Diffusion

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

nsteps = 30001
stride = 300
obs_stride = 1

box_lengths = [150.0,150.0,150.0]
Temp=293.15
eta=1e-21
dt = 0.01

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)

A_pos = [[0.0,0.0,0]]
A_types = ['Core_1']

Simulation.register_molecule_type('A', A_pos, A_types)

D_rr = [[0.005,0,0],[0,0.04,0],[0,0,0.1]]
D_tt = [[0.5,0,0],[0,0.4,0],[0,0,0.1]]

Simulation.set_diffusion_tensor('A', D_tt, D_rr)

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

import numpy as np
from pyrid.system.distribute_vol_util import random_quaternion

N = 1000

position = np.zeros((N,3), dtype = np.float64)
quaternion = np.zeros((N,4), dtype = np.float64)

for i in range(N):
    quaternion[i][:] = random_quaternion()

mol_type_idx = np.zeros(N, dtype = np.int64)

Simulation.add_molecules('Volume',0, position, quaternion, mol_type_idx)

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

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

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

Simulation.print_timer()

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

#%%

Evaluation.MSD(100, 2, Simulation, 'A')

Evaluation.plot_MSD(Simulation, 'A', save_fig = True)

#%%

Evaluation.P2(3100, 100, Simulation, 'A')

Evaluation.plot_P2(Simulation, 'A', save_fig = True, limits = [[0.0,30],[1e-3,1e0]])

../../_images/Diffusion_Validation.png — Fig. 35 **Mean squared displacement and rotational relaxation.**