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)
def timestep(sim, nSteps, dt):
for ii in range(nSteps):
advanceVelocity(sim.atoms, 0.5*dt)
advancePosition(sim, sim.atoms, dt)
# redistributeAtoms
sim.ePot = sim.pot.computeForce(sim.atoms)
advanceVelocity(sim.atoms, 0.5*dt)
#print('ke,pe = ',initatoms.kineticEnergy(sim)/sim.atoms.nAtoms,sim.ePot/sim.atoms.nAtoms)
sim.eKinetic = initatoms.kineticEnergy(sim)
def initValidate(sim):
ke = initatoms.kineticEnergy(sim)
pe = sim.ePot
print("Initial PE (cohesive energy) : ",pe/sim.atoms.nAtoms)
print("Initial energy : ",(ke+pe)/sim.atoms.nAtoms," atom count : ",sim.atoms.nAtoms)