def run_comd():
cmd = parseCommandLine()
# init subsystems
sim = simflat.initSimulation(cmd)
sim.ePot = sim.pot.computeForce(sim.atoms, sim)
sim.eKinetic = initatoms.kineticEnergy(sim)
initValidate(sim)
timestepTime = 0.0
timestepTimeOneIteration = 0.0
iStep = 0
for jStep in range(0, sim.nSteps, sim.printRate):
printInfo(sim, iStep, timestepTimeOneIteration)
start = time.clock()
timestep(sim, sim.printRate, sim.dt)
end = time.clock()
timestepTimeOneIteration = end - start
if jStep >= sim.nSkip * sim.printRate:
timestepTime += timestepTimeOneIteration
iStep += sim.printRate
printInfo(sim, iStep, timestepTimeOneIteration)
printPerformanceResult(sim, timestepTime)
