Scine::Kinetx  3.0.0
Kinetic models for reaction networks.
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Scine::Kinetx::Cvode::Impl Member List

This is the complete list of members for Scine::Kinetx::Cvode::Impl, including all inherited members.

_net (defined in Scine::Kinetx::IntegratorBase)Scine::Kinetx::IntegratorBaseprotected
abstol (defined in Scine::Kinetx::Cvode::Impl)Scine::Kinetx::Cvode::Impl
context (defined in Scine::Kinetx::Cvode::Impl)Scine::Kinetx::Cvode::Impl
cvode_mem (defined in Scine::Kinetx::Cvode::Impl)Scine::Kinetx::Cvode::Impl
f(const Eigen::VectorXd &concentrations) const Scine::Kinetx::IntegratorBaseprotected
fast_pow(const double &x, const int &n) (defined in Scine::Kinetx::IntegratorBase)Scine::Kinetx::IntegratorBaseinlineprotectedstatic
fDirected(const Eigen::VectorXd &concentrations) const Scine::Kinetx::IntegratorBaseprotected
fFlux(const Eigen::VectorXd &concentrationsT0, const Eigen::VectorXd &concentrationsT1) const Scine::Kinetx::IntegratorBaseprotected
fFluxDirected(const Eigen::VectorXd &concentrationsT0, const Eigen::VectorXd &concentrationsT1) const Scine::Kinetx::IntegratorBaseprotected
first_run (defined in Scine::Kinetx::Cvode::Impl)Scine::Kinetx::Cvode::Implmutable
g(const Eigen::VectorXd &concentrations) const Scine::Kinetx::IntegratorBaseprotected
gFlux(const Eigen::VectorXd &concentrationsT0, const Eigen::VectorXd &concentrationsT1, Eigen::VectorXd &flux, Eigen::VectorXd &forwardFlux, Eigen::VectorXd &backwardFlux) const Scine::Kinetx::IntegratorBaseprotected
Impl(Network &net) (defined in Scine::Kinetx::Cvode::Impl)Scine::Kinetx::Cvode::Implinline
Integrator()=default (defined in Scine::Kinetx::Integrator)Scine::Kinetx::Integrator
IntegratorBase(Network &net)Scine::Kinetx::IntegratorBase
jacobi(const Eigen::VectorXd &concentrations) const (defined in Scine::Kinetx::IntegratorBase)Scine::Kinetx::IntegratorBaseprotected
LS (defined in Scine::Kinetx::Cvode::Impl)Scine::Kinetx::Cvode::Implmutable
printHeader(const Eigen::VectorXd &y, const double dt, const double t) (defined in Scine::Kinetx::IntegratorBase)Scine::Kinetx::IntegratorBaseprotected
printTimeAndCheckConvergenceStep(const Eigen::VectorXd &y, const Eigen::VectorXd &yOld, Eigen::VectorXd &yMax, const unsigned int batchInterval, const unsigned int iBatch, const double dt, const double t, const double convergenceConcentrationChange) (defined in Scine::Kinetx::IntegratorBase)Scine::Kinetx::IntegratorBaseprotected
propagate(Eigen::VectorXd &concentrations, Eigen::VectorXd &yFlux, Eigen::VectorXd &rFlux, Eigen::VectorXd &rForwardFlux, Eigen::VectorXd &rBackwardFlux, double &t, double &dt) const Scine::Kinetx::Cvode::Implinlinevirtual
propagateY(Eigen::VectorXd &concentrations, double &tStart, double &dt) const (defined in Scine::Kinetx::Cvode::Impl)Scine::Kinetx::Cvode::Implinline
reltol (defined in Scine::Kinetx::Cvode::Impl)Scine::Kinetx::Cvode::Impl
rhs_func(realtype, N_Vector c, N_Vector g, void *user_data) (defined in Scine::Kinetx::Cvode::Impl)Scine::Kinetx::Cvode::Implinlinestatic
runIntegration(Eigen::VectorXd y, double tStart, double dt, Eigen::VectorXd &rFlux, Eigen::VectorXd &rForwardFlux, Eigen::VectorXd &rBackwardFlux, const unsigned int batchInterval=1000, const unsigned int nBatches=100000, const double convergenceConcentrationChange=1e-10)Scine::Kinetx::IntegratorBasevirtual
runIntegrationByTime(Eigen::VectorXd y, double tStart, double dt, Eigen::VectorXd &rFlux, Eigen::VectorXd &rForwardFlux, Eigen::VectorXd &rBackwardFlux, const double tMax, const unsigned int batchInterval=1000, const double convergenceConcentrationChange=1e-10)Scine::Kinetx::IntegratorBasevirtual
trackVertexAndEdgeFluxes(const Eigen::VectorXd &y, const Eigen::VectorXd &yInitial, Eigen::VectorXd &yFlux, Eigen::VectorXd &rFlux, Eigen::VectorXd &rForwardFlux, Eigen::VectorXd &rBackwardFlux, const double &dt) const Scine::Kinetx::IntegratorBaseprotected
y (defined in Scine::Kinetx::Cvode::Impl)Scine::Kinetx::Cvode::Impl
~Impl() (defined in Scine::Kinetx::Cvode::Impl)Scine::Kinetx::Cvode::Implinline