Date post: | 28-Mar-2015 |
Category: |
Documents |
Upload: | david-gill |
View: | 218 times |
Download: | 1 times |
Searching for Neighbor Atoms in Large-Scale
Atomistic Simulations
Wednesday, 10/30/2002
Interatomic Force Calculation in MD Simulation
A neighbor list is maintained for each atom to speed up force calculation.
€
Fi = fijj≠i
∑ Searching neighboring atoms
MPM: No Neighbor Particle Finding
€
M (n) = m( p)
n
∑ N (n,p)
€
F x(n) = m(p)N (n,p)bx
( p)
p
∑
F y(n) = m(p)N (n,p)by
( p)
p
∑
€
f x(n) =− V( p) σxx
( p)N,x(n,p) +σ xy
( p)N,y(n,p)
[ ]p
∑
f y(n) =− V( p) σxy
( p)N,x(n,p) +σ yy
( p)N,y(n,p)
[ ]p
∑
Interatomic Force Cut-off Radius
The size of the background grid equals the cut-off radius of the interatomic force.
Searing the Neighbor
Large-scale MD Simulation
Dynamically Update
Atoms List
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_c=linspace(0,0,ncell);plist_p=linspace(0,0,np);for p=1:np ix=ceil( x_p(p)/a ); iy=ceil( y_p(p)/a ); c=ncelly*(ix-1)+iy; plist_p(p)=plist_c(c); plist_c(c)=p;end
NeighborList
Initial Step
Neighbor List (Atom 1)
Neighbor List (Atom 2)
Neighbor List (Atom 3)
Neighbor List (Atom 4)
Any thing wrong?
Neighbor List (Atom 5)
Any thing wrong?
Neighbor List (Atom 6)
Anything wrong?
Neighbor List (Atom 7)
Neighbor List (Atom 8)
Neighbor List (Atom 9)
Neighbor List (Atom 10)
Neighbor List (Atom 11)
Neighbor List (Atom 12)
Anything wrong?
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_c=linspace(0,0,ncell);plist_p=linspace(0,0,np);for p=1:np ix=ceil( x_p(p)/a ); iy=ceil( y_p(p)/a ); c=ncelly*(ix-1)+iy; plist_p(p)=plist_c(c); plist_c(c)=p;end