Part I: Molecular Dynamics Animation
Animate molecular dynamics (MD) simulation, choosing either of the following two options.
Option 1: Combine md.c and atomv.c to write a C/OpenGL program for in situ animation of simulation, following the lecture note on “Visualizing Molecular Dynamics III—Animation”.
Option 2: Use the VMD software (http://www.ks.uiuc.edu/Research/vmd) to post-process simulation data, following the lecture note on “VMD Animation of Molecular Dynamics”. (For the simulation, use lmd.c instead of md.c for a better speed.)
Assignment: Demonstrate its execution on your laptop to me during the office hours.
Part II: Visualizing an Electronic Wave Function
Visualize the wave function of a photo-excited hole (i.e., absence of an electron) in the Gaussian-
cube file, http://cacs.usc.edu/education/cs596/src/viz/MoSe2-hole.cube, as an
isosurface, following the lecture note on “VMD Animation of Molecular Dynamics”.
Assignment: Demonstrate its execution on your laptop to me during the office hours.
Final-Project Ideas
You may extend this assignment to your final project by adding additional features such as:
Color-coding the atoms with their kinetic-energy values. (A nice visual demonstration of thermal equilibration may be obtained by initializing half the MD box at a high temperature and the other half at a low temperature and observing how these temperatures will equilibrate.)
Color-coding the atoms by mapping their 3D velocities to points in the RGB color cube.
Animate parallel MD code, pmd.c,1,2 or your own application.
How can you visualize (e.g., color-code) the 3´3 stress tensor,3-6
αβ
N
#
α β
1
α β
#
1 du &
&
(α, β = x, y, z) ,
σi
=
%vi vi
+
∑ rij
rij
%−
(
(
2
Ω %
≠
$
r dr 'r=r
(
$
j ( i )
ij '
of the i-th atom (i = 0, ..., N-1), where N is the total number of atoms, W = LxLyLz is the volume of the simulation box, rijα is the a-th component of the vector rij = ri − rj , and u(r) is the Lennard-Jones potential function?
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References
A. Sharma, et al., “Immersive and interactive exploration of billion-atom systems,” Presence: Teleoperators Virtual Env. 12, 85 (2003).
C. Zhang, et al., “ParaViz: a spatially decomposed parallel visualization algorithm using hierarchical visibility ordering,” Int’l J. Comput. Sci. 1, 407 (2007).
L. Hesselink, et al., “Research issues in vector and tensor field visualization,” IEEE Comput. Graphics Appl. 14, 76 (1993).
W. Ribarsky, et al., “Glyphmaker: creating customized visualizations of complex data,” IEEE Computer 27(7), 57 (1994).
A. Sigfridsson, et al., “Tensor field visualisation using adaptive filtering of noise fields combined with glyph rendering,” IEEE Visualization 2002 (IEEE, 2002) p. 371.
C. Zhang, et al., “Glyph-based comparative visualization for diffusion tensor fields,” IEEE T. Vis. Comput. Graphics 22, 797 (2016).
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