def compute_thermodynamics(rho, T, verbose=True):
beta = 1.0 / T
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_system(sim)
gr = compute_gr(sim, rho, beta, verbose=True)
virial, U_interact = calculate_thermodynamic_integrals(gr, rho, beta)
return virial, U_interact
def get_equilibrated_simulation(rho, T):
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)
for i in xrange(500):
if not i%10:
sim.config.randomize_velocities(T=T, mass=mass)
sim.cycle(50)
U = sim.evaluate_potential()
print 'equilibrate cycle i=%03d U=%.3f' % (i, U)
return sim
def compute_thermodynamics(rho, T, verbose=True):
beta = 1.0 / T
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_system(sim)
gr = compute_gr(sim, rho, beta, verbose=True)
virial, U_interact = calculate_thermodynamic_integrals(gr, rho, beta)
return virial, U_interact
from pyljfluid.components import (LJForceField, Config, MDSimulator,
StaticPairCorrelationCalculator)
import matplotlib.pyplot as plt
# Parameters
N = 1000
rho = 0.2
T = 1.5
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)
StaticPairCorrelationCalculator)
import matplotlib.pyplot as plt
# Parameters
N = 1000
rho = 0.2
T = 1.5
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())
