Related
help, please - I can't understand my own code! lol
I'm fairly new at python and after many trials and errors, I got my code to work, but there is one particular part of it I don't understand.
In the code below, I'm solving a fairly basic ODE through scipy's odeint-function. My goal is then to build on this blue-print for more complicated systems.
My question(s): How could I call the method .reaction_rate_simple without any arguments and without the closing parenthesis? What does this mean in python? Should I use a static method here somewhere?
If anyone has any feedback on this - maybe this is a crappy piece of code and there's a better way of solving it!
I am very thankful for any response and help!
import numpy as np
import matplotlib.pyplot as plt
from scipy.integrate import odeint
class batch_reator:
def __init__(self, C_init, volume_reactor, time_init, time_end):
self.C_init = C_init
self.volume = volume_reactor
self.time_init = time_init
self.time_end = time_end
self.operation_time = (time_end - time_init)
def reaction_rate_simple(self, concentration_t, t, stoch_factor, order, rate_constant):
reaction_rate = stoch_factor * rate_constant * (concentration_t ** order)
return reaction_rate
def equations_system(self, kinetics):
dCdt = kinetics
return dCdt
C_init = 200
time_init, time_end = 0, 1000
rate_constant, volume_reactor, order, stoch_factor = 0.0001, 10, 1, -1
time_span = np.linspace(time_init, time_end, 100)
Batch_basic = batch_reator(C_init, volume_reactor, time_init, time_end)
kinetics = Batch_basic.reaction_rate_simple
sol = odeint(Batch_basic.equations_system(kinetics), Batch_basic.C_init, time_span, args=(stoch_factor, order, rate_constant))
plt.plot(time_span, sol)
plt.show()
I assume you are referring to the line
kinetics = Batch_basic.reaction_rate_simple
You are not calling it, you are saving the method as a variable and then passing that method to equations_system(...), which simply returns it. I am not familiar with odeint, but according to the documentation, it accepts a callable, which is what you are giving it.
In python functions, lambdas, classes are all callable and can be assigned to variable and passed to functions and called as needed.
In this particular case the callback definition from the odeint docs say
func callable(y, t, …) or callable(t, y, …)
Computes the derivative of y at t. If the signature is callable(t, y, ...), then the argument tfirst must be set True.
So the first two arguments are passed in by odeint, and the other three are coming from the arguments specified by you.
1. The core problem and question
I will provide an executable example below, but let me first walk you through the problem first.
I am using solve_ivp from scipy.integrate to solve an initial value problem (see documentation). In fact I have to call the solver twice, to once integrate forward and once backward in time. (I would have to go unnecessarily deep into my concrete problem to explain why this is necessary, but please trust me here--it is!)
sol0 = solve_ivp(rhs,[0,-1e8],y0,rtol=10e-12,atol=10e-12,dense_output=True)
sol1 = solve_ivp(rhs,[0, 1e8],y0,rtol=10e-12,atol=10e-12,dense_output=True)
Here rhs is the right hand side function of the initial value problem y(t) = rhs(t,y). In my case, y has six components y[0] to y[5]. y0=y(0) is the initial condition. [0,±1e8] are the respective integration ranges, one forward and the other backward in time. rtol and atol are tolerances.
Importantly, you see that I flagged dense_output=True, which means that the solver does not only return the solutions on the numerical grids, but also as interpolation functions sol0.sol(t) and sol1.sol(t).
My main goal now is to define a piecewise function, say sol(t) which takes the value sol0.sol(t) for t<0 and the value sol1.sol(t) for t>=0. So the main question is: How do I do that?
I thought that numpy.piecewise should be tool of choice to do this for me. But I am having trouble using it, as you will see below, where I show you what I tried so far.
2. Example code
The code in the box below solves the initial value problem of my example. Most of the code is the definition of the rhs function, the details of which are not important to the question.
import numpy as np
from scipy.integrate import solve_ivp
# aux definitions and constants
sin=np.sin; cos=np.cos; tan=np.tan; sqrt=np.sqrt; pi=np.pi;
c = 299792458
Gm = 5.655090674872875e26
# define right hand side function of initial value problem, y'(t) = rhs(t,y)
def rhs(t,y):
p,e,i,Om,om,f = y
sinf=np.sin(f); cosf=np.cos(f); Q=sqrt(p/Gm); opecf=1+e*cosf;
R = Gm**2/(c**2*p**3)*opecf**2*(3*(e**2 + 1) + 2*e*cosf - 4*e**2*cosf**2)
S = Gm**2/(c**2*p**3)*4*opecf**3*e*sinf
rhs = np.zeros(6)
rhs[0] = 2*sqrt(p**3/Gm)/opecf*S
rhs[1] = Q*(sinf*R + (2*cosf + e*(1 + cosf**2))/opecf*S)
rhs[2] = 0
rhs[3] = 0
rhs[4] = Q/e*(-cosf*R + (2 + e*cosf)/opecf*sinf*S)
rhs[5] = sqrt(Gm/p**3)*opecf**2 + Q/e*(cosf*R - (2 + e*cosf)/opecf*sinf*S)
return rhs
# define initial values, y0
y0=[3.3578528933149297e13,0.8846,2.34921,3.98284,1.15715,0]
# integrate twice from t = 0, once backward in time (sol0) and once forward in time (sol1)
sol0 = solve_ivp(rhs,[0,-1e8],y0,rtol=10e-12,atol=10e-12,dense_output=True)
sol1 = solve_ivp(rhs,[0, 1e8],y0,rtol=10e-12,atol=10e-12,dense_output=True)
The solution functions can be addressed from here by sol0.sol and sol1.sol respectively. As an example, let's plot the 4th component:
from matplotlib import pyplot as plt
t0 = np.linspace(-1,0,500)*1e8
t1 = np.linspace( 0,1,500)*1e8
plt.plot(t0,sol0.sol(t0)[4])
plt.plot(t1,sol1.sol(t1)[4])
plt.title('plot 1')
plt.show()
3. Failing attempts to build piecewise function
3.1 Build vector valued piecewise function directly out of sol0.sol and sol1.sol
def sol(t): return np.piecewise(t,[t<0,t>=0],[sol0.sol,sol1.sol])
t = np.linspace(-1,1,1000)*1e8
print(sol(t))
This leads to the following error in piecewise in line 628 of .../numpy/lib/function_base.py:
TypeError: NumPy boolean array indexing assignment requires a 0 or 1-dimensional input, input has 2 dimensions
I am not sure, but I do think this is because of the following: In the documentation of piecewise it says about the third argument:
funclistlist of callables, f(x,*args,**kw), or scalars
[...]. It should take a 1d array as input and give an 1d array or a scalar value as output. [...].
I suppose the problem is, that the solution in my case has six components. Hence, evaluated on a time grid the output would be a 2d array. Can someone confirm, that this is indeed the problem? Since I think this really limits the usefulness of piecewiseby a lot.
3.2 Try the same, but just for one component (e.g. for the 4th)
def sol4(t): return np.piecewise(t,[t<0,t>=0],[sol0.sol(t)[4],sol1.sol(t)[4]])
t = np.linspace(-1,1,1000)*1e8
print(sol4(t))
This results in this error in line 624 of the same file as above:
ValueError: NumPy boolean array indexing assignment cannot assign 1000 input values to the 500 output values where the mask is true
Contrary to the previous error, unfortunately here I have so far no idea why it is not working.
3.3 Similar attempt, however first defining functions for the 4th components
def sol40(t): return sol0.sol(t)[4]
def sol41(t): return sol1.sol(t)[4]
def sol4(t): return np.piecewise(t,[t<0,t>=0],[sol40,sol41])
t = np.linspace(-1,1,1000)
plt.plot(t,sol4(t))
plt.title('plot 2')
plt.show()
Now this does not result in an error, and I can produce a plot, however this plot doesn't look like it should. It should look like plot 1 above. Also here, I so far have no clue what is going on.
Am thankful for help!
You can take a look to numpy.piecewise source code. There is nothing special in this function so I suggest to do everything manually.
def sol(t):
ans = np.empty((6, len(t)))
ans[:, t<0] = sol0.sol(t[t<0])
ans[:, t>=0] = sol1.sol(t[t>=0])
return ans
Regarding your failed attempts. Yes, piecewise excpect functions return 1d array. Your second attempt failed because documentation says that funclist argument should be list of functions or scalars but you send the list of arrays. Contrary to the documentation it works even with arrays, you just should use the arrays of the same size as t < 0 and t >= 0 like:
def sol4(t): return np.piecewise(t,[t<0,t>=0],[sol0.sol(t[t<0])[4],sol1.sol(t[t>=0])[4]])
I'm using right now the scipy.integrate.quad to successfully integrate some real integrands. Now a situation appeared that I need to integrate a complex integrand. quad seems not be able to do it, as the other scipy.integrate routines, so I ask: is there any way to integrate a complex integrand using scipy.integrate, without having to separate the integral in the real and the imaginary parts?
What's wrong with just separating it out into real and imaginary parts? scipy.integrate.quad requires the integrated function return floats (aka real numbers) for the algorithm it uses.
import scipy
from scipy.integrate import quad
def complex_quadrature(func, a, b, **kwargs):
def real_func(x):
return scipy.real(func(x))
def imag_func(x):
return scipy.imag(func(x))
real_integral = quad(real_func, a, b, **kwargs)
imag_integral = quad(imag_func, a, b, **kwargs)
return (real_integral[0] + 1j*imag_integral[0], real_integral[1:], imag_integral[1:])
E.g.,
>>> complex_quadrature(lambda x: (scipy.exp(1j*x)), 0,scipy.pi/2)
((0.99999999999999989+0.99999999999999989j),
(1.1102230246251564e-14,),
(1.1102230246251564e-14,))
which is what you expect to rounding error - integral of exp(i x) from 0, pi/2 is (1/i)(e^i pi/2 - e^0) = -i(i - 1) = 1 + i ~ (0.99999999999999989+0.99999999999999989j).
And for the record in case it isn't 100% clear to everyone, integration is a linear functional, meaning that ∫ { f(x) + k g(x) } dx = ∫ f(x) dx + k ∫ g(x) dx (where k is a constant with respect to x). Or for our specific case ∫ z(x) dx = ∫ Re z(x) dx + i ∫ Im z(x) dx as z(x) = Re z(x) + i Im z(x).
If you are trying to do a integration over a path in the complex plane (other than along the real axis) or region in the complex plane, you'll need a more sophisticated algorithm.
Note: Scipy.integrate will not directly handle complex integration. Why? It does the heavy lifting in the FORTRAN QUADPACK library, specifically in qagse.f which explicitly requires the functions/variables to be real before doing its "global adaptive quadrature based on 21-point Gauss–Kronrod quadrature within each subinterval, with acceleration by Peter Wynn's epsilon algorithm." So unless you want to try and modify the underlying FORTRAN to get it to handle complex numbers, compile it into a new library, you aren't going to get it to work.
If you really want to do the Gauss-Kronrod method with complex numbers in exactly one integration, look at wikipedias page and implement directly as done below (using 15-pt, 7-pt rule). Note, I memoize'd function to repeat common calls to the common variables (assuming function calls are slow as if the function is very complex). Also only did 7-pt and 15-pt rule, since I didn't feel like calculating the nodes/weights myself and those were the ones listed on wikipedia, but getting reasonable errors for test cases (~1e-14)
import scipy
from scipy import array
def quad_routine(func, a, b, x_list, w_list):
c_1 = (b-a)/2.0
c_2 = (b+a)/2.0
eval_points = map(lambda x: c_1*x+c_2, x_list)
func_evals = map(func, eval_points)
return c_1 * sum(array(func_evals) * array(w_list))
def quad_gauss_7(func, a, b):
x_gauss = [-0.949107912342759, -0.741531185599394, -0.405845151377397, 0, 0.405845151377397, 0.741531185599394, 0.949107912342759]
w_gauss = array([0.129484966168870, 0.279705391489277, 0.381830050505119, 0.417959183673469, 0.381830050505119, 0.279705391489277,0.129484966168870])
return quad_routine(func,a,b,x_gauss, w_gauss)
def quad_kronrod_15(func, a, b):
x_kr = [-0.991455371120813,-0.949107912342759, -0.864864423359769, -0.741531185599394, -0.586087235467691,-0.405845151377397, -0.207784955007898, 0.0, 0.207784955007898,0.405845151377397, 0.586087235467691, 0.741531185599394, 0.864864423359769, 0.949107912342759, 0.991455371120813]
w_kr = [0.022935322010529, 0.063092092629979, 0.104790010322250, 0.140653259715525, 0.169004726639267, 0.190350578064785, 0.204432940075298, 0.209482141084728, 0.204432940075298, 0.190350578064785, 0.169004726639267, 0.140653259715525, 0.104790010322250, 0.063092092629979, 0.022935322010529]
return quad_routine(func,a,b,x_kr, w_kr)
class Memoize(object):
def __init__(self, func):
self.func = func
self.eval_points = {}
def __call__(self, *args):
if args not in self.eval_points:
self.eval_points[args] = self.func(*args)
return self.eval_points[args]
def quad(func,a,b):
''' Output is the 15 point estimate; and the estimated error '''
func = Memoize(func) # Memoize function to skip repeated function calls.
g7 = quad_gauss_7(func,a,b)
k15 = quad_kronrod_15(func,a,b)
# I don't have much faith in this error estimate taken from wikipedia
# without incorporating how it should scale with changing limits
return [k15, (200*scipy.absolute(g7-k15))**1.5]
Test case:
>>> quad(lambda x: scipy.exp(1j*x), 0,scipy.pi/2.0)
[(0.99999999999999711+0.99999999999999689j), 9.6120083407040365e-19]
I don't trust the error estimate -- I took something from wiki for recommended error estimate when integrating from [-1 to 1] and the values don't seem reasonable to me. E.g., the error above compared with truth is ~5e-15 not ~1e-19. I'm sure if someone consulted num recipes, you could get a more accurate estimate. (Probably have to multiple by (a-b)/2 to some power or something similar).
Recall, the python version is less accurate than just calling scipy's QUADPACK based integration twice. (You could improve upon it if desired).
I realize I'm late to the party, but perhaps quadpy (a project of mine) can help. This
import quadpy
import numpy
val, err = quadpy.quad(lambda x: numpy.exp(1j * x), 0, 1)
print(val)
correctly gives
(0.8414709848078964+0.4596976941318605j)
I'm stucked trying to use the numpy.linalg functions to solve a big system of linear equations.
For instance, I've been trying to use:
numpy.linalg.solve
numpy.linalg.cg
numpy.linalg.inv
Among others, and none of these functions return anything. The program seems to abort raising no error or warning at all.
To demonstrate, I have this piece of code to create my A matrix:
import numpy
from intertools import product
indices = numpy.arange(x_steps * y_steps).reshape(x_steps, y_steps)
a = numpy.zeros((x_steps * y_steps, x_steps * y_steps))
for x, y in product(range(x_steps), range(y_steps)):
neighbors_x = indices[x, max(0, y-1):y+2].flatten()
neighbors_y = indices[max(0, x-1):x+2, y].flatten()
current = indices[x, y]
a[current, neighbors_x] = 1.0
a[current, neighbors_y] = 1.0
a[current, current] = -4.0
h = (x_dim / x_steps) * (y_dim / y_steps)
a /= h
Withx_dim = y_dim = 12 and x_steps = y_steps = 100.
The code works just fine. When I try to calculate det(A) I get 0.0144, which is correct.
But the system is never solved.
Then I tried to calculate the inverse of A:
print 'inv'
z = numpy.linalg.inv(a)
print 'here'
And 'here' is never printed, and no error is raised at all. I see the first print and then it appears on the console The program finished with code 0. As I said, I tried to solve the system with the conjugate gradient method too and the same occurs. It is weird, because I didn't get any error/warning to help me to find what is wrong.
I strongly think this is a memory problem (I am running my code in a 64bits Windows 8.1 -- 4GB RAM -- with a 32bits Numpy -- 64 generated a lot of incompatibilities here) but I really don't know if there is a way to solve it. If that is the problem, the Conjugate gradient method shouldn't be able to solve this, since that is its purpose?
Thank you in advance.
The (brief) documentation for scipy.integrate.ode says that two methods (dopri5 and dop853) have stepsize control and dense output. Looking at the examples and the code itself, I can only see a very simple way to get output from an integrator. Namely, it looks like you just step the integrator forward by some fixed dt, get the function value(s) at that time, and repeat.
My problem has pretty variable timescales, so I'd like to just get the values at whatever time steps it needs to evaluate to achieve the required tolerances. That is, early on, things are changing slowly, so the output time steps can be big. But as things get interesting, the output time steps have to be smaller. I don't actually want dense output at equal intervals, I just want the time steps the adaptive function uses.
EDIT: Dense output
A related notion (almost the opposite) is "dense output", whereby the steps taken are as large as the stepper cares to take, but the values of the function are interpolated (usually with accuracy comparable to the accuracy of the stepper) to whatever you want. The fortran underlying scipy.integrate.ode is apparently capable of this, but ode does not have the interface. odeint, on the other hand, is based on a different code, and does evidently do dense output. (You can output every time your right-hand-side is called to see when that happens, and see that it has nothing to do with the output times.)
So I could still take advantage of adaptivity, as long as I could decide on the output time steps I want ahead of time. Unfortunately, for my favorite system, I don't even know what the approximate timescales are as functions of time, until I run the integration. So I'll have to combine the idea of taking one integrator step with this notion of dense output.
EDIT 2: Dense output again
Apparently, scipy 1.0.0 introduced support for dense output through a new interface. In particular, they recommend moving away from scipy.integrate.odeint and towards scipy.integrate.solve_ivp, which as a keyword dense_output. If set to True, the returned object has an attribute sol that you can call with an array of times, which then returns the integrated functions values at those times. That still doesn't solve the problem for this question, but it is useful in many cases.
Since SciPy 0.13.0,
The intermediate results from the dopri family of ODE solvers can
now be accessed by a solout callback function.
import numpy as np
from scipy.integrate import ode
import matplotlib.pyplot as plt
def logistic(t, y, r):
return r * y * (1.0 - y)
r = .01
t0 = 0
y0 = 1e-5
t1 = 5000.0
backend = 'dopri5'
# backend = 'dop853'
solver = ode(logistic).set_integrator(backend)
sol = []
def solout(t, y):
sol.append([t, *y])
solver.set_solout(solout)
solver.set_initial_value(y0, t0).set_f_params(r)
solver.integrate(t1)
sol = np.array(sol)
plt.plot(sol[:,0], sol[:,1], 'b.-')
plt.show()
Result:
The result seems to be slightly different from Tim D's, although they both use the same backend. I suspect this having to do with FSAL property of dopri5. In Tim's approach, I think the result k7 from the seventh stage is discarded, so k1 is calculated afresh.
Note: There's a known bug with set_solout not working if you set it after setting initial values. It was fixed as of SciPy 0.17.0.
I've been looking at this to try to get the same result. It turns out you can use a hack to get the step-by-step results by setting nsteps=1 in the ode instantiation. It will generate a UserWarning at every step (this can be caught and suppressed).
import numpy as np
from scipy.integrate import ode
import matplotlib.pyplot as plt
import warnings
def logistic(t, y, r):
return r * y * (1.0 - y)
r = .01
t0 = 0
y0 = 1e-5
t1 = 5000.0
#backend = 'vode'
backend = 'dopri5'
#backend = 'dop853'
solver = ode(logistic).set_integrator(backend, nsteps=1)
solver.set_initial_value(y0, t0).set_f_params(r)
# suppress Fortran-printed warning
solver._integrator.iwork[2] = -1
sol = []
warnings.filterwarnings("ignore", category=UserWarning)
while solver.t < t1:
solver.integrate(t1, step=True)
sol.append([solver.t, solver.y])
warnings.resetwarnings()
sol = np.array(sol)
plt.plot(sol[:,0], sol[:,1], 'b.-')
plt.show()
result:
The integrate method accepts a boolean argument step that tells the method to return a single internal step. However, it appears that the 'dopri5' and 'dop853' solvers do not support it.
The following code shows how you can get the internal steps taken by the solver when the 'vode' solver is used:
import numpy as np
from scipy.integrate import ode
import matplotlib.pyplot as plt
def logistic(t, y, r):
return r * y * (1.0 - y)
r = .01
t0 = 0
y0 = 1e-5
t1 = 5000.0
backend = 'vode'
#backend = 'dopri5'
#backend = 'dop853'
solver = ode(logistic).set_integrator(backend)
solver.set_initial_value(y0, t0).set_f_params(r)
sol = []
while solver.successful() and solver.t < t1:
solver.integrate(t1, step=True)
sol.append([solver.t, solver.y])
sol = np.array(sol)
plt.plot(sol[:,0], sol[:,1], 'b.-')
plt.show()
Result:
FYI, although an answer has been accepted already, I should point out for the historical record that dense output and arbitrary sampling from anywhere along the computed trajectory is natively supported in PyDSTool. This also includes a record of all the adaptively-determined time steps used internally by the solver. This interfaces with both dopri853 and radau5 and auto-generates the C code necessary to interface with them rather than relying on (much slower) python function callbacks for the right-hand side definition. None of these features are natively or efficiently provided in any other python-focused solver, to my knowledge.
Here's another option that should also work with dopri5 and dop853. Basically, the solver will call the logistic() function as often as needed to calculate intermediate values so that's where we store the results:
import numpy as np
from scipy.integrate import ode
import matplotlib.pyplot as plt
sol = []
def logistic(t, y, r):
sol.append([t, y])
return r * y * (1.0 - y)
r = .01
t0 = 0
y0 = 1e-5
t1 = 5000.0
# Maximum number of steps that the integrator is allowed
# to do along the whole interval [t0, t1].
N = 10000
#backend = 'vode'
backend = 'dopri5'
#backend = 'dop853'
solver = ode(logistic).set_integrator(backend, nsteps=N)
solver.set_initial_value(y0, t0).set_f_params(r)
# Single call to solver.integrate()
solver.integrate(t1)
sol = np.array(sol)
plt.plot(sol[:,0], sol[:,1], 'b.-')
plt.show()