From owner-chemistry.,at,.ccl.net Thu Aug 25 07:58:00 2016 From: "Brian Skinn bskinn++alum.mit.edu" To: CCL Subject: CCL:G: Constrained optimization and frequency calculation Message-Id: <-52360-160825073538-25247-Fb6F9LPm7gfPrelA5BzhAA+/-server.ccl.net> X-Original-From: Brian Skinn Content-Type: multipart/alternative; boundary=001a113cd7aea5ba9f053ae3cbdb Date: Thu, 25 Aug 2016 07:35:11 -0400 MIME-Version: 1.0 Sent to CCL by: Brian Skinn [bskinn*_*alum.mit.edu] --001a113cd7aea5ba9f053ae3cbdb Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dr. Jensen, Apologies for the pedantry, but is "one-dimensional quantity" the proper term? Wouldn't, say, "order-one tensor quantity" be more accurate? That is to say, the gradient and each of the normal modes are individually 3N-dimensional, order-one tensor quantities, are they not? Best regards, Brian On Wed, Aug 24, 2016 at 3:27 PM, Frank Jensen frj=3D=3D=3Dchem.au.dk < owner-chemistry+/-ccl.net> wrote: > Gaussian by default assumes that the frequency analysis is done at a > stationary point, and projects out the T+R to get 3N-6 frequencies. > > If you are at a non-stationary point, use Freq=3DProjected to also projec= t > out the gradient, and thus get 3N-7 frequencies. > > Note that this provides 3N-7 frequencies, regardless of the number of > geometry constraints imposed, since the non-zero gradient is still only a > one-dimensional quantity. > > > > Frank > > > > Frank Jensen > > Assoc. Prof., Vice-Chair > > Dept. of Chemistry > > Aarhus University > > http://old.chem.au.dk/~frj > > > > *From:* owner-chemistry+frj=3D=3Dchem.au.dk+/-ccl.net [mailto: > owner-chemistry+frj=3D=3Dchem.au.dk+/-ccl.net] *On Behalf Of *Ankur Gupta > ankkgupt**umail.iu.edu > *Sent:* 24. august 2016 20:00 > *To:* Frank Jensen > *Subject:* CCL:G: Constrained optimization and frequency calculation > > > > Hello, > > Thank you Prof. Dr. M. Swart for answering my question. I found Baker's > paper really helpful. It discusses constrained optimization thoroughly bu= t > it does not focus much on normal mode analysis. I am more concerned about > the frequencies that we get from the Hessian after constrained > optimization. The algorithm for constrained optimization has been > implemented in most of the computational chemistry software. But I am not > able to understand the frequencies that it shows after the constrained > optimization. > > Thank you > > Ankur > > > > On Sat, Aug 20, 2016 at 5:03 AM, Marcel Swart marcel.swart/./icrea.cat < > owner-chemistry[-]ccl.net> wrote: > > Dear Ankur, > > > > I would suggest to have a look at PQS (Baker, Pulay and co-workers) or > QUILD (Swart and co-workers). > > Both use Baker=E2=80=99s elegant solution to constrained optimizations. > > > > Baker, "Constrained optimization in delocalized internal coordinates=E2= =80=9D > > Journal of Computational Chemistry 18, 1079 (1997) > > http://dx.doi.org/10.1002/(SICI)1096-987X(199706)18:8% > 3C1079::AID-JCC12%3E3.0.CO;2-8 > > > > PQS: > > http://www.pqs-chem.com/capabilities.php > > > > QUILD: > > http://www.marcelswart.eu/quild > > https://www.scm.com/documentation/Quild/index/index > > > > Marcel > > > > On 19 Aug 2016, at 22:33, Ankur Kumar Gupta ankkgupt*indiana.edu < > owner-chemistry*ccl.net> wrote: > > > > > Sent to CCL by: "Ankur Kumar Gupta" [ankkgupt||indiana.edu] > Hello, > > I have been reading about constrained optimization. I have read several > papers related to the topic including the classic Reaction path Hamiltoni= an > for polyatomic molecules by Miller et al. This and other research article= s > describe what is known as 'projection operator' method to do optimization > keeping one or more internal coordinates constant. Theoretically, we shou= ld > get 3N-6 non-zero eigenvalues from the force constant matrix (for a > molecule having N nuclei) but if we apply m number of constraints in the > molecule, we should obtain 3N-6-m non-zero eigenvalues (frequencies). Als= o, > in cases where the constraint corresponds to a non-equilibrium geometry, > there will be coupling between rotational and vibrational motion due to > which the number of non-zero eigenvalues might change. But for the sake o= f > simplicity, we can talk about equilibrium geometries only. I use Gaussian > 09 and I observed that the number of non-zero eigenvalues did not change > after constrained optimization. ! > I know there are many computational chemistry softwares out there and I > would like to know if there is a software which can do constrained > optimization correctly and give me the right number and magnitude of > eigenvalues (frequencies) after the optimization. > > Thank you > Ankur > > > > -=3D This is automatically added to each message by the mailing script = =3D-> 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>
> > > > _____________________________________ > Prof. Dr. Marcel Swart, FRSC > > ICREA Research Professor at > Institut de Qu=C3=ADmica Computacional i Cat=C3=A0lisi (IQCC) > Univ. Girona (Spain) > > COST Action CM1305 (ECOSTBio) chair > Girona Seminar 2016 organizer > > IQCC director > > RSC Advances associate editor > > Young Academy of Europe member > > > > web > http://www.marcelswart.eu > vCard > addressbook://www.marcelswart.eu/MSwart.vcf > > > > > > > > --001a113cd7aea5ba9f053ae3cbdb Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dr. Jensen,

Apologies for the pedantry,= but is "one-dimensional quantity" the proper term?=C2=A0 Wouldn&= #39;t, say, "order-one tensor quantity" be more accurate?

That is to say, the gradient and each of the normal modes= are individually 3N-dimensional, order-one tensor quantities, are they not= ?


Best regards,
Brian

On Wed, A= ug 24, 2016 at 3:27 PM, Frank Jensen frj=3D=3D=3Dchem.au.dk <owner-chemistry+/-ccl.net> wrote:

Gaussian by default assum= es that the frequency analysis is done at a stationary point, and projects = out the T+R to get 3N-6 frequencies.

If you are at a non-stati= onary point, use Freq=3DProjected to also project out the gradient, and thu= s get 3N-7 frequencies.

Note that this provides 3= N-7 frequencies, regardless of the number of geometry constraints imposed, = since the non-zero gradient is still only a one-dimensional quantity.

=C2=A0

Frank

=C2=A0

Frank Jensen

Assoc. Prof., Vice-Chair<= u>

Dept. of Chemistry=

Aarhus University<= u>

http://old.chem.au.dk/~frj

=C2=A0

From: owner-ch= emistry+frj=3D=3Dch= em.au.dk+/-ccl.net [mailto:owner-chemistry+frj=3D=3Dchem.au.dk+/-ccl.net] On Behalf Of Ankur Gupta ankkgupt**umail.iu.edu
Sent: 24. august 2016 20:00
To: Frank Jensen
Subject: CCL:G: Constrained optimization and frequency calculation

=C2=A0

Hello,<= /p>

Thank you Prof. Dr. M= . Swart for answering my question. I found Baker's paper really helpful= . It discusses constrained optimization thoroughly but it does not focus mu= ch on normal mode analysis. I am more concerned about the frequencies that we get from the Hessian after constrained optim= ization. The algorithm for constrained optimization has been implemented in= most of the computational chemistry software. But I am not able to underst= and the frequencies that it shows after the constrained optimization.

Thank you

Ankur

=C2=A0

On Sat, Aug 20, 2016 at 5:03 AM, Marcel Swart marcel= .swart/./icrea.cat <<= a href=3D"mailto:owner-chemistry[-]ccl.net" target=3D"_blank">owner-chemist= ry[-]ccl.net> wrote:

Dear Ankur,

=C2=A0

I would suggest to have a look at PQS (Baker, Pulay = and co-workers) or QUILD (Swart and co-workers).

Both use Baker=E2=80=99s elegant solution to constra= ined optimizations.

=C2=A0

Baker, "Constrained optimization in delocalized= internal coordinates=E2=80=9D

Journal of Computational Chemistry 18, 1079 (1997)

=C2=A0

PQS:

=C2=A0

QUILD:

=C2=A0

Marcel

=C2=A0

On 19 Aug 2016, at 22:33, Ankur Kumar Gupta ankkgupt= *indiana.edu <owner-chemistry*ccl= .net> wrote:

=C2=A0


Sent to CCL by: "Ankur Kumar Gupta" [ankkgupt||indiana.edu]
Hello,

I have been reading about constrained optimization. I have read several pap= ers related to the topic including the classic Reaction path Hamiltonian fo= r polyatomic molecules by Miller et al. This and other research articles de= scribe what is known as 'projection operator' method to do optimization keeping one or more internal coord= inates constant. Theoretically, we should get 3N-6 non-zero eigenvalues fro= m the force constant matrix (for a molecule having N nuclei) but if we appl= y m number of constraints in the molecule, we should obtain 3N-6-m non-zero eigenvalues (frequencies). Also, in cases= where the constraint corresponds to a non-equilibrium geometry, there will= be coupling between rotational and vibrational motion due to which the num= ber of non-zero eigenvalues might change. But for the sake of simplicity, we can talk about equilibrium geom= etries only. I use Gaussian 09 and I observed that the number of non-zero e= igenvalues did not change after constrained optimization. !
I know there are many computational chemistry softwares out there and I wou= ld like to know if there is a software which can do constrained optimizatio= n correctly and give me the right number and magnitude of eigenvalues (freq= uencies) after the optimization.

Thank you
Ankur



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_____________________________________
Prof. Dr. Marcel Swart, FRSC

ICREA Research Professor at
Institut de Qu=C3=ADmica Computacional i Cat=C3=A0lisi (IQCC)
Univ. Girona (Spain)

COST Action CM1305 (ECOSTBio) chair
Girona Seminar 2016 organizer

IQCC director<= /u>

RSC Advances associate e= ditor

Young Academy of Europe = member

=C2=A0

=C2=A0

=C2=A0


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