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>
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Date: Thu, 6 Sep 2012 19:49:00 +0300
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Sent to CCL by: Amir Bernat [bernat^post.bgu.ac.il]
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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> &lt;<a href=3D"mail=
to:owner-chemistry+*+ccl.net">owner-chemistry+*+ccl.net</a>&gt; wrote:<br>&gt;<=
br>
&gt; Sent to CCL by: &quot;Bradley =A0 Welch&quot; [bwelch5 _ <a href=3D"ht=
tp://slu.edu">slu.edu</a>]<br>&gt; Hey everyone,<br>&gt;<br>&gt; I&#39;ve d=
one a few polarizability calculations with Gaussian and other programs. One=
 thing I&#39;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&#39;=
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>
&gt;<br>&gt;<br>&gt; Bradley Welch<br>&gt; Saint Louis University.<br>&gt;<=
br>&gt;<br>&gt;<br>&gt; -=3D This is automatically added to each message by=
 the mailing script =3D-<br>&gt; To recover the email address of the author=
 of the message, please change<br>
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et</a> or use:<br>
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ry/sub_unsub.shtml">http://www.ccl.net/chemistry/sub_unsub.shtml</a><br>
&gt;<br>&gt; Before posting, check wait time at: <a href=3D"http://www.ccl.=
net">http://www.ccl.net</a><br>&gt;<br>&gt; Job: <a href=3D"http://www.ccl.=
net/jobs">http://www.ccl.net/jobs</a><br>&gt; Conferences: <a href=3D"http:=
//server.ccl.net/chemistry/announcements/conferences/">http://server.ccl.ne=
t/chemistry/announcements/conferences/</a><br>
&gt;<br>&gt; Search Messages: <a href=3D"http://www.ccl.net/chemistry/searc=
hccl/index.shtml">http://www.ccl.net/chemistry/searchccl/index.shtml</a><br=
>&gt;<br>&gt;<br>&gt=
; =A0 =A0 =A0 <a href=3D"http://www.ccl.net/spammers.txt">http://www.ccl.ne=
t/spammers.txt</a><br>
&gt;<br>&gt; RTFI: <a href=3D"http://www.ccl.net/chemistry/aboutccl/instruc=
tions/">http://www.ccl.net/chemistry/aboutccl/instructions/</a><br>&gt;<br>=
&gt;<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>
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Date: Thu, 6 Sep 2012 19:21:54 -0400
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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>
>