Transcription of How does classical MD work? - LAMMPS
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How does classical MD work? - LAMMPS
How does classical MD work? classical MD basicsEach of N particles is a point massatomgroup of atoms (united atom)macro- or meso- particleParticles interact via empirical force lawsall physics in energy potential forcepair-wise forces (LJ, Coulombic)many-body forces (EAM, Tersoff, REBO)molecular forces (springs, torsions)long-range forces (Ewald)Integrate Newton s equations of motionF = maset of 3N coupled ODEsadvance as far in time as possibleProperties via time-averaging ensemblesnapshots (vs MC sampling)MD timestepVelocity-Verlet formulation:update V by 1/2 step (using F)update X (using V)build neighbor lists (occasionally)compute F (using X)apply constraints & boundary conditions (on F)update V by 1/2 step (using new F)output and diagnosticsCPU time break-down:inter-particle forces = 80%neighbor lists = 15%everything else = 5%Aside on MD integration schemesMost MD codes use some form of explicit Stormer-VerletOnly second-order: E=| E E0| t2 Global stability trumps local accuracy of high-order schemesCan be shown that for Hamiltonian equations of motion,Stormer-Verlet exactly conserves a shadow Hamiltonian andE Es O( t2)For users: no energy drift over millions of timestepsFor developers: easy to decouple integration scheme fromefficient algorithms for force evaluation, parallelization32 atom LJ cluster200M timesteps t= issuesAre always limited in number of atoms and length of time youcan simulateThese have a larg
Global stability trumps local accuracy of high-order schemes ... glass relaxation (seconds to decades) rheological experiments (Hz to KHz) ... Muller-Plathe via x viscosity Green-Kubo via x ave/correlate. Examples of rheological simulations Polymer aggregation under shear.
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