Hard-Sphere Fluid

import pyrid as prd

file_path='Files//'
fig_path = 'Figures//'
file_name='Hard_Sphere_Fluid'

nsteps = 2e3
stride = 20
obs_stride = 200
box_lengths = [75.0,75.0,75.0]
Temp=293.15
eta=1e-21
dt = 0.1

Simulation = prd.Simulation(box_lengths = box_lengths,
                            dt = dt,
                            Temp = Temp,
                            eta = eta,
                            stride = stride,
                            write_trajectory = True,
                            file_path = file_path,
                            file_name = file_name,
                            fig_path = fig_path,
                            boundary_condition = 'periodic',
                            nsteps = nsteps,
                            seed = 0,
                            length_unit = 'nanometer',
                            time_unit = 'ns')

Simulation.register_particle_type('Core_1', 2.5) # (Name, Radius)
Simulation.register_particle_type('Core_2', 5.0) # (Name, Radius)

A_pos = [[0.0,0.0,0.0]]
A_types = ['Core_1']
Simulation.register_molecule_type('A', A_pos, A_types)
D_tt, D_rr = prd.diffusion_tensor(Simulation, 'A')
Simulation.set_diffusion_tensor('A', D_tt, D_rr)

B_pos = [[0.0,0.0,0.0]]
B_types = ['Core_2']
Simulation.register_molecule_type('B', B_pos, B_types)
D_tt, D_rr = prd.diffusion_tensor(Simulation, 'B')
Simulation.set_diffusion_tensor('B', D_tt, D_rr)

prd.plot.plot_mobility_matrix('A', Simulation, save_fig = False, show = True)

k=100.0 #kJ/(avogadro*nm^2)

Simulation.add_interaction('harmonic_repulsion', 'Core_1', 'Core_1', {'k':k}, bond = False)
Simulation.add_interaction('harmonic_repulsion', 'Core_1', 'Core_2', {'k':k}, bond = False)
Simulation.add_interaction('harmonic_repulsion', 'Core_2', 'Core_2', {'k':k}, bond = False)

points, points_types, quaternion = Simulation.distribute('PDS', 'Volume', 0, ['A', 'B'], [1500,125], clustering_factor=1.0, max_trials=300)

Simulation.add_molecules('Volume',0, points, quaternion, points_types)

prd.plot.plot_scene(Simulation, save_fig = True)

Simulation.observe_rdf(rdf_pairs = [['A','A'],['A','B'],['B','B']], rdf_bins = [100,100,100], rdf_cutoff = [20.0,22.5,25.0], stride = obs_stride)

Simulation.observe('Orientation', molecules = ['A', 'B'], obs_stride = obs_stride)

Simulation.observe('Position', molecules = ['A', 'B'], obs_stride = obs_stride)

Simulation.run(progress_stride = 1000, out_linebreak = False)

Simulation.print_timer()

Evaluation = prd.Evaluation()
Evaluation.load_file(file_name)

Evaluation.plot_rdf([['A','A']], steps = range(5,10), average = True, save_fig = True)

Evaluation.plot_rdf([['A','B']], steps = range(5,10), average = True, save_fig = True)

Evaluation.plot_rdf([['B','B']], steps = range(5,10), average = True, save_fig = True)

Fig. 36 Radial distribution functions.