From chemistry-request@www.ccl.net Tue Sep 1 02:46:25 1998 Received: from bacchus.pc1.uni-duesseldorf.de (root@bacchus.pc1.uni-duesseldorf.de [134.99.152.11]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id CAA08329 Tue, 1 Sep 1998 02:46:18 -0400 (EDT) Received: from bacchus.pc1.uni-duesseldorf.de (jochen@localhost [127.0.0.1]) by bacchus.pc1.uni-duesseldorf.de (8.8.7/8.8.7) with SMTP id IAA27912; Tue, 1 Sep 1998 08:45:54 +0200 From: Jochen Kuepper Reply-To: jochen@uni-duesseldorf.de To: viki@poodle.fh.huji.ac.il (Victoria Buch) Subject: Re: CCL:Linux on Alpha, math library Date: Fri, 8 Oct 2134 15:00:38 +0200 X-Mailer: KMail [version 0.7.9] Content-Type: text/plain Cc: CCL References: <199808290928.MAA06442@poodle.fh.huji.ac.il> MIME-Version: 1.0 Message-Id: <98090108455400.25801@bacchus.pc1.uni-duesseldorf.de> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by www.ccl.net id CAA08330 On Sat, 29 Aug 1998 Victoria Buch wrote: >> Igor J. Barani writes: >> > I have just recently installed Linux on a DEC Alpha and when I compile >> > several programs in fortran on it, they seem to compile to twice the >> > size and require 9 times as long to run than on DEC UNIX. Do you have >> > any idea why this may be so and how I may be able to speed up the >> > processes? Any suggestions would be greatly appreciated. Thank you. >We have just been there. You have the latest Red Hat Linux, dont you? >So: the latest math library libm version 2.0.7 from gnu is messed up. >Our system menager installed old version 2.0.1 - works faster by a factor 2. >More generally our sexperience suggests that >Alpha / Linux for FP operations is good only >for simple operations + - * / . My simulation >programs are still 40% below >the performance of Alpha-DEC, and only 10% faster than Petium II (400MHz) >which is more than 2 times cheaper. Disappointing. >Good luck. Victoria The slowdown of the math-library is due to bug-fixes. The old glibc based math-libs do have problems with wrong results for sqrt ( and others ) ! So you have to decide wether you use correct code or ( little ) faster code that might produce wrong answers. I would suggest to use the newest possible libm, if you are really for speed you might consider recompiling it with optimization turned high (v.i.). More important, there are replacement libraries for the more important math routines, that are hand-optimized assembler. IIRC, one of them is based on code Cray developed for their Alpha based machines. You can use both of them, since each one only provides a subset of functions in the next slower one (libm <- libfm <- libffm ) ! Look at http://people.frankfurt.netsurf.de/Joachim.Wesner/ Another important fact is the compiler to use. egcs-1.1pre is really stable for me, you might consider using it since there are very usefull new optimization passes. Also check your code and the compiler flags you are using, consider -fno-exceptions, -fno-rtti, ... and all the other -m, -f, -O options and take all these that will speed up your programs ! Hope it helps and you all get more power out of your Alpha-toys. If you need some more info, feel free to ask ( Victoria, aren't you in D"usseldorf right now ? ) Greetings, Jochen ----------------------------------------------------------------------- Jochen K"upper Heinrich-Heine-Universit"at D"usseldorf jochen@uni-duesseldorf.de Institut f"ur Physikalische Chemie I Universit"atsstr. 1, Geb 26.43 Raum 02.29 phone ++49-211-8113681 40225 D"usseldorf fax ++49-211-8115195 Germany http://www-public.rz.uni-duesseldorf.de/~jochen ----------------------------------------------------------------------- From chemistry-request@www.ccl.net Tue Sep 1 04:58:31 1998 Received: from rzusuntk.unizh.ch (rzumail2.unizh.ch [130.60.128.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id EAA08806 Tue, 1 Sep 1998 04:58:29 -0400 (EDT) Received: [from rzurs10.unizh.ch (mbeck@rzurs10.unizh.ch [130.60.68.60]) by rzusuntk.unizh.ch (8.8.5/SMI-5.25) with ESMTP id KAA08879 for ; Tue, 1 Sep 1998 10:58:28 +0200 (MET DST)] Received: from localhost (mbeck@localhost) by rzurs10.unizh.ch (AIX4.2/UCB 8.7/8.7) with SMTP id KAA74572 for ; Tue, 1 Sep 1998 10:58:27 +0200 (MEST) X-Authentication-Warning: rzurs10.unizh.ch: mbeck owned process doing -bs Date: Tue, 1 Sep 1998 10:58:27 +0200 (MEST) From: "Michael E. Beck" To: computational chemistry mailing list Subject: SPARTAN and CI Message-ID: Dear CCLs, I've got a problem understanding SPARTANS CI--output. Imagine you are performing a MNDO calculation on water. Orbitals 1 to 4 are doubly occupied. Now you want to do singles and doubles configuration interaction with orbitals 3 to 6 active. For the ground state, Spartan gives the following CI-wavefunction (the complete output is given below): 0 -0.998742 => that's the ground state (HF) determinant 1 0.003359 => a singly excited determinant 3 0.003359 => a singly excited determinant 9 0.017222 => a doubly excited determinant 12 0.032083 => a doubly excited determinant 23 0.031287 => a doubly excited determinant 26 0.013703 => a doubly excited determinant Thus the _singly_ excited determinants 1 and 3 enter the groundstate wavefunction with 0.003359. How's that possible? Thank's for your help Michael ___________________________________________________________________ Dr. Michael E. Beck | privat: Organisch--Chemisches Institut | Zschokkestr. 12a Theoretische Gruppe, Prof. W. Thiel | CH--8037 Zuerich Universitaet Zuerich | +41-1-271-54-39 Winterthurerstr. 190 |___________________________ CH--8057 Zuerich Tel.: +41-1-635-6117 web : www.unizh.ch/oci/group.pages/ thiel/persons/beck/ Fax.: 6836 mail: mbeck@oci.unizh.ch ___________________________________________________________________ Here's the complete SPARTAN output SPARTAN SEMIEMPIRICAL PROGRAM: SGI/R10K Release 5.0.3 (Job run on ocisgi30) Calculation started: Fri Aug 14 12:23:03 1998 Run type: Single point energy Model: RHF/MNDO Number of shells: 4 3 S shells 1 P shells Number of basis functions: 6 Number of electrons: 8 Use of molecular symmetry enabled Molecular charge: 0 Spin multiplicity: 1 Cartesian Coordinates (Angstroms) Atom Label X Y Z -- -------- ------------- ------------- ------------- H H1 0.0000000 -0.7570569 0.1874133 O O1 0.0000000 0.0000000 -0.3748267 H H2 0.0000000 0.7570569 0.1874133 Point Group = CNV Order = 2 Nsymop = 4 This system has 2 degrees of freedom Interatomic distances (Angstroms) 1 2 3 1 0.000000 0.943000 1.514114 2 0.943000 0.000000 0.943000 3 1.514114 0.943000 0.000000 Angle 3 2 1 is 106.800 degrees Angle 3 1 2 is 36.600 degrees Angle 2 3 1 is 36.600 degrees Highest occupied MO = #4 Huckel Guess... Guess energy = -474.011396062 cycle # 1 Energy = -499.548338849 cycle # 2 Energy = -500.382719238 cycle # 3 Energy = -500.467977346 cycle # 4 Energy = -500.482152185 cycle # 5 Energy = -500.484942669 pseudo cycle # 6 Energy = -500.485511347 pseudo cycle # 7 Energy = -500.485628130 pseudo cycle # 8 Energy = -500.485652173 pseudo cycle # 9 Energy = -500.485657128 pseudo Final Energy = -500.485658153 (rechecking after pseudodiagonalization) Converged in 9 cycles Convergence critera met in 9 cycles ... Electronic energy = -500.485658 eV Core repulsion energy = 149.060825 eV Total Energy = -351.424834 eV Performing integral transformation ... Constructing singles ... Constructing doubles ... CI calculation performed using orbitals 3 to 6 Slater Determinants State type configuration ----------------------------------------------------------------- 0 Ground state 11 00 11 00 1 Single 01 10 11 00 2 Single 01 01 11 00 3 Single 11 00 01 10 4 Single 11 00 01 01 5 Single 10 10 11 00 6 Single 10 01 11 00 7 Single 11 00 10 10 8 Single 11 00 10 01 9 Double 01 10 01 10 10 Double 01 10 01 01 11 Double 01 01 01 10 12 Double 01 01 01 01 13 Double 00 11 11 00 14 Double 01 10 10 10 15 Double 01 10 10 01 16 Double 01 01 10 10 17 Double 01 01 10 01 18 Double 10 10 01 10 19 Double 10 10 01 01 20 Double 10 01 01 10 21 Double 10 01 01 01 22 Double 11 00 00 11 23 Double 10 10 10 10 24 Double 10 10 10 01 25 Double 10 01 10 10 26 Double 10 01 10 01 Heats of Formation: HF -60.938 kcal/mol CI -62.320 kcal/mol Eigenvalues and eigenvectors of the CI matrix ... 0 1 2 3 4 5 eig: -0.059920 6.310075 7.511671 7.528376 8.243903 9.449156 OS: 0.123017 0.146661 0.000000 0.000000 0.758494 nm: 196.511126 165.076454 164.710152 150.414189 131.228648 spin: no yes no yes no --------------------------------------------------------------------------- 0 -0.998742 0.000000 0.000000 0.000000 0.000000 0.000000 1 0.003359 0.000000 0.000000 0.000000 0.000000 -0.707107 2 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 3 0.003359 0.000000 0.000000 0.000000 0.000000 0.707107 4 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 5 0.000000 0.705760 0.706022 0.000000 0.000000 0.000000 6 0.000000 0.000000 0.000000 0.704836 -0.705693 0.000000 7 0.000000 -0.705760 0.706022 0.000000 0.000000 0.000000 8 0.000000 0.000000 0.000000 -0.704836 -0.705693 0.000000 9 0.017222 0.000000 0.000000 0.000000 0.000000 0.000000 10 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 11 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 12 0.032083 0.000000 0.000000 0.000000 0.000000 0.000000 13 0.000000 0.000000 0.000000 -0.010847 0.009463 0.000000 14 0.000000 -0.019114 0.009315 0.000000 0.000000 0.000000 15 0.000000 0.000000 0.000000 -0.029136 -0.025788 0.000000 16 0.000000 0.000000 0.000000 0.047322 0.035251 0.000000 17 0.000000 -0.039215 0.038023 0.000000 0.000000 0.000000 18 0.000000 -0.019114 -0.009315 0.000000 0.000000 0.000000 19 0.000000 0.000000 0.000000 -0.047322 0.035251 0.000000 20 0.000000 0.000000 0.000000 0.029136 -0.025788 0.000000 21 0.000000 -0.039215 -0.038023 0.000000 0.000000 0.000000 22 0.000000 0.000000 0.000000 0.010847 0.009463 0.000000 23 0.031287 0.000000 0.000000 0.000000 0.000000 0.000000 24 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 25 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 26 0.013703 0.000000 0.000000 0.000000 0.000000 0.000000 6 7 8 9 10 11 eig: 10.257741 10.323881 11.782136 15.801429 16.092334 16.430589 OS: 2.631401 0.813497 2.937839 0.000000 0.000000 0.000000 nm: 120.884315 120.109872 105.244074 78.473915 77.055325 75.468995 spin: no yes yes no no yes --------------------------------------------------------------------------- 0 0.000000 -0.007135 0.000000 0.000000 0.000000 0.018663 1 0.000000 -0.703839 0.000000 0.000000 0.000000 0.014371 2 -0.706960 0.000000 -0.701960 0.000000 0.012296 0.000000 3 0.000000 -0.703839 0.000000 0.000000 0.000000 0.014371 4 0.706960 0.000000 -0.701960 0.000000 -0.012296 0.000000 5 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 6 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 7 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 8 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 9 0.000000 -0.066444 0.000000 0.000000 0.000000 -0.112892 10 0.009163 0.000000 -0.083163 0.000000 0.100365 0.000000 11 0.009163 0.000000 0.083163 0.000000 0.100365 0.000000 12 0.000000 -0.064357 0.000000 0.000000 0.000000 0.082687 13 0.000000 0.000000 0.000000 -0.408248 0.000000 0.000000 14 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 15 0.000000 0.000000 0.000000 0.408248 0.000000 0.000000 16 0.000000 0.000000 0.000000 0.408248 0.000000 0.000000 17 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 18 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 19 0.000000 0.000000 0.000000 0.408248 0.000000 0.000000 20 0.000000 0.000000 0.000000 0.408248 0.000000 0.000000 21 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 22 0.000000 0.000000 0.000000 -0.408248 0.000000 0.000000 23 0.000000 0.024536 0.000000 0.000000 0.000000 0.815618 24 -0.011107 0.000000 0.018348 0.000000 -0.699840 0.000000 25 -0.011107 0.000000 -0.018348 0.000000 -0.699840 0.000000 26 0.000000 0.003261 0.000000 0.000000 0.000000 -0.560736 12 13 14 15 16 17 eig: 17.333535 18.020974 19.015929 19.183426 19.365041 19.379897 OS: 0.000000 0.000000 0.000000 0.000000 0.000015 0.000000 nm: 71.537628 68.808711 65.208489 64.639131 64.032912 63.983829 spin: no no no yes yes yes --------------------------------------------------------------------------- 0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1 0..000000 0.000000 0.000000 0.000000 0.000000 0.000000 2 0.000000 0.000000 0.000000 0.000000 0.029411 0.000000 3 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 4 0.000000 0.000000 0.000000 0.000000 0.029411 0.000000 5 0.007689 0.000000 0.000000 0.000000 0.000000 -0.014835 6 0.000000 0.006805 0.001475 -0.004125 0.000000 0.000000 7 -0.007689 0.000000 0.000000 0.000000 0.000000 -0.014835 8 0.000000 -0.006805 -0.001475 -0.004125 0.000000 0.000000 9 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 10 0.000000 0.000000 0.000000 0.000000 -0.093752 0.000000 11 0.000000 0.000000 0.000000 0.000000 0.093752 0.000000 12 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 13 0.000000 0.674224 0.207141 -0.569009 0.000000 0.000000 14 -0.571169 0.000000 0.000000 0.000000 0.000000 -0.571916 15 0.000000 0.153504 -0.586804 -0.369139 0.000000 0.000000 16 0.000000 0.147691 -0.335784 -0.199871 0.000000 0.000000 17 0.416782 0.000000 0.000000 0.000000 0.000000 0.415562 18 -0.571169 0.000000 0.000000 0.000000 0.000000 0.571916 19 0.000000 -0.147691 0.335784 -0.199871 0.000000 0.000000 20 0.000000 -0.153504 0.586804 -0.369139 0.000000 0.000000 21 0.416782 0.000000 0.000000 0.000000 0.000000 -0.415562 22 0.000000 -0.674224 -0.207141 -0.569009 0.000000 0.000000 23 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 24 0.000000 0.000000 0.000000 0.000000 0.700247 0.000000 25 0.000000 0.000000 0.000000 0.000000 -0.700247 0.000000 26 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 18 19 20 21 22 23 eig: 19.943584 20.380517 20.803840 22.406845 22.832961 23.342782 OS: 0.000001 0.000000 0.000006 0.000000 0.000003 0.000000 nm: 62.175385 60.842420 59.604381 55.340231 54.307455 53.121346 spin: yes no no yes yes no --------------------------------------------------------------------------- 0 -0.023708 0.000000 0.000000 0.000000 0.000000 0.000000 1 -0.020550 0.000000 0.000000 0.000000 0.000000 0.000000 2 0.000000 0.000000 0.000000 0.000000 0.000000 0.007492 3 -0.020550 0.000000 0.000000 0.000000 0.000000 0.000000 4 0.000000 0.000000 0.000000 0.000000 0.000000 -0.007492 5 0.000000 0.000000 0.042943 0.000000 0.036228 0.000000 6 0.000000 0.056191 0.000000 -0.044499 0.000000 0.000000 7 0.000000 0.000000 -0.042943 0.000000 0.036228 0.000000 8 0.000000 -0.056191 0.000000 -0.044499 0.000000 0.000000 9 0.071421 0.000000 0.000000 0.000000 0.000000 0.000000 10 0.000000 0.000000 0.000000 0.000000 0.000000 0.699888 11 0.000000 0.000000 0.000000 0.000000 0.000000 0.699888 12 0.123133 0.000000 0.000000 0.000000 0.000000 0.000000 13 0.000000 0.048965 0.000000 -0.097326 0.000000 0.000000 14 0.000000 0.000000 0.416415 0.000000 -0.415722 0.000000 15 0.000000 0.362282 0.000000 0.443176 0.000000 0.000000 16 0.000000 -0.602658 0.000000 -0.540502 0.000000 0.000000 17 0.000000 0.000000 0.569873 0.000000 -0.570844 0.000000 18 0.000000 0.000000 0.416415 0.000000 0.415722 0.000000 19 0.000000 0.602658 0.000000 -0.540502 0.000000 0.000000 20 0.000000 -0.362282 0.000000 0.443176 0.000000 0.000000 21 0.000000 0.000000 0.569873 0.000000 0.570844 0.000000 22 0.000000 -0.048965 0.000000 -0.097326 0.000000 0.000000 23 -0.561260 0.000000 0.000000 0.000000 0.000000 0.000000 24 0.000000 0.000000 0.000000 0.000000 0.000000 0.100504 25 0.000000 0.000000 0.000000 0.000000 0.000000 0.100504 26 -0.814443 0.000000 0.000000 0.000000 0.000000 0.000000 24 25 26 eig: 23.750830 26.793754 27.275329 OS: 0.000000 0.001123 0.000135 nm: 52.208701 46.279442 45.462329 spin: yes yes yes --------------------------------------------------------------------------- 0 0.004494 0.000000 -0.039162 1 0.006874 0.000000 0.062632 2 0.000000 -0.079923 0.000000 3 0.006874 0.000000 0.062632 4 0.000000 -0.079923 0.000000 5 0.000000 0.000000 0.000000 6 0.000000 0.000000 0.000000 7 0.000000 0.000000 0.000000 8 0.000000 0.000000 0.000000 9 -0.775560 0.000000 -0.613148 10 0.000000 0.695913 0.000000 11 0.000000 -0.695913 0.000000 12 0.615096 0.000000 -0.771030 13 0.000000 0.000000 0.000000 14 0.000000 0.000000 0.000000 15 0.000000 0.000000 0.000000 16 0.000000 0.000000 0.000000 17 0.000000 0.000000 0.000000 18 0.000000 0.000000 0.000000 19 0.000000 0.000000 0.000000 20 0.000000 0.000000 0.000000 21 0.000000 0.000000 0.000000 22 0.000000 0.000000 0.000000 23 -0.103953 0.000000 -0.085839 24 0.000000 0.096529 0.000000 25 0.000000 -0.096529 0.000000 26 0.096143 0.000000 -0.113204 eigenvalue 0 = -500.545578 eigenvalue 1 = -494.175583 eigenvalue 2 = -492.973987 eigenvalue 3 = -492.957282 eigenvalue 4 = -492.241755 eigenvalue 5 = -491.036502 eigenvalue 6 = -490.227917 eigenvalue 7 = -490.161777 eigenvalue 8 = -488.703522 eigenvalue 9 = -484.684229 eigenvalue 10 = -484.393324 eigenvalue 11 = -484.055070 eigenvalue 12 = -483.152123 eigenvalue 13 = -482.464684 eigenvalue 14 = -481.469729 eigenvalue 15 = -481.302232 eigenvalue 16 = -481.120617 eigenvalue 17 = -481.105761 eigenvalue 18 = -480.542074 eigenvalue 19 = -480.105141 eigenvalue 20 = -479.681818 eigenvalue 21 = -478.078813 eigenvalue 22 = -477.652697 eigenvalue 23 = -477.142876 eigenvalue 24 = -476.734828 eigenvalue 25 = -473.691904 eigenvalue 26 = -473.210329 Spin-allowed singlet excitations State Energy OS nm ----------------------------------------- 2 7.511671 0.146661 165.076454 7 10.323881 0.813497 120.109872 8 11.782136 2.937839 105.244074 Ground State Dipole Moment: u(x) = 0.000000 u(y) = 0.000000 u(z) = 1.773507 u(tot) = 1.773507 Ground State Atomic Charges Atom Population Charge ------------------------------ H 1 0.838358 0.161642 O 2 6.323284 -0.323284 H 3 0.838358 0.161642 Ground State Bond Order Matrix 1 2 3 --------------------------------------------------------------------------- 1 0.000000 0.966988 0.003462 2 0.966988 0.000000 0.966988 3 0.003462 0.966988 0.000000 State 2 Dipole Moment: u(x) = 0.000000 u(y) = 0.000000 u(z) = -0.321723 u(tot) = 0.321723 State 2 Atomic Charges ------------------------------ H 1 1.143015 -0.143015 O 2 5.713970 0.286030 H 3 1.143015 -0.143015 State 2 Bond Order Matrix 1 2 3 --------------------------------------------------------------------------- 1 0.000000 0.610875 0.059521 2 0.610875 0.000000 0.610875 3 0.059521 0.610875 0.000000 Gross electron populations over atoms (HF wavefunction): Atom Population Net charge ------------------------------ 1 0.837 0.163 2 6.326 -0.326 3 0.837 0.163 Bond Order Matrix 1 2 3 --------------------------------------------------------------------------- 1 0.000000 0.970036 0.003445 2 0.970036 0.000000 0.970036 3 0.003445 0.970036 0.000000 Dipole Moment: u(x) = 0.000000 u(y) = 0.000000 u(z) = 1.783296 u(tot) = 1.783296 Heat of Formation: -62.320 kcal/mol ** Archive file written to unit 12 ** Total Cpu time: 0 mins. 0.04 secs. Total Wall time: 0 mins. 0.18 secs. Calculation started: Fri Aug 14 12:23:03 1998 SPARTAN PROPERTIES PACKAGE: SGI/R10K Release 5.0.3 Total Cpu time: 0 mins. 0.00 secs. From chemistry-request@www.ccl.net Tue Sep 1 06:19:41 1998 Received: from ashura.qcl.t.u-tokyo.ac.jp (ashura.qcl.t.u-tokyo.ac.jp [133.11.70.129]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id GAA09109 Tue, 1 Sep 1998 06:19:39 -0400 (EDT) Received: from localhost (localhost [127.0.0.1]) by ashura.qcl.t.u-tokyo.ac.jp (8.8.8/3.6W-980805) with ESMTP id TAA35142 for ; Tue, 1 Sep 1998 19:19:33 +0900 Message-Id: <199809011019.TAA35142@ashura.qcl.t.u-tokyo.ac.jp> To: chemistry@www.ccl.net Date: Tue, 01 Sep 1998 19:19:32 +0900 From: AKINAGA Yoshinobu Dear sirs, I'm interested in the calculation of an impurity embedded in the solid or the electron gas, employing both the local gaussian type basis functions and non-local plane-wave basis functions. I want to know how to evaluate the matrix elements of the one-electron nuclear-repulsion operator between the gaussian function and the plane-wave such as , where R_p, r_a, and r indicates the center of the gaussian, electron-nuclear distance, and position vector of the electron originating from arbitrary origin (which is generally different from R_p or R_a), as well as the two-electron exchange integral between the gaussian and the plane-wave such as int(dr1dr2) phi_a(r1)exp(-ik_ir1) r12^(-1) phi_b(r2)exp(ik_jr2) where "phi" means gaussian basis function, a or b is index of phi, and i or j is index of plane-wave (wave vector). Any references are wellcome, and all replies will be summerized. Thanks in advance. best regards, Yoshinobu Akinaga Department of Applied Chemistry, Graduate School of Engineering, University of Tokyo, Tokyo 113, Japan tel : 03-3812-2111(7243), E-mail : akinaga@qcl.t.u-tokyo.ac.jp From chemistry-request@www.ccl.net Tue Sep 1 06:42:09 1998 Received: from ashura.qcl.t.u-tokyo.ac.jp (ashura.qcl.t.u-tokyo.ac.jp [133.11.70.129]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id GAA09147 Tue, 1 Sep 1998 06:42:07 -0400 (EDT) Received: from localhost (localhost [127.0.0.1]) by ashura.qcl.t.u-tokyo.ac.jp (8.8.8/3.6W-980805) with ESMTP id TAA37486; Tue, 1 Sep 1998 19:42:04 +0900 Message-Id: <199809011042.TAA37486@ashura.qcl.t.u-tokyo.ac.jp> To: CHEMISTRY@www.ccl.net cc: akinaga@qcl.t.u-tokyo.ac.jp Date: Tue, 01 Sep 1998 19:42:03 +0900 From: AKINAGA Yoshinobu Dear Sirs, I am interested in the calculation of an impurity embedded in a solid or an elecron gas, employing both gaussian basis functions and plane-wave basis functions. I want to know how to evaluate the matrix elements of one-electron integral of nuclear-repulsion between the gaussian and the plane-wave such as , as well as two-electron integrals, for example, the exchange integral between the gaussian functions and the plane-waves such as int(dr1dr2) phi_a(r1)exp(ik_i r1)r12^(-1)exp(-k_j r2)phi_b(r2), where "phi_a" means a primitive gaussian function whose index is a, and "k_i" means wave vector whose index is i. Any references is welcome. All responses sill be summerized. Thanks in advance. best regards, =============================================================== Yoshinobu Akinaga Department of Applied Chemistry, Graduate School of Engineering, University of Tokyo, Tokyo 113, Japan tel : 03-3812-2111(7243), E-mail : akinaga@qcl.t.u-tokyo.ac.jp =============================================================== From chemistry-request@www.ccl.net Tue Sep 1 11:28:18 1998 Received: from cz2.chem.niu.edu (cz2.chem.niu.edu [131.156.9.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id LAA12054 Tue, 1 Sep 1998 11:28:18 -0400 (EDT) Received: from cz.chem.niu.edu by cz2.chem.niu.edu via SMTP (920330.SGI/920502.SGI.AUTO) for CHEMISTRY@www.ccl.net id AA10628; Tue, 1 Sep 98 09:33:57 -0500 Received: from smb.chem.niu.edu by cz.chem.niu.edu via SMTP (920330.SGI/890607.SGI) (for @cz2.chem.niu.edu:CHEMISTRY@www.ccl.net) id AA08426; Tue, 1 Sep 98 10:37:23 -0500 Received: from smb by smb.chem.niu.edu via SMTP (940816.SGI.8.6.9/940406.SGI) for id KAA14012; Tue, 1 Sep 1998 10:26:56 -0500 Sender: smb@smb.chem.niu.edu Message-Id: <35EC123F.167E@smb.chem.niu.edu> Date: Tue, 01 Sep 1998 10:26:55 -0500 From: Steven Bachrach X-Mailer: Mozilla 3.01 (X11; I; IRIX 5.3 IP12) Mime-Version: 1.0 To: computational chemistry list Subject: ECCC5 Reminder Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit The Fifth Electronic Computational Chemistry Conference (ECCC-5) will be held from Nov. 2 through Nov. 30, 1998, wholely on the Interent. The conference covers all aspects of computational chemistry. Paticipants will be able to view articles and discuss them entirely though a web browser. As always, ECCC-5 has no registration fee. The deadline for receipt of an abstract for the conference is September 25, 1998. Complete details on how the conference will operate, abstract submission, and conference registration can be found at http://hackberry.chem.niu.edu/ECCC5/ or feel free to email with your questions or comments. We invite all interested parties to contribute to the conference and participate! Steven Bachrach on behalf of the ECCC5 Scientific Organizing Committee -- Steven Bachrach Department of Chemistry Northern Illinois University DeKalb, Il 60115 Phone: (815)753-6863 smb@smb.chem.niu.edu Fax: (815)753-4802 From chemistry-request@www.ccl.net Tue Sep 1 13:35:23 1998 Received: from darkwing.uoregon.edu (genghis@darkwing.uoregon.edu [128.223.142.13]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA13499 Tue, 1 Sep 1998 13:35:22 -0400 (EDT) Received: from localhost (genghis@localhost) by darkwing.uoregon.edu (8.8.8/8.8.8) with SMTP id KAA21433 for ; Tue, 1 Sep 1998 10:35:21 -0700 (PDT) Date: Tue, 1 Sep 1998 10:35:20 -0700 (PDT) From: "Dale A. Braden" To: cclpost Subject: fitting IR spectra Message-ID: Dear CCL, Does anyone know of a freeware program for Unix or Windows that will enable one to fit an IR spectrum to a series of Lorentzian peaks? Ideally, it should accept data as ascii x,y pairs (position, amplitude) and automatically generate an initial guess for band positions by doing some kind of peak pick. Best wishes to all, Dale Braden Department of Chemistry University of Oregon Eugene, OR 97403-1253 genghis@darkwing.uoregon.edu From chemistry-request@www.ccl.net Tue Sep 1 15:28:52 1998 Received: from email.nist.gov (email.nist.gov [129.6.2.7]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id PAA14318 Tue, 1 Sep 1998 15:28:51 -0400 (EDT) From: chem@feldmann.nist.gov Received: from feldmann.nist.gov (feldmann.nist.gov [129.6.178.78]) by email.nist.gov (8.8.8/8.8.8) with ESMTP id PAA06128; Tue, 1 Sep 1998 15:23:36 -0400 (EDT) Received: from localhost (chem@localhost) by feldmann.nist.gov (8.8.8+Sun/8.8.8) with SMTP id PAA21159; Tue, 1 Sep 1998 15:19:25 -0400 (EDT) Date: Tue, 1 Sep 1998 15:19:25 -0400 (EDT) To: lists , APPLSPEC@uga.cc.uga.edu, CHEMCHAT@UAFSYSB.UARK.EDU, CHEMIG@LIST.NIH.GOV, CHEMISTRY@www.ccl.net, CHMINF-L@LISTSERV.INDIANA.EDU, ICS-L@UMDD.UMD.EDU, isisforum-l@mdli.com, listproc@msi.com, listserver@ic.ac.uk, mailbase@mailbase.ac.uk, molecular-dynamics-news@mailbase.ac.uk, NATODATA@CC1.KULEUVEN.AC.BE, pdb-l@pdb.pdb.bnl.gov Subject: Internet Journal of Chemistry (IJC) Message-ID: Just a brief note to draw your attention to a new, fully peer-reviewed and, for now, FREE chemistry e-journal: The Internet Journal of Chemistry - IJC (available at http://www.ijc.com/). The IJC is available in e-form; there is no corresponding print version of the journal. Launched in January 1998, with 36 articles published as of the end of August 1998, the IJC is a repository for the latest chemistry research findings. The Internet Journal of Chemistry has been established for chemists all over the world to take advantage of this new medium of dissemination of scientific research and to encourage chemists to use this vital new research tool. The IJC is seeking new research papers for publication. Uniquely for authors, the Internet Journal of Chemistry offers: - complete integration of multimedia, interactive tools within the article - encourages java and javascript - accepts data files in any format - imposes no arbitrary "page" limits - copyright licenses with payment to authors Unique features of IJC for readers: - customized journal layout - customized content (units, reference formats, etc.) - user annotations of articles Other features (not necessarily unique to IJC) for authors - peer review rapid publication, typically 6 weeks from submission to publication cited in Chemical Abstracts only format restriction is the article must be written in HTML for readers - articles available in HTML, thereby readily available through a standard browser and standard browser customizations available (fonts, point size, etc.) free access through 1999 email update notification of newly published articles From chemistry-request@www.ccl.net Tue Sep 1 15:42:53 1998 Received: from beryl.kapatel.gr (mail@beryl.kapatel.gr [193.92.133.35]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id PAA14484 Tue, 1 Sep 1998 15:42:49 -0400 (EDT) Received: (from mail@localhost) by beryl.kapatel.gr (8.6.12/8.6.9) id WAA18048 for ; Tue, 1 Sep 1998 22:43:27 +0200 Received: from agate.kapatel.gr(193.92.133.34) by beryl.kapatel.gr via smap (V2.0) id xma018046; Tue, 1 Sep 98 22:43:21 +0200 Message-ID: <35ECDAAA.40E0@beryl.kapatel.gr> Date: Tue, 01 Sep 1998 22:42:02 -0700 From: Nicholas Harkiolakis Organization: Agricultural University of Athens X-Mailer: Mozilla 2.0 (Win95; I; 16bit) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Benchmark Functions for Minimization Algorithms Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Greetings all, I'm developing a new method for locating Global and Local minima and interested to compare it with other methods in a mathematical sense initialy. I would appreciate any recomentations - functions (single and multi variable) with well defined global and local minima, that will be widely accepted as benchmark functions for messuring the efficiency of an algorithm. Also I would wellcome any relevant data - refferences anyone wishes to share or recomend. My goal is to apply the algorithm for the refinement of protein models using the AMBER forcefield. Thanks in advance, Nick Harkiolakis e-mail : nick@beryl.kapatel.gr From chemistry-request@www.ccl.net Tue Sep 1 16:56:27 1998 Received: from jasper.uor.edu (JASPER.UOR.EDU [192.251.139.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id QAA15949 Tue, 1 Sep 1998 16:56:26 -0400 (EDT) Received: by jasper.uor.edu; id AA19017; Tue, 1 Sep 1998 13:57:38 -0700 Message-Id: <35EC5F9D.3678@uor.edu> Date: Tue, 01 Sep 1998 13:57:01 -0700 From: Barbara Murray Reply-To: bmurray@jasper.uor.edu Organization: University of Redlands To: CHEMISTRY@www.ccl.net Subject: Summary: looking for molecular modeling program on web or free-long! References: <199807141406.KAA13368@www.ccl.net> Sometime ago I asked the following question and got many helpful answers. I ended up using isis/draw and weblab viewer both free to download. This is long > Barbara Murray wrote: > > > I am part of a national committee running an undergraduate > > pharmaceutical course on-line in the fall. We will be taking the > > students through all the steps that are involved in getting a drug to > > market. One of the things we want the students to do is to be able to > > draw and look at their chosen molecule in some sort of modeling > > program. Now, they don't really need to do calculations on this > > molecule; just look at it and move it around. Calculations would only > > be icing on the cake. > > Check out Chem3D at our website www.camsoft.com or www.chem3d.com. ChemOffice Net 4.5 will allow you to sketch molecules in 2D using ChemDraw Net and build 3D models (with a six heavy atom) limit using Chem3D Net. Chem3D Net will also allow visualization (including surface visualization) of molecules stored in various formats. > Chem3D Std which is available at the student price of $79 allows model building and 2D to 3D conversion and MM2 calculations. > For more information checkout our web site or send email to info@camsoft.com > > Kam Chana > CambridgeSoft Corporation > from wware@world.std.com > I wrote a Java program that might do some of what you want. Because it's > written in Java, you can run it on most browsers simply by visiting the > web page at http://world.std.com/~wware/ncad.html. > > The thing it doesn't do is to load and save molecule files (e.g. PDBs) > from your machine. Partly this is my laziness, and partly it's the Java > security model. But if you express interest, I might get motivated to > put in a load/save feature. > Your recent message to the CCL about the on-line pharmaceutical course you > are running was forwarded on to me. > > In looking for desktop modeling software, I would like to invite you to > consider the WebLab ViewerPro, Molecular Simulation's desktop 3D chemical > visualization software program. The WebLab Viewer a member of a suite of > products designed to enable chemical modeling, simulation, and > visualization on the web. > > As a native desktop software program, the ViewerPro works as a browser > helper application that will allow for the visualization, manipulation, > and > analysis of chemical structures accessed on the Internet. In addition to > reading a wide range of file formats, the ViewerPro includes tools for > sketching molecular structures. It is also integrated with the most > popular 2D drawing packages, allowing the user to convert a 2D sketch into > a 3D structure with a simple cut and paste. > > At your earliest convenience, please give me a call or drop me a note. I > would appreciate the opportunity to discuss how the Viewer, and perhaps > other MSI solutions, might assist you in your efforts. > > I look forward to hearing from you. > > Sincerely, > > John Wintersteen > Product Manager, WebLab Viewer Products > Molecular Simulations Inc. > 9685 Scranton Road > San Diego, CA 92121-3752 > 619-799-5791 > http://www.msi.com/viewer > > Here are some sites with molecular modelling programs-some for > free, some you have to purchase: > > http://world.std.com/%7Ewware/ncad.html > http://www.carol.com/mass.shtml > http://www.gaussian.com/ > > Some sites containing information on aspects of computers- > chemical reactions. > > http://chemistry.gsu.edu/post_docs/koen/wsoftwar.html > http://www.digichem.co.uk/msover.html > > Computer-assisted synthesis planning > http://www.caos.kun.nl/ > http://www.shef.ac.uk/~chem/chemdex/computational.html > > Combinatorial chemistry > > http://www.msi.com/corp/pdf/c2_builder_modules.pdf > > Let me know how you get on. > > Dr Andrew Czarn > Nanotechnologist > > > I can't help you with your specific questions, but the CMS Molecular > Biology Resource web site at http://www.sdsc.edu/ResTools/ should be > useful to you. > > It is a compendium of electronic and Internet-accessible tools and > resources for Molecular Biology, Biotechnology, Molecular Evolution, > Biochemistry, and Biomolecular Modeling. > > This was recently reviewed (July 10) in the NetWatch column of > _Science_, the weekly publication of the American Association for the > Advancement of Science: > > The site is a functional listing of public-domain Web tools > in the domain of molecular biology. "The 1900 or so links > here are organized according to the task at hand, whether > it's identifying a protein based on its peptide fragment map, > scouring a gene for coding regions, predicting a protein's > 3D structure, or doing a phylogenetic analysis," writes the > NetWatch column's editor, Jocelyn Kaiser. > > As Chris explains at the site, he began collecting these > resources and organizing them in this way in 1995, while he > was in the Department of Biochemistry at the University of > Nebraska, Lincoln. It has been updated five times, with the > latest update occurring after Chris came to SDSC in June 1996. > The site is mirrored at 11 sites around the world. > > Molecular Science is one of SDSC's "Thrust Areas". > > - Wayne Schroeder - > San Diego Supercomputer Center > http://www.sdsc.edu/~schroede > from dough@mdli.com > I would recommend ISIS/Draw to draw in structures, then transfer molfiles > to MSI's Weblab viewer, will pop them into 3D and display in a highly > interactive manner, including surfaces. Both ISIS Draw and Weblab viewer > lite are available free on the web. > > Hello, > > over the last year i have also been trying to find a free/cheap > modeling program for structure visualization etc. the only free program > I found is Molgen, however, it is DOS based and difficult to use. the > solution i have settled on is ChemSite. the price is about $100 per > copy but it decreases when a large number of copies are purchased. > concerning ease of use, it is not as intuitive as i would like, but it > is fairly straight forward to build a structure, minimize it and then > view it. the web site is > > http://www.webcom.com/molvis/ > > as part of the course i teach i have developed a de novo drug design > lab which is based on a simplified receptor; the receptor is an actual > chemical, however, it is very 2D in nature and, thus, easy to analyze. > if you are intereted i would be happy to send you more info. > > alex > > -- > Alex MacKerell, Ph.D. > Associate Professor > School of Pharmacy > University of Maryland > 20 North Pine Street > Baltimore, MD 21201 > 410-706-7442 > 410-706-0346 (fax) > > alex@mmiris.ab.umd.edu or > alex@rx.umaryland.edu > http://www.pharmacy.ab.umd.edu/~alex/ > from snmjohnson@iclub.org > I find ISIS/Draw to be pretty useful for generating 2D & 3D structures. > It will > allow you to create a 2D structure which can be exported & inserted into > Word > documents and such, and as far as the 3D stuff goes, after you make your > 2D > diagram, you can then view the structure with RasMol. > > Oh yeah, and it's free. :) > > You can find it at the following location: > > http://www.mdli.com/download/idrawdown.html > > > Sean Johnson > Barbara- > I too have been looking for a "free" program for building > molecules. > Unfortunately there is none that is currently supported. There was a > program called Molden that is free, but I tried to download it and install > it, and the installation failed. Searching for Molden on www might get > you > there. It may also be referred to in the ccl archive. There is also a > site > that will build it for you as I understand, but that is not satisfying for > a > course. Alas I do not know the address for this site. > The cheapest molecule building programs that give you 3D viewable > molecules in formats that can be either directly output to PDB format or > easily converted are Spartan (Mac or PC) and HyperChem-"Chemlite" actually > (PC only). The prices are $300 and $150 respectively. Chemlite also > sells > for around $70 for students. Spartan has a more powerful builder with > templates and the $300 version (there is a more powerful version for $445) > would be excellent for your class. Unfortunately, $300 is a tough pill > for > an undergrad to swallow. Spartan can export to PDB format. Chemlite does > not and you would have to use Babelwin if you want your students to view > their molecules with chime or rasmol. $70 is about the cost of a > textbook. > Chemlite/Hyperchem's builder is by far easier for students to learn, so if > you are looking for a quick return for your students, Chemlite is your > program. By the way, with both of these programs you get molecular > mechanics, and with Spartan you get Quantum mechanical optimizations too. > Chemlite has a nonoptimizing extended huckel module. > Finally, there is a program called Sculpt, but it is >$500 as I > recall. It is a good program an has a good builder module. > > If you figure something out, please let me know. I would be happy > to follow up on anything I have said here. Good luck! > > > Cheers, > > Jim > > James M. Lo Bue > Assistant Professor of Chemistry > Georgia Southern University > P. O. Box 8064 > Statesboro, GA 30460 > Ph: 912-681-0398 Fax: 912-681-0699 > > from adam@cherwell.com > Barbara > > Take a look at ChemSymphony: > > http://www.chemsymphony.com/ > > You will be particularly interested in the Extranet section and the > example > of well known drugs in the gallery > > http://www.chemsymphony.com/gallery/pharmas/index.html > > ChemSymphony Beans is a toolkit. You could use our 3D sketcher (see the > MOPAC example) to do this. But note that ChemSymphony Beans is a toolkit > so > you would need to invest some time in building the site to do exactly what > you want. It sounds quite ambitious to me (I mean the expectation of your > students are quite high)! > > I will be interested ot learn how you decide to do this. > > Regards > > Adam > > > > Chemsymphony is everything you ask for and more (it does > optimisations via MOPAC). It can be found at > > www.chemsymphony.com > > It is totally web based with molecules drawn online, calculations > submitted an results retreived back into the applet. Check out > the "extranet" section. > > Regards > Carl > > P.S. I have no affiliation with the company > > --------------------------------------------------------------- > |E-mail for life: carl.windsor@bigfoot.com | > -- > > Barbara, > > Its not really what you're looking for, but in a (local) course that I run > here at Bradford, students use ISIS Draw (free and downloadable) to draw > 2D structures and then cut-and-paste these into MSI's WebLabViewer > (free and downloadable) to display, rotate, etc in 3D. It's all simple > stuff that we do - but one of our aims is to get the students to > draw molecules using 2D drawing packages as well. In your case this > means getting the students to download 2 pieces of software - probably > not ideal - and construction of the molecules occurs in 2D rather than > 3D. > > If you come across any free JAVA-based packages that allow construction > of molecules in 3D I'd love to hear about them. > > Regards, > > Steve > > // Email : S.W.Doughty@bradford.ac.uk \\ > // WWW : http://abbot.pharm.brad.ac.uk/ \\ > ---------------------------------------------------------------- > > > May I suggest you look at these two options: > 1 - Molecules-3D (v2.5) a very inexpensive 3D model building program ($49 > student > price) > http://www.molecules.com/m3d_sefs.htm > 2 - WebMolecules - an online VRML-based visualization Library (plug-in > req'd) > http://www.molecules.com/vrmlmols/index.html > > > -- > David Segrist > Molecular Arts Technical Support > > ---------------------------------------------------------------- > Molecular Arts Corporation | > Hanover Corporate Centre, Suite 1000 | http://www.molecules.com > 1532 East Katella Avenue | Main: (714) 634-8100 > Anaheim, California 92805-6627 USA | FAX: (714) 634-1999 > ---------------------------------------------------------------- > from haun@intsim.com > HI Dr. Murray, > > I would suggest that you have a look at our software, SCULPT. SCULPT > allows you to take a structure, view it in 3D. In addition, it is > equippied with some very simple toolsdriven by a mouse; it allows you to > bend and twist portions of the structure while simultaneously giving you > visual feedback on steric forces. It uses Amber and UFF for > minimizations. > This is great for exploring secondary structures and receptor sites. If > your focus will be on small structures, it allows the user to > superposition > flexible structures for conformational analyses. It is a great tool for > students and more professional chemists and biochemists. > > For file compatibility it reads: PDB, MDL Mol (copies and pastes from ISIS > Draw), and (copies and pastes) CS Chem3D files. Thus it supports, ISIS, > ChemWindows, CS Office. The new beta version 2.6 for Windows also has hot > linking capabilities with MDL's Chime, beta 2.0. Incidentally, this > version of Chime also has a sculpting function to it - choose the right > button on the mouse. > > We also offer a great 3D builder called ChemBuilder3D which allows the > user > to build small molecules by a fragment library. It also has MM3 and UFF > and allows you to change torsion angles and conformations (cis to trans) > > If you are interested, please contact me and/or visit our web site > http://www.intsim.com for more information and a free trial. > > Best regards, > > Dan Haun > -- *********************************************************************** Barbara Murray bmurray@uor.edu Chemistry Department 909-793-2121 ext 2374 University of Redlands FAX 909-793-2029 1200 E Colton, PO Box 3080 Redlands, CA 92373-0999 From chemistry-request@www.ccl.net Tue Sep 1 17:27:21 1998 Received: from jazz.ucc.uno.edu (jazz.ucc.uno.edu [137.30.1.6]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id RAA16480 Tue, 1 Sep 1998 17:27:17 -0400 (EDT) Received: from slater (slater.chem.uno.edu) by jazz.ucc.uno.edu (PMDF V5.1-10 #D3119) with SMTP id <01J1ARC2LCJK9EK9GS@jazz.ucc.uno.edu> for CHEMISTRY@www.ccl.net; Tue, 1 Sep 1998 16:24:13 CST Date: Tue, 01 Sep 1998 16:22:08 -0500 From: Howard Alper Subject: Units and parameterization Sender: heacm@jazz.ucc.uno.edu To: CHEMISTRY@www.ccl.net Cc: heacm@jazz.ucc.uno.edu Message-id: <35EC6580.7566@uno.edu> Organization: University of New Orleans Hello, I have a question concerning the parameterization of simulation forcefields, the size of the parameters, and the units. Forcefields are parameterized such that one gets energies in kcal/mole (or kj/mole) even though one is simulating a number of particles much less than Avogadro's number, so that the actual energy is more like whatever number of kcal/mole/6.02 * 10 ** 23, for example. As some examples of consequences of this way of parameterizing forcefields, consider a simulation of N water molecules (my favorite!) If one want to compare to the experimental potential energy (in kcal/mole), one does not use the total energy of the N molecules in the simulation, but the total energy/N. Likewise, if one wanted the heat capacity, that would involve differences of fluctuations in the energy/particle, not the total computed energy of the system of N molecules. My question is: does anyone know the exact reasons for or derivation for the above methods (conventions?) of calculating properties from simulations? I am trying to explain this to someone who is very new to simulation, but it seems like I "know what to do" by some process of osmosis, and I do not remember being taught directly how to calculate things like E or Cp, so I end up saying " I just know". I am sure that there is a rational reason or process behind what is done, I just can't make it clear. Any explanations or references would be most welcome. Thanks, Howard -- Howard E. Alper, Ph.D. Dept. of Chemistry and The Advanced Materials Research Institute University of New Orleans New Orleans, LA 70148 504-280-7216 - Helping molecules find happiness for almost a 5th of a century. From chemistry-request@www.ccl.net Tue Sep 1 23:38:31 1998 Received: from mailrelay1.cc.columbia.edu (cu41754@mailrelay1.cc.columbia.edu [128.59.35.143]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id XAA18804 Tue, 1 Sep 1998 23:38:31 -0400 (EDT) Received: from still3.chem.columbia.edu (still3.chem.columbia.edu [128.59.112.36]) by mailrelay1.cc.columbia.edu (8.8.5/8.8.5) with SMTP id XAA10114; Tue, 1 Sep 1998 23:38:31 -0400 (EDT) Received: by still3.chem.columbia.edu (950413.SGI.8.6.12/930416.SGI.AUTO) id XAA08678; Tue, 1 Sep 1998 23:38:31 -0400 Date: Tue, 1 Sep 1998 23:38:31 -0400 From: shenkin@still3.chem.columbia.edu (Peter Shenkin) Message-Id: <199809020338.XAA08678@still3.chem.columbia.edu> To: chemistry@www.ccl.net, Knegtel Ronald Subject: Re: CCL:Summary cavities in protein-ligand complexes And whatever happened to Voronoi polynomials? -P. *** "Freedom's just another word for nothing left to lose." (B. Yeltsin)*** *Peter Shenkin; Chemistry, Columbia U.; shenkin@columbia.edu (212)854-5143* *MacroModel WWW page: http://www.columbia.edu/cu/chemistry/mmod/mmod.html * From chemistry-request@www.ccl.net Tue Sep 1 23:41:50 1998 Received: from deews1.dent.okayama-u.ac.jp (deews1.dent.okayama-u.ac.jp [150.46.202.36]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id XAA18817 Tue, 1 Sep 1998 23:41:44 -0400 (EDT) Received: from [150.46.162.70] ([150.46.162.70]) by deews1.dent.okayama-u.ac.jp (8.8.8/3.6W) with SMTP id MAA21839 for ; Wed, 2 Sep 1998 12:42:53 +0900 (JST) Message-Id: <199809020342.MAA21839@deews1.dent.okayama-u.ac.jp> Date: Wed, 2 Sep 1998 12:50:21 +0900 To: CHEMISTRY@www.ccl.net From: ep7@dent.okayama-u.ac.jp (masamura) Subject: CCL:Molpro I used molpro. However, the following error is detected. Please help me. submit: Syntax error: "export Project WorkDir" submit: Unable to process contents of command file "molpro.cmd" +1 #!/bin/ksh +2 ################################################################ +3 ############################################ +4 # # +5 #This is a sample shell script for running a meldf job. +6 # # +7 #--------------------------------------------------------------# +8 # # +9 #History: made by Prof.S.Ikuta for single SDCI--mrsdci ru +10 # # +11 ################################################################ +12 ########################################### +13 #set -v +14 #--------------------------------------------------------------# +15 # Job definitions # +16 #--------------------------------------------------------------# +17 Project='96oh-w3' +18 CurrDir=$PWD +19 WorkDir=/scratch/$Project +20 export Project WorkDir +21 print 'Start of job:' $Project +22 print 'Current directory:' $CurrDir +23 print 'Scratch directory;' $WorkDir +24 #---------------------------------------------------------------# +25 # Prologue +26 #---------------------------------------------------------------# +27 export +28 PATH=$PATH:$CurrDir:/home/center/ikuta/molpro96:/home/center/ikuta/molpr o96/ +29 bin:/home/center/ikuta/molpro96/lib:/usr/local/bin +30 export MOLPRO96=/home/center/ikuta/molpro96 +31 export TMPDIR=$WorkDir +32 trap 'exit' ERR +33 rm -fr /scratch/$Project +34 rm -fr $WorkDir +35 mkdir $WorkDir +36 cd $WorkDir +37 #---------------------------------------------------------------# +38 #Start executing meldf job # +39 #---------------------------------------------------------------# +40 molpro <$CurrDir/$Project.conf1.cation.mrcid.com +41 ls -l $WorkDir +42 # Epilogue +43 #---------------------------------------------------------------# +44 cd - +45 rm -r $WorkDir +46 #--------------------------------------------------------------# +47 # Finished, now cleanup. # +48 #-------------------------------------------------------------# +49 exit +1 ***,OH-(H2O)3 (C3) CCSD(T)/AUG-cc-pVDZ (96oh-w3.com) +2 memory,80,M +3 GPRINT,ORBITAL,CIVECTOR,REF; +4 R2=0.9723 ang +5 R4=1.7208 ang +6 R6=1.0065 ang +7 R7=0.9742 ang +8 T4=127.4 degree +9 T6=158.5 degree +10 T7=100.6 degree +11 N6=-166.8 degree +12 N7=35.2 degree +13 geometry={O1; +14 H2,O1,R2; +15 X3,H2,1.0,O1,120.0; +16 H4,O1,R4,H2,T4,X3,180.0; +17 X5,O4,1.0,O1, 90.0,H2, 180.0; +18 O6,O4, R6,O1, T6,H2, N6; +19 H7,O6, R7,H4, T7,O1, N7; +20 H8,O1, R4,H2, T4,X3,60.0; +21 X9,H8, 1.0, O1, 90.0, H2, 180.0; +22 O10,H8, R6,O1, T6,H2, N6; +23 H11,O10,R7,H8, T7,O1, N7; +24 H12,O1, R4, H2, T4,X3, -60.0; +25 X13,H12,1.0, O1, 90.0,H2, 180.0; +26 O14,H12, R6,O1,T6,H2,N6; +27 H15,O14, R7,H12, T7,O1, N7} +28 basis=avdz +29 int +30 +31 hf;occ,16;closed,16; +32 +33 ccsd(t);maxit,50 +34 +35 --- *********************************************************** Masao Masamura Okayama University ep7@dent.okayama-u.ac.jp FAX: 81-86-235-6714 TEL: 81-86-235-6712 *********************************************************** From chemistry-request@www.ccl.net Wed Sep 2 03:40:15 1998 Received: from aitana.cpd.ua.es (aitana.cpd.ua.es [193.145.233.5]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id DAA19484 Wed, 2 Sep 1998 03:40:12 -0400 (EDT) Received: from fisic1.ua.es (fisic1.ua.es [193.145.230.65]) by aitana.cpd.ua.es (AIX4.2/UCB 8.7/8.7) with SMTP id JAA27894; Wed, 2 Sep 1998 09:33:20 +0200 (METDST) Received: from localhost by fisic1.ua.es; (5.65/1.1.8.2/18Oct95-0850PM) id AA01419; Wed, 2 Sep 1998 09:36:02 +0200 Sender: juancar@fisic1.ua.es Message-Id: <35ECF562.2781@fisic1.ua.es> Date: Wed, 02 Sep 1998 09:36:02 +0200 From: Juan Carlos Sancho To: chemistry@www.ccl.net Cc: alexei@paladium.enscm.fr, kochw@argon.chem.tu-berlin.de Subject: CCL: Multideterminantal DFT Recently the application of single-determinant KS theory to the calculation of potential energy curves hace been critically analyzed in Chem. Phys. Lett. 288 (1998), 418-422. Both the non-polarized and restricted results show that the one-determinant approach is unable to provide potential energy curves for the ground state. These deficiencies can not be corrected by the correlation potential without explicitly including a dependence on more Slater determinants (GVB-PP or more advanced multiconfigurational wavefunction). The problem can be treated from differents point of view, depending if you are interested in applications or in the fundamentals. In order to obtain physically acceptable results it is neccesary to include information about the two-body density matrix in the coalescence point (also called on-top pair density). This facts show clearly the many-determinant nature of the problem. Nowadays there are several attempts to enhance the knowledge about the sittuation together with the above mentioned article and the previoulsy appeared in the CCL, - on-top pair density: J.P.Perdew, A.Savin and K.Burke, Phys. Rev A 51 (1995), 4531. F.Moscardo and A.J.Perez-Jimenez, Int. J. Quantum Chem. 67 (1998), 143. - combining multiconfigurational wavefunctions with DFT: N.O.J.Malcom abd J.J.W.McDouall, Chem. Phys. Lett. 282 (1998), 121. B.Miehlich, H.Stoll and A.Savin, Mol. Phys. 91 (1997), 527. T.Leininger, H.Stoll, A.Savin, Chem. Phys. Lett. 275 (1997), 151 I am very interested in this topic because is a main point in this group, so I acknowledge to maintain an estimulating discussion through this CCL. Thanks. Juan Carlos ---------------------------------------------------------------------- J.C. Sancho-Garcia Dpto. Quimica-Fisica Universidad de Alicante Apartado 99, 03080 Alicante SPAIN juancar@fisic1.ua.es ---------------------------------------------------------------------- From chemistry-request@www.ccl.net Wed Sep 2 08:20:30 1998 Received: from dfw-ix6.ix.netcom.com (dfw-ix6.ix.netcom.com [206.214.98.6]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id IAA20498 Wed, 2 Sep 1998 08:20:26 -0400 (EDT) Received: (from smap@localhost) by dfw-ix6.ix.netcom.com (8.8.4/8.8.4) id HAA02024 for ; Wed, 2 Sep 1998 07:19:48 -0500 (CDT) Received: from bst-ma3-06.ix.netcom.com(205.186.73.102) by dfw-ix6.ix.netcom.com via smap (V1.3) id rma001991; Wed Sep 2 07:19:12 1998 Received: by localhost with Microsoft MAPI; Wed, 2 Sep 1998 08:20:46 -0400 Message-ID: <01BDD64A.95A3B5E0.kmtakita@knowledgefoundation.com> From: Kim Takita To: "'chemistry@www.ccl.net'" Subject: low k dielectrics & copper Date: Wed, 2 Sep 1998 08:18:01 -0400 Is anyone in this group working on low k dielectrics (or copper)? I'm looking for information on this subject, particularly organizations pursuing low-k. Also, thank you to those who responded with survey questions on discovery methodologies. They are still trickling in. Once it's completed will post summary. ------------------------------------------------------------------------ ---------- Kim Takita Vice President The Knowledge Foundation, Inc. 101 Merrimac Street Boston, MA 02114 Phone: 617-367-7979 ext. 202 Fax: 617-367-7912 E-Mail: kmtakita@knowledgefoundation.com http://www.knowledgefoundation.com From chemistry-request@www.ccl.net Wed Sep 2 09:56:53 1998 Received: from bdh8.na.pg.com (bdh8.na.pg.com [192.44.184.137]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA21552 Wed, 2 Sep 1998 09:56:37 -0400 (EDT) Received: from pandora.na.pg.com (pandora.na.pg.com [155.126.79.1]) by bdh8.na.pg.com (8.8.8/8.8.8) with ESMTP id JAA28845 for ; Wed, 2 Sep 1998 09:50:03 -0400 (EDT) Received: from morpheus (morpheus [137.176.2.89]) by pandora.na.pg.com (8.8.8/8.8.8) with SMTP id JAA11480; Wed, 2 Sep 1998 09:55:43 -0400 (EDT) Sender: laidig@pg.com Message-ID: <35ED4F07.6231@pg.com> Date: Wed, 02 Sep 1998 09:58:31 -0400 From: Bill Laidig To: chemistry@www.ccl.net CC: laidig@pg.com Subject: charges fro X-ray All, I was wondering if anyone knows of any work, etc. in extracting quantities such as partially atomic charges, etc. from experimental densities obtained by small molecule crystallography. Also, if anyone knows of any X-ray programs that do this or of any utilities that extract information such as ESP's, etc., from the x-ray data that can be passed into a standard QC code. Thanks in advance, Bill P.S. I know such quantities as partial atomic charges are not uniquely defined, but, analogously to QC, for a given definition useful trends, etc. may be deduced. -- ************************************************************************ * "Like jewels in a crown, the precious stones glittered in the * * queen's round metal hat." - Jack Handey * * * * Bill Laidig * * The Procter & Gamble Co. tel 513-627-2857 fax - 1233 * * Miami Valley Laboratories laidig@pg.com (preferred) * * P.O. Box 538707 laidig.wd@pg.com * * Cincinnati, OH 45253-8707 * ************************************************************************ From chemistry-request@www.ccl.net Wed Sep 2 10:23:54 1998 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA21800 Wed, 2 Sep 1998 10:23:53 -0400 (EDT) Received: from bacchus.pc1.uni-duesseldorf.de (root@bacchus.pc1.uni-duesseldorf.de [134.99.152.11]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id KAA17499 for ; Wed, 2 Sep 1998 10:23:50 -0400 (EDT) Received: from bacchus.pc1.uni-duesseldorf.de (jochen@localhost [127.0.0.1]) by bacchus.pc1.uni-duesseldorf.de (8.8.7/8.8.7) with SMTP id QAA09580; Wed, 2 Sep 1998 16:23:29 +0200 From: Jochen Kuepper Reply-To: jochen@uni-duesseldorf.de To: "Marc N." Subject: Re: CCL:Re: CCL:Linux on Alpha, math library Date: Wed, 2 Sep 1998 16:22:32 +0200 Content-Type: text/plain Cc: CHEMISTRY@ccl.net References: Message-Id: <98090216232804.09006@bacchus.pc1.uni-duesseldorf.de> On Mon, 31 Aug 1998 Marc N. wrote: >On Sat, 29 Aug 1998, Victoria Buch wrote: >Well, this seems to be somewhat of an oversimplification. Indeed, the >libraries are very important, and so one can probably say that the >standard libraries that come with [Red Hat] Linux/Alpha are good only for >"simple operations + - * /". > >However, with the right, i.e., optimized libraries, we've found, e.g., >Gaussian 94 on a 500MHz Alpha/Linux box to be 2.5 times as fast as on a >400MHz Pentium II Linux system. Are you using the optimzed libfm and libffm math libraries ? (See my other posting). Greetings, Jochen ----------------------------------------------------------------------- Jochen K"upper Heinrich-Heine-Universit"at D"usseldorf jochen@uni-duesseldorf.de Institut f"ur Physikalische Chemie I Universit"atsstr. 1, Geb 26.43 Raum 02.29 phone ++49-211-8113681 40225 D"usseldorf fax ++49-211-8115195 Germany http://www-public.rz.uni-duesseldorf.de/~jochen ----------------------------------------------------------------------- From chemistry-request@www.ccl.net Wed Sep 2 10:54:46 1998 Received: from chemistry.leeds.ac.uk (chmsun1.leeds.ac.uk [129.11.12.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA23583 Wed, 2 Sep 1998 10:54:44 -0400 (EDT) Received: from miris7.leeds.ac.uk.chem.leeds.ac.uk (miris7.leeds.ac.uk [129.11.12.23]) by chemistry.leeds.ac.uk (8.8.8/8.8.8) with SMTP id PAA01870 for ; Wed, 2 Sep 1998 15:54:42 +0100 (BST) Date: Wed, 2 Sep 1998 15:54:42 +0100 (BST) Message-Id: <199809021454.PAA01870@chemistry.leeds.ac.uk> From: Stuart Green To: chemistry@www.ccl.net Subject: Thiophosphate AMBER parameters I'm trying to locate some parameters for thiophosphates (or phosphorothioates) suitable for the AMBER94/96 forcefield. After a literature search I couldn't find anything useful. Has anyone derived such parameters before? Are they willing to share? Cheers, Stuart -- Dr. Stuart M. Green S.M.Green@chem.leeds.ac.uk School of Chemistry University of Leeds Tel +44 113 233 6596 Leeds, LS2 9JT, England Fax +44 113 233 6563 From chemistry-request@www.ccl.net Wed Sep 2 13:40:16 1998 Received: from interlock.amoco.com (interlock.amoco.com [192.195.167.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id NAA09421 Wed, 2 Sep 1998 13:40:13 -0400 (EDT) Received: by interlock.amoco.com id MAA27267 (InterLock SMTP Gateway 3.0 for CHEMISTRY@www.ccl.net); Wed, 2 Sep 1998 12:40:03 -0500 Message-Id: <199809021740.MAA27267@interlock.amoco.com> From: jtgolab@amoco.com (Joe Golab) Date: Wed, 2 Sep 1998 12:49:33 -0500 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: CHEMISTRY@www.ccl.net Subject: SPRING ACS Call For Papers (COMP) Cc: paul.mathias@aspentech.com, jtgolab@amoco.com !!! CALL FOR PAPERS 1999 Spring National ACS Meeting (March 21-25) !!! "Bridging the Gap between Modeling in Chemistry and Engineering" (COMP) >>>>> SUBMISSION DEADLINE November 9, 1998 <<<<< Molecular modeling and simulation have reached levels of sophistication and accuracy that make them increasingly useful and even essential tools for chemists and chemical engineers. At the same time, the methods, capabilities, and limitations are often not yet well-known. More importantly, chemists and chemical engineers have evolved different approaches to the problem and the communication between the two groups is limited and inadequate. As part of the 1999 Spring National ACS Meeting (March 21-25) in Anahiem, a symposium will be held on "Bridging the Gap between Modeling in Chemistry and Engineering". The purpose of the symposium is to foster the development of an efficient dialogue between practitioners in both chemistry and engineering modeling which leads to real links that are exploitable to industrial, government, and academic affairs. The goal of the session is to educate potential, novice, and expert modelers by emphasizing how methods and successes have helped (or have the potential to help) the two fields. Contributed papers should focus on applications and new developments that highlight overlap with and support of other areas of modeling. Feel free to identify how modeling is implemented in your organization, share achievements, and philosophize on future challenges or rewards. It is anticipated that the audience will consist of those who need to understand possible uses and results and those who simply want to learn about the area. We are seeking papers on the following topics: Thermochemistry, Kinetics, Physical Properties, Catalysis, Forcefields, Process Screening, Solvation, Adsorption, Polymers & Copolymers, Phase and Multicomponent Equilibria, Surfactants, Materials, and Tools. We strongly encourage you to submit a suitable paper for this session. Papers will be accepted for review by contacting either one of us using the information below. The submission deadline is November 9, 1998 and should include a title and abstract. Please distribute this information to other researchers in industry, academia, and national labs. Thank you for your consideration. Joseph T. Golab Paul M. Mathias Amoco Corporation Aspen Technology, Inc. MAIL CODE D-5 150 West Warrenville Road Ten Canal Park Naperville, Illinois 60563 Cambridge, MA 02141-2201 Tel: (630) 961-7878 Tel: (617) 949-1727 Fax: (630) 961-6223 Fax: (617) 949-0727 Email: jtgolab@amoco.com Email: Paul.Mathias@AspenTech.com -- :Joe jtgolab@amoco.com (630) 961-7878 +---------------------------------------------+ | Just because something doesn't do what you | | planned it to do doesn't mean it's useless. | | - Thomas Edison | +---------------------------------------------+ From chemistry-request@www.ccl.net Wed Sep 2 15:31:33 1998 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id PAA17940 Wed, 2 Sep 1998 15:31:32 -0400 (EDT) Received: from cliff.acs.oakland.edu (cliff.acs.oakland.edu [141.210.10.111]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id PAA01351 for ; Wed, 2 Sep 1998 15:31:30 -0400 (EDT) Received: from ouchem.chem.oakland.edu (ouchem.chem.oakland.edu [141.210.108.5]) by cliff.acs.oakland.edu (8.8.8/8.8.8) with SMTP id PAA31415 for ; Wed, 2 Sep 1998 15:31:31 -0400 (EDT) Received: by ouchem.chem.oakland.edu; id AA24784; Wed, 2 Sep 1998 15:31:31 -0400 From: "Brent H. Besler" Message-Id: <9809021931.AA24784@ouchem.chem.oakland.edu> Subject: Gaussian 98 on Intel/Linux Platform To: chemistry@ccl.net Date: Wed, 2 Sep 1998 15:31:30 -0500 (EDT) I noticed that Gaussian 98 is now using the Portland Group Fortan compiler rather than f2c/gcc. When I did some tests, I was getting about a 30% speed increase over f2c/gcc when testing with a program which calculated overlap integrals over Slater orbitals. This is a real rough estimate, so I would be curious as to the performance increase with G98. From chemistry-request@www.ccl.net Wed Sep 2 03:40:15 1998 Received: from aitana.cpd.ua.es (aitana.cpd.ua.es [193.145.233.5]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id DAA19484 Wed, 2 Sep 1998 03:40:12 -0400 (EDT) Received: from fisic1.ua.es (fisic1.ua.es [193.145.230.65]) by aitana.cpd.ua.es (AIX4.2/UCB 8.7/8.7) with SMTP id JAA27894; Wed, 2 Sep 1998 09:33:20 +0200 (METDST) Received: from localhost by fisic1.ua.es; (5.65/1.1.8.2/18Oct95-0850PM) id AA01419; Wed, 2 Sep 1998 09:36:02 +0200 Sender: juancar@fisic1.ua.es Message-Id: <35ECF562.2781@fisic1.ua.es> Date: Wed, 02 Sep 1998 09:36:02 +0200 From: Juan Carlos Sancho X-Mailer: Mozilla 3.04Gold (X11; I; OSF1 V3.2 alpha) Mime-Version: 1.0 To: chemistry@www.ccl.net Cc: alexei@paladium.enscm.fr, kochw@argon.chem.tu-berlin.de Subject: CCL: Multideterminantal DFT Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Recently the application of single-determinant KS theory to the calculation of potential energy curves hace been critically analyzed in Chem. Phys. Lett. 288 (1998), 418-422. Both the non-polarized and restricted results show that the one-determinant approach is unable to provide potential energy curves for the ground state. These deficiencies can not be corrected by the correlation potential without explicitly including a dependence on more Slater determinants (GVB-PP or more advanced multiconfigurational wavefunction). The problem can be treated from differents point of view, depending if you are interested in applications or in the fundamentals. In order to obtain physically acceptable results it is neccesary to include information about the two-body density matrix in the coalescence point (also called on-top pair density). This facts show clearly the many-determinant nature of the problem. Nowadays there are several attempts to enhance the knowledge about the sittuation together with the above mentioned article and the previoulsy appeared in the CCL, - on-top pair density: J.P.Perdew, A.Savin and K.Burke, Phys. Rev A 51 (1995), 4531. F.Moscardo and A.J.Perez-Jimenez, Int. J. Quantum Chem. 67 (1998), 143. - combining multiconfigurational wavefunctions with DFT: N.O.J.Malcom abd J.J.W.McDouall, Chem. Phys. Lett. 282 (1998), 121. B.Miehlich, H.Stoll and A.Savin, Mol. Phys. 91 (1997), 527. T.Leininger, H.Stoll, A.Savin, Chem. Phys. Lett. 275 (1997), 151 I am very interested in this topic because is a main point in this group, so I acknowledge to maintain an estimulating discussion through this CCL. Thanks. Juan Carlos ---------------------------------------------------------------------- J.C. Sancho-Garcia Dpto. Quimica-Fisica Universidad de Alicante Apartado 99, 03080 Alicante SPAIN juancar@fisic1.ua.es ---------------------------------------------------------------------- From chemistry-request@www.ccl.net Wed Sep 2 03:45:54 1998 Received: from ashura.qcl.t.u-tokyo.ac.jp (ashura.qcl.t.u-tokyo.ac.jp [133.11.70.129]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id DAA19512 Wed, 2 Sep 1998 03:45:50 -0400 (EDT) Received: from localhost (localhost [127.0.0.1]) by ashura.qcl.t.u-tokyo.ac.jp (8.8.8/3.6W-980805) with ESMTP id QAA28668; Wed, 2 Sep 1998 16:45:46 +0900 Message-Id: <199809020745.QAA28668@ashura.qcl.t.u-tokyo.ac.jp> To: chemistry@www.ccl.net cc: akinaga@qcl.t.u-tokyo.ac.jp Subject: matrix elements with GTO and PW Date: Wed, 02 Sep 1998 16:45:46 +0900 From: AKINAGA Yoshinobu Dear Sirs, I am interested in the calculation of an impurity embedded in a solid or an elecron gas, employing both gaussian type functions (GTO) and plane-wave (PW) basis functions. I want to know how to evaluate the matrix elements of one-electron integral of nuclear-repulsion between the gaussian and the plane-wave such as , as well as two-electron integrals, for example, the integral between the gaussian functions and the plane-waves such as int(dr1dr2) phi_a(r1)exp(ik_i r1)r12^(-1)exp(-k_j r2)phi_b(r2), where "phi_a" means a primitive gaussian function whose index is a, and "k_i" means wave vector whose index is i. Any references is welcome. All responses sill be summerized. Thanks in advance. best regards, =============================================================== Yoshinobu Akinaga Department of Applied Chemistry, Graduate School of Engineering, University of Tokyo, Tokyo 113, Japan tel : 03-3812-2111(7243), E-mail : akinaga@qcl.t.u-tokyo.ac.jp =============================================================== From chemistry-request@www.ccl.net Wed Sep 2 08:20:30 1998 Received: from dfw-ix6.ix.netcom.com (dfw-ix6.ix.netcom.com [206.214.98.6]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id IAA20498 Wed, 2 Sep 1998 08:20:26 -0400 (EDT) Received: (from smap@localhost) by dfw-ix6.ix.netcom.com (8.8.4/8.8.4) id HAA02024 for ; Wed, 2 Sep 1998 07:19:48 -0500 (CDT) Received: from bst-ma3-06.ix.netcom.com(205.186.73.102) by dfw-ix6.ix.netcom.com via smap (V1.3) id rma001991; Wed Sep 2 07:19:12 1998 Received: by localhost with Microsoft MAPI; Wed, 2 Sep 1998 08:20:46 -0400 Message-ID: <01BDD64A.95A3B5E0.kmtakita@knowledgefoundation.com> From: Kim Takita To: "'chemistry@www.ccl.net'" Subject: low k dielectrics & copper Date: Wed, 2 Sep 1998 08:18:01 -0400 X-Mailer: Microsoft Internet E-mail/MAPI - 8.0.0.4211 Encoding: 18 TEXT Is anyone in this group working on low k dielectrics (or copper)? I'm looking for information on this subject, particularly organizations pursuing low-k. Also, thank you to those who responded with survey questions on discovery methodologies. They are still trickling in. Once it's completed will post summary. ------------------------------------------------------------------------ ---------- Kim Takita Vice President The Knowledge Foundation, Inc. 101 Merrimac Street Boston, MA 02114 Phone: 617-367-7979 ext. 202 Fax: 617-367-7912 E-Mail: kmtakita@knowledgefoundation.com http://www.knowledgefoundation.com From chemistry-request@www.ccl.net Wed Sep 2 09:56:53 1998 Received: from bdh8.na.pg.com (bdh8.na.pg.com [192.44.184.137]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA21552 Wed, 2 Sep 1998 09:56:37 -0400 (EDT) Received: from pandora.na.pg.com (pandora.na.pg.com [155.126.79.1]) by bdh8.na.pg.com (8.8.8/8.8.8) with ESMTP id JAA28845 for ; Wed, 2 Sep 1998 09:50:03 -0400 (EDT) Received: from morpheus (morpheus [137.176.2.89]) by pandora.na.pg.com (8.8.8/8.8.8) with SMTP id JAA11480; Wed, 2 Sep 1998 09:55:43 -0400 (EDT) Sender: laidig@pg.com Message-ID: <35ED4F07.6231@pg.com> Date: Wed, 02 Sep 1998 09:58:31 -0400 From: Bill Laidig X-Mailer: Mozilla 3.01SC-SGI (X11; I; IRIX64 6.2 IP28) MIME-Version: 1.0 To: chemistry@www.ccl.net CC: laidig@pg.com Subject: charges fro X-ray Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit All, I was wondering if anyone knows of any work, etc. in extracting quantities such as partially atomic charges, etc. from experimental densities obtained by small molecule crystallography. Also, if anyone knows of any X-ray programs that do this or of any utilities that extract information such as ESP's, etc., from the x-ray data that can be passed into a standard QC code. Thanks in advance, Bill P.S. I know such quantities as partial atomic charges are not uniquely defined, but, analogously to QC, for a given definition useful trends, etc. may be deduced. -- ************************************************************************ * "Like jewels in a crown, the precious stones glittered in the * * queen's round metal hat." - Jack Handey * * * * Bill Laidig * * The Procter & Gamble Co. tel 513-627-2857 fax - 1233 * * Miami Valley Laboratories laidig@pg.com (preferred) * * P.O. Box 538707 laidig.wd@pg.com * * Cincinnati, OH 45253-8707 * ************************************************************************ From chemistry-request@www.ccl.net Wed Sep 2 10:23:54 1998 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA21800 Wed, 2 Sep 1998 10:23:53 -0400 (EDT) Received: from bacchus.pc1.uni-duesseldorf.de (root@bacchus.pc1.uni-duesseldorf.de [134.99.152.11]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id KAA17499 for ; Wed, 2 Sep 1998 10:23:50 -0400 (EDT) Received: from bacchus.pc1.uni-duesseldorf.de (jochen@localhost [127.0.0.1]) by bacchus.pc1.uni-duesseldorf.de (8.8.7/8.8.7) with SMTP id QAA09580; Wed, 2 Sep 1998 16:23:29 +0200 From: Jochen Kuepper Reply-To: jochen@uni-duesseldorf.de To: "Marc N." Subject: Re: CCL:Re: CCL:Linux on Alpha, math library Date: Wed, 2 Sep 1998 16:22:32 +0200 X-Mailer: KMail [version 0.7.9] Content-Type: text/plain Cc: CHEMISTRY@ccl.net References: MIME-Version: 1.0 Message-Id: <98090216232804.09006@bacchus.pc1.uni-duesseldorf.de> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by www.ccl.net id KAA21801 On Mon, 31 Aug 1998 Marc N. wrote: >On Sat, 29 Aug 1998, Victoria Buch wrote: >Well, this seems to be somewhat of an oversimplification. Indeed, the >libraries are very important, and so one can probably say that the >standard libraries that come with [Red Hat] Linux/Alpha are good only for >"simple operations + - * /". > >However, with the right, i.e., optimized libraries, we've found, e.g., >Gaussian 94 on a 500MHz Alpha/Linux box to be 2.5 times as fast as on a >400MHz Pentium II Linux system. Are you using the optimzed libfm and libffm math libraries ? (See my other posting). Greetings, Jochen ----------------------------------------------------------------------- Jochen K"upper Heinrich-Heine-Universit"at D"usseldorf jochen@uni-duesseldorf.de Institut f"ur Physikalische Chemie I Universit"atsstr. 1, Geb 26.43 Raum 02.29 phone ++49-211-8113681 40225 D"usseldorf fax ++49-211-8115195 Germany http://www-public.rz.uni-duesseldorf.de/~jochen ----------------------------------------------------------------------- From chemistry-request@www.ccl.net Wed Sep 2 10:26:02 1998 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA21834 Wed, 2 Sep 1998 10:26:01 -0400 (EDT) Received: from bacchus.pc1.uni-duesseldorf.de (root@bacchus.pc1.uni-duesseldorf.de [134.99.152.11]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id KAA18213 for ; Wed, 2 Sep 1998 10:25:56 -0400 (EDT) Received: from bacchus.pc1.uni-duesseldorf.de (jochen@localhost [127.0.0.1]) by bacchus.pc1.uni-duesseldorf.de (8.8.7/8.8.7) with SMTP id QAA09590 for ; Wed, 2 Sep 1998 16:25:31 +0200 From: Jochen Kuepper Reply-To: jochen@uni-duesseldorf.de To: CCL Subject: Re: Linux on Alpha, math library Date: Sat, 9 Oct 2134 22:52:41 +0200 X-Mailer: KMail [version 0.7.9] Content-Type: text/plain MIME-Version: 1.0 Message-Id: <98090216253100.09585@bacchus.pc1.uni-duesseldorf.de> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by www.ccl.net id KAA21835 Sorry if that goes to the list twice, I haven't gotten it back from the list yet. ---------- Forwarded Message, on Tue, 01 Sep 1998 Jochen Kuepper wrote: ---------- On Sat, 29 Aug 1998 Victoria Buch wrote: >> Igor J. Barani writes: >> > I have just recently installed Linux on a DEC Alpha and when I compile >> > several programs in fortran on it, they seem to compile to twice the >> > size and require 9 times as long to run than on DEC UNIX. Do you have >> > any idea why this may be so and how I may be able to speed up the >> > processes? Any suggestions would be greatly appreciated. Thank you. >We have just been there. You have the latest Red Hat Linux, dont you? >So: the latest math library libm version 2.0.7 from gnu is messed up. >Our system menager installed old version 2.0.1 - works faster by a factor 2. >More generally our sexperience suggests that >Alpha / Linux for FP operations is good only >for simple operations + - * / . My simulation >programs are still 40% below >the performance of Alpha-DEC, and only 10% faster than Petium II (400MHz) >which is more than 2 times cheaper. Disappointing. >Good luck. Victoria The slowdown of the math-library is due to bug-fixes. The old glibc based math-libs do have problems with wrong results for sqrt ( and others ) ! So you have to decide wether you use correct code or ( little ) faster code that might produce wrong answers. I would suggest to use the newest possible libm, if you are really for speed you might consider recompiling it with optimization turned high (v.i.). More important, there are replacement libraries for the more important math routines, that are hand-optimized assembler. IIRC, one of them is based on code Cray developed for their Alpha based machines. You can use both of them, since each one only provides a subset of functions in the next slower one (libm <- libfm <- libffm ) ! Look at http://people.frankfurt.netsurf.de/Joachim.Wesner/ Another important fact is the compiler to use. egcs-1.1pre is really stable for me, you might consider using it since there are very usefull new optimization passes. Also check your code and the compiler flags you are using, consider -fno-exceptions, -fno-rtti, ... and all the other -m, -f, -O options and take all these that will speed up your programs ! Hope it helps and you all get more power out of your Alpha-toys. If you need some more info, feel free to ask ( Victoria, aren't you in D"usseldorf right now ? ) Greetings, Jochen ----------------------------------------------------------------------- Jochen K"upper Heinrich-Heine-Universit"at D"usseldorf jochen@uni-duesseldorf.de Institut f"ur Physikalische Chemie I Universit"atsstr. 1, Geb 26.43 Raum 02.29 phone ++49-211-8113681 40225 D"usseldorf fax ++49-211-8115195 Germany http://www-public.rz.uni-duesseldorf.de/~jochen ----------------------------------------------------------------------- From chemistry-request@www.ccl.net Wed Sep 2 10:54:46 1998 Received: from chemistry.leeds.ac.uk (chmsun1.leeds.ac.uk [129.11.12.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA23583 Wed, 2 Sep 1998 10:54:44 -0400 (EDT) Received: from miris7.leeds.ac.uk.chem.leeds.ac.uk (miris7.leeds.ac.uk [129.11.12.23]) by chemistry.leeds.ac.uk (8.8.8/8.8.8) with SMTP id PAA01870 for ; Wed, 2 Sep 1998 15:54:42 +0100 (BST) Date: Wed, 2 Sep 1998 15:54:42 +0100 (BST) Message-Id: <199809021454.PAA01870@chemistry.leeds.ac.uk> From: Stuart Green To: chemistry@www.ccl.net Subject: Thiophosphate AMBER parameters I'm trying to locate some parameters for thiophosphates (or phosphorothioates) suitable for the AMBER94/96 forcefield. After a literature search I couldn't find anything useful. Has anyone derived such parameters before? Are they willing to share? Cheers, Stuart -- Dr. Stuart M. Green S.M.Green@chem.leeds.ac.uk School of Chemistry University of Leeds Tel +44 113 233 6596 Leeds, LS2 9JT, England Fax +44 113 233 6563 From chemistry-request@www.ccl.net Wed Sep 2 03:45:54 1998 Received: from ashura.qcl.t.u-tokyo.ac.jp (ashura.qcl.t.u-tokyo.ac.jp [133.11.70.129]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id DAA19512 Wed, 2 Sep 1998 03:45:50 -0400 (EDT) Received: from localhost (localhost [127.0.0.1]) by ashura.qcl.t.u-tokyo.ac.jp (8.8.8/3.6W-980805) with ESMTP id QAA28668; Wed, 2 Sep 1998 16:45:46 +0900 Message-Id: <199809020745.QAA28668@ashura.qcl.t.u-tokyo.ac.jp> To: chemistry@www.ccl.net cc: akinaga@qcl.t.u-tokyo.ac.jp Subject: matrix elements with GTO and PW Date: Wed, 02 Sep 1998 16:45:46 +0900 From: AKINAGA Yoshinobu Dear Sirs, I am interested in the calculation of an impurity embedded in a solid or an elecron gas, employing both gaussian type functions (GTO) and plane-wave (PW) basis functions. I want to know how to evaluate the matrix elements of one-electron integral of nuclear-repulsion between the gaussian and the plane-wave such as , as well as two-electron integrals, for example, the integral between the gaussian functions and the plane-waves such as int(dr1dr2) phi_a(r1)exp(ik_i r1)r12^(-1)exp(-k_j r2)phi_b(r2), where "phi_a" means a primitive gaussian function whose index is a, and "k_i" means wave vector whose index is i. Any references is welcome. All responses sill be summerized. Thanks in advance. best regards, =============================================================== Yoshinobu Akinaga Department of Applied Chemistry, Graduate School of Engineering, University of Tokyo, Tokyo 113, Japan tel : 03-3812-2111(7243), E-mail : akinaga@qcl.t.u-tokyo.ac.jp =============================================================== From chemistry-request@www.ccl.net Wed Sep 2 22:07:11 1998 Received: from ns.DKFZ-Heidelberg.DE (ns.dkfz-heidelberg.de [192.55.188.199]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id WAA26655 Wed, 2 Sep 1998 22:07:10 -0400 (EDT) Received: from cvx12.inet.dkfz-heidelberg.de (cvx12.inet.dkfz-heidelberg.de [193.174.51.101]) by ns.DKFZ-Heidelberg.DE (8.8.8/8.8.8/DKFZ-8.8.8) with ESMTP id EAA23820 for ; Thu, 3 Sep 1998 04:06:40 +0200 (MET DST) Received: from localhost (localhost [[UNIX: localhost]]) by cvx12.inet.dkfz-heidelberg.de (8.8.8/8.8.8/DKFZ-8.8.8) with SMTP id EAA11438 for ; Thu, 3 Sep 1998 04:06:39 +0200 (METDST) Date: Thu, 3 Sep 1998 04:06:38 +0200 (METDST) From: Emadeddin Tajkhorshid To: chemistry@www.ccl.net Subject: OOP calculation Message-ID: Dear CCL I have a question about calculating out of plane force constants. Is there any experimental which can be used to derive these forces? or can we calculate them? If yes how? Thanx for your help Emad Tajkhorshid Dept. Mol. Biophysics, German Cancer Research center, Heidelberg, Germany Tel: +49 6221 422340, Fax: +40 6221 422333, Email: E.Tajkhorshid@DKFZ-Heidelberg.de From chemistry-request@www.ccl.net Wed Sep 2 13:40:16 1998 Received: from interlock.amoco.com (interlock.amoco.com [192.195.167.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id NAA09421 Wed, 2 Sep 1998 13:40:13 -0400 (EDT) Received: by interlock.amoco.com id MAA27267 (InterLock SMTP Gateway 3.0 for CHEMISTRY@www.ccl.net); Wed, 2 Sep 1998 12:40:03 -0500 Message-Id: <199809021740.MAA27267@interlock.amoco.com> Received: by interlock.amoco.com (Protected-side Proxy Mail Agent-4); Wed, 2 Sep 1998 12:40:03 -0500 Received: by interlock.amoco.com (Protected-side Proxy Mail Agent-3); Wed, 2 Sep 1998 12:40:03 -0500 Received: by interlock.amoco.com (Protected-side Proxy Mail Agent-2); Wed, 2 Sep 1998 12:40:03 -0500 Received: by interlock.amoco.com (Protected-side Proxy Mail Agent-1); Wed, 2 Sep 1998 12:40:03 -0500 From: jtgolab@amoco.com (Joe Golab) Date: Wed, 2 Sep 1998 12:49:33 -0500 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: CHEMISTRY@www.ccl.net Subject: SPRING ACS Call For Papers (COMP) Cc: paul.mathias@aspentech.com, jtgolab@amoco.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii !!! CALL FOR PAPERS 1999 Spring National ACS Meeting (March 21-25) !!! "Bridging the Gap between Modeling in Chemistry and Engineering" (COMP) >>>>> SUBMISSION DEADLINE November 9, 1998 <<<<< Molecular modeling and simulation have reached levels of sophistication and accuracy that make them increasingly useful and even essential tools for chemists and chemical engineers. At the same time, the methods, capabilities, and limitations are often not yet well-known. More importantly, chemists and chemical engineers have evolved different approaches to the problem and the communication between the two groups is limited and inadequate. As part of the 1999 Spring National ACS Meeting (March 21-25) in Anahiem, a symposium will be held on "Bridging the Gap between Modeling in Chemistry and Engineering". The purpose of the symposium is to foster the development of an efficient dialogue between practitioners in both chemistry and engineering modeling which leads to real links that are exploitable to industrial, government, and academic affairs. The goal of the session is to educate potential, novice, and expert modelers by emphasizing how methods and successes have helped (or have the potential to help) the two fields. Contributed papers should focus on applications and new developments that highlight overlap with and support of other areas of modeling. Feel free to identify how modeling is implemented in your organization, share achievements, and philosophize on future challenges or rewards. It is anticipated that the audience will consist of those who need to understand possible uses and results and those who simply want to learn about the area. We are seeking papers on the following topics: Thermochemistry, Kinetics, Physical Properties, Catalysis, Forcefields, Process Screening, Solvation, Adsorption, Polymers & Copolymers, Phase and Multicomponent Equilibria, Surfactants, Materials, and Tools. We strongly encourage you to submit a suitable paper for this session. Papers will be accepted for review by contacting either one of us using the information below. The submission deadline is November 9, 1998 and should include a title and abstract. Please distribute this information to other researchers in industry, academia, and national labs. Thank you for your consideration. Joseph T. Golab Paul M. Mathias Amoco Corporation Aspen Technology, Inc. MAIL CODE D-5 150 West Warrenville Road Ten Canal Park Naperville, Illinois 60563 Cambridge, MA 02141-2201 Tel: (630) 961-7878 Tel: (617) 949-1727 Fax: (630) 961-6223 Fax: (617) 949-0727 Email: jtgolab@amoco.com Email: Paul.Mathias@AspenTech.com -- :Joe jtgolab@amoco.com (630) 961-7878 +---------------------------------------------+ | Just because something doesn't do what you | | planned it to do doesn't mean it's useless. | | - Thomas Edison | +---------------------------------------------+ From chemistry-request@www.ccl.net Wed Sep 2 22:17:37 1998 Received: from mail1.javanet.com (mail1.javanet.com [205.219.162.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id WAA26703 Wed, 2 Sep 1998 22:17:36 -0400 (EDT) Received: from monaco (ct-hartford-us1242.javanet.com [209.150.34.105]) by mail1.javanet.com (8.8.8/8.7) with SMTP id WAA05623 for ; Wed, 2 Sep 1998 22:17:36 -0400 (EDT) Message-Id: <3.0.6.32.19980902221548.0090d520@mail.javanet.com> X-Sender: gusev@mail.javanet.com X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Wed, 02 Sep 1998 22:15:48 -0400 To: chemistry@www.ccl.net From: Vladimir Gusev Subject: Carbon nano-tube coordinates algorithm Dear CCL, Does anybody have a freely available source code/algorithm for generating carbon nano-tubes? The language is not important. I would appreciate any pointers. Vladimir Gusev From chemistry-request@www.ccl.net Wed Sep 2 15:31:33 1998 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id PAA17940 Wed, 2 Sep 1998 15:31:32 -0400 (EDT) Received: from cliff.acs.oakland.edu (cliff.acs.oakland.edu [141.210.10.111]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id PAA01351 for ; Wed, 2 Sep 1998 15:31:30 -0400 (EDT) Received: from ouchem.chem.oakland.edu (ouchem.chem.oakland.edu [141.210.108.5]) by cliff.acs.oakland.edu (8.8.8/8.8.8) with SMTP id PAA31415 for ; Wed, 2 Sep 1998 15:31:31 -0400 (EDT) Received: by ouchem.chem.oakland.edu; id AA24784; Wed, 2 Sep 1998 15:31:31 -0400 From: "Brent H. Besler" Message-Id: <9809021931.AA24784@ouchem.chem.oakland.edu> Subject: Gaussian 98 on Intel/Linux Platform To: chemistry@ccl.net Date: Wed, 2 Sep 1998 15:31:30 -0500 (EDT) X-Mailer: ELM [version 2.4 PL21] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit I noticed that Gaussian 98 is now using the Portland Group Fortan compiler rather than f2c/gcc. When I did some tests, I was getting about a 30% speed increase over f2c/gcc when testing with a program which calculated overlap integrals over Slater orbitals. This is a real rough estimate, so I would be curious as to the performance increase with G98. From chemistry-request@www.ccl.net Wed Sep 2 15:47:10 1998 Received: from helix.nih.gov (helix.nih.gov [128.231.2.3]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id PAA19217 Wed, 2 Sep 1998 15:47:10 -0400 (EDT) Received: (from mn1@localhost) by helix.nih.gov (8.8.5/8.8.5) id PAA19102; Wed, 2 Sep 1998 15:47:04 -0400 (EDT) Date: Wed, 2 Sep 1998 15:47:04 -0400 (EDT) From: "Marc N." To: chemistry@www.ccl.net cc: "M. Nicklaus" , viki@poodle.fh.huji.ac.il, pis_diez@nahuel.biol.unlp.edu.ar, jochen@uni-duesseldorf.de, kedziora@chem.nwu.edu Subject: Re: CCL:Linux on Alpha, math library Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Several people asked me about the "optimized libraries" from my previous posting - > However, with the right, i.e., optimized libraries, we've found, e.g., > Gaussian 94 on a 500MHz Alpha/Linux box to be 2.5 times as fast as on a > 400MHz Pentium II Linux system. Many of the matrix operations of G94, which consume a large part of the CPU cycles for many (most?) G94 jobs, are handled by library functions of the BLAS3 type (Basic Linear Algebra Subprograms, level 3). In fact, it is one single BLAS3 routine that is centrally used by G94, DGEMM (Double-precision GEneral Matrix-Matrix). On Digital Unix (DU), this routine is part of DEC's proprietary DXML (Digital Extended Math Library). Kazushige Goto has hand-coded a DGEMM routine for 21164 CPUs in assembler, and placed it under GNU Library Public License. It is available at ftp://ftp.eni.co.jp/.2/Linux-Alpha-JP/ftp.statabo.rim.or.jp/BLAS/ It has been clocked at 780 MFlops on a 600 MHz 21164 Alpha machine. This version of DGEMM can be used to replace the one in DXML. On Alpha/Linux, DXML doesn't run, so DXML has to be replaced there anyway. A ready-made library, which can be used as a direct replacement for DXML in G94 (edit alpha-osf1.make and recompile), has been placed by Bob Williams in ftp://rw.usuf2.usuhs.mil/pub/libdgemm/ The fastest version there is libdgemm-980415-2-coff-gnu.a (37 Kb). However, please note that in order to make a Alpha/Linux version of G94, you still need a DU system for compilation, and quite a few other requirements have to be fulfilled. More on this can be found in "Computational Chemistry on Commodity-Type Computers", Marc C. Nicklaus, Robert W. Williams, Bruno Bienfait, Eric S. Billings, and Milan Hodoscek, JCICS (in press), which also just came on-line on ACS's Web site at http://pubs.acs.org/subscribe/journals/jcisd8/browse_asap.html. Hope this helps, Marc ------------------------------------------------------------------------ Marc C. Nicklaus National Institutes of Health E-mail: mn1@helix.nih.gov Bldg 37, Rm 5B29 Phone: (301) 402-3111 37 Convent Dr, MSC 4255 Fax: (301) 496-5839 BETHESDA, MD 20892-4255 USA http://rex.nci.nih.gov/RESEARCH/basic/medchem/mcnbio.htm Laboratory of Medicinal Chemistry, National Cancer Institute ------------------------------------------------------------------------ From chemistry-request@www.ccl.net Wed Sep 2 22:07:11 1998 Received: from ns.DKFZ-Heidelberg.DE (ns.dkfz-heidelberg.de [192.55.188.199]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id WAA26655 Wed, 2 Sep 1998 22:07:10 -0400 (EDT) Received: from cvx12.inet.dkfz-heidelberg.de (cvx12.inet.dkfz-heidelberg.de [193.174.51.101]) by ns.DKFZ-Heidelberg.DE (8.8.8/8.8.8/DKFZ-8.8.8) with ESMTP id EAA23820 for ; Thu, 3 Sep 1998 04:06:40 +0200 (MET DST) Received: from localhost (localhost [[UNIX: localhost]]) by cvx12.inet.dkfz-heidelberg.de (8.8.8/8.8.8/DKFZ-8.8.8) with SMTP id EAA11438 for ; Thu, 3 Sep 1998 04:06:39 +0200 (METDST) Date: Thu, 3 Sep 1998 04:06:38 +0200 (METDST) From: Emadeddin Tajkhorshid To: chemistry@www.ccl.net Subject: OOP calculation Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL I have a question about calculating out of plane force constants. Is there any experimental which can be used to derive these forces? or can we calculate them? If yes how? Thanx for your help Emad Tajkhorshid Dept. Mol. Biophysics, German Cancer Research center, Heidelberg, Germany Tel: +49 6221 422340, Fax: +40 6221 422333, Email: E.Tajkhorshid@DKFZ-Heidelberg.de From chemistry-request@www.ccl.net Wed Sep 2 22:17:37 1998 Received: from mail1.javanet.com (mail1.javanet.com [205.219.162.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id WAA26703 Wed, 2 Sep 1998 22:17:36 -0400 (EDT) Received: from monaco (ct-hartford-us1242.javanet.com [209.150.34.105]) by mail1.javanet.com (8.8.8/8.7) with SMTP id WAA05623 for ; Wed, 2 Sep 1998 22:17:36 -0400 (EDT) Message-Id: <3.0.6.32.19980902221548.0090d520@mail.javanet.com> X-Sender: gusev@mail.javanet.com X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Wed, 02 Sep 1998 22:15:48 -0400 To: chemistry@www.ccl.net From: Vladimir Gusev Subject: Carbon nano-tube coordinates algorithm Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear CCL, Does anybody have a freely available source code/algorithm for generating carbon nano-tubes? The language is not important. I would appreciate any pointers. Vladimir Gusev