From owner-chemistry@ccl.net Wed Sep 16 07:25:00 2015 From: "Marco Fus marco.fuse=-=unimi.it" To: CCL Subject: CCL:G: Nuclear and electronic contribution in APTs and AATs Message-Id: <-51743-150916044721-13293-IzfIU0SEw1VFQJZs89gltw-.-server.ccl.net> X-Original-From: "Marco Fus " Date: Wed, 16 Sep 2015 04:47:19 -0400 Sent to CCL by: "Marco Fus " [marco.fuse[a]unimi.it] Dear CCLers: I would like to estimate the nuclear and the electronic contribution for the electric and magnetic dipole transition moments associated with a vibrational transition. I'm using gaussian g09 for dft vcd calculation of some molecular system, with iop(7/33=1) I was able to obtain cartesian coordinates of the electronic and magnetic dipole transition moment, but not information on their components. Do you know if it is possible obtain such information in output by IOPs or read it from formatted checkpoint file? Otherwise do you know if it is possible print out the atomic polar tensor and the atomic axial tensor? Thanks Marco Fus marco.fuse#%#unimi.it universit degli studi di Milano From owner-chemistry@ccl.net Wed Sep 16 08:00:00 2015 From: "Peter Jarowski peterjarowski ~~ gmail.com" To: CCL Subject: CCL:G: Case Studies of QM Computational Chemistry in Reactivity Message-Id: <-51744-150916053556-1114-aBBmRyDympMQMQK6dntJ4A]~[server.ccl.net> X-Original-From: Peter Jarowski Content-Type: multipart/alternative; boundary=001a113ac3421f9d9c051fda0686 Date: Wed, 16 Sep 2015 11:35:49 +0200 MIME-Version: 1.0 Sent to CCL by: Peter Jarowski [peterjarowski-,-gmail.com] --001a113ac3421f9d9c051fda0686 Content-Type: text/plain; charset=UTF-8 Hello All: We are at 62 respondents. As I was limited in the question number I could not ask for you to identify who you are working for etc. This might cause statistical problems in the Survey as it might be possible that 40 respondents work for Gaussian or something like that. If you are aware of any clustering that I should know about please let me know. For example, if you distributed the survey to colleagues at your company that would be good for me to know. About 65% of you are using Gaussian. That seems right for QM people I suppose. I will wait for a few days and then make the results available. Best Regards, Peter On Tue, Sep 15, 2015 at 1:35 PM, Peter Jarowski peterjarowski()gmail.com < owner-chemistry]![ccl.net> wrote: > Dear All: > > Wow. 18 respondents in a matter of a few hours. Wasn't expecting that. > Thanks. Of course one person was only interested in Methamphetamine > synthesis. Thank you Breaking Bad for making a mockery of our discipline! > > Please keep it up: > > https://www.surveymonkey.com/r/35QL9ZH > > Best Regards, > > Peter > > On Tue, Sep 15, 2015 at 9:46 AM, Peter Jarowski peterjarowski=gmail.com < > owner-chemistry++ccl.net> wrote: > >> Dear CCLers: >> >> I want to thank everyone for their responses to my question. In general, >> for theorists, we were able to stay on topic. When we forayed the >> discussion was quite heated, interesting and fun to watch. For my part, I >> am about to publish a paper with atomic charge analysis and now I am >> worried! I hope I land on the right side in the review process:) >> >> I am now writing again to see if we can refine the discussion further as >> I have enough responses regrading key examples of the utility of QM in >> predicting experimental (kinetic) outcomes. >> >> I have built a 9 question (not 10 as promised by Survey Monkey) survey to >> help us see where QM is in industry. Each question has an "other" section >> so please feel free to fill in. Once I have at least 50 respondents I will >> publish the metrics here on CCL. >> >> Here is the link: >> >> https://www.surveymonkey.com/r/35QL9ZH >> >> It will take a few minutes and should be rewarding to all. >> >> I look forward to your responses. For data scientists I think a more >> formulaic and quantifiable approach makes sense. >> >> Best Regards, >> >> Peter >> >> >> > --001a113ac3421f9d9c051fda0686 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hello All:

We are at= 62 respondents. As I was limited in the question number I could not ask fo= r you to identify who you are working for etc. This might cause statistical= problems in the Survey as it might be possible that 40 respondents work fo= r Gaussian or something like that. If you are aware of any clustering that = I should know about please let me know. For example, if you distributed the= survey to colleagues at your company that would be good for me to know.
About 65% of you are using Gaussian. That seems right for QM pe= ople I suppose.

I will wait for a few days and then make the r= esults available.

Best Regards,

Peter

On Tue, Sep 15, 201= 5 at 1:35 PM, Peter Jarowski peterjarowski()gm= ail.com <owner-chemistry]![ccl.net> wrote:
Dear All:
=
Wow. 18 respondents in a matter of a few hours. Wasn't expect= ing that. Thanks. Of course one person was only interested in Methamphetami= ne synthesis. Thank you Breaking Bad for making a mockery of our discipline= !

Please keep it up:

https://www.surveymonkey.com/r/35QL9ZH

Best Regards,

Peter

On Tue, Sep 15, 2015 at 9:46 A= M, Peter Jarowski peterjarowski=3Dgmail.com <owner-chemistry++ccl.net> wrote:=
Dear CCLers:

I want to thank everyone for thei= r responses to my question. In general, for theorists, we were able to stay= on topic. When we forayed the discussion was quite heated, interesting and= fun to watch. For my part, I am about to publish a paper with atomic charg= e analysis and now I am worried! I hope I land on the right side in the rev= iew process:)

I am now writing again to see if we can refine t= he discussion further as I have enough responses regrading key examples of = the utility of QM in predicting experimental (kinetic) outcomes.

I have built a 9 question (not 10 as promised by Survey Monkey) survey t= o help us see where QM is in industry. Each question has an "other&quo= t; section so please feel free to fill in. Once I have at least 50 responde= nts I will publish the metrics here on CCL.

Here is the link:<= br>
It will = take a few minutes and should be rewarding to all.

I loo= k forward to your responses. For data scientists I think a more formulaic a= nd quantifiable approach makes sense.

Best Regards,
Peter




--001a113ac3421f9d9c051fda0686-- From owner-chemistry@ccl.net Wed Sep 16 08:35:01 2015 From: "Mohan maruthi sena maruthi.sena- -gmail.com" To: CCL Subject: CCL:G: Symmetry constraint during scan calculation Message-Id: <-51745-150916073133-12938-8WaBJT6SEMvr4XgcXtrXiA!A!server.ccl.net> X-Original-From: Mohan maruthi sena Content-Type: multipart/alternative; boundary=94eb2c0846acac95e8051fdba316 Date: Wed, 16 Sep 2015 17:01:27 +0530 MIME-Version: 1.0 Sent to CCL by: Mohan maruthi sena [maruthi.sena]![gmail.com] --94eb2c0846acac95e8051fdba316 Content-Type: text/plain; charset=UTF-8 Hello all, Thanks for a reply. I am writing reply so late because I have tried and optimized the system using the symmetry keyword. I have still some doubt regarding symmetry scan calculations, 1) I have given symmetry=follow key word in g09 input file and it has followed the initial symmetry. Suppose my initial symmetry is octahedral and if I want to scan an angle in d3h symmetry, How can I mention this point group in input file. Is there in any option to mention point group in g09? Thanks for a reply in advance, Mohan On Sat, Sep 12, 2015 at 7:51 PM, Robert Molt r.molt.chemical.physics% gmail.com wrote: > > Sent to CCL by: Robert Molt [r.molt.chemical.physics#gmail.com] > if you start in a symmetry point group in Gaussian, you tend to follow it > by default. You can make this more explicit by using the symmetry keyword > in Gaussian (check the manual for details). > > > On 9/12/15 7:34 AM, Mohan maruthi sena maruthi.sena,,gmail.com wrote: > >> Hi all, >> I am trying to perform a scan calculation for SF6 molecule >> using Gaussian09. I have optimized the molecule and the symmetry of the >> molecule is octahedral. I want to perform scan of angle [FSF] calculation >> by imposing D3h symmetry constraint on the molecule [and also keeping bond >> length fixed]. How can I do this g09? [option in input file]. >> >> Thanks for a reply in advance, >> >> Regards, >> Mohan >> > > -- > Dr. Robert Molt Jr. > Visiting Associate Professor of Chemistry > Department of Chemistry & Chemical Biology > Indiana University-Purdue University Indianapolis > LD 326 > 402 N. Blackford St. > Indianapolis, IN 46202http://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > --94eb2c0846acac95e8051fdba316 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hello all,
=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 Thanks for = a reply. I am writing reply so late because I have tried and optimized the = system using the symmetry keyword. I have still some doubt regarding symmet= ry scan calculations,


1) I have given symmetry=3Dfollow ke= y word in g09 input file and it has followed the initial symmetry. Suppose = my initial symmetry is octahedral and if I want to scan an angle=C2=A0 in d= 3h symmetry, How can I mention this point group in input file. Is there in = any option to mention point group in g09?


Thanks for= a reply in advance,
Mohan

=

On= Sat, Sep 12, 2015 at 7:51 PM, Robert Molt r.molt.chemical.physics%gmail.com <= ;owner-chemist= ry(a)ccl.net> wrote:

Sent to CCL by: Robert Molt [r.molt.chemical.physics#gmail.com]
if you start in a symmetry point group in Gaussian, you tend to follow it b= y default. You can make this more explicit by using the symmetry keyword in= Gaussian (check the manual for details).


On 9/12/15 7:34 AM, Mohan maruthi sena maruthi.sena,,gmail.com wrote:
Hi all,
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 I am trying to perform a scan calculatio= n for SF6 molecule using Gaussian09. I have optimized the molecule and the = symmetry of the molecule is octahedral. I want to perform scan of angle [FS= F] calculation by imposing D3h symmetry constraint on the molecule [and als= o keeping bond length fixed].=C2=A0 =C2=A0How can I do this g09? [option in= input file].

Thanks for a reply in advance,

Regards,
Mohan

--
Dr. Robert Molt Jr.
Visiting Associate Professor of Chemistry
Department of Chemistry & Chemical Biology
Indiana University-Purdue University Indianapolis
LD 326
402 N. Blackford St.
Indianapolis, IN 46202



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--94eb2c0846acac95e8051fdba316-- From owner-chemistry@ccl.net Wed Sep 16 12:23:01 2015 From: "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor+/-fluor.quimica.uniovi.es" To: CCL Subject: CCL:G: Symmetry constraint during scan calculation Message-Id: <-51746-150916120217-32372-2paSq879ptwHNRCdIMl+bQ(-)server.ccl.net> X-Original-From: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal Content-disposition: inline Content-transfer-encoding: 8BIT Content-type: text/plain; charset=iso-8859-1 Date: Wed, 16 Sep 2015 17:44:57 +0200 MIME-version: 1.0 Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor * fluor.quimica.uniovi.es] On Wed, Sep 16, 2015 at 05:01:27PM +0530, Mohan maruthi sena maruthi.sena- -gmail.com wrote: > 1) I have given symmetry=follow key word in g09 input file and it has > followed the initial symmetry. Suppose my initial symmetry is octahedral > and if I want to scan an angle in d3h symmetry, How can I mention this > point group in input file. Is there in any option to mention point group in > g09? Mohan, Symmetry is recognized by gaussian g09 from the geometry of your system. That differs in many other codes (gamess for instance) where the symmetry can be given beforehand to simplify entering the geometry. If you want to see is your system in unstable against a D3h deformation you should try a small D3h deformation before optimizing the geometry. Analyzing the frequency vibrations will also give you a hint of the instability. Remember that QM codes use symmetry to reduce the computer time for obtaing the integrals required to compute energy, gradient and hessian of the problem. You can force g09 to avoid symmetry by nosymm. Check input: Good luck, Víctor Luaña -- . . "In science a person can be convinced by a good argument. / `' \ That is almost impossible in politics or religion" /(o)(o)\ (Adapted from Carl Sagan) /`. \/ .'\ "Lo mediocre es peor que lo bueno, pero también es peor / '`'` \ que lo malo, porque la mediocridad no es un grado, es una | \'`'`/ | actitud" -- Jorge Wasenberg, 2015 | |'`'`| | (Mediocre is worse than good, but it is also worse than \/`'`'`'\/ bad, because mediocrity is not a grade, it is an attitude) ===(((==)))==================================+========================= ! Dr.Víctor Luaña, in silico chemist & prof. !"I have two kinds of problems, ! Departamento de Química Física y Analítica ! the urgent and the important. ! Universidad de Oviedo, 33006-Oviedo, Spain ! The urgent are not important, ! e-mail: victor[A]fluor.quimica.uniovi.es ! and the important are never ! phone: +34-985-103491 fax: +34-985-103125 ! urgent. +--------------------------------------------+ (Dwight D. Eisenhower) GroupPage : http://azufre.quimica.uniovi.es/ From owner-chemistry@ccl.net Wed Sep 16 14:37:01 2015 From: "Raghu R raghu.rama.chem[]gmail.com" To: CCL Subject: CCL:G: Symmetry constraint during scan calculation Message-Id: <-51747-150916143544-13245-vS6wvg2lmmd8TdzBoFhOgw,+,server.ccl.net> X-Original-From: Raghu R Content-Type: multipart/alternative; boundary=001a113436fe99a9d2051fe19033 Date: Wed, 16 Sep 2015 20:35:37 +0200 MIME-Version: 1.0 Sent to CCL by: Raghu R [raghu.rama.chem-,-gmail.com] --001a113436fe99a9d2051fe19033 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Mohan, Do you want to compute the single point energies along the path connecting the Oh minima to a D3h structure with fixed S-F lengths? If so, you will need a good z-matrix, perhaps with several dummy atoms. You might still need to vary more than one angle and may be even a dihedral angle to go > from a octahedron to a triangular prism. Best, Raghu ------- Dr. Raghunathan Ramakrishnan Institute of Physical Chemistry University of Basel Klingelbergstrasse 80 CH4056 Basel Switzerland https://sites.google.com/site/raghucompchem/home On Wed, Sep 16, 2015 at 1:31 PM, Mohan maruthi sena maruthi.sena- -gmail.co= m wrote: > Hello all, > Thanks for a reply. I am writing reply so late because I > have tried and optimized the system using the symmetry keyword. I have > still some doubt regarding symmetry scan calculations, > > > 1) I have given symmetry=3Dfollow key word in g09 input file and it has > followed the initial symmetry. Suppose my initial symmetry is octahedral > and if I want to scan an angle in d3h symmetry, How can I mention this > point group in input file. Is there in any option to mention point group = in > g09? > > > Thanks for a reply in advance, > Mohan > > > On Sat, Sep 12, 2015 at 7:51 PM, Robert Molt r.molt.chemical.physics% > gmail.com wrote: > >> >> Sent to CCL by: Robert Molt [r.molt.chemical.physics#gmail.com] >> if you start in a symmetry point group in Gaussian, you tend to follow i= t >> by default. You can make this more explicit by using the symmetry keywor= d >> in Gaussian (check the manual for details). >> >> >> On 9/12/15 7:34 AM, Mohan maruthi sena maruthi.sena,,gmail.com wrote: >> >>> Hi all, >>> I am trying to perform a scan calculation for SF6 molecule >>> using Gaussian09. I have optimized the molecule and the symmetry of the >>> molecule is octahedral. I want to perform scan of angle [FSF] calculati= on >>> by imposing D3h symmetry constraint on the molecule [and also keeping b= ond >>> length fixed]. How can I do this g09? [option in input file]. >>> >>> Thanks for a reply in advance, >>> >>> Regards, >>> Mohan >>> >> >> -- >> Dr. Robert Molt Jr. >> Visiting Associate Professor of Chemistry >> Department of Chemistry & Chemical Biology >> Indiana University-Purdue University Indianapolis >> LD 326 >> 402 N. Blackford St. >> Indianapolis, IN 46202 >> >> >> >> -=3D This is automatically added to each message by the mailing script = =3D- >> E-mail to subscribers: CHEMISTRY-*-ccl.net or use:>> >> E-mail to administrators: CHEMISTRY-REQUEST-*-ccl.net or usehttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: >> http://server.ccl.net/chemistry/announcements/conferences/>> >> >> > --001a113436fe99a9d2051fe19033 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Mohan,

Do you want to compute the sing= le point energies along the path connecting the Oh minima to a D3h structur= e with fixed S-F lengths? If so, you will need a good z-matrix, perhaps wit= h several dummy atoms. You might still need to vary more than one angle and= may be even a dihedral angle to go from a octahedron to a triangular prism= .

Best,
Raghu

-= ------
Dr. Raghunathan Ramakrishnan
Institute of Physical Chemistry
University of Basel
Klingelbergstrasse 80
CH4056 Basel
Switzerland
https://sites.google.com/site/raghuco= mpchem/home


On Wed, Sep 16, 2015 at 1:31 PM, Mohan maruthi sena maruthi.se= na- -gmail.com <owner-chemistry|ccl= .net> wrote:
Hello all,
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 Thanks for a reply. I am w= riting reply so late because I have tried and optimized the system using th= e symmetry keyword. I have still some doubt regarding symmetry scan calcula= tions,


1) I have given symmetry=3Dfollow key word in g09 i= nput file and it has followed the initial symmetry. Suppose my initial symm= etry is octahedral and if I want to scan an angle=C2=A0 in d3h symmetry, Ho= w can I mention this point group in input file. Is there in any option to m= ention point group in g09?


Thanks for a reply in adv= ance,
Mohan

=

On Sat, Sep 12, 2= 015 at 7:51 PM, Robert Molt r.molt.chemical.physics%gmail.com <owner-chemistry-*-ccl.net> wrote:

Sent to CCL by: Robert Molt [r.molt.chemical.physics#gmail.com]
if you start in a symmetry point group in Gaussian, you tend to follow it b= y default. You can make this more explicit by using the symmetry keyword in= Gaussian (check the manual for details).


On 9/12/15 7:34 AM, Mohan maruthi sena maruthi.sena,,gmail.com wrote:
Hi all,
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 I am trying to perform a scan calculatio= n for SF6 molecule using Gaussian09. I have optimized the molecule and the = symmetry of the molecule is octahedral. I want to perform scan of angle [FS= F] calculation by imposing D3h symmetry constraint on the molecule [and als= o keeping bond length fixed].=C2=A0 =C2=A0How can I do this g09? [option in= input file].

Thanks for a reply in advance,

Regards,
Mohan

--
Dr. Robert Molt Jr.
Visiting Associate Professor of Chemistry
Department of Chemistry & Chemical Biology
Indiana University-Purdue University Indianapolis
LD 326
402 N. Blackford St.
Indianapolis, IN 46202



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--001a113436fe99a9d2051fe19033--