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()
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()