#include <set>
#include <vector>
#include <sstream>
#include <fstream>
#include <cstdlib>
#include <new>
#include "copasi/trajectory/CTrajectoryMethod.h"
#include "copasi/utilities/CVersion.h"
#include "copasi/utilities/CMatrix.h"
#include "copasi/utilities/CDependencyGraph.h"
#include "copasi/utilities/CIndexedPriorityQueue.h"
#include "copasi/utilities/CCopasiVector.h"
#include "CInterpolation.h"

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Classes
class	CHybridMethodODE45

class	CHybridODE45Balance

class	CHybridODE45MetabFlag

struct	CHybridMethodODE45::Data

Macros
#define	CONTINUE 1

#define	DETERMINISTIC 1

#define	FAST 1

#define	HAS_ERR -1

#define	HAS_EVENT 2

#define	HYBRID 2

#define	INT_EPSILON 0.1

#define	INTERP_RECORD_NUM 6

#define	MAX_STEPS 1000000

#define	NEW_STEP 3

#define	RANDOM_SEED 1

#define	REACH_END_TIME 0

#define	SLOW 0

#define	STOCHASTIC 0

#define	SUBTYPE 1

#define	USE_RANDOM_SEED false

Typedefs
typedef void(*	pEvalF )(const C_INT , const double , const double , double )

Macro Definition Documentation

#define CONTINUE 1

Definition at line 83 of file CHybridMethodODE45.h.

Referenced by CHybridMethodODE45::doSingleStep(), and CHybridMethodODE45::integrateDeterministicPart().

#define DETERMINISTIC 1

Definition at line 75 of file CHybridMethodODE45.h.

Referenced by CHybridMethodODE45::doSingleStep(), and CHybridMethodODE45::setupMethod().

#define FAST 1

Definition at line 71 of file CHybridMethodODE45.h.

Referenced by CHybridMethodODE45::setupCalculateSet(), CHybridMethodODE45::setupMetabFlags(), and CHybridMethodODE45::setupReactionFlags().

#define HAS_ERR -1

Definition at line 81 of file CHybridMethodODE45.h.

Referenced by CHybridMethodODE45::integrateDeterministicPart().

#define HAS_EVENT 2

Definition at line 84 of file CHybridMethodODE45.h.

Referenced by CHybridMethodODE45::doSingleStep(), and CHybridMethodODE45::integrateDeterministicPart().

#define HYBRID 2

Definition at line 76 of file CHybridMethodODE45.h.

Referenced by CHybridMethodODE45::doSingleStep(), and CHybridMethodODE45::setupMethod().

#define INT_EPSILON 0.1

Definition at line 55 of file CHybridMethodODE45.h.

#define INTERP_RECORD_NUM 6

Definition at line 80 of file CHybridMethodODE45.h.

Referenced by CHybridMethodODE45::doInverseInterpolation(), and CHybridMethodODE45::initMethod().

#define MAX_STEPS 1000000

CHybridMethodODE45

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

File name: CHybridMethodODE45.h Author: Shuo Wang Email: shuow.nosp@m.ang..nosp@m.learn.nosp@m.er@g.nosp@m.mail..nosp@m.com

Last change: 26, Aug 2013 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 54 of file CHybridMethodODE45.h.

#define NEW_STEP 3

Definition at line 85 of file CHybridMethodODE45.h.

Referenced by CHybridMethodODE45::doSingleStep(), CHybridMethodODE45::initMethod(), and CHybridMethodODE45::integrateDeterministicPart().

#define RANDOM_SEED 1

Definition at line 67 of file CHybridMethodODE45.h.

#define REACH_END_TIME 0

Definition at line 82 of file CHybridMethodODE45.h.

Referenced by CHybridMethodODE45::integrateDeterministicPart().

#define SLOW 0

Definition at line 70 of file CHybridMethodODE45.h.

Referenced by CHybridMethodODE45::evalF(), CHybridMethodODE45::getReactionIndex4Hybrid(), CHybridMethodODE45::outputDebug(), CHybridMethodODE45::setupMetabFlags(), and CHybridMethodODE45::setupReactionFlags().