From chemistry-request@ccl.net Thu Sep 26 09:42:46 1991 Date: 26 Sep 91 09:28 LCL From: PA13808%UTKVM1.BITNET@OHSTVMA.ACS.OHIO-STATE.EDU To: CHEMISTRY@ccl.net Subject: BITNET mail follows Status: R HOMOS AND LUMOS I agree with everything that Michael Frisch said and would like to a add the following concerning the meaning of LUMOS. If you look at what yo you are doing when you perform HF calculations on a neutral molecule you will see that you iterate using the ground state bond order matrix and that the unoccupied orbitals are largely determined by the requiremen ts that they be orthogonal to both the ground state orbitals and with eac other. This is the chief reason why you should not compare MOs from calc using diff basis sets. IF you add diffuse orbitals the will mix in a and also depress the energy purely by this orthogonality requirement. It is also possible that the added basis will create a new virtual MO which is lower in energy than what was the LUMO. This will now become the new LUMO.To sort this out you need to do Anions with diffuse functions and that is not easy. Mine hardly ever converge smoothly. Another problem, especially for molecules with low lying LUMOS is that you are locked in to a particular config by the initial choice of a particular HOMO and LUMO, the no matter how you do the calc you will end up with the wrong LUMO and HOMO. Most abinitio programs allow you switch the occupation of MOs but it is a tricky business, but you must be aware of this problem. As soon as you get away from hydrocarbons, for which the pairing theorem holds,you can easily get answers which are physically meningless. This is MY view. For a more optimistic view look at papers by Ken Jordan(PTTSBURGH) in CHEM REV and ACC Chem RES a few years ago ALSO a very recent paper on sigma * MOs by semiemp methods E lindholm J phys CHEM vol 95 p3923 1991. John E. BLOOR(BLOOR AT UTKVM1) PS I have just remembered that Fukui was awarded the Noble prize for his frontier orbital model using HOMOs and LUMOs so they must have some value. BY the way to those of you who are privileged to be invited to suggest potential Noble prize winners its time to have another theoretical chemist. From chemistry-request@ccl.net Thu Sep 26 12:46:18 1991 Date: Thu, 26 Sep 91 12:36:46 EDT From: (Andrew Fant) @umbc3.umbc.edu To: chemistry@ccl.net Subject: RE:Nobel Prizers Status: R How about a joint Nobel to John Pople and Michael Dewar for their success in making computational tools available to the experimentalist and for their efforts to bring theoretical methods to bear on problems that non- physical chemists are interested (i.e. organic mechanisms). I would not, however, want to be in the same room as the two of them as they wait to receive the award, or before they give their lectures. Just another uninvolved opinion +---------------------------------------------------------------------------+ Andy "The Fantom" Fant (fant@{umbc2,umbc3,chem3}.umbc.edu) Disclaimer: My writings are definitive, reality is often inaccurate "It is my supposition that the universe is not only queerer than we imagine, It is queerer than we CAN imagine." - J.B.S. Haldane From chemistry-request@ccl.net Thu Sep 26 13:15:13 1991 Date: Thu, 26 Sep 1991 12:59 EDT From: "DOUGLAS A. SMITH" Subject: AVS Clearinghouse To: chemistry@ccl.net Status: R I know that NCSC is being set up as a National AVS Clearinghouse, but it seems that they will be handling finished products, whether they be full applications or individual modules, for distribution, perhaps along the lines of QCPE. In my discussions with several people (who shall remain nameless so that all flames are directed to me only), the desire/need for a different type of clearinghouse has arisen. Namely, a place where people can submit algorithms, subroutines, and other submodular pieces of code. Programmers and users alike could access these codes, obtain them via ftp, and use them in their own creations (giving credit where due, of course). In principle, this would not even have to be limited to AVS, but could be used for any code. I, of course, am interested in the chemistry aspects, but I can see that others can/could/would write non-discipline specific code which would be appropriate. Does such a thing as this exist, at NCSC or anywhere else? Is there much interest is such a thing? There has been some talk about setting this up here at the University of Toledo, since we are a beta site for the AVS Chemistry Developer's Kit, are working with MSI-Polygen, and just plain develop code. Please address all comments and questions to the net - I would like to see a healthy discussion, since I am sure there are issues and items I have not even begun to think about. Doug Smith Assistant Professor of Chemistry The University of Toledo Toledo, OH 43606-3390 voice 419-537-2116 fax 419-537-4033 email fax0236@uoft02.utoledo.edu From chemistry-request@ccl.net Thu Sep 26 13:56:40 1991 Date: Thu, 26 Sep 91 10:46:06 PDT From: ross@zeno.mmwb.ucsf.EDU (Bill Ross) To: chemistry@ccl.net Subject: code repository Status: R I think a code repository is an excellent idea. While on the subject, how about extending it to include input for calculations, e.g. enough info to reproduce a charge calcn for a residue + the resulting charges + the parameter file(s) used for annealing or perturbing a structure and any labor-representative PDB files. Maybe throw in text from resulting paper(s). These could be viewed both as demos and labor saving devices to avoid typing in parameters from other people's papers, especially in cases people use the same software or have translation routines. Each contribution could be bundled into a compressed tar file. Bill Ross From chemistry-request@ccl.net Thu Sep 26 14:20:08 1991 From: bernhold@orange.qtp.ufl.edu Date: Thu, 26 Sep 1991 14:10:07 -0400 To: chemistry@ccl.net, fant@chem3.umbc.edu Subject: Theoretical chemistry Nobel prize Status: R On Sep 26 12:36pm, (Andrew Fant) wrote: > How about a joint Nobel to John Pople and Michael Dewar for their success > in making computational tools available to the experimentalist and for > their efforts to bring theoretical methods to bear on problems that non- > physical chemists are interested (i.e. organic mechanisms). No disrespect to Dewar or Pople intended, but I think that this would be a great _disservice_ to the theoretical chemistry community. What you suggest is recognizing people for _popularizing_ codes and there by the computational methods they embody. Some of these methods were developed by Dewar and Pople; many others were developed by others and have been incorporated into the programs they distribute. Advances in theoretical chemistry are largely incremental these days. I'm not saying Dewar and Pople don't deserve recognition, but there are _many_ other people involved in producing what is now a common tool. Surely there is a more appropriate way to recognize their contributions. In fact I seem to recall that Pople just recently received an ACS award for Computers in Chemistry (I can't find the announcement, so this is probably not exactly right) -- that's more like it. I realize that many people on this list are primarily consumers of computational chemistry rather than developers. My remarks are from the perspective of somone who's been working in quantum chemistry for some time. Just like when you buy a car -- you see the dealer, but not usually the manufacturing process. Nevertheless, you don't imagine that the dealer is entirely responsible for creating the car. -- David Bernholdt bernhold@qtp.ufl.edu Quantum Theory Project bernhold@ufpine.bitnet University of Florida Gainesville, FL 32611 904/392 6365 From NU019228@VM1.NoDak.EDU Thu Sep 26 14:53:53 1991 Date: Thu, 26 Sep 91 13:42:40 CDT From: "Mark S. Gordon" Organization: North Dakota Higher Education Computer Network Subject: Re: Theoretical chemistry Nobel prize To: Dave , chemistry@ccl.net, fant@chem3.umbc.edu, Status: R I took the suggestion for a joint Nobel prize for Michael Dewar and John Pople to recognize much more than the computer codes they distribute. Both Dewar and Pople would, I think, refer to their many seminal contribtions to theoretical chemistry, not to their computer codes, as their main contributions, if they were asked. I think there are very few who have contributed as much insight to chemistry as these two. Mark Gordon From chemistry-request@ccl.net Thu Sep 26 15:00:17 1991 Date: Thu, 26 Sep 91 14:53:13 EDT From: Kevin Moore To: chemistry@ccl.net Subject: AVS Clearinghouse Status: R Doug, NCSC will be handling any AVS module which is placed in the public domain. In general, this will not include algorithms, subroutines, etc which are not built as an AVS module. As the AVS clearinghouse, we will be taking modules built for any platform and porting them to the platforms of each of the AVS consortium members (currently includes: Stardent, DEC, HP, IBM, CONVEX, Evans & Sutherland and Set Technologies). The modules will be made available to the public upon receipt and verification that they work. Through an anonymous ftp site, users will be able to obtain the modules (a working executable), including the source and any available documentation. It sounds like your idea is slightly different from what we will be doing, in that we will not be taking general subroutines and converting them to AVS modules (as a practice). We do have a program which will take a routine not written as an AVS module and convert it to a module, but I doubt we will spend a lot of time doing this (as one can imagine the possible problems with such a code). The contact for the AVS center here at NCSC is David Bennett. Feel free to contact him with specific questions about our procedures at davidb@ncsc.org or (919)248-1182. Kevin Moore NCSC Scientific Support kmoore@ncsc.org (919)248-1179 ------------------------- Date: Thu, 26 Sep 1991 12:59 EDT From: "DOUGLAS A. SMITH" X-Envelope-To: chemistry@ccl.net X-Vms-To: IN%"chemistry@ccl.net" Sender: chemistry-request@ccl.net Precedence: bulk I know that NCSC is being set up as a National AVS Clearinghouse, but it seems that they will be handling finished products, whether they be full applications or individual modules, for distribution, perhaps along the lines of QCPE. In my discussions with several people (who shall remain nameless so that all flames are directed to me only), the desire/need for a different type of clearinghouse has arisen. Namely, a place where people can submit algorithms, subroutines, and other submodular pieces of code. Programmers and users alike could access these codes, obtain them via ftp, and use them in their own creations (giving credit where due, of course). In principle, this would not even have to be limited to AVS, but could be used for any code. I, of course, am interested in the chemistry aspects, but I can see that others can/could/would write non-discipline specific code which would be appropriate. Does such a thing as this exist, at NCSC or anywhere else? Is there much interest is such a thing? There has been some talk about setting this up here at the University of Toledo, since we are a beta site for the AVS Chemistry Developer's Kit, are working with MSI-Polygen, and just plain develop code. Please address all comments and questions to the net - I would like to see a healthy discussion, since I am sure there are issues and items I have not even begun to think about. Doug Smith Assistant Professor of Chemistry The University of Toledo Toledo, OH 43606-3390 voice 419-537-2116 fax 419-537-4033 email fax0236@uoft02.utoledo.edu From jkl@ccl.net Thu Sep 26 16:11:07 1991 Date: Thu, 26 Sep 91 15:43:45 -0400 From: jkl@ccl.net Subject: Re: Nobel Prize To: chemistry@ccl.net Status: R Forwarding another voice on Nobel Prize in ComputChem: ---------- Begin Forwarded Message ---------- >From bbesler@ouchem.chem.oakland.edu Thu Sep 26 15:25:24 1991 Date: Thu, 26 Sep 91 15:26:44 -0400 From: bbesler@ouchem.chem.oakland.edu (Brent H. Besler) To: chemistry-request@ccl.net Subject: Nobel Prize If there is going to be a computational quantum chemistry nobel prize, the following people should receive the award jointly: Pople, Dewar, H.F. Schaefer, H.C. Handy, Pulay(?). There are too many groups which are responsible for developments in quantum chemistry to award a prize that does not have major exclusions. ----------- End Forwarded Message ----------- From rl@cgl.ucsf.EDU Thu Sep 26 16:15:21 1991 Date: Thu, 26 Sep 91 13:16:47 -0700 From: rl@cgl.ucsf.edu (Robert Langridge) To: chemistry@ccl.net, jkl@ccl.net Subject: Re: Nobel Prize Status: R I'm not going to enter into the discussion of who, if anyone, deserves a Nobel Prize for computational quantum chemistry, but remind some of the recent posters that Stockholm limits each award to a maximum of three recipients. This has led to some arguable inequities, such as the award of the prize for quantum electrodynamics to Feynman, Tomonaga and Schwinger. They all certainly deserved the award, but it must have taken some very fine hair-splitting to eliminate Freeman Dyson. While we are on the subject - my favorite Nobel trivia question: When did Uhlenbeck and Goudschmidt win the Nobel Prize for the discovery of electron spin? Bob Langridge Phone: +1 415 476-2630, -1540, -5128 Computer Graphics Laboratory FAX: +1 415 476-0688 University of California E-Mail: rl@cgl.ucsf.edu San Francisco CA 94143-0446 From chemistry-request@ccl.net Thu Sep 26 16:42:21 1991 From: bernhold@orange.qtp.ufl.edu Date: Thu, 26 Sep 1991 16:29:56 -0400 To: chemistry@ccl.net Subject: Nbel Prize Status: R On Sep 26 3:43pm, bbesler@ouchem.chem.oakland.edu (Brent H. Besler) wrote: > If there is going to be a computational quantum chemistry nobel prize, the > following people should receive the award jointly: Pople, Dewar, H.F. Schaefer, > H.C. Handy, Pulay(?). There are too many groups which are responsible for > developments in quantum chemistry to award a prize that does not have major > exclusions. To my thinking, there are a great many others who should be on this list too. Consider, for _example_: Hartree, Fock, Slater, Lowdin, Longuet-Higgins, Shavitt, Paldus, Cizek, Roothaan, Davidson,... Can you honestly leave people like this out? A list like this could go on forever! -- David Bernholdt bernhold@qtp.ufl.edu Quantum Theory Project bernhold@ufpine.bitnet University of Florida Gainesville, FL 32611 904/392 6365 From chemistry-request@ccl.net Thu Sep 26 18:03:11 1991 Date: Thu, 26 Sep 1991 15:54 EDT From: "DOUGLAS A. SMITH" Subject: Re: AVS Clearinghouse To: MARTIN@cmda.abbott.com Status: R Yvonne: Sorry! Sometimes, when I get talking about a subject I forget that not everyone knows what it is. Application Visualization System, or AVS, is a set of tools, libraries, routines, etc. for filtering, mapping, and rendering data. Programming is through a graphical interface in which users pick AVS modules from a menu and the linking of the code in these modules is (almost) automatic. The resulting executable flow network (hence the name of the programming environment - the Network Editor) can be used, saved, modified, etc. Think of it as the next generation graphics environment after Silicon Graphics GL (my opinion, of course, and not necessarily something with which every one would agree). I hope Joe Leonard of Stardent is keeping up with this - may he could add something to what I have said. One addition - even though SGI has just announced that they will be making GL a more open system on more platforms, AVS already exists on most platforms - Stardent, Cray, Convex, IBM, SGI (yes!), DEC, and probably more that I am not thinking of. Doug Smith From chemistry-request@ccl.net Thu Sep 26 20:10:26 1991 Date: Thu, 26 Sep 91 16:55:56 -0700 From: pak@cgl.ucsf.edu (Peter Kollman) To: chemistry@ccl.net Subject: nobel prize prejudice Status: R I would like to add my two cents to the discussion about the nobel prize. I agree with Mark Gordon that both Pople and Dewar should be recognized for their science, not the popularity of their codes. But perhaps people don't realize that Pople has contributed in a seminal way to the theory of the structure of liquid water and statistical mechanics of dense gases, to NMR theory(Pople, Schneider and Bernstein, that classical text), to semi-empirical quantum chemistry and to ab initio quantum chemistry. MIchael Dewar is clearly one of the top figures in the world in theoretical chemistry but to my way of thinking, Pople's contributions are head and shoulders above the rest, in terms of total and breadth. He would be a fitting member of the cast of nobel laureates in this area, viz. Pauling(albeit his prize was not for the theory),Mulliken,Hoffmann/Fukui... From chemistry-request@ccl.net Thu Sep 26 21:44:18 1991 Date: Thu, 26 Sep 91 21:34:05 -0400 From: zheng@retina.chem.psu.edu (Ya-Jun Zheng) Status: R I think we should stop worrying who should win the Nobel prize. Before making any comment, we should know all the facts about one person's contribution. For example, what about the Pi-complex theory and the PMO theory? Yajun From chemistry-request@ccl.net Thu Sep 26 22:51:11 1991 From: Elizabeth Chelkowska Subject: Re: Nobel Prize in Chemistry To: CHEMISTRY@ccl.net Date: Fri, 27 Sep 91 12:43:02 EST Status: R ^I took the suggestion for a joint Nobel prize for Michael Dewar and John ^Pople to recognize much more than the computer codes they distribute. Both ^Dewar and Pople would, I think, refer to their many seminal contribtions ^to theoretical chemistry, not to their computer codes, as their main ^contributions, if they were asked. I think there are very few who have ^contributed as much insight to chemistry as these two. ^ ^Mark Gordon ^ I think Mark made a very important point: Nobel Prize in Chemistry is for recognition of contributions in CHEMICAL SCIENCES (I know, it is a very broad term. However, in case of theoretical chemistry the computer codes are tools only :-) ). Perhaps Stockholm should consider introduction of a new Nobel Prize - in Computer Sciences. Many good wishes Elizabeth =============================================================================== Elizabeth Chelkowska "It is also a good rule not to put Chemistry, University of Tasmania too much confidence in experimental GPO Box 252C, HOBART, Tas.7001 results until they have been confirmed Australia by theory." ryba@tasman.cc.utas.edu.au Sir Arthur Eddington ===============================================================================