From owner-chemistry@ccl.net Sat Nov 23 17:58:00 2013 From: "Cory Pye cpye---ap.smu.ca" To: CCL Subject: CCL:G: Failure Restarting Gaussian 09 Jobs Message-Id: <-49362-131121144042-27322-6bAn2uemoNggSMc2e4EUAg|,|server.ccl.net> X-Original-From: Cory Pye Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Thu, 21 Nov 2013 15:55:41 -0400 (AST) MIME-Version: 1.0 Sent to CCL by: Cory Pye [cpye\a/ap.smu.ca] Greetings from down the road. I think the problem comes from your use of ctrl-C. If you do a hard interrupt on a Gaussian job, it sometimes crashes in the middle of writing to the checkpoint file, or before it has a chance to. In other cases, the queueing system kills a job after say 48:00:00 hours, but the job hasn't yet finished, or it is in the middle of writing to the checkpoint file. It should work if you let the Gaussian program die on its own, as then it will write what it needs to the checkpoint file before error termination. -Cory On Wed, 20 Nov 2013, Douglas B. Staple dstaple^_^dal.ca wrote: > > Sent to CCL by: "Douglas B. Staple" [dstaple[*]dal.ca] > Hi Andrew, > > Yes, I can find the checkpoint file, but apparently Gaussian can't. > Good idea to try an absolute path, I didn't know that was possible. I > tried: > %Chk=/home/dstaple/temp/benzene > and > %Chk=/home/dstaple/temp/benzene.chk > > Unfortunately both gave the same error as before. > > Thanks, > > Doug > > > > > -- > Douglas B. Staple, Dr. rer. nat. > Department of Physics and Atmospheric Science > Dalhousie University > Halifax NS B3H 4R2 > Canada > > > > On 2013-11-20 1:03 PM, Andrew Yeung wrote: > > Hi Douglas > > > > Can Gaussian find the checkpoint file? Can you? > > > > How about using an explicit reference to the checkpoint file rather > > than an implicit reference? > > > > My checkpoint files have an extension of .chk. I'm not sure if > > Gaussian expects it. > > > > Andrew Yeung > > Donald J. Darensbourg Research Group > > Department of Chemistry, Texas A&M University > > 3255 TAMU > > College Station, TX 77843-3255 > > > > Tel: 979 845 4837 > > Fax: 979 845 0158 > > > > On 2013-11-20 10:11 AM, Douglas B. Staple dstaple^^^dal.ca wrote: > >> Sent to CCL by: "Douglas B. Staple" [dstaple~~dal.ca] > >> For some reason I can't get Gaussian 09 to restart jobs that are > >> prematurely terminated. Here is a test job: > >> http://myweb.dal.ca/~dstaple/benzene.gjf > >> Obviously the real jobs that are causing me issues are larger than > >> benzene, but the errors are exactly the same. > >> > >> I terminate the geometry optimization by hitting ctrl+C and then try > >> to restart the job using a new benzene.gjf file with the following form: > >> %NProcShared=8 > >> %Mem=10GB > >> %Chk=benzene > >> # PBEPBE/AUG-cc-pVDZ SCF(NoVarAcc,Fermi,XQC) > >> Integral(Grid=UltraFine,Acc2E=12) Opt=Restart > >> > >> I've tried various modifications to the route line, such as: > >> # SCF(NoVarAcc,Fermi,XQC) Integral(Grid=UltraFine,Acc2E=12) Opt=Restart > >> or: > >> # PBEPBE/AUG-cc-pVDZ SCF(NoVarAcc,Fermi,XQC) > >> Integral(Grid=UltraFine,Acc2E=12) Opt Geom=AllCheck Guess=Read > >> > >> Each time, I get output that contains the error "FileIO operation on > >> non-existent file", ultimately terminating in a segmentation > >> violation. I uploaded typical output (stdout and stderr) here: > >> http://myweb.dal.ca/~dstaple/benzene.e > >> http://myweb.dal.ca/~dstaple/benzene.o > >> > >> To make matters worse, the "real" jobs I'm interested in restarting > >> are multi-part jobs consisting of geometry optimization plus polarity > >> calculation, i.e. more like: > >> http://myweb.dal.ca/~dstaple/benzene_multipart.gjf > >> I know this changes things, but until I can get a geometry > >> optimization to restart it seems senseless to look at the multi-part > >> jobs. > >> > >> What am I doing wrong? > >> > >> Thanks, > >> > >> Douglas Staple > >> dstaple]*[dal.ca> > ************* ! 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) From owner-chemistry@ccl.net Sat Nov 23 18:33:00 2013 From: "Jandir Joaquim Passos jandirj_-_hotmail.com" To: CCL Subject: CCL: DCV4T:C60 Message-Id: <-49363-131123163924-14590-sio+KXhBFPkf/hV0+JZjfQ-*-server.ccl.net> X-Original-From: "Jandir Joaquim Passos" Date: Sat, 23 Nov 2013 16:39:23 -0500 Sent to CCL by: "Jandir Joaquim Passos" [jandirj..hotmail.com] I`m studying about organic sollar cells and my system just chosen for it is the DCV4:C60. Well, for begin my studies I need of cartesian coordinates of this system(I use TURBOMOLE). So, I glad if anyone can help me. Regards, Jandir From owner-chemistry@ccl.net Sat Nov 23 19:08:00 2013 From: "Julien Thibault tchetchenko%gmail.com" To: CCL Subject: CCL: API for the Basis Set Exchange Message-Id: <-49364-131123164541-25062-HOJV7llBnpjLB91k3jRRRA|,|server.ccl.net> X-Original-From: Julien Thibault Content-Type: multipart/alternative; boundary=001a1132e6e20a20f404ebdf0d72 Date: Sat, 23 Nov 2013 14:45:35 -0700 MIME-Version: 1.0 Sent to CCL by: Julien Thibault [tchetchenko=gmail.com] --001a1132e6e20a20f404ebdf0d72 Content-Type: text/plain; charset=ISO-8859-1 Hi, I was wondering if anybody was aware of an open-source distribution of the the basis set exchange database (https://bse.pnl.gov/bse/portal) so that people can install it locally and/or access the database through an API (REST? Java?) Regards, ~Julien -- Julien Thibault University of Utah Department of Biomedical Informatics Salt Lake City, UT --001a1132e6e20a20f404ebdf0d72 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hi,=A0
I was wondering if anybody was aware of an open= -source distribution of the the basis set exchange database (https://bse.pnl.gov/bse/portal) so that pe= ople can install it locally and/or access the database through an API (REST= ? Java?)
Regards,
~Julien

--
Juli= en Thibault
University of Utah
Department of Biomedical Informatics<= br>Salt Lake City, UT
--001a1132e6e20a20f404ebdf0d72-- From owner-chemistry@ccl.net Sat Nov 23 19:43:00 2013 From: "Jandir Joaquim Passos jandirpassos%%yahoo.com.br" To: CCL Subject: CCL: DCV4T:C60 Message-Id: <-49365-131123164907-25268-48I3mMBZGFFlBr2hE6JfTA_+_server.ccl.net> X-Original-From: "Jandir Joaquim Passos" Date: Sat, 23 Nov 2013 16:49:06 -0500 Sent to CCL by: "Jandir Joaquim Passos" [jandirpassos%%yahoo.com.br] I`m studying about organic sollar cells and my system just chosen for it is the DCV4:C60. Well, for begin my studies I need of cartesian coordinates of this system(I use TURBOMOLE). So, I glad if anyone can help me. Regards, Jandir From owner-chemistry@ccl.net Sat Nov 23 22:43:00 2013 From: "mike Andaham mymagnussen],[hotmail.com" To: CCL Subject: CCL:G: PES of a triatomic molecule Message-Id: <-49366-131123175401-6112-qLsWPmA03E5mP1+jlbmL+g]|[server.ccl.net> X-Original-From: "mike Andaham" Date: Sat, 23 Nov 2013 17:54:00 -0500 Sent to CCL by: "mike Andaham" [mymagnussen a hotmail.com] Hi all, I am quite new to Gaussian and I encountered a problem. I am trying to run a PES of the C-C-Cl molecule. The problem is that this molecule has a 2Sigma and 2PI states almost isoenergetic and, in fact, the 2PI splits into two components, one with a 2A' symmetry that should interact with the 2A' (from the 2sigma). I am able to obtain the two minimum (one is linear the other bent) but when I run a PES scan (with the opt=modredundant) it stops with an error when it reaches the 180 degrees (with a linear error). This is one of the most important parts, I wonder if there any way of doing the PES including the 180 degrees? (so far I can do it from 120 to 178 degrees). I tried opt=z-matrix, opt=modredundant, sc=qf, with symmetry, no symmetry.... by the way, I am scanning the angle and the C-C bond leaving the C-Cl to optimize. Additionally, how can I get the correct symmetry of the PI upon splitting? (renner-teller effect). If I could get one I think that the other is simply using the guess=alter, but I can not get any symmetry for this state (it gives some unknown symmetry orbitals). Thanks, Mike From owner-chemistry@ccl.net Sat Nov 23 23:18:01 2013 From: "Sreeja S sreejas++acsir.res.in" To: CCL Subject: CCL:G: UV Vis Spectrum and HOMO-LUMO Band gap of molecule Message-Id: <-49367-131123224340-7117-l5oLo9itXFejfOI0sVxG8w++server.ccl.net> X-Original-From: "Sreeja S" Date: Sat, 23 Nov 2013 22:43:38 -0500 Sent to CCL by: "Sreeja S" [sreejas*o*acsir.res.in] Dear Sir/Madam, I am using Gaussian09 with GaussView 5.0 and I am new to the field of computational chemistry. I require to find the optical properties of a molecule - the HOMO - LUMO Band gap. How can this be determined when the alpha and beta orbitals are filled unequally and end at different energies? Also I tried to get the UV-Vis spectra by choosing ZINDO and CIS but after Calculations, the UV - Vis spectra option was not active. Kindly advise me on what to do as this is urgently required for my project. Please tell me what are the settings required in GaussView input file as I have very little knowledge in this regard. Thanks in advance. Best Regards, Sreeja M.Tech - Ph.D student in Renewable Energy Academy of Scientific and Industrial Research, Council of Scientific and Industrial Research