numberofsteps = int(traj[traj.find("ion")+3:traj.find("S")])
print numberofsteps
center = zeros( (nmolecules,3) , float)
for i in range(nmolecules):
universe.addObject(Molecule('water', position = Vector(i*lattice_spacing, 0., 0.)))
center[i][0] = i*lattice_spacing
for atom in universe.atomList():
atom.setNumberOfBeads(P)
natoms = len(universe.atomList())
universe.setForceField(mbpolForceField(universe))
#This is the conversion factor to Units of K
Kper1overcm=11604.505/8065.54445
conv=Kper1overcm/1.196e-2
#print 1./(Units.k_B*0.37*Units.K)
#print traj
#rotskipval=float(argv[2])
mbpol_test=True
if mbpol_test:
trajectory = Trajectory(universe, traj)
else:
trajectory = Trajectory(None, traj)
print 'test'
npoints = len(trajectory)
theta_rad, k_theta))
elif fftype == "q-spc-fw":
ff.append(HarmonicBondForceField([a_list[0], a_list[2]], r_eq,
k_r))
ff.append(HarmonicBondForceField([a_list[1], a_list[2]], r_eq,
k_r))
ff.append(
HarmonicAngleForceField([a_list[0], a_list[2], a_list[1]],
theta_rad, k_theta))
es = ElectrostaticForceField(universe, fraction, o_charge)
ff.append(es)
lj = LennardJonesForceField(universe, epsilon, sigma)
ff.append(lj)
else:
ff.append(mbpolForceField(universe))
universe.setForceField(CompoundForceField(*ff))
trajectory = Trajectory(universe, traj)
###################################################
npoints = len(trajectory)
universe = trajectory.universe
natoms = universe.numberOfAtoms()
time = trajectory.time
np = universe.numberOfPoints()
P = np / natoms
kjtokcal = 0.239001
print Units.k_B
# Print averages of the quantu energy estimator
