Molecular dynamics

simple visualization of live MD simulation visualisation



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# Run if you need extra packages: numba and scipy
!pip install scipy numba



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from IPython.display import clear_output

import numpy as np
from MD_utils import lennardjones, simple_molecule_vis
from scipy.constants import N_A
epsilon = 0.9959
sigma = 0.3405
k_B = 0.008311
M = 39.948

initial condition



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plt = simple_molecule_vis(bs=1)



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plt.plot.display()



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import numpy  as np
# bs jest rozmiarem kostki w której znajdują się cząstki.  
nx = 8
dx = sigma *1.2
bs = dx*nx 
box = np.array([bs,bs,bs])
try:
    plt.update_box(bs=bs)
    print("no plot object")
except:
    pass

Nparticles = nx**3
print(Nparticles)

U = np.zeros((3,Nparticles))
l = 0
for i in range(nx):
    for j in range(nx):
        for k in range(nx):
            U[:,l] = (dx*i-dx*(nx/2-0.50),dx*j-dx*(nx/2-0.5),dx*k-dx*(nx/2-0.5))
            l+=1
V = np.zeros_like(U)
plt.pkts.positions = U.T.copy()
plt.pkts.point_size = .3
plt.pkts.colors = 0xff0000*np.ones(Nparticles)



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box = np.array([bs,bs,bs])
%time Epot, F, Vir = lennardjones(U, box,sigma = 0.3405, epsilon=0.9959)



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V = 0.1*(np.random.randn(3,Nparticles)-0.5)



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%%time
# Start simulation

import time 
n_steps = 1520
dt = 0.005
N = Nparticles

box = np.array([bs,bs,bs])
plt.update_box(bs=bs)

(epot,F,Vir) = lennardjones(U,box,sigma = 0.3405, epsilon=0.9959)
traj = []
for i in range(n_steps):
    U += V * dt + 0.5 * F/M * dt * dt
    F0 = F[:]

    (epot, F, Vir) = lennardjones(U, box,sigma = 0.3405, epsilon=0.9959)
    
    V += 0.5 * (F + F0)/M * dt
    U -= bs*np.rint(U/bs)
    
    traj.append(U[:,233].copy())
    
    if i%10==0:
        T = M*np.sum(V**2)/(k_B*(3*N-6))  
        P = 1/bs**3*(  N*k_B*T + 1/3.*Vir )
        Ek = 0.5*M*np.sum(V**2)
        plt.pkts.positions = U.T.copy()
        plt.pkts.colors = (np.sum((V**2),axis=0)/10.0* 0xffffff).astype(np.int64)
        plt.update_box(bs=bs)
        clear_output(wait=True)
     
        print(i,epot,Ek,epot+Ek,"T=",T,"P=",P)
        print("Vir:",Vir)
        print("bs:",bs)
    
traj = np.array(traj)

The trajectory of a single atom



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import k3d



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plt_traj = k3d.points(traj.copy(), color=0xffff00, point_size=.05)
plt.plot += plt_traj



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