Jiggling & Wiggling

2006/02/15

Atomeye generated coloring file

Filed under: Molecular Dynamics, Molecular Modeling, Ni3Al, Software — roylez @ 9:14 上午

atomeye generated coloring file

Originally uploaded by roylez.

It is really a long time since my last post about research stuff, emmh?
This pix is generated using the shear-strain coloring in atomeye, and it shows the cross section of a Ni3Al column in compression test. From it you can easily tell that the most highly stressed area is actully the surface.

2005/12/21

AtomEye: the software that those MIT guys use to plot atom

Filed under: Molecular Dynamics, Molecular Modeling — roylez @ 7:21 上午

AtomEye: the software that those MIT guys use to plot atom

Originally uploaded by roylez.

The day before yesterday, I had a very nice talk with Dr. Yunzhi Wang

from Ohio State University. Today I search for his homepage and find

another person in his department who interests me a lot.

http://www.mse.eng.ohio-state.edu/fac_staff/faculty/li/index.htmlx

Ju Li the assistant professor from MIT, who is the author of AtomEye, a

molecular modeling software. This software is exactly what those mit

guys used in their famous demonstration of dislocation multiplication.

This software is extremely small, about 3.5MB. And it is relies greatly

on command line. Luckily there is a well-written user manual for it on

the website.

http://164.107.79.177/Archive/Graphics/A/

2005/11/28

A PyMol generated gif file

Filed under: Molecular Dynamics, Molecular Modeling, Ni3Al — roylez @ 5:30 上午

A PyMol generated gif fileOriginally uploaded by roylez.

This is the gif file showing how dislocation would grow in a

twenty-Angstrom radius Ni3Al sample when compressed. It is quite

impressive, beautifully shows how dislocations and slip planes grow and

interact with each other.

I have tried to use Protein Explorer before turning to PyMol. PE, as I

think, is too much tricky to manipulate and very picky on browser as

well. But all the things in PyMol are easy, you simply click some thing,

almost everything can be done! I do not know why there is even less

document on PyMol on the net than rasmol and PE. Perhaps that is due to

PyMol is a young software, hmmm?

Python rocks, sourceforge rocks!

2005/11/23

Coordinate number method

Filed under: Molecular Dynamics, Molecular Modeling, Ni3Al — roylez @ 2:59 上午

Coordinate number methodOriginally uploaded by roylez.

This is picture is plotted completely at the same step as last one. This

time I use the coordinate number method to plot it. It is beautiful as I

have imagined.

2005/11/22

What the hell is it? Some kind of visual maze?

Filed under: Molecular Dynamics, Molecular Modeling, Ni3Al — roylez @ 6:19 上午

What the hell is it? Some kind of visual maze?

Originally uploaded by roylez.

My supervisor ask me to plot out the morphology of the dislocation in

the compression simulation of Ni3Al. I got this when trying that using

relative displacement method. It shows the cross section area, and looks

like a maze, isn’t it? Perhaps I should also try potential energy and

coordinate number, which might give me different image. Hmmm…

I think I am much nearer to the key.

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