def compute_gr(sim, rho, beta, verbose=True): gr_calc = StaticPairCorrelationCalculator(dr=gr_dr, r_max=sim.config.box_size / 2) for i in xrange(200): sim.cycle(20) gr_calc.accumulate_config(sim.config) if verbose: virial, U_interact = calculate_thermodynamic_integrals( gr_calc.get_accumulated(), rho, beta) print 'compute cycle i=%04d H=%.4f <virial>=%.3f <U_i>=%.3f' % ( i, sim.evaluate_hamiltonian(), virial, U_interact) return gr_calc.get_accumulated()
forcefield = LJForceField(sigma=1.0, epsilon=1.0, r_cutoff=2.5) r_neighbor_skin = 1.0 * forcefield.sigma mass = 48 * forcefield.epsilon * forcefield.sigma ** -2 dt = 0.032 # Initialize system config0 = Config.create(N=N, rho=rho, dt=dt, sigma=forcefield.sigma, T=T, mass=mass) sim = MDSimulator(config0, forcefield, mass=mass, r_skin=r_neighbor_skin) # Equilibrate for i in xrange(200): sim.config.randomize_velocities(T=T, mass=mass) sim.cycle(50) print 'equilibrate cycle i=%03d U=%.3f' % (i, sim.evaluate_potential()) # Compute g(r) gr_calc = StaticPairCorrelationCalculator(dr=0.01 * forcefield.sigma, r_max=config0.box_size / 2) for i in xrange(1000): print 'compute cycle i=%04d H=%.4f ' % (i, sim.evaluate_hamiltonian()) sim.cycle(25) gr_calc.accumulate_config(sim.config) gr = gr_calc.get_accumulated() # Plot g(r) plt.clf() plt.plot(gr.r, gr.g) plt.xlabel('Pair Separation, $r$ ($\sigma$)') plt.ylabel('Reduced Pair Density, $g(r)$') plt.show()
# Initialize system config0 = Config.create(N=N, rho=rho, dt=dt, sigma=forcefield.sigma, T=T, mass=mass) sim = MDSimulator(config0, forcefield, mass=mass, r_skin=r_neighbor_skin) # Equilibrate for i in xrange(200): sim.config.randomize_velocities(T=T, mass=mass) sim.cycle(50) print 'equilibrate cycle i=%03d U=%.3f' % (i, sim.evaluate_potential()) # Compute g(r) gr_calc = StaticPairCorrelationCalculator(dr=0.01 * forcefield.sigma, r_max=config0.box_size / 2) for i in xrange(1000): print 'compute cycle i=%04d H=%.4f ' % (i, sim.evaluate_hamiltonian()) sim.cycle(25) gr_calc.accumulate_config(sim.config) gr = gr_calc.get_accumulated() # Plot g(r) plt.clf() plt.plot(gr.r, gr.g) plt.xlabel('Pair Separation, $r$ ($\sigma$)') plt.ylabel('Reduced Pair Density, $g(r)$') plt.show()