From chemistry-request@server.ccl.net Fri Aug 25 04:34:32 2000 Received: from mail2.zrz.tu-berlin.de (mail2.zrz.TU-Berlin.DE [130.149.4.14]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA24069 for ; Fri, 25 Aug 2000 04:34:31 -0400 Received: from mailszrz.zrz.tu-berlin.de ([130.149.4.11]) by mail2.zrz.tu-berlin.de with esmtp (exim-3.16) id 13SEwR-0005H2-00; Fri, 25 Aug 2000 10:34:23 +0200 Received: from natrium.chem.tu-berlin.de ([130.149.42.210]) by mailszrz.zrz.tu-berlin.de with esmtp (exim-3.16) id 13SEwR-0006OS-00; Fri, 25 Aug 2000 10:34:23 +0200 Mime-Version: 1.0 X-Sender: chwu0531@mailszrz.zrz.tu-berlin.de Message-Id: In-Reply-To: <14755.61061.89062.707167@lrz.uni-muenchen.de> References: <14755.61061.89062.707167@lrz.uni-muenchen.de> Date: Fri, 25 Aug 2000 10:34:23 +0200 To: Eugene Leitl From: Christoph van =?iso-8859-1?Q?W=FCllen?= Subject: Re: CCL:Ahem, shouldn't we do something about it? Cc: chemistry@ccl.net Content-Type: text/plain; charset="us-ascii" As to the discussion of 'online publishing', my opinion is that if the contributions are not peer-reviewd (using the same quality standards as in the printed journals), there is always the risk that there will be some garbage among the contributions. In this case, not too many scientist will browse the contents. -- +---------------------------------+------------------------------------+ | Prof. Christoph van Wullen | Tele-Fon (+49) (0)30 314 27870 | | Technische Universitat Sekr. C3 | Tele-Fax (+49) (0)30 314 23727 | | Strasse des 17. Juni 135 | eMail: | | D-10623 Berlin, Germany | Christoph.vanWullen@TU-Berlin.DE | +---------------------------------+------------------------------------+ From chemistry-request@server.ccl.net Fri Aug 25 05:20:08 2000 Received: from wn1.sci.kun.nl (wn1.sci.kun.nl [131.174.8.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA24261 for ; Fri, 25 Aug 2000 05:20:08 -0400 Received: from studs3.sci.kun.nl by wn1.sci.kun.nl via studs3.sci.kun.nl [131.174.124.4] with ESMTP for id LAA29592 (8.8.8/3.29); Fri, 25 Aug 2000 11:19:59 +0200 (MET DST) From: "E.L. Willighagen" Received: by studs3.sci.kun.nl via egonw@localhost for chemistry@ccl.net id LAA01960 (8.8.8/3.1); Fri, 25 Aug 2000 11:19:58 +0200 (MET DST) Date: Fri, 25 Aug 2000 11:19:58 +0200 (MET DST) Message-Id: <200008250919.LAA01960@studs3.sci.kun.nl> To: chemistry@ccl.net Subject: re: Ahem, shouldn't we do something about it? > As to the discussion of 'online publishing', my opinion is that if the contributions > are not peer-reviewd (using the same quality standards as in the printed journals), > there is always the risk that there will be some garbage among the contributions. In this > case, not too many scientist will browse the contents. The Chemistry Preprint Server has a ranking mechanism, which allows readers to give a quality indication. But since these qualification is not only done by people in the same field of research it is very different from 'refereeing' in the sense it is done with journals... This could be circumvented by assining 'research interest' fields to persons and when this value is the same as for the article, extra weight can be given to the qualification... Egon From chemistry-request@server.ccl.net Fri Aug 25 05:48:45 2000 Received: from web1705.mail.yahoo.com (web1705.mail.yahoo.com [128.11.23.216]) by server.ccl.net (8.8.7/8.8.7) with SMTP id FAA24392 for ; Fri, 25 Aug 2000 05:48:44 -0400 Received: (qmail 15337 invoked by uid 60001); 25 Aug 2000 09:48:36 -0000 Message-ID: <20000825094836.15336.qmail@web1705.mail.yahoo.com> Received: from [161.142.4.9] by web1705.mail.yahoo.com; Fri, 25 Aug 2000 02:48:36 PDT Date: Fri, 25 Aug 2000 02:48:36 -0700 (PDT) From: sohail qamar Subject: enzyme SETUP To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear friend, I have a problem in setting up the model for enzyme using link edit parm.The charge is not 0.another thing is that i view in rasmol the chain is broken from various residues especially before or after HIP residues.If u are using leap i wellcome all suggestions. witj best regards, sohail. university sains malaysia. __________________________________________________ Do You Yahoo!? Yahoo! Mail - Free email you can access from anywhere! http://mail.yahoo.com/ From chemistry-request@server.ccl.net Fri Aug 25 06:16:47 2000 Received: from fecit-gate.fecit.co.uk (firewall-user@[193.119.134.250]) by server.ccl.net (8.8.7/8.8.7) with SMTP id GAA24536 for ; Fri, 25 Aug 2000 06:16:46 -0400 Received: by fecit-gate.fecit.co.uk; id LAA11810; Fri, 25 Aug 2000 11:23:05 +0100 Received: from suisei(192.168.101.50) by fecit-gate.fecit.co.uk via smap (V5.0) id xma011808; Fri, 25 Aug 00 11:22:23 +0100 Received: from fecit.co.uk (NT11.fecit.co.uk [192.168.101.116]) by suisei.fecit.co.uk (8.6.9/8.6.9) with ESMTP id LAA04799 for ; Fri, 25 Aug 2000 11:21:45 +0100 Message-ID: <39A64753.CA558D5F@fecit.co.uk> Date: Fri, 25 Aug 2000 11:15:47 +0100 From: Herbert Fruchtl Organization: Fujitsu European Centre for Information Technology X-Mailer: Mozilla 4.73 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Re: Ahem, shouldn't we do something about it? References: <14755.61061.89062.707167@lrz.uni-muenchen.de> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi there, I didn't follow the start of the discussion, so could somebody clarify if we talk about preprints of papers that a) possibly have been published in a journal b) possibly will be published in a journal c) are exclusively published on the web (making it an online journal) The questions associated with a) and b) mainly refer to the publishing policy of printed journals: a) Is this allowed? The journal owns the copyright. The author typically may give away copies, but publishing on the web is a step further. How do different journals handle this? From the user perspective, it's of course desirable, because not everybody has a well-stocked library in the same building (or the same city). b) Will journals accept something that's already on the web as "original and unpublished work"? c) The advantage is that it's faster than going through the refereeing and publishing process, and there are (rare) cases where more politics is involved than science. But won't it attract mainly the trash that would never make it past the referees? Archimedes Plutonium and friends (if you've ever read sci.physics, you know him)? I'm not sure if an open rating system would work either. Chances are that it will be hijacked by a few opinionated busybodies, while the majority of readers don't find time to submit a rating. Herbert From chemistry-request@server.ccl.net Fri Aug 25 10:44:58 2000 Received: from mcmail.cis.McMaster.CA (mattacf@mcmail.CIS.McMaster.CA [130.113.64.66]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA26479 for ; Fri, 25 Aug 2000 10:44:57 -0400 Received: from localhost (mattacf@localhost) by mcmail.cis.McMaster.CA with ESMTP id KAA29468 for ; Fri, 25 Aug 2000 10:44:45 -0400 (EDT) Date: Fri, 25 Aug 2000 10:44:45 -0400 (EDT) From: "C.F. Matta" To: CHEMISTRY@ccl.net Subject: Re: SUMMARY: How to rotate a PostScript file? In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Ups, forgot one more response..sorry about that: Response 10: Leif Norskov ========================= I think Corel Draw should be able to do it - but not for free. (check http://www.corel.com/) /Leif Norskov Novo Nordisk A/S LNL@novo.dk ___________________________________________________________________________ Cherif F. Matta tel. (905) 525-9140 ext. 22502 Chemistry Department fax (905) 522-2509 McMaster University _______________________ Hamilton, Ontario, CANADA L8S 4M1. | "Choice not chance ....................................................| determines one's Member of the Board of Governors of the University | destiny". Anonymous ___________________________________________________________________________ From chemistry-request@server.ccl.net Fri Aug 25 11:26:13 2000 Received: from Bayou.UH.EDU (root@Bayou.UH.EDU [129.7.1.7]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA26674 for ; Fri, 25 Aug 2000 11:26:13 -0400 Received: from [129.7.8.131] (K2.Chem.UH.EDU [129.7.8.131]) by Bayou.UH.EDU (8.8.8/8.8.8) with ESMTP id KAA05793; Fri, 25 Aug 2000 10:25:59 -0500 (CDT) User-Agent: Microsoft-Outlook-Express-Macintosh-Edition/5.02.2022 Date: Fri, 25 Aug 2000 10:26:01 -0500 Subject: Re: CCL:SUMMARY: How to rotate a PostScript file? From: Eric Bittner To: "C.F. Matta" , Message-ID: In-Reply-To: Mime-version: 1.0 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit on 8/25/00 9:44 AM, C.F. Matta at mattacf@mcmail.cis.McMaster.CA wrote: > > Ups, forgot one more response..sorry about that: > > Response 10: Leif Norskov > ========================= > I think Corel Draw should be able to do it - but not for free. > (check http://www.corel.com/) > > /Leif Norskov > Novo Nordisk A/S > LNL@novo.dk > > ___________________________________________________________________________ > > Cherif F. Matta tel. (905) 525-9140 ext. 22502 > Chemistry Department fax (905) 522-2509 > McMaster University _______________________ > Hamilton, Ontario, CANADA L8S 4M1. | "Choice not chance >> ....................................................| determines one's > Member of the Board of Governors of the University | destiny". Anonymous > ___________________________________________________________________________ > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To > Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > Hi, two free ways that work: you can rotate a PS file by simply editing it. It takes a bit of trial and error and you sort of have to know what to look for. use the graphics package in Latex to write a wrapper that loads the file, rotates it creates a dvi file with the new figure. This is really easy. As a last + costly method convert them to PDF (using acrobat distiller) and then edit the pdf file using adobe illustrator. -Cheers! ERB -- Prof. Eric R. Bittner Department of Chemistry Univ. of Houston http://eiger.chem.uh.edu/bittner/ From chemistry-request@server.ccl.net Fri Aug 25 12:51:24 2000 Received: from ivory.trentu.ca (trentu.ca [192.75.12.103]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA27046 for ; Fri, 25 Aug 2000 12:51:24 -0400 Received: from trentu.ca ([204.225.13.50]) by trentu.ca (PMDF V5.2-32 #29543) with ESMTP id <01JTDYVYHW62000FP6@trentu.ca> for chemistry@ccl.net; Fri, 25 Aug 2000 12:51:07 EDT Date: Fri, 25 Aug 2000 12:55:45 -0400 From: elewars Subject: SUMMARY DFT ORBITALS, WF To: chemistry@ccl.net Message-id: <39A6A510.163FFE7C@trentu.ca> MIME-version: 1.0 X-Mailer: Mozilla 4.7 [en] (WinNT; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en Friday, 2000 Aug 25 Hello, here is the summary of replies to my question about orbitals and wavefunctions in DFT. I got 12 replies: #1 D. Mathieu, #2 and #3 E. Scerri, #4 E. Proynov, #5 H. van Dam, #6 A. Bittner, #7 J. Spanget-Larsen, #8 U. Richter, #9 A. Shusterman, #10 K. Nguyen, #11 J. Smith, #12 R. Jensen. I hope no one has been overlooked. Thanks very much to all who responded. I don't think question 3 can really be answered definitively yet. I'll leave this topic with the thought that an electron density is an observable (it can be measured), while a wavefunction is a recipe, a prescription, a Vorschrift--use it in a certain way and you get the right answers. THE QUESTION Sat 2000 Aug 19 Hello, We know that in pure DFT (in contrast to wavefunction theory) there are are no orbitals and there is no wavefunction; the Kohn-Sham orbitals of current practical DFT methods were introduced to make the calculation of the electron density tractable. QUESTIONS (1) An important feature of ab initio (and semiempirical) calculations is that one can visualize the orbitals, particularly the HOMO and LUMO (frontier orbitals) and make chemical deductions. In a _pure_ DFT calculation a question about the shape and energy of these orbitals would be meaningless, right? (2) The Fukui function (R. G. Parr and W. Yang, J Am Chem Soc, 1984, 106, 4049) seems to be always discussed in the context of DFT; yet this function is "a chemical reactivity index in the sense of the frontier-electron theory of reactivity..." (R. G. Parr and W. Yang, "Density-Functional Theory of Atoms and Molecules", Oxford, New York, 1989, p. 101). But in pure DFT theory there are no frontier orbitals. Isn't this strange? (3) If, as has been suggested (Parr and Yang, "Density-Funtional Theory...", p. 53) wave mechanics can be reformulated without the wavefunction concept, what are we to make of the 80-year-old debate in physics and philosophy about the meaning of the wavefunction (wavefunction collapse, Schroedinger's cat, the many-worlds theory of QM, etc, etc, etc; see e.g. "Einstein, Bohr and the Quantum Dilemma", A. Whitaker, Cambridge University Press, Cambridge, 1996, and _many_ other books and papers...). Was this debate a meaningless exercise that would never have occurred if QM had been originally formulated in terms of electron (or more generally, particle) density rather than the wavefunction? Thanks, E. Lewars ==== THE REPLIES #1 Didier Mathieu, mathieu@ripault.cea.fr > In a _pure_ DFT > calculation a question about the shape and energy of these orbitals > would be meaningless, right? While the concept of orbitals is not necessary, it might be possible to define orbitals from the density obtained from "pure DFT"and its responses to changes of the Hamiltonian. It might then turn out that such orbitals, wile no physical observables, can be given some physical meaning a posteriori. > 1989, p. 101). But in pure DFT theory there are no frontier orbitals. > Isn't this strange? Why ? Fukui functions are defined independently of the notion of orbitals. Thus, I see them as an natural alternative - whithin DFT - to frontier orbitals and perturbation theory in order to interpret chemical reactivity. > papers...). Was this debate a meaningless exercise that would never have > occurred if QM had been originally formulated in terms of electron (or > more generally, particle) density rather than the wavefunction? In that case, I wonder how these physical concepts would have emerged. Clearly, the one-particule density is not suitable as it does not contains all the information about the system. However, QM has also been formulated in terms of the density matrix since the beginning. For me, probably for historical reasons, it is easier to grasp many QM ideas in terms of the wavefunction, also because some of the basic notions involve "interference effects", (sorry for being so conditioned by the wavefunction picture) and the phase of the wavefunction might be more suitable than the coherences of the density matrix to study them. On the other hand, in some cases, the influence of the environment on the quantum system considered is more naturally introduced in the density matrix formulation: for instance when adding the phenomenological relaxation rates T1 and T2 to the evolution equation in NMR. This sounds more natural than modifying the Shrodinger equation through adding a non-hermitian term to the hamiltonian. Cheers, Didier. === #2 Eric Scerri, scerri@purdue.edu But surely the shape of the electron density which would correspond to these orbitals could still be visualized if necessary, just as electron density can be in the ab initio wavefunction approaches. The two approaches are alternative ways of looking at the micro world. Whether one chooses to visualize, or not, is always an option in any theory. But perhaps you ar asking a more specific question like what do HOMO and LUMO electron density plots look like? Please clarify your question (1) eric scerri ------------------------------------------------- Eric Scerri PhD, Visiting Professor, Department of Chemistry & Biochemistry, UCLA, Los Angeles, CA 90095 USA --- I replied: Hello, I'll summarize the answers, maybe with some comments. But concerning your answer: in wavefunction theory we have a series of atomic or molecular orbitals, psi_1, psi_2,..., with increasing energy. I think that in a pure density functional theory we just have an electron density function, rho(r); not a series of electron densities. So there is no electron density rho_1 corresponding to a certain orbital , and another density rho_2 corresponding to another orbital, etc. Just one density function. But maybe I have overlooked something--so I am asking the chemical community for their thoughts. And it just occurrs to me that one might wonder how this fits in with photoelectron spectroscopy, which indicates that molecules have groups of electrons of different energies. thanks EL ==== #3 Eric Scerri I dont know enough about DFT to know the answer to this further point. I would guess that it is possible to recover some kind of shell tructure from DFT. Please let me know what you discover from others. I am also still puzzling over your No 3. You ask interesting philosophical questions. Please consider joining the Philchem list. the address can be found on the web pages for the International Society for the Philosophy of Chemistry after the section on the recent meeting in Poznan. ==== #4 Emil Proynov, proynov@chimie.umontreal.ca Dear Dr Elewards, I would suggest not to get so upset by those who claim that the Kohn-Sham (KS) determinantal wavefunction does not have a physical meaning. The SCF potential, as defined in the KS DFT scheme, determines a self-consistent field such that the KS determinant minimizes the electron kinetic energy and yields the exact electron density. It differs from the Hartree-Fock (HF) self-consistent field in what the latter is associated with the HF determinant (minimizes the total energy but does not yield the exact electron density). To any meaningful self-consistent field one can assign SCF one electron orbital picture with a portion of physical/chemical meaning in it. To my opinion there is nothing mysterious in the KS SCF field, just to keep in mind that it does not originate directly from the Schrodinger equation but from the Euler equation of the DFT variational task. It is true that in the latter one does not deal directly wavefunctions, but all the quantum mechanics with its postulates, theorems and paradoxes is hidden there in the exchange-correlation potential. You can find different opinions on this in the literature indeed. The matter is perhaps more complicated that I am trying to make it with this comment. Just to note that an increasing amount of theoretical studies use and refer explicitly to the KS SCF orbitals demonstrating their practical utility (see for example: I. Verdernikova et.al. Int. J. Quant. Chem. vol.77, 161 (2000)). Best wishes, Emil Proynov +-----------------------------+ | Emil Proynov | | proynov@chimie.umontreal.ca | +-----------------------------+ ===== #5 Hub van Dam, h.j.j.vandam@dl.ac.uk (Question 1) People try that sort of thing, yes. But I am not sure if this really works in cases where there is strong static correlation. In other words where you have a wavefunction (again) with multi configurations with large coefficients. (Q2) Yes, this seems very strange. (Q3) The 74 year old debate, autumn next year the Schroedinger equation will have been around for 75 years (I haven't heard any plans yet of how people want to commemorate this anniversary). I would like to think that quantum mechanics only obtained a firm foundation with Schroedingers wave-equations. Anyway, I don't think this was a meaningless exercise. Although the wavefunction in itself has no direct physical interpretation, we still need it to get the probability density right. I.e. the probability to find a particle at a certain point in space behaves like there is some superposition of waves involved. Trying to formulate quantum mechanics in terms of the electron density only, and at the same time including these superposition effects correctly is a far from trivial matter (I think it is save to say that this problem is unsolved). Therefore I think that although the wavefunction has not direct physical interpretation it is far from "meaningless" concept. Kind regards, Huub -- ======================================================================== Huub van Dam E-mail: h.j.j.vandam@dl.ac.uk CCLRC Daresbury Laboratory phone: +44-1925-603362 Daresbury, Warrington fax: +44-1925-603634 Cheshire, UK WA4 4AD ====== #6 Eric Bittner, bittner@uh.edu No, There is the issue of measurement, interference, causality, etc.. which you can not simply sweep under the rug by invoking a density. The debate over the ontology of quantum mechanics continues and is perhaps extremely relevant in the advent of quantum computers. Perhaps if your only interested in using quantum theory as an algorithm for making predictions about physical reality, the debate is pointless. However, if you really and truly want to understand the inner workings of nature, it is not. IF you do choose to only work with the density, rho(x), you are not representing the full physical picture. QM is completely formulated in terms of the density, which evolves under the continuity equation, AND the quantum Hamilton-Jacobi equation, \frac{\partial S}{\partial t} - H(p,q) - \frac{\hbar^2}{2m}\frac{1}{\sqrt{\rho}}\nabla^2 \sqrt{rho} = 0 where H(p,q) is the Hamiltonian with the canonical substitution p-> \nabla S/m and the last term is the quantum potential, Q. If you seek stationary states, i.e. d\rho/dt = 0, then the QHJ reduces to the time-independent Schrodinger equation. These equations of motion are easily derived from the Schrodinger eqn. by writing psi = R exp(i S/hbar) and defining the density as rho = |psi|^2. On the computational side of this: Bob Wyatt and I have recently developed methods to solve these equations of motion using ONLY the trajectories they imply...no wave function, no basis functions...only quantum paths. A pre-print version of one of our papers is included as an attachment (pdf format). -Cheers, Eric R. Bittner U. Houston -- Prof. Eric R. Bittner Department of Chemistry Univ. of Houston ========== #7 Jens Spanget-Larsen, jsl@virgil.ruc.dk (Q1) Or, in other words: "What Do the Kohn-Sham Orbitals and Eigenvalues Mean?". Stowasser and Hoffmann address this question in their recent paper - Ralf Stowasser & Roald Hoffmann: J. Am. Chem. Soc. 121, 3414-3420 (1999). Yours, Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Phone: +45 4674 2000 (RUC) Department of Chemistry +45 4674 2710 (direct) Roskilde University (RUC) Fax: +45 4674 3011 P.O.Box 260 E-Mail: JSL@virgil.ruc.dk DK-4000 Roskilde, Denmark ========= #8 Uwe Richter, uwe@nist.gov Hi, I'm very interested in answers to this questions. Please could you summarize or send me the responses directly? There are some people who even discuss virtual KS orbitals. Thanks, Uwe =========== #9 Alan Shusterman, Alan.Shusterman@directory.reed.edu These are great questions. I'd be grateful if you would pass along any answers you receive. Thanks, -Alan alan@reed.edu ==== Alan Shusterman Department of Chemistry Reed College Portland, OR ========= #10 Kiet Nguyen, Kiet.Nguyen@wpafb.af.mil Although there is considerable controversy in the literature concerning the meaning of Kohn-Sham orbitals, I think they are far from "meaningless". This topic has been carefully analyzed and reviewed.[1-5] Parr and Yang stated that "... one should expect no simple physical meaning for the Kohn-Sham orbital energies."[3] However, using the Janak theorem which "provides a meaning for the eigenvalues of the Kohn-Sham equation", they have connected the HOMO and LUMO energies to the ionization potential and electron affinity, respectively.[3] [1] E. J. Baerends and O. V. Gritsenko, J. Phys. Chem. A 101 (1997) 5383. [2] R. G. Parr and W. Yang, Density Functional Theory of Atoms and Molecules (University Press, Oxford, 1989). [3] J. P. Perdew, in: Density Functional Methods in Physics, edited by R. M. Dreizler and J. da Providencia New York, 1985), p. 265 [4] E. J. Baerends and O. V. Gritsenko, J. Phys. Chem. A 101 (1997) 5383. [5] R. Stowasser and R. Hoffman, J. Am. Chem. Soc. 121 (1999), 3414. Kiet A. Nguyen AFRL/MLPJ Laser Hardened Materials Branch Wright-Patterson AFB, OH 45433 Phone (937) 255-6671, Ext 3178 FAX (937) 255-1128 ========== #11 Jack Smith, Smithja@ucarb.com (We know that in pure DFT...no wavefunction) At least not explicitly. One-electron orbitals are not required for wavefunction theory either. I would say that the two approaches converge when you reduce it to N-electron density matrices (probably even at the 2-electron density matrix level). (The KS orbitals...electron density tractable) Particularly to make the kinetic energy part tractable. Orbitals also made wavefunction theory more tractable by introducing the pseudo-one-particle SCF equations, which further allowed for the formulation of the Roothan equations (for a basis set expansion approach). > My feeling is that Natural Orbitals from a CI calculation (eigenvectors of > 1-particle density matrix) should correspond to KS orbitals with > fractional occupations. Is there an analog to Natural Geminals (from the > 2-particle density matrix) in DFT? (In a pure DFT calc., a question about the shape and energy of these orbitals would be meaningless, right?) Orbitals, yes; orbital densities, no. The density differences between the neutral system and its various ionic states are in principle observable quantities (assuming you can get xray diffraction data for the ions). Under Koopmans' approximation these density differences should be the same as the orbital-derived densities. And the orbital energies should correspond to the ionization (electron attachment) energies. A similar correspondence can be defined for orbital density differences among different excited states. One thing that's missing from a pure density picture is the concept of overlap and orthogonality, which depend on the sign of the underlying one-electron orbitals (wavefunctions). Overlap is a key component of frontier orbital theory. Should it be? Is there a pure density analog? (The Fukui function.. But in a pure DFT theory these are no orbitals. Isn't this strange?) But there ARE frontier orbital DENSITIES. The +/- Fukui functions should correspond to the orbital densities mentioned above for whole electron changes (N +/-n). However, in an "open" sysem (in a Grand Canonical sense) where fractional electrons can come and go, the Fukui function can also be defined for infinitessimal changes in electron number - a continuous functional of the number of electrons. Thus, derivatives in the density wrt electron number can be defined even at N electrons. The corresponding derivative in energy would be the chemical potential, and the second derivative would be the hardness -- with no need to define a HOMO or LUMO and use crude finite difference approximations (along with Koopmans' approximation). > (3) > If, as has been suggested (Parr and Yang, "Density-Funtional Theory...", > p. 53) wave mechanics can be reformulated without the wavefunction > concept, what are we to make of the 80-year-old debate in physics and > philosophy about the meaning of the wavefunction (wavefunction collapse, > Schroedinger's cat, the many-worlds theory of QM, etc, etc, etc; see > e.g. "Einstein, Bohr and the Quantum Dilemma", A. Whitaker, Cambridge > University Press, Cambridge, 1996, and _many_ other books and > papers...). Was this debate a meaningless exercise that would never have > occurred if QM had been originally formulated in terms of electron (or > more generally, particle) density rather than the wavefunction? > It just means that all the debate is focused on the form of energy functional itself, the exchange and correlation parts in particular, rather than the wavefunction. One still has to explain the particle-wave duality of the electron beam experiments. The outcome is still probabilistic (non-deterministic for a given electron) whether you speak in terms of electron density or a wavefunction. The concepts of exchange and correlation are still very much "quantum" phenomena, whether you encapsulate in a quantum-constrained probabilistic wavefunction and a classical Hamiltonian (energy) operator, or in a classical-like probabilistic electron density and a quantum-constrained energy functional. DFT-KS and HF only converge when HF exchange is used, no correlation term is included, AND the Grand Canonical (GC) form of the density operator is used. DFT-KS and MC-SCF converge as the MC-SCF approach a full CI and the correlation functional approaches the "exact" expression, but again only if the GC form of the density operator is used. An interesting middle ground would be a Natural Orbital iteration on a small CI, or a VB wavefunction using non-orthogonal orbitals, or GC UHF using localized fractionally occupied nearly-orthogonal orbitals. (As you might tell, I'm a an advocate of the latter - which should have a correspondence with DFT-KS, given the right functional). My 2 cents' worth. - Jack -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Jack A. Smith || Union Carbide || Phone: (304) 747-5797 Catalyst Skill Center || FAX: (304) 747-4672 P.O. Box 8361 || S. Charleston, WV 25303 || smithja@ucarb.com -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- ===== #12 Roy Jensen, royj@uvic.ca Have you had any response to your questions. I would be very interested to hear the results. Please post a summary to the CCL. Roy Jensen =================== ================ ========= From chemistry-request@server.ccl.net Fri Aug 25 10:22:46 2000 Received: from mcmail.cis.McMaster.CA (mattacf@mcmail.CIS.McMaster.CA [130.113.64.66]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA26391 for ; Fri, 25 Aug 2000 10:22:46 -0400 Received: from localhost (mattacf@localhost) by mcmail.cis.McMaster.CA with ESMTP id KAA22272 for ; Fri, 25 Aug 2000 10:22:33 -0400 (EDT) Date: Fri, 25 Aug 2000 10:22:33 -0400 (EDT) From: "C.F. Matta" To: CHEMISTRY@ccl.net Subject: SUMMARY: How to rotate a PostScript file? In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, I would like to thank all those who kindly responded to my question: "how to rotate a postscript file": Rajendra Zope, Thomas Heine, Antonio Buljan, T. Daniel Crawford, Heidi M. Muchall, Xavier Fradera, David van der Spoel, Michael Braunschweig, Antonio Marquez Cruz. Thank you all. Here are their individual responses in the order received: Response 1: Rajendra Zope ========================== From: Rajendra Zope I am also in need of a package which can merge two or more postscript files into a single file. Please kindly notify me or summarize the responses to your querry. Rajendra Zope --------------------------------------------------------------------------- Rajendra Zope e-mail: rzope@cea.fr DRFMC/SI2A e-mail: zope@drfmc.ceng.cea.fr CEA-Grenoble Tel: 04 76 88 45 04 17, rue des Martyrs FAX: 04 76 88 51 60 F-38054 Grenoble Cedex 9 FRANCE -------------------------------------------------------------------- Response 2: Thomas Heine ======================== From: Thomas Heine 90 rotate (rotates by 90 degrees) 100 100 translate (translates in x/y direction which you will need to fix it to the place} Make sure to put it behind the bounding box (the stuff with the %) Thomas Response 3: Antonio Buljan ============================ From: Dr. Antonio Buljan the command is rotate alpha, where alpha is the angle. Now, alpha can be positive or negative. If you don't can do it, send the postscript file and I can fix it. I have some experience with this matter. Antonio Response 4: T. Daniel Crawford =============================== From: T. Daniel Crawford You could try (1) converting the PS file to a PNM using the pstopnm utility, (2) using pnmrotate to rotate the new image, and then (3) use pnmtops to convert back to a PS file. All three of these utilities are available on RedHat Linux systems, but I don't recall where to find them for other systems. A web search might help you there. -Daniel -- T. Daniel Crawford Department of Chemistry crawdad@vt.edu Virginia Polytechnic Institute and www.chem.vt.edu/chem-dept/crawford State University Response 5: Heidi M. Muchall ============================= From: Dr. Heidi M. Muchall just put 90 rotate for a counterclockwise rotation of 90 deg. or -90 rotate for clockwise. Any other angle will work, too. You might have to adjust the translate values, too. How's it going at Mac? Heidi ************************************************************* Dr. Heidi M. Muchall | e-mail: muchall@alcor.concordia.ca Assistant Professor | Department of Chemistry | and Biochemistry | Concordia University | phone: (514) 848-3342 Montreal, Quebec H3G 1M8 | Canada | fax: (514) 848-2868 ************************************************************* Response 6: Xavier Fradera ========================== From: Xavier Fradera you could also try using Gsview. I'm not sure about it, but I think it allows you to read a postscript file, change its orientation (i.e., portrait to landscape) and save it. Have a look at: http://www.cs.wisc.edu/~ghost/ Xavier. Response 7: David van der Spoel =============================== From: David van der Spoel put: rotate angle in front of the real code. Groeten, David. ________________________________________________________________________ Dr. David van der Spoel Biomedical center, Dept. of Biochemistry s-mail: Husargatan 3, Box 576, 75123 Uppsala, Sweden e-mail: spoel@xray.bmc.uu.se www: http://zorn.bmc.uu.se/~spoel phone: 46 18 471 4205 fax: 46 18 511 755 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Response 8: Michael Braunschweig ================================ From: michael braunschweig try the "rotation" package in latex. including the two ps files als pictures you can rotate them and create a new one. michael braunschweig department of chemistry university of dortmund germany Response 9: Antonio Marquez Cruz ================================ From: Antonio Marquez Cruz my $0.02 contribution: the command to rotate a file is x rotate where "x" is the rotation angle (positive as well as negative angles can be used). Try different values until you get the best fit of your two files. You may need also to translate your files at the same time. Dr. Antonio M. Marquez Dpt. of Physical Chemistry Dpto. de Quimica Fisica University of Seville Universidad de Sevilla E-41012 Seville (SPAIN) 41012-Sevilla Phone: 34-95-4557177 FAX: 34-95-4557174 ==================================================================== Cherif F. Matta ___________________________________________________________________________ Cherif F. Matta tel. (905) 525-9140 ext. 22502 Chemistry Department fax (905) 522-2509 McMaster University _______________________ Hamilton, Ontario, CANADA L8S 4M1. | "Choice not chance ....................................................| determines one's Member of the Board of Governors of the University | destiny". Anonymous ___________________________________________________________________________ From chemistry-request@server.ccl.net Fri Aug 25 10:34:48 2000 Received: from Bayou.UH.EDU (root@Bayou.UH.EDU [129.7.1.7]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA26447 for ; Fri, 25 Aug 2000 10:34:47 -0400 Received: from [129.7.8.131] (K2.Chem.UH.EDU [129.7.8.131]) by Bayou.UH.EDU (8.8.8/8.8.8) with ESMTP id JAA12126 for ; Fri, 25 Aug 2000 09:34:35 -0500 (CDT) User-Agent: Microsoft-Outlook-Express-Macintosh-Edition/5.02.2022 Date: Fri, 25 Aug 2000 09:34:36 -0500 Subject: On line preprint/reprint server. From: Eric Bittner To: Message-ID: Mime-version: 1.0 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit I've been following the discussion regarding a Chemistry Online preprint/reprint service. This already exists in the physics community and has been extremely successful and basically self reviewed. The URL is http://xxx.lanl.gov/ Sure, there is a lot of bolognia and you have to filter some of this out. But, it's a great way to get the really latest and greatest results and opinions. It's heavily theoretical (eq. quant-ph ) but there is certainly a healthy portion of experimental papers. Moreover, some of the best physics discussions I've seen have been posted on this server. Moreover, Phys. Rev. will consider postings to the LANL server as submissions if the author chooses to do inform PR of the posting. In fact, I have found that in some cases I have gotten *better* reviews (i.e. more critical) of preprints I've posted to LANL...often better and more critical than journal reviewers. (plus it's either in the open forum or by email. In either case, you know who your critics are.) Also, I've never seen "Archimedes Plutonium" or Mills (of Blacklight Power.com) post any thing on the server. I'd love to see Mills post his "hydrino" theory on the server. My $0.02 ERB -- Prof. Eric R. Bittner Department of Chemistry Univ. of Houston http://eiger.chem.uh.edu/bittner/ From chemistry-request@server.ccl.net Fri Aug 25 12:02:00 2000 Received: from lrz.uni-muenchen.de (root@A7ac0.pppool.de [213.6.122.192]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA26862 for ; Fri, 25 Aug 2000 12:01:57 -0400 Received: (from eugene.leitl@localhost) by lrz.uni-muenchen.de (8.8.8/8.8.8) id HAA19221; Fri, 25 Aug 2000 07:28:45 -0700 From: Eugene Leitl MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Message-ID: <14758.33437.452175.993925@lrz.uni-muenchen.de> Date: Fri, 25 Aug 2000 07:28:45 -0700 (PDT) To: CHEMICAL INFORMATION SOURCES DISCUSSION LIST Cc: Subject: Re: Chronicle: on Chem preprint servers In-Reply-To: References: X-Mailer: VM 6.71 under 21.1 (patch 4) "Arches" XEmacs Lucid Bachrach, Steven writes: > > First, NOTHING kept anyone from starting such an effort at any time in the > past. In fact, the Chemistry Preprint Server form ChemWeb is NOT the first > such effort in chemistry. Way back in 1994 and 1995 (ancient history on the > web), a Chemical Physics preprint server was enacted originating from Brown > University utilizing the same code as the LANL preprint server. This effort > was essentailly a failure as few authors submitted. I have a suspicion that the choice of the canonical publishing format used for http://xxx.lanl.gov (LaTeX), albeit being natural to physicists and mathematicians and convenient, since allowing automatical generation of multiple formats on the fly (necessary for future portability), was too intimidating for the typical chemist. AdobeAcrobat files (the de facto standard in online publishing) can be difficult to index/search, and I've noticed that some .pdf files do break GhostScript (a suite of applications created around a free PostScript interpreter) rendering. No robust OpenSource crossplatform reader is thus so far available, making .pdf a risky standard to adapt. (As far as I can tell .pdf prepared via the ps2pdf route renders ok with AdobeAcrobat). A scientific publishing standard has to be noncommercial, to guarantee its long-term readability. This can only be defined by a few-person independant commitee, who will also have to supply a demo implementation. > [...] > Third, there is no question that Chemweb is a subsidiary of Elsevier. > However, I question exactly what has been given to the Elsevier monopoly > here. When an author places an article into the preprint archive, the author > assigns no rights to Chemweb. The author retains the copyright and all > rights associated with the article. Elsevier cannot charge for access to the > article or reproduce it in any form without the express written consent of > the author. Chemweb (or Elsevier if you prefer) acts as the conduit for > access. Fairly subtle ad placement is the only source of income for Chemweb > for providing this service. (In the interest of full disclosure, I am on the > advisory board for the CPS.) I'd rather not give a single commercial body opportunity to establish itself as the de facto standard. Once a user base has been created, things will impercerceptibly start to change, commercial interests attempting to lock users into place, and to keep them there by balkanizing what for user's sake should remain a single community. Proprietary "standards" will be introduced, users will have to register themselves to allow tracking for marketing purposes, in absence of open mirrors, content is entirely at the publisher's mercy constituting a single-point failure, etc. The issue is much too important to be trusted to a single commercial vendor, however benign. As I understand, some of Elsevier's business practices are being frowned upon in the librarian/user community. Somehow, I do not believe that Elsevier's motives this time are entirely lily-white. > Lastly, my conclusion form the plenary session on online preprints was that > many people are unaware of what a preprint server is and what its > implications really are. Unquestionably, education of the chemical community > IS the first priority towards making any serious change to our publication > system. I concur with Steve Berry who argued at the plenary session that we > should be trying many different experiments, learning along the way, > adopting good things and throwing out those that fail. I view the CPS as > being one of the necessary experiments and hope that many more experiemnts > in publication (not just preprint severvices) will follow in the near > future. The question of peer-review in regards to e-preprint servers has come up in this thread. Both issues are independant of each other. A peer-review authority, whether commercial or free (as I understand peer reviewers are typically not being reimbursed for their pains) can of course digitally sign pointers to the documents in the public e-preprint archive, or store digitally signed peer-reviewed documents verbatim on their own server. I think it should be very possible to attract a minimal number of volunteer developers and have a sufficient number of administered storage and bandwidth donated for an alternative e-preprint server. Maybe it's time to move this to sourceforge. From chemistry-request@server.ccl.net Fri Aug 25 12:02:05 2000 Received: from [209.193.72.5] (boron.vcn.com [209.193.72.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA26868 for ; Fri, 25 Aug 2000 12:02:04 -0400 Received: from coffey.com (unverified [209.193.68.25]) by (Vircom SMTPRS 4.3.183) with ESMTP id for ; Fri, 25 Aug 2000 10:01:51 -0600 Message-ID: <39A699B5.5D3665D4@coffey.com> Date: Fri, 25 Aug 2000 10:07:19 -0600 From: phil stortz Reply-To: pstortz@coffey.com X-Mailer: Mozilla 4.7 (Macintosh; U; PPC) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Re: CCL:Ahem, shouldn't we do something about it? Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit there is always some garbage, particularly on the web. i'd rather read other opinions/research results and decide for myself. some garbage even gets through peer review. there could still be a mechanism to block papers from people who consistently post garbage, and who don't have any credentials. it would also be nice to have a brief summary of the authors credentials, even if not verified. it's been my experience that there are allot of politics involved with most of the science journals. Christoph van Wüllen wrote: > > As to the discussion of 'online publishing', my opinion is that if the contributions > are not peer-reviewd (using the same quality standards as in the printed journals), > there is always the risk that there will be some garbage among the contributions. In this > case, not too many scientist will browse the contents. -- "..a cynic is just a romantic who got mugged watching sausage being made last night" Klima and the Belmonts ("negations," 1964) From chemistry-request@server.ccl.net Fri Aug 25 14:57:33 2000 Received: from mta5.snfc21.pbi.net (mta5.snfc21.pbi.net [206.13.28.241]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA27884 for ; Fri, 25 Aug 2000 14:57:08 -0400 Received: from firstprinciples.com ([63.192.67.78]) by mta5.snfc21.pbi.net (Sun Internet Mail Server sims.3.5.2000.01.05.12.18.p9) with ESMTP id <0FZV00BIN2O4C4@mta5.snfc21.pbi.net> for chemistry@ccl.net; Fri, 25 Aug 2000 11:43:17 -0700 (PDT) Date: Fri, 25 Aug 2000 11:27:37 -0700 From: "Jason K. Perry" Subject: Ahem, shouldn't we do something about it? To: chemistry@ccl.net Reply-to: jkp@firstprinciples.com Message-id: <39A6BA99.DD9D9292@firstprinciples.com> Organization: First Principles Research, Inc. MIME-version: 1.0 X-Mailer: Mozilla 4.74 [en]C-PBI-NC404 (Win98; U) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en,pdf I'm a regular follower of the xxx.lanl.gov/cond-mat high temperature superconductivity e-print server (check out http://xxx.lanl.gov/list/cond-mat.supr-con/recent). The server has become a vital part of research in this particular field, where peer review is extremely slow (publication of theory papers routinely takes more than one year and is often subject to politics). There are no forums for ranking or commenting on the papers. It's just a fast delivery service for preprints. This, of course, is its biggest advantage. Some of the papers on this site have been uploaded after being accepted for publication in a journal, but most are uploaded in conjuction with journal submission. Physical Review even allows transfer of a paper directly from the Los Alamos server when submitting for publication on-line. The APS is definitely way ahead of the ACS in this arena. While I recognize that peer review is an important process for catching errors, and the papers on this site should be approached carefully, in general I like being able to judge for myself if a paper has merit or not. I definitely appreciate having access to the most cutting edge work in the field. I'm not sure yet how this might play out in chemistry. Research topics are much more diverse than in physics, and the review process is not quite as bad. This suggests the demand for an e-print server may be less. Still, I would like to see a server devoted to computational chemistry. Something in conjuction with CCL would be ideal... Jason Perry -- .................................................................. Jason K. Perry, Ph.D. First Principles Research, Inc. 8391 Beverly Blvd., #171, Los Angeles, CA 90048 phone (323) 465-9572 FAX (323) 465-2805 http://www.firstprinciples.com ..................................................................