From owner-chemistry@ccl.net Wed Nov 20 02:43:01 2013 From: "Andreas Klamt klamt~!~cosmologic.de" To: CCL Subject: CCL: COSMOlogic announces a free DEMO version of COSMOquick Message-Id: <-49350-131120024210-5089-nahKVnt8BIuUngbHtCQGCQ-.-server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Wed, 20 Nov 2013 08:42:05 +0100 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt()cosmologic.de] Dear CCLers, let me point you to a new demo version of our still quite new COSMOquick program: COSMOquick is a powerful COSMO-RS based toolbox without need for costly quantum chemistry calculations. It provides accurate solubility predictions, cocrystal screening, high quality QSPR descriptors for physicochemical properties, and much more. A DEMO version is available for download here: http://www.cosmologic.de/cosmoquick_demo The following tasks can be carried out with COSMOquick 1.2: - Solubility prediction using multiple reference solvents - QSPR predictions using multi-linear regression or random forest based models - Cocrystal screening, i.e. fast calculations of excess enthalpies - Sorption of small molecules in polymers or solvents - ADME property calculations, i.e. different partition coefficients and water solubility - Generation of approximate sigma-profiles from SMILES for use with COSMOtherm For more details and system requirements see www.cosmologic.de/cosmoquick Perhaps the one or the other likes to have a look. Best reagrds Andreas Klamt and Christoph Loschen From owner-chemistry@ccl.net Wed Nov 20 11:34:01 2013 From: "Douglas B. Staple dstaple^^^dal.ca" To: CCL Subject: CCL:G: Failure Restarting Gaussian 09 Jobs Message-Id: <-49351-131120111107-23704-Rkx2r1upRdWUOSK9oyMdNw||server.ccl.net> X-Original-From: "Douglas B. Staple" Date: Wed, 20 Nov 2013 11:11:05 -0500 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 From owner-chemistry@ccl.net Wed Nov 20 12:46:01 2013 From: "Douglas B. Staple dstaple^_^dal.ca" To: CCL Subject: CCL:G: Failure Restarting Gaussian 09 Jobs Message-Id: <-49352-131120121026-9158-hYmCJI9IMfLvJEJyvDfCJQ ~ server.ccl.net> X-Original-From: "Douglas B. Staple" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 20 Nov 2013 13:08:40 -0400 MIME-Version: 1.0 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>> >>