From Jeffrey.Gosper@brunel.ac.uk Thu Feb 20 05:24:25 1997 Received: from etamin.brunel.ac.uk for Jeffrey.Gosper@brunel.ac.uk by www.ccl.net (8.8.3/950822.1) id FAA11491; Thu, 20 Feb 1997 05:02:51 -0500 (EST) Received: from chem-pc-18 (actually chem-pc-18.brunel.ac.uk) by etamin.brunel.ac.uk with SMTP (PP); Thu, 20 Feb 1997 10:02:24 +0000 Date: Thu, 20 Feb 1997 10:02:18 GMT From: Jeffrey J Gosper Subject: Re: CCL:M:Constraints in MOPAC To: David Bevan cc: chemistry@www.ccl.net Message-ID: Priority: Normal MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII On Wed, 19 Feb 1997 15:52:02 -0500 David Bevan wrote: > From: David Bevan > Date: Wed, 19 Feb 1997 15:52:02 -0500 > Subject: CCL:M:Constraints in MOPAC > To: chemistry@www.ccl.net > > How does one constrain a dihedral angle during geometry optimization in > MOPAC 93? I am aware of PATH calculations in which a dihedral can be > changed and the geometry optimized at intervals of the reaction coordinate. > Is there a way to constrain a dihedral when not doing PATH calculations? If > so, is there a way to change the value of the constraining force? > > David Bevan > An optimization flag of 0 will maintain that particular variable. If all others have 1 flagged then you'll get selctive optimization. see http://www.brunel.ac.uk/depts/chem/ch241s/re_view/irc.htm for further details on MOPAC input files. /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ Dr. Jeff Gosper Dept. of Chemistry BRUNEL University Uxbridge Middx UB8 3PH, UK voice: 01895 274000 x2187 facsim: 01895 256844 internet/email/work: Jeffrey.Gosper@brunel.ac.uk internet/WWW: http://www.brunel.ac.uk/~castjjg Re_View's Home page (A molecular display/animation/analysis program): http://www.brunel.ac.uk/depts/chem/ch241s/re_view/re_view.htm \/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/ From Jeffrey.Gosper@brunel.ac.uk Thu Feb 20 06:24:25 1997 Received: from ceres.brunel.ac.uk for Jeffrey.Gosper@brunel.ac.uk by www.ccl.net (8.8.3/950822.1) id FAA11747; Thu, 20 Feb 1997 05:51:19 -0500 (EST) Received: from chem-pc-18 (actually chem-pc-18.brunel.ac.uk) by ceres.brunel.ac.uk with SMTP (PP); Thu, 20 Feb 1997 10:50:33 +0000 Date: Thu, 20 Feb 1997 10:50:27 GMT From: Jeffrey J Gosper Subject: Visualizing Hybrid orbitals To: CHEMISTRY@www.ccl.net Message-ID: Priority: Normal MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Dear all, I would like to know whether it is possible (and how) to visualize hybrid molecular orbitals rather than the the 'standard set' using MOPAC/PSI88 (or other readily available software). I have tried to include the LOCALIZE keyword along with the GRAPH option in MOPAC. However the orbitals obtain through the GRAPH/PSI88 combination seems to be uneffected by the LOACAIZE keyword. Any suggestions? /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ Dr. Jeff Gosper Dept. of Chemistry BRUNEL University Uxbridge Middx UB8 3PH, UK voice: 01895 274000 x2187 facsim: 01895 256844 internet/email/work: Jeffrey.Gosper@brunel.ac.uk internet/WWW: http://www.brunel.ac.uk/~castjjg Re_View's Home page (A molecular display/animation/analysis program): http://www.brunel.ac.uk/depts/chem/ch241s/re_view/re_view.htm \/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/ From citra@syrres.com Thu Feb 20 09:24:26 1997 Received: from syrres.syrres.com for citra@syrres.com by www.ccl.net (8.8.3/950822.1) id IAA12542; Thu, 20 Feb 1997 08:32:51 -0500 (EST) Date: Thu, 20 Feb 97 08:17 EST Message-ID: <9702200817.AA25563@syrres.syrres.com> Received: from syrres.com by syrres.syrres.com; Thu, 20 Feb 97 08:17 EST X-Sender: citra@srcinet.syrres.com X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: Mario Citra Subject: Transition probabilities using GAMESS gandalf7 wrote: My questions are: > 1. In GAMESS, what does "dipole length" and "dipole velocity", > calculated by "$TRANST", actually mean? Are either one of these the > transition dipole moment used to find the probability? You can apply the dipole moment operator in its position form (most common) or its velocity form to calculate the dipole strength of a transition. In the velocity form the integrals are solved by numerical methods and therefore the position form of the operator is employed for most applications. In certain areas such as vibrational circular dichroism theory nucleur velocity is incorperated into the wavefunction and the theory can be developed from the velocity form of the operator. Regards, Mario J. Citra MJC From trevor@euripides.gws.uky.edu Thu Feb 20 10:24:28 1997 Received: from euripides.gws.uky.edu for trevor@euripides.gws.uky.edu by www.ccl.net (8.8.3/950822.1) id JAA13092; Thu, 20 Feb 1997 09:45:29 -0500 (EST) Received: from euripides.gws.uky.edu (localhost [127.0.0.1]) by euripides.gws.uky.edu (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id JAA16212 for ; Thu, 20 Feb 1997 09:48:38 -0500 Sender: trevor@euripides.gws.uky.edu Message-ID: <330C6446.2781@euripides.gws.uky.edu> Date: Thu, 20 Feb 1997 09:48:38 -0500 From: Trevor Creamer Organization: Dept. of Biochemistry, University of Kentucky X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX 6.3 IP32) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: F77 on an R10000 O2 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit My apologies in advance if this is an inappropriate post... I have just migrated from a R4400 SGI platform running IRIX 5.3 to a new R10000 O2 running IRIX 6.3 and I'm having problems getting my (very standard) Fortran programs to compile in 64-bit mode. If I compile using: f77 -O3 -mips4 myprog.f (or f77 -O3 -64 myprog.f) I get the following error from the linker: ld64: FATAL 9: I/O error (/usr/lib64/crt1.o): No such file or directory f77 INTERNAL ERROR: /usr/lib32/cmplrs/ld64 returned non-zero status 32 Sure enough, crt1.o does not exist in /usr/lib64. I can compile with no problems using: f77 -O3 -32 myprog.f - crt1.o does exist in /usr/lib32. I have gone through the Development Option 7.0.1 and Developer Update Package (10/96) cd's throughly and there is nothing that hasn't been installed. Has anyone else run into this ? Any suggestions ? Cheers, Trevor ________________________________________________________________________ Trevor P. Creamer Kentucky Center for Email - trevor@euripides.gws.uky.edu Structural Biology Phone - (606) 323 6037 Dept. of Biochemistry Fax - (606) 323 1037 University of Kentucky Lexington, KY 40536-0084 http://euripides.gws.uky.edu/~trevor U.S.A. ________________________________________________________________________ From parviz@ENH.NIST.GOV Thu Feb 20 11:24:30 1997 Received: from ENH.NIST.GOV for parviz@ENH.NIST.GOV by www.ccl.net (8.8.3/950822.1) id LAA13909; Thu, 20 Feb 1997 11:12:34 -0500 (EST) Received: from h178076 (h178076.nist.gov) by ENH.NIST.GOV (PMDF V5.0-5 #10952) id <01IFMXL43T5S00AW4J@ENH.NIST.GOV> for chemistry@www.ccl.net; Thu, 20 Feb 1997 11:05:25 -0400 (EDT) Date: Thu, 20 Feb 1997 11:00:41 -0500 From: Parviz Subject: spin density X-Sender: parviz@mailserver.nist.gov To: chemistry@www.ccl.net Message-id: <01IFMXL48WEQ00AW4J@ENH.NIST.GOV> MIME-version: 1.0 X-Mailer: Windows Eudora Version 2.1.1 Content-type: text/plain; charset="us-ascii" Content-transfer-encoding: 7BIT spin-orbit coupling is important in "heavy" atoms and depends on the the magnitute of spin on the heavy atom. Some programs calculate the spin per atom; however, it is not clear to me that how these calculations are done. Here are some examples for discussions: 1. What are: (a) Total atomic spin densities and (b) Fermi contact analysis (atomic units) generated by GAUSSIAN-94 program? 2. Is it possible to get (a) from (b)? best wishes, parviz ---------------------------------------------- Parviz Hassanzadeh Physical and Chemical Properties Division National Institute of Standards and Technology Gaithersburg, MD 20899 phone: 301-975-2501 fax: 301-975-3670 e-mail: parviz.hassanzadeh@nist.gov ---------------------------------------------- From Jeffrey.Gosper@brunel.ac.uk Thu Feb 20 11:31:29 1997 Received: from etamin.brunel.ac.uk for Jeffrey.Gosper@brunel.ac.uk by www.ccl.net (8.8.3/950822.1) id KAA13647; Thu, 20 Feb 1997 10:46:50 -0500 (EST) Received: from chem-pc-18 (actually chem-pc-18.brunel.ac.uk) by etamin.brunel.ac.uk with SMTP (PP); Thu, 20 Feb 1997 15:45:38 +0000 Date: Thu, 20 Feb 1997 15:45:33 GMT From: Jeffrey J Gosper Subject: Re: CCL:trajectory calculations (fwd) To: JULANNA V GILBERT cc: CHEMISTRY@www.ccl.net Message-ID: Priority: Normal MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII On Tue, 18 Feb 1997 15:55:26 -0700 (MST) JULANNA V GILBERT wrote: > From: JULANNA V GILBERT > Date: Tue, 18 Feb 1997 15:55:26 -0700 (MST) > Subject: CCL:trajectory calculations (fwd) > To: CHEMISTRY@www.ccl.net > > > We are planning a graduatecourse in molecular dynamics/kinetics and want > to find software (PC) that will allow visualization of trajectories for > simple atom plus diatomic reactions over classical or quantum potential > energy surfaces. A program that demonstrates trajectories for atomic > scattering under various potential fields would also be useful. > > If anyone knows of such software (free or otherwise), please respond. > > Thank you, > > Julanna Gilbert > > The combination of GridView and Re_View (both Windows programs) can be used to display PESs (as contour maps) as well as showing structures and animations across the surface. A paper on this was published in ECCC3 by myself. The bonus is that both these programs are free to individual users (NB: Departmental and single PC licences are also very cheap). For further information on these see: http://www.brunel.ac.uk/depts/chem/ch241s/re_view/re_view.htm and http://www.brunel.ac.uk/depts/chem/ch241s/re_view/tagon.htm#gridview /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ Dr. Jeff Gosper Dept. of Chemistry BRUNEL University Uxbridge Middx UB8 3PH, UK voice: 01895 274000 x2187 facsim: 01895 256844 internet/email/work: Jeffrey.Gosper@brunel.ac.uk internet/WWW: http://www.brunel.ac.uk/~castjjg Re_View's Home page (A molecular display/animation/analysis program): http://www.brunel.ac.uk/depts/chem/ch241s/re_view/re_view.htm \/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/ From dons@hamilton.math.missouri.edu Thu Feb 20 13:24:30 1997 Received: from mail.missouri.edu for dons@hamilton.math.missouri.edu by www.ccl.net (8.8.3/950822.1) id NAA14930; Thu, 20 Feb 1997 13:05:09 -0500 (EST) Received: from hamilton.math.missouri.edu (hamilton.math.missouri.edu [128.206.72.117]) by mail.missouri.edu (8.8.5/8.8.5) with SMTP id MAA259242 for <@smtp.missouri.edu:chemistry@www.ccl.net>; Thu, 20 Feb 1997 12:05:06 -0600 Received: by hamilton.math.missouri.edu (940816.SGI.8.6.9/940406.SGI) for chemistry@www.ccl.net id MAA14942; Thu, 20 Feb 1997 12:03:35 -0600 From: "Don Steiger" Message-Id: <9702201203.ZM14940@hamilton.math.missouri.edu> Date: Thu, 20 Feb 1997 12:03:34 -0600 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net Subject: Gaussian94 and hyperpolarizability. Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Does anybody know how Gaussian94 calculates hyperpolarizabilies? The references given on the Gaussian94 Web page either do not address the issue or have not yet been published. Don Steiger dons@hamilton.math.missouri.edu -- Don Steiger From ren@chvzmw.chem.ncsu.edu Thu Feb 20 14:24:30 1997 Received: from chvzmw for ren@chvzmw.chem.ncsu.edu by www.ccl.net (8.8.3/950822.1) id OAA15582; Thu, 20 Feb 1997 14:01:46 -0500 (EST) From: Date: Thu, 20 Feb 1997 13:59:20 -0500 Message-Id: <97022013592001@chvzmw.chem.ncsu.edu> To: CHEMISTRY@www.ccl.net Subject: Help: QCPE crystal field program X-VMS-To: CHEMISTRY@www.ccl.net Hello: Are there people who have experience using the old QCPE program #216 "Crystal-Field Splitting Calculations for Trivalent Lanthanide Ions"? I have input problems. Thanks for your help. Jingqing Ren From decker@jcvsparc.chem.ualberta.ca Thu Feb 20 14:35:15 1997 Received: from quartz.ucs.ualberta.ca for decker@jcvsparc.chem.ualberta.ca by www.ccl.net (8.8.3/950822.1) id OAA15612; Thu, 20 Feb 1997 14:08:14 -0500 (EST) Received: from jcvsparc.chem.ualberta.ca (jcvsparc.chem.ualberta.ca [129.128.2.23]) by quartz.ucs.ualberta.ca (8.8.5/8.8.5) with ESMTP id MAA23414 for ; Thu, 20 Feb 1997 12:08:08 -0700 Received: (from decker@localhost) by jcvsparc.chem.ualberta.ca (8.6.9/8.6.9) id MAA03488 for chemistry@www.ccl.net; Thu, 20 Feb 1997 12:10:15 -0700 Date: Thu, 20 Feb 1997 12:10:15 -0700 From: Stephen Decker Message-Id: <199702201910.MAA03488@jcvsparc.chem.ualberta.ca> To: chemistry@www.ccl.net Subject: Atoms in Molecules in Gaussian94 Hello all, I was wondering if someone could help with a problem I seem to be having with the Gaussian94 implementation of Atoms in Molecules (AIM). I'm trying to use AIM to investigate the bonding in a transition metal complex containing an acetylene and CO ligands. The problem I'm having occurs after the critical points and interaction lines have been found, section II. BTW, 13 bond points and 1 ring point were found. After printing: 13 attractors - 13 bond point(s) + 1 ring point(s) - 0 cage point(s) = 1 the calculation quits with the following error message: FATAL ERROR: TOO MANY PATCHES The remaining steps in a successful analysis: III Properties of Attractors, and then IV Localized Orbitals and Covalent Bond Orders, aren't started. The system I'm looking at has a total of 13 atoms (and AIM found 13 attractors, so no non-nuclear attractors), 114 electrons and 193 basis functions. Does anybody know what the error means, what it is due to and how I can correct it? Is it due to some internal limitations on the system size or number of basis functions? Any help you can give me would be greatly appreciated. Thanks in advance, Stephen Decker Dept. of Chemistry, Univ. of Alberta, Edmonton, Canada decker@jcvsparc.chem.ualberta.ca From trevor@euripides.gws.uky.edu Thu Feb 20 15:24:30 1997 Received: from euripides.gws.uky.edu for trevor@euripides.gws.uky.edu by www.ccl.net (8.8.3/950822.1) id OAA15870; Thu, 20 Feb 1997 14:41:17 -0500 (EST) Received: from euripides.gws.uky.edu (localhost [127.0.0.1]) by euripides.gws.uky.edu (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id OAA02631 for ; Thu, 20 Feb 1997 14:44:32 -0500 Sender: trevor@euripides.gws.uky.edu Message-ID: <330CA9A0.167E@euripides.gws.uky.edu> Date: Thu, 20 Feb 1997 14:44:32 -0500 From: Trevor Creamer Organization: Dept. of Biochemistry, University of Kentucky X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX 6.3 IP32) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: F77 on an R10000 O2 Summary Content-Type: multipart/mixed; boundary="------------2781446B794B" This is a multi-part message in MIME format. --------------2781446B794B Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit -- ________________________________________________________________________ Trevor P. Creamer Kentucky Center for Email - trevor@euripides.gws.uky.edu Structural Biology Phone - (606) 323 6037 Dept. of Biochemistry Fax - (606) 323 1037 University of Kentucky Lexington, KY 40536-0084 http://euripides.gws.uky.edu/~trevor U.S.A. ________________________________________________________________________ --------------2781446B794B Content-Type: text/plain; charset=us-ascii; name="ccl" Content-Transfer-Encoding: 7bit Content-Disposition: inline; filename="ccl" Well, thanks for all the answers to my f77 compilation problems on an O2. I've appended the answers below for those who requested a summary. I've also included my original message at the very end. I gather there were two problems. Number one was that the 64-bit libraries are not loaded in the default installation. This was pointed out to me by a couple of people. Number two was pointed out by Omar Stradella from SGI (see below): apparently the O2's don't support 64-bit binaries (is this really true ?). You can take advantage of the mips4 instruction set using: f77 -n32 -mips4.... Thanks again, Trevor +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From: ps@ocisgi7.unizh.ch (Serge Pachkovsky) > I get the following error from the linker: > > ld64: FATAL 9: I/O error (/usr/lib64/crt1.o): No such file or directory > f77 INTERNAL ERROR: /usr/lib32/cmplrs/ld64 returned non-zero status 32 > > Sure enough, crt1.o does not exist in /usr/lib64. I can compile with no > problems using: Install compiler_dev.sw64.*, compiler_eoe.sw64.* and ftn_dev.sw64.* subsystems from your IDO CD. You might also want to install other 64-bit subsystems, such as complib.sw.sgimath_64, but these three are absolutely necessary to link -64 executables. Likewise, if you want to compile -n32 executables, install *.sw32.* subsystems. Generally, you can get a fairly good idea which subsystems you'd need by reading release notes (use relnotes or grelnotes, depending on your UI preferences). Regards, /Serge.P +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From: "Dr D.W. Lewis" We have had nothing but problems with this as well! The compilers are basically very poor (would SGI like to deny that?). The problem is mainly caused IMO (as I think you have noticed) by the 32-bit nature of Irix6.3 whilst the compiler is expecting an R10000 to support 64 bit stuff. The best I can do is say lower you optimisation to -O and it will probably work! I would check your code against another SG system as well if possible especially if you do ramp up the ooptimisation. I am getting rouding errors in some routines with -O3 on the O2. Having said that we have had reasonably good response from the software support at SGI - they seem aware and embarrassed at least. Raise it with them via their support line and see if you can get anything out of them. They jumped pretty quick when we said that the standard LAPACK routine failed to give correct test suite answers. I know its not much of a consolation but the C compiler seems better! But I won't be buying another O2...... ---------------------------------------------------------------------------- Dr. Dewi W. Lewis Dept of Materials Science and Metallurgy, Email: D.W.Lewis@msm.cam.ac.uk University of Cambridge, Pembroke St., Phone: +44 1223 3 34496 Cambridge, CB2 3QZ, UK Fax: +44 1223 3 34567 WWW: http://www-img.msm.cam.ac.uk/D.W.Lewis/ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From: Raf Bruyndonckx Hello Trevor, see if you can find "/usr/lib64/cmplrs/f77" , and if you have it, try that compiler. Otherwise, be sure you have all the 64-bit libraries and executables installed. Standard installation can skip some parts from the distribution and even using custom installation you miss sometimes a few. I hope this will help. Raf -- Raf Bruyndonckx Department of Inorganic Chemistry Univ Fribourg (Suisse) Perolles Tel: ++41 26 300 87 49 Fax: ++41 26 300 97 38 mailto:Raf.Bruyndonckx@unifr.ch http://www.unifr.ch/ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From: "Peter Shenkin" I seem to recall that this is due to some installation bug. Assuming you're under support, call SGI. Best, -P. -- ** Religion is OK, if practiced behind closed doors by consenting adults ** * Peter S. Shenkin; Chemistry, Columbia U.; 3000 Broadway, Mail Code 3153 * ** NY, NY 10027; shenkin@columbia.edu; (212)854-5143; FAX: 678-9039 *** MacroModel WWW page: http://www.cc.columbia.edu/cu/chemistry/mmod/mmod.html +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From: "Omar G. Stradella" Hi Trevor, The O2 does not support execution of 64 bit binaries. To take advantage of the new insctuction set anyway, compile with -n32 -mips4. Omar. +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ On Feb 20, 9:48am, Trevor Creamer wrote: > Subject: CCL:F77 on an R10000 O2 > My apologies in advance if this is an inappropriate post... > > I have just migrated from a R4400 SGI platform running IRIX 5.3 to a new > R10000 O2 running IRIX 6.3 and I'm having problems getting my (very > standard) Fortran programs to compile in 64-bit mode. If I compile > using: > > f77 -O3 -mips4 myprog.f (or f77 -O3 -64 myprog.f) > > I get the following error from the linker: > > ld64: FATAL 9: I/O error (/usr/lib64/crt1.o): No such file or directory > f77 INTERNAL ERROR: /usr/lib32/cmplrs/ld64 returned non-zero status 32 > > Sure enough, crt1.o does not exist in /usr/lib64. I can compile with no > problems using: > > f77 -O3 -32 myprog.f > > - crt1.o does exist in /usr/lib32. > > I have gone through the Development Option 7.0.1 and Developer Update > Package (10/96) cd's throughly and there is nothing that hasn't been > installed. Has anyone else run into this ? Any suggestions ? > Cheers, > Trevor --------------2781446B794B-- From GOSTOWSKIR@APSU01.APSU.EDU Thu Feb 20 16:24:30 1997 Received: from apsu01.apsu.edu for GOSTOWSKIR@APSU01.APSU.EDU by www.ccl.net (8.8.3/950822.1) id QAA16559; Thu, 20 Feb 1997 16:17:49 -0500 (EST) From: Received: from APSU01.APSU.EDU by APSU01.APSU.EDU (PMDF V5.0-4 #7156) id <01IFN62TGVZW000J6Y@APSU01.APSU.EDU> for chemistry@www.ccl.net; Thu, 20 Feb 1997 15:08:59 -0600 (CST) Date: Thu, 20 Feb 1997 15:08:59 -0600 (CST) Subject: removing dummy atoms To: chemistry@www.ccl.net Message-id: <01IFN62TGWXQ000J6Y@APSU01.APSU.EDU> X-VMS-To: IN%"chemistry@www.ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Does anyone have a suggestion for removing dummy atoms to facilitate display of MOPAC file in PCmodel. thanks, Rudy Gostowski From GOSTOWSKIR@APSU01.APSU.EDU Thu Feb 20 16:34:18 1997 Received: from apsu01.apsu.edu for GOSTOWSKIR@APSU01.APSU.EDU by www.ccl.net (8.8.3/950822.1) id QAA16572; Thu, 20 Feb 1997 16:17:53 -0500 (EST) From: Received: from APSU01.APSU.EDU by APSU01.APSU.EDU (PMDF V5.0-4 #7156) id <01IFN5U5FSYE000J6Y@APSU01.APSU.EDU> for chemistry@www.ccl.net; Thu, 20 Feb 1997 15:07:08 -0600 (CST) Date: Thu, 20 Feb 1997 15:07:08 -0600 (CST) Subject: Moledit for Windows problems To: chemistry@www.ccl.net Message-id: <01IFN5U5FTW8000J6Y@APSU01.APSU.EDU> X-VMS-To: IN%"chemistry@www.ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Moledit for Windows is a nice program but seems to have a few problems (???) These are mostly associated with trying to print. I can only accomplish by some combination of selecting print, closing the print manager, selecting print again (or print setup), and then closing Moledit. This does not work in all cases and sometimes it just locks up. The error messages given include: Das Drucken ist im Gang Or Allgemeine Schutzverletzung in Modul HPPCL5A.DRV bei 000E:2E92 Since I do not speak German this is not very useful. No insult intended to the programmer. Also, the "Help" will not work. If you have any ideas it would be appreciated as this is an excellant FREE solution to the input/output problem. thanks, Rudy Gostowski From mn1@helix.nih.gov Thu Feb 20 17:24:32 1997 Received: from helix.nih.gov for mn1@helix.nih.gov by www.ccl.net (8.8.3/950822.1) id QAA16625; Thu, 20 Feb 1997 16:28:09 -0500 (EST) Received: (from mn1@localhost) by helix.nih.gov (8.8.4/8.8.4) id QAA10277; Thu, 20 Feb 1997 16:27:56 -0500 (EST) Date: Thu, 20 Feb 1997 16:27:56 -0500 (EST) From: "M. Nicklaus" Message-Id: <199702202127.QAA10277@helix.nih.gov> To: CHEMISTRY@www.ccl.net Subject: G:Problem in DFT job Cc: mn1@helix.nih.gov Dear CCL'ers, I am trying to run an optimization (actually, a PES scan, but I don't even get that far), using the following route section: # B3LYP/6-31G(d) Guess=Read Opt=(VeryTight,CalcFC,AddRedundant) The job calculates one energy, and then crashes with the error message DenBas #2 allocation failure: iend,mxcore= 91944 17059 Error termination via Lnk1e in /usr/programs/g94/l1101.exe. (Previously, I ran the job with the exact same structure with the route section # B3LYP/6-31G(d) Guess=Read Opt=(Tight,AddRedundant) This job *didn't* crash; but then, the optimization never converged. This was the reason I switched to "VeryTight,CalcFC".) Any suggestions as to what's going wrong, and how to fix it? Thanks in advance for all responses. Marc ------------------------------------------------------------------------ Marc C. Nicklaus Lab. of Medicinal Chemistry e-mail: mn1@helix.nih.gov National Cancer Institute, NIH Phone: (301) 402-3111 Bldg 37, Rm 5B29 Fax: (301) 496-5839 BETHESDA, MD 20892-4255 USA WWW: http://www.nci.nih.gov/intra/lmch/MCNBIO.HTM ------------------------------------------------------------------------ From schrecke@t12.lanl.gov Thu Feb 20 17:32:13 1997 Received: from mailhost.lanl.gov for schrecke@t12.lanl.gov by www.ccl.net (8.8.3/950822.1) id QAA16741; Thu, 20 Feb 1997 16:43:46 -0500 (EST) Received: from [128.165.22.209] ([128.165.22.209]) by mailhost.lanl.gov (8.8.5/8.8.3) with SMTP id OAA07290 for ; Thu, 20 Feb 1997 14:43:46 -0700 (MST) Date: Thu, 20 Feb 1997 14:43:46 -0700 (MST) Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: CHEMISTRY@www.ccl.net From: schrecke@t12.lanl.gov (Georg Schreckenbach) Subject: DFT and ECP. Summary On Wednesday, I posted a question about the use of effective core potentials within DFT. A got a number of replies: special thanks to everybody who answered. This is my summary. If anybody wants to comment further on the matter, please do so! Yours, Georg ======================================================= Original question: I was thinking about the use of effective core potentials (ECPs, also called pseudopotentials -- I had posted a question and summary about the difference between these two terms a while ago in the CCL), and their application in density functional theory (DFT). Specifically, the usual ECPs are derived using Hartree-Fock (HF) type methods. Recently, one can see them being used in DFT applications, appareantly with success (e.g., Martin Kaupp's work). On a purely theoretical ground, however, one would assume that ECPs for DFT should be derived with a DFT based method. This could be pushed even further by making a separate ECP for each new functional in DFT. Has anybody done something like this? Are there any real, practical differences between HF-derived and DFT-derived ECPs when they are applied in DFT calculations (what does this do for geometries, energetics etc.)? I would appreciate references, but also any kind of experience, published or unpublished. I will summarize to the list if I get any answers. ======================================================= And the answers: From: Karl Irikura ON THE USE OF COMMON EFFECTIVE CORE POTENTIALS IN DENSITY-FUNCTIONAL CALCULATIONS .1. TEST CALCULATIONS ON TRANSITION-METAL CARBONYLS Vanwullen-C INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 58 (2) : pp147-152 EFFECTIVE CORE POTENTIALS FOR DFT CALCULATIONS Russo-TV Martin-RL Hay-PJ JOURNAL OF PHYSICAL CHEMISTRY 99 (47) : pp17085-17087 Good luck! Karl Irikura ---------------------------------------------- Dr. Karl K. Irikura Physical and Chemical Properties Division National Institute of Standards and Technology Gaithersburg, MD 20899 voice: 301-975-2510 fax: 301-975-3670 e-mail: karl.irikura@nist.gov ---------------------------------------------- ======================================================= [Comment by G.S.: I had forgotten to put the paper by Russo/ Hay/Martin into the question ... ] ======================================================= From: qiang@euch4e.chem.emory.edu > Has anybody done something like this? Yes, to my limited knowledge, at least Hay et. al. has done this sometime ago. I don't remember the exact reference, somewhere in JCP(or JPC, sorry!) '96 or '95. Search for author index. Roughly their results showed that original ECP still give quite reliable results when used with DFT. Yet indeed, they found some strange behavior as well. I don't know if any people has persued the issue systematically later on, but I guess it's certainly worth doing, since DFT stuff are more and more popular in transition metal studies. Hope this is helpful somehow. Good luck. ______________________________________________________________ Qiang Cui Dept. of Chem. Emory Univ. 508 Webster Dr. Apt.#2 Atlanta, GA 30322. Decatur, GA 30033. (404)-727-2381 (404)-636-6149 http://tswww.cc.emory.edu/~qcui ______________________________________________________________ ======================================================= From: "Dr. Heinz Schiffer" Hi George, everyone in the plane wave community does exactly that: create for each exchange-correlation functional your own pseudopotential. See, e.g.: S. Goedecker, M. Teter, J. Hutter Separable dual-space Gaussian pseudopotentials Phys. Rev. B, 54(3) (1996) 1703-1710 N. Troullier and Jose Luis Martins Efficient pseudopotentials for plane-wave calculations Phys. Rev. B, 43(3) (1991) 1993-2006 G. B. Bachelet, D. R. Hamann, and M. Schlueter Pseudopotentials that work: From H to Pu Phys. Rev. B., 26(8) (1982) 4199-4228 Recently, Christoph van Wuellen in Kutzelniggs group published a paper about the use of common ECPs for DFT calculations with Gaussian basis sets : Christoph van Wuellen On the use of common effective cor potentials in density functional calculations. I. Test calculations on transition-metal carbonyls Int. J. Quantum Chem. 58(2) (1996) 147-52 I think the main conclusion was, that those ECPs work just fine ! Cheers, Heinz -- Dr. Heinz Schiffer Phone ++49-69-305-2330 Hoechst CR&T Fax ++49-69-305-81162 Scientific Computing, G864 Email schiffer@h1tw0036.hoechst.com 65926 Frankfurt am Main schiffer@msmwia.hoechst.com ======================================================= From: lrbu00@xd88.kodak.com Salahub's group at U. of Montreal has a set of ECP's for deMon. Regards, John -- John M. McKelvey email: mckelvey@Kodak.COM Computational Science Laboratory phone: (716) 477-3335 2nd Floor, Bldg 83, RL Eastman Kodak Company Rochester, NY 14650-2216 ======================================================= From: kaupp@vsibm1.mpi-stuttgart.mpg.de (Martin Kaupp) Your question touches the transferability of ECPs derived at different computational levels (e.g. HF, different DFT variants, one may even think of CI approaches etc....). The general answer from our experience is that this depends on the ECP core sizes you employ (M. Kaupp, H.-J. Flad, A. K\"oster, H. Stoll, D. R. Salahub, unpublished results). We never got around to publish these test studies but hopefully will do so eventually.... For small core sizes typical for transition metal species, this transferability is essentially perfect. Apart from our own work in the context of NMR calculations, this has also been found by other authors, see e.g.: C. van W\"ullen Int. J. Quant. Chem., 1996, 58, 147. T. V. Russo, R. L. Martin, P. J. Hay J. Phys. Chem. 1995, 99, 17085. Many others have already used HF-derived ECPs in their DFT studies without even worrying about transferability. The main point in our experience is that electron correlation apparently does not affect the sizes of lower core shells very much (it may do so however for outer semi-core shells, cf. below). For larger core sizes (e.g. Ga+3, Zn+2, Na+1), we find that transferability starts to deteriorate. However, this is hardly surprising, as in post-HF calculations one gets problems at about the same point. With respect to deriving ECPs from DFT fits using different functionals, I know this is pursued by several groups in the solid-state community, usually in the context of plane wave basis sets. I don't have references at hand, unfortunately. However, the transferability between different DFT variants for a given core size should be even superior to HF->DFT or vice versa. Viele Gruesse, Martin ------------------------------------------------------------------ | Dr. Martin Kaupp | | Max-Planck-Institut fuer Festkoerperforschung, | | Heisenbergstrasse 1, D-70569 Stuttgart, Germany, | | Tel.: country-code+711/689-1532 | | Fax.: country-code+711/689-1562 | | email: kaupp@vsibm1.mpi-stuttgart.mpg.de | | | | and Institut fuer Theoretische Chemie, Universitaet Stuttgart, | | Pfaffenwaldring 55, D-70569 Stuttgart, Germany | | Tel.: country-code+711/685-4408 | | Fax.: country-code+711/685-4442 | | http://www.theochem.uni-stuttgart.de/~kaupp/ | | email: kaupp@theochem.uni-stuttgart.de | ------------------------------------------------------------------ ======================================================= End of summary ======================================================= -- +---------------------------------------------------------------------+ | Dr. Georg Schreckenbach Tel: (USA)-505-667 7605 | | Theoretical Chemistry T-12 FAX: (USA)-505-665 3909 | | M.S. B268 E-mail: schrecke@t12.lanl.gov | | Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, USA | +---------------------------------------------------------------------+ From jianwang@cgl.ucsf.EDU Thu Feb 20 18:24:32 1997 Received: from socrates.ucsf.EDU for jianwang@cgl.ucsf.EDU by www.ccl.net (8.8.3/950822.1) id SAA17473; Thu, 20 Feb 1997 18:02:43 -0500 (EST) Received: (from jianwang@localhost) by socrates.ucsf.EDU (8.8.5/GSC4.26) id PAA29509; Thu, 20 Feb 1997 15:02:40 -0800 (PST) Date: Thu, 20 Feb 1997 15:02:40 -0800 (PST) From: Jian Wang X-Sender: jianwang@socrates.ucsf.edu To: CHEMISTRY@www.ccl.net cc: amber@cgl.ucsf.edu Subject: mixed internal and cartesian coordinates Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL netters, Could someone point to me a fortran or c program that converts mixed cartesian and internal coordinates into cartesian coordinates? I know G9x can do the job. Are there any others? Thanks. ________________________________________________________________________ Jian Wang, Ph.D Department of Pharmaceutical Chemistry Tel: (415)-476-2597 (O) Box 0446, Room S-1019 (415)-752-2256 (H) University of California Fax: (415)-476-0668 (O) San Francisco, CA94143-0446 U.S.A. Email: jianwang@cgl.ucsf.edu _________________________________________________________________________ From alper@moldyn.com Thu Feb 20 21:24:31 1997 Received: from photon.com for alper@moldyn.com by www.ccl.net (8.8.3/950822.1) id UAA18175; Thu, 20 Feb 1997 20:53:35 -0500 (EST) Received: from bart.moldyn.com ([172.16.2.14]) by gateway.photon.com with SMTP id <5888-1>; Thu, 20 Feb 1997 17:44:14 -0800 Received: by bart.moldyn.com (940816.SGI.8.6.9/940406.SGI.AUTO) id UAA14908; Thu, 20 Feb 1997 20:57:58 -0500 From: alper@moldyn.com (Howard Alper) Message-Id: <199702210157.UAA14908@bart.moldyn.com> Subject: Experience with QM/MM CHARMM codes To: CHEMISTRY@www.ccl.net Date: Thu, 20 Feb 1997 17:57:55 -0800 Cc: alper@bart.moldyn.com (Howard Alper) X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Hello, I was wondering if anyone in CCL-land had experience with both semi-empirical and ab-initio versions of CHARMM's combined Quantum/Classical (QM/MM) forcefield code (for example versions c24b and c25a of CHARMM), both with respect to the basic behavior of the code, and the correctness of the results compared to experiment or theory. Thanks. As always, I will sunmmarize the responses for the list. Howard -- Dr. Howard Alper Moldyn Inc. 955 Massachusetts Avenue Fifth Floor Cambridge, MA 02139-3180 617-354-3124 x19 email: alper@moldyn.com - helping molecules find happiness for over a 10th of a century. From anti!anti.irkutsk.su!uucp@irnet.ru Thu Feb 20 21:38:08 1997 Received: from irnet.ru for anti!anti.irkutsk.su!uucp@irnet.ru by www.ccl.net (8.8.3/950822.1) id UAA18124; Thu, 20 Feb 1997 20:31:05 -0500 (EST) Received: from anti.UUCP (uuanti@localhost) by irnet.ru (8.7.3/8.7.3) with UUCP id JAA20781 for chemistry@www.ccl.net; Fri, 21 Feb 1997 09:26:37 +0800 (ISK) X-Authentication-Warning: irnet.ru: uuanti set sender to anti!anti.irkutsk.su!uucp using -f Received: by anti.irkutsk.su (UUPC/@ v6.14g, 06Jun95) id AA26488; Thu, 20 Feb 1997 17:26:05 +0800 (IRK) To: chemistry@www.ccl.net Cc: a:\email\ccl\request.out@irnet.ru Message-Id: Organization: ANGARSK TECHNOLOGICAL INSTITUTE From: "Leonid B. Krivdin" Date: Thu, 20 Feb 97 17:26:05 +0800 X-Mailer: BML [MS/DOS Beauty Mail v1.36h] Subject: 3D-drawing of MOs and LMOs Lines: 27 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Netters: I'm interested in 3D-drawing of canonical MOs, localization and 3D-drawing of the resulted localized MOs of the middle-size organic molecules at semiempirical level of approximation. Could anybody help to locate ftp/http sites of any non-commercial programs doing this job in a user-friendly manner under DOS/Windows/Linux? Thank you in advance, Leonid Krivdin. *************************************************** Dr Leonid B. Krivdin Professor of Chemistry Angarsk Technological Institute 60 Chaikovsky Ave. Angarsk 665835, Russia E-mail: krivdin@anti.irkutsk.su ***************************************************