 10024) with ESMTP id 21280-03; Fri, 4 Jun 2004 17:34:09 +0200 (DFT) Received: from mel (mel.informatik.uni-tuebingen.de [134.2.13.156]) by mx3.informatik.uni-tuebingen.de (Postfix) with ESMTP id 6A798149; Fri, 4 Jun 2004 17:34:08 +0200 (DFT) Date: Fri, 4 Jun 2004 17:34:07 +0200 (MST) From: Joerg Wegner To: jle$at$TheWorld.com Cc: chemistry$at$ccl.net Subject: Re: CCL:Why program in Java? In-Reply-To: <43165.130.36.62.126.1086349577.squirrel$at$www.TheWorld.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Virus-Scanned: by amavisd-new (McAfee AntiVirus) at informatik.uni-tuebingen.de X-Spam-Status: No, hits=5.4 required=7.5 tests=COMBINED_FROM,MY_BAD_DOT, NO_RDNS2,SMILEY autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi, i know only a VERY OLD summary, which was before the new JIT compiler, so it is definitely deprecated, also things like GCJ are not part of it, but ... it's the only study i know ... and be also critical when reading it: @ARTICLE{pre00, author = {L. Prechelt}, title = {{A}n empirical comparison of {C}, {C++}, {J}ava, {P}ython, {R}exx, and {T}cl}, journal = {IEEE Computer}, year = {2000}, volume = {33}, number = {10}, pages = {23--29}, groupsearch = {0}, contents = {c, c++, java, python, tcl, perl, rexx}, abstract = {Often heated, debates regarding different programming languages' effectiveness remain inconclusive because of scarce data and a lack of direct comparisons. The author addresses that challenge, comparatively analyzing 80 implementations of the phonecode program in seven different languages (C, C++, Java, Perl, Python, Rexx, and Tcl). Further, for each language, the author analyzes several separate implementations by different programmers. The comparison investigates several aspects of each language, including program length, programming effort, run-time efficiency, memory consumption, and reliability. The author uses comparisons to present insight into program language performance. For example, the study indicates that Java's memory overhead is still huge compared to C or C++, but its runtime efficiency has become quite acceptable. The scripting languages, however, offer reasonable alternatives to C and C++, even for tasks that must handle fair amounts of computation and data.}, topics = {c, c++, java, python, tcl, perl, rexx}, } Kind regards, Joerg On Fri, 4 Jun 2004 jle$at$TheWorld.com wrote: > Folks, I would appreciate pointers to any article/book discussing > the pros and cons of programming in Java. Either with regards to > other interpreted languages such as Python/Perl, or with regards > to compiled languages such as C/C++. Truly comparative articles > would be best, although evangelical texts would suffice (i.e. I've > read some of the XP literature :-). > > Thanks in advance! > > Joe > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY$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$nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > Dipl. Chem. Joerg K. Wegner Center of Bioinformatics Tuebingen (ZBIT) Department of Computer Architecture Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 29 78970 Fax: (+49/0) 7071 29 5091 E-Mail: mailto:wegnerj$at$informatik.uni-tuebingen.de WWW: http://www-ra.informatik.uni-tuebingen.de -- Never mistake motion for action. (E. Hemingway) Never mistake action for meaningful action. (Hugo Kubinyi,2004) From chemistry-request@ccl.net Fri Jun 4 18:18:37 2004 Received: from chem.udel.edu (chem.udel.edu [128.175.138.224]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i54NIaNh018845 for ; Fri, 4 Jun 2004 18:18:36 -0500 Received: from localhost (pradyu@localhost) by chem.udel.edu (8.9.3/8.9.3) with ESMTP id TAA344010 for ; Fri, 4 Jun 2004 19:43:15 -0400 (EDT) Date: Fri, 4 Jun 2004 19:43:14 -0400 From: "Pradyumna S. Singh" To: chemistry^at^ccl.net Subject: Del G from PCM In-Reply-To: <40C09355.314B368C^at^utdallas.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.6 required=7.5 tests=FVGT_s_SINGLE_LETTER 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, COuld somebody on the list tell me how I could obtain an explicit value for Delta G (solvation) using the PCM on Gaussian 03 ? G98 gave an explicit value, but G03 doesnt seem to be doing so. Thanks, Pradyumna From chemistry-request@ccl.net Fri Jun 4 22:39:24 2004 Received: from mx5.net.nih.gov (mailfwd.nih.gov [165.112.130.36]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i553dKNh029319 for ; Fri, 4 Jun 2004 22:39:20 -0500 Received: from mx5.net.nih.gov (localhost [127.0.0.1]) by mx5.net.nih.gov (8.12.10/8.12.8p1) with ESMTP id i553h2qB011520 for ; Fri, 4 Jun 2004 23:43:02 -0400 Received: from pollux.cber.nih.gov (pollux.cber.nih.gov [128.231.52.5]) by mx5.net.nih.gov (8.12.10/8.12.8p1) with ESMTP id i553gvd3011515 for ; Fri, 4 Jun 2004 23:42:57 -0400 Date: Fri, 4 Jun 2004 23:41:19 -0400 From: Rick Venable To: CHEMISTRY(at)ccl.net Subject: CCL: 3D Iso-valued Surfaces Message-ID: ReplyTo: Rick_Venable(at)nih.gov MIME-Version: 1.0 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 Can anyone recommend a good freeware graphics program for Linux or IRIX that can render iso-valued surfaces from a 3D grid dataset? I'm looking for something with a well documented input data format. I'd considered a QM orbital viewer, but my data units are quite a bit different. Regards, =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable(at)nih.gov ALT email: rvenable(at)speakeasy.org ------------------------------------- "Don't blame me, I voted for Kang." Homer =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=