From Steven.Creve@chem.kuleuven.ac.be Mon Mar 11 04:15:39 1996 Received: from hartree.quantchem.kuleuven.ac.b for Steven.Creve@chem.kuleuven.ac.be by www.ccl.net (8.7.1/950822.1) id DAA03234; Mon, 11 Mar 1996 03:57:43 -0500 (EST) Received: by hartree.quantchem.kuleuven.ac.be id AA32104 (5.67b/IDA-1.5 for Computational Chemistry List ); Mon, 11 Mar 1996 09:56:52 +0100 Date: Mon, 11 Mar 1996 09:56:51 +0100 (NFT) From: Steven Creve X-Sender: steven@hartree To: Computational Chemistry List Subject: CCL:G94:CCSD(T) Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Has anyone yet tried to run CCSD(T) jobs using Gaussian94/RevC.3 ? With the following input: $RunGauss %mem=3500000 %chk=test # CCSD(T)/6-31G** test scf=direct pop=none H2Si=CH2 + H. doublet 0 2 **Molecule specification** I get this output: ********************************************** Gaussian 94: IBM-RS6000-G94RevC.3 26-Sep-1995 11-Mar-1996 ********************************************** %mem=3500000 %chk=test Default route: SCF=Direct MP2=Direct ------------------------------------------ # CCSD(T)/6-31G** test scf=direct pop=none ------------------------------------------ L903/L905 and L906 can only do MP2. Error termination via Lnk1e in /soft/g94/l1.exe. I don't see any mistake in the input, so what is the problem? Steven -------------------------------------------------------------------------- Steven Creve steven.creve@chem.kuleuven.ac.be Labo Quantumchemie steven@hartree.quantchem.kuleuven.ac.be Celestijnenlaan 200F 3001-HEVERLEE tel: (32) (16) 32 73 93 BELGIUM fax: (32) (16) 32 79 92 From Armel.Lebail@cnrs-imn.fr Mon Mar 11 04:40:25 1996 Received: from naimn3.cnrs-imn.fr for Armel.Lebail@cnrs-imn.fr by www.ccl.net (8.7.1/950822.1) id EAA03255; Mon, 11 Mar 1996 04:01:43 -0500 (EST) From: Received: from naimn2 (naimn2.cnrs-imn.fr [194.214.57.34]) by naimn3.cnrs-imn.fr (8.6.10/jtpda-5.1-IMN) with SMTP id KAA31968 for ; Mon, 11 Mar 1996 10:01:05 +0100 Date: Mon, 11 Mar 1996 10:00:05 +0200 Message-Id: <96031110000555@naimn2.cnrs-imn.fr> To: CHEMISTRY@www.ccl.net Subject: Re: CCL:Making a crystal packing model in a computer X-VMS-To: SMTP%"CHEMISTRY@www.ccl.net" Dear H. Ogura, >Obviously, making such computer-based model is going to be a formidable >task. I have a few points for with I seek your advice. Programs calculating atomic coordinates are numerous and belong to different categories : distance calculation, structure display, structure refinement... At no cost for non-commercial users and even with sources, the list is long, see the well known Crystallography Virtual Library on the WEB : http://www.unige.ch/crystal/w3vlc/crystal_index.html and go to "software". > We would rather not use VRML... You should use it ! VRML applications are exploding with a lot of free stuff for all kind of operating systems and machines. You will find PDB to VRML converters, standalone (or plug-in) viewers distributed free with complete source (VRweb...), etc... A good crystallography-oriented entry point may be: http://fluo.univ-lemans.fr:8001/vrml/vrmlinfo.html A program which may do the whole job you need is STRUVIR, a STRUPLO to VRML converter for PC distributed with FORTRAN source, manual and examples. You have just to compile for your own UNIX machine. Available at the above address together with entries for other softwares as xtal-3d and certainly much more coming soon. Armel Le Bail - Laboratoire des Fluorures, CNRS-URA-449, Universite du Maine, 72017 Le Mans Cedex, FRANCE - armel@ONE.univ-lemans.fr or lebail@cnrs-imn.fr http://fluo.univ-lemans.fr:8001/ From owner-chemistry@ccl.net Mon Mar 11 04:50:33 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id DAA03164; Mon, 11 Mar 1996 03:30:44 -0500 (EST) Received: from aci.cvut.cz for strajbl@silicon.karlov.mff.cuni.cz by bedrock.ccl.net (8.7.1/950822.1) id DAA07919; Mon, 11 Mar 1996 03:30:33 -0500 (EST) Received: from ns.karlov.mff.cuni.cz by aci.cvut.cz (IBM VM SMTP V2R2) with TCP; Mon, 11 Mar 96 09:32:53 MET Received: from silicon.karlov.mff.cuni.cz by ns.karlov.mff.cuni.cz id aa22292; 11 Mar 96 9:22 MEZ Received: by silicon.karlov.mff.cuni.cz (940816.SGI.8.6.9/930416.SGI) for CHEMISTRY@ccl.net id HAA24872; Mon, 11 Mar 1996 07:38:46 -0800 From: Marek Strajbl Message-Id: <9603110738.ZM24870@silicon.karlov.mff.cuni.cz> Date: Mon, 11 Mar 1996 07:38:46 -0800 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: CHEMISTRY@ccl.net Subject: Summary: view spectrum Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear netters, this is a summary of replies to following posting: I am looking for X-windows program (freeware) for viewing spectra. What I need is just to view several spectra, possibly superimposed or windowed, and perform simple operations - scaling of spectrum, shrinking, zooming in and out, marking peaks etc. Preferably for X-windows or SGI platform. Format of data: XY ascii file or SpetraCalc format. On Mar 7, 2:10pm, James Vincent wrote: > Subject: Re: CCL:view spectrum > The general graphing program xmgr would probably work well. > It accepts data in a number of formats, allows you to easily mark > text anywhere on the graph. Perhaps this isn't what you meant but > it should be able to plot things in almost any way you like. > > Jim > > > Jim >-- End of excerpt from James Vincent On Mar 8, 9:23am, Carlo Nervi wrote: > Subject: Re: CCL:view spectrum > Dear Marek, > > > you could try http://chpc06.ch.unito.it/linux/linux_prg.html > a collection of Free Scientific Software available for > linux (but generally source code is availbale). > > Hope this help, > Carlo > > ---------------------------------------------------------------------------- > Dr. Carlo Nervi > Dipartimento di Chimica Inorganica, Chimica Fisica e Chimica dei Materiali, > via P. Giuria 7, 10125 Torino, ITALY > phone: (Italy)-11-6707508 | e-mail: nervi@chpc06.ch.unito.it > fax: (Italy)-11-6707855 | nervi@silver.ch.unito.it > http://chpc06.ch.unito.it/ >-- End of excerpt from Carlo Nervi On Mar 8, 9:47am, Marc-Andre Delsuc wrote: > Subject: Re: CCL:view spectrum > I don't know what you call 'spectra'. However, I am developping an NMR > processing software, working under Unix/Xwindow. > This program does what you say, of course, but actually does much more : > NMR processing (spectral analysis) of 1D, 2D and 3D NMR spectra; linear > prediction; maximum entropy; macro language; definable user interface; > etc.. > However it is free, and works on SGI, HP, Linux, SUN, etc... > If you fell like trying it, check : > ftp://tome.cbs.univ-montp1.fr/pub/gifa_v4 > > Good luck. > > _________________________________________________________________________ > Marc-Andre' Delsuc Centre de Biochimie Structurale > mad@cbs.univ-montp1.fr Faculte de Pharmacie > tel : (33) 67 04 34 36 15 av, Charles Flahault > fax : (33) 67 52 96 23 34060 Montpellier cedex > www : http://tome.cbs.univ-montp1.fr FRANCE > >-- End of excerpt from Marc-Andre Delsuc On Mar 8, 10:59am, jochen@sunserver1.rz.uni-duesseldorf.de wrote: > Subject: Re: CCL:view spectrum > Dear Marek, > > I am writing a program to display and fit high resolution LIF data > at the moment. You will be able to perform all the things you want to do > at a later stage (most things you are asking for should run within some > weeks). I am using Linux/XFree86 and the Motif toolkit. > > But I would also like to get information about existing programs, > since it would save me some time to take some routines out. > > Cheers, > Jochen > > > +-------------------------------------------+ > | Jochen Kuepper | > | | > | Heinrich-Heine-Universitaet Duesseldorf | > | Institut fuer Physikalische Chemie I | > | Universitaetsstrasse 26.43.02.29 | > | 40225 Duesseldorf | > | Germany | > | jochen@uni-duesseldorf.de | > | | > +-------------------------------------------+ >-- End of excerpt from jochen@sunserver1.rz.uni-duesseldorf.de On Mar 8, 12:35pm, Peter Gedeck wrote: > Subject: Re: CCL:view spectrum > I don't know of any special program for the display of spectra, but if you > use XY files you can always use GNUplot (several FTP-sites) or xmgr > (ftp://ftp.teleport.com/pub/users/pturner/acegr/ maybe now different). > The later requires Motif but this should be available on your SGI > platform. > > Yours, > > Peter >-- End of excerpt from Peter Gedeck From owner-chemistry@ccl.net Mon Mar 11 06:15:41 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id GAA04804; Mon, 11 Mar 1996 06:13:08 -0500 (EST) Received: from fstgds01.tu-graz.ac.at for hassler@fscm1.dnet.tu-graz.ac.at by bedrock.ccl.net (8.7.1/950822.1) id GAA08682; Mon, 11 Mar 1996 06:13:05 -0500 (EST) From: Received: from FSCM1.DECnet MAIL11D_V3 by fstgds01.tu-graz.ac.at (5.57/Ultrix3.0-C) id AA18316; Mon, 11 Mar 96 12:12:44 +0100 Date: Mon, 11 Mar 96 12:12:44 +0100 Message-Id: <9603111112.AA18316@fstgds01.tu-graz.ac.at> To: "chemistry@ccl.net."@FULTRX.dnet.tu-graz.ac.at Subject: MM3-parameters Dear members of CCL! I need MM3 parameters (stretching constants, torsional constants, bending parameters, etc.) for bonds containing Si,C,H,X (X=F,Cl,Br,I) (atoms arranged in all possible variations). Can you tell me, where I can find these parameters (literature, or another existing force field program already providing such parameters)? All replies are highly acknowledged! Best wishes to everyone Doz.Dr.K. Hassler Institut fuer Anorganische Chemie, Technische Universitaet Graz, Stremayrgasse 16 present e-mail: hassler@fscm1.tu-graz.ac.at From lliu@csb0.IPC.PKU.EDU.CN Mon Mar 11 07:15:43 1996 Received: from csb0.IPC.PKU.EDU.CN for lliu@csb0.IPC.PKU.EDU.CN by www.ccl.net (8.7.1/950822.1) id GAA05836; Mon, 11 Mar 1996 06:39:54 -0500 (EST) Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for chemistry@www.ccl.net id AA09540; Mon, 11 Mar 96 19:37:25 -0800 Date: Mon, 11 Mar 1996 19:37:24 -0800 (PST) From: Liu Liang To: chemistry@www.ccl.net Subject: Sybyl/Unity Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, I am going to use the Unity of Sybyl. As a beginner, I need some theoretic knowledge of the Unity. If you know where I can find the paper about it and successful examples, please send the message to lliu@ipc.pku.edu.cn. ------------------------------------------------------------------------------- Liu Liang( Leon Liu ) | Address Ph.D Student of Organic Chemistry | Building 30; Room 222 Chemistry Department | Peking University e-mail: lliu@ipc.pku.edu.cn | Beijing 100871 Phone: (86)10-2751490 | P. R. China ------------------------------------------------------------------------------- From juanca@daphne.qf.ub.es Mon Mar 11 11:15:43 1996 Received: from daphne.qf.ub.es for juanca@daphne.qf.ub.es by www.ccl.net (8.7.1/950822.1) id KAA10173; Mon, 11 Mar 1996 10:43:38 -0500 (EST) Received: from malva.qf.ub.es by daphne.qf.ub.es with SMTP (1.37.109.4/16.2) id AA04757; Mon, 11 Mar 96 16:40:16 +0100 X-Mailer: InterCon TCP/Connect II 2.2.1 Mime-Version: 1.0 Message-Id: <9603111643.AA19867@malva.qf.ub.es> Date: Mon, 11 Mar 1996 16:43:19 +0100 From: "Juan Carlos Paniagua" To: chemistry@www.ccl.net Cc: ccchuang@gate.sinica.edu.tw, gertvh@sci.kun.nl, hebant@ext.jussieu.fr, rgab@trpntech.com, wojnow@tiger.chem.uw.edu.pl, jordi@daphne.qf.ub.es Subject: CCL: 2nd summary: WYSIWYG LaTeX for Mac? Content-Type: Text/Plain; charset=US-ASCII Content-Disposition: Inline Dear CCL readers, I reproduce two interesting mails I received after sending my summary to the CCL. Thanks again. Original posting: > Does anybody know any WYSIWYG text editor for the Mac that > produces LaTeX code (something like wordperfect for the mac, that > allows viewing the codes in a separate window while you are writing)? > Expressionist generates LaTeX code, but it is not practical as > a text editor. Replies: ------------------------------------------------------------------------------ I noticed that people mentioned the text editor Alpha but did not mention that Alpha alone is not enough to work with LaTex. Along with Alpha you need a program like OzTex which compiles the raw LaTex and turns it into a .dvi file and also allows you to display that .dvi output in a Mac window. Alpha is set up to run OzTex (or any other LaTex compiler) from a menu option so it's relatively easy to compile the document when you want and makes Alpha feel like you're in a self-contained environment of sorts. Alpha also has a lot of support for LaTex commands from within its menus. Tom Pollard who responded to your message wrote pieces of that or maybe just the part for BibTex - I forget. Both Alpha and OzTex are shareware while TexTures is commercial software, I believe. Hope this helps. From: Bryan Marten ------------------------------------------------------------------------------ I think the most important one is missed in the summary. One Mac implimentation of LaTeX is called OzteX, available from ftp site "midway.uchicago.edu", in the pub/OzTeX/oztex directory. There are 3 versions, with the oldest version being freeware and newer versions shareware. I have not used OzTeX but many people used and praised it very much in the c.s.mac.apps group. If you search the hyperarchive for latex, you'll find a readme file that can lead you to it. From: Jie Yuan = www.uc.edu/~yuanj ------------------------------------------------------------------------------ From owner-chemistry@ccl.net Mon Mar 11 12:16:03 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id LAA11117; Mon, 11 Mar 1996 11:43:11 -0500 (EST) Received: from mailhub.cc.columbia.edu for shenkin@still3.chem.columbia.edu by bedrock.ccl.net (8.7.1/950822.1) id LAA15035; Mon, 11 Mar 1996 11:43:06 -0500 (EST) Received: from still3.chem.columbia.edu (still3.chem.columbia.edu [128.59.112.36]) by mailhub.cc.columbia.edu (8.7.3/8.7.3) with SMTP id LAA02690; Mon, 11 Mar 1996 11:43:00 -0500 (EST) Received: by still3.chem.columbia.edu (931110.SGI/930416.SGI.AUTO) for @mailhub.cc.columbia.edu:chemistry-request@www.ccl.net id AA03155; Mon, 11 Mar 96 11:42:59 -0500 Date: Mon, 11 Mar 96 11:42:59 -0500 From: shenkin@still3.chem.columbia.edu (Peter Shenkin) Message-Id: <9603111642.AA03155@still3.chem.columbia.edu> To: chemistry@ccl.net, chemistry-request@www.ccl.net Subject: Re: CCL:request for book recommendations I've found Loren Meissner's book to be most readable. You can breeze through it and understand F90 pretty well, if you already know f77. But this book isn't all-inclusive. Meissner's book is called "Fortran 90" and is published by PWS Publishing Company. A more inclusive reference that claims to cover everything in the standard is the "Fortran 90 Handbook", by Adams, Brainerd, Martin, Smith and Wagener. It's published by McGraw Hill. These same authors (or some of them) also have another book which is more tutorial in nature, but I've not seen this. There are a lot of others available, and you can find a list of them on the Fortran Marketplace WWW page; URL is: http://www.fortran.com/fortran/market.html Hope this helps, -P. **************** In Memorium, Minnie Pearl, 1913-1996, RIP ***************** *** Peter S. Shenkin, Box 768 Havemeyer Hall, Chemistry, Columbia Univ., *** *** NY, NY 10027; shenkin@columbia.edu; (212)854-5143; FAX: 678-9039 *** *** MacroModel home page: www.cc.columbia.edu/cu/chemistry/mmod/mmod.html*** From schrecke@zinc.chem.ucalgary.ca Mon Mar 11 14:15:44 1996 Received: from zinc.chem.ucalgary.ca for schrecke@zinc.chem.ucalgary.ca by www.ccl.net (8.7.1/950822.1) id NAA13735; Mon, 11 Mar 1996 13:59:40 -0500 (EST) From: Received: by zinc.chem.ucalgary.ca (AIX 3.2/UCB 5.64/4.03) id AA16614; Mon, 11 Mar 1996 11:48:57 -0700 Message-Id: <9603111848.AA16614@zinc.chem.ucalgary.ca> Subject: Summary: Conservation of Difficulty To: CHEMISTRY@www.ccl.net Date: Mon, 11 Mar 1996 11:48:56 -0700 (MST) Reply-To: schrecke@zinc.chem.ucalgary.ca (Georg Schreckenbach) X-Mailer: ELM [version 2.4 PL23] Content-Type: text Dear netters, here is my summary to the posting of the "Law of Conservation of Difficulty". I was truly amazed by the large number of responses I got. Appareantly, I found an interesting subject. Reading the responses was indeed a pleasure for me, therefore thanx to everybody who wrote! There are some really good thoughts hidden in this rather lengthy summary ... There seem to be two types of responses to this "conservation law". A number of writers agree (more or less) to my "law" and add some aspect or another to it. The other group points out that "Reducing the difficulty" is what science is all about, see, e.g., the example of the Maxwell equations in Vitaly Rassolov's mail. Before coming to the actual summary, I want to give proper credit, since I didn't "invent" this myself. Rather, I heard it in 1988 from Prof. H. Eschrig, Dresden, Germany. ---------------------------------------------------------------------- ---------------------------------------------------------------------- This was my original posting: ---------------------------------------------------------------------- ---------------------------------------------------------------------- Hi everybody, a couple of years ago, one of my theoretical physics professors cited the "Law of Conservation of Difficulty". I thought I should share this law with the computational chemistry community on the net. As the name suggests, the law states that the difficulty of a problem is conserved, no matter how you reformulate it. I will demonstrate this by a few examples. Take Density functional theory (DFT). We start off with the terribly complicated Schroedinger equation -- for the electrons in a molecule, say. We reformulate it in a very clever way to obtain DFT. Now what have we got? Indeed, we have a beautiful formulation of the same problem: the basic variable is the density, an observable that depends on three coordinates, rather than 3*N as is the case with the wave function. Thus, the problem has been simplified considerably. However, all the difficulty comes back in the exchange-correlation functional. (Remember that its functional form is unknown). Another example is given by Molecular Mechanics. Again, the very difficult problem of the time-dependent Schroedinger equation is reformulated as simple classical equations of motion. However, the difficulty is conserved. In this case, it pops up in the necessity to obtain reliable force fields. I suppose I have to modify the law somewhat since it is certainly possible to make life MORE complicated (by doing lots of stupid things). Maybe the "difficulty" is an entropy-like property? Does anybody want to comment on the above? If so, then I shall summarize to the net. In particular, I would like to get a reference ... Yours, Georg P.S. Don't take me too serious on this one ... ---------------------------------------------------------------------- ---------------------------------------------------------------------- And these are the various answers: ---------------------------------------------------------------------- ---------------------------------------------------------------------- Huang Tang writes: (tang@Xtended.chem.cornell.edu) Interesting law :-) I would go further to apply the law of ever increasing entropy: you never replace a single (complicated) work with a single simpler work. So, DFT and MM replace ab initio work with many, many trivial, time consuming small jobs to tackle each problem. On the human side, we diverse a single work supposedly done by computer (say solve the HFR equations) to many smaller jobs for us (constructing force field.) Cheers... Huang TANG ---------------------------------------------------------------------- Richard A Caldwell writes: This reads like it's related to what I have always called "Caldwell's First Law:" "To solve a problem, you must first create it." Have a good day, Dick CAldwell ---------------------------------------------------------------------- Randy J. Zauhar writes: George, That is an excellent observation. Indeed, I think there is an entropy/complexity issue in this. In a system with complex interactions (i.e. a system of protons and electrons) you can try to "condense" obervables together (as in your example of particle density in DFT) - neverthless, to make predictions about that system, your model must somehow take into account the information embodied in the various interactions found in the original system. If you are lucky, the information in those interactions is unimportant for the predictions you want to make, in which case you can create a simple and useful model - if not, then the complexity you threw away must be reintroduced somewhere else. I am sure that physicists with interest in information theory have thought long and hard about this. Regards, Randy All opinions expressed here are mine, not my employer's ///////////////////////////////////////////////////////////////////////// \\ Randy J. Zauhar, PhD | E-mail: zauhar@tripos.com // \\ Tripos, Inc. | : zauhar@crl.com // \\ 1699 S. Hanley Rd., Suite 303 | Phone: (314) 647-1099 Ext. 3382 // \\ St. Louis, MO 63144 | // ///////////////////////////////////////////////////////////////////////// ** ** ** "If you have conceptions of things that you can have no conception ** ** of, then the conception and the thing appear to co-incide." ** ** --- C.G. Jung ** ************************************************************************* ---------------------------------------------------------------------- Vitaly Rassolov writes (rassolov@chem.nwu.edu) As far as I remember, Mach (the same as in Mach number of hydrodynamics) said that the purpose of science is to save time. That is, by discovering general laws we spare followers from unnecessary details. It seems to me that such view of science is closely related to "Conservation of Difficulty": the purpose of science becomes the reduction of difficulty. Indeed, if we simply reformulate the problem, the degree of difficulty remains the same, so no science was per- formed. However, the truly valuable scientific contributions are precisely those which help to deal with difficulties. Maxwell equations, for instance, greatly simplify building of electrical devices (i.e. reduce difficulty in their construction). If one adheres to such view, the law on "Conservation of Difficulty" becomes the measure against which we can check the progress of science. Vitaly Rassolov Northwestern University ---------------------------------------------------------------------- "Robert W. Zoellner" writes Subject: Conservation of Difficulty, perhaps Just an aside to your perhaps basic law of nature: I recently built a deck outside of our house, and decided that digging the holes for the supports would be too difficult using only hand tools such as picks, shovels, and the like (even with my friend helping). So, I rented a gas-powered auger, for two men, to do the job. The upshot of all of this was our conclusion: The work needed to do a job does not change with the tools used: All that changes is the intensity of the work during the time needed to finish the job. We were just as tired after drilling one hole with the auger as we were after digging one hole with our hand tools. Thus, not only the conservation of difficulty, but a conservation of work and effort! A loose application to computational chemistry is possible, I suppose, in that you begin with semi-empirical methods because that is all that your computer can handle in a reasonable period of time, and then move to ab initio when you can afford to, but the overall effort required is probably about the same, especially when you factor in the time it took to get the proper computer for the job! Oh well.... Have fun with your question! Bob Z. ---------------------------------------------------------------------------------- Hugh Kennedy writes (P8946019@vmsuser.acsu.unsw.EDU.AU) Simplifications and compressions are always possible: that's what science is all about; without them, our models and calculations would be as complex as the natural systems we are trying to understand. Hugh Kennedy ---------------------------------------------------------------------------------- Dave Young writes: (this article was posted on the list and produced some spin-off discussion) Georg writes: > > a couple of years ago, one of my theoretical physics > professors cited the "Law of Conservation of Difficulty". > I thought I should share this law with the computational > chemistry community on the net. > > As the name suggests, the law states that the difficulty > of a problem is conserved, no matter how you reformulate it. > I will demonstrate this by a few examples. I will agree that there are very often trade offs in the difficulty of methods. However, I will not admit to any sort of law of conservation. Let me give a counter example. Consider the solution of the Schrodinger equation for the hydrogen atom. If we did not know the exact solution we could put incredible amounts of work into extremely accurate calculations using DFT, GTO expansions, cubic splines, polynomials, etc. Now consider how difficult hydrogen atom calculations could be even knowing the exact solution. The logarithm and exponential functions have proven so useful that they have been built into calculators and programming languages and reliably return results to the precision of the machine. If this were not the case, we would have to spend quite a bit of time making sure that we are accurately computing exponentials and logarithms, or we could have an enormous database holding a table of logarithms ( 60 years ago every scientist and engineer had a table of logarithms handy at all times ). Now extrapolate from our current state of theory. If we knew the exact analytic solution to the Schrodinger equation for molecules most of what we do now would be trivial on the smallest PC. This would still not prevent computational chemists from eating every bit of computer power in sight as they tried to either deal with relativistic effects or the transport of drugs through cell wall membranes. Although computers are incredibly powerful tools that I would not want to live without, they have also made us lazy. In the past such scientific problems would have either been shelved until the mathematicians had come up with a technique for solving it or scientists would have worked on it until a solution was found. Although numerical techniques allow us to jump past the development of mathematics, sooner or later we will have to go back and get the original problem right. I firmly believe that the Schrodinger equation will one day be as easily dealt with as trignometric functions on a calculator. Now ask your self two questions. 1. How important would it be to work on an analytic solution to the Schrodinger equation? 2. What would be the chances that you could get funding for this project? I will let you draw your own conclusions. Dave Young young@slater.cem.msu.edu ========================================================================== No assumption or approximation is reasonable for all cases. Corollary: Assumptions must be both rationalized and checked. But it is more important to check them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- David writes Equivalence of computational complexity is well known. If you could solve the traveling salesman problem, you could solve many other difficult computing problems. By gross extrapolation, not only have alot of smart people been trying to find simple analytical solutions to the solutions to the many body Schroedinger equation without success, many more people in other fields have been working on problems that are computationally equivalent, also without success. If there is a simple solution, finding it certainly is not easy! That most of the problems we have solved tend to have simple solutions (Occam's razor), does not imply that all problems have simple solutions. Maybe we just are not smart enough to solve the problems with really complicated solutions. The conclusion from computer science is that there seem to be whole classes of problems that are just plain hard. David -------------------------------------------------------------------------- Konrad Hinsen writes: Cc: chemistry@www.ccl.net > right. I firmly believe that the Schrodinger equation will one day > be as easily dealt with as trignometric functions on a calculator. Which means by numerical approximation ;-) Seriously, I wonder what your confidence is based on. Of course it may be possible to find further analytic solutions, but I don't see why this should necessarily be true. Much less do I see how you can make such a claim for *all* applications of the Schroedinger equation. Of course all this depends on what you call a "solution". In the case of trigonometry, all we have is a set of analytic relations between various functions that often occur together. With the exception of a few special cases, there is no "analytic" answer to a trigonometric problem, in the sense that the result cannot be expressed in simpler functions (i.e. sums, products, and powers). A comparative level of "solution" of the Schroedinger equation would be a safe numerical procedure that can find the solution to any problem to a specified accuracy. This procedure could then be put into the theoretical chemist's equivalent of a pocket calculator. If that's what you mean by solution, I agree that it will probably one day be available. ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsenk@ere.umontreal.ca Departement de chimie | Tel.: +1-514-343-6111 ext. 3953 Universite de Montreal | Fax: +1-514-343-7586 C.P. 6128, succ. Centre-Ville | Deutsch/Esperanto/English/Nederlands/ Montreal (QC) H3C 3J7 | Francais (phase experimentale) ------------------------------------------------------------------------------- Liang writes (liang@wavefun.com) On Mar 5, 12:48pm, wrote: > > a couple of years ago, one of my theoretical physics > professors cited the "Law of Conservation of Difficulty". > I thought I should share this law with the computational > chemistry community on the net. > > As the name suggests, the law states that the difficulty > of a problem is conserved, no matter how you reformulate it. > I will demonstrate this by a few examples. Seems that the difficulty of obtaining the exact solution is conserved. > > Take Density functional theory (DFT). We start off with the > terribly complicated Schroedinger equation -- for the electrons > in a molecule, say. We reformulate it in a very clever > way to obtain DFT. Now what have we got? Indeed, we have a > beautiful formulation of the same problem: the basic variable > is the density, an observable that depends on three coordinates, > rather than 3*N as is the case with the wave function. > Thus, the problem has been simplified considerably. > However, all the difficulty comes back in the exchange-correlation > functional. (Remember that its functional form is unknown). > Seemingly you are not enjoying the saved computer time for the O(N^4) HF exchange calculations and growingly feel annoyed by the inherited inaccuracy. The God solves SEs exactly and He bleesed by giving chances to measure the observables as His own SE solutions. The not blessed has to model the world approximately. I do not bother with this law. As long as there are still ways to go around the most difficult and possibilities to trade the last few percent accuracy for the time needed to draw a picture of any quality anyway. The real artists possess the perfectness and the exactness. > Another example is given by Molecular Mechanics. Again, the > very difficult problem of the time-dependent Schroedinger equation > is reformulated as simple classical equations of motion. > However, the difficulty is conserved. In this case, it pops up > in the necessity to obtain reliable force fields. > I dreamed of living a simple life: doing things with one method never trying a second. Will trust the ConsumersReport to find the best buys as long as the magzine is reliable. Buy the simplest camera equipted with the most sophisticated computer chip. If not yet available, demand one from the manufactures. > > I suppose I have to modify the law somewhat since it is certainly > possible to make life MORE complicated (by doing lots of stupid > things). Maybe the "difficulty" is an entropy-like property? > Agree. And I hear the LAWd saying: minimize the entropy on your own; let it grow elsewhere. The buddism advises not to take any initiatives so that the total entropy could be conserved. > > Does anybody want to comment on the above? > If so, then I shall summarize to the net. In particular, I > would like to get a reference ... > Done. > Yours, Georg > > P.S. Don't take me too serious on this one ... > It's really a fun to read the broadcasting and write the comments. Have a good day! Liang ------------------------------------------------------------------------------- Michael K. Gilson writes (gilson@indigo14.carb.nist.gov) The discussion raises the following possibly naive question: Are there mathematical problems that can be solved analytically, whose numerical solutions look like hard, NP-complete problems? Mike ------------------------------------------------------------------------------- Jan Reimers writes > Take Density functional theory (DFT). We start off with the > terribly complicated Schroedinger equation -- for the electrons > in a molecule, say. We reformulate it in a very clever > way to obtain DFT. Now what have we got? Indeed, we have a > beautiful formulation of the same problem: the basic variable > is the density, an observable that depends on three coordinates, > rather than 3*N as is the case with the wave function. > Thus, the problem has been simplified considerably. > However, all the difficulty comes back in the exchange-correlation > functional. (Remember that its functional form is unknown). I have never found DFT to be that beautiful, I don't understand what it contributes beyond what J.C. Salter already showed us years before with his Chi-alpha approximation to exchange function. Besides the reduction from 3N to 3 coordinates is essentially the one elctron approximation, The mean field approximation, the product wave function approximation, or whatever you want to call it. Its not specific to DFT. If Kohn and Sham told us how to evaluate the kinetic energy as a functional of the density, then I would say DFT was "beautiful". Since we don't know how to do this we expand the density as sum of occupied orbitals, and we are right back to Slaters formulation. In exchange (no pun intended) for making approximations you get reduced diffictulty. So in this sense DFT does not conserve difficulty. You appriximate Vxc with some empirical functional, and you fit the density and Vxc with an auxillary basis, and it all pays off by reducing an N**4 compution to and N**3 computation. Does saving computer time count as dercreased difficulty, our are you using a more abstract (subjective?) definition? > > P.S. Don't take me too serious on this one ... > OK +--------------------------------------+-------------------------------------+ | Jan N. Reimers, Research Scientist | Sorry, Don't have time to write the | | Moli Energy (1990) Ltd. B.C. Canada | usual clever stuff in this spot. | | janr@molienergy.bc.ca | | +--------------------------------------+-------------------------------------+ -------------------------------------------------------------------------------- John Reissner writes: What I always heard about "C.o.D" was that it referred to the fact that while solved problems seemed easy in retrospect, ("the easy problems have all been 'picked off'"), in fact historically all problems were equally difficult, i.e. just barely soluble. John John Reissner Pembroke State University Pembroke NC 28372 USA reissner@pembvax1.pembroke.edu vox: (910)521-6425 fax: (910)521-6649 -------------------------------------------------------------------------------- Ole Swang writes (oles@kjemi.uio.no) >As the name suggests, the law states that the difficulty >of a problem is conserved, no matter how you reformulate it. Interesting view, and the observation seems empirically true. As for reasons, I have the feeling that it doesn't necessarily express some mystical property of nature - except that nature is more compicated than any model we will ever come up with. I would like to put forth some loose thoughts: The criterion for good science is how good all the other scientists think it is. If you produce a successful simplification of a model, then it is possible to describe more complicated systems with it, and that will promptly be done. The level of complexity is limited to what the human brain can cope with; but in science, we always try to push our brains to the limit (or at least, we should try to do so). If a problem gets less complicated, we quickly finish it off and go for something bigger ... and then things are just as complex as they used to be. All the best, Ole Swang -------------------------------------------------------------------------------- Rene Fournier writes ( Subject: Law of conservation of difficulty: violations. On the same humoristic tone ... (I am citing the graph from memory from a very interesting lecture by P. O. Lowdin; my apologies for possible misrepresentation of his good words). I think there are important violations of the "law of conservation of difficulty". This happens when someone has a powerful intuition about how to solve a problem. Here is a humoristic illustration of this. The graph below pretends to show the error measured relative to experiment as a function of the level of theory. Contrary to expectation, accuracy does not improve monotonously with increasing sophistication of the theory: the graph is reminiscent of the radial part of a 3s function, not a 1s. The 3 nodal (zero-error) regions are where quantum chemists try to be. If you have poor physical/chemical intuition, or if you are obsessed with the fear of being largely in error, you have to settle for hard work and mathematical wizardry and painfully work your way down the x axis towards full CI calculations. If you're clever, AND willing to take the risk of saying a few foolish things from time to time, you can work in an intermediate region which you might call "HF/6-31G" (or, nowadays, B3LYP//6-31G ?). Only a handful of geniuses can work at "Pauling's level" and still be right most of the time. ^ | | | x x x |x (Beginning E |x / graduate students) r |x / r |x / o |x / (Experienced graduate students) r | x \ | x \ | x \ (Postdocs) | x \ / Really, REALLY tough | x x x / / fully ab initio | x Pauling's level x x / / calculation. | x of theory x x / / (tenured profs) | x / x x / | x / x | x / Full CI | x / x |---> x / 0| |x | | x | | x / ----|--|-x|--------|--x--|------------------|-----------------------------x--> |0 | x| | x | | Level of theory; | x x Computational effort | x x \ | x x \ | x x Hartree-Fock 6-31G | level of theory | Cheers, Rene. |---------------------------------|-----------------------------| | R. Fournier | fournier@physics.unlv.edu | | University of Nevada Las Vegas | fournie@ned1.sims.nrc.ca | | Department of Physics | | | 4505 Maryland Parkway | phone : (702) 895 1706 | | Las Vegas, NV 89154-4002 USA | FAX : (702) 895 0804 | |---------------------------------|-----------------------------| =========================================================================== =========================================================================== (End of summary) ============================================================================== Georg Schreckenbach Tel: (Canada)-403-220 8204 Department of Chemistry FAX: (Canada)-403-289 9488 University of Calgary Email: schrecke@zinc.chem.ucalgary.ca 2500 University Drive N.W., Calgary, Alberta, Canada, T2N 1N4 ============================================================================== From owner-chemistry@ccl.net Mon Mar 11 17:15:55 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id RAA16158; Mon, 11 Mar 1996 17:09:53 -0500 (EST) Received: from phem3 for R29CLOSE@ETSU.EAST-TENN-ST.EDU by bedrock.ccl.net (8.7.1/950822.1) id RAA25607; Mon, 11 Mar 1996 17:09:52 -0500 (EST) From: Received: from ETSU.EAST-TENN-ST.EDU (MAILER@ETSU) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #5888) id <01I27XH7VAI88WXNGK@phem3.acs.ohio-state.edu>; Mon, 11 Mar 1996 17:09:40 EST Received: from ETSU.EAST-TENN-ST.EDU (NJE origin R29CLOSE@ETSU) by ETSU.EAST-TENN-ST.EDU (LMail V1.2a/1.8a) with BSMTP id 6434; Mon, 11 Mar 1996 17:08:36 -0500 Date: Mon, 11 Mar 1996 16:43:19 -0500 (EST) Subject: Crystal Packing To: chemistry@ccl.net Message-id: <01I27XH8X2GM8WXNGK@phem3.acs.ohio-state.edu> Organization: East Tennessee State University X-Envelope-to: chemistry@ccl.net Content-transfer-encoding: 7BIT Reply to Hiroshi Ogura: I am amazed at how many people have written this group in the past few years about generating crystal structures. Each time someone responds with a hint about using a commercial package like Sybil or HyperChem. I don't have access to either of these programs, so have been working on this problems over the past few weeks. My solution was to take the old Oak Ridge packages like ORFEE and ORTEP and modify them to generate any number of unit cells. The appeal of using these packages is that one doesn't have to reinvent any codeing for mole- cular transformations. So far I have a simple FORTRAN program that takes the xyz coordinates from a crystal paper and generates the unit cell. For the old timers you know that the notation for the first molecule is 55501. If there are 4 molecules in the unit cell, these are just specified as 55502, 55503 and 55504. One can then move these up an axis (say b) by just specifying 565xx, etc. Real simple. My program does this and then outputs a file to BABEL. I then use BABEL to generate an ALCHEMY file. I use ALCHEMY to view the molecule. It works. But I can't streamline it because I don't have the BABEL source code. If I did, I could compile the whole. routine. So there are several steps involved, but it seems to work. I am sure that the people with commercial packages think this is all a waste of time. I realize that commercial packages can generate a unit cell from the xyz coordiates, but can they really generate several unit cells? This is really what's important if your looking for nearest neighbors. I looked at several packages that could not determine, for example, all the atoms 4-5 Angstroms from a particular part of any molecule. Since ORFEE is so good at doing this, I decided to modify the program rather that buy something that may or may not really work. If this is of interest to anyone, write me and I will send you the FORTRAN code. Regards, Dave Close.