Molecular Dynamics Basics (4.1, 4.2, 4.3) Liouville formulation (4.3.3) Multiple timesteps (15.3)

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Presentation transcript:

Molecular Dynamics Basics (4.1, 4.2, 4.3) Liouville formulation (4.3.3) Multiple timesteps (15.3)

2 Molecular Dynamics Theory: Compute the forces on the particles Solve the equations of motion Sample after some timesteps

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7 Molecular Dynamics Initialization –Total momentum should be zero (no external forces) –Temperature rescaling to desired temperature –Particles start on a lattice Force calculations –Periodic boundary conditions –Order NxN algorithm, –Order N: neighbor lists, linked cell –Truncation and shift of the potential Integrating the equations of motion –Velocity Verlet –Kinetic energy

8 Periodic boundary conditions

9 Lennard Jones potentials The truncated and shifted Lennard-Jones potential The truncated Lennard-Jones potential The Lennard-Jones potential

10 Phase diagrams of Lennard Jones fluids

11 Saving cpu time Cell listVerlet-list

12 Equations of motion Verlet algorithm Velocity Verlet algorithm

13 Lyaponov instability

14 Liouville formulation Depends implicitly on t Liouville operator Solution Beware: this solution is equally useless as the differential equation!

15 Shift of coordinatesShift of momenta Taylor expansion Let us look at them separately

16 We have noncommuting operators! Trotter identity

17 Velocity Verlet!

18 Velocity Verlet: vx=vx+delt*fx/2 x=x+delt*vx Call force(fx) vx=vx+delt*fx/2 Call force(fx) Do while (t<tmax) enddo

19 Liouville Formulation Velocity Verlet algorithm: Three subsequent coordinate transformations in either r or p of which the Jacobian is one: Area preserving Other Trotter decompositions are possible!

20 Multiple time steps What to use for stiff potentials: –Fixed bond-length: constraints (Shake) –Very small time step

21 Multiple Time steps Trotter expansion : Introduce: δt=Δt/n

22 Now n times : First

23 vx=vx+ddelt*fx_short/2 x=x+ddelt*vx Call force_short(fx_short) vx=vx+ddelt*fx_short/2 Call force(fx_long,f_short) Do ddt=1,n enddo vx=vx+delt*fx_long/2

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