Dear All,
Now, I am doing the simulation in the system containing Carbon atoms. I used the Tersoff potential as interatomic interaction. My initial configuration is Carbon rich 6*sqrt(3) R30. Then I do the equilibration at 300 K. First of all I only create the velocity at 300 K, then I run the equilibration for long enough MD steps. But, I feel something strange, because some of my carbon atoms jump far away from their initial region. Then, I change the way to do this, I start to create the velocity at 10 K and increase my temperature slowly to 300 K. But, I found that some atoms still jump. I think the attractive force is not high enough for my system, or maybe I should change the way to do the equilibration at 300 K. Do you have an Idea to solve this problem?
What I expect is for low temperature e.g. 300 K, the Carbon atoms do not move away from their region, but they prefer to move little around their original position.
Thanks for your answer and I do appreciate for it.
“I do need extra glue in my simulation” 
—> this line is just kidding.
rizal
Research Assistant, Complex Liquid Laboratory
National Central University Taiwan
Dear All,
Now, I am doing the simulation in the system containing Carbon atoms. I used
the Tersoff potential as interatomic interaction. My initial configuration
is Carbon rich 6*sqrt(3) R30. Then I do the equilibration at 300 K. First of
all I only create the velocity at 300 K, then I run the equilibration for
long enough MD steps. But, I feel something strange, because some of my
carbon atoms jump far away from their initial region. Then, I change the way
you have to be a bit more specific about what you mean by "jump".
is it a single long distance jump, that could just be a manifestation
of periodic boundary conditions, or that atoms separate from your
structure, which could be cause by "dangling" bonds or overlapping
atoms due to PBC.
to do this, I start to create the velocity at 10 K and increase my
temperature slowly to 300 K. But, I found that some atoms still jump. I
think the attractive force is not high enough for my system, or maybe I
should change the way to do the equilibration at 300 K. Do you have an Idea
to solve this problem?
What I expect is for low temperature e.g. 300 K, the Carbon atoms do not
move away from their region, but they prefer to move little around their
original position.
Thanks for your answer and I do appreciate for it.
"I do need extra glue in my simulation" ---> this line is just
kidding.
i recommend to stay away from superglue;
it may not look good to have a keyboard
stuck to your fingers... 
cheers,
axel.
Thanks Dr. Axel for your answer. The thing happen is some atoms separate quite far from their species in Z-direction. I do not apply the periodic boundary condition at Z-direction to make it like a surface. I have tried to consider the long range interaction by adding the distance of neighbor atoms, but it seems doesn’t work. The initial position of atoms has a quite far distance beyond the cutoff distance in formation hexagonal 6sqrt(3) x 6sqrt(3) R30. What I expect is after relaxation they will form diamondlike structure, like in the experiment. Unfortunately, I cannot find it in my simulation. The atoms start to jump after the hit another atoms because of random motion, then I tried to start from the low temperature e.g. 10 K, and the thing still happen.
Then I have an idea to just draw the result using GIMP and everything done. — just kidding.
Thanks for your answer, any suggestion will really help me.
rizal
2011/3/23 Axel Kohlmeyer <[email protected]>