Hi there.
On 1/20/11 5:29 PM, Li, Shunfang wrote:
My questions are the following:
1)Can we apply a constant initial velocity on some atoms of a system, in
a MD simulations performed by Siesta?
I know, the atoms are assigned random velocities drawn from the
Maxwell-Bolzmann distribution with the corresponding temperature in a MD
simulation, however, you know, the constraint of zero center of mass
velocity is imposed.
If you want to apply a constant *initial* velocity this is easily done
with a little trick.
You run a fake calculation at your interested target temperature. I call
it "fake", because you need this calculation only to have Siesta write
the XV file. You don't even need to converge the electronic density.
The XV file will contain the atomic positions (your initial coordinates
if you don't relax) and the velocities sampled form the
Maxwell-Boltzmann distribution, as you said.
You can edit that file and define the velocity you like for the atoms(s)
you like.
You are now ready to run your calculation, making sure you specify the
option MD.UseSaveXV true. In this way the initial positions and
velocities are read from the XV file.
This should do what you want.
2)Alternatively, can we apply external force on the atoms?
If it is okay, how to construct the input file? Or should we modify the
source code?
You should modify the source code, but the developers have prepared a
simple way for you to do it.
Edit the file constr.f in the Src folder and add the kind of constraint
that you like. If you add the line
fa(3,132) = 0.5
for instance, at each MD step the force along z of the atoms number 132
will be set to 0.5.
Don't forget to recompile Siesta and to specify the constraint:
%block GeometryConstraints
routine constr
%endblock GeometryConstraints
Good luck,
Riccardo
--
Riccardo Rurali
Institut de Ciència de Materials de Barcelona (ICMAB)
Consejo Superior de Investigaciones CientÃficas (CSIC)
Campus de Bellaterra
08193 Bellaterra (Barcelona)
Spain
tel.: +34 93 5801853 ext. 347
e-mail: [email protected]
http://www.icmab.es/dmmis/leem/
Man, the dope's that there's still hope
