#include <set>#include <vector>#include <sstream>#include <fstream>#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 "copasi/odepack++/CLSODA.h"#include "CHybridNextReactionLSODAMethod.h"
Go to the source code of this file.
Classes | |
| class | CHybridLSODABalance |
| class | CHybridLSODAStochFlag |
| class | CHybridMethodLSODA |
| struct | CHybridMethodLSODA::Data |
Macros | |
| #define | INT_EPSILON 0.1 |
| #define | LOWER_STOCH_LIMIT 800 |
| #define | MAX_STEPS 1000000 |
| #define | OUTPUT_COUNTER 100 |
| #define | PARTITIONING_INTERVAL 1 |
| #define | PARTITIONING_STEPSIZE 0.001 |
| #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 62 of file CHybridMethodLSODA.h.
| #define LOWER_STOCH_LIMIT 800 |
Definition at line 63 of file CHybridMethodLSODA.h.
| #define MAX_STEPS 1000000 |
This class implements an hybrid algorithm to simulate a biochemical system over time.
File name: CHybridMethodLSODA.h Author: Juergen Pahle Email: juergen.pahle@eml-r.villa-bosch.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 61 of file CHybridMethodLSODA.h.
| #define OUTPUT_COUNTER 100 |
Definition at line 69 of file CHybridMethodLSODA.h.
| #define PARTITIONING_INTERVAL 1 |
Definition at line 68 of file CHybridMethodLSODA.h.
| #define PARTITIONING_STEPSIZE 0.001 |
Definition at line 66 of file CHybridMethodLSODA.h.
Referenced by CHybridMethodLSODA::initializeParameter().
| #define RANDOM_SEED 1 |
Definition at line 73 of file CHybridMethodLSODA.h.
| #define RUNGE_KUTTA_STEPSIZE 0.001 |
Definition at line 65 of file CHybridMethodLSODA.h.
| #define SUBTYPE 1 |
Definition at line 71 of file CHybridMethodLSODA.h.
| #define UPPER_STOCH_LIMIT 1000 |
Definition at line 64 of file CHybridMethodLSODA.h.
| #define USE_RANDOM_SEED false |
Definition at line 72 of file CHybridMethodLSODA.h.
