1. ? Flow chart of a molecular dynamics simulation
2016/11/15
Name: _____________________________
Purpose: calculate energy and temperature time histories of Ar gas (n molecules).
Variables (vector): x[n], y[n], z[n], vx[n], vy[n], vz[n], fmx[n], fmy[n], fmz[n], dfmx[n][n], dfmy[n][n], dfmz[n][n].
Read Initial conditions, constants, parameters
Q: Describe the appropriate initial conditions for x, vx, fmx.
Q: What constants need to be defined?
(e.g. Boltzmann constant)
Q: What other simulation parameters are needed?
(e.g. number of timesteps)
Force computation
Q: Write down the analytical expression for the force (dfmx[i][j]) acting between the atoms at positions x[i], y[i], z[i] and x[j], y[j], z[j].
Q How do you account for the periodic boundary condition?
Force summation
Q: Complete the following c script to calculate the force acting on atom i.
for(i=1; i<=nmol-1; i++){ }
Velocity update
Q: Complete the following c script to update the velocity of atom i.
for(i=1; i<=nmol-1; i++){ }
Position update
Q: Complete the following c script to update the position of atom i.
Q How do you account for the periodic boundary condition?
for(i=1; i<=nmol-1; i++){ }
Write output data
Q: What information do you need to output and how frequently?
Plot
Energy, Temperature ?
Time