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feature/rapid equilibrium reactions for CSTR #324

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feature/rapid equilibrium reactions for CSTR #324

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6a4367e
Restart implementation
AntoniaBerger Jan 15, 2025
e17e097
changed residual, jacobi and jacobi derivativ to handle consvered moi…
AntoniaBerger Jan 21, 2025
bbb83bf
Progress of the week: add functionality for consisitent intialisation
AntoniaBerger Jan 24, 2025
0b3aaa4
edded leanConsistenInitalisationTimeDerivative, fixed some bugs
AntoniaBerger Jan 31, 2025
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8 changes: 8 additions & 0 deletions src/libcadet/Memory.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -353,6 +353,14 @@ namespace cadet

explicit operator T*() const { return _ptr; }

// method to copy elements from std::vector
void copyFromVector(const std::vector<T>& vec) {
if (vec.size() > _numElements) {
throw std::out_of_range("Vector size exceeds BufferedArray size");
}
std::copy(vec.begin(), vec.end(), _ptr);
}

private:
BufferedArray(T* ptr, unsigned int numElements) : _ptr(ptr), _numElements(numElements) { }

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27 changes: 25 additions & 2 deletions src/libcadet/model/ReactionModel.hpp
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Expand Up @@ -212,6 +212,14 @@ class IDynamicReactionModel

virtual int residualLiquidAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, double const* y,
double* res, double factor, LinearBufferAllocator workSpace) const = 0;


virtual int quasiStationaryFlux(double t, unsigned int secIdx, const ColumnPosition& colPos, active const* y,
Eigen::Map<Eigen::VectorXd> fluxes, std::vector<int> mapQSReac, LinearBufferAllocator workSpace) = 0;

virtual int quasiStationaryFlux(double t, unsigned int secIdx, const ColumnPosition& colPos, double const* y,
Eigen::Map<Eigen::VectorXd> fluxes, std::vector<int> mapQSReac, LinearBufferAllocator workSpace) = 0;


/**
* @brief Adds the analytical Jacobian of the reaction terms for one liquid phase cell
Expand All @@ -237,9 +245,19 @@ class IDynamicReactionModel
virtual void analyticJacobianLiquidAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, double const* y, double factor, linalg::BandMatrix::RowIterator jac, LinearBufferAllocator workSpace) const = 0;
virtual void analyticJacobianLiquidAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, double const* y, double factor, linalg::DenseBandedRowIterator jac, LinearBufferAllocator workSpace) const = 0;
virtual void analyticJacobianLiquidAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, double const* y, double factor, linalg::BandedSparseRowIterator jac, LinearBufferAllocator workSpace) const = 0;
#ifdef ENABLE_DG

virtual void analyticQuasiSteadyJacobianLiquid(double t, unsigned int secIdx, const ColumnPosition& colPos, double const* y, int state, int reaction, linalg::BandMatrix::RowIterator jac, LinearBufferAllocator workSpace) const = 0;
virtual void analyticQuasiSteadyJacobianLiquid(double t, unsigned int secIdx, const ColumnPosition& colPos, double const* y, int state, int reaction, linalg::DenseBandedRowIterator jac, LinearBufferAllocator workSpace) const = 0;
virtual void analyticQuasiSteadyJacobianLiquid(double t, unsigned int secIdx, const ColumnPosition& colPos, double const* y, int state, int reaction, linalg::BandedSparseRowIterator jac, LinearBufferAllocator workSpace) const = 0;

virtual void fillConservedMoietiesBulk(Eigen::MatrixXd& M, std::vector<int>& QSReaction, std::vector<int>& _QsCompBulk) = 0;

virtual void timeDerivativeQuasiStationaryReaction(double t, unsigned int secIdx, const ColumnPosition& colPos, double const* y, double* dReacDt, LinearBufferAllocator workSpace) = 0;

#ifdef ENABLE_DG
virtual void analyticJacobianLiquidAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, double const* y, double factor, linalg::BandedEigenSparseRowIterator jac, LinearBufferAllocator workSpace) const = 0;
#endif

#endif

/**
* @brief Evaluates the residual for one combined phase cell
Expand Down Expand Up @@ -314,6 +332,11 @@ class IDynamicReactionModel
* @return Number of reactions
*/
virtual unsigned int numReactionsCombined() const CADET_NOEXCEPT = 0;

/**
* @brief Returns wheather liquid reactions are in quasi-stationary state
* @return boolean
*/

protected:
};
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