AVS Modules						              Load_sim
North Carolina State University

NAME
	Load_sim - a module to present molecular dynamics data of
	 	  chain-like molecules.
SUMMARY
     Name	   Loadsim

     Type	   data

     Inputs	   x-y-z coordinate data in binary form

     Outputs	   geometry

     Parameters    Name			  Type			Default
		  Config File		  File Browser
		  Sleep 		  Toggle		   On
		  Apply PBC/Unfold Traj.  Choice		   Off
		  Bounding Box		  Toggle	 	   Off
		  Sticks Only   	  Toggle		   Off
		  New Colors		  One Shot	   
		  Show All		  One Shot
		  Square Wells  	  Toggle		   Off
		  Snapshot		  Oneshot	
		  Radius		  Float			   2.00
		  Kill Module		  Oneshot
		  Rewind/Fast Forward	  Panels


DESCRIPTION
	The Loadsim module will create a ball and stick geometry representation
	of molecular dynamics or Monte Carlo data. The ability
	to interactively select positions in the data file as well 
	as individual chains is advantageous for visualizing chain motions.
	Although written for visualizing simple chain-like molecules
 	it can be extended to other systems.

INPUTS
	The input data is a binary file generated from your Fortran or C
	simulation program and consists of header information
	followed by x,y,z coordinates. The source(read_conf.c) for data input
	expects binary data, but can be modified to read ascii files.
	The reason for this is to minimize storage space for very large
	coordinate data files. The data file should be structured as follows:

	Header:

	Number of Chains, Chain Length, Simulation Box Length, 
	Segment or Bead Radius, Number of H type beads(under development)

	Coordinates:

	Move Number,  Array of x coord., Array of y coord.
	Array of z coord.
	Move Number,  Array of x coord., Array of y coord.
	Array of z coord.
	......

	Your favorite data type for each of these variables may 
	be specified in the header file(mytypes.h). The default is to
	read data generated from a FORTRAN program with the following
	output statements:

	  REAL BOXL,RAD,X(N),Y(N),Z(N) 
	  INTEGER NCHN,ICHNLEN,MOVNUM
	  OPEN(UNIT=60,FORM='UNFORMATTED')
	  WRITE(60)NCHN,ICHNLEN,BOXL,RAD,INT(0)
	  WRITE(60)MOVNUM,X,Y,Z

PARAMETERS
	Config File
	   Use this file browser to select the input file.

	Sleep
	   Use this toggle to start/stop the program.

	Apply PBC/Unfold Traj
	   It is assumed that the coordinate data is the actual position
	   rather the the periodic one. This switch applies periodic boundary
	   conditions from the box length information contained in the header
	   portion of the input data.

	Bounding Box
	   Turn on/off the bounding box for the simulation.

	Sticks Only
	   Represent the chain as a series of sticks rather than
	   a ball and stick model.

	New Colors
	   Randomly generate new colors. Attempts to generate saturated colors.

	Show all Chains
	   Redraws all chains. Selected after picking one or more chains
	   from the system in order to restore the view of all chains.
	   The module uses upstream geometry to allow the visualization 
	   of one or more chains by simply selecting a chain.

	Square Wells
	   Draws a semi-transparent sphere 1.5*(ball radius) around each bead.

	Snapshot
	   Draws a tube of size Radius around a given chain.

	Radius
	   Adjust the radius of the tube from snapshot. Must be applied before
	   the tube is constructed.

	Rewind/Forward
	   Presents a control panel to allow selection of particular
	   frames from the data file.

OUTPUTS

	Geometry data suitable for geometry viewer

EXAMPLE	1

          Load Simulation 
             |
          Geometry Viewer


LIMITATIONS/NOTES


AVS Module
Prashant Gupta 
Steven Smith
North Carolina State University