COPASI API
4.16.103
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#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"
Go to the source code of this file.
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 *) |
#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 |
This class implements an hybrid algorithm to simulate a biochemical system over time.
File name: CHybridMethodODE45.h Author: Shuo Wang Email: shuow ang. learn er@g mail. 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().
#define STOCHASTIC 0 |
Definition at line 74 of file CHybridMethodODE45.h.
Referenced by CHybridMethodODE45::doSingleStep(), and CHybridMethodODE45::setupMethod().
#define SUBTYPE 1 |
Definition at line 65 of file CHybridMethodODE45.h.
#define USE_RANDOM_SEED false |
Definition at line 66 of file CHybridMethodODE45.h.
Definition at line 88 of file CHybridMethodODE45.h.