Program Listing for File sundials_matrix_wrapper.h
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#ifndef AMICI_SUNDIALS_MATRIX_WRAPPER_H
#define AMICI_SUNDIALS_MATRIX_WRAPPER_H
#include <sunmatrix/sunmatrix_band.h> // SUNMatrix_Band
#include <sunmatrix/sunmatrix_dense.h> // SUNMatrix_Dense
#include <sunmatrix/sunmatrix_sparse.h> // SUNMatrix_Sparse
#include <gsl/gsl-lite.hpp>
#include <vector>
#include <algorithm>
#include <assert.h>
#include "amici/vector.h"
namespace amici {
class SUNMatrixWrapper {
public:
SUNMatrixWrapper() = default;
SUNMatrixWrapper(sunindextype M, sunindextype N, sunindextype NNZ,
int sparsetype);
SUNMatrixWrapper(sunindextype M, sunindextype N);
SUNMatrixWrapper(sunindextype M, sunindextype ubw, sunindextype lbw);
SUNMatrixWrapper(const SUNMatrixWrapper &A, realtype droptol,
int sparsetype);
explicit SUNMatrixWrapper(SUNMatrix mat);
~SUNMatrixWrapper();
SUNMatrixWrapper(const SUNMatrixWrapper &other);
SUNMatrixWrapper(SUNMatrixWrapper &&other);
SUNMatrixWrapper &operator=(const SUNMatrixWrapper &other);
SUNMatrixWrapper &operator=(SUNMatrixWrapper &&other);
void reallocate(sunindextype nnz);
void realloc();
SUNMatrix get() const;
sunindextype rows() const {
assert(!matrix_ ||
(matrix_id() == SUNMATRIX_SPARSE ?
num_rows_ == SM_ROWS_S(matrix_) :
num_rows_ == SM_ROWS_D(matrix_)));
return num_rows_;
}
sunindextype columns() const {
assert(!matrix_ ||
(matrix_id() == SUNMATRIX_SPARSE ?
num_columns_ == SM_COLUMNS_S(matrix_) :
num_columns_ == SM_COLUMNS_D(matrix_)));
return num_columns_;
}
sunindextype num_nonzeros() const;
sunindextype num_indexptrs() const;
sunindextype capacity() const;
realtype *data();
const realtype *data() const;
realtype get_data(sunindextype idx) const{
assert(matrix_);
assert(matrix_id() == SUNMATRIX_SPARSE);
assert(idx < capacity());
assert(SM_DATA_S(matrix_) == data_);
return data_[idx];
}
realtype get_data(sunindextype irow, sunindextype icol) const{
assert(matrix_);
assert(matrix_id() == SUNMATRIX_DENSE);
assert(irow < rows());
assert(icol < columns());
return SM_ELEMENT_D(matrix_, irow, icol);
}
void set_data(sunindextype idx, realtype data) {
assert(matrix_);
assert(matrix_id() == SUNMATRIX_SPARSE);
assert(idx < capacity());
assert(SM_DATA_S(matrix_) == data_);
data_[idx] = data;
}
void set_data(sunindextype irow, sunindextype icol, realtype data) {
assert(matrix_);
assert(matrix_id() == SUNMATRIX_DENSE);
assert(irow < rows());
assert(icol < columns());
SM_ELEMENT_D(matrix_, irow, icol) = data;
}
sunindextype get_indexval(sunindextype idx) const {
assert(matrix_);
assert(matrix_id() == SUNMATRIX_SPARSE);
assert(idx < capacity());
assert(indexvals_ == SM_INDEXVALS_S(matrix_));
return indexvals_[idx];
}
void set_indexval(sunindextype idx, sunindextype val) {
assert(matrix_);
assert(matrix_id() == SUNMATRIX_SPARSE);
assert(idx < capacity());
assert(indexvals_ == SM_INDEXVALS_S(matrix_));
indexvals_[idx] = val;
}
void set_indexvals(const gsl::span<const sunindextype> vals) {
assert(matrix_);
assert(matrix_id() == SUNMATRIX_SPARSE);
assert(static_cast<sunindextype>(vals.size()) == capacity());
assert(indexvals_ == SM_INDEXVALS_S(matrix_));
std::copy_n(vals.begin(), capacity(), indexvals_);
}
sunindextype get_indexptr(sunindextype ptr_idx) const {
assert(matrix_);
assert(matrix_id() == SUNMATRIX_SPARSE);
assert(ptr_idx <= num_indexptrs());
assert(indexptrs_ == SM_INDEXPTRS_S(matrix_));
return indexptrs_[ptr_idx];
}
void set_indexptr(sunindextype ptr_idx, sunindextype ptr) {
assert(matrix_);
assert(matrix_id() == SUNMATRIX_SPARSE);
assert(ptr_idx <= num_indexptrs());
assert(ptr <= capacity());
assert(indexptrs_ == SM_INDEXPTRS_S(matrix_));
indexptrs_[ptr_idx] = ptr;
if (ptr_idx == num_indexptrs())
num_nonzeros_ = ptr;
}
void set_indexptrs(const gsl::span<const sunindextype> ptrs) {
assert(matrix_);
assert(matrix_id() == SUNMATRIX_SPARSE);
assert(static_cast<sunindextype>(ptrs.size()) == num_indexptrs() + 1);
assert(indexptrs_ == SM_INDEXPTRS_S(matrix_));
std::copy_n(ptrs.begin(), num_indexptrs() + 1, indexptrs_);
num_nonzeros_ = indexptrs_[num_indexptrs()];
}
int sparsetype() const;
void scale(realtype a);
void multiply(N_Vector c, const_N_Vector b, realtype alpha = 1.0) const;
void multiply(AmiVector& c, AmiVector const& b, realtype alpha = 1.0) const {
multiply(c.getNVector(), b.getNVector(), alpha);
}
void multiply(gsl::span<realtype> c, gsl::span<const realtype> b,
const realtype alpha = 1.0) const;
void multiply(N_Vector c,
const_N_Vector b,
gsl::span <const int> cols,
bool transpose) const;
void multiply(gsl::span<realtype> c,
gsl::span<const realtype> b,
gsl::span <const int> cols,
bool transpose) const;
void sparse_multiply(SUNMatrixWrapper &C,
const SUNMatrixWrapper &B) const;
void sparse_add(const SUNMatrixWrapper &A, realtype alpha,
const SUNMatrixWrapper &B, realtype beta);
void sparse_sum(const std::vector<SUNMatrixWrapper> &mats);
sunindextype scatter(const sunindextype k, const realtype beta,
sunindextype *w, gsl::span<realtype> x,
const sunindextype mark,
SUNMatrixWrapper *C, sunindextype nnz) const;
void transpose(SUNMatrixWrapper &C, const realtype alpha,
sunindextype blocksize) const;
void to_dense(SUNMatrixWrapper &D) const;
void to_diag(N_Vector v) const;
void zero();
SUNMatrix_ID matrix_id() const {return id_;};
void refresh();
private:
SUNMatrix matrix_ {nullptr};
SUNMatrix_ID id_ {SUNMATRIX_CUSTOM};
int sparsetype_ {CSC_MAT};
sunindextype num_nonzeros_ {0};
sunindextype capacity_ {0};
realtype *data_ {nullptr};
sunindextype *indexptrs_ {nullptr};
sunindextype *indexvals_ {nullptr};
sunindextype num_rows_ {0};
sunindextype num_columns_ {0};
sunindextype num_indexptrs_ {0};
void finish_init();
void update_ptrs();
void update_size();
bool ownmat = true;
};
} // namespace amici
namespace gsl {
inline span<realtype> make_span(SUNMatrix m)
{
switch (SUNMatGetID(m)) {
case SUNMATRIX_DENSE:
return span<realtype>(SM_DATA_D(m), SM_LDATA_D(m));
case SUNMATRIX_SPARSE:
return span<realtype>(SM_DATA_S(m), SM_NNZ_S(m));
default:
throw amici::AmiException("Unimplemented SUNMatrix type for make_span");
}
}
} // namespace gsl
#endif // AMICI_SUNDIALS_MATRIX_WRAPPER_H