From owner-chemistry@ccl.net Thu Nov 25 01:36:00 2010 From: "Horkel, Ernst ehorkel|-|ioc.tuwien.ac.at" To: CCL Subject: CCL:G: AW: G: Gaussian 09 - Problems with TDDFT geometry optimization Message-Id: <-43222-101125013413-22525-qnFGuHQYivgPpzzCA9hPVQ\a/server.ccl.net> X-Original-From: "Horkel, Ernst" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 25 Nov 2010 07:35:50 +0100 MIME-Version: 1.0 Sent to CCL by: "Horkel, Ernst" [ehorkel_._ioc.tuwien.ac.at] Hello, yes, this seems to bet he solution, I started a separated job last night and the frequencies are still alive and running :-). Thanks to you and Theis (private email communication) for help! Ernst _______________________________________________________________ Univ.Ass. Dipl.-Ing. Dr.techn. Ernst Horkel Institute of Applied Synthetic Chemistry, Vienna University of Technology Tel.: +43-1-58801-15411 Getreidemarkt 9/163OC, +43-644-60588-7122 A-1060 Vienna, Austria Fax: +43-1-58801-15499 email: ehorkel##ioc.tuwien.ac.at -----Ursprüngliche Nachricht----- Von: owner-chemistry+ehorkel==ioc.tuwien.ac.at##ccl.net [mailto:owner-chemistry+ehorkel==ioc.tuwien.ac.at##ccl.net] Im Auftrag von Jamin Krinsky krinsky.jamin%gmail.com Gesendet: Mittwoch, 24. November 2010 21:28 An: Horkel, Ernst Betreff: CCL:G: Gaussian 09 - Problems with TDDFT geometry optimization Sent to CCL by: Jamin Krinsky [krinsky.jamin#,#gmail.com] Dear Ernst, Nobody has replied to this so I'll give it an educated guess. It could be something about specifying what is actually two-part job, the "opt freq" keyword combination. Gaussian must do numerical frequencies for TD jobs and maybe the keywords generated automatically for the second (frequency) part are not compatible with that method. I would do the two parts separately anytime the first part works and the second doesn't. You already have the optimization part done, so make a copy of the .chk file from that job with a new name (newfile.chk for example below) and make a new input like this: %nprocshared=8 %mem=4GB %chk=newfile.chk # freq td=(singlets,nstates=6,root=1) hf/6-31g(d,p) geom=checkpoint guess=read frequency part of calc 0 1 {make sure to put a few blank lines here!!!} You could also include the "read" option in the TD keyword to save some time but I can't remember exactly how that ends up behaving in these kinds of jobs. Regards, Jamin On Mon, Nov 22, 2010 at 4:42 AM, Ernst Horkel ehorkel++ioc.tuwien.ac.at wrote: > > Sent to CCL by: "Ernst  Horkel" [ehorkel=-=ioc.tuwien.ac.at] > Dear all, > > I intend to simulate electronic spectra of organic compunds using TDDFT level of theory. For this purpose I want to perform a geometry optimization of the 1st excited state (of benzene as an example) and an vibrational analysis of the minimum found. Unfortunately, the job fails and I have no idea why. IMHO the first job (geometry optimization) succeeds, but the second one doesn't. > > I am using G09 on a 8 core Opteron machine (all 8 cores, 4 GB RAM) > > So this is the (partial) output: > > -----SNIP------- > >   D24       -0.00016   0.00000   0.00000   0.00007   0.00007  -0.00009 >         Item               Value     Threshold  Converged? >  Maximum Force            0.000048     0.000450     YES >  RMS     Force            0.000017     0.000300     YES >  Maximum Displacement     0.000107     0.001800     YES >  RMS     Displacement     0.000032     0.001200     YES >  Predicted change in Energy=-1.673574D-08 >  Optimization completed. >    -- Stationary point found. >                           ---------------------------- >                           !   Optimized Parameters   ! >                           ! (Angstroms and Degrees)  ! >  --------------------------                            -------------------------- >  ! Name  Definition              Value          Derivative Info.                ! >  -------------------------------------------------------------------------------- >  ! R1    R(1,2)                  1.4138         -DE/DX =    0.0                 ! > > -----SNAP----- > > so this seems to tell me geometry optimization is OK; > > -----SNIP------- > > ZZZY=              0.0003 XXYY=            -89.8781 XXZZ=            -63.1837 YYZZ=            -63.1836 >  XXYZ=             -0.0003 YYXZ=             -0.0010 ZZXY=              0.0000 >  N-N= 2.014646440196D+02 E-N=-9.396066542997D+02  KE= 2.300858570874D+02 >  1\1\GINC-MASTER\FOpt\RTD-HF-FC\6-31G(d,p)\C6H6\HANMIK\22-Nov-2010\0\\# >  opt freq td=(singlets,nstates=6,root=1) hf/6-31g(d,p) geom=connectivi >  ty\\benzol-test tddft\\0,1\C,6.5168316274,1.2693566194,0.001738384\C,7 >  .9306171845,1.2692925681,0.0021804376\C,8.637562195,2.4936128114,0.001 >  6217232\C,7.930730751,3.7180250171,0.0006395457\C,6.5169664187,3.71808 >  94956,0.0001753444\C,5.8100105637,2.4937526246,0.000783884\H,5.9799138 >  434,0.3394581721,0.0021016335\H,8.467444507,0.3393399532,0.0029641075\ >  H,9.7113385438,2.4935793196,0.0019875469\H,8.4676875942,4.6479015869,0 >  .0002526738\H,5.980104819,4.6480239866,-0.0007186233\H,4.7362355123,2. >  4938321253,0.0004983426\\Version=AM64L-G09RevA.02\State=1-A\HF=-230.70 >  92354\RMSD=2.128e-09\RMSF=3.164e-05\Dipole=0.0000005,0.,-0.0000154\PG= >  C01 [X(C6H6)]\\_._ > > >  The arm of the moral universe is long, but it bends toward justice. >  -- Martin Luther King, Jr. >  Job cpu time:  0 days  0 hours 12 minutes  2.7 seconds. >  File lengths (MBytes):  RWF=     47 Int=      0 D2E=      0 Chk=      5 Scr=      1 >  Normal termination of Gaussian 09 at Mon Nov 22 13:16:17 2010. >  Link1:  Proceeding to internal job step number  2. >  ---------------------------------------------------------------------- >  #N Geom=AllCheck Guess=TCheck SCRF=Check GenChk RTD-HF(FC)/6-31G(d,p) >  Freq >  ---------------------------------------------------------------------- >  QPErr --- A syntax error was detected in the input line. >  Check SCRF=Check GenChk RTD-HF(FC)/6-31G >                               ' >  Last state="GCL" >  TCursr= 1046 LCursr=   54 >  Error termination via Lnk1e in /opt/g09/l1.exe at Mon Nov 22 13:16:17 2010. >  Job cpu time:  0 days  0 hours  0 minutes  0.2 seconds. >  File lengths (MBytes):  RWF=     47 Int=      0 D2E=      0 Chk=      5 Scr=      1 > > ------SNAP------- > > This are the last lines of the log file; This tells me there is a syntax error, which I do not understand... > > Here is the (complete) input: > > > %nprocshared=8 > %mem=4GB > %chk=benzene_tddft.chk > # opt freq td=(singlets,nstates=6,root=1) hf/6-31g(d,p) geom=connectivity > > benzol-test tddft > > 0 1 >  C                  6.52617188    1.28567244    0.00167800 >  C                  7.92133188    1.28567244    0.00167800 >  C                  8.61886988    2.49342344    0.00167800 >  C                  7.92121588    3.70193244    0.00047900 >  C                  6.52639088    3.70185444    0.00000000 >  C                  5.82878988    2.49364844    0.00099600 >  H                  5.97641288    0.33335544    0.00212800 >  H                  8.47083988    0.33315944    0.00299300 >  H                  9.71854988    2.49350344    0.00231200 >  H                  8.47141588    4.65407544    0.00042000 >  H                  5.97626888    4.65413544   -0.00095300 >  H                  4.72918588    2.49383144    0.00081600 > >  1 2 1.5 6 1.5 7 1.0 >  2 3 1.5 8 1.0 >  3 4 1.5 9 1.0 >  4 5 1.5 10 1.0 >  5 6 1.5 11 1.0 >  6 12 1.0 >  7 >  8 >  9 >  10 >  11 >  12 > > Btw, the input was generated using GaussView 5.0; so it should be OK? > > So my questions are: > > 1.) is it possible to perform the job in the way I intend to? > 2.) is the input correct? > 3.) what else can be wrong? > > Any ideas or hints are really welcome. > > Thank you in advance, > > Ernst Horkel, > > ehorkel_._ioc.tuwien.ac.at>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txthttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Thu Nov 25 02:35:00 2010 From: "Tamas Gunda tgunda2\a/puma.unideb.hu" To: CCL Subject: CCL:G: Gaussian output problem Message-Id: <-43223-101125023117-21089-xBBwPnn+gjcOCqifGi3PHQ!A!server.ccl.net> X-Original-From: "Tamas Gunda" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Thu, 25 Nov 2010 08:31:09 +0100 MIME-Version: 1.0 Sent to CCL by: "Tamas Gunda" [tgunda2:-:puma.unideb.hu] Maciek, You can fix it in a few minutes with Mol2mol. It has an option to read any user defined format of coordinates. In this case the first and third data columns simply should be regarded as dummy data, so the program simply skipes them. Thus, the format string should be: d a d x y z (this is for dummy, atom numbers, dummy, x,y,z) Having inputted the data they can be outputted in many formats. Hava look at www.gunda.hu/mol2mol Tamas Gunda -------------------------------------------------- > From: "Maciej Maslyk maciejmarcin.maslyk .. ceu.es" Sent: Tuesday, November 23, 2010 14:45 PM To: "Gunda, Tamas E " Subject: CCL:G: Gaussian output problem > > Sent to CCL by: "Maciej Maslyk" [maciejmarcin.maslyk-,-ceu.es] > Hi everyone, > could you help me with one problem, please? Every time I'm running G03 job > I got problem with outputs. The problem is that I cannot extract > structures because there are stars **** instead of atom numbers higher > than 9999. Have you ever had this problem in your calculation if you had > more than 9999 atoms in the system? > > It looks like this in output: > 9995 1 20001030 -12.655571 46.600810 32.540627 > 9996 1 20001030 -12.533484 47.134581 33.952118 > 9997 8 20001021 2.441067 -19.529269 31.331119 > 9998 1 20001030 2.813824 -19.307495 32.184450 > 9999 1 20001030 1.933916 -20.325103 31.491166 > **** 8 20001021 37.587292 -11.572024 28.812192 > **** 1 20001030 37.333847 -11.927328 27.960694 > **** 1 20001030 38.095189 -12.272395 29.221488 > **** 8 20001021 23.735956 -43.072924 13.135294 > **** 1 20001030 23.388276 -42.182008 13.115359 > **** 1 20001030 22.974070 -43.624340 13.312930 > > Do you have any suggestions? > > Thanks in advance > > Maciek> > From owner-chemistry@ccl.net Thu Nov 25 04:48:00 2010 From: "turker akcay turkerakcay---hotmail.com" To: CCL Subject: CCL:G: ONIOM error Message-Id: <-43224-101125044628-1179-UZ1TQc86t5Y7AiMc9n8K8w]-[server.ccl.net> X-Original-From: "turker akcay" Date: Thu, 25 Nov 2010 04:46:25 -0500 Sent to CCL by: "turker akcay" [turkerakcay++hotmail.com] Dear CCLlers I have tried to optimize a structure containing copper metal in core center and I used the ONIOM method. But I met an error message. Could you help me, please ****************************************** %rwf=CuPc-OptIr-DFT631G-PM3MM-ultrafine.rwf %nosave %chk=C:\Users\TURKR\Desktop\PC yeni\ONIOM\CuPc-OptIr-DFT631G-PM3MM- ultrafine.chk %mem=100MW %nprocshared=1 Will use up to 1 processors via shared memory. Default route: MaxDisk=2000MB ---------------------------------------------------------------------- #p opt=(tight,maxcycle=512,gdiis) freq=noraman oniom(b3lyp/6-31g:pm3mm ) geom=connectivity int=ultrafine scf=maxcycle=512 ---------------------------------------------------------------------- 1/6=512,7=10,14=-1,18=20,19=11,26=3,38=1,52=2,57=2/1,3; 2/9=110,17=6,18=5,40=1/2; 1/6=512,14=-1,18=20,19=11,38=1,52=2,53=3172/20; .......... .......... ONIOM: Cut between C /H 10 and O 9 factor= 0.686809 0.686809 ONIOM: Cut between C /H 92 and O 91 factor= 0.686809 0.686809 ONIOM: Cut between C /H 131 and O 130 factor= 0.686809 0.686809 ONIOM: Cut between C /H 171 and O 170 factor= 0.686809 0.686809 ONIOM: saving gridpoint 17 ONIOM: generating point 3 -- low level on real system. Leave Link 120 at Thu Nov 25 11:42:56 2010, MaxMem= 104857600 cpu: 0.0 (Enter C:\G03W\l301.exe) Standard basis: VSTO-3G (5D, 7F) There are 620 symmetry adapted basis functions of A symmetry. Integral buffers will be 262144 words long. Raffenetti 2 integral format. Two-electron integral symmetry is turned on. 620 basis functions, 1860 primitive gaussians, 620 cartesian basis functions 326 alpha electrons 325 beta electrons nuclear repulsion energy 11121.7860281271 Hartrees. Warning! Cu atom 209 has 11 valence electrons but only 4 basis functions. This is less than a minimal basis set! IExCor= 0 DFT=F Ex=HF Corr=None ExCW=0 ScaHFX= 1.000000 ScaDFX= 1.000000 1.000000 1.000000 1.000000 IRadAn= 5 IRanWt= -1 IRanGd= 0 ICorTp=0 NAtoms= 209 NActive= 209 NUniq= 209 SFac= 1.00D+00 NAtFMM= 60 Big=T Leave Link 301 at Thu Nov 25 11:42:58 2010, MaxMem= 104857600 cpu: 0.0 (Enter C:\G03W\l401.exe) Simple Huckel Guess. NBasis= 620 NMin= 625 so simple Huckel guess is impossible. Error termination via Lnk1e in C:\G03W\l401.exe at Thu Nov 25 11:43:02 2010. Job cpu time: 0 days 0 hours 0 minutes 12.0 seconds. File lengths (MBytes): RWF= 52 Int= 0 D2E= 0 Chk= 1 Scr= 1 From owner-chemistry@ccl.net Thu Nov 25 09:30:01 2010 From: "Herbert Fruchtl herbert.fruchtl-.-st-andrews.ac.uk" To: CCL Subject: CCL: Question on calculation of charge center of electrons in a molecule Message-Id: <-43226-101125035702-4803-DoaHEffzPwSKE6uS41m7qA-,-server.ccl.net> X-Original-From: Herbert Fruchtl Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 25 Nov 2010 08:56:34 +0000 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl*_*st-andrews.ac.uk] I don't have time to look at the maths of it, but I think the centre of charge of the electron density should be identical to the centre of the Mulliken charges, which would be easy to calculate (analogous to the centre of mass). Herbert Gegham Galstyan gegham * chemie.fu-berlin.de wrote: > Sent to CCL by: "Gegham Galstyan" [gegham^_^chemie.fu-berlin.de] > Dear CCLers, > > I need to calculate the charge center of electrons in a small organic molecule. Is there any program that is able to do that? > Many thanks beforehand. > > Best wishes, > Gegham Galstyan > > Free University Berlin > Institut fr Chemie und Biochemie > Fabeckstrae 36a > 14195 Berlin > > mailto: gegham,,chemie.fu-berlin.de> > -- Herbert Fruchtl Senior Scientific Computing Officer School of Chemistry, School of Mathematics and Statistics University of St Andrews -- The University of St Andrews is a charity registered in Scotland: No SC013532 From owner-chemistry@ccl.net Thu Nov 25 12:00:00 2010 From: "=?ISO-8859-1?Q?Ulf_Ekstr=F6m?= ulfek(~)few.vu.nl" To: CCL Subject: CCL: Question on calculation of charge center of electrons in a molecule Message-Id: <-43227-101125115832-20540-OBtMms360IT1noGRDqvxNw()server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Ulf_Ekstr=F6m?= Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 25 Nov 2010 17:58:25 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Ulf_Ekstr=F6m?= [ulfek],[few.vu.nl] On Thu, Nov 25, 2010 at 9:56 AM, Herbert Fruchtl herbert.fruchtl-.-st-andrews.ac.uk wrote: > > Sent to CCL by: Herbert Fruchtl [herbert.fruchtl*_*st-andrews.ac.uk] > I don't have time to look at the maths of it, but I think the centre of > charge of the electron density should be identical to the centre of the > Mulliken charges, which would be easy to calculate (analogous to the centre > of mass). This will not work, for example if you have a single centre basis set all Mulliken charge would be on that center. What you should do is to compute the dipole moment of the molecule and use that to work out the center of charge. Sincerely, Ulf Ekstrom From owner-chemistry@ccl.net Thu Nov 25 17:24:00 2010 From: "rocky walden rocky.walden19%a%gmail.com" To: CCL Subject: CCL: suggestions needed..... Message-Id: <-43228-101125105247-8101-RwfKvVQGXEpiuB5zSlYXlw^-^server.ccl.net> X-Original-From: rocky walden Content-Type: multipart/alternative; boundary=00163642707e889dac0495e298e4 Date: Thu, 25 Nov 2010 16:52:41 +0100 MIME-Version: 1.0 Sent to CCL by: rocky walden [rocky.walden19=-=gmail.com] --00163642707e889dac0495e298e4 Content-Type: text/plain; charset=ISO-8859-1 Dear CCL users. Thank you for your valuable time. I am working on organometallic Compounds containing 6 carbon atoms with a Metal atom Pt, Re, pd. Now i am planning to optimize them geometrically. I am also looking forward to continue my work focusing the development of forcefields that which can explicitly to treat Metal atoms (like Pt, Pd, Os, Re, Ru, Fe) containing Organic compounds. So i kindly request all the computational chemistry experts. please suggest me how to start from scratch for the development of the forcefield for specially Metal atom containing Organic Compounds. I also kindly request you to post me some links or some references literature. This is very helpful to me. Excuse me for my bad english. Thank you in advance. Regards Walden --00163642707e889dac0495e298e4 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear CCL users.
=A0=A0 Thank you for your val= uable time.
=A0=A0 I am working on organometallic Compounds containing 6= carbon atoms with a Metal atom Pt, Re, pd.
=A0=A0 Now i am planning to = optimize them geometrically.
=A0=A0 I am also looking forward to continue my work focusing the developme= nt of forcefields that which can explicitly=A0 to treat Metal atoms (like P= t, Pd, Os, Re, Ru, Fe) containing Organic compounds.
=A0 So i kindly request all the computational chemistry experts. please sug= gest me how to start from scratch=A0 for the development of the forcefield = for specially Metal atom containing Organic Compounds.

I also kindly= request you to post me some links or some references literature.
This is very helpful to me.

Excuse me for my bad english.
Thank y= ou in advance.


Regards
Walden

=

--00163642707e889dac0495e298e4--