From chemistry-request@www.ccl.net Fri Nov 20 19:48:27 1998 Received: from ns01.sbphrd.com (firewall-user@ns01.sbphrd.com [208.198.64.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id TAA23712 Fri, 20 Nov 1998 19:48:26 -0500 (EST) Received: by ns01.sbphrd.com; id TAA06760; Fri, 20 Nov 1998 19:48:12 -0500 Received: from phinet.sbphrd.com(139.136.64.5) by ns01.sbphrd.com via smap (3.2) id xma006758; Fri, 20 Nov 98 19:47:55 -0500 Received: from phufs2.um.us.sbphrd.com by phinet.sbphrd.com; (/) id AA31974; Fri, 20 Nov 1998 19:47:55 -0500 Received: from phu198.um.us.sbphrd.com (phu198.um.us.sbphrd.com [139.136.98.47]) by phufs2.um.us.sbphrd.com (8.8.8/8.8.8/sbphrd/mh/19971204) with ESMTP id TAA12930 for ; Fri, 20 Nov 1998 19:47:55 -0500 (EST) From: M Dominic Ryan Received: (from ryanmd@localhost) by phu198.um.us.sbphrd.com (8.8.8/8.8.8) id TAA27263 for chemistry@www.ccl.net; Fri, 20 Nov 1998 19:49:19 -0500 (EST) Date: Fri, 20 Nov 1998 19:49:19 -0500 (EST) Message-Id: <199811210049.TAA27263@phu198.um.us.sbphrd.com> To: chemistry@www.ccl.net Subject: Travel Grants Available T R A V E L G R A N T S The Computers in Chemistry Division of American Chemical Society invites students presenting a paper at the spring meeting in Anaheim to apply for a travel grant. A limited number of grants of up to $500 will be awarded to selected students. 1. Candidates must be graduate students OR undergraduate students in good standing as confirmed by their department. 2. Students must have a supporting letter from their (primary) thesis advisor or the department chair if the latter is not possible (with an explanatory note). 3. No more than one award will be given to a research group. 4. Funds must be used to attend the Spring 1999 National meeting of the American Chemical Society. 5. Candidates must be presenting either an oral paper or a poster. 6. To apply, send letter of request, C.V. and supporting documents to the address below. Supporting Letters must be sent by mail (i.e. hard-copy). M. Dominic Ryan, UW2412 SmithKline Beecham Pharmaceuticals 709 Swedeland Rd King of Prussia, PA 19406 USA There is still limited time to submit a paper to either the General oral section or to the Posters. If you have already been accepted, forward your application for consideration. If you would like to present a paper, please forward both the grant application and the abstract form. Thank you. Dominic Ryan Program Chair Division of Computers in Chemistry American Chemical Society Fax: 610-270-4451 __ M. Dominic Ryan (610)-270-6529 SmithKline Beecham Pharmaceuticals Internet: ryanmd@mms.sbphrd.com King of Prussia, PA From chemistry-request@www.ccl.net Mon Nov 23 11:09:16 1998 Received: from hartree.chem.kuleuven.ac.be (hartree.quantchem.kuleuven.ac.be [134.58.49.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA07531 Mon, 23 Nov 1998 11:08:49 -0500 (EST) Received: from localhost (steven@localhost) by hartree.chem.kuleuven.ac.be (8.9.0/8.9.0) with ESMTP id QAA56914 for ; Mon, 23 Nov 1998 16:57:44 +0100 Date: Mon, 23 Nov 1998 16:57:44 +0100 (NFT) From: Steven Creve To: Computational Chemistry List Subject: CCL:DFT:local-nl, SUMMARY Message-ID: Hi, concerning the discussion "local <-> non-local in DFT", my first impression has been that there seems to be a lot of confusion on definitions in this area. I think that the best definitions and viewpoints are those offered by Keith Refson, Rene Fournier and Mark Casida, the first three answers given below. For the sake of completeness, I have also includede the other answers I received. I'd wish to thank all people who contributed to this interesting discussion on the CCL. Steven -------------------------------------------------------------------------- Steven Creve steven.creve@chem.kuleuven.ac.be Labo Quantumchemie Celestijnenlaan 200F 3001-HEVERLEE tel: (32) (16) 32 73 93 BELGIUM fax: (32) (16) 32 79 92 ================================================================= A N S W E R S (Refson, Fournier and Casida) ================================================================= > is the following correct: > > non-local means that the xc potential in point r depends not only on the > density in r (and also gradients of rho in r, ...) but also on the density > in other points r'. Exactly. in DFT, the LDA - local density approximation -- is precisely the statement that Exc[n(r)] = integral exc(n(r)) dr where on the LHS Exc is a functional of the charge density, ie it depends on the functional form of n(r) and exc(n) is a pure function of the charge density n at any point r. Nonlocality corresponds to increasing the *dimensionality* of the RHS so strictly, generalised gradient functionals which also depend on grad n are still local. Hartree-Fock exchange which depends (in the DFT formalism) on integral ex(n1(r1), n2(r2)) dr1 dr2 is nonlocal. Email: Keith.Refson@ | Tel: +44 1865 272026 | Dr Keith Refson, | earth.ox.ac.uk | Fax: +44 1865 272072 | Dept of Earth Sciences | Spam: root@cyberpromo.com | Parks Road, Oxford OX1 3PR, UK| ------------------------------------------------------------------ Local or nonlocal? Good question. "Gradient-corrected" functionals (Becke88, Perdew86, Perdew-Wang91, etc...) are often called "non-local" but in my opinion that's an unfortunate misuse of the term. I suppose they came to be called "non-local" because they are NOT the usual local density approximation (LDA). But "NOT the USUAL LDA" is not synonymous with "nonlocal". All functionals of the form b J[f(x)] = S ( F(x,f,f',f'',...,f(n)) ) dx a are local in the mathematical sense explained in I.M. Gelf'and S.V. Fomin, "Calculus of Variations" (Prentice-Hall, Englewood Cliffs, 1963). J[f(x)] is an integral between a and b; it can be broken into any number "n" of integrals on contiguous subdomains [a,c_1], [c_1,c_2], ... [c_(n-1),b], and the subdomains can be chosen as small as you wish. So you can decompose J into a sum of local contributions, irrespective of the order of derivatives in the integrand F. An example of nonlocal functional given by Gelf'and and Fomin is: S x sqrt(1+y'*y') dx J[y(x)] = ---------------------- S sqrt(1+y'*y') dx which gives the abscissa of the center of mass of a curve y(x). You can break the numerator and denominator into sums of local contributions, but you can not directly break J itself into sums of local contributions. I think the class of functionals J[f] = S S ( f(x) K(x,y) f(y) dx dy ) should also be called nonlocal (provided K(x,y) is "non-diagonal", i.e., K(x,y) is NOT delta(x,y)*K(x,x) ) If you go by the definition of "local and nonlocal" above, most functionals in common use (including LYP?) are local. -------------------------------------------------------------------- | Rene Fournier | Bureau/Office 303 Petrie | | Chemistry Dpt, York University | (416) 736 2100 Ext. 30687 | | 4700 Keele Street, Toronto | FAX: (416) 736-5936 | | Ontario, CANADA M3J 1P3 | e-mail: renef@yorku.ca | -------------------------------------------------------------------- ------------------------------------------------------------------ Exchange-correlation functionals may be classified as: 1) Local --- the exchange-correlation energy density functional at r, e_xc(r), depends only on the density at r. 2) Semi-local --- e_xc(r) depends only on the density and a finite number of its derivatives at r. 3) Nonlocal --- e_xc(r) depends on properties of the density at several values of r, typically involving an integral. (The restriction to a finite number of derivatives in (2) is because some integrals can be represented as a gradient expansion in an infinite number of derivatives.) The distinction between (2) and (3) is often not made, so that both are called "nonlocal". On the other hand, it is probably worth noting that the generalized gradient approximations (GGAs) fall under (2) and the older weighted density approximation falls under (3) and not (2), so the distinction has some value. Hope this helps, Mark.Casida@UMontreal.CA ================================================================== O T H E R A N S W E R S : ================================================================== > 1) what are the *exact* definitions of local vs. non-local? > This is an critical point in DFT. Nowadays, there is a great interest in properties of the exchange and correlation functionals like homogeneity and locality. From the DFT point of view, a functional is local when all the terms in the functional derivative, with the exception of the first, vanish. What does it means?. It can be presumed that we are dealing with non-local functionals, so we can suppose several non-local dependences (succesive derivatives of the density) in the exchange or correlation integrand. From here, the corresponding contribution to the functional derivative is obtained. The complete corrections to the first, local, term would reproduce the exact potential if DFT is exact. > > 2) is the LYP correlation functional, which incorporates gradient > corrections, local or non-local? > Following the previous discussion:non-local, since it will provide higher order corrections, non-local, to the local term in the correlation potential. Juan Carlos juancar@fisic1.ua.es ---------------------------------------------------------------------- >1) what are the *exact* definitions of local vs. non-local? The term "local" is used in dft to indicate that only the density is being considered to build the functionals. The term "non-local" is often (mis)used to indicate that gradient corrections to the density are also considered to write down the functionals. I prefer the term "gradient corrections to the density" since "non-local" actually means that one is modeling the exchange-correlation hole without any connection with the gradients just mentioned. >2) is the LYP correlation functional, which incorporates gradient >corrections, local or non-local? Well, the lyp c functional is both local and non-local because it has terms including both the density and its gradient. ------------------------------------------------------------------ In Hartree-Fock theory, the exchange potential is non-local, i.e. you need to know the wave function at point r and r' to be able to compute the exchange energy. In DFT theory, the exchange (or exchange-correlation) potential is local! It depends only on the properties of the electron density at point r where you want to compute the exchange energy. Words "local" and "non-local" frequently used in DFT are misleading because they do not refer to the potential but to the density! A local functional use only the value of the electron density at point r. A non-local functional use the electron density, but also its first, second, ... derivatives at point r. Hope this helps. ...Xav Ast. Pr. Xavier Assfeld Xavier.Assfeld@lctn.u-nancy.fr Laboratoire de Chimie theorique (T) 33 3 83 91 21 49 Universite Henri Poincare (F) 33 3 83 91 25 30 F-54506 Nancy BP 239 http://www.lctn.u-nancy.fr ------------------------------------------------------------------ I missed your original question. However, the definition of nonlocal depends upon who is using it. Some people consider gradient functionals as nonlocal, some call them quasilocal. I prefer to consider as local any functional whose density (i.e integrand) does not involve an integral. This would include gradient functionals. Nonlocal functionals are rare -- besides the classical coulomb energy J[[p(r)]. I've done some for magnetic responses, and for xc in the presence of a field, but not for the field free case. Hope this helps Fred Salsbury sals@rabi.cchem.berkeley.edu http://waugh.cchem.berkeley.edu/~sals ------------------------------------------------------------------ > is the following correct: > > non-local means that the xc potential in point r depends not only on the > density in r (and also gradients of rho in r, ...) but also on the density > in other points r'. No, that's incorrect. The xc potential of nonlocal functionals depends only on the density, gradient, laplacian at r. The reason why they are called non-local might be because to know gradient and laplacian of density at point r, you need to know their behaviors at other points, r', r", .... Shubin ------------------------------------------------------------------ > is the following correct: > > non-local means that the xc potential in point r depends not only on the > density in r (and also gradients of rho in r, ...) but also on the density > in other points r'. I don't believe so (but others can answer this better than I). I believe that non-local means that the energy functional depends on the density at r and the gradient of the density at r. The functional is independent of density at other points in space. Alan Alan Shusterman Dept of Chemistry Reed College Portland, OR www.reed.edu/~alan ------------------------------------------------------------------ > 1) what are the *exact* definitions of local vs. non-local? The word "local" is from the "local density approximations", which refers to a formulation of the density functional theory by Kohn and Sham, Phys. Rev. 140, A1133 (1965). It assumes that the exchange (and correlation) potential is a local operator as opposed to the nonlocal operator in the Hartree-Fock theory. This greatly simplifies the calculation of the exchange (correlation) energy but trimmed off subtle physical properties of the exchange-correlation holes of a realistic electron system. "Nonlocal" really means "not a local" and in practice, the "generalized gradient approximations". For the latter, the igonored properties of the exchange-correlation hole in the "local desnity approximations" have been recovered to a certain degree. Mainly, the rate of change of the density in the vicinity of the spatial point where the potential is calculated has been included: the gradient corrections. However, it is not a simple Taylor expansion! The spectra in wavelength space were critically examined and some spurious errors removed. These jargons have been used by physicists for more than two decades and their meanings becomes well known after hundreds of papers published debating the theory and the approximations in the '70s and '80s. As it is now popular in the computational chemistry world, probably, less confussion would be caused if these jargon words could be replaced with more self-interpreting phrases like "local..." or "local ... with gradient corrections", or "a hybrid of the exact Hartree exchange and the gradient corrected local density exchange-correlation potentials". > 2) is the LYP correlation functional, which incorporates gradient > corrections, local or non-local? > LYP is "nonlocal". > Liang Lou Wavefunction, Inc. ------------------------------------------------------------------ Hi, Steve. This term "non-local" is not correct in general because gradient potentials STILL local. LYP corr. correction includes both local and non-local terms. So, the "non-local" is used only to distinct >from pure local potentials (S, VWN) in LDA, -- Galina Orlova Vis. Res. Professor gorlova@qchem2.chembio.uoguelph.ca Department of Chemistry and Biochemistry University of Guelph Guelph, ON, N1G 2W1, Canada ph. (519) 824 4120 ext 3061 Fax (519) 766-1499 ------------------------------------------------------------------ I have always heard that local functionals are ones that use the electron density only and nonlocal functionals are those that use a gradient of electron density. It is not necessary to take into account the density at other points because the gradient gives an extrapolation to nearby points (to the extent that the density is approximately linear in a localized region). Dave Young youngd2@mail.auburn.edu ------------------------------------------------------------------ From chemistry-request@www.ccl.net Mon Nov 23 11:39:18 1998 Received: from eros.pquim.unam.mx (aspuru@eros.pquim.unam.mx [132.248.56.176]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA08472 Mon, 23 Nov 1998 11:39:18 -0500 (EST) Received: from localhost (aspuru@localhost) by eros.pquim.unam.mx (8.8.7/8.8.7) with ESMTP id KAA16015; Mon, 23 Nov 1998 10:33:52 -0600 Date: Mon, 23 Nov 1998 10:33:52 -0600 (CST) From: Alan Aspuru Guzik To: Pisanty Baruch Alejandro-FQ cc: computo_en_docencia@servidor.unam.mx, ajduven@semovm.semo.edu, chemistry@www.ccl.net Subject: CCL:Scientific Computing Service Course(s) -- appropriate content ? In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 19 Nov 1998, Pisanty Baruch Alejandro-FQ wrote: |software applications to solve problems arising in their laboratories. While |some programming experience may be necessary to solve small problems |or apply patches to programs where source code is available, this will |probably |be a small part of the tasks that they will have to do with computers. It dependes on whether they will use commercial operating systems such as Windows NT or if they are using free alternatives such as FreeBSD or Linux. Learning the basics of WHAT a programming language is makes them free to make a contribution to the global free software depot. (See http://SAL.Kachinatech.com for all the Scientific Applications / demo programs written under free licenses). | |It would seem to me that they will spend more of their time installing, |maintaining, |and configuring operating systems and self-contained application packages. It depends if those application packages are 4000 USD or 5000 USD. We in the developing countries cannot afford buying that stuff from outside. I think that in the long term, developing our own programs with our own resources will be more formative, and indeed cheapear and fruitful. |They will be interfacing computers to experimental equipment and installing |software that will run the instrument, collect the data, and reduce it. |They will be using software tools like Excel, SPSS, SAS, Origin, etc. to |analyze I agree with you in this aspect. Carlos Amador and I are experimenting in using Computer Science as an aid in our Kinematics and Dynamics course given here at UNAM. In the FIRST WEEK of the FIRST SEMESTER of class, we taught them how to numerically integrate and derivate using a spreadsheet. That gave them the insight of what VELOCITY and ACCELERATION are as derivatives of the position of a moving object. |data. Programming will probably be done using MathCAD, MATLAB or |Mathematica rather |than C or FORTRAN because of the built-in graphical interfaces for the display |of computed results. We chose to use an intermediate thing. There are programming languages that are not as intricate as C or C++ (the first, with difficult-to-teach-program and debug pointers, the second with the first inconvenience and a badly designed and difficult object oriented stuff), or Fortran. We thought first on using Java, but afterwards found that Python (http://www.python.org) is a VERY GOOD alternative, having numerical, computational chemistry, graphics visualization (we are specifically using VTK, http://www.kitware.com/vtk/), scientific (Vector, Tensor, etc) and is a language that we taught them in ONE saturday and some support sessions afterwards. |The problem space that those who teach service course(s) in computing |will have to be wider than the usual numerical analysis problems posed |for engineering students, physics and chemistry majors. There needs to |be attention to combinatorics, probability, and statistics. This is an I agree with you, some insight using simple Monte Carlo programs like calculating Pi by Monte Carlo, which as you see is fairly straightforward in Python: --------- >from math import * from string import * >from whrandom import * archivo=open('circulo.dat','r') linea = archivo.readline() linea = archivo.readline() r = atof(linea) print('QMCirculo 98') print('Radio a usar: ' + str(r)) linea = archivo.readline() linea = archivo.readline() n = atoi(linea) print('Numero de iteraciones: ' + str(n)) linea = archivo.readline() linea = archivo.readline() delta = atof(linea) print('El intervalo de confianza porcentual es: ' + str(100.0* (1 - delta)) + "%") # como inicializo las listas? punto = [0,0] n_circulo = 0 n_afuera = 0 a_circulo = 0 for i in range(n): punto[0] = random() punto[1] = random() if (sqrt(pow(punto[0],2)+pow(punto[1],2)) < r) : n_circulo = n_circulo + 1 # n_afuera = n - n_circulo # summary statistics a_circulo = (1.0 * n_circulo) / n print 'El area de la seccion es: ' + str(a_circulo) pi = (4.0 * a_circulo) print 'Pi es: ' + str(pi) #estimando la varianza varianza = (1.0 *n_circulo / n)*(1.0 - (1.0*n_circulo /n))/(n -1.0) print "La varianza es " + str(varianza) ---- with a data file like this one: ------ Radio del circulo 1.0 Numero de vueltas 10000 El delta 0.001 ---- (The delta parameter was not used, I planned to use it for confidence interval evaluation, but I did not finish that part of the code) Anyways, circulo.py was coded in 20 minutes... I think this kind of things and cellular automata games can be very good for simulating economics / population biology, etc... |important aspect in the course offered here since the majority of the |students are from cell and molecular biology, environmental science, and |geology. [The chemistry and physics students here take a pretty |traditional course in FORTRAN. Whether this is the best choice for all, |I have my doubts.] The course in question is a freshman level course. |Students are concurrently struggling with calculus at best. I'd have a second course in which Mathematica, Maple, Python and C are used as languages. I support the idea of not marrying to just one option. |I would welcome comments, critique, and suggestions on my comments from |list members. This list has subscribers from a number of disciplines |whose insights I would appreciate. I will summarize for the list. Well, this was only 0.02 c. I wait your reply, Alan Aspuru Guzik Student and TA, Theoretical Chemistry and Physics Department, Chemistry School, Universidad Nacional Autonoma de Mexico From chemistry-request@www.ccl.net Mon Nov 23 12:20:36 1998 Received: from ned1.sims.nrc.ca (ned1.sims.nrc.ca [132.246.108.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA10328 Mon, 23 Nov 1998 12:20:34 -0500 (EST) Received: (from zorka@localhost) by ned1.sims.nrc.ca (8.8.8/8.8.8) id MAA20065; Mon, 23 Nov 1998 12:20:33 -0500 (EST) Date: Mon, 23 Nov 1998 12:20:32 -0500 (EST) From: Zorka Smedarchina To: CHEMISTRY@www.ccl.net Subject: CCL: New software for tunneling dynamics. Message-ID: Dear colleagues, We would like to draw your attention to a recent software package developed by us. It is called DOIT (Dynamics Of Instanton Tunneling) and performs direct-dynamics calculations of rate constants and tunneling splittings which are due to tunneling of hydrogen/deuterium/tritium in polyatomic systems (molecules, clusters, complexes, etc.). The package can be useful to many researchers, especially those working with relatively large systems (potentially biologically-active). The code is based on a novel approach that utilizes instanton theory, uses standard output of quantum chemical calculations, and in all tests carried out so far proved to be more accurate and much faster than the code POLYRATE of Truhlar et al. when dealing with tunneling. It is on the net, at http://www.nrc.ca/sims under "New software...", available for (controlled) free distribution. For contacts please write to Zorka Smedarchina at Zorka.Smedarchina@nrc.ca Sincerely, Zorka Smedarchina, Antonio Fernandez-Ramos, Marek Zgierski and Willem Siebrand. Steacie Institute for Molecular Sciences, National Research Council of Canada, 100 Sussex Dr. Ottawa, Ont., K1A 0R6 Canada. From chemistry-request@www.ccl.net Tue Nov 24 13:14:24 1998 Received: from romeo.ic.ac.uk (romeo.ic.ac.uk [155.198.5.9]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id NAA06783 Tue, 24 Nov 1998 13:14:15 -0500 (EST) Received: from oban.cc.ic.ac.uk [155.198.5.28] by romeo.ic.ac.uk with smtp (Exim 1.62 #1) id 0ziMyc-0000Fj-00; Tue, 24 Nov 1998 18:14:14 +0000 Received: from sg1.cc.ic.ac.uk ([155.198.63.8] helo=cscmgb.cc.ic.ac.uk) by oban.cc.ic.ac.uk with esmtp (Exim 1.90 #1) id 0ziMyZ-00025O-00; Tue, 24 Nov 1998 18:14:11 +0000 Received: from [155.198.224.86] by cscmgb.cc.ic.ac.uk (980427.SGI.8.8.8/4.0) id SAA25068; Tue, 24 Nov 1998 18:14:10 GMT Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-Sender: rzepa@155.198.63.8 Message-Id: Date: Tue, 24 Nov 1998 18:19:51 +0000 To: CHEMISTRY@www.ccl.net, watoc@ic.ac.uk From: "Rzepa, Henry" Subject: WATOC99: Online registration for Posters and Oral presentations If you are considering visiting the WATOC99 congress and wish to submit either poster, or a request to make an oral presentation, please note that you can now submit this via the URL http://www.chemsoc.org/watoc99/ or directly via http://www.chemsoc.org/watoc99/home.htm (Closing date January 15, 1999). Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; mailto:rzepa@ic.ac.uk; Tel (44) 171 594 5774; Fax: (44) 171 594 5804. URL: http://www.ch.ic.ac.uk/rzepa/ If my digital email signature is invalid, download a new root at http://www.belsign.be/en/services/receive/install-ca.html From chemistry-request@www.ccl.net Tue Nov 24 14:37:32 1998 Received: from mx.seanet.com (dns2.seanet.com [199.181.164.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id OAA07430 Tue, 24 Nov 1998 14:37:31 -0500 (EST) Received: from biggeek ([150.215.151.125]) by mx.seanet.com (8.8.8/Seanet-8.7.3) with SMTP id LAA00933 for ; Tue, 24 Nov 1998 11:37:23 -0800 (PST) Message-ID: <000701be17e1$dc0fdc60$7d97d796@biggeek.wrq.com> From: "Mark Thompson" To: Subject: OpenGL graphics accelerators & PII Xeon 450 Date: Tue, 24 Nov 1998 11:37:23 -0800 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0004_01BE179E.CD8AF460" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 This is a multi-part message in MIME format. ------=_NextPart_000_0004_01BE179E.CD8AF460 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable =20 I'm looking at the 3D Labs 3D GMX2000 graphics card for = chemistry-related graphics applications written with openGL. Does anyone have any = experience with this particular card, or similar high-end openGL accelerator cards? I'd like to hear from you. =20 Also, I'd like to find more information on performance comparisons = between the Intel PII 450 MHz and the PII Xeon 450 MHz (both with 512K cache) with = the usual suite of computational chemistry programs (running either Linux or Win32)? = I've seen the DGAUSS performanance numbers on the Intel website, but would like to = hear other experiences as well. Thanks in advance. I'll summarize for the list. Mark Thompson ------=_NextPart_000_0004_01BE179E.CD8AF460 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
   
I'm looking at the 3D Labs  3D = GMX2000=20 graphics card for chemistry-related
graphics = applications=20 written with openGL.  Does anyone have any experience
with this particular card, or similar high-end = openGL=20 accelerator cards?
I'd like to hear from you. 
 
Also, I'd like to find more information on = performance=20 comparisons between the
Intel PII 450 MHz and the PII Xeon 450 MHz (both = with 512K=20 cache) with the usual suite
of computational chemistry programs (running either = Linux or=20 Win32)?  I've seen
the DGAUSS performanance numbers on the Intel = website, but=20 would like to hear other
experiences as well.
 
Thanks in advance.  I'll summarize for the=20 list.
 
Mark Thompson
 
------=_NextPart_000_0004_01BE179E.CD8AF460-- From chemistry-request@www.ccl.net Tue Nov 24 14:56:59 1998 Received: from mailbox.syr.edu (root@mailbox.syr.edu [128.230.1.5]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id OAA07583 Tue, 24 Nov 1998 14:56:59 -0500 (EST) Received: from [128.230.59.17] (jello.cat.syr.edu [128.230.59.17]) by mailbox.syr.edu (8.9.1/8.9.1) with ESMTP id OAA12724 for ; Tue, 24 Nov 1998 14:57:01 -0500 (EST) X-Sender: desingh@mailbox.syr.edu Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 24 Nov 1998 15:00:16 -0500 To: Computational Chemistry List From: Deepak Singh Subject: SGI Octane Hi folks, I am thinking of upgrading my current workstation from a SGI Indigo2 to a dual processor octane. I have never used one, so I would appreciate of someone told me what it was like and whether it is as good as it sounds. MY primary programs are MOPAC, gamess, QUANTA/CHARMm and INSIGHTII (the latter two require SGI's). Thanks Deepak. ********************************************************************** Deepak Singh Email: desingh@syr.edu Graduate Fellow URL: http://web.syr.edu/~desingh Department of Chemistry and Biochemistry, Tel: (315) 443 1739 -- work Syracuse University (315) 472 9659 -- home 1-014 Scitech Syracuse NY 13244 Fax: (315) 443 4070 "Violence is the last resort of the incompetent". -- Salvor Hardin ********************************************************************** From chemistry-request@www.ccl.net Tue Nov 24 14:58:17 1998 Received: from mailbox.syr.edu (root@mailbox.syr.edu [128.230.1.5]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id OAA07604 Tue, 24 Nov 1998 14:58:16 -0500 (EST) Received: from [128.230.59.17] (jello.cat.syr.edu [128.230.59.17]) by mailbox.syr.edu (8.9.1/8.9.1) with ESMTP id OAA13201 for ; Tue, 24 Nov 1998 14:58:19 -0500 (EST) X-Sender: desingh@mailbox.syr.edu Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 24 Nov 1998 15:01:33 -0500 To: Computational Chemistry List From: Deepak Singh Subject: MOPAC97 Hi again, Can anybody tell me where I can get the source code for MOPAC97 or MOPAC95? QCPE only goes upto MOPAC93. Regards Deepak. ********************************************************************** Deepak Singh Email: desingh@syr.edu Graduate Fellow URL: http://web.syr.edu/~desingh Department of Chemistry and Biochemistry, Tel: (315) 443 1739 -- work Syracuse University (315) 472 9659 -- home 1-014 Scitech Syracuse NY 13244 Fax: (315) 443 4070 "Violence is the last resort of the incompetent". -- Salvor Hardin ********************************************************************** From chemistry-request@www.ccl.net Tue Nov 24 16:28:32 1998 Received: from wavefun.com (wave-fw.wavefun.com [209.125.133.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id QAA08476 Tue, 24 Nov 1998 16:28:28 -0500 (EST) From: Date: Tue, 24 Nov 1998 13:27:56 -0800 Message-Id: <9811241327.ZM2336@wavefun.com > In-Reply-To: Steven Creve "CCL:CCL:DFT:local-nl, SUMMARY" (Nov 23, 4:57pm) References: Reply-To: liang@wavefun.com X-Mailer: Z-Mail-SGI (3.2S.3 08feb96 MediaMail) To: Steven Creve Subject: Re: CCL:CCL:DFT:local-nl, SUMMARY Cc: CHEMISTRY@www.ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii > > concerning the discussion "local <-> non-local in DFT", my first > impression has been that there seems to be a lot of confusion on > definitions in this area. ------------------------------- > Local or nonlocal? > > Good question. "Gradient-corrected" functionals (Becke88, Perdew86, > Perdew-Wang91, etc...) are often called "non-local" but in my > opinion that's an unfortunate misuse of the term. I suppose they > came to be called "non-local" because they are NOT the usual local > density approximation (LDA). But "NOT the USUAL LDA" is not > synonymous with "nonlocal". ------------------------------- > I have always heard that local functionals are ones that use the > electron density only and nonlocal functionals are those that use a > gradient of electron density. It is not necessary to take into account > the density at other points because the gradient gives an extrapolation to > nearby points (to the extent that the density is approximately linear in a > localized region). > I guess there is a misunderstanding (of the terms local vs. nonlocal) in other terms: physics vs. math. The Fock exchange potential is a nonlocal operator, with a nonlocality mathematically extending to infinity and physically to the point where the magnitude of an atomic wave function vanishes. Going with every electron there is a hole created by the Pauli exchange rules and the repulsions missing in the Hartree potential. The shape and range of this hole is determined not only by the carrying electron itself but all the surrounding electrons. This is where the nonlocality comes from. The electron system is highly responsive and the perturbations along the trajectory can be quickly damped (screened) out. The effective range of the xc hole is limited (may be described by a characteristic length). This may be regarded as a "short sightedness" of electron systems. And in fact, it has been shown that much of the semiquantitative success of the LDA can be explained by a spherical average made to the skewed and singularity plagued xc hole (a luck?). Assuming a "slowly varying" density for an atomic system is too crude. There have been many efforts to go beyond this restrictive framework. The goal is to take into account the nonlocality, up to a finite distance in accordance with the short sightedness of electrons in a pool. This can be done with the help of a generalized Taylor expansion for the density around the very point r. The r' dependence is absorbed in the derivative terms of r. The term "generalized" refers to a treatment of the singular points (cusps) within the xc hole (which is a function of r and r'). The gradient corrections as they stand involve local operators depending on r only. But physically, the properties of the xc hole in the vicinity of the spatial point r have been described correctly, as approved by the success of GGAs. Also, without an explicit r' dependence, much computational cost can be saved. In my perhaps misrepresented vocabulary, the word "nonlocal" is a physical term, with a meaning which can be read as "it takes some nonlocality into account and goes beyond the local density approximations". There may be misunderstaninding of the physics in the above descriptions. Any oppositions (fires), please, direct to my e-mail address liang@wavefun.com Thanks, Liang Lou From chemistry-request@www.ccl.net Tue Nov 24 20:36:21 1998 Received: from hisui.icrs.tohoku.ac.jp (hisui.icrs.tohoku.ac.jp [130.34.28.34]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id UAA09812 Tue, 24 Nov 1998 20:36:20 -0500 (EST) Received: from grampus.icrs.tohoku.ac.jp (grampus.icrs.tohoku.ac.jp [130.34.28.143]) by hisui.icrs.tohoku.ac.jp (8.8.8+2.7Wbeta7/3.6Wbeta7+P9711) with SMTP id KAA05095 for ; Wed, 25 Nov 1998 10:40:06 +0900 (JST) Message-Id: <199811250133.AA00095@grampus.icrs.tohoku.ac.jp> From: shuichi@icrs.tohoku.ac.jp (=?ISO-2022-JP?B?GyRCQmdfNxsoQg==?= =?ISO-2022-JP?B?IBskQj0oMGwbKEI=?=) Date: Wed, 25 Nov 1998 10:33:06 +0900 To: chemistry@www.ccl.net Subject: MM3 parameter for methyl benzylamine MIME-Version: 1.0 X-Mailer: AL-Mail32 Version 1.10 beta2 Content-Type: text/plain; charset=us-ascii Dear CCL member; I'm interested in the stereochemistry of methyl benzylamine derivatives. I'm going to do MM3 calculation to find the conformers of this molecule. But MM3 does not provide some torsion parameters for it. And I could not find the subjets of methyul benzylamine parameters in this CCL archives. Then I would like to ask you about the information of following torsion parameters; 2-1-9-3; C(sp2 alkene)-C(sp3)-N(sp2)-C(sp2 carbonyl) 2-2-1-9; C(sp2 alkene)- C(sp2 alkene)-C(sp3)-N(sp2) 2-1-9-28; C(sp2 alkene)-C(sp3)-N(sp2)-H(H-N-C=O amide) Any information and references are cordially invited. _________________________________________________ OSAWA, Shuichi Institute for Chemical Reaction Science Tohoku University Katahira 2 chome, Aoba-ku Sendai 980-8577 JAPAN E-mail: shuichi@icrs.tohoku.ac.jp From chemistry-request@www.ccl.net Tue Nov 24 23:01:51 1998 Received: from send206.yahoomail.com (send206.yahoomail.com [205.180.60.172]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id XAA10046 Tue, 24 Nov 1998 23:01:50 -0500 (EST) Message-ID: <19981125040224.7595.rocketmail@send206.yahoomail.com> Received: from [209.61.76.150] by send206.yahoomail.com; Tue, 24 Nov 1998 20:02:24 PST Date: Tue, 24 Nov 1998 20:02:24 -0800 (PST) From: Jeff Liu Subject: gaussian performance on various computers To: CHEMISTRY@www.ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi, all, I'm going to purchase a work station (with unix or linus system) for the calculation of polycyclic aromatic compounds using Gaussian. Can anyone provide information on how gaussian perform on different work stations and the requirement for these work stations? Thanks a lot. Jeff _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com