IntegratorsPython.cpp File Reference

#include <Kinetx/Integrator/CashKarp5.h>
#include <Kinetx/Integrator/Cvode.h>
#include <Kinetx/Integrator/ExplicitEuler.h>
#include <Kinetx/Integrator/ImplicitEuler.h>
#include <Kinetx/Integrator/Integrator.h>
#include <pybind11/eigen.h>
#include <pybind11/pybind11.h>
#include <pybind11/stl.h>
#include <iomanip>
#include <memory>

Include dependency graph for IntegratorsPython.cpp:

Enumerations
enum	IntegratorName { CashKarp5, ExplicitEuler, ImplicitEuler, CvodeBdf }
	Enum class for the different numerical integration schemes.

Functions
std::tuple< Eigen::MatrixXd, Eigen::MatrixXd, Eigen::MatrixXd, Eigen::MatrixXd >	integrateDifferentialEquations (Network &network, std::vector< double > yStart, const double tStart, const double dt, const IntegratorName integratorName, const unsigned int batchInterval=1000, const unsigned int nBatches=100000, const double convergenceConcentrationChange=1e-10, bool integrateByTime=false, double maxTime=1e+5)
	A helper function to integrate the rate equations of a given reaction network in a batch-wise fashion. This function keeps track of the maximum concentration for each species in between integration batches. More...
IntegratorName	resolveIntegratorName (std::string integrator)
	Resolve a string to its enum representation for the numerical integration schemes. More...
void	init_numerical_integration (pybind11::module &m)
	Python bindings for the numerical integration. More...

Detailed Description

Copyright

This code is licensed under the 3-clause BSD license.
Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
See LICENSE.txt for details.

Function Documentation

void init_numerical_integration

(

pybind11::module &

m

)

Python bindings for the numerical integration.

Parameters

m

std::tuple<Eigen::MatrixXd, Eigen::MatrixXd, Eigen::MatrixXd, Eigen::MatrixXd> integrateDifferentialEquations	(	Network &	network,
		std::vector< double >	yStart,
		const double	tStart,
		const double	dt,
		const IntegratorName	integratorName,
		const unsigned int	batchInterval = 1000,
		const unsigned int	nBatches = 100000,
		const double	convergenceConcentrationChange = 1e-10,
		bool	integrateByTime = false,
		double	maxTime = 1e+5
	)

A helper function to integrate the rate equations of a given reaction network in a batch-wise fashion. This function keeps track of the maximum concentration for each species in between integration batches.

Parameters

network	The reaction network.
yStart	The starting concentrations.
tStart	The starting time.
dt	The time step (note that this may be ignored by some numerical integration schemes)
integratorName	The enum for the integration scheme.
batchInterval	The number of propagation steps per batch.
nBatches	The maximum number of batches.
convergenceConcentrationChange	If the maximum change is concentration is lower than the given threshold. The integration is considered to be complete.
integrateByTime	If true, the numerical integration is done up to the specified maxTime.
maxTime	The maximum time to integrate. This is only used if integrateByTime is true.

Returns

A matrix of which the values of the first column are the final concentrations, the values of the second column are the maximum concentrations reached by the species, and the third column are the concentration flux through the species during the integration.

IntegratorName resolveIntegratorName

(

std::string

integrator

)

Resolve a string to its enum representation for the numerical integration schemes.

Parameters

integrator

The string.

Returns

The enum.