From ep7@dent.okayama-u.ac.jp Fri Jul 4 01:49:42 1997 Received: from deews1.dent.okayama-u.ac.jp for ep7@dent.okayama-u.ac.jp by www.ccl.net (8.8.3/950822.1) id BAA17718; Fri, 4 Jul 1997 01:40:02 -0400 (EDT) From: Received: from [150.46.140.80] (yobou2.dent.okayama-u.ac.jp [150.46.140.80]) by deews1.dent.okayama-u.ac.jp (8.7.5+2.6Wbeta6/3.3W9) with SMTP id OAA10444 for ; Fri, 4 Jul 1997 14:40:14 +0900 (JST) Message-Id: <199707040540.OAA10444@deews1.dent.okayama-u.ac.jp> Date: Fri, 4 Jul 1997 14:45:41 +0900 To: CHEMISTRY@www.ccl.net X-Sender: ep7@dent.okayama-u.ac.jp (Unverified) Subject: CCL: Gauss View MIME-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp X-Mailer: Eudora-J(1.3.8.5-J13) I would like to ask you about Gauss View. How can I use Gauss View ? For example, must we compile Gauss View with Gaussian 94 ? ============================================================================ ===== Masao Masamura Okayama University Dental School Department of Preventive Dentistry Shikata-cho,Okayama,700 Japan Fax: 81-86-225-3724 e-mail: ep7@dent.okayama-u.ac.jp ============================================================================ ===== From ccl@www.ccl.net Fri Jul 4 04:49:46 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id EAA18454; Fri, 4 Jul 1997 04:30:20 -0400 (EDT) Received: from voimax.voima.jkl.fi for eloranta@voimax.voima.jkl.fi by bedrock.ccl.net (8.8.6/950822.1) id EAA29964; Fri, 4 Jul 1997 04:30:18 -0400 (EDT) Received: (from eloranta@localhost) by voimax.voima.jkl.fi (8.8.5/8.8.5) id LAA15943 for chemistry@ccl.net; Fri, 4 Jul 1997 11:30:25 +0300 From: Jussi Eloranta Message-Id: <199707040830.LAA15943@voimax.voima.jkl.fi> Subject: SCI-PCM solvent model To: chemistry@ccl.net Date: Fri, 4 Jul 1997 11:30:25 +0300 (EET DST) Dear netters, Does anyone know references for the SCI-PCM solvent model as implemented in Gaussian 94? The Gaussian manual gives four references which all are under preparation and I was not able to find out if these have been published now. "Exploring Chemistry with Electronic Structure Methods (2nd ed.)" also points to one of these unpublished articles. Also a pointer to good review article on the solvent models would be very helpful. Regards, Jussi Eloranta / University of Jyvaskyla, Finland. From daizadeh@indigo.ucdavis.edu Fri Jul 4 14:49:50 1997 Received: from indigo.ucdavis.edu for daizadeh@indigo.ucdavis.edu by www.ccl.net (8.8.3/950822.1) id OAA21576; Fri, 4 Jul 1997 14:03:46 -0400 (EDT) Received: by indigo.ucdavis.edu (940816.SGI.8.6.9/940406.SGI.AUTO) id LAA13280; Fri, 4 Jul 1997 11:12:35 -0700 From: "Iraj Daizadeh" Message-Id: <9707041112.ZM13278@indigo.ucdavis.edu> Date: Fri, 4 Jul 1997 11:12:24 -0700 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: heifets@indigo.ucdavis.edu, stuchebr@indigo.ucdavis.edu, daizadeh@indigo.ucdavis.edu, leee@indigo.ucdavis.edu, CHEMISTRY@www.ccl.net Subject: 3-D Summary! Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Status: RO Content-Length: 10213 Hello. Below is a summary of the responses I have received concerning visualization of 3-D data, in particular, visualization of a 3-d flow field. I have also included possible solutions to a recent problem sent to the CCL which corresponds to a related aspect of data analysis; viz., visualization of some sort of iso-surface (generalized contouring). I have attempted to make all listings below as anonymous as possible (plagarism). For the most part, all programs shown below were compiled (or precompiled binaries used) on a SGI (SiliconGraphics,Inc.) R10000 running IRIX 6.2 (except for the Fortner products). I should note that there were many others I have tested as well; a list of those follow: Plotmtv - Great, almost as easy as xmgr!!!!!! YetAnoextHuckMolorbprog - Nice for display of band structures, etc. graph3d - robot - scian - tecate - tipsy - uncert - The last six are vacuous since either I do not remember the programs efficacy or there were compilation problems. Any questions, comments or concerns, please do not hesitate to send me an email. Iraj. Iraj Daizadeh Department of Chemistry University of California Davis, CA 95616 email: daizadeh@indigo.ucdavis.edu Phone: 916.754.8695 -------------------------------------------------------------------------------- Below was the problem: Hello. Would anyone know an easy-to-learn program that allows for visualizing data >from a file in 3-dimension Euclidean space something that looks like a fluid dynamics simulation? I started to write such a piece of code using Tcl/Tk but speed is of the essence (as always). Thanks in advance. Iraj Daizadeh Department of Chemistry University of California Davis, CA 95616 -------------------------------------------------------------------------------- #1) I use FAST, developed here, and available for free (I think). It does 3D scalar and vector fields on a wide variety of grids, including, of course, uniform cartesian. For some examples of what it can do for molecules, see http://science.nas.nasa.gov/~creon/papers/mgms96/ for availablitty of FAST, look at http://science.nas.nasa.gov/Software/FAST/ #2) Check out software at http://www.fortner.com/ I have never used their stuff, but it looks impressive (and they have been in business for a while). It is not free - but I think their main modules come as a package for less than $1,000. Fortner: http://www.fortner.com/docs/demos_all.html #3) Try pgplot. It's not available in netlib but it's excellent and free. See http://astro.caltech.edu/~tjp/pgplot/ It may not do *exactly* what you need but I think it'll come close, probably a lot closer than other free tools. #4) Sorry about the delay, but hours are not always so extensible as I might wish! Yes! VU can create pictures of 3-d fields using streamlines and/or vectors. Yes!! VU can displayed atoms and links between them using spheres and cylinders colored according to the usual standards. And Yes!!! you can put all of this on screen at the same time! We have created a couple of new images in the VU gallery representing small molecules in which a cutting plane is used to probe and visualize a scalar field. These are not big protein but rather small molecules, but the idea is the same. I invited you to go check again the VU home page at http://www.cerca.umontreal.ca/vu/gallery/ to check these new additions. VU is developped mainly for use in Computational Fluid Dynamics (CFD), but it also usefull for other application domains. It is being use extensively for chemistry applications here at Cerca and nearby universities, and also at the University of Hannover with AllChem (their web address is in VU HomePage). ** VU allows for 2-d and 3-d exploration of scalar fields as well as vector fields. Furthermore, VU can also display geometric entities such as curves and surfaces. ** Scalar fields can be probed/represented using either : - iso-surfaces in 3-d space, - iso-lines on arbitrary cutting planes - iso-lines on surfaces of constant coordinate from a structured grid. - graphs, i.e. continuously shaded images representing the values of a scalar field on cutting planes (or surfaces of constant coordinate from a structured grid). ** Vector fields can be probed/represented using either : - arrows (scalable) - streamlines in various number and location, all of which is specified interactivally. - dynamic particle tracing: non static images in which particle (represented as small spheres) are injected in various location to probe the vector fields. ** VU can extract information from these various fields and present them in a tabular form in a file or directly at the cursor location. ** VU uses `expressions' such as "sqrt(px*px+py*py+pz*pz)" to indicate color mapping, deformation or scaling factor for use in creating images (at least colorfull if not always meaningfull!). ** VU can also use transparency in any image, in order to be able able to `see' what is behind a cutting plane or an iso-surface. ** VU uses OpenGL and Motif (both fairly standard libraries) and works on UNIX workstations: IRIX, AIX, HP-UX, OSF1 and Linux. In a nutshell, VU can creates many and various images of 2-d and 3-d scalar and vector fields from a solution computed over a set of grid nodes. The input file for VU specifies the mesh used and the computed solution fields. You may see and read about some examples in the VU Web pages. However, if the fact that some of the web pages crucial for a full understanding of the capabilities of the program and of its input file might not be in english, you could forward a sample test case of your data to support_vu in order to establish its usuability in your case. Even if the documentation has not been yet completely translated and made avalailable on the Web, VU is nonetheless available in four languages: french, english, german and spanish. #5) IBM visualization data explorer/IRIS explorer will do. A while ago, i downloaded the comparison of these visualization softwares. Now I dont remember the URL. But u can find them in my homepage. http://144.16.73.100/~parthi/home.html and CLICK "visualization". u can see the comparison of four visualization softwares. #6) One possibility for almost all visualization tasks is to write a simple program to transform the data to a VRML file and then use a VRML browser to visualize it. For more information about VRML, look at the VRML repository (http://www.sdsc.edu/vrml/). For an example of code that generates VRML, look at the VRML module on my Python page (http://www.yi.com/home/HinsenKonrad/python.html). #7) I'm glad you enjoyed the site. I usually use Matlab or Mathematica to plot my vectors. Unfortunately, both of these programs are commercial so you must buy them. There may be shareware available on the internet to do the same thing. Happy hunting. #8) I don't know what your constraints are: systems, time, money, expertise ... but if I were in your position, I could knock out a visualization of "data from a file in 3-dimension Euclidean space something that looks like a fluid dynamics simulation" in 30-60 minutes using AVS. Have you any familiarity with it at all? There were other packages (IBM's Data Explorer and SGI's IRIS Explorer) which did much the same thing and were all the rage 3-4 years ago. #9) Vis5D will suit your needs if your data are sampled on a rectangular 3-D grid, and you have values for px, py and pz at each grid point. See Section 3.1 of the Vis5D README file for instructions about getting your data into Vis5D. I recommend map projection 0 (generic) and vertical coordinate system 0 (generic), since your data are not related to Earth coordinates (latitude and longitude). If you use the names 'U', 'V' and 'W' for px, py and pz then Vis5D will recognize these as the three components of a vector field. If you don't, then you can use the 'UVW VARS' widget to tell Vis5D which fields are vector components. In generic coordinates, vector components are in the units given for North, South, East, West, Top and Bottom bounds, per second. If you have a time sequence of data (i.e., a changing vector field), Vis5D will trace motion trajectories for you. You'll need to correctly assign dates and times to time steps to get realistic motions. If you only have one time step, you can still look at motion trajectories by just repeating the same data over a sequence of times. Good luck. #10) The purpose of this message is to give you a quick feeling for how the NCAR graphics package can be used to display graphs of your data from the Cray. The NCAR graphics package consists of libraries of C and Fortran callable subrou- tines for creating graphs and utilities for displaying them. #11) MSI's software developer's kit does exactly what you want. It includes an API set to visualize iso-surfaces, molecular structure, trajectories, normal modes, plots/graphs, etc. It also allows you in a few steps to put an interface together to any computational chemistry code. For general information about this toolkit visit: http://www.msi.com/support/sdk/ for specific information on plotting iso-surfaces visit: http://www.msi.com/support/sdk/users/examples/iso/README.html #12) Dear CCLers, although I'm pretty sure this question has been already posed (and I beg your pardon for posing it again), I have to ask about a 3D visualisation tool. I worked with SciAn, which is pretty good indeed, but the only existing version needs Z buffer and DGL. Looking on the net I found a software called vis5d, pretty good the same but tuned for metereological data and I found too time-expensive to adapt it to visualize orbitals, electronic density and so on. I'm using molden but I would like to find out soemthing more general (I'm trying to use ELF also, and this feature is not implemented in molden). The software I'm looking for should manage x,y,z,function_value in order to give isosurfaces of the function I'm trying to plot. Something not strictly platform-dependant would be very fine. Thank you for all the information you will provide. From ccl@www.ccl.net Sat Jul 5 11:50:02 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id KAA27154; Sat, 5 Jul 1997 10:57:43 -0400 (EDT) Received: from nz11.rz.uni-karlsruhe.de for Joachim.Schummer@geist-soz.uni-karlsruhe.de by bedrock.ccl.net (8.8.6/950822.1) id KAA12107; Sat, 5 Jul 1997 10:57:43 -0400 (EDT) Received: from ips01 (actually ips01.geist-soz.uni-karlsruhe.de) by nz11.rz.uni-karlsruhe.de with SMTP (PP); Sat, 5 Jul 1997 16:57:37 +0200 Message-ID: <33BECE09.6E31@geist-soz.uni-karlsruhe.de> Date: Sat, 05 Jul 1997 15:43:21 -0700 From: Joachim Schummer Reply-To: Joachim.Schummer@geist-soz.uni-karlsruhe.de Organization: Institute of Philosophy, University of Karlsruhe X-Mailer: Mozilla 3.01Gold [de] (Win16; I) MIME-Version: 1.0 To: CHEMISTRY list Subject: Urgent! Humanities are in danger of being dissolved Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, As a chemists and philosopher, now working on the philosophy of chemistry, I essentially depend on your support because of a disasterous university policy in Germany: ------------------------------------------------------------------------ Faculty of Humanities and Social Sciences in Karlsruhe is in danger of being dissolved ------------------------------------------------------------------------ The commission for university structural affairs of Baden-Wuerttemberg, Germany has recommended the government (June 21, 1997) to dissolve the Faculty of Humanities and Social Sciences at the University of Karlsruhe. In the disguise of an enlightened measure to improve the educational ressources of the country, the government obviously intends to take radical economy measures. Since most humanities departments and faculties have been shrunk to the very lowest level in this country during the last years, the commission's general recommendation to cut another 15-25 p.c. requires now for the first time the closure of a whole faculty. Please support the preservation of the Faculty of Humanities and Social Sciences! Complete our electronic form to require the government to preserve the humanities and social sciences in Karlsuhe: http://www.uni-karlsruhe.de/~philosophie/iinitiat.htm We run an electronic list of contributers in order to raise the public pressure. Responses from the international natural sciences community are particularily welcome. Please forward this message! Thank you very much for your help, Joachim Schummer ------------------------------------------------------------ Dr. Joachim Schummer Institute of Philosophy, University of Karlsruhe Postfach 69 80, D-76128 Karlsruhe, GERMANY Joachim.Schummer@geist-soz.uni-karlsruhe.de From yubofan@guomai.sh.cn Sun Jul 6 02:50:13 1997 Received: from gm-email.guomai.sh.cn for yubofan@guomai.sh.cn by www.ccl.net (8.8.3/950822.1) id CAA28729; Sun, 6 Jul 1997 02:02:28 -0400 (EDT) Received: from ------ ([210.0.0.14]) by gm-email.guomai.sh.cn (8.8.5/8.8.5) with ESMTP id OAA10202 for ; Sun, 6 Jul 1997 14:58:28 +0800 Message-Id: <199707060658.OAA10202@gm-email.guomai.sh.cn> From: "Yubo Fan" To: Subject: How long will it be took to calculate by D95 basis set than 3-21G*'s? Date: Sun, 6 Jul 1997 01:12:55 +0800 X-MSMail-Priority: Normal X-Priority: 3 X-Mailer: Microsoft Internet Mail 4.70.1161 MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi, everyone, I never use D95 basis set to calculate some systems before. Will it take for more time than to use some small basis sets, for example, 3-21G*? If you have some advices, please tell me. Thank you very much Y. FAN =================================================== FAN, Yubo Department of Chemistry Fudan University Shanghai, 200433 P. R. China Voice(86-21)65492222-4294 ===================================================