[Python] Simplify and generalize conversion of sparse matrices

include/cantera/cython/kinetics_utils.h

@@ -53,26 +53,12 @@ inline void sparseCscData(const Eigen::SparseMatrix<double>& mat,
     }
 }
 
-// Function which passes sparse matrix
-#define SPARSE_MATRIX(PREFIX, CLASS_NAME, FUNC_NAME) \
-    inline Eigen::SparseMatrix<double> PREFIX ## _ ## FUNC_NAME(Cantera::CLASS_NAME* object) \
-    { return object->FUNC_NAME(); }
-
-#define KIN_SPARSE_MATRIX(FUNC_NAME) SPARSE_MATRIX(kin, Kinetics, FUNC_NAME)
 #define KIN_1D(FUNC_NAME) ARRAY_FUNC(kin, Kinetics, FUNC_NAME)
 
-KIN_SPARSE_MATRIX(reactantStoichCoeffs)
-KIN_SPARSE_MATRIX(productStoichCoeffs)
-KIN_SPARSE_MATRIX(revProductStoichCoeffs)
-
 KIN_1D(getFwdRatesOfProgress)
 KIN_1D(getRevRatesOfProgress)
 KIN_1D(getNetRatesOfProgress)
 
-KIN_SPARSE_MATRIX(fwdRatesOfProgress_ddX)
-KIN_SPARSE_MATRIX(revRatesOfProgress_ddX)
-KIN_SPARSE_MATRIX(netRatesOfProgress_ddX)
-
 KIN_1D(getFwdRateConstants_ddT)
 KIN_1D(getFwdRateConstants_ddP)
 KIN_1D(getFwdRateConstants_ddC)
@@ -106,10 +92,6 @@ KIN_1D(getCreationRates)
 KIN_1D(getDestructionRates)
 KIN_1D(getNetProductionRates)
 
-KIN_SPARSE_MATRIX(creationRates_ddX)
-KIN_SPARSE_MATRIX(destructionRates_ddX)
-KIN_SPARSE_MATRIX(netProductionRates_ddX)
-
 KIN_1D(getCreationRates_ddT)
 KIN_1D(getDestructionRates_ddT)
 KIN_1D(getNetProductionRates_ddT)

interfaces/cython/cantera/kinetics.pxd

@@ -51,6 +51,19 @@ cdef extern from "cantera/kinetics/Kinetics.h" namespace "Cantera":
         void getDerivativeSettings(CxxAnyMap&) except +translate_exception
         void setDerivativeSettings(CxxAnyMap&) except +translate_exception
 
+        # Kinetics sparse matrices
+        CxxSparseMatrix reactantStoichCoeffs() except +translate_exception
+        CxxSparseMatrix productStoichCoeffs() except +translate_exception
+        CxxSparseMatrix revProductStoichCoeffs() except +translate_exception
+
+        CxxSparseMatrix fwdRatesOfProgress_ddX() except +translate_exception
+        CxxSparseMatrix revRatesOfProgress_ddX() except +translate_exception
+        CxxSparseMatrix netRatesOfProgress_ddX() except +translate_exception
+
+        CxxSparseMatrix creationRates_ddX() except +translate_exception
+        CxxSparseMatrix destructionRates_ddX() except +translate_exception
+        CxxSparseMatrix netProductionRates_ddX() except +translate_exception
+
 
 cdef extern from "cantera/kinetics/InterfaceKinetics.h":
     cdef cppclass CxxInterfaceKinetics "Cantera::InterfaceKinetics":
@@ -113,18 +126,6 @@ cdef extern from "cantera/cython/kinetics_utils.h":
     cdef void kin_getDestructionRates_ddC(CxxKinetics*, double*) except +translate_exception
     cdef void kin_getNetProductionRates_ddC(CxxKinetics*, double*) except +translate_exception
 
-    # Kinetics sparse matrices
-    cdef CxxSparseMatrix kin_reactantStoichCoeffs(CxxKinetics*) except +translate_exception
-    cdef CxxSparseMatrix kin_productStoichCoeffs(CxxKinetics*) except +translate_exception
-    cdef CxxSparseMatrix kin_revProductStoichCoeffs(CxxKinetics*) except +translate_exception
-
-    cdef CxxSparseMatrix kin_fwdRatesOfProgress_ddX(CxxKinetics*) except +translate_exception
-    cdef CxxSparseMatrix kin_revRatesOfProgress_ddX(CxxKinetics*) except +translate_exception
-    cdef CxxSparseMatrix kin_netRatesOfProgress_ddX(CxxKinetics*) except +translate_exception
-
-    cdef CxxSparseMatrix kin_creationRates_ddX(CxxKinetics*) except +translate_exception
-    cdef CxxSparseMatrix kin_destructionRates_ddX(CxxKinetics*) except +translate_exception
-    cdef CxxSparseMatrix kin_netProductionRates_ddX(CxxKinetics*) except +translate_exception
 
 
 ctypedef void (*kineticsMethod1d)(CxxKinetics*, double*) except +translate_exception
@@ -138,5 +139,4 @@ cdef class InterfaceKinetics(Kinetics):
 
 cdef np.ndarray get_species_array(Kinetics kin, kineticsMethod1d method)
 cdef np.ndarray get_reaction_array(Kinetics kin, kineticsMethod1d method)
-cdef np.ndarray get_dense(Kinetics kin, kineticsMethodSparse method)
-cdef tuple get_sparse(Kinetics kin, kineticsMethodSparse method)
+cdef get_from_sparse(CxxSparseMatrix&, int, int)

interfaces/cython/cantera/kinetics.pyx

@@ -31,11 +31,10 @@ cdef np.ndarray get_reaction_array(Kinetics kin, kineticsMethod1d method):
     method(kin.kinetics, &data[0])
     return data
 
-cdef np.ndarray get_dense(Kinetics kin, kineticsMethodSparse method):
-    cdef CxxSparseMatrix smat = method(kin.kinetics)
+cdef np.ndarray get_dense(CxxSparseMatrix& smat):
     cdef size_t length = smat.nonZeros()
     if length == 0:
-        return np.zeros((kin.n_reactions, 0))
+        return np.zeros((smat.rows(), 0))
 
     # index/value triplets
     cdef np.ndarray[int, ndim=1, mode="c"] rows = np.empty(length, dtype=c_int)
@@ -48,10 +47,7 @@ cdef np.ndarray get_dense(Kinetics kin, kineticsMethodSparse method):
         out[rows[i], cols[i]] = data[i]
     return out
 
-cdef tuple get_sparse(Kinetics kin, kineticsMethodSparse method):
-    # retrieve sparse matrix
-    cdef CxxSparseMatrix smat = method(kin.kinetics)
-
+cdef get_sparse(CxxSparseMatrix& smat):
     # pointers to values and inner indices of CSC storage
     cdef size_t length = smat.nonZeros()
     cdef np.ndarray[np.double_t, ndim=1] value = np.empty(length)
@@ -64,6 +60,14 @@ cdef tuple get_sparse(Kinetics kin, kineticsMethodSparse method):
     CxxSparseCscData(smat, &value[0], &inner[0], &outer[0])
     return value, inner, outer
 
+cdef get_from_sparse(CxxSparseMatrix& smat, int rows, int cols):
+    if _utils._USE_SPARSE:
+        tup = get_sparse(smat)
+        return _utils._scipy_sparse.csc_matrix(tup, shape=(rows, cols))
+    else:
+        return get_dense(smat)
+
+
 cdef class Kinetics(_SolutionBase):
     """
     Instances of class `Kinetics` are responsible for evaluating reaction rates
@@ -271,11 +275,8 @@ cdef class Kinetics(_SolutionBase):
             Method was changed to a property in Cantera 3.0.
         """
         def __get__(self):
-            if _utils._USE_SPARSE:
-                tup = get_sparse(self, kin_reactantStoichCoeffs)
-                shape = self.n_total_species, self.n_reactions
-                return _utils._scipy_sparse.csc_matrix(tup, shape=shape)
-            return get_dense(self, kin_reactantStoichCoeffs)
+            return get_from_sparse(self.kinetics.reactantStoichCoeffs(),
+                                   self.n_total_species, self.n_reactions)
 
     property reactant_stoich_coeffs3:
         """
@@ -308,11 +309,8 @@ cdef class Kinetics(_SolutionBase):
             Method was changed to a property in Cantera 3.0.
         """
         def __get__(self):
-            if _utils._USE_SPARSE:
-                tup = get_sparse(self, kin_productStoichCoeffs)
-                shape = self.n_total_species, self.n_reactions
-                return _utils._scipy_sparse.csc_matrix(tup, shape=shape)
-            return get_dense(self, kin_productStoichCoeffs)
+            return get_from_sparse(self.kinetics.productStoichCoeffs(),
+                                   self.n_total_species, self.n_reactions)
 
     property product_stoich_coeffs3:
         """
@@ -341,11 +339,8 @@ cdef class Kinetics(_SolutionBase):
         For sparse output, set ``ct.use_sparse(True)``.
         """
         def __get__(self):
-            if _utils._USE_SPARSE:
-                tup = get_sparse(self, kin_revProductStoichCoeffs)
-                shape = self.n_total_species, self.n_reactions
-                return _utils._scipy_sparse.csc_matrix(tup, shape=shape)
-            return get_dense(self, kin_revProductStoichCoeffs)
+            return get_from_sparse(self.kinetics.revProductStoichCoeffs(),
+                                   self.n_total_species, self.n_reactions)
 
     property forward_rates_of_progress:
         """
@@ -519,11 +514,8 @@ cdef class Kinetics(_SolutionBase):
         may be changed or removed without notice.
         """
         def __get__(self):
-            if _utils._USE_SPARSE:
-                tup = get_sparse(self, kin_fwdRatesOfProgress_ddX)
-                shape = self.n_reactions, self.n_total_species
-                return _utils._scipy_sparse.csc_matrix(tup, shape=shape)
-            return get_dense(self, kin_fwdRatesOfProgress_ddX)
+            return get_from_sparse(self.kinetics.fwdRatesOfProgress_ddX(),
+                                   self.n_reactions, self.n_total_species)
 
     property reverse_rates_of_progress_ddT:
         """
@@ -565,11 +557,8 @@ cdef class Kinetics(_SolutionBase):
         may be changed or removed without notice.
         """
         def __get__(self):
-            if _utils._USE_SPARSE:
-                tup = get_sparse(self, kin_revRatesOfProgress_ddX)
-                shape = self.n_reactions, self.n_total_species
-                return _utils._scipy_sparse.csc_matrix(tup, shape=shape)
-            return get_dense(self, kin_revRatesOfProgress_ddX)
+            return get_from_sparse(self.kinetics.revRatesOfProgress_ddX(),
+                                   self.n_reactions, self.n_total_species)
 
     property net_rates_of_progress_ddT:
         """
@@ -611,11 +600,8 @@ cdef class Kinetics(_SolutionBase):
         may be changed or removed without notice.
         """
         def __get__(self):
-            if _utils._USE_SPARSE:
-                tup = get_sparse(self, kin_netRatesOfProgress_ddX)
-                shape = self.n_reactions, self.n_total_species
-                return _utils._scipy_sparse.csc_matrix(tup, shape=shape)
-            return get_dense(self, kin_netRatesOfProgress_ddX)
+            return get_from_sparse(self.kinetics.netRatesOfProgress_ddX(),
+                                   self.n_reactions, self.n_total_species)
 
     property creation_rates_ddT:
         """
@@ -657,11 +643,8 @@ cdef class Kinetics(_SolutionBase):
         may be changed or removed without notice.
         """
         def __get__(self):
-            if _utils._USE_SPARSE:
-                tup = get_sparse(self, kin_creationRates_ddX)
-                shape = self.n_total_species, self.n_total_species
-                return _utils._scipy_sparse.csc_matrix(tup, shape=shape)
-            return get_dense(self, kin_creationRates_ddX)
+            return get_from_sparse(self.kinetics.creationRates_ddX(),
+                                   self.n_total_species, self.n_total_species)
 
     property destruction_rates_ddT:
         """
@@ -703,11 +686,8 @@ cdef class Kinetics(_SolutionBase):
         may be changed or removed without notice.
         """
         def __get__(self):
-            if _utils._USE_SPARSE:
-                tup = get_sparse(self, kin_destructionRates_ddX)
-                shape = self.n_total_species, self.n_total_species
-                return _utils._scipy_sparse.csc_matrix(tup, shape=shape)
-            return get_dense(self, kin_destructionRates_ddX)
+            return get_from_sparse(self.kinetics.destructionRates_ddX(),
+                                   self.n_total_species, self.n_total_species)
 
     property net_production_rates_ddT:
         """
@@ -749,11 +729,8 @@ cdef class Kinetics(_SolutionBase):
         may be changed or removed without notice.
         """
         def __get__(self):
-            if _utils._USE_SPARSE:
-                tup = get_sparse(self, kin_netProductionRates_ddX)
-                shape = self.n_total_species, self.n_total_species
-                return _utils._scipy_sparse.csc_matrix(tup, shape=shape)
-            return get_dense(self, kin_netProductionRates_ddX)
+            return get_from_sparse(self.kinetics.netProductionRates_ddX(),
+                                   self.n_total_species, self.n_total_species)
 
     property delta_enthalpy:
         """Change in enthalpy for each reaction [J/kmol]."""