COPASI API  4.16.103
Classes | Macros
CHybridMethod.h File Reference
#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
#define LOWER_STOCH_LIMIT   800
#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
#define RANDOM_SEED   1
#define RUNGE_KUTTA_STEPSIZE   0.001

Definition at line 62 of file CHybridMethod.h.

Referenced by CHybridMethod::initializeParameter().

#define SUBTYPE   1

Definition at line 66 of file CHybridMethod.h.

#define UPPER_STOCH_LIMIT   1000
#define USE_RANDOM_SEED   false