Description
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, c,1,2 or your own application.
- How can you visualize (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
- Sharma, et al., “Immersive and interactive exploration of billion-atom systems,” Presence: Teleoperators Virtual Env. 12, 85 (2003).
- Zhang, et al., “ParaViz: a spatially decomposed parallel visualization algorithm using hierarchical visibility ordering,” Int’l J. Comput. Sci. 1, 407 (2007).
- Hesselink, et al., “Research issues in vector and tensor field visualization,” IEEE Comput. Graphics Appl. 14, 76 (1993).
- Ribarsky, et al., “Glyphmaker: creating customized visualizations of complex data,” IEEE Computer 27(7), 57 (1994).
- Sigfridsson, et al., “Tensor field visualisation using adaptive filtering of noise fields combined with glyph rendering,” IEEE Visualization 2002 (IEEE, 2002) p. 371.
- Zhang, et al., “Glyph-based comparative visualization for diffusion tensor fields,” IEEE T. Vis. Comput. Graphics 22, 797 (2016).
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