# -------------------------------------------------------------
# Initial Configuration
# -------------------------------------------------------------
bulk_configuration = nlread('Polystyrene.hdf5')[-1]

# -------------------------------------------------------------
# OPLS-AA Calculator
# -------------------------------------------------------------
potential_builder = OPLSPotentialBuilder()
calculator = potential_builder.createCalculator(bulk_configuration)
bulk_configuration.setCalculator(calculator)

# -------------------------------------------------------------
# Molecular Dynamics
# -------------------------------------------------------------
initial_velocity = ConfigurationVelocities(
    remove_center_of_mass_momentum=True
)

method = NPTMartynaTobiasKlein(
    time_step=1*femtoSecond,
    reservoir_temperature=300*Kelvin,
    reservoir_pressure=1*bar,
    thermostat_timescale=100*femtoSecond,
    barostat_timescale=500*femtoSecond,
    initial_velocity=initial_velocity,
    heating_rate=0*Kelvin/picoSecond,
)

constraints = [FixCenterOfMass()]

md_trajectory = MolecularDynamics(
    bulk_configuration,
    constraints=constraints,
    trajectory_filename='Polystyrene_Trajectory.hdf5',
    steps=100000,
    log_interval=10,
    trajectory_interval=1000,
    method=method
)

# -------------------------------------------------------------
# Calculate End to End Distance
# -------------------------------------------------------------
analyzer = FreeVolume(
      md_trajectory,
      start_time=0*ps,
      end_time=100*ps,
      time_resolution=10*ps,
      overlap_ratio=1.0,
      samples=10000
)
free_volume_ratio = analyzer.ratio()
time = analyzer.times().convertTo(ps)

# -------------------------------------------------------------
# Plot The Results
# -------------------------------------------------------------
import pylab
pylab.figure()
pylab.plot(time, free_volume_ratio)
pylab.xlabel('Time / ps')
pylab.ylabel('Free volume ratios')
pylab.savefig('Free_Volume_Ratio_Plot.png')