Graeme Ackland March 2010 Molecular Dynamics "Everything is made of atoms." Molecular dynamics simulates the motions of atoms according to the forces between them 1. Define positions of atoms 2. Calculate forces between them 3. Solve Newton’s equations of motion 4. Move atoms goto 1 ) ( ij i i i r U r m F Interatomic Potential – the only approximation
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Graeme Ackland March 2010 Molecular Dynamics "Everything is made of atoms." Molecular dynamics simulates the motions of atoms according to the forces between.
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Graeme AcklandMarch 2010
Molecular Dynamics
"Everything is made of atoms." Molecular dynamics simulates the motions of atoms
according to the forces between them
1. Define positions of atoms
2. Calculate forces between them
3. Solve Newton’s equations of motion
4. Move atoms
goto 1
)( ijiii rUrmF
Interatomic Potential – the only approximation
Graeme AcklandMarch 2010
Periodic Boundary Conditions
109 atoms - < micron
Looking beyond the boundary see an image of the atoms in the other side.
Least constraining boundary: all atoms are equivalent
Infinitely repeated array of supercells
Graeme AcklandMarch 2010
Finding the neighbours
Atoms interact with all others: time ~N2
Atoms only interact with nearby: time: ~N
A scheme for finding and maintaining neighbour lists.
Neighbourlist moves with the atom
Link cells are fixed in space
Graeme AcklandMarch 2010
Integration Schemes
Lots of mathematical schemes…
Runge-Kutta, Predictor-corrector, etc…
(integration error pushed to arbitrary order)
Generally use Verlet(integration error second order for