From owner-chemistry@ccl.net Mon Dec 1 13:40:01 2014
From: "Mikael Johansson mikael.johansson(0)iki.fi" <owner-chemistry * server.ccl.net>
To: CCL
Subject: CCL: Jmol script for plotting 3D vectors on molecules: jvec2jmol
Message-Id: <-50784-141201132704-18194-9zUnCXGfQDLavvFBqBypyA * server.ccl.net>
X-Original-From: Mikael Johansson <mikael.johansson,+,iki.fi>
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Date: Mon, 1 Dec 2014 20:26:53 +0200 (EET)
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Sent to CCL by: Mikael Johansson [mikael.johansson[]iki.fi]
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Hello All,
Just in case someone happens to find it useful:
I couldn't find a quick and simple way to visualize vector data together
with molecules, especially in 3D; while the failure might very well be due
to a deficiency in googling skill, I made an attempt at creating a tool.
If you have a file wih vector data in six columns, in the simple format
x.coord y.coord z.coord d.x d.y d.z
the jvec2jmol script transform the vectors into Jmol script form for quick
visualization. At simplest, the syntax would be:
jvec2jmol.py data.txt data.jmol; jmol -s data.jmol
You will probably want to display some molecule as well, of course. The
default values of the script are biased towards displaying magnetically
induced current vectors, but are easily adjustable.
jvec2jmol has a few colour gradient options, and a rudimentary
understanding of translucency. It even comes with a quick but not
necessarily dirty mini-tutorial.
The script can be downloaded here; the .tar.gz file contains some simple
examples:
http://www.iki.fi/~mpjohans/scripts/
Of course, comments, bug reports, etc, are welcome.
Cheers,
Mikael J.
--
Dr. Mikael Johansson
Computational Biocatalysis
Department of Chemistry
Technische Universit�t M�nchen
mikael.johansson .. iki.fi
http://www.iki.fi/~mpjohans/
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From owner-chemistry@ccl.net Mon Dec 1 14:37:01 2014
From: "Igors Mihailovs igors.mihailovs0++gmail.com" <owner-chemistry[-]server.ccl.net>
To: CCL
Subject: CCL:G: Freezing the density of a fragment
Message-Id: <-50785-141201141658-17727-ZcdsQ4KBQdws4tc6NHn4Ng[-]server.ccl.net>
X-Original-From: Igors Mihailovs <igors.mihailovs0*|*gmail.com>
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Date: Mon, 1 Dec 2014 20:22:08 +0200
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Sent to CCL by: Igors Mihailovs [igors.mihailovs0 . gmail.com]
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Good day to everybody,
Is it possible to freeze electron density of some fragment during a
multi-molecular calculation, treating this fragment only as a source of
external potential? In Gaussian or some another program? Because it would
let us to run some very costly calculations, iteratively optimizing
electron density of each part... Thanks in advance!
With best regards,
Igors Mihailovs
Institute of Solid State Physics,
University of Latvia
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<div dir=3D"ltr"><div>Good day to everybody,<br><br></div>Is it possible to=
freeze electron density of some fragment during a multi-molecular calculat=
ion, treating this fragment only as a source of external potential? In Gaus=
sian or some another program? Because it would let us to run some very cost=
ly calculations, iteratively optimizing electron density of each part... Th=
anks in advance!<br><br clear=3D"all"><div><div><div><div><div class=3D"gma=
il_signature">With best regards,<br>Igors Mihailovs<br>Institute of Solid S=
tate Physics,<br></div><div class=3D"gmail_signature">University of Latvia<=
br></div><div class=3D"gmail_signature"><br></div></div>
</div></div></div></div>
--089e0158b86a80dd2f05092bb1d1--
From owner-chemistry@ccl.net Mon Dec 1 18:45:01 2014
From: "Fedor Goumans goumans]-[scm.com" <owner-chemistry ~~ server.ccl.net>
To: CCL
Subject: CCL:G: Freezing the density of a fragment
Message-Id: <-50786-141201162906-12123-JZnyi3qFLczR9KNSDtkp5A ~~ server.ccl.net>
X-Original-From: Fedor Goumans <goumans:+:scm.com>
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Date: Mon, 01 Dec 2014 22:28:58 +0100
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Sent to CCL by: Fedor Goumans [goumans .. scm.com]
Dear Igor,
You can use Frozen-Density Embedding, or subsystem DFT, with ADF to do
just that.
In the current implementation you can freeze the densities of different
subsystems so long as they are not covalently bound (with the exception
of '3-FDE' as applied to proteins).
Look at papers by (amongst others) Christoph Jacob, Johannes Neugebauer,
Michele Pavanello, Luuk Visscher, Tomasz Wesolowski on the
implementation in ADF and various applications.
A recent review: Jacob & Neugebauer, WIREs:CMS 4, 325 (2013) (doi:
10.1002/wcms.1175)
With kind regards,
Fedor
On 12/1/2014 7:22 PM, Igors Mihailovs igors.mihailovs0++gmail.com wrote:
> Good day to everybody,
>
> Is it possible to freeze electron density of some fragment during a
> multi-molecular calculation, treating this fragment only as a source
> of external potential? In Gaussian or some another program? Because it
> would let us to run some very costly calculations, iteratively
> optimizing electron density of each part... Thanks in advance!
>
> With best regards,
> Igors Mihailovs
> Institute of Solid State Physics,
> University of Latvia
>
--
Dr. T. P. M. (Fedor) Goumans
Business Developer
Scientific Computing & Modelling NV (SCM)
Vrije Universiteit, FEW, Theoretical Chemistry
De Boelelaan 1083
1081 HV Amsterdam, The Netherlands
T +31 20 598 7625
https://www.scm.com
https://twitter.com/SCM_Amsterdam