def plotShiftedPotentialDiff(minDist,
maxDist,
chartName,
filename="plotPotentialDiff"):
shift = MDFunctions.LennardJonesPotential(3, constants.eps, constants.sig)
series = np.linspace(2.8, 3.1, 100)
pot = MDFunctions.LennardJonesPotential(series, constants.eps,
constants.sig, 0)
pot2 = MDFunctions.LennardJonesPotential(series, constants.eps,
constants.sig, shift)
diff = pot - pot2
plt.subplot(1, 1, 1)
plt.title(chartName)
plt.plot(series, pot, label=f'Non shifted')
plt.plot(series, pot2, label=f'Shifted')
plt.plot(series, diff, label=f'Difference between shifted and non shifted')
plt.xlabel('distance (sigmas)')
plt.ylabel('force')
plt.legend()
plt.savefig(f'./fig/{filename}.jpg')
plt.show()
def plotPotential(minDist, maxDist, chartName, filename="plotPotential"):
series = np.linspace(minDist, maxDist, 100)
pot = MDFunctions.LennardJonesPotential(series, constants.eps,
constants.sig)
shiftedPot = MDFunctions.LennardJonesPotential(series, constants.eps,
constants.sig,
constants.cutOffRange)
#plt.subplot(1,1,1)
plt.title(chartName)
plt.plot(series, pot, label=f'Unmodified')
plt.plot(series, shiftedPot, label=f'Shifted')
plt.xlabel('distance (sigmas)')
plt.ylabel('force')
plt.legend()
plt.savefig(f'./fig/{filename}.jpg')
plt.show()
def eulerCromer(p, n, dt, particles, eps, sig):
scaleBy = 24
acc_vec = np.array([0.0, 0.0, 0.0])
pot = 0.
for op in particles:
if op is p:
continue
distvec = np.subtract(p.x[n], op.x[n])
dist = np.sqrt(distvec[0]**2 + distvec[1]**2 + distvec[2]**2)
forcescalar = 2 * (dist**-12) - dist**-6
acc_vec += forcescalar * (distvec / dist**2.0)
pot += MDFunctions.LennardJonesPotential(dist, eps, sig)
p.p[n + 1] = pot
p.a[n + 1] = scaleBy * acc_vec
p.v[n + 1] = p.v[n] + dt * p.a[n + 1]
p.x[n + 1] = p.x[n] + dt * p.v[n + 1]
return p
def euler(p, n, dt, particles, eps, sig):
scaleBy = 24
acc_vec = np.array([0.0, 0.0, 0.0])
pot = 0.
#for op in particles:
plen = len(particles)
for op in particles:
if op is p:
continue
distvec = np.subtract(p.x[n], op.x[n])
dist = np.sqrt(distvec[0]**2 + distvec[1]**2 + distvec[2]**2)
# pointTo = np.linalg.norm(distvec)
forcescalar = 2 * (dist**-12) - dist**-6
acc_vec = forcescalar * (distvec / dist**2)
pot = MDFunctions.LennardJonesPotential(dist, eps, sig)
#Initial particle
p.p[n + 1] += pot
p.a[n + 1] += scaleBy * acc_vec
p.v[n + 1] += p.v[n] + dt * p.a[n + 1]
p.x[n + 1] += p.x[n] + dt * p.v[n]
p.swap(n + 1)
