From owner-chemistry@ccl.net Tue Mar 27 07:51:00 2012 From: "sobereva sobjubao]~[yahoo.com.cn" To: CCL Subject: CCL:G: Bader Analysis Message-Id: <-46571-120327064939-12334-8HnALMx1b9pubuSC/3FIbw-x-server.ccl.net> X-Original-From: sobereva Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Tue, 27 Mar 2012 18:49:28 +0800 (CST) MIME-Version: 1.0 Sent to CCL by: sobereva [sobjubao:+:yahoo.com.cn] Hi, You may have interest to try Multiwfn, which can realize AIM analysis too (except for basin integral, but will be supported in the future). Multiwfn is an interactive program, its use is as easy as AIM2000, the results can be directly visualized by built-in graphical module. Besides, Multiwfn outperforms AIM2000 remarkably in calculation speed. A tutorial for performing AIM analysis is given in Section 4.2.1 of Multiwfn manual. The methods of generating .wfn file by Gaussian and GAMESS(US) are described at the head of Chapter 4 of the manual. For those quantum chemistry programs that don't support exporting .wfn file but support exporting Molden input file (e.g. Molpro, Molcas), you can make use Molden2aim program to obtain .wfn file, see Section 5.1 of Multiwfn manual. Multiwfn can be freely downloaded at http://multiwfn.codeplex.com, J. Comp. Chem., 33, 580 is an introductory paper for this program. By the way, if the two atoms you are interested in are non-covalently interacted, a method based on reduced density gradient proposed by Yang group (JACS,132,6498) may be more useful than AIM analysis, the theoretical background and practical applications of this analysis method have been given in Section 4.100.1 of Multiwfn manual. Tian Lu School of Chemical and Biological Engineering University of Science and Technology Beijing No.30, XueYuan road, HaiDian district, Beijing, P. R. China --- On Sat, 3/24/12, ili jordak ilijordak*yahoo.fr wrote: > From: ili jordak ilijordak*yahoo.fr > Subject: CCL: Bader Analysis > To: "Lu, Tian " > Date: Saturday, March 24, 2012, 2:19 AM > > Sent to CCL by: "ili  jordak" [ilijordak%%yahoo.fr] > I would like to make a calculation by the theory of Bader > (with the AIM2000 software) to obtain direct evidence of > interaction between two atoms. > Could you help me to create a file (*.aim or *.wfn) or tell > me how I can do to make this calculation ?. > > > > -= 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> > E-mail to subscribers: CHEMISTRY]_[ccl.net > or use: >      > > E-mail to administrators: CHEMISTRY-REQUEST]_[ccl.net > or use >      >      >      > > > From owner-chemistry@ccl.net Tue Mar 27 10:27:00 2012 From: "Cory Pye cpye : ap.smu.ca" To: CCL Subject: CCL:G: Opt with Full point group Symmetry in G09 Message-Id: <-46572-120327102538-22089-cjurB8JNzss1Ykx9cqOyPg^^server.ccl.net> X-Original-From: Cory Pye Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Tue, 27 Mar 2012 11:34:54 -0300 (ADT) MIME-Version: 1.0 Sent to CCL by: Cory Pye [cpye|,|ap.smu.ca] Hello Mi, I recommend the use of opt=z-matrix and a very carefully constructed z-matrix. -Cory Pye On Sun, 25 Mar 2012, Mi Yang agri_chemist%x%yahoo.com wrote: > > Sent to CCL by: "Mi Yang" [agri_chemist++yahoo.com] > Dear CCL Colleagues, > I am desperately trying to optimized a C 40 fulleren molecules with D5H symmetry. But after my > several calculations with different coordinates it reduces the symmetry C2H in final geometry. I > checked CCL archives and used some helpful keywords like symm=loose and iop(2/17=xx), > iop(2/18=xx) upto 1 etc. > > Do Gaussian has ability to optimized only some systems in their Largest Abelian subgroup instead of > full point group...? > In my comparison of systems same point group is necessary so how can I optimized the above Fulleren > 40 (D5H) system in G09...? > Any comment or recommendation will be highly appreciating..... > > MiYang> > ************* ! 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 Tue Mar 27 21:03:00 2012 From: "Hugo Alejandro Jimenez Vazquez hjimenez],[woodward.encb.ipn.mx" To: CCL Subject: CCL:G: Opt with Full point group Symmetry in G09 Message-Id: <-46573-120327122149-7303-9BGHuwkY1fveVVdk5+YRjQ!=!server.ccl.net> X-Original-From: Hugo Alejandro Jimenez Vazquez Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Tue, 27 Mar 2012 10:46:00 -0600 (CST) MIME-Version: 1.0 Sent to CCL by: Hugo Alejandro Jimenez Vazquez [hjimenez,+,woodward.encb.ipn.mx] Although MiYang does not mention it, I would guess that he is using diffuse functions in the basis set employed in his (her?) calculations. I am also trying to do calculations on fullerenes, and I have found that the inclusion of diffuse functions breaks the symmetry of the wavefunction with respect to the symmetry of the molecule under analysis. Gaussian says that "the density has only Abelian symmetry" and in an optimization the point group of the molecule changes to that of the density with the corresponding increase in computational cost. I have not found a way to solve this problem other than getting rid of the diffuse functions from the basis set, although I am still looking. I asked for advise from Gaussian, but they could not help me. The problem is not particular to Gaussian 09; previous versions of Gaussian also exhibit the same behavior. Another solution would be to use a larger basis set withouth the use of diffuse functions. I have not tried Cory's suggestion though, but I believe that the outcome would be the same. Regards, -- --- Hugo A. Jimenez Vazquez hjimenez###woodward.encb.ipn.mx Departamento de Quimica Organica ENCB-IPN Mexico On Tue, 27 Mar 2012, Cory Pye cpye : ap.smu.ca wrote: > > Sent to CCL by: Cory Pye [cpye|,|ap.smu.ca] > Hello Mi, > > I recommend the use of opt=z-matrix and a very carefully constructed z-matrix. > > -Cory Pye > > On Sun, 25 Mar 2012, Mi Yang agri_chemist%x%yahoo.com wrote: > > > > > Sent to CCL by: "Mi Yang" [agri_chemist++yahoo.com] > > Dear CCL Colleagues, > > I am desperately trying to optimized a C 40 fulleren molecules with D5H symmetry. But after my > > several calculations with different coordinates it reduces the symmetry C2H in final geometry. I > > checked CCL archives and used some helpful keywords like symm=loose and iop(2/17=xx), > > iop(2/18=xx) upto 1 etc. > > > > Do Gaussian has ability to optimized only some systems in their Largest Abelian subgroup instead of > > full point group...? > > In my comparison of systems same point group is necessary so how can I optimized the above Fulleren > > 40 (D5H) system in G09...? > > Any comment or recommendation will be highly appreciating..... > > > > MiYang> > > > > ************* ! 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 Tue Mar 27 21:38:00 2012 From: "Jim Kress ccl_nospam%x%kressworks.com" To: CCL Subject: CCL:G: Bader Analysis Message-Id: <-46574-120327122427-8620-9Ep1ymlGYRPMV5enu3A23Q===server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 27 Mar 2012 12:24:14 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam%%kressworks.com] Unfortunately, since Multiwfn seems to require that the user have Gaussian installed, you have limited the scope of available users to those who own and have installed Gaussian. That leads to a couple of questions: 1) What version of Gaussian is required? 2) Is the program unusable for people who do not have Gaussian or who (like me) have been "banned" by Gaussian? Jim > -----Original Message----- > From: owner-chemistry+ccl_nospam==kressworks.com|a|ccl.net > [mailto:owner-chemistry+ccl_nospam==kressworks.com|a|ccl.net] On Behalf > Of sobereva sobjubao]~[yahoo.com.cn > Sent: Tuesday, March 27, 2012 6:49 AM > To: Kress, Jim > Subject: CCL:G: Bader Analysis > > > Sent to CCL by: sobereva [sobjubao:+:yahoo.com.cn] Hi, > > You may have interest to try Multiwfn, which can realize AIM analysis too > (except for basin integral, but will be supported in the future). Multiwfn is an > interactive program, its use is as easy as AIM2000, the results can be directly > visualized by built-in graphical module. Besides, Multiwfn outperforms > AIM2000 remarkably in calculation speed. > > A tutorial for performing AIM analysis is given in Section 4.2.1 of Multiwfn > manual. The methods of generating .wfn file by Gaussian and GAMESS(US) > are described at the head of Chapter 4 of the manual. For those quantum > chemistry programs that don't support exporting .wfn file but support > exporting Molden input file (e.g. Molpro, Molcas), you can make use > Molden2aim program to obtain .wfn file, see Section 5.1 of Multiwfn manual. > > Multiwfn can be freely downloaded at http://multiwfn.codeplex.com, J. > Comp. Chem., 33, 580 is an introductory paper for this program. > > By the way, if the two atoms you are interested in are non-covalently > interacted, a method based on reduced density gradient proposed by Yang > group (JACS,132,6498) may be more useful than AIM analysis, the theoretical > background and practical applications of this analysis method have been > given in Section 4.100.1 of Multiwfn manual. > > Tian Lu > > School of Chemical and Biological Engineering University of Science and > Technology Beijing No.30, XueYuan road, HaiDian district, Beijing, P. R. China > > --- On Sat, 3/24/12, ili jordak ilijordak*yahoo.fr > wrote: > > > From: ili jordak ilijordak*yahoo.fr > > Subject: CCL: Bader Analysis > > To: "Lu, Tian " > > Date: Saturday, March 24, 2012, 2:19 AM > > > > Sent to CCL by: "ili  jordak" [ilijordak%%yahoo.fr] I would like to > > make a calculation by the theory of Bader (with the AIM2000 software) > > to obtain direct evidence of interaction between two atoms. > > Could you help me to create a file (*.aim or *.wfn) or tell me how I > > can do to make this calculation ?. > > > > > > > > -= 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 a sign. You can > > also> E-mail to subscribers: CHEMISTRY a ccl.net or use: > >      > > > E-mail to administrators: CHEMISTRY-REQUEST a ccl.net or use > >      >      >      To > recover the email address of the author of the message, please change the > strange characters on the top line to the |a| sign. You can also look up the X- > Original-From: line in the mail header.> From owner-chemistry@ccl.net Tue Mar 27 22:13:00 2012 From: "Jim Kress ccl_nospam[a]kressworks.com" To: CCL Subject: CCL:G: Bader Analysis Message-Id: <-46575-120327123815-10125-o7zm+v1H9iLgK/qYSNhPCg:+:server.ccl.net> X-Original-From: "Jim Kress" Date: Tue, 27 Mar 2012 12:38:12 -0400 Sent to CCL by: "Jim Kress" [ccl_nospam{:}kressworks.com] Unfortunately, since Multiwfn seems to require that the user have Gaussian installed, you have limited the scope of available users to those who own and have installed Gaussian. That leads to a couple of questions: 1) What version of Gaussian is required? 2) Is the program unusable for people who do not have Gaussian or who (like me) have been "banned" by Gaussian? Jim > -----Original Message----- > Subject: CCL:G: Bader Analysis > > > Sent to CCL by: sobereva [sobjubao:+:yahoo.com.cn] Hi, > > You may have interest to try Multiwfn, which can realize AIM analysis too > (except for basin integral, but will be supported in the future). Multiwfn is an > interactive program, its use is as easy as AIM2000, the results can be directly > visualized by built-in graphical module. Besides, Multiwfn outperforms > AIM2000 remarkably in calculation speed. > > A tutorial for performing AIM analysis is given in Section 4.2.1 of Multiwfn > manual. The methods of generating .wfn file by Gaussian and GAMESS(US) > are described at the head of Chapter 4 of the manual. For those quantum > chemistry programs that don't support exporting .wfn file but support > exporting Molden input file (e.g. Molpro, Molcas), you can make use > Molden2aim program to obtain .wfn file, see Section 5.1 of Multiwfn manual. > > Multiwfn can be freely downloaded at http://multiwfn.codeplex.com, J. > Comp. Chem., 33, 580 is an introductory paper for this program. > > By the way, if the two atoms you are interested in are non-covalently > interacted, a method based on reduced density gradient proposed by Yang > group (JACS,132,6498) may be more useful than AIM analysis, the theoretical > background and practical applications of this analysis method have been > given in Section 4.100.1 of Multiwfn manual. > > Tian Lu > > School of Chemical and Biological Engineering University of Science and > Technology Beijing No.30, XueYuan road, HaiDian district, Beijing, P. R. China > From owner-chemistry@ccl.net Tue Mar 27 22:48:00 2012 From: "Dr. Vitaly V. Chaban vvchaban]-[gmail.com" To: CCL Subject: CCL:G: hybrid functionals in periodic calculations in Gaussian Message-Id: <-46576-120327223542-5550-R8tSXgpo7fOe8TzbI3M3xw],[server.ccl.net> X-Original-From: "Dr. Vitaly V. Chaban" Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 27 Mar 2012 22:34:54 -0400 MIME-Version: 1.0 Sent to CCL by: "Dr. Vitaly V. Chaban" [vvchaban::gmail.com] Dear All -- Would anyone please suggest if this is possible to make hybrid functionals work adequately in periodic calculations with the Gaussian 09 software? Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA