def oppg_4_3(return_protein):
T_step = -30 # increase the temp by this amount each iteration
N = 15
T_max = 1500
d = 600
N_T = (T_max // abs(T_step))
count = 0
# Matrix with all diameters for all twists and temp
length = np.zeros((N_T, d))
# Vector with mean energy for each temp
L_mean = np.zeros(N_T)
# Calculate energy
protein = Protein(N, T_max)
for j in range(T_max, -T_step, T_step):
print(j)
protein.change_temp(j)
for i in range(0, d):
protein.twist()
length[count][i] = protein.diameter()
L_mean[count] = np.mean(length[count])
count += 1
protein.change_temp(10**(-6))
for i in range(0, d):
protein.twist()
length[N_T - 1] = protein.diameter()
L_mean[N_T - 1] = np.mean(length[N_T - 1])
L_mean = L_mean[::-1]
# Create temp vector for plotting the mean diameter
x = np.arange(0, T_max, -T_step)
# Plot the mean diameter
plt.figure('exercise-4-3')
plt.title('Mean diameter')
plt.grid()
plt.xlabel('T')
plt.ylabel('$<$L$>$')
plt.plot(x, L_mean, color='#000000', linestyle='-')
plt.show()
if return_protein:
return protein, N
def oppg_4_1():
T_step = -30 # increase the temp by this amount each iteration
N = 15
T_max = 1500
d = 600
N_T = (T_max // abs(T_step)) * d
count = 0
# Vector with energy
energy = np.zeros(N_T)
# Calculate energy
protein = Protein(N, T_max)
for j in range(T_max, -T_step, T_step):
print(j)
protein.change_temp(j)
for i in range(0, d):
protein.twist()
energy[count] = protein.energy()
count += 1
protein.change_temp(10**(-6))
for i in range(0, d):
protein.twist()
energy[count] = protein.energy()
count += 1
# Create temp vector for plotting the energy
x = np.arange(0, N_T)
# Plot the energy
plt.figure('exercise-4-1')
plt.title('Protein energy')
plt.grid()
plt.xlabel('# twists')
plt.ylabel('Energy')
labels = []
for i in range(0, N_T, d):
if (i % (N_T / 10)) == 0:
labels.append(str(i))
else:
labels.append("")
plt.xticks(np.arange(0, N_T, d), labels)
plt.plot(x, energy, color='#000000', linestyle='-', linewidth=0.3)
plt.show()
def oppg_4_2():
T_step = -30 # increase the temp by this amount each iteration
N = 30
T_max = 1500
d = 600
N_T = (T_max // abs(T_step))
count = 0
# Matrix with all energies for all twists and temp
epsilon = np.zeros((N_T, d))
# Vector with mean energy for each temp
e_mean = np.zeros(N_T)
# Calculate energy
protein = Protein(N, T_max)
for j in range(T_max, -T_step, T_step):
print(j)
protein.change_temp(j)
for i in range(0, d):
protein.twist()
epsilon[count][i] = protein.energy()
e_mean[count] = np.mean(epsilon[count])
count += 1
protein.change_temp(10**(-6))
for i in range(0, d):
protein.twist()
epsilon[N_T - 1] = protein.energy()
e_mean[N_T - 1] = np.mean(epsilon[N_T - 1])
e_mean = e_mean[::-1]
# Create temp vector for plotting the mean energy
x = np.arange(0, T_max, -T_step)
# Plot the mean energy
plt.figure('exercise-4-2')
plt.title('Mean energy')
plt.grid()
plt.xlabel('T')
plt.ylabel('$<$E$>$')
plt.plot(x, e_mean, color='#000000', linestyle='-')
plt.show()