#include "trajectory/CTrajectoryMethod.h"
#include <set>
#include <vector>
#include <iostream>
#include <fstream>
#include "utilities/CVersion.h"
#include "utilities/CMatrix.h"
#include "utilities/CDependencyGraph.h"
#include "utilities/CIndexedPriorityQueue.h"
#include "utilities/CCopasiVector.h"
#include "CHybridNextReactionRKMethod.h"

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Classes
class	CHybridBalance

class	CHybridMethod

class	CHybridStochFlag

Macros
#define	INT_EPSILON 0.1

#define	LOWER_STOCH_LIMIT 800

#define	MAX_STEPS 1000000

#define	OUTPUT_COUNTER 100

#define	PARTITIONING_INTERVAL 1

#define	RANDOM_SEED 1

#define	RUNGE_KUTTA_STEPSIZE 0.001

#define	SUBTYPE 1

#define	UPPER_STOCH_LIMIT 1000

#define	USE_RANDOM_SEED false

Macro Definition Documentation

#define INT_EPSILON 0.1

Definition at line 59 of file CHybridMethod.h.

Referenced by CHybridMethod::checkModel(), CHybridMethodLSODA::checkModel(), and CHybridMethodODE45::checkModel().

#define LOWER_STOCH_LIMIT 800

Definition at line 60 of file CHybridMethod.h.

Referenced by CHybridMethod::initializeParameter(), and CHybridMethodLSODA::initializeParameter().

#define MAX_STEPS 1000000

CHybridMethod

This class implements an hybrid algorithm to simulate a biochemical system over time.

File name: CHybridMethod.h Author: Juergen Pahle Email: juerg.nosp@m.en.p.nosp@m.ahle@.nosp@m.eml-.nosp@m.r.vil.nosp@m.la-b.nosp@m.osch..nosp@m.de

Last change: 15, December 2004

(C) European Media Lab 2003. Partition the system into a deterministic part and a stochastic part. That is, every reaction is either classified deterministic or stochastic. Deterministic reactions involve only those metabolites (on substrate and product side), which have a high particle number. Therefore it is legal to integrate this part of the system with e.g. a numerical integrator. The concentration and relative particle number change should be low enough, so that the probabilities of all the reactions in the system show only little changes. The stochastic reactions must be simulated with an exact stochastic method (e.g. next reaction method (Gibson)), because their firing changes the reaction probabilities in the system significantly.

Definition at line 58 of file CHybridMethod.h.

Referenced by CHybridMethodODE45::initializeParameter(), CHybridMethod::initializeParameter(), and CHybridMethodLSODA::initializeParameter().

#define OUTPUT_COUNTER 100

Definition at line 64 of file CHybridMethod.h.

#define PARTITIONING_INTERVAL 1

Definition at line 63 of file CHybridMethod.h.

Referenced by CHybridMethod::initializeParameter(), and CHybridMethodLSODA::initializeParameter().

#define RANDOM_SEED 1

Definition at line 68 of file CHybridMethod.h.

Referenced by CHybridMethodODE45::initializeParameter(), CHybridMethod::initializeParameter(), and CHybridMethodLSODA::initializeParameter().

#define RUNGE_KUTTA_STEPSIZE 0.001

Definition at line 62 of file CHybridMethod.h.