From owner-chemistry@ccl.net Thu Sep 6 12:01:00 2012 From: "Bradley Welch bwelch5[a]slu.edu" <owner-chemistry[]server.ccl.net> To: CCL Subject: CCL:G: ab initio polarizability calculations? Message-Id: <-47541-120906115942-14777-wo8EtxncjgcFiIjWBzm4Sw[]server.ccl.net> X-Original-From: "Bradley Welch" <bwelch5++slu.edu> Date: Thu, 6 Sep 2012 11:59:41 -0400 Sent to CCL by: "Bradley Welch" [bwelch5 _ slu.edu] Hey everyone, I've done a few polarizability calculations with Gaussian and other programs. One thing I've noticed is all these programs have to do multiple calculations to give you a polarizability. Is there a paper(or papers) that describes the general method of how these programs calculate polarizability? I'm assuming it has to consider the field in the x,y,z directions, and combinations of others, but I would like to figure out exactly how it does it. I'm not doing frequency dependent polarizability, only the static polarizability. Bradley Welch Saint Louis University. From owner-chemistry@ccl.net Thu Sep 6 12:52:00 2012 From: "Amir Bernat bernat-x-post.bgu.ac.il" <owner-chemistry!^!server.ccl.net> To: CCL Subject: CCL:G: ab initio polarizability calculations? Message-Id: <-47542-120906124906-25491-4hV/lBfe+6IEa3QubQxWAQ!^!server.ccl.net> X-Original-From: Amir Bernat <bernat#post.bgu.ac.il> Content-Type: multipart/alternative; boundary=bcaec54eeae2a3bda604c90b44d1 Date: Thu, 6 Sep 2012 19:49:00 +0300 MIME-Version: 1.0 Sent to CCL by: Amir Bernat [bernat^post.bgu.ac.il] --bcaec54eeae2a3bda604c90b44d1 Content-Type: text/plain; charset=ISO-8859-1 Hello, I just got this reply From the Gaussian help Email a few days ago: In Gaussian09, the combination of Placzek invariants (a2, b2) used to compute the Raman scattering activity, depolarization ratios (polarized and unpolarized) for each normal mode i, is as follows: a2_i = Sum_xy (1/9)*(dalpha_xx * dalpha_yy) b2_i = Sum_xy (1/2)*(3*dalpha_xy * dalpha_xy - dalpha_xx * dalpha_yy) where dalpha_xx = derivative the the polarizability with respect to the ith normal mode. Raman Activity = 45*a2_i + 7*b2_i Depolar (P) = 3*b2_i/(45*a2_i + 4*b2_i) Depolar (U) = 6*b2_i/(45*a2_i + 7*b2_i) The a2 and b2 invariants are not individually printed during a Freq=Raman calculation. The polarizability derivatives for each normal mode can however be printed using IOp(7/33=1). One could write a script which would extract these tensors, form the invariants and then combine them according to your particular optical setup. The individual a2 and b2 invariants are however printed (labeled Alpha2 and Beta2, respectively) if Freq=ROA is requested. This option is much more computationally demanding as the electric dipole - magnetic dipole and electric dipole - electric quadrupole polarizability derivatives are computed as well. Amir On Thu, Sep 6, 2012 at 6:59 PM, Bradley Welch bwelch5[a]slu.edu < owner-chemistry+*+ccl.net> wrote: > > Sent to CCL by: "Bradley Welch" [bwelch5 _ slu.edu] > Hey everyone, > > I've done a few polarizability calculations with Gaussian and other programs. One thing I've noticed is all these programs have to do multiple calculations to give you a polarizability. Is there a paper(or papers) that describes the general method of how these programs calculate polarizability? I'm assuming it has to consider the field in the x,y,z directions, and combinations of others, but I would like to figure out exactly how it does it. I'm not doing frequency dependent polarizability, only the static polarizability. > > > Bradley Welch > Saint Louis University.> > -- -- Amir Bernat http://physweb.bgu.ac.il/~bernat/ --bcaec54eeae2a3bda604c90b44d1 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable <div dir=3D"ltr"><div>Hello,</div><div><br></div>I just got this reply From= the Gaussian help Email a few days ago:<br><br><br><blockquote style=3D"ma= rgin:0px 0px 0px 40px;border:none;padding:0px">In Gaussian09, the combinati= on of Placzek invariants (a2, b2) used<br> to<br>compute the Raman scattering activity, depolarization ratios (polariz= ed<br>and unpolarized) for each normal mode i, is as follows: =A0<br>a2_i = =3D Sum_xy (1/9)*(dalpha_xx * dalpha_yy)<br>b2_i =3D Sum_xy (1/2)*(3*dalpha= _xy * dalpha_xy - dalpha_xx * dalpha_yy)<br> where dalpha_xx =3D derivative the the polarizability with respect to the<b= r>ith normal mode.<br><br>Raman Activity =3D 45*a2_i + 7*b2_i<br>Depolar (P= ) =3D 3*b2_i/(45*a2_i + 4*b2_i)<br>Depolar (U) =3D 6*b2_i/(45*a2_i + 7*b2_i= )<br> <br>The a2 and b2 invariants are not individually printed during a<br>Freq= =3DRaman calculation. =A0The polarizability derivatives for each<br>normal<= br>mode can however be printed using IOp(7/33=3D1). =A0One could write a<br= >script<br> which would extract these tensors, form the invariants and then combine<br>= them according to your particular optical setup. =A0<br>The individual a2 a= nd b2 invariants are however printed (labeled Alpha2<br>and Beta2, respecti= vely) if Freq=3DROA is requested. =A0This option is<br> much<br>more computationally demanding as the electric dipole - magnetic di= pole<br>and electric dipole - electric quadrupole polarizability derivative= s are<br>computed as well.=A0</blockquote><div style><br></div><div style> <br></div><div style>Amir=A0<br><br>On Thu, Sep 6, 2012 at 6:59 PM, Bradley= Welch bwelch5[a]<a href=3D"http://slu.edu">slu.edu</a> <<a href=3D"mail= to:owner-chemistry+*+ccl.net">owner-chemistry+*+ccl.net</a>> wrote:<br>><= br> > Sent to CCL by: "Bradley =A0 Welch" [bwelch5 _ <a href=3D"ht= tp://slu.edu">slu.edu</a>]<br>> Hey everyone,<br>><br>> I've d= one a few polarizability calculations with Gaussian and other programs. One= thing I've noticed is all these programs have to do multiple calculati= ons to give you a polarizability. Is there a paper(or papers) that describe= s the general method of how these programs calculate polarizability? I'= m assuming it has to consider the field in the x,y,z directions, and combin= ations of others, but I would like to figure out exactly how it does it. I&= #39;m not doing frequency dependent polarizability, only the static polariz= ability.<br> ><br>><br>> Bradley Welch<br>> Saint Louis University.<br>><= br>><br>><br>> -=3D This is automatically added to each message by= the mailing script =3D-<br>> To recover the email address of the author= of the message, please change<br> ><br>= ><br>><br>> = E-mail to subscribers: <a href=3D"mailto:CHEMISTRY+*+ccl.net">CHEMISTRY+*+ccl.n= et</a> or use:<br> > =A0 =A0 =A0 <a href=3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_message= ">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a><br>><br>> E-mai= l to administrators: <a href=3D"mailto:CHEMISTRY-REQUEST+*+ccl.net">CHEMISTRY= -REQUEST+*+ccl.net</a> or use<br> > =A0 =A0 =A0 <a href=3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_message= ">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a><br>><br>> Subsc= ribe/Unsubscribe:<br>> =A0 =A0 =A0 <a href=3D"http://www.ccl.net/chemist= ry/sub_unsub.shtml">http://www.ccl.net/chemistry/sub_unsub.shtml</a><br> ><br>> Before posting, check wait time at: <a href=3D"http://www.ccl.= net">http://www.ccl.net</a><br>><br>> Job: <a href=3D"http://www.ccl.= net/jobs">http://www.ccl.net/jobs</a><br>> Conferences: <a href=3D"http:= //server.ccl.net/chemistry/announcements/conferences/">http://server.ccl.ne= t/chemistry/announcements/conferences/</a><br> ><br>> Search Messages: <a href=3D"http://www.ccl.net/chemistry/searc= hccl/index.shtml">http://www.ccl.net/chemistry/searchccl/index.shtml</a><br= >><br>><br>>= ; =A0 =A0 =A0 <a href=3D"http://www.ccl.net/spammers.txt">http://www.ccl.ne= t/spammers.txt</a><br> ><br>> RTFI: <a href=3D"http://www.ccl.net/chemistry/aboutccl/instruc= tions/">http://www.ccl.net/chemistry/aboutccl/instructions/</a><br>><br>= ><br><br><br><br>-- <br><br>-- <br>Amir Bernat<br><a href=3D"http://phys= web.bgu.ac.il/~bernat/">http://physweb.bgu.ac.il/~bernat/</a><br> </div></div> --bcaec54eeae2a3bda604c90b44d1-- From owner-chemistry@ccl.net Thu Sep 6 17:49:00 2012 From: "jax cho cneks2012|a|gmail.com" <owner-chemistry+*+server.ccl.net> To: CCL Subject: CCL: Charmm code Message-Id: <-47543-120906163142-11968-6B+q8iuLoo9qqyczmVCjlw+*+server.ccl.net> X-Original-From: "jax cho" <cneks2012 .. gmail.com> Date: Thu, 6 Sep 2012 16:31:36 -0400 Sent to CCL by: "jax cho" [cneks2012%gmail.com] Hello, I am reading charmm code and wondering if anyone could give me a hint about subrouteine estrbnd of file escalar_mm. this subroutine should involve three atoms (idx, jdx and kdx) since it is related with one angle. The gradient, however, relates to four atoms, indexed with idx,jdx,kdx and additional ldx. Could anyone tell me what this ldx refer to? Thanks. Jax From owner-chemistry@ccl.net Thu Sep 6 19:24:00 2012 From: "Venable, Richard (NIH/NHLBI) E venabler===nhlbi.nih.gov" <owner-chemistry]^[server.ccl.net> To: CCL Subject: CCL: Charmm code Message-Id: <-47544-120906192224-23526-4t2QiOIB6le03FCDAa5FiQ]^[server.ccl.net> X-Original-From: "Venable, Richard (NIH/NHLBI) [E]" <venabler()nhlbi.nih.gov> Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 6 Sep 2012 19:21:54 -0400 MIME-Version: 1.0 Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler(_)nhlbi.nih.gov] I suggest posting such specific questions on the CHARMM forums at www.charmm.org Perhaps the code is working with the dihedral angle, which is defined by four atoms. -- Rick Venable 5635 FL/T906 Membrane Biophysics Section NIH/NHLBI Lab. of Computational Biology Bethesda, MD 20892-9314 U.S.A. (301) 496-1905 venabler AT nhlbi*nih*gov On 9/6/12 4:31 PM, "jax cho cneks2012|a|gmail.com" <owner-chemistry|*|ccl.net> wrote: > >Sent to CCL by: "jax cho" [cneks2012%gmail.com] >Hello, > >I am reading charmm code and wondering if anyone could give me a hint >about subrouteine estrbnd of file escalar_mm. > >this subroutine should involve three atoms (idx, jdx and kdx) since it is >related with one angle. The gradient, however, relates to four atoms, >indexed with idx,jdx,kdx and additional ldx. Could anyone tell me what >this ldx refer to? > >Thanks. > >Jax> >