- From the project
This project simulates water molecules whose
random motion is partially constrained in one direction.
Molecules are treated as points that have
a certain potential that governs their motion.
The directional constraint is established by parallel lines with
a Lennard-Jones potential.
I worked with the following people on this project:
- Dr. K. Smith - Furnished
the topic of this research project, a working simulation to start
from, and invaluable help in understanding the code involved.
- Dr. D. Banks - Described
project and goals, provided guidance and assistance through development.
Computational Simulation Program
- The simulation uses the "moldy" molecular dynamics simulation written
by Keith Refson, and modified by Dr. Smith.
- Homepage of Moldy
This program was modified to be fitted with an Open Inventor view of
the simulation by Dr. K. Smith. She provided me with a simulation
of the molecules diffusing un-impeded. It was my task to take the simulation
further, adding surface "tissue" to interact with the molecules.
- Modified Inventor viewer to allow for arbritrary number of water
- Added function to read in description of lines from a file. Each
line has a postion, direction, and repulsion factor.
- Inventor viewer displays the lines.
- The lines repel the water molecules. Since the state begins far
from equilibrium, the repulsive force of the bars is slowly scaled up
to 100% in order to prevent excessive velocities. There is a readout
of the scale in the bottom left-hand corner.
- Added glyph representing global molecular velocity. Each molecule's
velocity contributes a bump to the glyph. Large protrusions on the glyph
indicate a large number of molecules moving in that direction. This glyph
is always viewable in the lower left-hand corner of the screen, and may
be viewed larger by zooming out on the viewer (yes, out).
- I would like to work on these things.
- Fix camera-alignment of glyph in lower left. Right now it rotates with
the camera, but in the wrong directions.
- Study and debug the glyph. Is it correct? The results are surprising
so I wonder.
Zoomed out to see
The shots below show the program running with two different
line configurations. See the top views to see the layout of the lines.
- Coming soon.
- final.tar.gz (2.9MB)