I'm working on a physics simulation where particles collide together and I need to calculate the resulting velocities of the particles after the collision. For that, the following formulas are given (I have to use these, I've found other equations online which caused me different problems):
I've tried to recreate them like this:
def reflect_particle_velocity(Pa, Pb, Va, Vb, Ma, Mb):
Vas = (np.sqrt(np.square(Va[0]) + np.square(Va[1])))
Vbs = (np.sqrt(np.square(Vb[0]) + np.square(Vb[1])))
Prel = [np.abs(Pa[0] - Pb[0]), np.abs(Pa[1] - Pb[1])]
Vrel = [np.abs(Va[0] - Vb[0]), np.abs(Va[1] - Vb[1])]
dotFactor = np.dot(Vrel, Prel) / np.dot(Prel , Prel)
MaFact = (2 * Mb) / (Ma + Mb)
MbFact = (2 * Ma) / (Ma + Mb)
NewVa = [(Vas - (MaFact * dotFactor)) * Prel[0], (Vas - (MaFact * dotFactor)) * Prel[1]]
NewVb = [(Vbs + (MbFact * dotFactor)) * Prel[0], (Vbs + (MbFact * dotFactor)) * Prel[1]]
return NewVa, NewVb
Where Pa is the 2D position of the first particle, Pb is the 2D position of the second particle, Va is the 2D velocity of the first particle, Vb is the 2D velocity of the second particle, Pa is the 2D position of the first particle, Pb is the 2D position of the second particle, Ma is the mass of the first particle and Mb is the mass of the second particle.
Using this code I get the following readings:
The green line being the total energy in the system. As you can see it's increasing massively, infact, the first few values are around 200 slowly going upward. What I've noticed is that somehow my code increases the velocity too much. either that or I've created a working perpetual motion machine...
What have I done wrong?
EDIT:
Here is the code used for generating data/displaying the energy over time:
import numpy as np
import matplotlib.pyplot as plt
def step(pos, vel, mas, Na, Nb, R, dt, boxX, boxY):
pos = step_particles_pos(pos, vel, dt)
vel = step_particles_vel(vel, dt)
vel = check_collisions_bbox(pos, vel, boxX, boxY, Na + Nb)
vel = check_collisions_particles(pos, vel, mas, Na, Nb, R)
return pos, vel
def step_particles_pos(pos, vel, dt):
#return np.array([pos[:, 0] + (vel[:, 0] * dt), pos[:, 1] + (vel[:, 1] * dt) - 0.5 * (9.8 * np.square(dt))])
pos[:, 0] = pos[:, 0] + (vel[:, 0] * dt)
pos[:, 1] = pos[:, 1] + (vel[:, 1] * dt) - 0.5 * (9.8 * np.square(dt))
return pos
def step_particles_vel(vel, dt):
vel[:, 1] = vel[:, 1] - (9.8 * dt)
return vel
def check_collisions_bbox(pos, vel, boxX, boxY, N):
posMaskNy = np.zeros(np.shape(pos))
posMaskPx = np.zeros(np.shape(pos))
posMaskPy = np.zeros(np.shape(pos))
posMaskNy = np.where(pos < 0, 1, posMaskNy)
posMaskPx = np.where(pos > boxX, 1, posMaskPx)
posMaskPy = np.where(pos > boxY, 1, posMaskPy)
posMaskPx[:, 1] = 0
posMaskPy[:, 0] = 0
posMask = posMaskNy + posMaskPx + posMaskPy
posMask = np.where(posMask != 0, -1, posMask)
posMask = np.where(posMask == 0, 1, posMask)
vel = vel * posMask
return vel
def reflect_particle_velocity(Pa, Pb, Va, Vb, Ma, Mb):
Vas = (np.sqrt(np.square(Va[0]) + np.square(Va[1])))
Vbs = (np.sqrt(np.square(Vb[0]) + np.square(Vb[1])))
Prel = [np.abs(Pa[0] - Pb[0]), np.abs(Pa[1] - Pb[1])]
Vrel = [np.abs(Va[0] - Vb[0]), np.abs(Va[1] - Vb[1])]
dotFactor = np.dot(Vrel, Prel) / np.dot(Prel , Prel)
MaFact = (2 * Mb) / (Ma + Mb)
MbFact = (2 * Ma) / (Ma + Mb)
NewVa = [(Vas - (MaFact * dotFactor)) * Prel[0], (Vas - (MaFact * dotFactor)) * Prel[1]]
NewVb = [(Vbs + (MbFact * dotFactor)) * Prel[0], (Vbs + (MbFact * dotFactor)) * Prel[1]]
return NewVa, NewVb
def check_collisions_particles(pos, vel, mas, Na, Nb, R):
A = pos[:, 0]
B = pos[:, 1]
Xdiff = np.abs(A - A[:, np.newaxis])
Ydiff = np.abs(B - B[:, np.newaxis])
diff = np.triu(np.sqrt(np.square(Xdiff) + np.square(Ydiff)))
diffMask = np.where(diff == 0 , R + 1, diff)
diffMask = np.where(diffMask <= R , -1, diffMask)
diffMask = np.where(diffMask > R , 0, diffMask)
invertIDs = np.argwhere(diffMask)
for int in invertIDs:
vel[int[0]], vel[int[1]] = reflect_particle_velocity(pos[int[0]],
pos[int[1]],
vel[int[0]],
vel[int[1]],
mas[int[0]],
mas[int[1]])
return vel
def get_kinetic_energy(vel, M, start, end):
N = end - start
results = np.zeros(N)
factor = ( 1 / (2 * N) ) * M
for i in range(0, N):
results[i] = factor * np.dot(np.abs(vel[i]), np.abs(vel[i]))
return results
def get_potential_energy(pos, M, start, end):
N = end - start
results = np.zeros(N)
factor = ( 1 / N ) * M * 9.8
for i in range(0, N):
results[i] = factor * pos[i][1]
return results
def get_average(a, n):
sum = 0
for i in range(0, int(n)):
sum = sum + a[i]
return sum / n
Na = 30 # number of A particles
Nb = 30 # number of B particles
Ma = 0.025 # weight of A particles
Mb = 0.05 # weight of B particles
R = 0.04 # particle radius
T = 100 # simulation time
dt = 0.004 # time increments
dts = 0.04 # measurement increments
stept = T / dt # number of cycles in simulation
steps = T / dts # number of measurements
ints = stept / steps # interval between measurements
samples = 0 # number of measurements taken
qTimes = 10 # inverval of quiver display
qStep = T / qTimes # number of steps between quiver displays
boxX = 8 # width of the bounding box
boxY = 16 # height of the bounding box
# generate random starting positions/velocities
# for the amount of particles in the simulation.
posX = np.random.rand(Na + Nb)
posY = np.random.rand(Na + Nb)
velX = np.random.rand(Na + Nb)
velY = np.random.rand(Na + Nb)
MA = np.full(Na, Ma)
MB = np.full(Nb, Mb)
mas = np.concatenate((MA, MB), axis=0)
timespace = np.linspace(0, T, int(steps))
# merge the two arrays into one containing tuples.
pos = np.array((posX * boxX, posY * boxY)).T
vel = np.array([velX, velY]).T
KEa = np.zeros(int(steps))
KEb = np.zeros(int(steps))
PEa = np.zeros(int(steps))
PEb = np.zeros(int(steps))
TE = np.zeros(int(steps))
# cycle stept amount of times
for i in range(0, int(stept)):
# update all particles
pos, vel = step(pos, vel, mas, Na, Nb, R, dt, boxX, boxY)
if i % ints == 0:
KEa[samples] = get_average(get_kinetic_energy(vel, Ma, 0, Na), Na)
KEb[samples] = get_average(get_kinetic_energy(vel, Mb, Na, Na + Nb), Nb)
PEa[samples] = get_average(get_potential_energy(pos, Ma, 0, Na), Na)
PEb[samples] = get_average(get_potential_energy(pos, Mb, Na, Na + Nb), Nb)
TE[samples] = KEa[samples] + KEb[samples] + PEa[samples] + PEb[samples]
samples = samples + 1
#Energy over Time plot
plt.figure(figsize=(10, 6))
plt.tick_params(axis='both', labelsize=14)
plt.grid(True)
plt.xlabel('Time', fontsize=16)
plt.ylabel('Energy', fontsize=16)
plt.plot(timespace, KEa, color="royalblue")
plt.plot(timespace, KEb, color="navy")
plt.plot(timespace, PEa, color="gold")
plt.plot(timespace, PEb, color="yellow")
plt.plot(timespace, TE, color="green")
plt.show()
Related
I used the RK4 method to calculate the radiated spectrum for a two-
level system in quantum mechanics in matplotlib. I also want to plot
the signal along the vertical axis together in the same figure, but
my code doesn’t implement it. The code is provided below (I also
attached the original figure (Fig. (a)). In general, some clear
explanation to plot another x,y-axis as in the first attached figure.
Many thanks to all in advance.
[enter image description here]
[enter image description here]
: https://i.stack.imgur.com/lYLCs.jpg.
enter image description here
The goals of this code are:
1) Numerical calculation of the Bloch equations and 2) Calculated
the radiated spectra from a two-level system.
Numerical calculation was performed using RK4 method. The Fast
Fourier Transform (FFT) was also been used.
import numpy as np
from scipy.integrate import odeint
import matplotlib.pyplot as plot
import math
from scipy.fftpack import*
plot.rcParams.update({'font.size': 16})
# Parameters
n= 30 # Number of optical cycles.
Om0 = 1.5/27.2114 # Carrier frequency.
Om = Om0 # Transition frequency.
dt = 0.1 # Time step.
E0 = 1#np.sqrt(I/I0) # Electric peak
t = np.arange(0,2*np.pi*n/Om0,0.01) # Time in x-axis data.
d = 1.0 # Dipole moment.
h_par = 1.0 # The reduced Planck constant (=1 in a.u.)
E = E0 * np.cos(Om0*t) # Electric pulse.
OmR = d*E/h_par # Rabi Flopping frequency.
N = np.size(t) # Total number of samples.
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
## Numerical solutions using RK4 method.
# Define Bloch system
def f1(t,u,v,w):
return Om * v
def f2(t,u,v,w):
return -Om * u -2 * (E0*np.cos(Om0*t)) * w
def f3(t,u,v,w):
return 2 * (E0*np.cos(Om0*t)) * v
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
def integrate(u0,v0,w0):
u = np.zeros(N)
v = np.zeros(N) # Filled with arrays with zeros.
w = np.zeros(N)
u[0] = u0 # Construct initial conditions.
v[0] = v0
w[0] = w0
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# The fourth-order Runge-Kutta coefficients (RK4)
for i in range(N-1):
k1u = dt * f1(t[i], u[i], v[i], w[i])
k1v = dt * f2(t[i], u[i], v[i], w[i])
k1w = dt * f3(t[i], u[i], v[i], w[i])
k2u = dt * f1(t[i] + 0.5 * dt, u[i] + 0.5 * k1u, v[i] + 0.5 * k1v, w[i] + 0.5 * k1w)
k2v = dt * f2(t[i] + 0.5 * dt, u[i] + 0.5 * k1u, v[i] + 0.5 * k1v, w[i] + 0.5 * k1w)
k2w = dt * f3(t[i] + 0.5 * dt, u[i] + 0.5 * k1u, v[i] + 0.5 * k1v, w[i] + 0.5 * k1w)
k3u = dt * f1(t[i] + 0.5 * dt, u[i] + 0.5 * k2u, v[i] + 0.5 * k2v, w[i] + 0.5 * k2w)
k3v = dt * f2(t[i] + 0.5 * dt, u[i] + 0.5 * k2u, v[i] + 0.5 * k2v, w[i] + 0.5 * k2w)
k3w = dt * f3(t[i] + 0.5 * dt, u[i] + 0.5 * k2u, v[i] + 0.5 * k2v, w[i] + 0.5 * k2w)
k4u = dt * f1(t[i] + dt, u[i] + k3u, v[i] + k3v,w[i] + k3w)
k4v = dt * f2(t[i] + dt, u[i] + k3u, v[i] + k3v,w[i] + k3w)
k4w = dt * f3(t[i] + dt, u[i] + k3u, v[i] + k3v,w[i] + k3w)
u[i + 1] = u[i] + (k1u + 2 * k2u + 2 * k3u + k4u)/6
v[i + 1] = v[i] + (k1v + 2 * k2v + 2 * k3v + k4v)/6
w[i + 1] = w[i] + (k1w + 2 * k2w + 2 * k3w + k4w)/6
return u,v,w
# Initial conditions
u1,v1, w1 = integrate(0.0,0.0,-1.0)
## Fast Fourier Transform (FFT).
# Frequency domain.
dom = 2*np.pi/(t[-1]-t[0]) # Frequency step.
om = np.arange(-N/2, N/2)*dom # Generate
frequency axis data.
FFT_u1 = fftshift(fft(u1))*dt/np.sqrt(2*np.pi)
S = np.abs(FFT_u1)
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
P = np.log10((S)**2) # Power spectrum of a two-level system.
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# Plotting results
font = {'family': 'serif',
'color': 'darkred',
'weight': 'normal',
'size': 16,
}
fig, ax = plot.subplots(1, 1, figsize =(8,6),
dpi=300) # Resolution.
#ax.plot(om/Om0,P, linestyle='-', c='black')
#ax.set_xlabel('$\omega/\omega_0$', fontdict=font)
#ax.set_ylabel(r"$log\mid P \mid^2$", fontdict=font)
ax.set_xlim(0.0,20.0)
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# Contour plot
y = np.linspace(0,20,1000)
P2 = np.log10((S)**2)*E
cp = ax.contour(om/Om0,y/Om0, P2)
fig.colorbar(cp) # Add a colorbar to a plot
fig.suptitle('Numerical Solutions.', fontdict=font)
plot.tight_layout()
plot.show()
The function HH_model(I,area_factor) has as return value the number of spikes which are triggered by n runs. Assuming 1000 runs, there are 157 times that max(v[]-v_rest) > 60, then the return value of HH_model(I,area_factor) is 157.
Now I know value pairs from another model - the x-values are related to the stimulus I, while the y-values are the number of spikes.
I have written these values as a comment under the code. I want to choose my input parameters I and area_factor in a way that the error to the data is as small as possible. I have no idea how I should do this optimization.
import matplotlib.pyplot as py
import numpy as np
import scipy.optimize as optimize
# HH parameters
v_Rest = -65 # in mV
gNa = 1200 # in mS/cm^2
gK = 360 # in mS/cm^2
gL = 0.3*10 # in mS/cm^2
vNa = 115 # in mV
vK = -12 # in mV
vL = 10.6 # in mV
#Number of runs
runs = 1000
c = 1 # in uF/cm^2
ROOT = False
def HH_model(I,area_factor):
count = 0
t_end = 10 # in ms
delay = 0.1 # in ms
duration = 0.1 # in ms
dt = 0.0025 # in ms
area_factor = area_factor
#geometry
d = 2 # diameter in um
r = d/2 # Radius in um
l = 10 # Length of the compartment in um
A = (1*10**(-8))*area_factor # surface [cm^2]
I = I
C = c*A # uF
for j in range(0,runs):
# Introduction of equations and channels
def alphaM(v): return 12 * ((2.5 - 0.1 * (v)) / (np.exp(2.5 - 0.1 * (v)) - 1))
def betaM(v): return 12 * (4 * np.exp(-(v) / 18))
def betaH(v): return 12 * (1 / (np.exp(3 - 0.1 * (v)) + 1))
def alphaH(v): return 12 * (0.07 * np.exp(-(v) / 20))
def alphaN(v): return 12 * ((1 - 0.1 * (v)) / (10 * (np.exp(1 - 0.1 * (v)) - 1)))
def betaN(v): return 12 * (0.125 * np.exp(-(v) / 80))
# compute the timesteps
t_steps= t_end/dt+1
# Compute the initial values
v0 = 0
m0 = alphaM(v0)/(alphaM(v0)+betaM(v0))
h0 = alphaH(v0)/(alphaH(v0)+betaH(v0))
n0 = alphaN(v0)/(alphaN(v0)+betaN(v0))
# Allocate memory for v, m, h, n
v = np.zeros((int(t_steps), 1))
m = np.zeros((int(t_steps), 1))
h = np.zeros((int(t_steps), 1))
n = np.zeros((int(t_steps), 1))
# Set Initial values
v[:, 0] = v0
m[:, 0] = m0
h[:, 0] = h0
n[:, 0] = n0
### Noise component
knoise= 0.0005 #uA/(mS)^1/2
### --------- Step3: SOLVE
for i in range(0, int(t_steps)-1, 1):
# Get current states
vT = v[i]
mT = m[i]
hT = h[i]
nT = n[i]
# Stimulus current
IStim = 0
if delay / dt <= i <= (delay + duration) / dt:
IStim = I # in uA
else:
IStim = 0
# Compute change of m, h and n
m[i + 1] = (mT + dt * alphaM(vT)) / (1 + dt * (alphaM(vT) + betaM(vT)))
h[i + 1] = (hT + dt * alphaH(vT)) / (1 + dt * (alphaH(vT) + betaH(vT)))
n[i + 1] = (nT + dt * alphaN(vT)) / (1 + dt * (alphaN(vT) + betaN(vT)))
# Ionic currents
iNa = gNa * m[i + 1] ** 3. * h[i + 1] * (vT - vNa)
iK = gK * n[i + 1] ** 4. * (vT - vK)
iL = gL * (vT-vL)
Inoise = (np.random.normal(0, 1) * knoise * np.sqrt(gNa * A))
IIon = ((iNa + iK + iL) * A) + Inoise #
# Compute change of voltage
v[i + 1] = (vT + ((-IIon + IStim) / C) * dt)[0] # in ((uA / cm ^ 2) / (uF / cm ^ 2)) * ms == mV
# adjust the voltage to the resting potential
v = v + v_Rest
# test if there was a spike
if max(v[:]-v_Rest) > 60:
count += 1
return count
# some datapoints from another model out of 1000 runs. ydata means therefore 'count' out of 1000 runs.
# xdata = np.array([0.92*I,0.925*I,0.9535*I,0.975*I,0.9789*I,I,1.02*I,1.043*I,1.06*I,1.078*I,1.09*I])
# ydata = np.array([150,170,269,360,377,500,583,690,761,827,840])
EDIT:
import matplotlib.pyplot as plt
import numpy as np
from scipy.optimize import minimize
# HH parameters
v_Rest = -65 # in mV
gNa = 120 # in mS/cm^2
gK = 36 # in mS/cm^2
gL = 0.3 # in mS/cm^2
vNa = 115 # in mV
vK = -12 # in mV
vL = 10.6 # in mV
#Number of runs
runs = 1000
c = 1 # in uF/cm^2
def HH_model(x,I,area_factor):
count = 0
t_end = 10 # in ms
delay = 0.1 # in ms
duration = 0.1 # in ms
dt = 0.0025 # in ms
area_factor = area_factor
#geometry
d = 2 # diameter in um
r = d/2 # Radius in um
l = 10 # Length of the compartment in um
A = (1*10**(-8))*area_factor # surface [cm^2]
I = I*x
C = c*A # uF
for j in range(0,runs):
# Introduction of equations and channels
def alphaM(v): return 12 * ((2.5 - 0.1 * (v)) / (np.exp(2.5 - 0.1 * (v)) - 1))
def betaM(v): return 12 * (4 * np.exp(-(v) / 18))
def betaH(v): return 12 * (1 / (np.exp(3 - 0.1 * (v)) + 1))
def alphaH(v): return 12 * (0.07 * np.exp(-(v) / 20))
def alphaN(v): return 12 * ((1 - 0.1 * (v)) / (10 * (np.exp(1 - 0.1 * (v)) - 1)))
def betaN(v): return 12 * (0.125 * np.exp(-(v) / 80))
# compute the timesteps
t_steps= t_end/dt+1
# Compute the initial values
v0 = 0
m0 = alphaM(v0)/(alphaM(v0)+betaM(v0))
h0 = alphaH(v0)/(alphaH(v0)+betaH(v0))
n0 = alphaN(v0)/(alphaN(v0)+betaN(v0))
# Allocate memory for v, m, h, n
v = np.zeros((int(t_steps), 1))
m = np.zeros((int(t_steps), 1))
h = np.zeros((int(t_steps), 1))
n = np.zeros((int(t_steps), 1))
# Set Initial values
v[:, 0] = v0
m[:, 0] = m0
h[:, 0] = h0
n[:, 0] = n0
### Noise component
knoise= 0.0005 #uA/(mS)^1/2
### --------- Step3: SOLVE
for i in range(0, int(t_steps)-1, 1):
# Get current states
vT = v[i]
mT = m[i]
hT = h[i]
nT = n[i]
# Stimulus current
IStim = 0
if delay / dt <= i <= (delay + duration) / dt:
IStim = I # in uA
else:
IStim = 0
# Compute change of m, h and n
m[i + 1] = (mT + dt * alphaM(vT)) / (1 + dt * (alphaM(vT) + betaM(vT)))
h[i + 1] = (hT + dt * alphaH(vT)) / (1 + dt * (alphaH(vT) + betaH(vT)))
n[i + 1] = (nT + dt * alphaN(vT)) / (1 + dt * (alphaN(vT) + betaN(vT)))
# Ionic currents
iNa = gNa * m[i + 1] ** 3. * h[i + 1] * (vT - vNa)
iK = gK * n[i + 1] ** 4. * (vT - vK)
iL = gL * (vT-vL)
Inoise = (np.random.normal(0, 1) * knoise * np.sqrt(gNa * A))
IIon = ((iNa + iK + iL) * A) + Inoise #
# Compute change of voltage
v[i + 1] = (vT + ((-IIon + IStim) / C) * dt)[0] # in ((uA / cm ^ 2) / (uF / cm ^ 2)) * ms == mV
# adjust the voltage to the resting potential
v = v + v_Rest
# test if there was a spike
if max(v[:]-v_Rest) > 60:
count += 1
return count
def loss(parameters, model, x_ref, y_ref):
# unpack multiple parameters
I, area_factor = parameters
# compute prediction
y_predicted = np.array([model(x, I, area_factor) for x in x_ref])
# compute error and use it as loss
mse = ((y_ref - y_predicted) ** 2).mean()
return mse
# some datapoints from another model out of 1000 runs. ydata means therefore 'count' out of 1000 runs.
xdata = np.array([0.92,0.925,0.9535, 0.975, 0.9789, 1])
ydata = np.array([150,170,269, 360, 377, 500])
y_data_scaled = ydata / runs
y_predicted = np.array([HH_model(x,I=10**(-3), area_factor=1) for x in xdata])
parameters = (10**(-3), 1)
mse0 = loss(parameters, HH_model, xdata, y_data_scaled)
# compute the parameters that minimize the loss (alias, the error between the data and the predictions of the model)
optimum = minimize(loss, x0=np.array([10**(-3), 1]), args=(HH_model, xdata, y_data_scaled))
# compute the predictions with the optimized parameters
I = optimum['x'][0]
area_factor = optimum['x'][1]
y_predicted_opt = np.array([HH_model(x, I, area_factor) for x in xdata])
# plot the raw data, the model with handcrafted guess and the model with optimized parameters
fig, ax = plt.subplots(1, 1)
ax.set_xlabel('input')
ax.set_ylabel('output predictions')
ax.plot(xdata, y_data_scaled, marker='o')
ax.plot(xdata, y_predicted, marker='*')
ax.plot(xdata, y_predicted_opt, marker='v')
ax.legend([
"raw data points",
"initial guess",
"predictions with optimized parameters"
])
I started using your function,
then I noticed it was very slow to execute.
Hence, I decided to show the process with a toy (linear) model.
The process remains the same.
import numpy as np
import matplotlib.pyplot as plt
from scipy.optimize import minimize
def loss(parameters, model, x_ref, y_ref):
# unpack multiple parameters
m, q = parameters
# compute prediction
y_predicted = np.array([model(x, m, q) for x in x_ref])
# compute error and use it as loss
mse = ((y_ref - y_predicted) ** 2).mean()
return mse
# load a dataset to fit a model
x_data = np.array([0.92, 0.925, 0.9535, 0.975, 0.9789, 1, 1.02, 1.043, 1.06, 1.078, 1.09])
y_data = np.array([150, 170, 269, 360, 377, 500, 583, 690, 761, 827, 840])
# normalise the data - input is already normalised
y_data_scaled = y_data / 1000
# create a model (linear, as an example) using handcrafted parameters, ex:(1,1)
linear_fun = lambda x, m, q: m * x + q
y_predicted = np.array([linear_fun(x, m=1, q=1) for x in x_data])
# create a function that given a model (linear_fun), a dataset(x,y) and the parameters, compute the error
parameters = (1, 1)
mse0 = loss(parameters, linear_fun, x_data, y_data_scaled)
# compute the parameters that minimize the loss (alias, the error between the data and the predictions of the model)
optimum = minimize(loss, x0=np.array([1, 1]), args=(linear_fun, x_data, y_data_scaled))
# compute the predictions with the optimized parameters
m = optimum['x'][0]
q = optimum['x'][1]
y_predicted_opt = np.array([linear_fun(x, m, q) for x in x_data])
# plot the raw data, the model with handcrafted guess and the model with optimized parameters
fig, ax = plt.subplots(1, 1)
ax.set_xlabel('input')
ax.set_ylabel('output predictions')
ax.plot(x_data, y_data_scaled, marker='o')
ax.plot(x_data, y_predicted, marker='*')
ax.plot(x_data, y_predicted_opt, marker='v')
ax.legend([
"raw data points",
"initial guess",
"predictions with optimized parameters"
])
# Note1: good practise is to validate your model with a different set of data,
# respect to the one that you have used to find the parameters
# here, however, it is shown just the optimization procedure
# Note2: in your case you should use the HH_model instead of the linear_fun
# and I and Area_factor instead of m and q.
Output:
-- EDIT: To use the HH_model:
I went deeper in your code,
I tried few values for area and stimulus
and I executed a single run of HH_Model without taking the threshold.
Then, I checked the predicted dynamic of voltage (v):
the sequence is always diverging ( all values become nan after few steps )
if you have an initial guess for stimulus and area that could make the code to work, great.
if you have no idea of the order of magnitude of these parameters
the unique solution I see is a grid search over them - just to find this initial guess.
however, it might take a very long time without guarantee of success.
given that the code is based on a physical model, I would suggest to:
1 - find pen and paper a reasonable values.
2 - check that this simulation works for these values.
3 - then, run the optimizer to find the minimum.
Or, worst case scenario, reverse engineer the code and find the value that makes the equation to converge
Here the refactored code:
import math
import numpy as np
# HH parameters
v_Rest = -65 # in mV
gNa = 1200 # in mS/cm^2
gK = 360 # in mS/cm^2
gL = 0.3 * 10 # in mS/cm^2
vNa = 115 # in mV
vK = -12 # in mV
vL = 10.6 # in mV
# Number of runs
c = 1 # in uF/cm^2
# Introduction of equations and channels
def alphaM(v):
return 12 * ((2.5 - 0.1 * (v)) / (np.exp(2.5 - 0.1 * (v)) - 1))
def betaM(v):
return 12 * (4 * np.exp(-(v) / 18))
def betaH(v):
return 12 * (1 / (np.exp(3 - 0.1 * (v)) + 1))
def alphaH(v):
return 12 * (0.07 * np.exp(-(v) / 20))
def alphaN(v):
return 12 * ((1 - 0.1 * (v)) / (10 * (np.exp(1 - 0.1 * (v)) - 1)))
def betaN(v):
return 12 * (0.125 * np.exp(-(v) / 80))
def predict_voltage(A, C, delay, dt, duration, stimulus, t_end):
# compute the timesteps
t_steps = t_end / dt + 1
# Compute the initial values
v0 = 0
m0 = alphaM(v0) / (alphaM(v0) + betaM(v0))
h0 = alphaH(v0) / (alphaH(v0) + betaH(v0))
n0 = alphaN(v0) / (alphaN(v0) + betaN(v0))
# Allocate memory for v, m, h, n
v = np.zeros((int(t_steps), 1))
m = np.zeros((int(t_steps), 1))
h = np.zeros((int(t_steps), 1))
n = np.zeros((int(t_steps), 1))
# Set Initial values
v[:, 0] = v0
m[:, 0] = m0
h[:, 0] = h0
n[:, 0] = n0
# Noise component
knoise = 0.0005 # uA/(mS)^1/2
for i in range(0, int(t_steps) - 1, 1):
# Get current states
vT = v[i]
mT = m[i]
hT = h[i]
nT = n[i]
# Stimulus current
if delay / dt <= i <= (delay + duration) / dt:
IStim = stimulus # in uA
else:
IStim = 0
# Compute change of m, h and n
m[i + 1] = (mT + dt * alphaM(vT)) / (1 + dt * (alphaM(vT) + betaM(vT)))
h[i + 1] = (hT + dt * alphaH(vT)) / (1 + dt * (alphaH(vT) + betaH(vT)))
n[i + 1] = (nT + dt * alphaN(vT)) / (1 + dt * (alphaN(vT) + betaN(vT)))
# Ionic currents
iNa = gNa * m[i + 1] ** 3. * h[i + 1] * (vT - vNa)
iK = gK * n[i + 1] ** 4. * (vT - vK)
iL = gL * (vT - vL)
Inoise = (np.random.normal(0, 1) * knoise * np.sqrt(gNa * A))
IIon = ((iNa + iK + iL) * A) + Inoise #
# Compute change of voltage
v[i + 1] = (vT + ((-IIon + IStim) / C) * dt)[0] # in ((uA / cm ^ 2) / (uF / cm ^ 2)) * ms == mV
# stop simulation if it diverges
if math.isnan(v[i + 1]):
return [None]
# adjust the voltage to the resting potential
v = v + v_Rest
return v
def HH_model(stimulus, area_factor, runs=1000):
count = 0
t_end = 10 # in ms
delay = 0.1 # in ms
duration = 0.1 # in ms
dt = 0.0025 # in ms
area_factor = area_factor
# geometry
d = 2 # diameter in um
r = d / 2 # Radius in um
l = 10 # Length of the compartment in um
A = (1 * 10 ** (-8)) * area_factor # surface [cm^2]
stimulus = stimulus
C = c * A # uF
for j in range(0, runs):
v = predict_voltage(A, C, delay, dt, duration, stimulus, t_end)
if max(v[:] - v_Rest) > 60:
count += 1
return count
And the attempt to run one simulation:
import time
from ex_21.equations import c, predict_voltage
area_factor = 0.1
stimulus = 70
# input signal
count = 0
t_end = 10 # in ms
delay = 0.1 # in ms
duration = 0.1 # in ms
dt = 0.0025 # in ms
# geometry
d = 2 # diameter in um
r = d / 2 # Radius in um
l = 10 # Length of the compartment in um
A = (1 * 10 ** (-8)) * area_factor # surface [cm^2]
C = c * A # uF
start = time.time()
voltage_dynamic = predict_voltage(A, C, delay, dt, duration, stimulus, t_end)
elapse = time.time() - start
print(voltage_dynamic)
Output:
[None]
I am trying to make a plot of a projectile motion of a mass which is under the effect of gravitational, buoyancy and drag force. Basically, I want to show effects of the buoyancy and drag force on flight distance, flight time and velocity change on plotting.
import matplotlib.pyplot as plt
import numpy as np
V_initial = 30 # m/s
theta = np.pi/6 # 30
g = 3.711
m =1
C = 0.47
r = 0.5
S = np.pi*pow(r, 2)
ro_mars = 0.0175
t_flight = 2*(V_initial*np.sin(theta)/g)
t = np.linspace(0, t_flight, 200)
# Drag force
Ft = 0.5*C*S*ro_mars*pow(V_initial, 2)
# Buoyant Force
Fb = ro_mars*g*(4/3*np.pi*pow(r, 3))
x_loc = []
y_loc = []
for time in t:
x = V_initial*time*np.cos(theta)
y = V_initial*time*np.sin(theta) - (1/2)*g*pow(time, 2)
x_loc.append(x)
y_loc.append(y)
x_vel = []
y_vel = []
for time in t:
vx = V_initial*np.cos(theta)
vy = V_initial*np.sin(theta) - g*time
x_vel.append(vx)
y_vel.append(vy)
v_ch = [pow(i**2+ii**2, 0.5) for i in x_vel for ii in y_vel]
tau = []
for velocity in v_ch:
Ft = 0.5*C*S*ro_mars*pow(velocity, 2)
tau.append(Ft)
buoy = []
for velocity in v_ch:
Fb = ro_mars*g*(4/3*np.pi*pow(r, 3))
buoy.append(Fb)
after this point, I couldn't figure out how to plot to a projectile motion under this forces. In other words, I'm trying to compare the projectile motion of the mass under three circumstances
Mass only under the effect of gravity
Mass under the effect of gravity and air resistance
Mass under the effect of gravity, air resistance, and buoyancy
You must calculate each location based on the sum of forces at the given time. For this it is better to start from calculating the net force at any time and using this to calculate the acceleration, velocity and then position. For the following calculations, it is assumed that buoyancy and gravity are constant (which is not true in reality but the effect of their variability is negligible in this case), it is also assumed that the initial position is (0,0) though this can be trivially changed to any initial position.
F_x = tau_x
F_y = tau_y + bouyancy + gravity
Where tau_x and tau_y are the drag forces in the x and y directions, respectively. The velocities, v_x and v_y, are then given by
v_x = v_x + (F_x / (2 * m)) * dt
v_y = v_y + (F_y / (2 * m)) * dt
So the x and y positions, r_x and r_y, at any time t are given by the summation of
r_x = r_x + v_x * dt
r_y = r_y + v_y * dt
In both cases this must be evaluated from 0 to t for some dt where dt * n = t if n is the number of steps in summation.
r_x = r_x + V_i * np.cos(theta) * dt + (F_x / (2 * m)) * dt**2
r_y = r_y + V_i * np.sin(theta) * dt + (F_y / (2 * m)) * dt**2
The entire calculation can actually be done in two lines,
r_x = r_x + V_i * np.cos(theta) * dt + (tau_x / (2 * m)) * dt**2
r_y = r_y + V_i * np.sin(theta) * dt + ((tau_y + bouyancy + gravity) / (2 * m)) * dt**2
Except that v_x and v_y require updating at every time step. To loop over this and calculate the x and y positions across a range of times you can simply follow the below (edited) example.
The following code includes corrections to prevent negative y positions, since the given value of g is for the surface or Mars I assume this is appropriate - when you hit zero y and try to keep going you may end up with a rapid unscheduled disassembly, as we physicists call it.
Edit
In response to the edited question, the following example has been modified to plot all three cases requested - gravity, gravity plus drag, and gravity plus drag and buoyancy. Plot setup code has also been added
Complete example (edited)
import numpy as np
import matplotlib.pyplot as plt
def projectile(V_initial, theta, bouyancy=True, drag=True):
g = 9.81
m = 1
C = 0.47
r = 0.5
S = np.pi*pow(r, 2)
ro_mars = 0.0175
time = np.linspace(0, 100, 10000)
tof = 0.0
dt = time[1] - time[0]
bouy = ro_mars*g*(4/3*np.pi*pow(r, 3))
gravity = -g * m
V_ix = V_initial * np.cos(theta)
V_iy = V_initial * np.sin(theta)
v_x = V_ix
v_y = V_iy
r_x = 0.0
r_y = 0.0
r_xs = list()
r_ys = list()
r_xs.append(r_x)
r_ys.append(r_y)
# This gets a bit 'hand-wavy' but as dt -> 0 it approaches the analytical solution.
# Just make sure you use sufficiently small dt (dt is change in time between steps)
for t in time:
F_x = 0.0
F_y = 0.0
if (bouyancy == True):
F_y = F_y + bouy
if (drag == True):
F_y = F_y - 0.5*C*S*ro_mars*pow(v_y, 2)
F_x = F_x - 0.5*C*S*ro_mars*pow(v_x, 2) * np.sign(v_y)
F_y = F_y + gravity
r_x = r_x + v_x * dt + (F_x / (2 * m)) * dt**2
r_y = r_y + v_y * dt + (F_y / (2 * m)) * dt**2
v_x = v_x + (F_x / m) * dt
v_y = v_y + (F_y / m) * dt
if (r_y >= 0.0):
r_xs.append(r_x)
r_ys.append(r_y)
else:
tof = t
r_xs.append(r_x)
r_ys.append(r_y)
break
return r_xs, r_ys, tof
v = 30
theta = np.pi/4
fig = plt.figure(figsize=(8,4), dpi=300)
r_xs, r_ys, tof = projectile(v, theta, True, True)
plt.plot(r_xs, r_ys, 'g:', label="Gravity, Buoyancy, and Drag")
r_xs, r_ys, tof = projectile(v, theta, False, True)
plt.plot(r_xs, r_ys, 'b:', label="Gravity and Drag")
r_xs, r_ys, tof = projectile(v, theta, False, False)
plt.plot(r_xs, r_ys, 'k:', label="Gravity")
plt.title("Trajectory", fontsize=14)
plt.xlabel("Displacement in x-direction (m)")
plt.ylabel("Displacement in y-direction (m)")
plt.ylim(bottom=0.0)
plt.legend()
plt.show()
Note that this preserves and returns the time-of-flight in the variable tof.
Using vector notation, and odeint.
import numpy as np
from scipy.integrate import odeint
import scipy.constants as SPC
import matplotlib.pyplot as plt
V_initial = 30 # m/s
theta = np.pi/6 # 30
g = 3.711
m = 1 # I assume this is your mass
C = 0.47
r = 0.5
ro_mars = 0.0175
t_flight = 2*(V_initial*np.sin(theta)/g)
t = np.linspace(0, t_flight, 200)
pos0 = [0, 0]
v0 = [np.cos(theta) * V_initial, np.sin(theta) * V_initial]
def f(vector, t, C, r, ro_mars, apply_bouyancy=True, apply_resistance=True):
x, y, x_prime, y_prime = vector
# volume and surface
V = np.pi * 4/3 * r**3
S = np.pi*pow(r, 2)
# net weight bouyancy
if apply_bouyancy:
Fb = (ro_mars * V - m) * g *np.array([0,1])
else:
Fb = -m * g * np.array([0,1])
# velocity vector
v = np.array([x_prime, y_prime])
# drag force - corrected to be updated based on current velocity
# Ft = -0.5*C*S*ro_mars*pow(V_initial, 2)
if apply_resistance:
Ft = -0.5*C*S*ro_mars* v *np.linalg.norm(v)
else:
Ft = np.array([0, 0])
# resulting acceleration
x_prime2, y_prime2 = (Fb + Ft) / m
return x_prime, y_prime, x_prime2, y_prime2
sol = odeint(f, pos0 + v0 , t, args=(C, r, ro_mars))
plt.plot(sol[:,0], sol[:, 1], 'g', label='tray')
plt.legend(loc='best')
plt.xlabel('x')
plt.ylabel('y')
plt.grid()
plt.show()
Note that I corrected your drag force to use the actual (not initial) velocity, I do not know if that was your mistake or it was on purpose.
Also please check the documentation for odeint to understand better how to turn a second order ODE (like the one in your problem) to a first order vector ODE.
To remove air resistance or bouyancy, set apply_bouyancy and apply_resistance to True or False by adding them to the args=(...)
Now that my perlin generator is 'working' I created noise, to find that it is nothing like what I see on the internets...
My noise:
Notice the streaks:
What I am aiming to get (obviously with corresponding colour):
1:
Why does mine look so noisy and nasty?
Code (sorry for no stub, the Perlin noise makes up most of the program so it's important to include the full program):
from PIL import Image
from tkinter import filedialog
from random import randint, random
#Initialise width / height
width = 625
height = 625
#Import gradient picture - 200*1 image used to texture perlin noise
#R,G,B,Alpha
gradient = Image.open("image.png")
gradlist = list(gradient.getdata())
#Create new image
img = Image.new('RGBA', (width, height), color=(255, 255, 255, 255))
#Perlin noise modules --------------------------------------------------------------------------------------------------------
#Modules
from random import sample
from math import floor
p = sample([x for x in range(0, (width * height))], (width * height)) * 2
#Antialising
def fade(t):
retval = 6*(t**5) - 15*(t**4) + 10*(t**3)
return retval
#Linear interpolation
def lerp(t,a,b):
retval = a + (t * (b - a))
return retval
#Clever bitwise hash stuff - picks a unit vector from 12 possible - (1,1,0),(-1,1,0),(1,-1,0),(-1,-1,0),(1,0,1),(-1,0,1),(1,0,-1),(-1,0,-1),(0,1,1),(0,-1,1),(0,1,-1),(0,-1,-1)
def grad(hash, x, y, z):
h = hash % 15
if h < 8:
u = x
else:
u = y
if h < 4:
v = y
elif h in (12, 14):
v = x
else:
v = z
return (u if (h & 1) == 0 else -u) + (v if (h & 2) == 0 else -v)
#Perlin function
def perlin(x,y,z):
ix = int(floor(x)) & 255
iy = int(floor(y)) & 255
iz = int(floor(z)) & 255
x -= int(floor(x))
y -= int(floor(y))
z -= int(floor(z))
u = fade(x)
v = fade(y)
w = fade(z)
#Complicated hash stuff
A = p[ix] + iy
AA = p[A] + iz
AB = p[A + 1] + iz
B = p[ix + 1] + iy
BA = p[B] + iz
BB = p[B + 1] + iz
return -lerp(w, lerp(v, lerp(u, grad(p[AA], x, y, z),grad(p[BA], x - 1, y, z)),lerp(u, grad(p[AB], x, y - 1, z),grad(p[BB], x - 1, y - 1, z))),lerp(v, lerp(u, grad(p[AA + 1], x, y, z - 1),grad(p[BA + 1], x - 1, y, z - 1)), lerp(u, grad(p[AB + 1], x, y - 1, z - 1),grad(p[BB + 1], x - 1, y - 1, z - 1))))
def octavePerlin(x,y,z,octaves,persistence):
total = 0
frequency = 1
amplitude = 1
maxValue = 0
for x in range(octaves):
total += perlin(x * frequency, y * frequency, z * frequency) * amplitude
maxValue += amplitude
amplitude *= persistence
frequency *= 2
return total / maxValue
z = random()
img.putdata([gradlist[int(octavePerlin((x + random() - 0.5) / 1000, (y + random() - 0.5) / 1000, z, 4, 2) * 100 + 100)] for x in range(width) for y in range(height)])
img.save(filedialog.asksaveasfilename() + ".png", "PNG")
For my physics degree, I have to take some Python lessons. I'm an absolute beginner and as such, I can't understand other answers. The code is to plot an object's trajectory with air resistance. I would really appreciate a quick fix - I think it has something to do with the time variable being too small but increasing it doesn't help.
import matplotlib.pyplot as plt
import numpy as np
import math # need math module for trigonometric functions
g = 9.81 #gravitational constant
dt = 1e-3 #integration time step (delta t)
v0 = 40 # initial speed at t = 0
angle = math.pi/4 #math.pi = 3.14, launch angle in radians
time = np.arange(0, 10, dt) #time axis
vx0 = math.cos(angle)*v0 # starting velocity along x axis
vy0 = math.sin(angle)*v0 # starting velocity along y axis
xa = vx0*time # compute x coordinates
ya = -0.5*g*time**2 + vy0*time # compute y coordinates
def traj_fric(angle, v0): # function for trajectory
vx0 = math.cos(angle) * v0 # for some launch angle and starting velocity
vy0 = math.sin(angle) * v0 # compute x and y component of starting velocity
x = np.zeros(len(time)) #initialise x and y arrays
y = np.zeros(len(time))
x[0], y[0], 0 #projecitle starts at 0,0
x[1], y[1] = x[0] + vx0 * dt, y[0] + vy0 * dt # second elements of x and
# y are determined by initial
# velocity
i = 1
while y[i] >= 0: # conditional loop continuous until
# projectile hits ground
gamma = 0.005 # constant of friction
height = 100 # height at which air friction disappears
f = 0.5 * gamma * (height - y[i]) * dt
x[i + 1] = (2 * x[i] - x[i - 1] + f * x[i - 1])/1 + f # numerical integration to find x[i + 1]
y[i + 1] = (2 * y[i] - y[i - 1] + f * y[i - 1] - g * dt ** 2)/ 1 + f # and y[i + 1]
i = i + 1 # increment i for next loop
x = x[0:i+1] # truncate x and y arrays
y = y[0:i+1]
return x, y, (dt*i), x[i] # return x, y, flight time, range of projectile
x, y, duration, distance = traj_fric(angle, v0)
fig1 = plt.figure()
plt.plot(xa, ya) # plot y versus x
plt.xlabel ("x")
plt.ylabel ("y")
plt.ylim(0, max(ya)+max(ya)*0.2)
plt.xlim(0, distance+distance*0.1)
plt.show()
print "Distance:" ,distance
print "Duration:" ,duration
n = 5
angles = np.linspace(0, math.pi/2, n)
maxrange = np.zeros(n)
for i in range(n):
x,y, duration, maxrange [i] = traj_fric(angles[i], v0)
angles = angles/2/math.pi*360 #convert rad to degress
print "Optimum angle:", angles[np.where(maxrange==np.max(maxrange))]
The error is:
File "C:/Python27/Lib/site-packages/xy/projectile_fric.py", line 43, in traj_fric
x[i + 1] = (2 * x[i] - x[i - 1] + f * x[i - 1])/1 + f # numerical integration to find x[i + 1]
IndexError: index 10000 is out of bounds for axis 0 with size 10000
This is pretty straightforward. When you have a size of 10000, element index 10000 is out of bounds because indexing begins with 0, not 1. Therefore, the 10,000th element is index 9999, and anything larger than that is out of bounds.
Mason Wheeler's answer told you what Python was telling you. The problem occurs in this loop:
while y[i] >= 0: # conditional loop continuous until
# projectile hits ground
gamma = 0.005 # constant of friction
height = 100 # height at which air friction disappears
f = 0.5 * gamma * (height - y[i]) * dt
x[i + 1] = (2 * x[i] - x[i - 1] + f * x[i - 1])/1 + f # numerical integration to find x[i + 1]
y[i + 1] = (2 * y[i] - y[i - 1] + f * y[i - 1] - g * dt ** 2)/ 1 + f # and y[i + 1]
i = i + 1 # increment i for next loop
The simple fix is to change the loop to something like (I don't know Python syntax, so bear with me):
while (y[i] >= 0) and (i < len(time)):
That will stop the sim when you run out of array, but it will (potentially) also stop the sim with the projectile hanging in mid-air.
What you have here is a very simple ballistic projectile simulation, modeling atmospheric friction as a linear function of altitude. QUALITATIVELY, what is happening is that your projectile is not hitting the ground in the time you allowed, and you are attempting to overrun your tracking arrays. This is caused by failure to allow sufficient time-of-flight. Observe that the greatest possible time-of-flight occurs when atmospheric friction is zero, and it is then trivial to compute a closed-form upper bound for time-of-flight. You then use that upper bound as your time, and you will allocate sufficient array space to simulate the projectile all the way to impact.
enter code heredef data_to_array(total):
random.shuffle(total)
X = np.zeros((len(total_train), 224, 224, 3)).astype('float')
y = []
for i, img_path in enumerate(total):
img = cv2.imread('/content/gdrive/My Drive/PP/Training/COVID/COVID-19 (538).jpg')
img = cv2.resize(img, (224, 224))
X[i] = img - 1
if len(re.findall('covid', '/content/gdrive/My Drive/PP/Training/COVID/COVID-19 (538).jpg')) == 3:
y.append(0)
else:
y.append(1)
y = np.array(y)
return X, y
X_train, y_train = data_to_array(total_train)
X_test, y_test = data_to_array(total_val)