Jiggling & Wiggling

February 15, 2006

Atomeye generated coloring file

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

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.

November 28, 2005

A PyMol generated gif file

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

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!

November 23, 2005

Coordinate number method

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

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.

November 22, 2005

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

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

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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