From chemistry-request@server.ccl.net Sun Sep 5 00:40:00 1999 Received: from mail.chat.ru (gnu.chat.ru [212.24.32.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id AAA09391 for ; Sun, 5 Sep 1999 00:40:00 -0400 Received: from [62.76.11.201] (helo=chat.ru) by mail.chat.ru with smtp (Exim 2.12 #3) id 11NU3E-000I0Q-00 for CHEMISTRY@ccl.net; Sun, 5 Sep 1999 08:37:18 +0400 Date: Sun, 5 Sep 1999 10:33:48 +0500 From: "Qadir K. Timerghazin" X-Mailer: The Bat! (v1.036) S/N B2B97075 Reply-To: "Qadir K. Timerghazin" Priority: Normal Message-ID: <19440.990905@chat.ru> To: CHEMISTRY@ccl.net Subject: NBO summary Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, Some days ago I posted questions about NBO method: QKT> 1. Is it correct to perform NBO analysis of density obtained from DFT QKT> calculation? I mean not only Natural Populational Analysis but also QKT> NHO and NBOs. QKT> 2. After NBO analysis we obtain a set of NHOs and NBOs constructed >>from s, p, d, etc. orbitals. What kind of functions describe this QKT> basic orbitals? Are these Slater orbitals or simply orbitals of QKT> H-atom? If I want to visualize NBOs what fonctions should I use? Many thanks to Eric Glendening and Alan Shusterman who replied me: *************************************************************** Eric D. Glendening: >> 1. Is it correct to perform NBO analysis of density obtained from DFT >> calculation? I mean not only Natural Populational Analysis but also >> NHO and NBOs. EG> The NBO methods can be applied to any density, SCF, MPn, DFT, etc.. EG> There's nothing inappropriate in doing so. >> 2. After NBO analysis we obtain a set of NHOs and NBOs constructed >> >from s, p, d, etc. orbitals. What kind of functions describe this >> basic orbitals? Are these Slater orbitals or simply orbitals of >> H-atom? If I want to visualize NBOs what fonctions should I use? EG> All orbital sets in NBO analysis are ultimately linear combinations EG> of the atomic orbital basis functions (probably Gaussian functions) EG> used in the calculation. NBO will, on request, print the various EG> transformation matrices that it has computed. For example, use EG> the AONHO keyword to print the transformation from AOs to NHOs. EG> The PLOT keyword is also useful. This keyword causes the program to EG> write a series of files to disk that can be used as input for an EG> orbital plotter (ORBPLT) for visualizing NAOs, NHOs, NBO, etc. You EG> might contact Frank Weinhold (weinhold@chem.wisc.edu) about this EG> program. *************************************************************** Alan Shusterman: >>>Is it correct to perform NBO analysis of density obtained from DFT calculation? >>>I mean not only Natural Populational Analysis but also NHO and NBOs. AS> This is an interesting question and I once asked an 'NBO expert' for the answer, but his AS> reply was either lost or not given. AS> My own feeling is this: the NBO analysis uses the elements of the density matrix which AS> are derived in turn from the occupied Kohn-Sham orbitals. Since the KS orbitals should AS> give a good AS> description of the electron density distribution (even better than HF?), the KS AS> density matrix should be useful and so should the analysis of the matrix. The "problem" AS> for me, if there is one, is AS> exactly what do the NHO and NBO analyses do with the density matrix and does that make AS> sense? AS> There are certainly parts of the NBO analysis that might NOT make a lot of sense if AS> DFT models are used. For example, NBO reports 2nd-order perturbation energies for AS> interactions between filled AS> and empty NBO. The perturbation energies depend on the orbital energies, and KS AS> orbital energies are nothing like HF orbital energies so I would expect DFT and HF AS> results to be very different. >>>After NBO analysis we obtain a set of NHOs and NBOs constructed from s, p, d, etc. >>>orbitals. What kind of functions describe this basic orbitals? Are these Slater orbitals >>> or simply orbitals of >>>H-atom? If I want to visualize NBOs what fonctions should I use? AS> The NAO, NHO, and NBO are constructed from the basis set used in your original DFT AS> (or HF) calculation. If you used the STO-3G basis set then these are STO-3G functions. AS> Hardly any calculations AS> use real Slater orbitals or H-atom orbitals, so it is unlikely that the NBO would be AS> based on these. If you want to make pictures of the NBO, apply the NBO mixing AS> coefficients to the basis set AS> you used for your calculation. ******************************************************************* With best regards, Qadir mailto:qt@chat.ru From chemistry-request@server.ccl.net Sun Sep 5 15:25:44 1999 Received: from mail.rdc2.on.home.com (ha1.rdc2.on.home.com [24.9.0.15]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA13257 for ; Sun, 5 Sep 1999 15:25:44 -0400 Received: from simbiosys.ca ([24.112.43.127]) by mail.rdc2.on.home.com (InterMail v4.01.01.07 201-229-111-110) with ESMTP id <19990905192132.ICGN22922.mail.rdc2.on.home.com@simbiosys.ca>; Sun, 5 Sep 1999 12:21:32 -0700 Sender: zsolt@ccl.net Message-ID: <37D2C2F6.40ACB15F@simbiosys.ca> Date: Sun, 05 Sep 1999 15:22:30 -0400 From: Zsolt Zsoldos Organization: SimBioSys Inc. X-Mailer: Mozilla 4.05C-SGI [en] (X11; I; IRIX64 6.5 IP28) MIME-Version: 1.0 To: Joe M Leonard , chemistry@ccl.net Subject: Re: CCL:Linux questions References: <199909050222.WAA03707@world.std.com> Content-Type: multipart/mixed; boundary="------------33874C89E17B1E168169D298" This is a multi-part message in MIME format. --------------33874C89E17B1E168169D298 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Joe M Leonard wrote: > > Folks, > > Are there any technical reasons for picking RedHat 6.0 vs. > SuSE 6.2? Or, do they basically contains the same, pretty > much up-to-date components...? > There are versions of each distribution, that contain basically the same libraries and server code. However, I am not sure, that RedHat 6.0 is equivalent with the 6.2 version of SuSE. I do not have first hand experience with SuSE, but I seem to recall, that SuSE 6.1 was the equivalent of RedHat 6.0. In general, many people say, that RedHat releases are frequently more buggy than other distributions (e.g. SuSE or Caldera), because they pick the latest (frequently still experimental or beta) versions of every component - while others tend to go for more established, better tested packages. I am running RedHat 6.0 and Caldera 2.2, they both seem to be compatible and I did not experience stability problems either. > Also, has anybody had any luck porting "large, significant" > OpenGL/IRIX applications to Linux? If so, which version(s) > of OpenGL, combined with which graphics cards did you use? > Was Mesa able to deliver, or did you have to purchase a "real" > OpenGL? I am familiar with the compute performance vis-a-vis > IRIX boxes - what were the OpenGL/graphics performance > comparisons? > I have ported a 200K lines of code system from IRIX, which is client/server, the server code is C++, the client UI is Java, the 3D graphics code is again C++ (VTK based). The whole port took about a week (mainly makefile editing, some minor C++ modifications because the egcs compiler was more strict about ANSI compliance than the MipsPro compiler on IRIX). For the OpenGL, I have tried 4 different systems: 1. Metro OpenGL software, 2. Metro Extreme 3D hardware accelerated (beta version), 3. XiG Accelerated X software OpenGL, and 4. XiG 3D hardware accelerated OpenGL (limited availability technology demo). Solutions 2 & 4 (hw accel) were tried on an ELSA Gloria L/MX OpenGL accelerator graphics card (3DLabs Glint 500 MX + Delta chipset). The software renderings were tried on the same hardware (dual Pentium II at 350MHz 128MB RAM) as well as on a laptop (Pentium II at 366MHz 160MB RAM). The speed of the software versions were better than an Indy workstation, the hardware accelerated speeds were comparable to an Indigo2 Impact graphics performance. For precise numeric comparison, I have run the VTK speed benchmark, for which results on various platform are available: http://www-sop.inria.fr/caiman/personnel/Robert.Riviere/vtk/sphere-bench/ The results for the above mentioned 4 OpenGL libraries: 1. Metro software: 69 kpolys/s 2. Metro hw.accel: 147 kpolys/s 3. XiG software: 77 kpolys/s 4. XiG hw.accel: 145 kpolys/s Important note, is that the hw.accel. results are greatly affected by the size of the rendering window, because the currently available (beta version) drivers do not support DMA - slowing down the pixel transfer rate substantially. On very small window, it is possible to reach 946 kpolys/s on the same benchmark (same large number of geometry primitives rendered). In comparison, my Indigo2 Impact gives 221 kpolys/s on the same benchmark regardless of the size of the window. This means, once the final drivers with DMA are released by Metro and XiG, we can expect the PC/Linux solution to beat the SGI Impact graphics by large margin. I do not have measurements on Mesa, but from the VTK benchmark results page (link above) it appears that a pure Mesa on a PII 300MHz gets a 38 kpolys/s, but on an AMD K6-III-400 Mhz with 3Dnow optimisation it gets 74 kpolys/s. So, it seems that the XiG software is better on a slower CPU and no 3Dnow optimisation. Interesting to note, that the same benchmark gives an amazing 2236 kpolys/s result on the SGI Visual Workstation under NT. With SGI's recent linux support, we can hope that they will come out with a linux OpenGL library soon for that hardware. That would be a real screamer beating Onyx InfiniteReality2 results! Best regards, Zsolt Zsoldos --------------33874C89E17B1E168169D298 Content-Type: text/x-vcard; charset=us-ascii; name="vcard.vcf" Content-Transfer-Encoding: 7bit Content-Description: Card for Zsoldos, Zsolt Content-Disposition: attachment; filename="vcard.vcf" begin: vcard fn: Zsolt Zsoldos n: Zsoldos;Zsolt org: SimBioSys Inc. adr: 716 Peter Robertson Blvd;;;Brampton;Ontario;L6R 1L6;Canada email;internet: zsolt@simbiosys.ca title: President tel;work: (905) 793 8617 tel;fax: (905) 793 4996 tel;home: (905) 793 0599 note;quoted-printable:http://www.simbiosys.ca/=0D=0A= Private email: zzsolt@home.com=0D=0A= x-mozilla-cpt: ;0 x-mozilla-html: TRUE version: 2.1 end: vcard --------------33874C89E17B1E168169D298--