Refactor: smoother conversion from SUNMatrixWrapper to SUNMatrix (#2317)

Adds an implicit conversion function to SUNMatrixWrapper make things more readable.

include/amici/rdata.h

@@ -576,7 +576,7 @@ class ReturnData : public ModelDimensions {
 
         if (!this->J.empty()) {
             SUNMatrixWrapper J(nx_solver, nx_solver);
-            model.fJ(t_, 0.0, x_solver_, dx_solver_, xdot, J.get());
+            model.fJ(t_, 0.0, x_solver_, dx_solver_, xdot, J);
             // CVODES uses colmajor, so we need to transform to rowmajor
             for (int ix = 0; ix < model.nx_solver; ix++)
                 for (int jx = 0; jx < model.nx_solver; jx++)

include/amici/sundials_matrix_wrapper.h

@@ -72,6 +72,11 @@ class SUNMatrixWrapper {
 
     ~SUNMatrixWrapper();
 
+    /**
+     * @brief Conversion function.
+     */
+    operator SUNMatrix() { return get(); };
+
     /**
      * @brief Copy constructor
      * @param other

src/model.cpp

@@ -2249,7 +2249,7 @@ void Model::fdJydy(int const it, AmiVector const& x, ExpData const& edata) {
 
             auto tmp_sparse = SUNMatrixWrapper(tmp_dense, 0.0, CSC_MAT);
             auto ret = SUNMatScaleAdd(
-                1.0, derived_state_.dJydy_.at(iyt).get(), tmp_sparse.get()
+                1.0, derived_state_.dJydy_.at(iyt), tmp_sparse
             );
             if (ret != SUNMAT_SUCCESS) {
                 throw AmiException(
@@ -2897,7 +2897,7 @@ void Model::fdwdp(realtype const t, realtype const* x) {
     }
 
     if (always_check_finite_) {
-        checkFinite(derived_state_.dwdp_.get(), ModelQuantity::dwdp, t);
+        checkFinite(derived_state_.dwdp_, ModelQuantity::dwdp, t);
     }
 }
 
@@ -2943,7 +2943,7 @@ void Model::fdwdx(realtype const t, realtype const* x) {
     }
 
     if (always_check_finite_) {
-        checkFinite(derived_state_.dwdx_.get(), ModelQuantity::dwdx, t);
+        checkFinite(derived_state_.dwdx_, ModelQuantity::dwdx, t);
     }
 }
 
@@ -2960,7 +2960,7 @@ void Model::fdwdw(realtype const t, realtype const* x) {
     );
 
     if (always_check_finite_) {
-        checkFinite(dwdw_.get(), ModelQuantity::dwdw, t);
+        checkFinite(dwdw_, ModelQuantity::dwdw, t);
     }
 }
 

src/model_dae.cpp

@@ -14,7 +14,7 @@ void Model_DAE::fJ(
     realtype t, realtype cj, const_N_Vector x, const_N_Vector dx,
     const_N_Vector /*xdot*/, SUNMatrix J
 ) {
-    fJSparse(t, cj, x, dx, derived_state_.J_.get());
+    fJSparse(t, cj, x, dx, derived_state_.J_);
     derived_state_.J_.refresh();
     auto JDense = SUNMatrixWrapper(J);
     derived_state_.J_.to_dense(JDense);
@@ -88,7 +88,7 @@ void Model_DAE::fJv(
     N_Vector Jv, realtype cj
 ) {
     N_VConst(0.0, Jv);
-    fJSparse(t, cj, x, dx, derived_state_.J_.get());
+    fJSparse(t, cj, x, dx, derived_state_.J_);
     derived_state_.J_.refresh();
     derived_state_.J_.multiply(Jv, v);
 }
@@ -135,7 +135,7 @@ void Model_DAE::fJDiag(
     realtype const t, AmiVector& JDiag, realtype const /*cj*/,
     AmiVector const& x, AmiVector const& dx
 ) {
-    fJSparse(t, 0.0, x.getNVector(), dx.getNVector(), derived_state_.J_.get());
+    fJSparse(t, 0.0, x.getNVector(), dx.getNVector(), derived_state_.J_);
     derived_state_.J_.refresh();
     derived_state_.J_.to_diag(JDiag.getNVector());
     if (checkFinite(JDiag.getVector(), ModelQuantity::JDiag) != AMICI_SUCCESS)
@@ -355,7 +355,7 @@ void Model_DAE::fJB(
     realtype t, realtype cj, const_N_Vector x, const_N_Vector dx,
     const_N_Vector /*xB*/, const_N_Vector /*dxB*/, SUNMatrix JB
 ) {
-    fJSparse(t, cj, x, dx, derived_state_.J_.get());
+    fJSparse(t, cj, x, dx, derived_state_.J_);
     derived_state_.J_.refresh();
     auto JBDense = SUNMatrixWrapper(JB);
     derived_state_.J_.transpose(JBDense, -1.0, nxtrue_solver);
@@ -376,7 +376,7 @@ void Model_DAE::fJSparseB(
     realtype t, realtype cj, const_N_Vector x, const_N_Vector dx,
     const_N_Vector /*xB*/, const_N_Vector /*dxB*/, SUNMatrix JB
 ) {
-    fJSparse(t, cj, x, dx, derived_state_.J_.get());
+    fJSparse(t, cj, x, dx, derived_state_.J_);
     derived_state_.J_.refresh();
     auto JSparseB = SUNMatrixWrapper(JB);
     derived_state_.J_.transpose(JSparseB, -1.0, nxtrue_solver);
@@ -387,7 +387,7 @@ void Model_DAE::fJvB(
     const_N_Vector dxB, const_N_Vector vB, N_Vector JvB, realtype cj
 ) {
     N_VConst(0.0, JvB);
-    fJSparseB(t, cj, x, dx, xB, dxB, derived_state_.JB_.get());
+    fJSparseB(t, cj, x, dx, xB, dxB, derived_state_.JB_);
     derived_state_.JB_.refresh();
     derived_state_.JB_.multiply(JvB, vB);
 }
@@ -397,7 +397,7 @@ void Model_DAE::fxBdot(
     const_N_Vector dxB, N_Vector xBdot
 ) {
     N_VConst(0.0, xBdot);
-    fJSparseB(t, 1.0, x, dx, xB, dxB, derived_state_.JB_.get());
+    fJSparseB(t, 1.0, x, dx, xB, dxB, derived_state_.JB_);
     derived_state_.JB_.refresh();
     fM(t, x);
     derived_state_.JB_.multiply(xBdot, xB);
@@ -454,7 +454,7 @@ void Model_DAE::fqBdot_ss(
 
 void Model_DAE::fJSparseB_ss(SUNMatrix JB) {
     /* Just pass the model Jacobian on to JB */
-    SUNMatCopy(derived_state_.JB_.get(), JB);
+    SUNMatCopy(derived_state_.JB_, JB);
     derived_state_.JB_.refresh();
 }
 
@@ -465,7 +465,7 @@ void Model_DAE::writeSteadystateJB(
     /* Get backward Jacobian */
     fJSparseB(
         t, cj, x.getNVector(), dx.getNVector(), xB.getNVector(),
-        dxB.getNVector(), derived_state_.JB_.get()
+        dxB.getNVector(), derived_state_.JB_
     );
     derived_state_.JB_.refresh();
     /* Switch sign, as we integrate forward in time, not backward */
@@ -491,7 +491,7 @@ void Model_DAE::fsxdot(
         // the same for all remaining
         fM(t, x);
         fdxdotdp(t, x, dx);
-        fJSparse(t, 0.0, x, dx, derived_state_.J_.get());
+        fJSparse(t, 0.0, x, dx, derived_state_.J_);
         derived_state_.J_.refresh();
     }
 

src/model_ode.cpp

@@ -14,7 +14,7 @@ void Model_ODE::fJ(
 void Model_ODE::fJ(
     realtype t, const_N_Vector x, const_N_Vector /*xdot*/, SUNMatrix J
 ) {
-    fJSparse(t, x, derived_state_.J_.get());
+    fJSparse(t, x, derived_state_.J_);
     derived_state_.J_.refresh();
     auto JDense = SUNMatrixWrapper(J);
     derived_state_.J_.to_dense(JDense);
@@ -77,7 +77,7 @@ void Model_ODE::fJv(
     const_N_Vector v, N_Vector Jv, realtype t, const_N_Vector x
 ) {
     N_VConst(0.0, Jv);
-    fJSparse(t, x, derived_state_.J_.get());
+    fJSparse(t, x, derived_state_.J_);
     derived_state_.J_.refresh();
     derived_state_.J_.multiply(Jv, v);
 }
@@ -355,7 +355,7 @@ void Model_ODE::fJB(
     realtype t, const_N_Vector x, const_N_Vector /*xB*/,
     const_N_Vector /*xBdot*/, SUNMatrix JB
 ) {
-    fJSparse(t, x, derived_state_.J_.get());
+    fJSparse(t, x, derived_state_.J_);
     derived_state_.J_.refresh();
     auto JDenseB = SUNMatrixWrapper(JB);
     derived_state_.J_.transpose(JDenseB, -1.0, nxtrue_solver);
@@ -373,14 +373,14 @@ void Model_ODE::fJSparseB(
     realtype t, const_N_Vector x, const_N_Vector /*xB*/,
     const_N_Vector /*xBdot*/, SUNMatrix JB
 ) {
-    fJSparse(t, x, derived_state_.J_.get());
+    fJSparse(t, x, derived_state_.J_);
     derived_state_.J_.refresh();
     auto JSparseB = SUNMatrixWrapper(JB);
     derived_state_.J_.transpose(JSparseB, -1.0, nxtrue_solver);
 }
 
 void Model_ODE::fJDiag(realtype t, N_Vector JDiag, const_N_Vector x) {
-    fJSparse(t, x, derived_state_.J_.get());
+    fJSparse(t, x, derived_state_.J_);
     derived_state_.J_.refresh();
     derived_state_.J_.to_diag(JDiag);
 }
@@ -390,14 +390,14 @@ void Model_ODE::fJvB(
     const_N_Vector xB
 ) {
     N_VConst(0.0, JvB);
-    fJSparseB(t, x, xB, nullptr, derived_state_.JB_.get());
+    fJSparseB(t, x, xB, nullptr, derived_state_.JB_);
     derived_state_.JB_.refresh();
     derived_state_.JB_.multiply(JvB, vB);
 }
 
 void Model_ODE::fxBdot(realtype t, N_Vector x, N_Vector xB, N_Vector xBdot) {
     N_VConst(0.0, xBdot);
-    fJSparseB(t, x, xB, nullptr, derived_state_.JB_.get());
+    fJSparseB(t, x, xB, nullptr, derived_state_.JB_);
     derived_state_.JB_.refresh();
     derived_state_.JB_.multiply(xBdot, xB);
 }
@@ -456,7 +456,7 @@ void Model_ODE::fqBdot_ss(realtype /*t*/, N_Vector xB, N_Vector qBdot) const {
 
 void Model_ODE::fJSparseB_ss(SUNMatrix JB) {
     /* Just copy the model Jacobian */
-    SUNMatCopy(derived_state_.JB_.get(), JB);
+    SUNMatCopy(derived_state_.JB_, JB);
     derived_state_.JB_.refresh();
 }
 
@@ -468,7 +468,7 @@ void Model_ODE::writeSteadystateJB(
     /* Get backward Jacobian */
     fJSparseB(
         t, x.getNVector(), xB.getNVector(), xBdot.getNVector(),
-        derived_state_.JB_.get()
+        derived_state_.JB_
     );
     derived_state_.JB_.refresh();
     /* Switch sign, as we integrate forward in time, not backward */
@@ -492,7 +492,7 @@ void Model_ODE::fsxdot(
         // we only need to call this for the first parameter index will be
         // the same for all remaining
         fdxdotdp(t, x);
-        fJSparse(t, x, derived_state_.J_.get());
+        fJSparse(t, x, derived_state_.J_);
         derived_state_.J_.refresh();
     }
     if (pythonGenerated) {

src/newton_solver.cpp

@@ -108,7 +108,7 @@ void NewtonSolver::computeNewtonSensis(
 NewtonSolverDense::NewtonSolverDense(Model const& model)
     : NewtonSolver(model)
     , Jtmp_(model.nx_solver, model.nx_solver)
-    , linsol_(SUNLinSol_Dense(x_.getNVector(), Jtmp_.get())) {
+    , linsol_(SUNLinSol_Dense(x_.getNVector(), Jtmp_)) {
     auto status = SUNLinSolInitialize_Dense(linsol_);
     if (status != SUNLS_SUCCESS)
         throw NewtonFailure(status, "SUNLinSolInitialize_Dense");
@@ -117,26 +117,26 @@ NewtonSolverDense::NewtonSolverDense(Model const& model)
 void NewtonSolverDense::prepareLinearSystem(
     Model& model, SimulationState const& state
 ) {
-    model.fJ(state.t, 0.0, state.x, state.dx, xdot_, Jtmp_.get());
+    model.fJ(state.t, 0.0, state.x, state.dx, xdot_, Jtmp_);
     Jtmp_.refresh();
-    auto status = SUNLinSolSetup_Dense(linsol_, Jtmp_.get());
+    auto status = SUNLinSolSetup_Dense(linsol_, Jtmp_);
     if (status != SUNLS_SUCCESS)
         throw NewtonFailure(status, "SUNLinSolSetup_Dense");
 }
 
 void NewtonSolverDense::prepareLinearSystemB(
     Model& model, SimulationState const& state
 ) {
-    model.fJB(state.t, 0.0, state.x, state.dx, xB_, dxB_, xdot_, Jtmp_.get());
+    model.fJB(state.t, 0.0, state.x, state.dx, xB_, dxB_, xdot_, Jtmp_);
     Jtmp_.refresh();
-    auto status = SUNLinSolSetup_Dense(linsol_, Jtmp_.get());
+    auto status = SUNLinSolSetup_Dense(linsol_, Jtmp_);
     if (status != SUNLS_SUCCESS)
         throw NewtonFailure(status, "SUNLinSolSetup_Dense");
 }
 
 void NewtonSolverDense::solveLinearSystem(AmiVector& rhs) {
     auto status = SUNLinSolSolve_Dense(
-        linsol_, Jtmp_.get(), rhs.getNVector(), rhs.getNVector(), 0.0
+        linsol_, Jtmp_, rhs.getNVector(), rhs.getNVector(), 0.0
     );
     Jtmp_.refresh();
     // last argument is tolerance and does not have any influence on result
@@ -167,7 +167,7 @@ NewtonSolverDense::~NewtonSolverDense() {
 NewtonSolverSparse::NewtonSolverSparse(Model const& model)
     : NewtonSolver(model)
     , Jtmp_(model.nx_solver, model.nx_solver, model.nnz, CSC_MAT)
-    , linsol_(SUNKLU(x_.getNVector(), Jtmp_.get())) {
+    , linsol_(SUNKLU(x_.getNVector(), Jtmp_)) {
     auto status = SUNLinSolInitialize_KLU(linsol_);
     if (status != SUNLS_SUCCESS)
         throw NewtonFailure(status, "SUNLinSolInitialize_KLU");
@@ -177,9 +177,9 @@ void NewtonSolverSparse::prepareLinearSystem(
     Model& model, SimulationState const& state
 ) {
     /* Get sparse Jacobian */
-    model.fJSparse(state.t, 0.0, state.x, state.dx, xdot_, Jtmp_.get());
+    model.fJSparse(state.t, 0.0, state.x, state.dx, xdot_, Jtmp_);
     Jtmp_.refresh();
-    auto status = SUNLinSolSetup_KLU(linsol_, Jtmp_.get());
+    auto status = SUNLinSolSetup_KLU(linsol_, Jtmp_);
     if (status != SUNLS_SUCCESS)
         throw NewtonFailure(status, "SUNLinSolSetup_KLU");
 }
@@ -189,18 +189,18 @@ void NewtonSolverSparse::prepareLinearSystemB(
 ) {
     /* Get sparse Jacobian */
     model.fJSparseB(
-        state.t, 0.0, state.x, state.dx, xB_, dxB_, xdot_, Jtmp_.get()
+        state.t, 0.0, state.x, state.dx, xB_, dxB_, xdot_, Jtmp_
     );
     Jtmp_.refresh();
-    auto status = SUNLinSolSetup_KLU(linsol_, Jtmp_.get());
+    auto status = SUNLinSolSetup_KLU(linsol_, Jtmp_);
     if (status != SUNLS_SUCCESS)
         throw NewtonFailure(status, "SUNLinSolSetup_KLU");
 }
 
 void NewtonSolverSparse::solveLinearSystem(AmiVector& rhs) {
     /* Pass pointer to the linear solver */
     auto status = SUNLinSolSolve_KLU(
-        linsol_, Jtmp_.get(), rhs.getNVector(), rhs.getNVector(), 0.0
+        linsol_, Jtmp_, rhs.getNVector(), rhs.getNVector(), 0.0
     );
     // last argument is tolerance and does not have any influence on result
 
@@ -211,7 +211,7 @@ void NewtonSolverSparse::solveLinearSystem(AmiVector& rhs) {
 void NewtonSolverSparse::reinitialize() {
     /* partial reinitialization, don't need to reallocate Jtmp_ */
     auto status = SUNLinSol_KLUReInit(
-        linsol_, Jtmp_.get(), Jtmp_.capacity(), SUNKLU_REINIT_PARTIAL
+        linsol_, Jtmp_, Jtmp_.capacity(), SUNKLU_REINIT_PARTIAL
     );
     if (status != SUNLS_SUCCESS)
         throw NewtonFailure(status, "SUNLinSol_KLUReInit");

src/sundials_linsol_wrapper.cpp

@@ -161,7 +161,7 @@ SUNLinSolBand::SUNLinSolBand(N_Vector x, SUNMatrix A)
 
 SUNLinSolBand::SUNLinSolBand(AmiVector const& x, int ubw, int lbw)
     : A_(SUNMatrixWrapper(x.getLength(), ubw, lbw)) {
-    solver_ = SUNLinSol_Band(const_cast<N_Vector>(x.getNVector()), A_.get());
+    solver_ = SUNLinSol_Band(const_cast<N_Vector>(x.getNVector()), A_);
     if (!solver_)
         throw AmiException("Failed to create solver.");
 }
@@ -170,7 +170,7 @@ SUNMatrix SUNLinSolBand::getMatrix() const { return A_.get(); }
 
 SUNLinSolDense::SUNLinSolDense(AmiVector const& x)
     : A_(SUNMatrixWrapper(x.getLength(), x.getLength())) {
-    solver_ = SUNLinSol_Dense(const_cast<N_Vector>(x.getNVector()), A_.get());
+    solver_ = SUNLinSol_Dense(const_cast<N_Vector>(x.getNVector()), A_);
     if (!solver_)
         throw AmiException("Failed to create solver.");
 }
@@ -187,7 +187,7 @@ SUNLinSolKLU::SUNLinSolKLU(
     AmiVector const& x, int nnz, int sparsetype, StateOrdering ordering
 )
     : A_(SUNMatrixWrapper(x.getLength(), x.getLength(), nnz, sparsetype)) {
-    solver_ = SUNLinSol_KLU(const_cast<N_Vector>(x.getNVector()), A_.get());
+    solver_ = SUNLinSol_KLU(const_cast<N_Vector>(x.getNVector()), A_);
     if (!solver_)
         throw AmiException("Failed to create solver.");
 
@@ -197,7 +197,7 @@ SUNLinSolKLU::SUNLinSolKLU(
 SUNMatrix SUNLinSolKLU::getMatrix() const { return A_.get(); }
 
 void SUNLinSolKLU::reInit(int nnz, int reinit_type) {
-    int status = SUNLinSol_KLUReInit(solver_, A_.get(), nnz, reinit_type);
+    int status = SUNLinSol_KLUReInit(solver_, A_, nnz, reinit_type);
     if (status != SUNLS_SUCCESS)
         throw AmiException("SUNLinSol_KLUReInit failed with %d", status);
 }

tests/cpp/unittests/testMisc.cpp

@@ -681,7 +681,7 @@ TEST(UnravelIndex, UnravelIndexSunMatDense)
     A.set_data(2, 1, 5);
 
     for(int i = 0; i < 6; ++i) {
-        auto idx = unravel_index(i, A.get());
+        auto idx = unravel_index(i, A);
         EXPECT_EQ(A.get_data(idx.first, idx.second), i);
     }
 }
@@ -706,7 +706,7 @@ TEST(UnravelIndex, UnravelIndexSunMatSparse)
     D.set_data(2, 1, 0);
     D.set_data(3, 1, 0);
 
-    auto S = SUNSparseFromDenseMatrix(D.get(), 1e-15, CSC_MAT);
+    auto S = SUNSparseFromDenseMatrix(D, 1e-15, CSC_MAT);
 
     EXPECT_EQ(unravel_index(0, S), std::make_pair((sunindextype) 2, (sunindextype) 0));
     EXPECT_EQ(unravel_index(1, S), std::make_pair((sunindextype) 3, (sunindextype) 0));
@@ -720,8 +720,8 @@ TEST(UnravelIndex, UnravelIndexSunMatSparseMissingIndices)
 {
     // Sparse matrix without any indices set
     SUNMatrixWrapper mat = SUNMatrixWrapper(2, 3, 2, CSC_MAT);
-    EXPECT_EQ(unravel_index(0, mat.get()), std::make_pair((sunindextype) -1, (sunindextype) -1));
-    EXPECT_EQ(unravel_index(1, mat.get()), std::make_pair((sunindextype) -1, (sunindextype) -1));
+    EXPECT_EQ(unravel_index(0, mat), std::make_pair((sunindextype) -1, (sunindextype) -1));
+    EXPECT_EQ(unravel_index(1, mat), std::make_pair((sunindextype) -1, (sunindextype) -1));
 }