From chemistry-request@server.ccl.net Sat Jul 31 01:55:37 1999 Received: from matrix.chem.jyu.fi (matrix.chem.jyu.fi [130.234.8.17]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA26156 for ; Sat, 31 Jul 1999 01:55:36 -0400 Received: (from eloranta@localhost) by matrix.chem.jyu.fi (8.9.3/8.9.3) id IAA20508; Sat, 31 Jul 1999 08:49:31 +0300 From: Jussi Eloranta Message-Id: <199907310549.IAA20508@matrix.chem.jyu.fi> Subject: Re: CCL:Large matrix diagonalization. To: jochen@uni-duesseldorf.de (Jochen Kuepper) Date: Sat, 31 Jul 1999 08:49:31 +0300 (EEST) Cc: daizadeh@nucleus.harvard.edu (Iraj Daizadeh), chemistry@ccl.net In-Reply-To: <99073009311801.12040@bacchus.pc1.uni-duesseldorf.de> from "Jochen Kuepper" at Jul 30, 1999 09:29:56 AM X-Mailer: ELM [version 2.5 PL0pre8] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit > >On Don, 29 Jul 1999 Iraj Daizadeh wrote: > >>For my phd dissertation, we spent quite some time diagonalizing SPARSE >>matrices of the order of 1000x1000 or so...The diagonalization process was >>performed by a routine called cboris (fortran code): > >>It is included in the QCPE > >>This routine is not faster than the diagonalization packages that come >>with blas or something or that sort... > >So why have you used it ? What's it advantage to LAPACK algorithms ? > LAPACK can not deal with sparse matrices for the general case. A good pick would be ARPACK which works on top of LAPACK and BLAS. It supports parallelism too. Note that ARPACK routines are iterative in nature and therefore allows to find some specified eigen states. Regards, Jussi Eloranta Dept. of Chemistry Univeristy of Jyvaskyla Finland ps. http://www.caam.rice.edu/~kristyn/parpack_home.html From chemistry-request@server.ccl.net Fri Jul 30 14:48:45 1999 Received: from alchemy.chem.utoronto.ca (alchemy.chem.utoronto.ca [142.150.224.224]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA21788 for ; Fri, 30 Jul 1999 14:48:45 -0400 Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.9.3/8.9.3) id OAA27833 for chemistry@ccl.net; Fri, 30 Jul 1999 14:43:27 -0400 (EDT) Date: Fri, 30 Jul 1999 14:43:27 -0400 (EDT) From: "E. Lewars" Message-Id: <199907301843.OAA27833@alchemy.chem.utoronto.ca> To: chemistry@ccl.net Subject: NMR CHEMICAL SHIFTS--SUMMARY(2) 1999 July 30 Hello, I can't remember if I sent this summary to the comp chem nerwork already; anyway, there is a new reply that just came (#6). Thanks E. Lewars ======================= 1999 July 26 REPLIES TO QUESTION ABOUT MP2- cf. HF-LEVEL NMR CHEMICAL SHIFTS THE QUESTION: > Hello, I read somewhere that NMR chemical shifts calc at the MP2 level are > somewhat better than at the HF level. Has anyone a reference to this? > Thanks. Thanks very much to all who responded. As you see, I got a lot of information. For people who wish to look at just a few of the refs, I might suggest: J. Gauss. JCP 99 3629 (1993) Cheesman et al JCP 104 5497 (1996) (I haven't yet got hold of the J. Gauss paper in Ber. Bunsenges. Phys. Chem.) The Chem Rev 1999 review is physical-theoretical rather than a presentation and analysis of calculated chemical shifts. I did a few calcs on B3LYP/6-31G* geometries, using the G94 default algorithm and the HF/6-31G* and HF/6-311+G(2d,p) wavefunctions. There was not that much difference between the two basis sets, although the latter took a lot longer. I was astonished at how accurate the chemical shifts were. ------------- THE ANSWERS (#1--#6): 1999 July MP2 cf. HF NMR SHIFTS #1 Matthias Hofmann > Hello, I read somewhere that NMR chemical shifts calc at the MP2 level are > somewhat better than at the HF level. Has anyone a reference to this? > Thanks. One early example is: Decisive Electron Correlation Effects on Computed 11B und 13C NMR Chemical Shifts. Application of the GIAO-MP2 Method to Boranes and Carbaboranes. M. Bue\237hl, J. Gauss, M. Hofmann, P. v. R. Schleyer, J. Am. Chem. Soc., 1993, 115, 12385-12390. For other nuclei you might search for early papers by J. Gauss, who first implemented the GIAO-MP2 methods (and higher correlated methods) in ACES2. Regards, Matthias -------------------------------------------------------------------- Dr. Matthias Hofmann | phone: 706 542-7748 Ctr. for Comp. Quantum Chem. | fax: 706 542-0406 University of Georgia | e-mail: hofmann2@zopyros.ccqc.uga.edu Athens, GA 30602-2525 | http://zopyros.ccqc.uga.edu ============----------------------------------------------------------- #2 Michael D. Bartberger Jul 21 '99 at 10:42 pm Hello: You might check the references of J. Gauss; he, along with John Stanton have published a number of papers (I include references below) on the computation of checmical shifts with MBPT. Also R.J. Bartlett and coworkers have investigated shifts and coupling constants at the CC level. A lot of this is nicely summarized in a recent Chem. Rev. article by Helgaker et al., 1999, v. 99, 293-352. Other possibly useful references follow. Best regards, -Mike Bartberger UCLA +-----------------------------------------------------------------+ | Michael D. Bartberger, Ph.D. | | NIH Postdoctoral Fellow TEL: 310.206.0553 | | Department of Chemistry and Biochemistry FAX: 310.206.1843 | | University of California, Los Angeles | | Los Angeles, California 90095-1569 mdb@chem.ucla.edu | +-----------------------------------------------------------------+ Kollwitz, M; Haser, M; Gauss, J. Non-Abelian point group symmetry in direct second-order many-body perturbation theory calculations of NMR chemical shifts. JOURNAL OF CHEMICAL PHYSICS, 1998 MAY 22, V108 N20:8295-8301. Gauss, J; Stanton, JF. Electron correlation effects on the calculated C-13 NMR spectra of vinyl cations. THEOCHEM-JOURNAL OF MOLECULAR STRUCTURE, 1997 JUN 30, V398:73-80. STANTON JF; GAUSS J; SIEHL HU. CCSD(T) CALCULATION OF NMR CHEMICAL SHIFTS - CONSISTENCY OF CALCULATED AND MEASURED C-13 CHEMICAL SHIFTS IN THE 1-CYCLOPROPYLCYCLOPROPYLIDENEMETHYL CATION. CHEMICAL PHYSICS LETTERS, 1996 NOV 15, V262 N3-4:183-186. KOLLWITZ M; GAUSS J. A DIRECT IMPLEMENTATION OF THE GIAO-MBPT(2) METHOD FOR CALCULATING NMR CHEMICAL SHIFTS - APPLICATION TO THE NAPHTHALENIUM AND ANTHRACENIUM IONS. CHEMICAL PHYSICS LETTERS, 1996 OCT 4, V260 N5-6:639-646. GAUSS J. ACCURATE CALCULATION OF NMR CHEMICAL SHIFTS. BERICHTE DER BUNSEN-GESELLSCHAFT-PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 1995 AUG, V99 N8:1001-1008. BUHL M; GAUSS J; STANTON JF. ACCURATE COMPUTATIONS OF SE-77 NMR CHEMICAL SHIFTS WITH THE GIAO-CCSD METHOD. CHEMICAL PHYSICS LETTERS, 1995 JUL 21, V241 N3:248-252. SIEHL HU; MULLER T; GAUSS J; BUZEK P; and others. CYCLOPROPYLCYCLOPROPYLIDENEMETHYL CATION - A UNIQUE STABILIZED VINYL CATION CHARACTERIZED BY NMR SPECTROSCOPY AND QUANTUM CHEMICAL AB INITIO CALCULATIONS. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1994 JUL 13, V116 N14:6384-6387. BUHL M; GAUSS J; HOFMANN M; SCHLEYER PV. DECISIVE ELECTRON CORRELATION EFFECTS ON COMPUTED B-11 AND C-13 NMR CHEMICAL SHIFTS - APPLICATION OF THE GIAO-MP2 METHOD TO BORANES AND CARBABORANES. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1993 DEC 29, V115 N26:12385-12390. SCHLEYER PV; GAUSS J; BUHL M; GREATREX R; and others. EVEN MORE RELIABLE NMR CHEMICAL SHIFT COMPUTATIONS BY THE GIAO-MP2 METHOD. JOURNAL OF THE CHEMICAL SOCIETY-CHEMICAL COMMUNICATIONS, 1993 DEC 7, N23:1766-1768. SIEBER S; SCHLEYER PV; GAUSS J. THE ACCURATE C(2V) PHENONIUM AND BENZENONIUM ION STRUCTURES CONFIRMED BY CORRELATED GIAO-MP2 NMR CHEMICAL SHIFT CALCULATIONS. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1993 JUL 28, V115 N15:6987-6988. Pub type: Note. GAUSS J; SCHNEIDER U; AHLRICHS R; DOHMEIER C; and others. AL-27 NMR SPECTROSCOPIC INVESTIGATION OF ALUMINUM(I) COMPOUNDS - ABINITIO CALCULATIONS AND EXPERIMENT. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1993 MAR 24, V115 N6:2402-2408. GAUSS J. CALCULATION OF NMR CHEMICAL SHIFTS AT 2ND-ORDER MANY-BODY PERTURBATION THEORY USING GAUGE-INCLUDING ATOMIC ORBITALS. CHEMICAL PHYSICS LETTERS, 1992 APR 17, V191 N6:614-620. PERERA SA; BARTLETT RJ. STRUCTURE AND NMR SPECTRA OF THE 2-NORBORNYL CARBOCATION - PREDICTION OF (1)J((CC)-C-13-C-13) FOR THE BRIDGED, PENTACOORDINATE CARBON ATOM. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1996 AUG 21, V118 N33:7849-7850. PERERA SA; BARTLETT RJ; SCHLEYER PV. PREDICTED NMR COUPLING CONSTANTS AND SPECTRA FOR ETHYL CARBOCATION - A FINGERPRINT FOR NONCLASSICAL HYDROGEN-BRIDGED STRUCTURES. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1995 AUG 16, V117 N32:8476-8477. Pub type: Note. =============== #3 MP2 NMR chemical shifts MONACO@CHEMNA.DICHI.UNINA.IT Jul 22 '99 at 9:32 am Hi although they were more concerned with MCSCF, the group of Kutzelnigg has investigated the effect of correlation on the chemical shifts. So you can look at its bibliography. As far as I remember, the effects were not amazing. Of course when the ground state and the first excited ones are very near in energy, correlation may play a role and paramagnetic contributions become more difficult to compute. Good luck Guglielmo Monaco Dip. di Chimica Universit\340 di Napoli ITALY ============= #4 schrecke@t12mail.lanl.gov Hi, while I can't find the original references in the moment, I would suggest to start with some reviews on ab initio NMR calculations: J. Gauss, Ber. Bunsenges. Phys. Chem. 1995, 99, 1001 T. Helgaker et al., Chem.Rev.1999, 99, 293 Both should have something on your question or, at least, give you further references. Besides, some limited SCF-MP2 comparison is also in B=FChl et al= . J. Phys. Chem. 1995, 99, 4000. Best regards, Georg P.S. Please summarize to the CCL. -------------------- Dr. Georg Schreckenbach Tel: (USA)-505-667 7605 Theoretical Chemistry T-12 FAX: (USA)-505-665 3909 M.S. B268, Los Alamos National E-mail: schrecke@t12.lanl.gov Laboratory, Los Alamos, New Mexico, 87545, USA Internet: http://www.t12.lanl.gov/home/schrecke/ ***new location!*** =================== #5 Doug Fox Jul 22 '99 at 12:47 (noon) Errol, Check J. Gauss, JCP vol 99 3629 (1993). We draw from this and compare it with DFT methods in Cheesman et.al. JCP vol 104, 5497 (1996). Schleyer has also made comparisons in some of his Boron work but I don't have a good reference. Douglas J. Fox Director of Technical Support help@gaussian.com ========================== #6 Date: Thu, 29 Jul 1999 17:02:04 +0100 (CET) Subject: Re: CCL:SUMMARY OF NMR SHIFTS, MP2 cf. HF To: elewars@alchemy.chem.utoronto.ca Dear friend, I would like to call your attention on a recent paper by our group (Chem.Phys.Lett. 298,113-119, 1998) showing that the PBE1PBE functional (an hybrid based on the PBE model of Perdew et al.) provides improved NMR chemical shifts with respect to other functionals. Note th at this is also the case for other propeties (J.Chem.Phys. 110,6158-6170, 1999), polarizabilities (Chem.Phys.Lett.307,265-271,1999) and UV spectra (J.Chem.Phys. number of August 15, 1999 and other papers in press). Best regards Enzo -------------------------------------------------------------------------- Vincenzo Barone full professor of Theoretical Chemistry -------------------------------------------------------------------------- Dipartimento di Chimica | phone: +39-081-5476503 Universita' Federico II | fax: +39-081-5527771 via Mezzocannone 4 | e-mail: enzo@chemna.dichi.unina.it I-80134 Napoli, Italy | enzo@napo.dichi.unina.it -------------------------------------------------------------------------- From chemistry-request@server.ccl.net Fri Jul 30 15:28:35 1999 Received: from bioc1.msi.com (bioc1.msi.com [146.202.0.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA22049 for ; Fri, 30 Jul 1999 15:28:32 -0400 Received: (from daemon@localhost) by bioc1.msi.com (980427.SGI.8.8.8/970903.SGI.AUTOCF) id MAA28234 for ; Fri, 30 Jul 1999 12:23:53 -0700 (PDT) Received: from johnw-pc.msi.com(146.202.12.17) by bioc1.msi.com via smap (V2.0) id xma028231; Fri, 30 Jul 99 12:23:31 -0700 Received: by localhost with Microsoft MAPI; Fri, 30 Jul 1999 12:31:27 -0700 Message-ID: <01BEDA87.71C79D20.johnw@msi.com> From: John Wintersteen Reply-To: "Viewer_Pro (E-mail)" To: "'chemistry@ccl.net'" Subject: CCL: WebLab Viewer 3.5 released by MSI Date: Fri, 30 Jul 1999 12:28:35 -0700 Organization: Molecular Simulations Inc. X-Mailer: Microsoft Internet E-mail/MAPI - 8.0.0.4211 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Molecular Simulations Inc. is pleased to announce the availability of the WebLab ViewerPro 3.5. The WebLab ViewerPro is a PC based 3D molecular visualization and chemical communication application. Features added to this new version include hardware stereo support for enhanced 3D visualization, molecular superimposition, a structure monitor for displaying under/over valanced atoms, a command processor for entering ViewerPro script commands from the interface. Usability enhancements include a measure button for quickly measuring distances, angles, dihedrals. Objects definition have been added to PDB, MSF (Quanta), MSI, and CAR file importers for defining backbone, side chain, Hydrophobic, hydrophilic, acid, and basic groups. Numerous improvements to file importers and usability features have also been added. For more information about WebLab Viewer products and download options please visit the WebLab Viewer web site. A free, 30 day trial version of the WebLab ViewerPro is also available from MSI's web site at: http://www.msi.com/viewer Sincerely, WebLab Viewer Product Team Molecular Simulations Inc. 800-461-4525 From chemistry-request@server.ccl.net Fri Jul 30 15:30:48 1999 Received: from postoffice.npac.syr.edu (postoffice.npac.syr.edu [128.230.7.230]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA22071 for ; Fri, 30 Jul 1999 15:30:48 -0400 Received: from snake.npac.syr.edu (snake.npac.syr.edu [128.230.162.60]) by postoffice.npac.syr.edu (8.9.3/8.9.3) with ESMTP id PAA20701; Fri, 30 Jul 1999 15:21:13 -0400 (EDT) Received: from localhost (bernhold@localhost) by snake.npac.syr.edu (8.9.3/8.9.3) with SMTP id PAA05169; Fri, 30 Jul 1999 15:21:13 -0400 (EDT) Message-Id: <199907301921.PAA05169@snake.npac.syr.edu> X-Authentication-Warning: snake.npac.syr.edu: bernhold@localhost didn't use HELO protocol Reply-to: bernhold@npac.syr.edu To: MChalla@t12.lanl.gov cc: chemistry@ccl.net, jochen@uni-duesseldorf.de, daizadeh@nucleus.harvard.edu cc: bernhold@npac.syr.edu Subject: Re: roll your own rant (was Large matrix diagonalization). In-reply-to: <9907301248420C.09427@ice.lanl.gov> MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-ID: <5164.933362472.1@snake.npac.syr.edu> Date: Fri, 30 Jul 1999 15:21:12 -0400 From: "David E. Bernholdt" Hi Matt, Actually, as much as it may surprise people, I agree with virtually everything you said. If someone takes a careful and thorough look at what's already out there, and determines that nothing meets their needs, then they must certainly roll their own in some fashion. It is those who don't look and instead reinvent the wheel (or borrow an old squared-off wheel >from some old comp. chem. code) that I have a quarrel with. Likewise I think those who treat linear algebra routines as a black box are asking for trouble, but that's quite different from having to write it yourself. Once you have determined that something new must be done, I still think its worth trying to interest an NA person in the problem, but it sounds like I've had better luck than you :-) I suppose it also depends on how central the problem you've encountered is to what you want to do. Indeed, sometimes you can't afford to wait. But I think a key point to observe is that historically, NA folks have invested a lot of effort on problems relevant to say fluid dynamics or finite element methods and less to those relevant to chemistry. And I believe one of the primary reasons for this is that we chemists have not made a sufficient effort to bring our problems to the attention of the NA community. The more we do this, the more chemistry-related problems will be treated as a matter of course ny the NA folks, and then the next time we've got a problem, maybe we _will_ find a ready-made solution in the NA community. David -- David E. Bernholdt | Email: bernhold@npac.syr.edu Northeast Parallel Architectures Center | Phone: +1 315 443 3857 111 College Place, Syracuse University | Fax: +1 315 443 1973 Syracuse, NY 13244-4100 | URL: http://www.npac.syr.edu From chemistry-request@server.ccl.net Sat Jul 31 12:56:13 1999 Received: from cerberus.ulaval.ca (cerberus.ulaval.ca [132.203.250.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA30953 for ; Sat, 31 Jul 1999 12:56:12 -0400 Received: from fluor.chm.ulaval.ca (fluor.chm.ulaval.ca [132.203.70.9]) by cerberus.ulaval.ca (8.8.7/8.7.3) with ESMTP id NAA15013 for ; Sat, 31 Jul 1999 13:00:50 -0400 (EDT) Received: (from anh@localhost) by fluor.chm.ulaval.ca (8.6.12/8.6.12) id MAA29842 for chemistry@ccl.net; Sat, 31 Jul 1999 12:28:05 -0400 From: "Nguyen N. Anh" Message-Id: <9907311228.ZM29840@fluor.chm.ulaval.ca> Date: Sat, 31 Jul 1999 12:28:01 -0400 X-Mailer: Z-Mail (3.2.1 6apr95 MediaMail) To: chemistry@ccl.net Subject: CASSCF-right energy Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear cclers, I'm doing CASSCF calculations with G94 and getting the following lines: ------------- 2ND ORD PT ENERGY CV 0.000000 CU 0.000000 UV -0.000186 TOTAL 0.499662 ITN= 1 MaxIt=999 E= 0.4998474810 DE= 5.00D-01 Acc= 1.00D-05 ITN= 2 MaxIt=999 E= 0.4660556090 DE=-3.38D-02 Acc= 1.00D-05 ITN= 3 MaxIt=999 E= 0.4999700399 DE= 3.39D-02 Acc= 1.00D-05 ITN= 4 MaxIt=999 E= 0.4996883687 DE=-2.82D-04 Acc= 1.00D-05 ITN= 5 MaxIt=999 E= 0.4996964720 DE= 8.10D-06 Acc= 1.00D-05 ... DO AN EXTRA-ITERATION FOR FINAL PRINTING FINAL EIGENVALUES AND EIGENVECTORS VECTOR EIGENVALUES CORRESPONDING EIGENVECTOR 1 -1.3618045 -0.43997634E-02 0.99633020 -0.85479675E-01 MCSCF converged. ----------------------- G94 returns 2 energies: one after each iteration (0.4996964720 in this case), and the other is written with CI coefficients (-1.3618045 in this case). Normally these 2 energies must be the same, but it is not the case in this job. I want to know which one is the right energy. Why is a such discrepancy? Thank you very much -- Nguyen Nam Anh Quebec, Canada E-mail: anh@chm.ulaval.ca WWW: http://promethium.chm.ulaval.ca/~anh/ From chemistry-request@server.ccl.net Sat Jul 31 12:58:12 1999 Received: from theo1.theochem.tu-muenchen.de (theo2.theochem.tu-muenchen.de [129.187.191.1]) by server.ccl.net (8.8.7/8.8.7) with SMTP id MAA31009 for ; Sat, 31 Jul 1999 12:58:10 -0400 From: kcharoen@theochem.tu-muenchen.de Received: from theo3.theochem.tu-muenchen.de (theo3.theochem.tu-muenchen.de [129.187.157.6]) by theo1.theochem.tu-muenchen.de (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id SAA29582 for ; Sat, 31 Jul 1999 18:52:40 +0200 Received: by theo3.theochem.tu-muenchen.de (SMI-8.6/SMI-SVR4) id SAA06309; Sat, 31 Jul 1999 18:53:19 +0200 Date: Sat, 31 Jul 1999 18:53:19 +0200 Message-Id: <199907311653.SAA06309@theo3.theochem.tu-muenchen.de> To: chemistry@ccl.net Subject: is TINKER dead ? X-Sun-Charset: US-ASCII Dear CCL members, I do apologize if this question is out of scope but I am in desparate need for the access of TINKER program at the http://dasher.wustl.edu/tinker with no success along the whole week. Is such server out of service now or Prof. Jay Ponder (developer of the program) move out of St. Louis already. Search engine nevertheless point me to other places where TINKER located apart from the mentioned site. Thank you in advance for a kind help. Best wishes, Teerakiat