def getting_it_all(my, dt, beta, N, S0, I0,
R0): #since im doing it twice, I made a function
p = SIR_class(my, dt, beta, N)
solver = RungeKutta4(p)
solver.set_initial_condition([S0, I0, R0])
t = np.linspace(0, N * dt, N + 1)
u, t = solver.solve(t)
S = u[:, 0]
I = u[:, 1]
R = u[:, 2]
#unpacking u with the variables I need
plot_SIR(S, I, R, t) #plotting this S
def solve_SEIR(T, dt, S_0, E2_0):
"""Solves the differential equation given initial conditions and time"""
# Initial conditions and time
initial_conditions = [S_0, 0, E2_0, 0, 0, 0]
times = np.linspace(0, T, int(T / dt) + 1)
# Uses RungeKutta4 to solve
solver = RungeKutta4(SEIR)
solver.set_initial_condition(initial_conditions)
u, t = solver.solve(times)
return u, t
def test_asymptotic_limit():
U0 = [1, 1]
f = Problem(tau_A=8, tau_B=40)
from ODESolver import RungeKutta4
solver = RungeKutta4(f)
solver.set_initial_condition(U0)
dt = 10 / 60.0 # minutes
T = 50 # 50 min
n = int(round(T / float(dt)))
import numpy as np
time_points = np.linspace(0, T, n + 1)
u, t = solver.solve(time_points)
# Plot
u_A = u[:, 0]
u_B = u[:, 1]
assert f.test_asymptotic_limit(u_A, u_B, tol=0.001)
from matplotlib.pyplot import plot, show, legend
plot(t, u_A, t, u_B)
legend(['u_A', 'u_B'], loc='lower left')
show()
S, I, R, V = u
new_S = -self.beta * S * I - self.p(t, self.vt) * S
new_I = self.beta * S * I - self.my * I
new_R = self.my * I
new_V = self.p(t, self.vt) * S
return new_S, new_I, new_R, new_V
if __name__ == "__main__":
max_infected = np.zeros(32)
qq = 0
a = False
for i in range(32):
plt.clf()
problem = SIRV2(0.1, 0.5, 0.0005, 120, p, i)
solver = RungeKutta4(problem)
solver.set_initial_condition([1500, 1, 0, 0])
t = np.linspace(0, 60, 121)
u, t = solver.solve(t)
S = u[:, 0]
I = u[:, 1]
R = u[:, 2]
V = u[:, 3]
max_infected[i] = np.amax(I)
q = np.amax(I)
tol = 0.5
if abs(qq - q) < tol and a == False:
ii = i
print "when we have vacinated %d days, from day 6, to day %d, we have the most effective vaccination period" % (
u_k = u[k, :]
u_k_minus_1 = u[k - 1, :]
test = np.abs(np.sum(u_k_minus_1) - np.sum(u_k))
tol = 1e-9
msg = "They aint the same bro. THEY AINT THE SAME"
if test < tol:
return False
else:
print(msg)
return True
U0 = (7000, 30, 0, 0)
swaggyboi = RungeKutta4(solvelolve)
swaggyboi.set_initial_condition(U0)
u, t = swaggyboi.solve(t, terminate=terminate)
def plottelott(u, t):
S = []
I = []
R = []
D = []
for i in range(len(u)):
S.append(u[i][0])
I.append(u[i][1])
R.append(u[i][2])
D.append(u[i][3])
if __name__ == "__main__":
n = 240 #number of points
alpha = 0.0016#chance that a human kills a zmobie
sigma = 2.0 #number of new people
gammaS = 0.014#chance that a susceptible human dies
gamma1 = 0.014#chance that an infected human dies
p = 1#chance that an human zombie turns into a zombie
beta = 0.0012 #chance of human turning zombie
T = 24 #time in hours
S0 = 10 #start humans
I0 = 0 #start infected
Z0 = 100 #start zombies
R0 = 0 #start removed
p = SIZR_class(alpha, sigma, gamma1, gammaS, p, beta, n)
solver = RungeKutta4(p)
solver.set_initial_condition([S0, I0, Z0, R0])
t = np.linspace(0, T, n+1)
u, t = solver.solve(t)
#using ODESolver and RungeKutta to get the values I need
S = u[:, 0]
I = u[:, 1]
Z = u[:, 2]
R = u[:, 3]
#unpacking the values
plot4zombie(t, S, I, Z, R)
#plotting the thing
"""
terminal > python SIZR.py
from ODESolver import ODESolver, ForwardEuler, RungeKutta4
def f(u, t):
M = 1 # SolarMasses
G = 4 * pi**2 # AU^3/(yr^2*SM)
x, y, vx, vy = u
dx = vx
dy = vy
radius = sqrt(x**2 + y**2)
dvx = -G * M * x / radius**2
dvy = -G * M * y / radius**2
return [dx, dy, dvx, dvy]
planet = RungeKutta4(f)
x = 1
y = 0 # AU
vx = 0
vy = 2 * pi # AU/yr
U0 = [x, y, vx, vy]
planet.set_initial_condition(U0)
time_points = linspace(0, 10, 1001)
u, t = planet.solve(time_points)
x, y, vx, vy = u[:, 0], u[:, 1], u[:, 2], u[:, 3]
plt.plot(x, y)
plt.axis('equal')
plt.show()
class SIR:
def __init__(self, beta, nu):
self.beta = beta
self.nu = nu
def __call__(self, u, t):
S, I, R = u[0], u[1], u[2]
dS = -self.beta * S * I
dI = self.beta * S * I - self.nu * I
dR = self.nu * I
return [dS, dI, dR]
S0 = 1000
I0 = 1
R0 = 0
model = SIR(beta=0.001, nu=1 / 7.0)
solver = RungeKutta4(model)
solver.set_initial_condition([S0, I0, R0])
time_points = np.linspace(0, 100, 101)
u, t = solver.solve(time_points)
S = u[:, 0]
I = u[:, 1]
R = u[:, 2]
plt.plot(t, S, t, I, t, R)
plt.show()
class Decay:
def __init__(self, a):
self.a = a
def __call__(self, u, t):
return -self.a * u
#b
decay_inst = Decay(a)
#c
T = 20000
tp = np.linspace(1, T, T / 500)
RK = RungeKutta4(decay_inst)
RK.set_initial_condition(u0)
u, t = RK.solve(tp)
def exact(t):
return np.exp(-a * t)
print(
f"Difference between exact, {exact(T):.5f}, and approxiamate {u[len(u)-1]:.5f}, is {np.abs(exact(T) - u[len(u)-1]):.5f} after {T} years. limited to decimals"
)
plt.plot(t, u, label="approximate fraction of particals that remain")
plt.plot(t, exact(t), label="Exact fraction of particals that remain", ls="--")
plt.subplot(4, 1, 1)
plt.title("RungeKutta2")
for i in n:
t = np.linspace(-17, 17, i)
RK2 = RungeKutta2(f)
RK2.set_initial_condition(y0)
u, t = RK2.solve(t)
plt.plot(t, u, label=f"n = {i} steps")
plt.legend()
plt.subplot(4, 1, 2)
plt.title("RungeKutta4")
for i in n:
t = np.linspace(-17, 17, i)
RK4 = RungeKutta4(f)
RK4.set_initial_condition(y0)
u, t = RK4.solve(t)
plt.plot(t, u, label=f"n = {i} steps")
plt.legend()
plt.subplot(4, 1, 3)
plt.title("Heun")
for i in n:
t = np.linspace(-17, 17, i)
H = Heun(f)
H.set_initial_condition(y0)
u, t = H.solve(t)
plt.plot(t, u, label=f"n = {i} steps")
plt.legend()
test_Cooling()
#c)
T0 = 95 #temperature when t=0 in C
t1 = 15; T1 = 92 #temperature after 15 seconds in C
U0 = T0
dt = t1; tstop = 3600
N = int (tstop/dt)
timepoints = np.linspace(0, tstop, N)
for color, Ts in zip([ "slateblue", "darkorange"], [20,25]):
h = estimate_h(t1, Ts, T0, T1)
cool = Cooling(h, Ts)
dTdt = RungeKutta4(cool)
dTdt.set_initial_condition(U0)
u, t = dTdt.solve(timepoints, cool.terminate)
print(f"Surrounding temperature: {Ts}. Coffee temperature when poured into the cup: {u[0]}◦C. After 15 sec: {u[1]}")
plt.plot(t, u, f"{color}", label = f"Ts = {Ts}")
plt.legend()
plt.xlabel("time (seconds)")
plt.ylabel("Temperature (◦C)")
plt.title("Solutions-Newton’s law of cooling")
plt.show()
"""
(plot)
from ODESolver import RungeKutta4
import numpy as np
import matplotlib.pyplot as plt
def SIR_model(u, t):
beta = 0.001
nu = 1 / 7.0
S, I, R = u[0], u[1], u[2]
dS = -beta * S * I
dI = beta * S * I - nu * I
dR = nu * I
return [dS, dI, dR]
S0 = 1000
I0 = 1
R0 = 0
solver = RungeKutta4(SIR_model)
solver.set_initial_condition([S0, I0, R0])
time_points = np.linspace(0, 100, 101)
u, t = solver.solve(time_points)
S = u[:, 0]
I = u[:, 1]
R = u[:, 2]
plt.plot(t, S, t, I, t, R)
plt.show()
seconds = 10
time_array = linspace(0, seconds, timepoints)
V0 = 8 # Voltage of battery when on
def Q_der(Q,t): # Definition of Q'(t)
return (V0 - Q/C)/R
# __Exercise a__
def Q_exact(t): # Q(t) exact (only for charge-up).
return (Q0 - C*V0)*exp(-t/(R*C)) + C*V0
circuit_FE = ForwardEuler(Q_der)
circuit_FE.set_initial_condition(Q0)
Q_FE, t = circuit_FE.solve(time_array)
circuit_RK4 = RungeKutta4(Q_der)
circuit_RK4.set_initial_condition(Q0)
Q_RK4, t = circuit_RK4.solve(time_array)
plt.plot(t, Q_FE, label='$Q(t)$, Forward Euler')
plt.plot(t, Q_RK4, label='$Q(t)$, Runge Kutta 4')
many_time_steps = linspace(0, seconds, 1001) # For analytical solution.
plt.plot(many_time_steps, Q_exact(many_time_steps), label='$Q(t)$, exact')
plt.xlabel('Time [seconds]')
plt.ylabel('Electric charge [colomb]')
plt.title('Charging capasitor')
plt.legend()
plt.savefig('fig_E2.1.pdf')
plt.clf()
# __Exercise b__