[Openmd-users] OpenMD stuntDoubles and visualizing the result

[Dan Gezelter]

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:

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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
************************************************