From owner-chemistry@ccl.net Tue Apr 4 00:44:00 2006 From: "Shenggang Li shenggangli%x%gmail.com" To: CCL Subject: CCL: program to calculate Frank-Condon factors Message-Id: <-31407-060403191139-15658-jpOf5g7kpubsofrvT1EjdQ : server.ccl.net> X-Original-From: "Shenggang Li" Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 3 Apr 2006 17:12:12 -0500 MIME-Version: 1.0 Sent to CCL by: "Shenggang Li" [shenggangli-x-gmail.com] Dear Maciej, Dr. P.-N. Roy's program is currently maintained by Dr. D.-S. Yang's group at the University of Kentucky (dyang0{:}uky.edu). Although I am involved in further development of the program, you should contact him about Dr. Roy's program. Also, we are about to release an updated version of the program, which is largely rewritten. Thanks! On 4/3/06, Maciej Haranczyk maharan:_:chem.univ.gda.pl wrote: > Sent to CCL by: Maciej Haranczyk [maharan.{:}.chem.univ.gda.pl] > Dear All, > > I would like to simulate photoelectron spectrum of small anionic molecule. > I am looking for a program to calculate Frank-Condon factors in the > multidimentional case. Could anyone recommend me such program ? > > I know there was a program by professor P-N Roy but I am not able to > contact professor Roy nor can I find the program on the web. > > Any help will be appreciated. > > Thanks, > Maciej > > -- > > Maciek Haranczyk > maharan*o*chem.univ.gda.pl> > > > -- Shenggang Li Shelby Hall L103A Department of Chemistry University of Alabama Tuscaloosa, AL 35487-0336 Office: 205-348-4906 From owner-chemistry@ccl.net Tue Apr 4 02:41:00 2006 From: "XunLei Ding dxl^^^ustc.edu.cn" To: CCL Subject: CCL: convert pseudo format from castep to pwscf Message-Id: <-31408-060403125313-31970-Rvre4mP3Un5ZbAo6rjMoiw^^^server.ccl.net> X-Original-From: "XunLei Ding" Content-Type: text/plain Date: Mon, 03 Apr 2006 23:47:10 +0800 Sent to CCL by: "XunLei Ding" [dxl=-=ustc.edu.cn] Dear all, I want to do a calculation using pwscf with the same pseudopotential provided in castep software. How can I convert the pseudo from castep format into pwscf format? Is there any software or tools for this problem? Thank you! Yours, Ding From owner-chemistry@ccl.net Tue Apr 4 03:29:00 2006 From: "Gunda Tamás tgunda2005++puma.unideb.hu" To: CCL Subject: CCL: XYZ to PDB translation Message-Id: <-31409-060402180040-28545-kTTB3WWR72C6rcqjbzfyug=-=server.ccl.net> X-Original-From: "Gunda Tamás" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Sun, 2 Apr 2006 23:22:30 +0200 MIME-Version: 1.0 Sent to CCL by: "Gunda Tamás" [tgunda2005\a/puma.unideb.hu] Try Mol2Mol http://web.interware.hu/frenzy/mol2mol Tamas E. Gunda ----- Original Message ----- > From: "Mikhail Ladanov mladanov:mail.usf.edu" To: "Gunda, Tamas E " Sent: Friday, March 31, 2006 21:03 Subject: CCL: XYZ to PDB translation > Sent to CCL by: "Mikhail Ladanov" [mladanov/./mail.usf.edu] > I work with MD simulations of system with very big number of atoms. > Im trying to translate my XYZ file into PDB using OpenBabel 2.0 > As soon as I have a file of size about 15-20 Mb, Babel results with segmentation fault. > I have therefore 2 questions: > 1. Is there any way to make OpenBabel work with big files without any errors? > 2. Is there any other utility I could translate XYZ to PDB with?> > > > From owner-chemistry@ccl.net Tue Apr 4 07:44:00 2006 From: "John McKelvey jmmckel]^[attglobal.net" To: CCL Subject: CCL: TDDFT for Large Unsaturated pi-Systems Message-Id: <-31410-060404073204-18843-HoDEEnBG54Dl6BhfKvDBdQ*server.ccl.net> X-Original-From: John McKelvey Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 04 Apr 2006 07:25:51 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel*_*attglobal.net] Dear Sue, I would check on some recent papers by Stefan Grimme. He has studied TDDFT and choice of functionals quite extensively. Cheers, John McKelvey Sue L chsue2004/./yahoo.com wrote: >Sent to CCL by: "Sue L" [chsue2004|-|yahoo.com] >Does anyone know which DFT functional in TDDFT is suitable to calculate the singlet-singlet excitations for large unsaturated pi-systems? B3LYP usually underestimate the excitation energies for these systems > >Thank you very much > >Sue> > > > > > > From owner-chemistry@ccl.net Tue Apr 4 08:19:00 2006 From: "makowskm(!)chemia.uj.edu.pl" To: CCL Subject: CCL: TDDFT for Large Unsaturated pi-Systems Message-Id: <-31411-060404075041-24471-kE6HsFgQB4BnX5brtgHYUA^^^server.ccl.net> X-Original-From: makowskm[#]chemia.uj.edu.pl Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-2 Date: Tue, 4 Apr 2006 13:07:10 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: makowskm**chemia.uj.edu.pl If you mean polyenes for example - the answer is none. There were some papers claiming that Tamm-Dancoff approximation to TDDFT combined with non-hybrid functionals gave decent excitation energies. > Sent to CCL by: "Sue L" [chsue2004|-|yahoo.com] > Does anyone know which DFT functional in TDDFT is suitable to calculate > the singlet-singlet excitations for large unsaturated pi-systems? B3LYP > usually underestimate the excitation energies for these systems > > Thank you very much > > Sue> > > > -- Dr Marcin Makowski Jagiellonian University Department of Theoretical Chemistry email:makowskm[-]chemia.uj.edu.pl or Kyushu University email:marcin[-]cube.kyushu-u.ac.jp From owner-chemistry@ccl.net Tue Apr 4 09:29:00 2006 From: "XunLei Ding dxl%ustc.edu.cn" To: CCL Subject: CCL: how to add a background charge density in castep Message-Id: <-31412-060404034140-19240-cbXAvwQ4KVSSmkz4khgnVA*|*server.ccl.net> X-Original-From: "XunLei Ding" Content-Type: text/plain Date: Tue, 04 Apr 2006 15:41:31 +0800 Sent to CCL by: "XunLei Ding" [dxl!^!ustc.edu.cn] Dear All, How to introduce a background charge density in castep to compensating the net charge of a supercell? For example, Na-doped ZnO supercell(the charge of impurity Na=-1). Thank you! Yours, Ding From owner-chemistry@ccl.net Tue Apr 4 11:42:01 2006 From: "Luca Bertini luca.bertini||istm.cnr.it" To: CCL Subject: CCL: TDDFT for Large Unsaturated pi-Systems Message-Id: <-31413-060404101427-30467-yyiaQa/TLlivRPq0zoEFUw^-^server.ccl.net> X-Original-From: "Luca Bertini" Content-Type: text/plain; charset=iso-8859-1 Date: Tue, 4 Apr 2006 15:31:03 +0200 MIME-Version: 1.0 Sent to CCL by: "Luca Bertini" [luca.bertini ~ istm.cnr.it] Furthemore is known that the adiabatic exchange-correlation kernel is wrong for excited states with non-negligible double-excitation character, as it is the case of polyenes. therefore is not only a problem of DFT functional but also a problem of the TDDFT method. Luca ---------- Original Message ----------- > From: "makowskm(!)chemia.uj.edu.pl" To: "Bertini, Luca " Sent: Tue, 4 Apr 2006 08:24:11 -0400 Subject: CCL: TDDFT for Large Unsaturated pi-Systems > Sent to CCL by: makowskm**chemia.uj.edu.pl > If you mean polyenes for example - the answer is none. There were > some papers claiming that Tamm-Dancoff approximation to TDDFT > combined with non-hybrid functionals gave decent excitation energies. > > Sent to CCL by: "Sue L" [chsue2004|-|yahoo.com] > > Does anyone know which DFT functional in TDDFT is suitable to calculate > > the singlet-singlet excitations for large unsaturated pi-systems? B3LYP > > usually underestimate the excitation energies for these systems > > > > Thank you very much > > > > Sue> > > > > > > > > -- > Dr Marcin Makowski > Jagiellonian University > Department of Theoretical Chemistry > email:makowskm]![chemia.uj.edu.pl > or > Kyushu University > email:marcin]![cube.kyushu-u.ac.jp > > -= This is automatically added to each message by the mailing script > =- To recover the email address of the author of the message, please > change the strange characters on the top line to the () sign. You can > also> > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+ ------- End of Original Message ------- From owner-chemistry@ccl.net Tue Apr 4 13:18:01 2006 From: "makowskm##chemia.uj.edu.pl" To: CCL Subject: CCL: TDDFT for Large Unsaturated pi-Systems Message-Id: <-31414-060404131438-15753-FWLMdzf50W7buyiUUMCtIg(a)server.ccl.net> X-Original-From: makowskm^-^chemia.uj.edu.pl Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-2 Date: Tue, 4 Apr 2006 19:14:31 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: makowskm_+_chemia.uj.edu.pl For polyenes it's a little bit counterintuitive. The excitation energy for doubly excited A_g state is usually not so bad (but optimal geometry is not so good), but strong B_u is severely too low. Definitely, it's still the problem with functionals, but saying that TDDFT is just wrong for states dominated by double excitations is not absolutely true. > Sent to CCL by: "Luca Bertini" [luca.bertini ~ istm.cnr.it] > > Furthemore is known that the adiabatic exchange-correlation kernel is > wrong > for excited states with non-negligible double-excitation character, as it > is > the case of polyenes. therefore is not only a problem of DFT functional > but > also a problem of the TDDFT method. > > Luca > > ---------- Original Message ----------- >> From: "makowskm(!)chemia.uj.edu.pl" > To: "Bertini, Luca " > Sent: Tue, 4 Apr 2006 08:24:11 -0400 > Subject: CCL: TDDFT for Large Unsaturated pi-Systems > >> Sent to CCL by: makowskm**chemia.uj.edu.pl >> If you mean polyenes for example - the answer is none. There were >> some papers claiming that Tamm-Dancoff approximation to TDDFT >> combined with non-hybrid functionals gave decent excitation energies. >> > Sent to CCL by: "Sue L" [chsue2004|-|yahoo.com] >> > Does anyone know which DFT functional in TDDFT is suitable to >> calculate >> > the singlet-singlet excitations for large unsaturated pi-systems? >> B3LYP >> > usually underestimate the excitation energies for these systems >> > >> > Thank you very much >> > >> > Sue> >> > >> > >> > >> >> -- >> Dr Marcin Makowski >> Jagiellonian University >> Department of Theoretical Chemistry >> email:makowskm]![chemia.uj.edu.pl >> or >> Kyushu University >> email:marcin]![cube.kyushu-u.ac.jp >> >> -= This is automatically added to each message by the mailing script >> =- To recover the email address of the author of the message, please >> change the strange characters on the top line to the ^ sign. You can >> also> >> Search Messages: http://www.ccl.net/htdig (login: ccl, Password: >> search)> >> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- >> +-+ > ------- End of Original Message -------> > > > -- Dr Marcin Makowski Jagiellonian University Department of Theoretical Chemistry email:makowskm\a/chemia.uj.edu.pl or Kyushu University email:marcin\a/cube.kyushu-u.ac.jp From owner-chemistry@ccl.net Tue Apr 4 14:01:02 2006 From: "Guilherme Menegon Arantes dinamica===webcable.com.br" To: CCL Subject: CCL:G: G03 "Error in orthogonal basis" + Bad length for file. Message-Id: <-31415-060404135153-1681-FTtaKQ2a6xfrUo7w0B13iA**server.ccl.net> X-Original-From: Guilherme Menegon Arantes Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Tue, 4 Apr 2006 13:51:45 -0300 MIME-Version: 1.0 Sent to CCL by: Guilherme Menegon Arantes [dinamica~!~webcable.com.br] Hi there list, Any tip about the following error seen in Gaussian 03 (B.04) on a SGI Altix running SUSE LINUX Enterprise Server 9 (ia64), kernel 2.6.5-7.201-rtgfx: (Enter /usr/local/g03/l302.exe) NPDir=0 NMtPBC= 1 NCelOv= 1 NCel= 1 NClECP= 1 NCelD= 1 NCelK= 1 NCelE2= 1 NClLst= 1 CellRange= 0.0. One-electron integrals computed using PRISM. Error in orthogonal basis= 4.77D+01 with 295 functions, increasing threshold to 2.00D-06. Error in orthogonal basis= 9.49D+01 with 295 functions, increasing threshold to 4.00D-06. ... Error in orthogonal basis= 9.49D+01 with 295 functions, increasing threshold to 5.24D-01. Error in orthogonal basis= 9.49D+01 with 288 functions, increasing threshold to 1.05D+00. Error in orthogonal basis= 2.27D+01 with 145 functions, increasing threshold to 2.10D+00. Error in orthogonal basis= 2.22D+01 with 30 functions, increasing threshold to 4.19D+00. Error in orthogonal basis= 2.13D+00 with 1 functions, increasing threshold to 8.39D+00. Bad length for file. FileIO: IOper= 1 IFilNo(1)= -685 Len= 0 IPos= 0 Q= 1142739344 dumping /fiocom/, unit = 1 NFiles = 46 SizExt = 524288 WInBlk = 2048 defal = T LstWrd = 9723904 FType=2 FMxFil=10000 ... Base 20480 End 65536 End1 65536 Wr Pntr 20480 Rd Pntr 20480 Length 45056 Error termination in NtrErr: NtrErr Called from FileIO. --------------------------------------------------------- This job route session: %nosave %mem=97440512 %chk=temp/oi.chk #p mp2/6-311+G(df,p) maxdisk=1920mw scan counterpoise=2 --------------------------------------------------------- What puzzles me is that this looks like a disk/scratch file error, but there is plenty of space and the files never get bigger than 1GB (not at this stage of the calculation!). This "Error in orthogonal basis" appears to be caused by a linear dependence in the basis set (not seen in G98 for the same job). If I tunr off this lin. dep. check (using iop(3/32=2)), the SCF does not converge. I googled around and also looked in the Gaussian web site, but no help. Thanks for your attention, Guilherme Menegon Arantes Sao Paulo, Brasil ______________________________________________________ From owner-chemistry@ccl.net Tue Apr 4 14:54:00 2006 From: "Young Leh youngleh%%gmail.com" To: CCL Subject: CCL: How to fix atoms at specific position in GaussView Message-Id: <-31416-060404145240-32207-SwQ5wiDvGaGHMUpi0uw3IA:_:server.ccl.net> X-Original-From: "Young Leh" Date: Tue, 4 Apr 2006 14:52:39 -0400 Sent to CCL by: "Young Leh" [youngleh^-^gmail.com] Dear CCLer, I am currently building a cluster model cut from a lattice structure. So, I need to fix all the outside atoms in its original postions in crystals. The experiment data for those atoms in cartesian coordinate is available. However, I can not find any place in GaussView to constrain the atoms. Does anybody know if GaussView can do this at all? If not, could sombody please recommend some visual interface that can achieve this goal. Thanks for the suggestions. Sincerely, Young Leh From owner-chemistry@ccl.net Tue Apr 4 15:28:01 2006 From: "david.giesen###kodak.com" To: CCL Subject: CCL: TDDFT for Large Unsaturated pi-Systems Message-Id: <-31417-060404102941-2137-yGBoDJIRPx4qWZyVcjwL2g- -server.ccl.net> X-Original-From: david.giesen[a]kodak.com Content-Type: text/plain; charset="US-ASCII" Date: Tue, 4 Apr 2006 09:42:26 -0400 MIME-Version: 1.0 Sent to CCL by: david.giesen a kodak.com It's hard to know exactly what you are looking for as "large unsaturated pi-systems" is a broad class. But the paper below shows some nice results with TD-PBE0/6-311+G(2d,p)//PBE0/6-311G(d,p) for thioindigo dyes. Dave Thioindigo Dyes: Highly Accurate Visible Spectra with TD-DFT Jacquemin, D.; Preat, J.; Wathelet, V.; Fontaine, M.; Perpete, E. A. J. Am. Chem. Soc.; (Article); 2006; 128(6); 2072-2083. DOI: 10.1021/ja056676h "Sue L chsue2004/./yahoo.com" Sent by: owner-chemistry^^ccl.net 04/03/2006 10:59 PM Please respond to "CCL Subscribers" To "Giesen, David J " cc Subject CCL: TDDFT for Large Unsaturated pi-Systems Sent to CCL by: "Sue L" [chsue2004|-|yahoo.com] Does anyone know which DFT functional in TDDFT is suitable to calculate the singlet-singlet excitations for large unsaturated pi-systems? B3LYP usually underestimate the excitation energies for these systems Thank you very much Suehttp://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 Tue Apr 4 16:03:01 2006 From: "Gustavo Seabra gustavo.seabra]-[gmail.com" To: CCL Subject: CCL:G: program to calculate Frank-Condon factors Message-Id: <-31418-060404122607-4610-HcTo80TbjVEB3eXn7vnZgA_._server.ccl.net> X-Original-From: "Gustavo Seabra" Content-Type: multipart/alternative; boundary="----=_Part_28019_13626859.1144164094166" Date: Tue, 4 Apr 2006 11:21:34 -0400 MIME-Version: 1.0 Sent to CCL by: "Gustavo Seabra" [gustavo.seabra]=[gmail.com] ------=_Part_28019_13626859.1144164094166 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Maciej, During my Ph.D. I wrote a program that calculates x-ray photoelectron intensities from the Dyson orbitals generated by a electron propagator calculation in Gaussian. It works for soft x-ray (like Mg-K_alpha, where th= e wavelength is smaller than the molecule dimensions) and uses a plane wave o= r orthogonalized plane wave to represent the photoelectron. I haven't tested, but it's possible that it will work with anions at lower photon energies. You can see some results at: "Electron Propagator Theory Calculations of Molecular Photoionization Cross Sections: The First-Row Hydrides", G. M. Seabra, I.G. Kaplan, V. G. Zakrzewski and J. V. Ortiz, J. Chem. Phys., 121 (9), 4243 -- 4145 (2004) Of course, since it is coded in Gaussian, you will probably need access to Gaussian code to compile it. If you think this can be useful for you, you can contact me directly for more details. HTH, Gustavo. On 4/3/06, Maciej Haranczyk maharan:_:chem.univ.gda.pl < owner-chemistry/a\ccl.net> wrote: > > Sent to CCL by: Maciej Haranczyk [maharan./a\.chem.univ.gda.pl] > Dear All, > > I would like to simulate photoelectron spectrum of small anionic molecule= . > I am looking for a program to calculate Frank-Condon factors in the > multidimentional case. Could anyone recommend me such program ? > > I know there was a program by professor P-N Roy but I am not able to > contact professor Roy nor can I find the program on the web. > > Any help will be appreciated. > > Thanks, > Maciej > > -- > > Maciek Haranczyk > maharan*o*chem.univ.gda.pl > ------=_Part_28019_13626859.1144164094166 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Maciej,

During my Ph.D. I wrote a program that calculates x-ray phot= oelectron intensities from the Dyson orbitals generated by a electron propa= gator calculation in Gaussian. It works for soft x-ray (like Mg-K_alpha, wh= ere the wavelength is smaller than the molecule dimensions) and uses a plan= e wave or orthogonalized plane wave to represent the photoelectron. I haven= 't tested, but it's possible that it will work with anions at lower photon = energies. You can see some results at:

"Electron Propagator Theory Calculations of Molecular Ph= otoionization Cross Sections: The First-Row Hydrides", G. M. Seabra, I= .G. Kaplan, V. G. Zakrzewski and J. V. Ortiz, J. Chem. Phys., 121 (9), 4243= -- 4145 (2004)

Of course, since it is coded in Gaussian, you will probably need ac= cess to Gaussian code to compile it.

If you think this can be useful= for you, you can contact me directly for more details.

HTH,

Gustavo.

On 4/3/06, Maciej Haranczyk maharan:_:chem.univ.gda.pl < owner-chemistry/a\ccl.net> wrote:
Sent to CCL by: Maciej Haranczyk [maharan./a\.che= m.univ.gda.pl]
Dear All,

I would like to simulate photoelectron spectrum of sma= ll anionic molecule.
I am looking for a program to calculate Frank-Condo= n factors in the
multidimentional case. Could anyone recommend me such p= rogram ?

I know there was a program by professor P-N Roy but I am not able t= o
contact professor Roy nor can I find the program on the web.

An= y help will be appreciated.

Thanks,
Maciej

--

Maci= ek Haranczyk
maharan*o*chem.univ.gda.pl
=

------=_Part_28019_13626859.1144164094166-- From owner-chemistry@ccl.net Tue Apr 4 23:13:00 2006 From: "Carlos Silva Lopez csilval{=}uvigo.es" To: CCL Subject: CCL: TDDFT for Large Unsaturated pi-Systems Message-Id: <-31419-060404110605-7921-8pF/qKXZfvpkajLefYGJIg(-)server.ccl.net> X-Original-From: Carlos Silva Lopez Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Tue, 04 Apr 2006 09:12:54 -0500 MIME-Version: 1.0 Sent to CCL by: Carlos Silva Lopez [csilval_-_uvigo.es] Look at this paper and references therein http://www3.interscience.wiley.com/cgi-bin/fulltext/112139058/HTMLSTART ZINDO is cheap and seems to work awesomely Sue L chsue2004/./yahoo.com wrote: >Sent to CCL by: "Sue L" [chsue2004|-|yahoo.com] >Does anyone know which DFT functional in TDDFT is suitable to calculate the singlet-singlet excitations for large unsaturated pi-systems? B3LYP usually underestimate the excitation energies for these systems > >Thank you very much > >Sue> > > > > -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Carlos Silva Lopez Researcher University of Minnesota Phone : (612) 625-6317 Department of Chemistry Fax : (612) 626-7541 207 Pleasant St. SE e-mail: silva028=-=tc.umn.edu Minneapolis, MN USA 55455-0431 http://riesling.chem.umn.edu/~carlos ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~