From owner-chemistry@ccl.net Tue Mar 24 04:43:01 2009 From: "Jon Wright jon{:}gate.sinica.edu.tw" To: CCL Subject: CCL:G: NBO 3.1 in gaussian : d-elements Message-Id: <-38915-090324044110-25756-gK1ftkuwBwW0CU+N/IJaxg#%#server.ccl.net> X-Original-From: Jon Wright Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 24 Mar 2009 16:05:15 +0800 MIME-Version: 1.0 Sent to CCL by: Jon Wright [jon::gate.sinica.edu.tw] Karine, Have you tried a slightly older version of Gaussian? Only last week I emailed them beacause one of our students has been getting very different numbers for Zn in an NBO analysis between g03e1 and g03d2, perhaps you are seeing the same problem he has. I have emailed Gaussian and they are looking into it, perhaps you can also email them with your numbers so that if it is really a problem with g03e1 as our seems to be they know and can check and they might make it a higher priority. Jon > Sent to CCL by: "Karine Costuas" [kcostuas^-^univ-rennes1.fr] > Dear CCLers, > > > We recently bought the GENNBO 5.0. We are currently studying a problem of reactivity in Fe containing complexes with Gaussian. We were surprized to have really different NBO analysis between the NBO 3.1 included in Gaussian 03, and the NBO 5.0 (post-treatment of the file47 obtained with archive keyword). > > Here are the atomic charges we obtained for two characteristic atoms: > > Gaussian 03 E.01 (B3LYP, LANL2DZ + pol) > NBO 3.1: Fe -1.010, C -0.218 > NBO 5.0: Fe -0.167, C -0.158 > > Gaussian 03 E.01 (B3LYP, AHLRICHS DZ all electrons) (same atoms, same geometry) > NBO 3.1: Fe -0.648, C -0.182 > NBO 5.0: Fe +0.414, C -0.38 > > We are facing the same problems for ruthenium systems. I must confess I have difficulties to understand what's going on. Does anyone know if NBO 3.1 takes correctly into accound d orbitals. Moreover, does anyone already face such a change in charges just by modifying the atomic basis set? > > Thanks in advance, sincerely, > > Karine Costuas > CNRS researcher, University of Rennes 1 > France (research in danger here!) > From owner-chemistry@ccl.net Tue Mar 24 05:42:00 2009 From: "Anindita De anindita/./iitk.ac.in" To: CCL Subject: CCL:G: J calculation Message-Id: <-38916-090324035610-21633-FwP/soB0O1X1jLrZz765Yg{:}server.ccl.net> X-Original-From: "Anindita De" Date: Tue, 24 Mar 2009 03:56:05 -0400 Sent to CCL by: "Anindita De" [anindita,,iitk.ac.in] Dear All, I want to determine the J value of an antiferromagnetically coupled dimer using Gaussian 03 programme.Can anyone tell me how to do it ? Regards, Anindita From owner-chemistry@ccl.net Tue Mar 24 07:31:00 2009 From: "Barbara Jagoda-Cwiklik barbara^fh.huji.ac.il" To: CCL Subject: CCL:G: about l502.exe error Message-Id: <-38917-090324072450-6999-CHX/7O48sygNDgN7PGo5Bg{:}server.ccl.net> X-Original-From: Barbara Jagoda-Cwiklik Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 24 Mar 2009 13:18:01 +0200 MIME-Version: 1.0 Sent to CCL by: Barbara Jagoda-Cwiklik [barbara^fh.huji.ac.il] On Mon, Mar 23, 2009 at 10:41 PM, gungun lin lingungun*|*163.com wrote: > > Sent to CCL by: "gungun lin" [lingungun##163.com] > Hi, all: > i have solved the problem l103.exe error with the suggestions by Ol Ga and Denis. > but now i have faced a new problem which obsessed me a whole day. > > Cycle 1 Pass 1 IDiag 1: > FoFCou: FMM=T IPFlag= 0 FMFlag= 990000 FMFlg1= 4097 > NFxFlg= 0 DoJE=T BraDBF=F KetDBF=F FulRan=T. > Symmetry not used in FoFCou. > FMM levels: 4 Number of levels for PrismC: 2 > RepCel: MaxNCR= 5 NClRep= 5 NMtPBC= 5. > Spurious integrated density or basis function: > NE= 78 NElCor= 0 El error=1.98D-01 rel=2.54D-03 Tolerance=1.00D-03 > Shell 18 absolute error=3.64D-02 Tolerance=1.20D-02 > Shell 3 signed error=3.06D-02 Tolerance=1.00D-01 > Inaccurate quadrature in CalDSu. > Error termination via Lnk1e in C:\G03W\l502.exe at Mon Mar 23 21:33:27 2009. > Job cpu time: 0 days 0 hours 11 minutes 48.0 seconds. > File lengths (MBytes): RWF= 265 Int= 0 D2E= 0 Chk= 1 Scr= 1 > --------------------------------------------------------- > > > your suggestions will be appreciated! thanks a lot! > Dear Lin Gungun, You might have seen this page already, but maybe some solutions will be useful to you: http://people.uleth.ca/~stacey.wetmore/errors.html Good luck, Basia -- Barbara Jagoda-Cwiklik, Ph.D The Fritz Haber Research Center for Molecular Dynamics Institute of Chemistry The Hebrew University of Jerusalem Jerusalem, ISRAEL e-mail: barbara##fh.huji.ac.il From owner-chemistry@ccl.net Tue Mar 24 09:05:01 2009 From: "Alex Rudn rudikk99:-:yahoo.com" To: CCL Subject: CCL:G: Process number 3 did not complete successfully. Message-Id: <-38918-090324090148-22903-9RcC0W859CjylMy+pE63nw]![server.ccl.net> X-Original-From: "Alex Rudn" Date: Tue, 24 Mar 2009 09:01:43 -0400 Sent to CCL by: "Alex Rudn" [rudikk99!=!yahoo.com] Dear all, I keep getting the same type of error, submitting my jobs on cluster, I have a feeling that this is something specific for that machine because i run one of the file - with the very same input file on my laptop and it works. Any suggestions how to avoid this error are welcome. ############### ###submission: ################ I have 2 scripts one called asub and the other asub_script asub: #!/bin/tcsh # constants set SCRIPTFILE=asub_script set BSUBCALLBASE='bsub -M 104000 -q' set BSUBQUEUEPRODUCTION=p4-mp4 set BSUBQUEUETEST=p4-short # uncomment this line if testing #set BSUBQUEUE=$BSUBQUEUETEST # uncomment this line if running in production set BSUBQUEUE=$BSUBQUEUEPRODUCTION echo submitting: $BSUBCALLBASE $BSUBQUEUE $SCRIPTFILE # submit the job $BSUBCALLBASE $BSUBQUEUE $SCRIPTFILE ###################### and asub_script: #!/bin/tcsh # constants set WORKDIR=`pwd` echo workdir: $WORKDIR set INEXTENSION=.gjf echo inextension: $INEXTENSION set OUTEXTENSION=.out echo outextension: $OUTEXTENSION # create a working area in local scratch space set SCRATCHDIR=/scratch/$USER mkdir -p $SCRATCHDIR #copy all the source input files to the scratch directory, overwriting cp -f *$INEXTENSION $SCRATCHDIR/ #go to the scratch directory cd $SCRATCHDIR #loop through the source input files #can also be hardcoded as 'foreach INPUTFILE (*.gjf)' foreach INPUTFILE (`ls *$INEXTENSION`) echo inputfile: $INPUTFILE set OUTPUTBASE=`basename $INPUTFILE $INEXTENSION` echo outputbase: $OUTPUTBASE set INPUT=$WORKDIR/$INPUTFILE echo input: $INPUT set OUTPUT=$WORKDIR/$OUTPUTBASE$OUTEXTENSION echo output: $OUTPUT # invoke gaussian (either g98 or g03) g98 <$INPUT>$OUTPUT # print message echo output is in /`hostname -s`$SCRATCHDIR end ############### ###input: ############### %chk=1_C6H5NH2.chk %mem=26MW %nproc=4 # opt=calcfc rb3lyp/6-31+g(d) freq=noraman Title Card Required 0 1 Geometry ############### ###error msg: ############### There are 353 symmetry adapted basis functions of A symmetry. Crude estimate of integral set expansion from redundant integrals=1.000. Integral buffers will be 262144 words long. Raffenetti 2 integral format. Two-electron integral symmetry is turned on. 353 basis functions 604 primitive gaussians 60 alpha electrons 60 beta electrons nuclear repulsion energy 1109.3846698641 Hartrees. One-electron integrals computed using PRISM. Fell through 180 loop in KntVR1. Error termination via Lnk1e in /usr/local/apps/gaussian-98/g98/l302.exe. Job cpu time: 0 days 0 hours 0 minutes .0 seconds. File lengths (MBytes): RWF= 10 Int= 0 D2E= 0 Chk= 8 Scr= 1 Process number 3 did not complete successfully. Error termination via Lnk1e in /usr/local/apps/gaussian-98/g98/l302.exe. Job cpu time: 0 days 0 hours 0 minutes 1.4 seconds. File lengths (MBytes): RWF= 10 Int= 0 D2E= 0 Chk= 8 Scr= 1 From owner-chemistry@ccl.net Tue Mar 24 10:08:01 2009 From: "Saurabh Agrawal Saurabh.Agrawal _ ucdconnect.ie" To: CCL Subject: CCL: RUTILE 110 SURFACE Message-Id: <-38919-090324100322-3766-RCJJW6YIH2T2Zco3kzQUeA=-=server.ccl.net> X-Original-From: Saurabh Agrawal Content-language: en Content-type: multipart/alternative; boundary="Boundary_(ID_1Orkzk8V6IiX2G4St/fgzQ)" Date: Tue, 24 Mar 2009 14:03:07 +0000 (GMT) MIME-version: 1.0 Sent to CCL by: Saurabh Agrawal [Saurabh.Agrawal^ucdconnect.ie] This is a multi-part message in MIME format. --Boundary_(ID_1Orkzk8V6IiX2G4St/fgzQ) Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: QUOTED-PRINTABLE Content-disposition: inline Hello, Thank you Dr Stephen Todd, Dr. Andreas Bick and Dave for your respons= e and help. Sincere regards, Saurabh ----- Original Message ----- =46rom: "Close, David M. CLOSED%mail.etsu.edu" Date: Monday, March 23, 2009 8:31 pm Subject: CCL: RUTILE 110 SURFACE To: "Agrawal, Saurabh " > Saurabh: > =A0 You need to look in a book on cry= stallography.=A0 Rutile forms in tetragonal prisms.=A0 The plane you = want (1,1,0) is the cleavage plane. > Anyway, these three numbers ar= e the Miller indices. =A0=A0The plane you are looking for is one full= lattice spacing in the a-direction, one full lattice spacing in the = b-direction, an no displacement in the c-direction. If you have acces= s to an elementary graphics program, you can input the coordinates yo= u supplied, the lattice constants you supplied, and the program will = draw the unit cell.=A0 From this you can determine the cleavage plane= . > =A0 Regards, Dave Close. =A0 > From: owner-chemistry+closed= =3D=3Detsu.edu^^^ccl.net [mailto:owner-chemistry+closed=3D=3Detsu.edu= ^^^ccl.net] On Behalf Of Saurabh Agrawal Saurabh.Agrawal:+:ucdconnect= .ie > Sent: Monday, March 23, 2009 9:07 AM > To: Close, David M. > Subject: CCL: RUTILE 110 SURFACE =A0 > Dear CCL Subscribers, =20 > I am trying to make 110 rutile surface form the 1x1 lattice coordi= nates given below. I could replicate the surface using moe software. = But I am not sure which side of the surface is 110. Any information o= r tutorial helpful to solve this problem would be of much help for me= . =20 =20 > HETATM=A0=A0=A0 1 TI=A0=A0=A0=A0 *=A0=A0=A0=A0 1=A0=A0=A0=A0=A0= =A0 0.000=A0=A0 0.000=A0=A0 0.000=A0 1.00=A0 0.00=A0=A0=A0=A0=A0=A0= =A0=A0=A0 TI=A0=20 > HETATM=A0=A0=A0 2 O=A0=A0=A0=A0=A0 *=A0=A0=A0=A0 1=A0=A0=A0=A0= =A0=A0 1.400=A0=A0 1.400=A0=A0 0.000=A0 1.00=A0 0.00=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0 O=A0=20 > HETATM=A0=A0=A0 3 O=A0=A0=A0=A0=A0 *=A0=A0=A0=A0 1=A0=A0=A0=A0= =A0 -1.400=A0 -1.400=A0=A0 0.000=A0 1.00=A0 0.00=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0 O=A0=20 > HETATM=A0=A0=A0 4 TI=A0=A0=A0=A0 *=A0=A0=A0=A0 1=A0=A0=A0=A0=A0= =A0 2.296=A0=A0 2.296=A0=A0 0.000=A0 1.00=A0 0.00=A0=A0=A0=A0=A0=A0= =A0=A0=A0 TI=A0=20 > HETATM=A0=A0=A0 5 O=A0=A0=A0=A0=A0 *=A0=A0=A0=A0 1=A0=A0=A0=A0= =A0 -0.896=A0=A0 0.896=A0 -1.479=A0 1.00=A0 0.00=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0 O=A0=20 > HETATM=A0=A0=A0 6 O=A0=A0=A0=A0=A0 *=A0=A0=A0=A0 1=A0=A0=A0=A0= =A0=A0 0.896=A0 -0.896=A0 -1.479=A0 1.00=A0 0.00=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0 O=A0=20 > END =20 > Thanking you in advance. =20 > Saurabh =20 Saurabh Agrawal, PhD Student, Department of Chemical and Bioprocess Engineering, UCD, Belfield, Dublin-4, Ireland --Boundary_(ID_1Orkzk8V6IiX2G4St/fgzQ) Content-type: text/html; charset=us-ascii Content-transfer-encoding: QUOTED-PRINTABLE Content-disposition: inline Hello,

Thank you Dr Stephen Todd, Dr. Andreas Bick and Dav= e for your response and help.

Sincere regards,

Saurabh<= br>




----- Original Message -----
From: "= Close, David M. CLOSED%mail.etsu.edu" <owner-chemistry..ccl.net>=
Date: Monday, March 23, 2009 8:31 pm
Subject: CCL: RUTILE 110 = SURFACE
To: "Agrawal, Saurabh " <Saurabh.Agrawal..ucdcon= nect.ie>

=

=

> Saurabh:

> <= /font>  You need to look in a book on crystallography.  Rut= ile forms in tetragonal prisms.  The plane you want (1,1,0) is t= he cleavage plane.

> Anyway, these three numbers are the Mille= r indices.   The plane you are looking for is one full latt= ice spacing in the a-direction, one full lattice spacing in the b-dir= ection, an no displacement in the c-direction. If you have access to = an elementary graphics program, you can input the coordinates you sup= plied, the lattice constants you supplied, and the program will draw = the unit cell.  From this you can determine the cleavage plane.<= o:p>

>= ;   Regards, Dave Close.

&nb= sp;

> From: owner-ch= emistry+closed=3D=3Detsu.edu^^^ccl.net [mailto:owner-chemistry+closed= =3D=3Detsu.edu^^^ccl.net] On Behalf Of Saurabh Agrawal Saurabh= .Agrawal:+:ucdconnect.ie
> Sent: Monday, March 23, 2009 9:07 AM
> To: Close, Da= vid M.
> = Subject: CCL: RUTILE 110 SURFACE

<= p class=3D"MsoNormal"> 

<= font style=3D"font-style: normal; font-weight: normal; background-col= or: rgb(245, 248, 240); font-size: 14px;">> Dear CCL Subscr= ibers,

> I am trying to make 110 rutile surface form the 1x1 lattice coordin= ates given below. I could replicate the surface using moe software. B= ut I am not sure which side of the surface is 110. Any information or= tutorial helpful to solve this problem would be of much help for me.=


> = HETATM    1 TI     *  &= nbsp;  1       0.000   0= .000   0.000  1.00  0.00    &= nbsp;     TI 
> HETATM    2 O  = ;    *     1   &nbs= p;   1.400   1.400   0.000  1.00&n= bsp; 0.00          = O 
> = HETATM    3 O      * &nb= sp;   1      -1.400  -1.400&n= bsp;  0.000  1.00  0.00     &= nbsp;     O 
> HETATM    4 TI  = ;   *     1    &nbs= p;  2.296   2.296   0.000  1.00  0= .00          TI  > HETATM = ;   5 O      *   &n= bsp; 1      -0.896   0.896  -= 1.479  1.00  0.00       =     O 
> HETATM    6 O    = ;  *     1     &nbs= p; 0.896  -0.896  -1.479  1.00  0.00  &= nbsp;        O 
> END

> Thanking you in advance= .

> Sau= rabh

 =

Saurabh Agrawal,
PhD Student,
Department of Chemical an= d Bioprocess Engineering,
UCD, Belfield,
Dublin-4, Ireland
--Boundary_(ID_1Orkzk8V6IiX2G4St/fgzQ)-- From owner-chemistry@ccl.net Tue Mar 24 13:15:01 2009 From: "Anu Bamgbelu anubamgbelu~!~yahoo.com" To: CCL Subject: CCL:G: TD-DFT Message-Id: <-38920-090324130034-13784-+PuBWMeW6n3BXZDYsiUzyw]=[server.ccl.net> X-Original-From: Anu Bamgbelu Content-Type: multipart/alternative; boundary="0-1838130578-1237910423=:38905" Date: Tue, 24 Mar 2009 09:00:23 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Anu Bamgbelu [anubamgbelu * yahoo.com] --0-1838130578-1237910423=:38905 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi, You can check this journal for the theory and applications of TDDFT. The Journal of Chemical Physics 124, 094107 (2006). Hope it helps thanks anu --- On Fri, 3/20/09, taner atalar taneratalar%%gmail.com wrote: > From: taner atalar taneratalar%%gmail.com Subject: CCL:G: TD-DFT To: "Adegoke, Anu " Date: Friday, March 20, 2009, 1:02 AM Hi, =A0 I am the beginner for the TD-DFT learning by using the Gaussian 03 w, so ar= e there any good sources and/or references for learning TD-DFT (freely avai= lable) ? =A0 Also any=A0useful=A0materials=A0about the Gaussian usage and about=A0output= interpretation=A0for this method (TD-DFT) ? =A0 I tried to do some calculations by using TD-DFT with Gaussian 03 W, unfortu= nately all the my calculations terminated with errors. =A0 Any suggestions? or Any help ? =A0 =A0 Thank you very much in advance, =A0 Taner Atalar=0A=0A=0A --0-1838130578-1237910423=:38905 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hi,
You can check this journal for the theory and applications of TDDFT.
The Journal of Chemical Physics 124, 094107 (2006).
Hope it helps
thanks
anu

--- On Fri, 3/20/09, taner atalar taneratalar%%gmail.com= <owner-chemistry#%#ccl.net> wrote:

From: taner atalar taneratalar%%gmail.com <own= er-chemistry#%#ccl.net>
Subject: CCL:G: TD-DFT
To: "Adegoke, Anu -id= #44i-" <anubamgbelu#%#yahoo.com>
Date: Friday, March 20, 2009, 1:02 = AM

Hi,
 
I am the beginner for the TD-DFT learning by using the Gaussian 03 w, = so are there any good sources and/or references for learning TD-DFT (freely= available) ?
 
Also any useful materials about the Gaussian usage and = about output interpretation for this method (TD-DFT) ?
 
I tried to do some calculations by using TD-DFT with Gaussian 03 W, un= fortunately all the my calculations terminated with errors.
 
Any suggestions? or Any help ?
 
 
Thank you very much in advance,
 
Taner Atalar

=0A=0A=0A= =0A --0-1838130578-1237910423=:38905-- From owner-chemistry@ccl.net Tue Mar 24 17:13:01 2009 From: "Starr Hazard hazards]^[musc.edu" To: CCL Subject: CCL:G: gaussian versus gamess commands Message-Id: <-38921-090324170833-11409-gu7g1hgt+uOKLCJ49kwThg/./server.ccl.net> X-Original-From: "Starr Hazard" Date: Tue, 24 Mar 2009 17:08:28 -0400 Sent to CCL by: "Starr Hazard" [hazards()musc.edu] Folks, I have a Gaussian *.com file as a template for a process I wish to explore. I do not have a Gaussian License. I have installed GAMESS and I am trying to task GAMESS as nearly as possible to perform the Gaussian procedure. The Gaussian *.com file has this line #MP2/6-31G* OPT POP=(MK,DIPOLE) DENSITY=CURRENT How would I translate these two elements "POP=(MK,DIPOLE)", "DENSITY=CURRENT" into comparable elements of a GAMESS *inp file? Thanks, Starr