Searching for Neighbor Atoms in Large-Scale Atomistic Simulations Wednesday, 10/30/2002.
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Transcript of Searching for Neighbor Atoms in Large-Scale Atomistic Simulations Wednesday, 10/30/2002.
![Page 1: Searching for Neighbor Atoms in Large-Scale Atomistic Simulations Wednesday, 10/30/2002.](https://reader035.fdocuments.in/reader035/viewer/2022062404/5515d7d5550346dd6f8b4947/html5/thumbnails/1.jpg)
Searching for Neighbor Atoms in Large-Scale
Atomistic Simulations
Wednesday, 10/30/2002
![Page 2: Searching for Neighbor Atoms in Large-Scale Atomistic Simulations Wednesday, 10/30/2002.](https://reader035.fdocuments.in/reader035/viewer/2022062404/5515d7d5550346dd6f8b4947/html5/thumbnails/2.jpg)
Interatomic Force Calculation in MD Simulation
A neighbor list is maintained for each atom to speed up force calculation.
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Fi = fijj≠i
∑ Searching neighboring atoms
![Page 3: Searching for Neighbor Atoms in Large-Scale Atomistic Simulations Wednesday, 10/30/2002.](https://reader035.fdocuments.in/reader035/viewer/2022062404/5515d7d5550346dd6f8b4947/html5/thumbnails/3.jpg)
MPM: No Neighbor Particle Finding
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M (n) = m( p)
n
∑ N (n,p)
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F x(n) = m(p)N (n,p)bx
( p)
p
∑
F y(n) = m(p)N (n,p)by
( p)
p
∑
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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
∑
![Page 4: Searching for Neighbor Atoms in Large-Scale Atomistic Simulations Wednesday, 10/30/2002.](https://reader035.fdocuments.in/reader035/viewer/2022062404/5515d7d5550346dd6f8b4947/html5/thumbnails/4.jpg)
Interatomic Force Cut-off Radius
The size of the background grid equals the cut-off radius of the interatomic force.
![Page 5: Searching for Neighbor Atoms in Large-Scale Atomistic Simulations Wednesday, 10/30/2002.](https://reader035.fdocuments.in/reader035/viewer/2022062404/5515d7d5550346dd6f8b4947/html5/thumbnails/5.jpg)
Searing the Neighbor
![Page 6: Searching for Neighbor Atoms in Large-Scale Atomistic Simulations Wednesday, 10/30/2002.](https://reader035.fdocuments.in/reader035/viewer/2022062404/5515d7d5550346dd6f8b4947/html5/thumbnails/6.jpg)
Large-scale MD Simulation
![Page 7: Searching for Neighbor Atoms in Large-Scale Atomistic Simulations Wednesday, 10/30/2002.](https://reader035.fdocuments.in/reader035/viewer/2022062404/5515d7d5550346dd6f8b4947/html5/thumbnails/7.jpg)
Dynamically Update
Atoms List
![Page 8: Searching for Neighbor Atoms in Large-Scale Atomistic Simulations Wednesday, 10/30/2002.](https://reader035.fdocuments.in/reader035/viewer/2022062404/5515d7d5550346dd6f8b4947/html5/thumbnails/8.jpg)
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
![Page 9: Searching for Neighbor Atoms in Large-Scale Atomistic Simulations Wednesday, 10/30/2002.](https://reader035.fdocuments.in/reader035/viewer/2022062404/5515d7d5550346dd6f8b4947/html5/thumbnails/9.jpg)
NeighborList
Initial Step
![Page 10: Searching for Neighbor Atoms in Large-Scale Atomistic Simulations Wednesday, 10/30/2002.](https://reader035.fdocuments.in/reader035/viewer/2022062404/5515d7d5550346dd6f8b4947/html5/thumbnails/10.jpg)
Neighbor List (Atom 1)
![Page 11: Searching for Neighbor Atoms in Large-Scale Atomistic Simulations Wednesday, 10/30/2002.](https://reader035.fdocuments.in/reader035/viewer/2022062404/5515d7d5550346dd6f8b4947/html5/thumbnails/11.jpg)
Neighbor List (Atom 2)
![Page 12: Searching for Neighbor Atoms in Large-Scale Atomistic Simulations Wednesday, 10/30/2002.](https://reader035.fdocuments.in/reader035/viewer/2022062404/5515d7d5550346dd6f8b4947/html5/thumbnails/12.jpg)
Neighbor List (Atom 3)
![Page 13: Searching for Neighbor Atoms in Large-Scale Atomistic Simulations Wednesday, 10/30/2002.](https://reader035.fdocuments.in/reader035/viewer/2022062404/5515d7d5550346dd6f8b4947/html5/thumbnails/13.jpg)
Neighbor List (Atom 4)
Any thing wrong?
![Page 14: Searching for Neighbor Atoms in Large-Scale Atomistic Simulations Wednesday, 10/30/2002.](https://reader035.fdocuments.in/reader035/viewer/2022062404/5515d7d5550346dd6f8b4947/html5/thumbnails/14.jpg)
Neighbor List (Atom 5)
Any thing wrong?
![Page 15: Searching for Neighbor Atoms in Large-Scale Atomistic Simulations Wednesday, 10/30/2002.](https://reader035.fdocuments.in/reader035/viewer/2022062404/5515d7d5550346dd6f8b4947/html5/thumbnails/15.jpg)
Neighbor List (Atom 6)
Anything wrong?
![Page 16: Searching for Neighbor Atoms in Large-Scale Atomistic Simulations Wednesday, 10/30/2002.](https://reader035.fdocuments.in/reader035/viewer/2022062404/5515d7d5550346dd6f8b4947/html5/thumbnails/16.jpg)
Neighbor List (Atom 7)
![Page 17: Searching for Neighbor Atoms in Large-Scale Atomistic Simulations Wednesday, 10/30/2002.](https://reader035.fdocuments.in/reader035/viewer/2022062404/5515d7d5550346dd6f8b4947/html5/thumbnails/17.jpg)
Neighbor List (Atom 8)
![Page 18: Searching for Neighbor Atoms in Large-Scale Atomistic Simulations Wednesday, 10/30/2002.](https://reader035.fdocuments.in/reader035/viewer/2022062404/5515d7d5550346dd6f8b4947/html5/thumbnails/18.jpg)
Neighbor List (Atom 9)
![Page 19: Searching for Neighbor Atoms in Large-Scale Atomistic Simulations Wednesday, 10/30/2002.](https://reader035.fdocuments.in/reader035/viewer/2022062404/5515d7d5550346dd6f8b4947/html5/thumbnails/19.jpg)
Neighbor List (Atom 10)
![Page 20: Searching for Neighbor Atoms in Large-Scale Atomistic Simulations Wednesday, 10/30/2002.](https://reader035.fdocuments.in/reader035/viewer/2022062404/5515d7d5550346dd6f8b4947/html5/thumbnails/20.jpg)
Neighbor List (Atom 11)
![Page 21: Searching for Neighbor Atoms in Large-Scale Atomistic Simulations Wednesday, 10/30/2002.](https://reader035.fdocuments.in/reader035/viewer/2022062404/5515d7d5550346dd6f8b4947/html5/thumbnails/21.jpg)
Neighbor List (Atom 12)
Anything wrong?
![Page 22: Searching for Neighbor Atoms in Large-Scale Atomistic Simulations Wednesday, 10/30/2002.](https://reader035.fdocuments.in/reader035/viewer/2022062404/5515d7d5550346dd6f8b4947/html5/thumbnails/22.jpg)
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