From owner-chemistry@ccl.net Thu May 20 09:29:00 2010 From: "Berger Raphael berger%a%chem.helsinki.fi" To: CCL Subject: CCL:G: frequency.log to shifted coord.xyz Message-Id: <-41899-100520084151-2109-rzScLnB16JK1ng4xaeSNwg||server.ccl.net> X-Original-From: Berger Raphael Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII Date: Thu, 20 May 2010 15:05:17 +0300 (EEST) MIME-Version: 1.0 Sent to CCL by: Berger Raphael [berger-#-chem.helsinki.fi] Dear CCL-readers, I'm searching for a nice tool, prefreably script-type for generating shifted xyz coordinate files from a gaussian type log file from a normal mode analyses. Does anyone know about such a programme? Best regards BR From owner-chemistry@ccl.net Thu May 20 10:08:00 2010 From: "Naser Eltaher Eltayeb nasertaha90=-=yahoo.co.uk" To: CCL Subject: CCL:G: Fluorescence in G09 Message-Id: <-41900-100519204312-13576-hdN1LSKqVTWH+277rHtkfQ#server.ccl.net> X-Original-From: "Naser Eltaher Eltayeb" Date: Wed, 19 May 2010 20:43:11 -0400 Sent to CCL by: "Naser Eltaher Eltayeb" [nasertaha90 * yahoo.co.uk] Hi All I saw in the Gaussian09 new features a nice graph showing a good matching between experimental and calculated emission and absorption spectra. Anyone have idea about how to calculate the emission spectra using 09? and what is the keyword? I know this function is not available in G03. Thank you From owner-chemistry@ccl.net Thu May 20 13:10:00 2010 From: "Adam Tenderholt atenderholt|a|gmail.com" To: CCL Subject: CCL:G: frequency.log to shifted coord.xyz Message-Id: <-41901-100520130932-32374-q7WCQBJchYjE5tu8ipngBA . server.ccl.net> X-Original-From: Adam Tenderholt Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 20 May 2010 10:09:22 -0700 MIME-Version: 1.0 Sent to CCL by: Adam Tenderholt [atenderholt|a|gmail.com] Distorting a molecule along a normal mode is really straight-forward with cclib and the python bindings for openbabel. Example python code for doing this is: -- import sys > from cclib.parser import ccopen > from cclib.bridge import makeopenbabel import openbabel as ob parser =3D ccopen(sys.argv[1]) data =3D parser.parse() distort =3D data.atomcoords[0] - data.vibdisps[0] obmol =3D makeopenbabel(distort, data.atomnos) obconv =3D ob.OBConversion() ok =3D obconv.SetOutFormat("XYZ") obconv.WriteFile(obmol, "distorted.xyz") --- Note that this script takes the logfile of a frequency calculation (any fully supported by cclib) as its first argument, and distorts along the first normal mode (i.e. data.vibdisps[0]). Adam On Thu, May 20, 2010 at 5:05 AM, Berger Raphael berger%a%chem.helsinki.fi wrote: > > Sent to CCL by: Berger Raphael [berger-#-chem.helsinki.fi] > Dear CCL-readers, > > I'm searching for a nice tool, prefreably script-type for > generating shifted xyz coordinate files from a gaussian type > log file from a normal mode analyses. > Does anyone know about such a programme? > > Best regards > =A0 =A0 =A0 =A0BR > > > > -=3D This is automatically added to each message by the mailing script = =3D-> =A0 =A0> =A0 =A0=A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.= shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> =A0 =A0> > > From owner-chemistry@ccl.net Thu May 20 14:32:01 2010 From: "Jamin Krinsky jamink*|*berkeley.edu" To: CCL Subject: CCL: Correction for syntax in G09 RFO opt keyword Message-Id: <-41902-100520142947-10360-TIgZ6GOAU5D2gPFZzYR0Og/./server.ccl.net> X-Original-From: Jamin Krinsky Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 20 May 2010 11:29:37 -0700 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [jamink]|[berkeley.edu] Dear CCL subscribers, I had posted a while back a suggestion to use the RFO option for the OPT keyword to get around a problem in G09 where optimizations crash with an "error in coordinate system" message. Somehow the server messed up my post and the version that reached you all contained the string 3DRFO. This option does NOT exist. I checked and it is correct in the version I wrote and sent, but anyway sorry for any confusion this may have caused. Regards, Jamin -- Jamin L Krinsky, Ph.D. Molecular Graphics and Computation Facility 175 Tan Hall, University of California, Berkeley, CA 94720 jamink_+_berkeley.edu, 510-643-0616 http://glab.cchem.berkeley.edu From owner-chemistry@ccl.net Thu May 20 19:57:01 2010 From: "Dvir Doron dvir.doron_+_gmail.com" To: CCL Subject: CCL: Computing heats of formation Message-Id: <-41903-100520123657-11242-NdxvZKHcHP3M8VOgnxItog|a|server.ccl.net> X-Original-From: "Dvir Doron" Date: Thu, 20 May 2010 12:36:56 -0400 Sent to CCL by: "Dvir Doron" [dvir.doron~~gmail.com] Hi, According to the common procedure for predicting enthalpies of formation, the computed energy difference between the molecule and its constituent atoms is added to the experimental enthalpy of formation determined for the identical atoms. When it comes to calculate the electronic energy associated with the constituent atoms within a certain molecule, how should one treat these individual atoms in terms of the chosen level of theory and spin-state? Thanks, Dvir From owner-chemistry@ccl.net Thu May 20 20:32:01 2010 From: "bicz]_[kom-net.pl" To: CCL Subject: CCL:G: Fluorescence in G09 Message-Id: <-41904-100520142609-9031-4VcqPwsuMzSIxtRy8SKCoQ~~server.ccl.net> X-Original-From: bicz_._kom-net.pl Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-2 Date: Thu, 20 May 2010 19:26:03 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: bicz,kom-net.pl Please take a look at the white paper available at http://idea.sns.it/download Regards, Malgorzata > > Sent to CCL by: "Naser Eltaher Eltayeb" [nasertaha90 * yahoo.co.uk] > Hi All > > I saw in the Gaussian09 new features a nice graph showing a good matching > between experimental and calculated emission and absorption spectra. > Anyone have idea about how to calculate the emission spectra using 09? and > what is the keyword? I know this function is not available in G03. > > Thank you> > >