Questions
Why is energy stability important
Mention an advantage and a disadvantage of
classical molecular dynamics.
What is MD?
We are theoretical physicists.
MD are theoretical simulations aiming to
describe and explain a multitude of
phenomena.
Motivation
Representative for many of the calculations
we do
Classical dynamics
Li ,
i=1
and Hamiltonian
get momentum
pi (ri , ri , t) =
ri
H=
ri pi L
H
ri =
p
Potential
The potential is the most complicated part.
At any time it depends on the position of
all other particles.
Classical vs ab-initio
Very fast
Can handle systems
Slow
10^3 atoms if one has
Potential dependent
Wrong
Solves the
up to 10^10 atoms
Schrdinger/Dirac
equations for the
electrons. Results are
very accurate.
V (rij ) = 4
12
6
6
12
rij
rij
0.1
Vr
0.0
0.1
0.2
0.3
0.4
2.5
3.0
3.5
4.0
r
4.5
5.0
The MD cycle
Implementation
Performance
400
Version 1
Time1000 steps s
300
200
100
0
0
3
4
Atoms x1000
V eV
0.0
0.1
0.2
0.3
0.4
3
Cutoff
Version 2
Only evaluate forces if the distance is
smaller than cutoff
400
Time1000 steps s
300
Version 1
Version 2 Cutoff
200
100
0
0
3
4
Atoms x1000
Version 3
Neighbourcells
Divide the simulation box into cells of size
slightly larger than the cutoff
Implementation
Parallel model
One block handles a cell
Each thread handles an atom, and calculates
the potential from all the atoms in its own
and neighbouring cells
first integrator
second integrator
force calculations
Stability
Its faster!
100
Time1000 steps s
80
60
Version 1
Version 2, Cutoff
Version 3, Cells
40
20
0
0
10
15
Atoms x1000
20
25
Reflection
The GPU is very fast
Naive implementation is easy to do
Optimized implementation become
increasingly harder to debug
Questions?