# STM:The CAVE and Immersadesk

# Introduction

Scientific visualization is a powerful method to display the results of computer simulations and/or experimental measurements. The functionality of the Application Visualization System (AVS) from Advanced Visual Systems, Inc. modules have been ported to the Immersadesk© environment from Pyramid Systems, Inc.

There are two applications, one called IMolecule for the display of the geometric structure of molecules and the other is IMD for the display of the results of molecular dynamics simulations.

# IMolecule

The IMolecule application code is designed to read geometric structure information of a molecule from a variety of file formats. For more information see the SC97 presentation.

For these displays, the visualization process begins by reading the structural information and other output data from the calculation. The data is currently displayed using traditional ball and stick models. The size of the atom is determined from the van der Waals radii, and one can input coordinates in either Bohrs or Angstroms.

To run type:

`IMolecule filename filetype units`

Navigation throughout the molecule is accomplished by:

1. Button 1: Toggle between rotation on or off (initially off). This follows the position of the wand.
2. Button 2: Toggle between scale and translation (initially scale). The actual functionality is controlled only by the joystick.
3. Button 3: Reset to initial configuration.

The program currently can read structural information from the following types of files:

1. Plain XYZ Coordinates called PlainCoord. Atom types are specified by the numerical entry in periodic table.
2. XYZ Coordinates called coord. Atom types specified by atomic name as a character string.
3. Gaussian© Cube Files called Cube.
4. Brookhaven Protein Data Bank called pdb.
5. GAMESS Coordinates via a PERL script called PGamess.
6. GAMESS Plotting Option called Gamess Cube.
7. MSI DCAR called Dcar.
8. DMOL XYZ called DMOL_XYZ.
9. Mopac Electrostatic Potential called Mopac ESP.
10. Mopac coordinates called Mopac XYZ.
11. MOL2 called mol2.
12. MOL called mol.
13. CHEM3D called Chem3d.
14. Molecular Mechanics Code MM3 called mm3.

# IMD

The IMD application code is designed to read the results of a molecular dynamics (MD) simulation of spherically symmetric, electrically neutral atom system interacting via a Lennard-Jones potential. The atoms are displayed as spheres, colored by the magnitude of the velocity. (Red being the fastest and blue being the slowest). For more information see the SC97 presentation.

The executable file is CaveDyn0, which is set to read the file `mdvis.dat.kenf_N64` 1000 time steps 64 particles. The source file is CaveDyn0.c for the the CaveDyn0 executable and lastly, a Makefile to make the executable, make cave0 to make the CaveDyn0 executable.