class MDSim:
def __init__(self, numpyart, rho, temp, force, stepsize=0.001):
"""Initializes the various parts of an MD simulation.
Parameters:
numpyart: Number of particles
rho : Density
temp : Temperature
force: A force model
stepsize: Time step
"""
self.geometry = CubicLattice( numpyart, rho ) # Initialize a geometry,
# in this case a cubic lattice.
self.system = Ensemble( self.geometry, temp ) # Create an ensemble to
# store information about
# the simulation.
self.solver = VeloVerlet( self.system, force, stepsize ) # Create the sampler class.
self.sampler = Sampler()
def run( self, nsteps, tSet):
"""Simulates N steps of the simulation."""
# Equilibration Run.
print "equilibrating %i steps" % (nsteps/2)
for n in range(0,nsteps/2,2):
self.solver.step()
if( n % 1000 == 0 ):
#self.system.setT(tSet)
print "step = %05i, temp = %12.7f" % (n, self.system.getT())
print "Equilibration done."
# Production Run.
for n in range(nsteps/2, nsteps+1):
# sample every 100 steps but only after nsteps / 2 equilibration steps
if( n % fil == 0 and n > nsteps / 2 ):
U = copy.deepcopy(self.system.getPos())
#Sampling
self.sampler.sampleData( U[0], U[1], U[2],
self.system.getEpot(),
self.system.getEkin(),
self.system.getT(),
self.system.getP(),
copy.deepcopy(self.system.getVel()) )
# print every 500 steps
if( n % 1000 == 0 ):
print "step = %05i, temp = %12.7f" % (n, self.system.getT())
self.solver.step() # take a simulation step
def __init__(self, numpyart, rho, temp, force, stepsize=0.001):
"""Initializes the various parts of an MD simulation.
Parameters:
numpyart: Number of particles
rho : Density
temp : Temperature
force: A force model
stepsize: Time step
"""
self.geometry = CubicLattice( numpyart, rho ) # Initialize a geometry,
# in this case a cubic lattice.
self.system = Ensemble( self.geometry, temp ) # Create an ensemble to
# store information about
# the simulation.
self.solver = VeloVerlet( self.system, force, stepsize ) # Create the sampler class.
self.sampler = Sampler()