From chemistry-request@www.ccl.net Fri Feb 26 19:24:25 1999 Received: from alchemy.chem.utoronto.ca (alchemy.chem.utoronto.ca [142.150.224.224]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id TAA24552 Fri, 26 Feb 1999 19:24:25 -0500 (EST) Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.8.7/8.7.3) id TAA16975 for chemistry@www.ccl.net; Fri, 26 Feb 1999 19:24:25 -0500 (EST) Date: Fri, 26 Feb 1999 19:24:25 -0500 (EST) From: "E. Lewars" Message-Id: <199902270024.TAA16975@alchemy.chem.utoronto.ca> To: chemistry@www.ccl.net Subject: MOLWIN PROBLEMS--THANKS; HOW TO GET MOLWIN 1999 Feb 26 Thanks to *everyone* who responded to my question (below) about problems applying Molwin to Gaussian 98W output. I apologize to people whose replies I may have omitted here (an oversight on my part). I am still looking at the problem, which seems a bit odd. In response to a question about where to get Molwin, I have put that info' after the responses, below. Thanks again. E. Lewars ================= Question: 1999 Feb 20 Hello, Some readers may be familiar with the Windows program Molwin which visualizes Gaussian output (regardless of the platform on which the Gaussian calc was done) for publishable illustrations and allows you to animate the frequencies. For G94 freqs in contrast to G92, the keyword freq(HPMode) is needed [high-precision mode, the long form of freq output]. I now find that with G98W Molwin not only won't visualize the molecule or animate the freqs; it can't even recognize there is a Gaussian output job in its directory. I've tried to see what format change from G94W to G98W is causing the problem; no luck. Any suggestions? Thanks E. Lewars ==================================================== RESPONSES: #1 Hi, I'm using g98 in an sgi box and animate some of the jobs with XMOL. I had the same problem, and see that in the output after the input orientation label, the xyz coordinates include now an atom type field, and shifts the coordinates to the right. If you have the source code of molwin, you could change the routine that reads the gaussian output files. Hope this helps a bit, Edgar Arcia Edgar Arcia edgar.arcia@pnl.gov =========== #2 Feb 22 (46) Re: CCL:G:G98W and MOLWINCommand: Read MessageMessage 2/12 from Nathaniel Feb 22 '99 at 9:33 am Date: Mon, 22 Feb 1999 09:33:31 GMT To: elewars@alchemy.chem.utoronto.ca Subject: Re: CCL:G:G98W and MOLWIN Reply-To: Noj.Malcolm@man.ac.uk I'm not sure if this is your problem, but this may be due the the new 'atom type ' field in the cartesian coords spec. (used for the oniom stuff i guess). If you are hacking in the molwin source then you may just require an extra field after the atomic number. noj -- Dr. Noj Malcolm Theory Group, Dept. of Chemistry, University of Manchester, Oxford Road, line 1 [h for help]Manchester. M13 9PL e-mail noj.malcolm@man.ac.uk ========== #3 Feb 22 Konstantin N. Kudi (49) Re: G98W and MOLWINCommand: Read MessageMessage 3/12 from Konstantin N. Kudin Feb 22 '99 at 1:51 pm X-Authentication-Warning: spca.ruf.rice.edu: kostya owned process doing -bs Date: Mon, 22 Feb 1999 13:51:06 -0600 (CST) The most probable cause of the failure is the change of the geometry output. Compare: (g94) Input orientation: ---------------------------------------------------------- Center Atomic Coordinates (Angstroms) Number Number X Y Z ---------------------------------------------------------- 1 14 -.104121 .000000 -.753677 g98: Input orientation: --------------------------------------------------------------------- Center Atomic Atomic Coordinates (Angstroms) Number Number Type X Y Z --------------------------------------------------------------------- 1 14 0 .544305 .000000 .000000 There is an extra column for Atomic Type. Sincerely, Konstantin Kudin. =============== Getting Molwin: The Windows program MolWin will accept Cartesians, Gaussian opt or freq jobs or PDB and give attractive ball-and-stick pictures. The molecule can be rotated with a mouse and the atom and bond sizes can be adjusted. The pictures can be sent to WordPerfect (and other programs, I suppose) and edited with bond lengths, angles, etc., then printed for publication-quality illustrations. Unfortunately you can't _query_ Molwin for geometry. The info' below applies to G92 and G94. FREQS: MolWin will also accept Gaussian 92 freq output, show the molecule, and let you animate the vibrational frequencies. For G94, use the keyword requesting the long form of freq output: freq(HPMode) MolWin was written by Dr Pavel Ganelin of the Catholic University of America, 48ganelin@cua.edu It should be obtainable from oak.oakland.edu/simtel/win3/chem/molwin23.zip If it isn't there, look in the CCL archives or post a query to CCL. ==== NOTE: the inconveniently big Gaussian output can be made much smaller with an editor and still be read by MolWin; the essential parts are the Cartesian coordinates and the "long form" of the freqs, as shown in the example below. (G94 requires freq(HPMode) to print the long form.) This speeds up MolWin's reading of the file (which also takes up maybe 20 times less space on your hard drive). E. Lewars ----- O=C=N-C=O radical, freqs, MP2/6-31G* G92 1997 Oct 29 Copyright (c) 1992, Gaussian, Inc. All Rights Reserved. ---------------------------------------------- # freq MP2/6-31G* scf=direct maxdisk=100000000 ---------------------------------------------- ------------------------------------------------- Radical (mult = 2) O=C-N-C=O; input: MP2 geom, Cs ------------------------------------------------- STOICHIOMETRY C2NO2(2) FRAMEWORK GROUP C1[X(C2NO2)] DEG. OF FREEDOM 9 FULL POINT GROUP C1 NOP 1 LARGEST ABELIAN SUBGROUP C1 NOP 1 LARGEST CONCISE ABELIAN SUBGROUP C1 NOP 1 Standard orientation: ---------------------------------------------------------- Center Atomic Coordinates (Angstroms) Number Number X Y Z ---------------------------------------------------------- 1 6 -1.174440 -.367072 .000001 2 7 -.015605 .421966 .000000 3 6 1.164572 .050862 .000002 4 8 -2.304558 .011849 -.000001 5 8 2.325613 -.143912 -.000002 ---------------------------------------------------------- Rotational constants (GHZ): 112.9395192 2.4738711 2.4208440 Full mass-weighted force constant matrix: Low frequencies --- -13.6556 -.1619 -.0003 .0015 .0029 4.7354 Low frequencies --- 120.4172 170.4701 535.5204 0Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering activities (A**4/AMU), Raman depolarization ratios, reduced masses (AMU), force constants (mDyne/A) and normal coordinates: 1 2 3 4 5 ?A ?A ?A ?A ?A Frequencies --- 120.4057 170.4700 535.5204 591.8592 620.1372 Reduced masses --- 13.9540 14.5297 14.3216 12.6558 12.5723 Force constants --- .1192 .2488 2.4199 2.6120 2.8487 IR Intensities --- 2.3268 2.9694 5.9691 20.2035 14.1247 Raman Activities --- .0000 .0000 .0000 .0000 .0000 Depolarizations --- .0000 .0000 .0000 .0000 .0000 Coord Atom Element: 1 1 6 .00000 -.26971 -.30050 .00000 -.13003 2 1 6 .00000 -.14004 .44819 .00000 -.26110 3 1 6 .65818 .00000 .00000 .11988 .00000 1 2 7 .00000 .00026 .23642 .00000 -.07108 2 2 7 .00000 -.65058 .00889 .00000 -.28206 3 2 7 .36625 .00000 .00000 .31270 .00000 1 3 6 .00000 .09881 .31110 .00000 .18291 2 3 6 .00000 -.23159 .05483 .00000 .83428 3 3 6 .10397 .00000 .00000 -.87904 .00000 1 4 8 .00000 -.09710 -.57371 .00000 .00325 2 4 8 .00000 .40135 -.29511 .00000 .11300 3 4 8 -.55495 .00000 .00000 -.04104 .00000 1 5 8 .00000 .22509 .35877 .00000 .01930 2 5 8 .00000 .44702 -.09006 .00000 -.29610 3 5 8 -.33747 .00000 .00000 .33683 .00000 6 7 8 9 ?A ?A ?A ?A Frequencies --- 928.4373 1431.1212 1926.1061 2367.9502 Reduced masses --- 13.0098 14.4817 13.3669 12.7576 Force constants --- 6.6073 17.4752 29.2174 42.1469 IR Intensities --- 86.7287 88.0603 833.9814 744.9082 Raman Activities --- .0000 .0000 .0000 .0000 Depolarizations --- .0000 .0000 .0000 .0000 Coord Atom Element: 1 1 6 -.35954 .14062 -.76457 -.09516 2 1 6 -.66815 .19793 .24065 .06066 3 1 6 .00000 .00000 .00000 .00000 1 2 7 .00216 -.79373 .06901 -.32161 2 2 7 .52839 .01082 -.00153 .04951 3 2 7 .00000 .00000 .00000 .00000 1 3 6 .12483 -.06339 -.11284 .84912 2 3 6 -.12940 -.04048 .01577 -.15434 3 3 6 .00000 .00000 .00000 .00000 1 4 8 -.10391 .10564 .54936 .07336 2 4 8 .15569 -.02097 -.18872 -.02558 3 4 8 .00000 .00000 .00000 .00000 1 5 8 .27811 .53131 .04850 -.35744 2 5 8 -.01992 -.10663 -.00232 .05252 3 5 8 .00000 .00000 .00000 .00000 0Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering activities (A**4/AMU), Raman depolarization ratios, reduced masses (AMU), force constants (mDyne/A) and normal coordinates: 1 2 3 ?A ?A ?A Frequencies -- 120.4057 170.4700 535.5204 THIS MOLECULE IS AN ASYMMETRIC TOP. ROTATIONAL SYMMETRY NUMBER 1. ROTATIONAL TEMPERATURES (KELVIN) 5.42021 .11873 .11618 ROTATIONAL CONSTANTS (GHZ) 112.93952 2.47387 2.42084 ZERO-POINT VIBRATIONAL ENERGY 51989.8 (JOULES/MOL) 12.42585 (KCAL/MOL) .0198018 (HARTREE/PARTICLE) 0Berny optimization. 0No z-matrix variables hence no action by Optmz. GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad 1\1\UNIVERSITY OF TORONTO CHEMISTRY DEPARTMENT-ALCHEMY\FREQ\UMP2-FC\6-31G(D)\C2N 1O2(2)\ELEWARS\29-Oct-1997\0\\# FREQ MP2/6-31G* SCF=DIRECT MAXDISK=100000000\\Ra dical (mult = 2) O=C-N-C=O; input: MP2 geom, Cs\\0,2\C,0,-0.01192,-1.17592,-0.36 21\N,0,0.01389,-0.01389,0.4218\C,0,0.00152,1.16477,0.04611\O,0,0.0007,-2.30449,0 .0212\O,0,-0.00505,2.32501,-0.15327\\Version=HP-PARisc-HPUX-G92RevC.3\HF=-279.85 86329\MP2=-280.6037662\PUHF=-279.862544\PMP2-0=-280.6066228\S2=0.772\S2-1=0.76\S 2A=0.75\RMSD=5.145e-09\RMSF=1.253e-04\Dipole=-0.0045844,0.4907865,-0.1392956\Dip WHEN HAVING A MEETING OF THE MINDS, MAKE SURE YOU HAVE THE EQUIPMENT FOR IT. Job cpu time: 0 days 3 hours 56 minutes 41.5 seconds. File lengths (MBytes): RWF= 647 Int= 0 D2E= 0 Chk= 1 Scr= 0 0Normal termination of Gaussian 92.