Searching for Neighbor Atoms in Large-Scale Atomistic Simulations

1
Searching for Neighbor Atoms in Large-Scale
Atomistic Simulations
Wednesday, 10/30/2002
2
Interatomic Force Calculation in MD Simulation
Searching neighboring atoms
A neighbor list is maintained for each atom to
speed up force calculation.
3
MPM No Neighbor Particle Finding
4
Interatomic Force Cut-off Radius
The size of the background grid equals the
cut-off radius of the interatomic force.
5
Searing the Neighbor
6
Large-scale MD Simulation
7
Dynamically Update Atoms List
8
Put Particles Into Cells
ncell is the total number of cells np is the
total number of particles a is the size of a
cell ncelly is the number of cells in y
direction plist_clinspace(0,0,ncell) plist_pl
inspace(0,0,np) for p1np ixceil( x_p(p)/a
) iyceil( y_p(p)/a )
cncelly(ix-1)iy plist_p(p)plist_c(c)
plist_c(c)p end
9
NeighborListInitial Step
10
Neighbor List (Atom 1)
11
Neighbor List (Atom 2)
12
Neighbor List (Atom 3)
13
Neighbor List (Atom 4)
Any thing wrong?
14
Neighbor List (Atom 5)
Any thing wrong?
15
Neighbor List (Atom 6)
Anything wrong?
16
Neighbor List (Atom 7)
17
Neighbor List (Atom 8)
18
Neighbor List (Atom 9)
19
Neighbor List (Atom 10)
20
Neighbor List (Atom 11)
21
Neighbor List (Atom 12)
Anything wrong?
22
Put Particles Into Cells
ncell is the total number of cells np is the
total number of particles a is the size of a
cell ncelly is the number of cells in y
direction plist_clinspace(0,0,ncell) plist_pl
inspace(0,0,np) for p1np ixceil( x_p(p)/a
) iyceil( y_p(p)/a )
cncelly(ix-1)iy plist_p(p)plist_c(c)
plist_c(c)p end