[Openmd-users] OpenMD stuntDoubles and visualizing the result

[Amila Kasunjith]

Dear Professor Dan Gezelter,

Thank you very much for your kind reply. This the first time that Sri
Lankan University is trying to build nano-particle simulation. Therefore we
are facing lot of troubles.

I have some more question regarding the OpenMD input file.


   1. In StuntDouble by using pv or pvqj we can define the position of each
   atom. As I feel it is very much difficult to hand written position of each
   atom. Is there any software for this. cant we do this work using PackMole.
   2. I also confused with the guidelines at the internet. "
   http://openmd.org/?cat=4"  Building and equilibrating a gold
   nanooparticle in OpenMD steps from 2 to down. from where do we have to call
   these commands
   3. finally I had a problem in Installing the software after running the
   command "make", It gives me error after installing  97%


I am very much thank full to you If you can provide me necessary
information on these maters

Thank you

Best Regards
Kasun
ᐧ

On 8 February 2015 at 22:34, Dan Gezelter <gezelter at nd.edu> wrote:

> Dear Kasun,
>
>   One easy way to visualize what the StuntDoubles are doing is to use the
> Dump2XYZ program that is built with openmd:
>
>   Dump2XYZ -i file.dump -o file.xyz -m -b
>
> The flags that are relevant here are:
>
>   -i         input dump file
>   -o         output file name
>   -b         Convert to base atom type  (default=off)
>   -m         map to the periodic box  (default=off)
>
> xyz files can be read in vmd and Jmol, and that's one of the primary ways
> of visualizing the output of a md, dump or eor file.
>
> The StuntDouble lines typically have one of two forms:
>
>   index pv    x y z  vx vy vz
>
> or
>
>   index pvqj  x y z  vx vy vz  qw qx qy qz  jx jy jz
>
> The first form (pv) is for StuntDoubles without internal structure like
> regular atoms.  It provides the index number of the StuntDouble, followed
> by a field specifier (pv = positions & velocities).  The next three fields
> are physical locations (in angstroms) of the StuntDouble, and then the
> following three fields are velocities (in angstroms/fs).
>
> The second form (pvqj) is used for StuntDoubles that have orientational
> degrees of freedom (for example: water, dipoles, or rigid bodies).  In this
> form, the field specifier (pvqj = positions, velocities, quaternions &
> angular momenta).
>
> The quaternions are a compact representation of the rotation matrix (A)
> that converts between body-fixed and space-frame coordinate systems:
>
>
>
>
> The jx, jy, and jz are body-fixed angular momenta for that StuntDouble.
>
> One of the nice features of Dump2XYZ is the automatic mapping of atoms in
> a rigid body into atomic positions in 3-D.  This program will probably help
> you significantly in trying to visualize your results.
>
> Best regards,
>
>  --Dan Gezelter
>
>
> > On Feb 7, 2015, at 5:05 AM, Amila Kasunjith <kasunjithamila at gmail.com>
> wrote:
> >
> > Hi.
> > I'm kasunjith, graduate from faculty of engineering University of
> Ruhuna. We are interested to model a Water-TiO2 mixture using OpenMD. We
> encounter some problem in stuntDoubles and visualizing the results.
> >
> > We need clear format of stuntDoubles in order to have develop a clear
> simulation. we are also interested to know about the method of visualizing
> the out put results.
> >
> > We are much thank full to you if you can provide me details on above
> matters
> >
> > thank you
> >
> > Best regards
> > Kasun
> >
> > --
> > K.A. Amila Kasunjith
> > B. Sc in Eng Undergraduate
> > Department of Mechanical and Manufacturing Engineering,
> > Faculty of Engineering,
> > University of Ruhuna.
> > Gall
> > Sri Lanka
> > 0712787343(mobile)
>
>
>
> ***********************************************
>   J. Daniel Gezelter
>   Associate Professor
>   Department of Chemistry and Biochemistry
>   251 Nieuwland Science Hall
>   University of Notre Dame
>   Notre Dame, IN 46556-5670
>
>   phone:  +1 (574) 631-7595
>   e-mail: gezelter at nd.edu
>   web:    http://www.nd.edu/~gezelter
> ************************************************
>
>
>
>
>
>


-- 
*K.A. Amila Kasunjith*
B. Sc in Eng Undergraduate
Department of Mechanical and Manufacturing Engineering,
Faculty of Engineering,
University of Ruhuna.
Gall
Sri Lanka
0712787343(mobile)
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