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