COPASI API
4.16.103
|
#include <CState.h>
Public Member Functions | |
C_FLOAT64 * | beginDependent () |
const C_FLOAT64 * | beginDependent () const |
C_FLOAT64 * | beginFixed () |
const C_FLOAT64 * | beginFixed () const |
C_FLOAT64 * | beginIndependent () |
const C_FLOAT64 * | beginIndependent () const |
CState () | |
CState (const CState &src) | |
C_FLOAT64 * | endDependent () |
const C_FLOAT64 * | endDependent () const |
C_FLOAT64 * | endFixed () |
const C_FLOAT64 * | endFixed () const |
C_FLOAT64 * | endIndependent () |
const C_FLOAT64 * | endIndependent () const |
size_t | getNumDependent () const |
size_t | getNumFixed () const |
size_t | getNumIndependent () const |
size_t | getNumVariable () const |
const C_FLOAT64 & | getTime () const |
bool | isValid () const |
CState & | operator= (const CState &rhs) |
void | setTime (const C_FLOAT64 &time) |
~CState () | |
Protected Member Functions | |
C_FLOAT64 * | resize (const size_t &size) |
void | updateIterator (const size_t &numIndependent, const size_t &numDependent, const size_t &numFixed) |
Private Attributes | |
C_FLOAT64 * | mpBeginDependent |
C_FLOAT64 * | mpBeginFixed |
C_FLOAT64 * | mpBeginIndependent |
C_FLOAT64 * | mpEnd |
C_FLOAT64 * | mpValues |
size_t | mSize |
bool | mUpdateDependentRequired |
Friends | |
class | CStateTemplate |
std::ostream & | operator<< (std::ostream &os, const CState &s) |
CState::CState | ( | ) |
CState::CState | ( | const CState & | src | ) |
CState::~CState | ( | ) |
C_FLOAT64 * CState::beginDependent | ( | ) |
Retrieve the array of pointers of values of all dependent entities, which are only dependent species for a reduced model.
Definition at line 330 of file CState.cpp.
References mpBeginDependent.
Referenced by CHybridMethodODE45::outputState(), and CModel::updateSimulatedValues().
const C_FLOAT64 * CState::beginDependent | ( | ) | const |
Retrieve the array of pointers of values of all dependent entities, which are only dependent species for a reduced model.
Definition at line 337 of file CState.cpp.
References mpBeginDependent.
C_FLOAT64 * CState::beginFixed | ( | ) |
Retrieve the array of pointers of values of all fixed entities.
Definition at line 332 of file CState.cpp.
References mpBeginFixed.
Referenced by CHybridMethodODE45::outputState(), and CLsodaMethod::stateChanged().
const C_FLOAT64 * CState::beginFixed | ( | ) | const |
Retrieve the array of pointers of values of all fixed entities.
Definition at line 339 of file CState.cpp.
References mpBeginFixed.
C_FLOAT64 * CState::beginIndependent | ( | ) |
Retrieve the array of pointers of values of all independent entities.
Definition at line 328 of file CState.cpp.
References mpBeginIndependent.
Referenced by CSteadyStateMethod::allPositive(), CLyapWolfMethod::calculate(), CModel::calculateJacobian(), CModel::calculateJacobianX(), CMathModel::calculateRootJacobian(), CNewtonMethod::containsNaN(), CHybridMethodODE45::doInverseInterpolation(), CTauLeapMethod::doSingleStep(), CCopasiXMLParser::InitialStateElement::end(), CLyapWolfMethod::evalF(), CHybridMethodODE45::evalF(), CHybridMethodLSODA::integrateDeterministicPart(), CHybridMethodODE45::integrateDeterministicPart(), CTSSAMethod::integrationMethodStart(), CTrajectoryMethodDsaLsodar::CPartition::intialize(), CHybridMethodODE45::outputState(), CLsodaMethod::peekAhead(), CNewtonMethod::processInternal(), CCrossSectionTask::relativeDifferenceOfStates(), CTrajectoryMethodDsaLsodar::CPartition::rePartition(), CNewtonMethod::solveJacobianXeqB(), CTauLeapMethod::start(), CStochDirectMethod::start(), CLyapWolfMethod::start(), CTrajAdaptiveSA::start(), CLsodaMethod::start(), CTrajectoryMethodDsaLsodar::start(), CLsodaMethod::stateChanged(), CHybridMethod::step(), CHybridMethodLSODA::step(), CStochMethod::step(), CNewtonMethod::targetFunction(), and CTauLeapMethod::updateSystem().
const C_FLOAT64 * CState::beginIndependent | ( | ) | const |
Retrieve the array of pointers of values of all independent entities.
Definition at line 335 of file CState.cpp.
References mpBeginIndependent.
C_FLOAT64 * CState::endDependent | ( | ) |
Retrieve pointer just beyond the values of all dependent entities.
Definition at line 331 of file CState.cpp.
References mpBeginFixed.
Referenced by CSteadyStateMethod::allPositive(), and CHybridMethodODE45::outputState().
const C_FLOAT64 * CState::endDependent | ( | ) | const |
Retrieve pointer just beyond the values of all dependent entities.
Definition at line 338 of file CState.cpp.
References mpBeginFixed.
C_FLOAT64 * CState::endFixed | ( | ) |
Retrieve pointer just beyond the values of all fixed entities.
Definition at line 333 of file CState.cpp.
References mpEnd.
Referenced by CHybridMethodODE45::outputState(), and CLsodaMethod::stateChanged().
const C_FLOAT64 * CState::endFixed | ( | ) | const |
Retrieve pointer just beyond the values of all fixed entities.
Definition at line 340 of file CState.cpp.
References mpEnd.
C_FLOAT64 * CState::endIndependent | ( | ) |
Retrieve pointer just beyond the values of all independent entities.
Definition at line 329 of file CState.cpp.
References mpBeginDependent.
Referenced by CNewtonMethod::containsNaN(), CHybridMethodODE45::outputState(), and CCrossSectionTask::relativeDifferenceOfStates().
const C_FLOAT64 * CState::endIndependent | ( | ) | const |
Retrieve pointer just beyond the values of all independent entities.
Definition at line 336 of file CState.cpp.
References mpBeginDependent.
size_t CState::getNumDependent | ( | ) | const |
Retrieve the number of dependent entities.
Definition at line 344 of file CState.cpp.
References mpBeginDependent, and mpBeginFixed.
Referenced by CSteadyStateTask::initialize(), CHybridMethodODE45::outputState(), and resize().
size_t CState::getNumFixed | ( | ) | const |
Retrieve the number of fixed entities.
Definition at line 348 of file CState.cpp.
References mpBeginFixed, and mpEnd.
Referenced by resize().
size_t CState::getNumIndependent | ( | ) | const |
Retrieve the number of independent entities.
Definition at line 342 of file CState.cpp.
References mpBeginDependent, and mpBeginIndependent.
Referenced by CModel::calculateJacobian(), CModel::calculateJacobianX(), CMathModel::calculateRootJacobian(), CSteadyStateTask::initialize(), CTSSAMethod::integrationMethodStart(), CLyapMethod::isValidProblem(), CHybridMethodODE45::outputState(), CLyapTask::process(), resize(), CLyapWolfMethod::start(), and CLsodaMethod::start().
size_t CState::getNumVariable | ( | ) | const |
Retrieve the number of variable entities, i.e., the sum of independent and dependent variables.
Definition at line 346 of file CState.cpp.
References mpBeginFixed, and mpBeginIndependent.
const C_FLOAT64 & CState::getTime | ( | ) | const |
Retrieve the time of the state
Definition at line 325 of file CState.cpp.
References mpValues.
Referenced by CHybridMethodODE45::doSingleStep(), CTrajectoryMethodDsaLsodar::fireReaction(), CTSSATask::initialize(), CTrajectoryTask::initialize(), CCrossSectionTask::initialize(), CHybridMethodLSODA::integrateDeterministicPart(), CHybridMethodODE45::integrateDeterministicPart(), CTSSAMethod::integrationMethodStart(), CTimeSeries::output(), CHybridMethod::outputData(), CHybridMethodLSODA::outputData(), CHybridMethod::outputDebug(), CHybridMethodODE45::outputDebug(), CHybridMethodLSODA::outputDebug(), CHybridMethodODE45::outputState(), CHybridMethod::partitionSystem(), CLsodaMethod::peekAhead(), CSteadyStateTask::process(), CHybridMethod::start(), CStochDirectMethod::start(), CLyapWolfMethod::start(), CTrajAdaptiveSA::start(), CStochMethod::start(), CLsodaMethod::start(), CLsodaMethod::stateChanged(), CTauLeapMethod::step(), CHybridMethod::step(), CStochDirectMethod::step(), CTrajAdaptiveSA::step(), CStochMethod::step(), CLsodaMethod::step(), and CTrajectoryMethodDsaLsodar::step().
bool CState::isValid | ( | ) | const |
Check whether the current state is valid (contains no NaN)
Definition at line 351 of file CState.cpp.
References C_FLOAT64, mpBeginDependent, and mpBeginIndependent.
Referenced by CSteadyStateTask::process(), and CLsodaMethod::step().
Assignment operator
const | CState & rhs |
Definition at line 303 of file CState.cpp.
References C_FLOAT64, mpBeginDependent, mpBeginFixed, mpBeginIndependent, mpEnd, mpValues, mSize, mUpdateDependentRequired, and pdeletev.
|
protected |
Definition at line 365 of file CState.cpp.
References C_FLOAT64, getNumDependent(), getNumFixed(), getNumIndependent(), min, mpValues, mSize, pdeletev, and updateIterator().
Referenced by CStateTemplate::resize().
Set the time of the state
const | C_FLOAT64 & time |
Definition at line 326 of file CState.cpp.
References mpValues.
Referenced by CLyapWolfMethod::calculate(), CHybridMethodODE45::doInverseInterpolation(), CHybridNextReactionLSODAMethod::doSingleStep(), CHybridNextReactionRKMethod::doSingleStep(), CHybridMethodODE45::doSingleStep(), CTrajectoryMethodDsaLsodar::doSingleStep(), CTrajAdaptiveSA::doSingleTauLeapStep(), CLyapWolfMethod::evalF(), CLsodaMethod::evalF(), CHybridMethodLSODA::evalF(), CHybridMethodODE45::evalF(), CTrajectoryMethodDsaLsodar::evalF(), CTSSAMethod::evalF(), CLsodaMethod::evalR(), CHybridMethodLSODA::integrateDeterministicPart(), CHybridMethodODE45::integrateDeterministicPart(), CTSSAMethod::integrationStep(), CLsodaMethod::peekAhead(), CSteadyStateTask::process(), CModel::setInitialState(), CTauLeapMethod::step(), CHybridMethod::step(), CHybridMethodLSODA::step(), CStochDirectMethod::step(), CLyapWolfMethod::step(), CTrajAdaptiveSA::step(), CStochMethod::step(), CLsodaMethod::step(), and CTrajectoryMethodDsaLsodar::step().
|
protected |
Update the pointers to the different types of entities
const | size_t & numIndependent |
const | size_t & numDependent |
const | size_t & numFixed |
Definition at line 388 of file CState.cpp.
References mpBeginDependent, mpBeginFixed, mpBeginIndependent, mpEnd, and mpValues.
Referenced by CStateTemplate::reorder(), and resize().
|
friend |
|
friend |
Definition at line 398 of file CState.cpp.
|
private |
Pointer to the beginning of values of dependent entities.
Definition at line 485 of file CState.h.
Referenced by beginDependent(), endIndependent(), getNumDependent(), getNumIndependent(), isValid(), operator=(), and updateIterator().
|
private |
Pointer to the beginning of values of fixed entities.
Definition at line 490 of file CState.h.
Referenced by beginFixed(), endDependent(), getNumDependent(), getNumFixed(), getNumVariable(), operator=(), and updateIterator().
|
private |
Pointer to the beginning of values of independent entities.
Definition at line 480 of file CState.h.
Referenced by beginIndependent(), getNumIndependent(), getNumVariable(), isValid(), operator=(), and updateIterator().
|
private |
Pointer just beyond the values of fixed entities.
Definition at line 495 of file CState.h.
Referenced by endFixed(), getNumFixed(), operator<<(), operator=(), and updateIterator().
|
private |
Array of entity values
Definition at line 470 of file CState.h.
Referenced by CState(), getTime(), operator<<(), operator=(), resize(), setTime(), updateIterator(), and ~CState().
|
private |
Size of the state
Definition at line 475 of file CState.h.
Referenced by CState(), operator=(), and resize().
|
private |
Indicates whether the state is of a reduced or complete model
Definition at line 500 of file CState.h.
Referenced by operator=().