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Change in coordinate density for np.meshgrid() in matplotlib

I am plotting a vector field using the numpy function quiver() and it works. But I would like to emphasize the cowlick in the following plot:
I am not sure how to go about it, but increasing the density of arrows in the center could possibly do the trick. To do so, I would like to resort to some option within np.meshgrid() that would allow me to get more tightly packed x,y coordinate points in the center. A linear, quadratic or other specification does not seem to be built in. I am not sure if sparse can be modified to this end.
The code:
lim = 10
int = 0.22 *lim
x,y = np.meshgrid(np.arange(-lim, lim, int), np.arange(-lim, lim, int))
u = 3 * np.cos(np.arctan2(y,x)) - np.sqrt(x**2+y**2) * np.sin(np.arctan2(y,x))
v = 3 * np.sin(np.arctan2(y,x)) + np.sqrt(x**2+y**2) * np.cos(np.arctan2(y,x))
color = x**2 + y**2
plt.rcParams["image.cmap"] = "Greys_r"
mult = 1
plt.figure(figsize=(mult*lim, mult*lim))
plt.quiver(x,y,u,v,color, linewidths=.006, lw=.1)
plt.show()
Closing the loop on this, thanks to the accepted answer I was able to finally strike a balance between the density of the mesh as I learned from to do from #flwr and keeping the "cowlick" structure of the vector field conspicuous (avoiding the radial structure around the origin as much as possible):

You can construct the points whereever you want to calculate your field on and quivers will be happy about it. The code below uses polar coordinates and stretches the radial coordinate non-linearly.
import numpy as np
import matplotlib.pyplot as plt
lim = 10
N = 10
theta = np.linspace(0.1, 2*np.pi, N*2)
stretcher_factor = 2
r = np.linspace(0.3, lim**(1/stretcher_factor), N)**stretcher_factor
R, THETA = np.meshgrid(r, theta)
x = R * np.cos(THETA)
y = R * np.sin(THETA)
# x,y = np.meshgrid(x, y)
r = x**2 + y**2
u = 3 * np.cos(THETA) - np.sqrt(r) * np.sin(THETA)
v = 3 * np.sin(THETA) + np.sqrt(r) * np.cos(THETA)
plt.rcParams["image.cmap"] = "Greys_r"
mult = 1
plt.figure(figsize=(mult*lim, mult*lim))
plt.quiver(x,y,u,v,r, linewidths=.006, lw=.1)
Edit: Bug taking meshgrid twice

np.meshgrid just makes a grid of the vectors you provide.
What you could do is contract this regular grid in the center to have more points in the center (best visible with more points), e.g. like so:
# contract in the center
a = 0.5 # how far to contract
b = 0.8 # how strongly to contract
c = 1 - b*np.exp(-((x/lim)**2 + (y/lim)**2)/a**2)
x, y = c*x, c*y
plt.plot(x,y,'.k')
plt.show()
Alternatively you can x,y cooridnates that are not dependent on a grid at all:
x = np.random.randn(500)
y = np.random.randn(500)
plt.plot(x,y,'.k')
plt.show()
But I think you'd prefer a slightly more regular patterns you could look into poisson disk sampling with adaptive distances or something like that, but the key point here is that for using quiver, you can use ANY set of coordinates, they do not have to be in a regular grid.

Planetary orbit shown as linear graph using rk4

I am trying to simulate the orbit of a planet around a star using the Runge-Kutta 4 method. After speaking to tutors my code should be correct. However, I am not generating my expected 2D orbital plot but instead a linear plot. This is my first time using solve_ivp to solve a second order differential. Can anyone explain why my plots are wrong?
import numpy as np
import matplotlib.pyplot as plt
from scipy.integrate import solve_ivp
# %% Define derivative function
def f(t, z):
x = z[0] # Position x
y = z[1] # Position y
dx = z[2] # Velocity x
dy = z[3] # Velocity y
G = 6.674 * 10**-11 # Gravitational constant
M = 2 # Mass of binary stars in solar masses
c = 2*G*M
r = np.sqrt(y**2 + x**2) # Distance of planet from stars
zdot = np.empty(6) # Array for integration solutions
zdot[0] = x
zdot[1] = y
zdot[2] = dx # Velocity x
zdot[3] = dy #Velocity y
zdot[4] = (-c/(r**3))*(x) # Acceleration x
zdot[5] = (-c/(r**3))*(y) # Acceleration y
return zdot
# %% Define time spans, initial values, and constants
tspan = np.linspace(0., 10000., 100000000)
xy0 = [0.03, -0.2, 0.008, 0.046, 0.2, 0.3] # Initial positions x,y in R and velocities
# %% Solve differential equation
sol = solve_ivp(lambda t, z: f(t, z), [tspan[0], tspan[-1]], xy0, t_eval=tspan)
# %% Plot
#plot
plt.grid()
plt.subplot(2, 2, 1)
plt.plot(sol.y[0],sol.y[1], color='b')
plt.subplot(2, 2, 2)
plt.plot(sol.t,sol.y[2], color='g')
plt.subplot(2, 2, 3)
plt.plot(sol.t,sol.y[4], color='r')
plt.show()

With the ODE function as given, you are solving in the first components the system
xdot = x
ydot = y
which has well-known exponential solutions. As the exponential factor is the same long both solutions, the xy-plot will move along a line through the origin.
The solution is of course to fill zdot[0:2] with dx,dy, and zdot[2:4] with ax,ay or ddx,ddy or however you want to name the components of the acceleration. Then the initial state also has only 4 components. Or you need to make and treat position and velocity as 3-dimensional.
You need to put units to your constants and care that all use the same units. G as cited is in m^3/kg/s^2, so that any M you define will be in kg, any length is in m and any velocity in m/s. Your constants might appear ridiculously small in that context.
It does not matter what the comment in the code says, there will be no magical conversion. You need to use actual conversion computations to get realistic numbers. For instance using the numbers
G = 6.67408e-11 # m^3 s^-2 kg^-1
AU = 149.597e9 # m
Msun = 1.988435e30 # kg
hour = 60*60 # seconds in an hour
day = hour * 24 # seconds in one day
year = 365.25*day # seconds in a year (not very astronomical)
one could guess that for a sensible binary system of two stars of equal mass one has
M = 2*Msun # now actually 2 sun masses
x0 = 0.03*AU
y0 = -0.2*AU
vx0 = 0.008*AU/day
vy0 = 0.046*AU/day
For the position only AU makes sense as unit, the speed could also be in AU/hour. By https://math.stackexchange.com/questions/4033996/developing-keplers-first-law and Cannot get RK4 to solve for position of orbiting body in Python the speed for a circular orbit of radius R=0.2AU around a combined mass of 2*M is
sqrt(2*M*G/R)=sqrt(4*Msun*G/(0.2*AU)) = 0.00320 * AU/hour = 0.07693 AU/day
which is ... not too unreasonable if the given speeds are actually in AU/day. Invoke the computations from https://math.stackexchange.com/questions/4050575/application-of-the-principle-of-conservation to compute if the Kepler ellipse would look sensible
r0 = (x0**2+y0**2)**0.5
dotr0 = (x0*vx0+y0*vy0)/r0
L = x0*vy0-y0*vx0 # r^2*dotphi = L constant, L^2 = G*M_center*R
dotphi0 = L/r0**2
R = L**2/(G*2*M)
wx = R/r0-1; wy = -dotr0*(R/(G*2*M))**0.5
E = (wx*wx+wy*wy)**0.5; psi = m.atan2(wy,wx)
print(f"half-axis R={R/AU} AU, eccentr. E={E}, init. angle psi={psi}")
print(f"min. rad. = {R/(1+E)/AU} AU, max. rad. = {R/(1-E)/AU} AU")
which returns
half-axis R=0.00750258 AU, eccentr. E=0.96934113, init. angle psi=3.02626659
min. rad. = 0.00380969 AU, max. rad. = 0.24471174 AU
This gives an extremely thin ellipse, which is not that astonishing as the initial velocity points almost directly to the gravity center.
orbit variants with half-day steps marked, lengths in AU
If the velocity components were swapped one would get
half-axis R=0.07528741 AU, eccentr. E=0.62778767, init. angle psi=3.12777251
min. rad. = 0.04625137 AU, max. rad. = 0.20227006 AU
This is a little more balanced.

Is there a way to plot Nullclines of a nonlinear system of ODEs

So I am trying to plot the nullclines of a system of ODEs, however I can't seem to plot them in the correct way. When I plot them, I manage to plot them according to time (t vs x and t vs y) but not at (x vs y). I'm not really sure how to explain it, and I think it would be better to just show it. I am trying to replicate this. The equations and parameters are given, however this was done in a program called XPP (I'll post these at the bottom), and there are some parameters that i don't understand what they mean.
My entire code is:
import numpy as np
from scipy import integrate
import matplotlib.pyplot as plt
# define system in terms of a Numpy array
def Sys(X, t=0):
# here X[0] = x and x[1] = y
#protien [] is represented with y, and mRNA [] is represented by x
return np.array([ (k1*S*Kd**p)/(Kd**p + X[1]**p) - kdx*X[0], ksy*X[0] - (k2*ET*X[1])/(Km + X[1])])
#variables
k1=.1
S=1
Kd=1
kdx=.1
p=2
ksy=1
k2=1
ET=1
Km=1
# generate 1000 linearly spaced numbers for x-axes
t = np.linspace(0, 50,100)
# initial values
Sys0 = np.array([1, 0])
#Solves the ODE
X, infodict = integrate.odeint(Sys, Sys0, t, full_output = 1, mxstep = 50000)
#assigns appropriate equations to x and y
x,y = X.T
#plot's the graph
fig = plt.figure(figsize=(15,5))
fig.subplots_adjust(wspace = 0.5, hspace = 0.3)
ax1 = fig.add_subplot(1,2,1)
ax1.plot(x, color="blue")
ax1.plot(y, color = 'red')
ax1.set_xlabel("Protien concentration")
ax1.set_ylabel("mRNA concentration")
ax1.set_title("Phase space")
ax1.grid()
The given equations and parameters are:
model for a simple negative feedback loop
protein (y) inhibits the synthesis of its mRNA (x)
dx/dt = k1SKd^p/(Kd^p + y^p) - kdx*x
dy/dt = ksyx - k2ET*y/(Km + y)
p k1=0.1, S=1, Kd=1, kdx=0.1, p=2
p ksy=1, k2=1, ET=1, Km=1
# XP=y, YP=x, TOTAL=100, METH=stiff, XLO=0, XHI=4, YLO=0, YHI=1.05 (I don't exactly understand what is going on here)
Again, this uses a program called XPP or WINPP.
Any help with this would be appreciated, the original paper I am trying to replicate this from is : Design principles of biochemical oscillators by Bela Novak and John J. Tyson

projectile motion simple simulation using numpy matplotlib python

I am trying to graph a projectile through time at various angles. The angles range from 25 to 60 and each initial angle should have its own line on the graph. The formula for "the total time the projectile is in the air" is the formula for t. I am not sure how this total time comes into play, because I am supposed to graph the projectile at various times with various initial angles. I imagine that I would need x,x1,x2,x3,x4,x5 and the y equivalents in order to graph all six of the various angles. But I am confused on what to do about the time spent.
import numpy as np
import matplotlib.pylab as plot
#initialize variables
#velocity, gravity
v = 30
g = -9.8
#increment theta 25 to 60 then find t, x, y
#define x and y as arrays
theta = np.arange(25,65,5)
t = ((2 * v) * np.sin(theta)) / g #the total time projectile remains in the #air
t1 = np.array(t) #why are some negative
x = ((v * t1) * np.cos(theta))
y = ((v * t1) * np.sin(theta)) - ((0.5 * g) * (t ** 2))
plot.plot(x,y)
plot.show()

First of all g is positive! After fixing that, let's see some equations:
You know this already, but lets take a second and discuss something. What do you need to know in order to get the trajectory of a particle?
Initial velocity and angle, right? The question is: find the position of the particle after some time given that initial velocity is v=something and theta=something. Initial is important! That's the time when we start our experiment. So time is continuous parameter! You don't need the time of flight.
One more thing: Angles can't just be written as 60, 45, etc, python needs something else in order to work, so you need to write them in numerical terms, (0,90) = (0,pi/2).
Let's see the code:
import numpy as np
import matplotlib.pylab as plot
import math as m
#initialize variables
#velocity, gravity
v = 30
g = 9.8
#increment theta 25 to 60 then find t, x, y
#define x and y as arrays
theta = np.arange(m.pi/6, m.pi/3, m.pi/36)
t = np.linspace(0, 5, num=100) # Set time as 'continous' parameter.
for i in theta: # Calculate trajectory for every angle
x1 = []
y1 = []
for k in t:
x = ((v*k)*np.cos(i)) # get positions at every point in time
y = ((v*k)*np.sin(i))-((0.5*g)*(k**2))
x1.append(x)
y1.append(y)
p = [i for i, j in enumerate(y1) if j < 0] # Don't fall through the floor
for i in sorted(p, reverse = True):
del x1[i]
del y1[i]
plot.plot(x1, y1) # Plot for every angle
plot.show() # And show on one graphic

You are making a number of mistakes.
Firstly, less of a mistake, but matplotlib.pylab is supposedly used to access matplotlib.pyplot and numpy together (for a more matlab-like experience), I think it's more suggested to use matplotlib.pyplot as plt in scripts (see also this Q&A).
Secondly, your angles are in degrees, but math functions by default expect radians. You have to convert your angles to radians before passing them to the trigonometric functions.
Thirdly, your current code sets t1 to have a single time point for every angle. This is not what you need: you need to compute the maximum time t for every angle (which you did in t), then for each angle create a time vector from 0 to t for plotting!
Lastly, you need to use the same plotting time vector in both terms of y, since that's the solution to your mechanics problem:
y(t) = v_{0y}*t - g/2*t^2
This assumes that g is positive, which is again wrong in your code. Unless you set the y axis to point downwards, but the word "projectile" makes me think this is not the case.
So here's what I'd do:
import numpy as np
import matplotlib.pyplot as plt
#initialize variables
#velocity, gravity
v = 30
g = 9.81 #improved g to standard precision, set it to positive
#increment theta 25 to 60 then find t, x, y
#define x and y as arrays
theta = np.arange(25,65,5)[None,:]/180.0*np.pi #convert to radians, watch out for modulo division
plt.figure()
tmax = ((2 * v) * np.sin(theta)) / g
timemat = tmax*np.linspace(0,1,100)[:,None] #create time vectors for each angle
x = ((v * timemat) * np.cos(theta))
y = ((v * timemat) * np.sin(theta)) - ((0.5 * g) * (timemat ** 2))
plt.plot(x,y) #plot each dataset: columns of x and columns of y
plt.ylim([0,35])
plot.show()
I made use of the fact that plt.plot will plot the columns of two matrix inputs versus each other, so no loop over angles is necessary. I also used [None,:] and [:,None] to turn 1d numpy arrays to 2d row and column vectors, respectively. By multiplying a row vector and a column vector, array broadcasting ensures that the resulting matrix behaves the way we want it (i.e. each column of timemat goes from 0 to the corresponding tmax in 100 steps)
Result:

Color matplotlib quiver field according to magnitude and direction

I'm attempting to achieve the same behavior as this function in Matlab, whereby the color of each arrow corresponds to both its magnitude and direction, essentially drawing its color from a wheel. I saw this question, but it only seems to work for barbs. I also saw this answer, but quiver complains that the color array must be two-dimensional.
What is the best way to compute C for matplotlib.pyplot.quiver, taking into account both magnitude and direction?

Even though this is quite old now, I've come across the same problem. Based on matplotlibs quiver demo and my own answer to this post, I created the following example. The idea is to convert the angle of a vector to the color using HSV colors Hue value. The absolute value of the vector is used as the saturation and the value.
import numpy as np
import matplotlib.colors
import matplotlib.pyplot as plt
def vector_to_rgb(angle, absolute):
"""Get the rgb value for the given `angle` and the `absolute` value
Parameters
----------
angle : float
The angle in radians
absolute : float
The absolute value of the gradient
Returns
-------
array_like
The rgb value as a tuple with values [0..1]
"""
global max_abs
# normalize angle
angle = angle % (2 * np.pi)
if angle < 0:
angle += 2 * np.pi
return matplotlib.colors.hsv_to_rgb((angle / 2 / np.pi,
absolute / max_abs,
absolute / max_abs))
X = np.arange(-10, 10, 1)
Y = np.arange(-10, 10, 1)
U, V = np.meshgrid(X, Y)
angles = np.arctan2(V, U)
lengths = np.sqrt(np.square(U) + np.square(V))
max_abs = np.max(lengths)
c = np.array(list(map(vector_to_rgb, angles.flatten(), lengths.flatten())))
fig, ax = plt.subplots()
q = ax.quiver(X, Y, U, V, color=c)
plt.show()
The color wheel is the following. The code for generating it is mentioned in the Edit.
Edit
I just noticed, that the linked matlab function "renders a vector field as a grid of unit-length arrows. The arrow direction indicates vector field direction, and the color indicates the magnitude". So my above example is not really what is in the question. Here are some modifications.
The left graph is the same as above. The right one does, what the cited matlab function does: A unit-length arrow plot with the color indicating the magnitude. The center one does not use the magnitude but only the direction in the color which might be useful too. I hope other combinations are clear from this example.
import numpy as np
import matplotlib.colors
import matplotlib.pyplot as plt
def vector_to_rgb(angle, absolute):
"""Get the rgb value for the given `angle` and the `absolute` value
Parameters
----------
angle : float
The angle in radians
absolute : float
The absolute value of the gradient
Returns
-------
array_like
The rgb value as a tuple with values [0..1]
"""
global max_abs
# normalize angle
angle = angle % (2 * np.pi)
if angle < 0:
angle += 2 * np.pi
return matplotlib.colors.hsv_to_rgb((angle / 2 / np.pi,
absolute / max_abs,
absolute / max_abs))
X = np.arange(-10, 10, 1)
Y = np.arange(-10, 10, 1)
U, V = np.meshgrid(X, Y)
angles = np.arctan2(V, U)
lengths = np.sqrt(np.square(U) + np.square(V))
max_abs = np.max(lengths)
# color is direction, hue and value are magnitude
c1 = np.array(list(map(vector_to_rgb, angles.flatten(), lengths.flatten())))
ax = plt.subplot(131)
ax.set_title("Color is lenth,\nhue and value are magnitude")
q = ax.quiver(X, Y, U, V, color=c1)
# color is length only
c2 = np.array(list(map(vector_to_rgb, angles.flatten(),
np.ones_like(lengths.flatten()) * max_abs)))
ax = plt.subplot(132)
ax.set_title("Color is direction only")
q = ax.quiver(X, Y, U, V, color=c2)
# color is direction only
c3 = np.array(list(map(vector_to_rgb, 2 * np.pi * lengths.flatten() / max_abs,
max_abs * np.ones_like(lengths.flatten()))))
# create one-length vectors
U_ddash = np.ones_like(U)
V_ddash = np.zeros_like(V)
# now rotate them
U_dash = U_ddash * np.cos(angles) - V_ddash * np.sin(angles)
V_dash = U_ddash * np.sin(angles) + V_ddash * np.cos(angles)
ax = plt.subplot(133)
ax.set_title("Uniform length,\nColor is magnitude only")
q = ax.quiver(X, Y, U_dash, V_dash, color=c3)
plt.show()
To plot the color wheel use the following code. Note that this uses the max_abs value from above which is the maximum value that the color hue and value can reach. The vector_to_rgb() function is also re-used here.
ax = plt.subplot(236, projection='polar')
n = 200
t = np.linspace(0, 2 * np.pi, n)
r = np.linspace(0, max_abs, n)
rg, tg = np.meshgrid(r, t)
c = np.array(list(map(vector_to_rgb, tg.T.flatten(), rg.T.flatten())))
cv = c.reshape((n, n, 3))
m = ax.pcolormesh(t, r, cv[:,:,1], color=c, shading='auto')
m.set_array(None)
ax.set_yticklabels([])

I don't know if you've since found that quiver with matplotlib 1.4.x has 3d capability. This capability is limited when attempting to colour the arrows however.
A friend and I write the following script (in half an hour or so) to plot my experiment data using hex values from a spreadsheet, for my thesis. We're going to make this more automated once we're done with the semester but the issue with passing a colour map to quiver is that it can't accept a vector form for some reason.
This link is to my git repository where the code I used, slightly neatened up by another friend, is hosted.
I hope I can save someone the time it took me.