From owner-chemistry@ccl.net Wed Jun 28 00:12:00 2006 From: "JunJun Liu ljjlp03#%#gmail.com" To: CCL Subject: CCL:G: G03: IEEE divide by zero Message-Id: <-32039-060627235746-31141-srS2Vp8m66V5TLMDE2Nu7A~~server.ccl.net> X-Original-From: "JunJun Liu" Content-Transfer-Encoding: 8bit Content-Type: text/plain; format=flowed; delsp=yes; charset=utf-8 Date: Wed, 28 Jun 2006 00:11:38 -0300 MIME-Version: 1.0 Sent to CCL by: "JunJun Liu" [ljjlp03__gmail.com] Hi all, I got the following message when doing PES scan with ONIOM. "IEEE divide by zero"? What does it mean? Any helps are highly appreciated! ======================= GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Berny optimization. Internal Forces: Max 0.020397238 RMS 0.003229077 Search for a local minimum. Step number 212 out of a maximum of 382 All quantities printed in internal units (Hartrees-Bohrs-Radians) Update second derivatives using D2CorX and points212211 Energy Rises -- skip Quadratic search. Skip linear search -- no minimum in search direction. Steepest descent instead of Quadratic search. Maximum step size ( 0.707) exceeded in Quadratic search. -- Step size scaled by 0.018 Steepest descent step scaled to max of 0.05000. Iteration 1 RMS(Cart)= 0.00031999 RMS(Int)= 0.00036811 Iteration 2 RMS(Cart)= 0.00046601 RMS(Int)= 0.00022147 Iteration 3 RMS(Cart)= 0.00003230 RMS(Int)= 0.00019215 Iteration 4 RMS(Cart)= 0.00035422 RMS(Int)= 0.00009485 Iteration 5 RMS(Cart)= 0.00001649 RMS(Int)= 0.00009311 PROGRAM ABORTED : IEEE divide by zero PROCEDURE TRACEBACK: (0) 0x400000000015f1f0 FTN_GETARITRAP + 0x570 [/opt/cluster/apps/g03-C.02.M1/g03/l103.exe] (1) 0x400000000015ff70 U_CATCH_ARITHMETIC_TRAP + 0x3b0 [/opt/cluster/apps/g03-C.02.M1/g03/l103.exe] (2) 0xe000000190002660 _user_sendsig + 0x2660 [***_Kernel_Gateway_***] (3) 0x40000000001ace12 bend_ + 0x772 [/opt/cluster/apps/g03-C.02.M1/g03/l103.exe] (4) 0x40000000001a97c0 formb_ + 0x920 [/opt/cluster/apps/g03-C.02.M1/g03/l103.exe] (5) 0x400000000025e800 formcb_ + 0xa0 [/opt/cluster/apps/g03-C.02.M1/g03/l103.exe] (6) 0x400000000026bb80 redq2x_ + 0xcc0 [/opt/cluster/apps/g03-C.02.M1/g03/l103.exe] (7) 0x400000000025ddd0 redcar_ + 0x350 [/opt/cluster/apps/g03-C.02.M1/g03/l103.exe] (8) 0x40000000002aa7f0 grdopt_ + 0x5870 [/opt/cluster/apps/g03-C.02.M1/g03/l103.exe] (9) 0x400000000014f0b0 optmz_ + 0x58d0 [/opt/cluster/apps/g03-C.02.M1/g03/l103.exe] (10) 0x40000000000f0db0 ml103 + 0x1d0 [/opt/cluster/apps/g03-C.02.M1/g03/l103.exe] (11) 0xc00000000004e070 main_opd_entry + 0x50 [/usr/lib/hpux64/dld.so] ========== From owner-chemistry@ccl.net Wed Jun 28 04:38:01 2006 From: "=?iso-8859-15?q?=D6d=F6n_Farkas?= farkas!^!chem.elte.hu" To: CCL Subject: CCL:G: Gaussian individual basis set Message-Id: <-32040-060627174937-24648-fwbd616JxCCIVBSj8pwLhQ||server.ccl.net> X-Original-From: =?iso-8859-15?q?=D6d=F6n_Farkas?= Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-15" Date: Tue, 27 Jun 2006 18:58:28 +0200 MIME-Version: 1.0 Sent to CCL by: =?iso-8859-15?q?=D6d=F6n_Farkas?= [farkas-,-chem.elte.hu] Hi Alessandro, Just one comment: when a standard basis set, like 6-31G(d) is used with Gen than the "6D" keyword should also be applied, since Gen defaults to 5D while the original 6-31G uses 6D by default. Ödön On Tuesday 27 June 2006 17:58, Alessandro Contini alessandro.contini-.-unimi.it wrote: > Sent to CCL by: Alessandro Contini [alessandro.contini]=[unimi.it] > Hi Orlin, > this is possible in gaussian by using the keyword gen, as in the > following input example: > > %chk=test.chk > %mem=256MB > %nproc=1 > # opt freq b3lyp/gen geom=checkpoint guess=read > > title > > 0 1 > > C H O 0 > 6-31G(d) > **** > Fe 0 > 6-311+G(3df,2p) > **** > > > In this case the 6-31G* basis is applied to carbon oxigen (and H) atoms, > while a more extended basis is applied to iron (NB just an example!!) > It's also possible to apply a basis set on single atoms by specifing > their number (see the on line manual at > http://www.gaussian.com/g_ur/k_gen.htm. ) > > Hope this help > > Alessandro > > > > > > Il giorno mar, 27/06/2006 alle 08.08 -0400, Orlin Blajiev > > blajiev=-=vub.ac.be ha scritto: > > Sent to CCL by: Orlin Blajiev [blajiev_+_vub.ac.be] > > Hi, > > > > Thank you for the answer. I was wondering is not it possible to have an > > individual basis set assingment for Ag in particular or for each atom > > in the structure. It is a possibility in the case of GAMESS, for > > example. There every atom can be given its own basis set. Therefore, > > 6-31 can be used for light ones and lesser for the transition metals. > > > > Orlin > > > > kefalidi(a)chem.auth.gr wrote: > > > Sent to CCL by: kefalidi-*-chem.auth.gr > > > Hi Orlin, > > > > > > The basis set you asked for the Ag atom is not available because Ag is > > > a second > > > row transition metal. For information about all the basis set that you > > > can use for the Ag atom or any other atom, you can visit the site > > > http://www.emsl.pnl.gov/forms/basisform.html > > > > > > Christos > > > > > > Quoting "Orlin Blajiev blajiev_-_vub.ac.be" : > > >> Sent to CCL by: Orlin Blajiev [blajiev- -vub.ac.be] > > >> Hi, > > >> > > >> I will appreciate some help with the following question. I have the > > >> following input for Gaussian-how can I ask for a individual basis > > >> set for Ag as 6-31 is not available for it. > > >> > > >> %chk=clBHA.chk > > >> %mem=20000000 > > >> # opt freq b3lyp/6-31g(d) formcheck output=wfn > > >> > > >> XX clBHAN311.log > > >> > > >> 0 1 > > >> O 1.03535 -1.04284 0.02249 > > >> C 0.41990 0.04621 0.23888 > > >> C -1.06633 0.06016 0.14887 > > >> C -1.75191 -1.11823 0.41903 > > >> C -3.13397 -1.16168 0.35358 > > >> C -3.82195 -0.01875 0.00104 > > >> C -3.16803 1.15775 -0.29437 > > >> C -1.78409 1.19172 -0.22084 > > >> N 1.03103 1.15471 0.56393 > > >> H 0.53306 1.97165 0.81387 > > >> O 2.41620 1.28733 0.63971 > > >> Ag 3.35043 -0.74343 0.20642 > > >> H -1.19437 -1.99336 0.67135 > > >> H -3.66278 -2.06484 0.56731 > > >> Cl -5.62080 -0.06847 -0.08841 > > >> H -3.71992 2.02505 -0.58447 > > >> H -1.27777 2.09764 -0.48124 -- Odon Farkas Associate Professor Laboratory of Chemical Informatics Institute of Chemistry Eötvös Loránd University, Budapest 1/A Pázmány Péter sétány H-1117 Budapest, Hungary From owner-chemistry@ccl.net Wed Jun 28 06:09:00 2006 From: "Irena Efremenko irena.efremenko~!~weizmann.ac.il" To: CCL Subject: CCL:G: NBO visualization Message-Id: <-32041-060627150951-7661-gxeahQjuLmkszjMomR8L4A:_:server.ccl.net> X-Original-From: Irena Efremenko Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 27 Jun 2006 21:12:44 +0300 MIME-Version: 1.0 Sent to CCL by: Irena Efremenko [irena.efremenko.^.weizmann.ac.il] Hi, Search CCL archive. This is quoted from recent post: By default, natural orbitals are not included in the checkpoint file. Use a second job step of this form to place the natural orbitals into the checkpoint file: --Link1-- %Chk=name # IOP(4/5=8,4/38=-1) Guess=(Read,Save,Only) Geom=AllCheck Run the formchk utility on the resulting checkpoint file to prepare the orbitals for visualization. Hope it helps. Irena Eva B lter eva.berssen()mail.uni-oldenburg.de wrote: > Sent to CCL by: "Eva B lter" [eva.berssen|*|mail.uni-oldenburg.de] > Hello! > > I want to plot some G03-generated NBO results with regular programms like Chem3D or others. Trying to visualize some Orbitals ore binding parameters with Molekel failed because of the choice of the basis sets (I used the gen key). > The normal fchk-files only plot the mulliken informations. Is it possible to verify the calculations to get the wanted NBO-informations in an fchk file ore are there other possibilties to plot the informations? > Thank you and greetings > > Eva Blter> > -- ****** Dr. Irena Efremenko Dept. of Organic Chemistry Weizmann Institute of Science 76100 Rehovot, Israel Phone: +972 8 9343680 FAX: +972 8 9344142 Email: irena.efremenko^weizmann.ac.il ****** From owner-chemistry@ccl.net Wed Jun 28 08:31:00 2006 From: "Alessandro Contini alessandro.contini---unimi.it" To: CCL Subject: CCL:G: Gaussian individual basis set Message-Id: <-32042-060628081756-10475-J6a86/9Zlre9zqGUS4Gmrg ~~ server.ccl.net> X-Original-From: Alessandro Contini Content-transfer-encoding: 8BIT Content-type: text/plain; charset=utf-8 Date: Wed, 28 Jun 2006 14:09:59 +0200 MIME-version: 1.0 Sent to CCL by: Alessandro Contini [alessandro.contini-$-unimi.it] Hi Ă–dön, absolutely right, thanks for the comment. Regards, Alessandro Il giorno mer, 28/06/2006 alle 07.35 -0400, Ă–dön Farkas farkas!^! chem.elte.hu ha scritto: > Sent to CCL by: =?iso-8859-15?q?=D6d=F6n_Farkas?= [farkas-,-chem.elte.hu] > > Hi Alessandro, > > Just one comment: when a standard basis set, like 6-31G(d) is used with Gen > than the "6D" keyword should also be applied, since Gen defaults to 5D while > the original 6-31G uses 6D by default. > > dn > > On Tuesday 27 June 2006 17:58, Alessandro Contini > alessandro.contini-.-unimi.it wrote: > > Sent to CCL by: Alessandro Contini [alessandro.contini]=[unimi.it] > > Hi Orlin, > > this is possible in gaussian by using the keyword gen, as in the > > following input example: > > > > %chk=test.chk > > %mem=256MB > > %nproc=1 > > # opt freq b3lyp/gen geom=checkpoint guess=read > > > > title > > > > 0 1 > > > > C H O 0 > > 6-31G(d) > > **** > > Fe 0 > > 6-311+G(3df,2p) > > **** > > > > > > In this case the 6-31G* basis is applied to carbon oxigen (and H) atoms, > > while a more extended basis is applied to iron (NB just an example!!) > > It's also possible to apply a basis set on single atoms by specifing > > their number (see the on line manual at > > http://www.gaussian.com/g_ur/k_gen.htm. ) > > > > Hope this help > > > > Alessandro > > > > > > > > > > > > Il giorno mar, 27/06/2006 alle 08.08 -0400, Orlin Blajiev > > > > blajiev=-=vub.ac.be ha scritto: > > > Sent to CCL by: Orlin Blajiev [blajiev_+_vub.ac.be] > > > Hi, > > > > > > Thank you for the answer. I was wondering is not it possible to have an > > > individual basis set assingment for Ag in particular or for each atom > > > in the structure. It is a possibility in the case of GAMESS, for > > > example. There every atom can be given its own basis set. Therefore, > > > 6-31 can be used for light ones and lesser for the transition metals. > > > > > > Orlin > > > > > > kefalidi(a)chem.auth.gr wrote: > > > > Sent to CCL by: kefalidi-*-chem.auth.gr > > > > Hi Orlin, > > > > > > > > The basis set you asked for the Ag atom is not available because Ag is > > > > a second > > > > row transition metal. For information about all the basis set that you > > > > can use for the Ag atom or any other atom, you can visit the site > > > > http://www.emsl.pnl.gov/forms/basisform.html > > > > > > > > Christos > > > > > > > > Quoting "Orlin Blajiev blajiev_-_vub.ac.be" : > > > >> Sent to CCL by: Orlin Blajiev [blajiev- -vub.ac.be] > > > >> Hi, > > > >> > > > >> I will appreciate some help with the following question. I have the > > > >> following input for Gaussian-how can I ask for a individual basis > > > >> set for Ag as 6-31 is not available for it. > > > >> > > > >> %chk=clBHA.chk > > > >> %mem=20000000 > > > >> # opt freq b3lyp/6-31g(d) formcheck output=wfn > > > >> > > > >> XX clBHAN311.log > > > >> > > > >> 0 1 > > > >> O 1.03535 -1.04284 0.02249 > > > >> C 0.41990 0.04621 0.23888 > > > >> C -1.06633 0.06016 0.14887 > > > >> C -1.75191 -1.11823 0.41903 > > > >> C -3.13397 -1.16168 0.35358 > > > >> C -3.82195 -0.01875 0.00104 > > > >> C -3.16803 1.15775 -0.29437 > > > >> C -1.78409 1.19172 -0.22084 > > > >> N 1.03103 1.15471 0.56393 > > > >> H 0.53306 1.97165 0.81387 > > > >> O 2.41620 1.28733 0.63971 > > > >> Ag 3.35043 -0.74343 0.20642 > > > >> H -1.19437 -1.99336 0.67135 > > > >> H -3.66278 -2.06484 0.56731 > > > >> Cl -5.62080 -0.06847 -0.08841 > > > >> H -3.71992 2.02505 -0.58447 > > > >> H -1.27777 2.09764 -0.48124 > > -- > Odon Farkas > Associate Professor > Laboratory of Chemical Informatics > Institute of Chemistry > Etvs Lornd University, Budapest > 1/A Pzmny Pter stny > H-1117 Budapest, Hungary> > > From owner-chemistry@ccl.net Wed Jun 28 11:11:02 2006 From: "d n Farkas farkas::chem.elte.hu" To: CCL Subject: CCL: G03: IEEE divide by zero Message-Id: <-32043-060628044156-9663-Hgy/nodtYijSnfRONwBHdA..server.ccl.net> X-Original-From: " d n Farkas" Date: Wed, 28 Jun 2006 04:41:55 -0400 Sent to CCL by: " d n Farkas" [farkas|*|chem.elte.hu] Hi, This is very likely related to a linear bend (bond angle which become linear), post the original structure to be sure. Best wishes, dn From owner-chemistry@ccl.net Wed Jun 28 19:03:01 2006 From: "Cory Pye cpye###crux.smu.ca" To: CCL Subject: CCL:G: Gaussian "gauopt utility" Message-Id: <-32044-060628150145-31098-Y8XOOA6B41dGXMIAu8GbyQ*o*server.ccl.net> X-Original-From: Cory Pye Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Wed, 28 Jun 2006 15:03:04 -0300 (ADT) MIME-Version: 1.0 Sent to CCL by: Cory Pye [cpye{=}crux.smu.ca] On Tue, 27 Jun 2006, FAVRE Georges 210344 georges.favre_+_cea.fr wrote: > Sent to CCL by: "FAVRE Georges 210344" [georges.favre:cea.fr] > Dear CCL > > 3 3 T 0.0 0.0 > 7.66V 2.25V 1.24V > # RHF/Gen Test > ... > 1 0 > sto 1s 2 <1 12.10> > sto 2sp 2 <2 12.10> > **** > 2 0 > sto 1s 2 <3 12.10> > **** > 3 0 > sto 1s 2 <3 12.10> > **** > > > > What does the parameter 12.10 mean? I don't understand these values > since they don't have any appearance in the STO-2G basis. 12.10 stands for the Fortran fixed format F12.10, i.e. a field length of 12, with up to 10 points after the decimal. 0 1 2 3 123456789012345678901234567890123456 7.66V 2.25V 1.24V | | | | start of field > Another point which bothers me is the values used for the variables: > 7.66V 2.25V 1.24V > Does anyone could explain me what these values correspond to? > The STO-NG basis sets are optimized for a zeta = 1. Least squares fits of N-Gaussians with an r^2 weighing factor. The values 7.66, 2.25, and 1.24 are the initial values for the optimization corresponding to the oxygen 1s, the oxygen 2sp, and the hysdrogen 1s shells. I am in the process of extending these basis sets to the rest of the periodic table. > > > Thanks and have a great day! > > Regards, > > > Georges Favre> > > ************* ! Dr. Cory C. Pye ***************** ! Associate Professor *** ** ** ** ! Theoretical and Computational Chemistry ** * **** ! Department of Chemistry, Saint Mary's University ** * * ! 923 Robie Street, Halifax, NS B3H 3C3 ** * * ! cpye#%#crux.stmarys.ca http://apwww.stmarys.ca/~cpye *** * * ** ! Ph: (902)-420-5654 FAX:(902)-496-8104 ***************** ! ************* ! Les Hartree-Focks (Apologies to Montreal Canadien Fans)