1. Searching for Neighbor Atoms in Large-Scale Atomistic Simulations Wednesday, 10/30/2002

2. Interatomic Force Calculation in MD Simulation A neighbor list is maintained for each atom to speed up force calculation. Searching neighboring atoms

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_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

9. Neighbor List Initial 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_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