Is it possible to solve a time delay differential equations using C++ Boost - odeint
library ? For an instance below equation:
x'(t) = r*x(t)*(1 - x(t-tau)),
where tau is a constant value for time delay.
Yes, you can. But odeint is not explicitly designed for DDEs. There are two possibilities to solve DDEs with odeint:
You consider x and its discretized history as dependend variables and use directly the steppers.
You consider only x as dependent variable and pass the history with the system function (your r.h.s.). But in this case you should only use steppers which evaluate the state at multiplies of you timesteps, like Euler or RK2.
If I have time I will write a more concrete answer, maybe with some code snippets.
Related
I am trying to solve an ODE of the form: (d/dt) x = A * x
given the square matrix A and the vector x at t=0 in sympy. The system I am studying has more than 50 equations.
As I defined it above, I believe these equations are linear, homogeneous, and first-order. When I looked in the sympy documentation, I found something similar ("system_of_odes_linear_neq_order1_type1"). I defined the system and am trying to solve with a command like so:
sympy.dsolve(system,hint='system_of_odes_linear_neq_order1_type1')
The script has been running for a while without terminating so I'm getting a bit worried. On second look, I saw the system being called "nonhomogeneous" in the documentation:
https://www.cfm.brown.edu/people/dobrush/am33/SymPy/part2.html#sympy.solvers.ode._linear_neq_order1_type1
Why is it called "nonhomogeneous" here? Is type of solver I used incorrect and should I redefine the system/solver? I don't see many other options for systems of differential equations where there are more than 3 equations.
Introduction
Let’s assume that I need the Jacobian matrix for the following set of ODE:
dxdt[ 0 ] = -90.0 * x[0] - 50.0 * x[1];
dxdt[ 1 ] = x[0] + 3*x[1];
dxdt[ 2 ] = x[1] + 50*x[2];
In Matlab/Octave this would be pretty easy:
syms x0 x1 x2;
f = [-90.0*x0-50.0*x1, x0+3*x1, x1+50*x2]
v=[x0, x1, x2]
fp = jacobian(f,v)
This would results with following output matrix:
[-90 -50 0 ]
[ 1 3 0 ]
[ 0 1 50]
What I need
Now I want to reproduce the same results in C++. I can’t compute the Jacobian before and hard-code it, as it will depend for example on user inputs and time. So my question is: How to do this? Usually for mathematics operations, I use the Boost library, however in this case I can’t find any solution. There’s only short note about this in implicit systems, but the following code doesn’t work:
sys.second( x , jacobi , t )
It also requests the time (t), so it probably doesn’t generate an analytic form of solution. Do I misunderstand the documentations? Or should I use another function? I would prefer to stay within Boost, as I need the Jacobian as ublas::matrix and I want to avoid conversion.
EDIT:
More specific I will use Jacobian inside rosenbrock4 ODE solver. Example here - lines 47-52. I need automatic generation of this structure as the ODE set may be changed later and I want to avoid manually rewriting Jacobian ever time. Also some variables inside ODE definitions are not constant in time.
I know this is long after the fact, but I have recently been wanting to do the same thing and have come across many auto differentiation (AD) libraries that do this pretty well. I have mostly been using Eigen's AD because I am already using Eigen everywhere. Here's an example of how you can use Eigen's AD to get the jacobian like you asked.
There's also a long list of c++ AD libraries on autodiff.org.
Hope this helps someone!
The Jacobian is based on derivatives of the function. If the function f is only known at run-time (and there are no constraints such as linearity), you have to automatise the differentiation. If you want this to happen exactly (as opposed to a numerical estimation), you need to use symbolic computation. Look for example here and here for libraries supporting this.
Note that the Jacobian usually depends on the state and the time, so it’s impossible to represent it as a constant matrix (such as in your example), unless your problem is so boring that you can solve it analytically anyway.
I have a cyclic program in C++ which includes composing of a function (every time it is different) and further minimization of it. Composing of a function is implemented with GiNaC package (symbolic expressions).
I tried to minimize functions using Matlab fmincon function but it ate all the memory while converting string to lambda function (functions are rather complicated). And I couldn't manage to export function from C++ to Matlab in any way but as a string.
Is there any way to compose a complicated function (3 variables, sin-cos-square root etc.) and minimize it without determing gradient by myself because I don't know how functions look before running the program?
I also looked at NLopt and as I understood it requires gradients to be writte by programmer.
Most optimization algorithms do require the gradient. However, if it's impossible to 'know' it directly, you may evaluate it considering a small increment of every coordinate. If your F function depends on coordinates of x vector, you may approximate the i's component of you gradient vector G as
x1 = x;
x1[i] += dx;
G[i] = (F(x1) - F(x))/dx;
where dx is some small increment. Although such a calculation is approximate it's usually absolutely good for a minimum finding provided that dx is small enough.
I am trying to solve two point boundary problem with odeint. My equation has the form of
y'' + a*y' + b*y + c = 0
It is pretty trivial when I have boundary conditions of y(x_1) = y_1 , y'(x_2) = y_2, but when boundary conditions are y(x_1) = y_1 , y(x_2) = y_2 I am lost. Does anybody know the way to deal with problems like this with odeint or other scientific library?
In this case you need a shooting method. odeint does not have such a method, it solved the initial value problem (IVP) which is your first case. I think in the Numerical Recipies this method is explained and you can use Boost.Odeint to do the time stepping.
An alternative and more efficient method to solve this type of problem is finite differences or finite elements method. For finite differences you can check Numerical Recipes. For finite elements I recommend dealii library.
Another approach is to use b-splines: Assuming you do know the initial x0 and final xfinal points of integration, then you can expand the solution y(x) in a b-spline basis, defined over (x0,xfinal), i.e.
y(x)= \sum_{i=1}^n A_i*B_i(x),
where A_i are constant coefficients to be determined, and B_i(x) are b-spline basis (well defined polynomial functions, that can be differentiated numerically). For scientific applications you can find an implementation of b-splines in GSL.
With this substitution the boundary value problem is reduced to a linear problem, since (am using Einstein summation for repeated indices):
A_i*[ B_i''(x) + a*B_i'(x) + b*B_i(x)] + c =0
You can choose a set of points x and create a linear system from the above equation. You can find information for this type of method in the following review paper "Applications of B-splines in Atomic and Molecular Physics" - H Bachau, E Cormier, P Decleva, J E Hansen and F Martín
http://iopscience.iop.org/0034-4885/64/12/205/
I do not know of any library solving directly this problem, but there are several libraries for B-splines (I recommend GSL for your needs), that will allow you to form the linear system. See this stackoverflow question:
Spline, B-Spline and NURBS C++ library
I just implemented the numerical integration for a set of coupled ODEs
from a discretized PDE using the odeint C++ library. It works nicely and
is lightning fast, but there is one issue:
My system of ODEs has, so-called, absorbing boundary conditions: the time
derivatives of my state variable, n, which is a vector of N doubles
(a population density) gets calculated in the system function, but before that happens
(or after the time integration) I would like to set:
n[N]=n[N-2];
n[N-1]=n[N-2];
However, of course this doesn't work because the state variable in the system
function is declared as const, and it looks as if this could not be changed
other than through meddling with the library... is there any way around this?
I should mention that setting dndt[N] and dndt[N-1] to zero might look like a
solution, but it doesn't really help as it defies the concept of absorbing boundary
conditions (n[N] and n[N-1] would then always have the values they had at t=0, rather
then the value of n[N-2] at any point in time), and so I'd really prefer to change n.
Thanks for any help!
Regards,
Michael
Usually absorbing boundary condition manifests itself in the equations of motion. n[N] = n[N-1] = n[N-2], so can insert n[N]=n[N-2] and n[N-1]=n[N-2] into the equation for dndt[N-2].
For example, the discrete Laplacian Lx[i] = x[i+1]-2 x[i] +x[i-1] with absorbing boundaries x[n]=x[n-1] can be written as Lx[n-1] = x[n-2] - x[n-1]. The equation for x[n] can then be omitted.