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

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

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MPM: No Neighbor Particle Finding

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Interatomic Force Cut-off Radius The size of the background grid equals the cut-off radius of the interatomic force.

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Searing the Neighbor

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Large-scale MD Simulation

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Dynamically Update Atoms List

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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

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Neighbor List Initial Step

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Neighbor List (Atom 1)

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Neighbor List (Atom 2)

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Neighbor List (Atom 3)

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Neighbor List (Atom 4) Any thing wrong?

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Neighbor List (Atom 5) Any thing wrong?

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Neighbor List (Atom 6) Anything wrong?

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Neighbor List (Atom 7)

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Neighbor List (Atom 8)

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Neighbor List (Atom 9)

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Neighbor List (Atom 10)

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Neighbor List (Atom 11)

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Neighbor List (Atom 12) Anything wrong?

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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

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Molecular dynamics (MD) simulations A deterministic method based on the solution of Newton’s equation of motion F i = m i a i for the ith particle; the.

Molecular dynamics (MD) simulations A deterministic method based on the solution of Newton’s equation of motion F i = m i a i for the ith particle; the.

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