Optimizing the performance of molecular dynamics ...
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Optimizing the performance of molecular dynamics ...
qResults ØScalability ØOptimizing the performance ØPhysics properties
qConclusion and discussion
Background qGeologic storage of carbon dioxide requires further understanding of a chemical system containing water, carbon dioxide and hydrocarbons; qSystematic studies on such system via MD require hundreds simulations with different T, P and composition; qMD are computationally expensive; qOptimizing performance of MD Simulation is important! c/o wiki.
Molecular Dynamics q3N second order coupled, nonlinear, ordinary differential equations; qNewton’s equation 𝐹 = 𝑚 $ 𝑎, 𝑎 =
'( ')
qForce from potential energy 𝐹⃗- = −
=
'*+ ; * ') 5
/ 𝑉(𝑟⃗ /01
);
qInitial position and velocity + Velocity Verlet algorithm solves the problem (in serial). Symplectic integrator: Energy conservation; Numerical stable; Time reversibility.
Molecular Dynamics—pair interaction qTotal potential energy of the system:
qShort-ranged interaction:
ØDirect sum is 𝑂(𝑁 9 ); ØIntroducing cutoff distance due to fast decay of LJ potential; ØVerlet list and cell list are combined to efficiently find neighbors within cutoff; ØResulting 𝑂(𝑁) complexity in CPU and memory. c/o D. Frenkel
