From owner-chemistry@ccl.net Tue Oct 3 01:10:01 2006 From: "fuji fuji yamafuji6!^!yahoo.com" To: CCL Subject: CCL: Ground to excited state Transition electric dipole moments in g03 Message-Id: <-32692-061003010640-20272-cKobmiCCY5LrWMnaphiI3g::server.ccl.net> X-Original-From: "fuji fuji" Date: Tue, 3 Oct 2006 01:06:38 -0400 Sent to CCL by: "fuji fuji" [yamafuji6!=!yahoo.com] Dear CCL members, I am doing TDDFT calculations on a ligand alone and ligand flanking with two nucleobases. My TDDFT calculation gave me the following output : 1) Ligand alone: Ground to excited state Transition electric dipole moments (Au): state X Y Z Osc. 1 -2.0448 -0.0698 -0.0003 0.4146 .............. 2) Ligand flanking with two nucleobases: Ground to excited state Transition electric dipole moments (Au): state X Y Z Osc. 0.4683 -1.5561 -0.2660 0.2680 .............. In the calculation of ligand alone, the transition dipole lie on the XY plane and ligand flanking with two nucleobases shows Z polarization. My question is how to calculate/represent this Z polatisation in terms of degree? I need to calculate this to explain the charge transfer character between the nucleobase and the ligand. Say for example I have found that the transition dipole is 25 degree out of plane, indicating that it has significant charge-transfer character... in a paper by J.M.Jean and K.B.Hall, PNAS 2001 vol.98, no.1, 37-41. Thanks in advance. Best Regards From owner-chemistry@ccl.net Tue Oct 3 01:44:00 2006 From: "Nehru Viji Shankaran chat2viji ~~ gmail.com" To: CCL Subject: CCL: fortran doubt Message-Id: <-32693-061003012912-981-Y43T7QKpP4tzckOQKIuedQ]|[server.ccl.net> X-Original-From: "Nehru Viji Shankaran" Date: Tue, 3 Oct 2006 01:29:12 -0400 Sent to CCL by: "Nehru Viji Shankaran" [chat2viji(-)gmail.com] Dear all, Fortran is very new to me. I had a doubt in the following statement IF(YZA.LT.2.D-2)then IF(YZA.LT.1.D-4) what does this mean. this statement is from MOPAC subroutine gmetry.for. kindly reply me, thanks in advance. Nehru Viji Shankaran nehruviji!=!yahoo.co.in chat2viji!=!yahoo.co.in From owner-chemistry@ccl.net Tue Oct 3 02:47:00 2006 From: "Ulrike Salzner salzner(!)fen.bilkent.edu.tr" To: CCL Subject: CCL:G: simulation of UV spectra Message-Id: <-32694-061003012231-27882-Ro5g4j9SkwqoMAa1VVtstg---server.ccl.net> X-Original-From: Ulrike Salzner Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Tue, 03 Oct 2006 08:22:21 +0300 Mime-Version: 1.0 Sent to CCL by: Ulrike Salzner [salzner . fen.bilkent.edu.tr] Hello, is there are program that can simulate UV-spectra of open-shell systems > from G03 (TD) calculations? I have Gaussum but it can do only closed- shell species. Can GaussView do it? Thanks for suggestions, Ulrike -- Ulrike Salzner Associate Professor Department of Chemistry Bilkent University 06800 Bilkent, Ankara Turkey From owner-chemistry@ccl.net Tue Oct 3 04:16:01 2006 From: "Michel Petitjean ptitjean,itodys.jussieu.fr" To: CCL Subject: CCL: fortran doubt Message-Id: <-32695-061003041031-9021-sY0f/B+VKit+lcn3g2/sLw^_^server.ccl.net> X-Original-From: Michel Petitjean Date: Tue, 3 Oct 2006 10:10:03 +0200 (MEST) Sent to CCL by: Michel Petitjean [ptitjean*|*itodys.jussieu.fr] To: chemistry||ccl.net Subj: CCL: Re: fortran doubt Dear Nehru, Some lines may be missing, but the meaning of these tests seems obvious. Please post more source lines to explain your doubt. Remarks: In order to parametrise the programme, an experienced programmer would have declared the constants "2.D-2" and "1.D-4" in a DATA statement, either in the subroutine itself, or in some calling routine and passing them in arguments (the meaning of the arguments being explained again in the called subroutine). Furthermore he would have inserted some comments to explain the meaning of the two constants and why they are set to these particular values. Best regards, Michel Petitjean, Email: petitjean||itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean||ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html Sent to CCL by: "Nehru Viji Shankaran" [chat2viji(-)gmail.com] > Dear all, > > Fortran is very new to me. I had a doubt in the following statement > > IF(YZA.LT.2.D-2)then > IF(YZA.LT.1.D-4) > > what does this mean. > > this statement is from MOPAC subroutine gmetry.for. > > kindly reply me, > thanks in advance. > > Nehru Viji Shankaran > nehruviji\a/yahoo.co.in From owner-chemistry@ccl.net Tue Oct 3 05:11:00 2006 From: "Stan van Gisbergen vangisbergen[A]scm.com" To: CCL Subject: CCL: Non-Linear Optical Property Calculations Message-Id: <-32696-061003041623-9554-TNwH5DBcrmT+xZQwPCkzlw#%#server.ccl.net> X-Original-From: Stan van Gisbergen Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed Date: Tue, 3 Oct 2006 09:23:14 +0200 Mime-Version: 1.0 (Apple Message framework v619.2) Sent to CCL by: Stan van Gisbergen [vangisbergen()scm.com] Dear Jose Font, The Amsterdam Density Functional (ADF) program package can efficiently calculate dynamic (frequency-dependent) first hyperpolarizability tensors analytically using Time-Dependent DFT and the (2n+1) rule of perturbation theory. Several third-order dynamic properties can also be obtained by finite difference (calculating beta in small static electric fields). The first application of this was to show that gamma of C60 was not as large as some experimentalists were thinking: Physical Review Letters, 1997. 78: p. 3097. See also the ADF user's guide, HYPERPOL keyword: http://www.scm.com/Doc/Doc2006.01/ADF/ADFUsersGuide/page125.html If you have further questions, let me know. Best regards, Stan van Gisbergen On Oct 2, 2006, at 9:10 PM, Jose Font jose_font!=!urmc.rochester.edu wrote: > Sent to CCL by: "Jose Font" [jose_font() urmc.rochester.edu] > I am developing an interest in in calculating second/third nonlinear > optical susceptibilities in quantum dots. > > The plan is to use known software to calculate these properties on > systems that are known to test the software. The second step is to > design new quantum dots on the computer and determine if they have the > appropriate properties. If they do, on the scale of the computer, > they will be sybthesized and tested experimentally for the properties > to make sure that the scale for the calculations correlate to the > 'bulk' scale. > > What academic software is available? What commercial software is > recommended? > > Is there a paper that goes into the details of calculating the > properties? > > Thanks - Jose Font > > email: jose_font,urmc.rochester.edu> To recover the email address of the author of the message, please > change> > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+ > > > > Dr. S.J.A. van Gisbergen       Scientific Computing & Modelling NV Theoretical Chemistry, Vrije Universiteit De Boelelaan 1083 1081 HV Amsterdam The Netherlands                                 vangisbergen(_)scm.com   http://www.scm.com T: +31-20-5987626     F: +31-20-5987629       From owner-chemistry@ccl.net Tue Oct 3 05:56:00 2006 From: "Herbert Fruchtl herbert.fruchtl^_^st-andrews.ac.uk" To: CCL Subject: CCL: fortran doubt Message-Id: <-32697-061003053854-26918-taquGaRCuZgQZdOp2wtNPA],[server.ccl.net> X-Original-From: Herbert Fruchtl Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 03 Oct 2006 10:34:53 +0100 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl!=!st-andrews.ac.uk] This is not the place for a discussion about Fortran programming style, but: - if you want to declare a constant somewhere else, it should be a PARAMETER, not DATA. - if it's only used once, "hiding" the value somewhere else only makes it more difficult to understand the program, so the use of literal constants seems OK here. The meaning of these constants is probably "a fairly small value that has proved to prevent trouble". Don't know if it makes sense to add this as a comment to every line of code where you do something like this. Today (in Fortran 95) one would do it differently, but MOPAC was largely written in the seventies, with some parts even older. The lines Nehru included seem to be already from a slightly more modern version, where the original GOTO structure of the code (I looked it up in MOPAC 6) was replaced with if/then constructs. Herbert Michel Petitjean ptitjean,itodys.jussieu.fr wrote: > Sent to CCL by: Michel Petitjean [ptitjean*|*itodys.jussieu.fr] > To: chemistry{}ccl.net > Subj: CCL: Re: fortran doubt > > Dear Nehru, > > Some lines may be missing, but the meaning of these tests seems obvious. > Please post more source lines to explain your doubt. > > Remarks: > In order to parametrise the programme, an experienced programmer > would have declared the constants "2.D-2" and "1.D-4" in a DATA statement, > either in the subroutine itself, or in some calling routine > and passing them in arguments (the meaning of the arguments being > explained again in the called subroutine). > Furthermore he would have inserted some comments to explain the meaning > of the two constants and why they are set to these particular values. > > Best regards, > > Michel Petitjean, Email: petitjean{}itodys.jussieu.fr > ITODYS (CNRS, UMR 7086) ptitjean{}ccr.jussieu.fr > 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 > 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 > http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html > > Sent to CCL by: "Nehru Viji Shankaran" [chat2viji(-)gmail.com] >> Dear all, >> >> Fortran is very new to me. I had a doubt in the following statement >> >> IF(YZA.LT.2.D-2)then >> IF(YZA.LT.1.D-4) >> >> what does this mean. >> >> this statement is from MOPAC subroutine gmetry.for. >> >> kindly reply me, >> thanks in advance. >> >> Nehru Viji Shankaran >> nehruviji\a/yahoo.co.in> > > -- Herbert Fruchtl EaStCHEM Fellow School of Chemistry University of St Andrews From owner-chemistry@ccl.net Tue Oct 3 10:00:01 2006 From: "John McKelvey jmmckel]![attglobal.net" To: CCL Subject: CCL: Dual dual-core AMD performance Message-Id: <-32698-061003092011-9549-iXdCCVzPCADFWmys5e0WPQ.@.server.ccl.net> X-Original-From: John McKelvey Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 03 Oct 2006 09:16:49 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel%a%attglobal.net] Hello! Could I get some comments and/or references related to the performance of various ab-initio/DFT programs on SMP AMD dual-core, and dual-dual-core hardware? Many thanks! John McKelvey From owner-chemistry@ccl.net Tue Oct 3 12:43:00 2006 From: "=?ISO-8859-1?Q?=D6d=F6n?= Farkas farkas_+_chem.elte.hu" To: CCL Subject: CCL: Question on Oniom calculation with gaussian 03 Message-Id: <-32699-061003100430-15422-Fbx80C5mJa6X5Wl7w61t4Q,server.ccl.net> X-Original-From: =?ISO-8859-1?Q?=D6d=F6n?= Farkas Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Tue, 03 Oct 2006 16:04:20 +0200 Mime-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?=D6d=F6n?= Farkas [farkas|a|chem.elte.hu] Hi, It seems that the semiempirical (AM1) SCF did not converge on the medium or high layer. Double check the charge/multplicity for the corresponding layer and you may also try changing the layers to get more reasonable structures. Good luck, Ă–dön On Mon, 2006-10-02 at 08:46 -0400, cercis morera morera2004+/-yahoo.com wrote: > Sent to CCL by: cercis morera [morera2004**yahoo.com] > --0-80013413-1159785688=:54197 > Content-Type: text/plain; charset=iso-8859-1 > Content-Transfer-Encoding: 8bit > > Hello everybody, Im doing an Oniom calculation with 3 layers, and I get the following message > ALL CONVERGERS ARE NOW FORCED ON SHIFT=1000, PULAY ON, CAMP-KING ON AND ITERATION COUNTER RESET > > the previous message is present in the output after every cycle of 3-point extrapolation > and finally it shows the following error > Error in Pulay, LFock= 5 NFock1= 7 EMat(L,L)= 5.85D-15 > Error termination via Lnk1e in h:\program files\l402.exe at Sun Oct 1 18:37:38 2006. > Job cpu time: 0 days 7 hours 7 minutes 24.0 seconds. > File lengths (MBytes): RWF= 50 Int= 0 D2E= 0 Chk= 30 Scr= > here is the keywords I used : > # ONIOM (B3lyp/6-31g:AM1:UFF) opt test > Somebody have already meet this kind of problems???? > > Thank you in advance !!!!!!! > > > > > --------------------------------- > Do you Yahoo!? > Everyone is raving about the all-new Yahoo! Mail. > --0-80013413-1159785688=:54197 > Content-Type: text/html; charset=iso-8859-1 > Content-Transfer-Encoding: 8bit > >
Hello everybody, Im doing an Oniom calculation with 3 layers, and I get the following message
ALL CONVERGERS ARE NOW FORCED ON SHIFT=1000, PULAY ON, CAMP-KING ON AND ITERATION COUNTER RESET
 
the previous message is present in the output after every cycle of 3-point extrapolation
and finally it shows the following error 
  Error in Pulay, LFock= 5 NFock1= 7 EMat(L,L)= 5.85D-15
Error termination via Lnk1e in h:\program files\l402.exe at Sun Oct 1 18:37:38 2006.
Job cpu time:  0 days  7 hours  7 minutes 24.0 seconds.
File lengths (MBytes):  RWF=     50 Int=      0 D2E=      0 Chk=     30 Scr=
here is the keywords I used :
# ONIOM (B3lyp/6-31g:AM1:UFF) opt test
Somebody have already  meet this kind of problems????
 
Thank you in > advance !!!!!!!

>

Do you Yahoo!?
Everyone is raving about the all-new Yahoo! Mail. > --0-80013413-1159785688=:54197--> > > -- Ödön Farkas Research associate professor Deparment of Organic Chemistry, Institute of Chemistry, Eötvös Loránd University, Budapest Address: 1/A Pázmány Péter sétány, H-1117 Budapest, Hungary Phone: +36-1-372-2570 Cell phone: +36-30-255-3111 Fax: +36-1-372-2620 URL: http://organ.elte.hu/farkas From owner-chemistry@ccl.net Tue Oct 3 14:47:01 2006 From: "Jozsef Csontos jozsefcsontos(!)creighton.edu" To: CCL Subject: CCL:G: Dual dual-core AMD performance Message-Id: <-32700-061003143859-10911-ZKaNj6/eCbAbEJfojBfS1w%server.ccl.net> X-Original-From: Jozsef Csontos Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Tue, 03 Oct 2006 12:47:10 -0500 Mime-Version: 1.0 Sent to CCL by: Jozsef Csontos [jozsefcsontos{=}creighton.edu] Hi, dual dual-core Opteron (Gaussian03, 33 atoms (17 heavy), tight optimization, 287 basis function) link speedups #ofCPUs link502 link703 1 1.0 1.0 2 1.8 1.8 4 3.5 3.2 Good luck, Jozsef On Tue, 2006-10-03 at 10:22 -0400, John McKelvey jmmckel]![attglobal.net wrote: > Sent to CCL by: John McKelvey [jmmckel%a%attglobal.net] > Hello! > > Could I get some comments and/or references related to the performance > of various ab-initio/DFT programs on SMP AMD dual-core, and > dual-dual-core hardware? > > Many thanks! > > John McKelvey> > > -- Jozsef Csontos, Ph.D. Department of Biomedical Sciences Creighton University, Omaha, NE From owner-chemistry@ccl.net Tue Oct 3 17:06:01 2006 From: "Alex A. Granovsky gran ~ classic.chem.msu.su" To: CCL Subject: CCL:G: Dual dual-core AMD performance Message-Id: <-32701-061003165338-11762-AQM8xQq2kzV6k2+NjhUjfw^-^server.ccl.net> X-Original-From: "Alex A. Granovsky" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="koi8-r" Date: Tue, 3 Oct 2006 23:24:58 +0400 MIME-Version: 1.0 Sent to CCL by: "Alex A. Granovsky" [gran * classic.chem.msu.su] Hi, some data for PC GAMESS on Pentium D, dual-core Opterons and Xeons (Dempsey and Woodcrest) can be found at http://classic.chem.msu.su/gran/gamess/ in the "Performance" section Best regards, Alex Granovsky ----- Original Message ----- > From: "Jozsef Csontos jozsefcsontos(!)creighton.edu" To: "Granovsky, Alex, A. " Sent: Tuesday, October 03, 2006 10:59 PM Subject: CCL:G: Dual dual-core AMD performance > Sent to CCL by: Jozsef Csontos [jozsefcsontos{=}creighton.edu] > Hi, > > dual dual-core Opteron (Gaussian03, 33 atoms (17 heavy), tight > optimization, 287 basis function) > > link speedups > #ofCPUs link502 link703 > 1 1.0 1.0 > 2 1.8 1.8 > 4 3.5 3.2 > > Good luck, > > Jozsef > > On Tue, 2006-10-03 at 10:22 -0400, John McKelvey jmmckel]![attglobal.net > wrote: > > Sent to CCL by: John McKelvey [jmmckel%a%attglobal.net] > > Hello! > > > > Could I get some comments and/or references related to the performance > > of various ab-initio/DFT programs on SMP AMD dual-core, and > > dual-dual-core hardware? > > > > Many thanks! > > > > John McKelvey> > > > > > -- > Jozsef Csontos, Ph.D. > > Department of Biomedical Sciences > Creighton University, > Omaha, NE> > > >