COPASI API  4.16.103
Classes | Macros | Typedefs
CHybridMethodODE45.h File Reference
#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
#define DETERMINISTIC   1
#define FAST   1
#define HAS_ERR   -1

Definition at line 81 of file CHybridMethodODE45.h.

Referenced by CHybridMethodODE45::integrateDeterministicPart().

#define HAS_EVENT   2
#define HYBRID   2
#define INT_EPSILON   0.1

Definition at line 55 of file CHybridMethodODE45.h.

#define INTERP_RECORD_NUM   6
#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
#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
#define STOCHASTIC   0
#define SUBTYPE   1

Definition at line 65 of file CHybridMethodODE45.h.

#define USE_RANDOM_SEED   false

Definition at line 66 of file CHybridMethodODE45.h.

Typedef Documentation

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

Definition at line 88 of file CHybridMethodODE45.h.