Fixes on AMG + documentation + AMG report

src/FiniteDifference/Derivative.hpp

@@ -8,11 +8,6 @@
 #ifndef OPENFPM_NUMERICS_SRC_FINITEDIFFERENCE_DERIVATIVE_HPP_
 #define OPENFPM_NUMERICS_SRC_FINITEDIFFERENCE_DERIVATIVE_HPP_
 
-#define CENTRAL 0
-#define CENTRAL_B_ONE_SIDE 1
-#define FORWARD 2
-#define BACKWARD 3
-#define CENTRAL_SYM 4
 
 #include "util/mathutil.hpp"
 #include "Vector/map_vector.hpp"
@@ -20,6 +15,7 @@
 #include "FiniteDifference/util/common.hpp"
 #include "util/util_num.hpp"
 #include <unordered_map>
+#include "FD_util_include.hpp"
 
 /*! \brief Derivative second order on h (spacing)
  *

src/FiniteDifference/FDScheme_unit_tests.hpp

@@ -23,21 +23,23 @@ constexpr unsigned int V = 0;
 
 struct sys_nn
 {
-	// dimensionaly of the equation (2D problem 3D problem ...)
+	//! dimensionaly of the equation (2D problem 3D problem ...)
 	static const unsigned int dims = 2;
-	// number of fields in the system
+	//! number of degree of freedoms
 	static const unsigned int nvar = 1;
+
 	static const unsigned int ord = EQS_FIELD;
 
-	// boundary at X and Y
+	//! boundary at X and Y
 	static const bool boundary[];
 
-	// type of space float, double, ...
+	//! type of space float, double, ...
 	typedef float stype;
 
-	// Base grid
+	//! Base grid
 	typedef grid_dist_id<dims,stype,scalar<float>,CartDecomposition<2,stype> > b_grid;
 
+	//! specify that we are on testing
 	typedef void testing;
 };
 
@@ -45,21 +47,22 @@ const bool sys_nn::boundary[] = {NON_PERIODIC,NON_PERIODIC};
 
 struct sys_pp
 {
-	// dimensionaly of the equation (2D problem 3D problem ...)
+	//! dimensionaly of the equation (2D problem 3D problem ...)
 	static const unsigned int dims = 2;
-	// number of fields in the system
+	//! number of degree of freedom in the system
 	static const unsigned int nvar = 1;
 	static const unsigned int ord = EQS_FIELD;
 
-	// boundary at X and Y
+	//! boundary at X and Y
 	static const bool boundary[];
 
-	// type of space float, double, ...
+	//! type of space float, double, ...
 	typedef float stype;
 
-	// Base grid
+	//! Base grid
 	typedef grid_dist_id<dims,stype,scalar<float>,CartDecomposition<2,stype> > b_grid;
 
+	//! Indicate we are on testing
 	typedef void testing;
 };
 
@@ -69,23 +72,26 @@ const bool sys_pp::boundary[] = {PERIODIC,PERIODIC};
 
 struct syss_nn
 {
-	// dimensionaly of the equation (2D problem 3D problem ...)
+	//! dimensionaly of the equation (2D problem 3D problem ...)
 	static const unsigned int dims = 2;
-	// number of fields in the system
+	//! Degree of freedom in the system
 	static const unsigned int nvar = 1;
+
 	static const unsigned int ord = EQS_FIELD;
 
+	//! Indicate that the type of grid is staggered
 	static const unsigned int grid_type = STAGGERED_GRID;
 
-	// boundary at X and Y
+	//! boundary at X and Y
 	static const bool boundary[];
 
-	// type of space float, double, ...
+	//! type of space float, double, ...
 	typedef float stype;
 
-	// Base grid
+	//! Base grid
 	typedef grid_dist_id<dims,stype,scalar<float>,CartDecomposition<2,stype> > b_grid;
 
+	//! Indicate we are on testing
 	typedef void testing;
 };
 
@@ -93,23 +99,25 @@ const bool syss_nn::boundary[] = {NON_PERIODIC,NON_PERIODIC};
 
 struct syss_pp
 {
-	// dimensionaly of the equation (2D problem 3D problem ...)
+	//! dimensionaly of the equation (2D problem 3D problem ...)
 	static const unsigned int dims = 2;
-	// number of fields in the system
+	//! number of fields in the system
 	static const unsigned int nvar = 1;
 	static const unsigned int ord = EQS_FIELD;
 
+	//! Indicate the grid is staggered
 	static const unsigned int grid_type = STAGGERED_GRID;
 
-	// boundary at X and Y
+	//! boundary at X and Y
 	static const bool boundary[];
 
-	// type of space float, double, ...
+	//! type of space float, double, ...
 	typedef float stype;
 
-	// Base grid
+	//! Base grid
 	typedef grid_dist_id<dims,stype,scalar<float>,CartDecomposition<2,stype> > b_grid;
 
+	//! Indicate we are on testing
 	typedef void testing;
 };
 

src/FiniteDifference/Laplacian.hpp

@@ -8,6 +8,9 @@
 #ifndef OPENFPM_NUMERICS_SRC_FINITEDIFFERENCE_LAPLACIAN_HPP_
 #define OPENFPM_NUMERICS_SRC_FINITEDIFFERENCE_LAPLACIAN_HPP_
 
+#include "FD_util_include.hpp"
+#include "util/util_num.hpp"
+#include "FiniteDifference/eq.hpp"
 
 /*! \brief Laplacian second order on h (spacing)
  *

src/FiniteDifference/eq_unit_test_3d.hpp

@@ -193,8 +193,7 @@ template<typename solver_type,typename lid_nn_3d> void lid_driven_cavity_3d()
 	fd.impose(v_z(), 0.0, EQ_3, {-1,-1,-1},{sz[0]-1,sz[1]-1,-1});
 
 	solver_type solver;
-	solver.best_solve();
-	auto x = solver.solve(fd.getA(),fd.getB());
+	auto x = solver.try_solve(fd.getA(),fd.getB());
 
 	// Bring the solution to grid
 	fd.template copy<velocity,pressure>(x,{0,0},{sz[0]-1,sz[1]-1,sz[2]-1},g_dist);

src/Makefile.am

@@ -2,7 +2,7 @@
 LINKLIBS = $(HDF5_LDFLAGS)  $(HDF5_LIBS) $(OPENMP_LDFLAGS) $(LIBHILBERT_LIB) $(PETSC_LIB) $(SUITESPARSE_LIBS) $(LAPACK_LIBS) $(BLAS_LIBS)  $(METIS_LIB) $(PARMETIS_LIB) $(DEFAULT_LIB) $(PTHREAD_LIBS) $(OPT_LIBS) $(BOOST_LDFLAGS) $(BOOST_PROGRAM_OPTIONS_LIB) $(BOOST_IOSTREAMS_LIB) $(LIBQUADMATH) $(OPENMP_LDFLAGS) $(LIBIFCORE)
 
 noinst_PROGRAMS = numerics
-numerics_SOURCES = main.cpp ../../openfpm_vcluster/src/VCluster/VCluster.cpp ../../openfpm_devices/src/memory/HeapMemory.cpp ../../openfpm_devices/src/memory/PtrMemory.cpp ../../openfpm_devices/src/Memleak_check.cpp
+numerics_SOURCES = main.cpp Solvers/petsc_solver_unit_tests.cpp  ../../openfpm_vcluster/src/VCluster/VCluster.cpp ../../openfpm_devices/src/memory/HeapMemory.cpp ../../openfpm_devices/src/memory/PtrMemory.cpp ../../openfpm_devices/src/Memleak_check.cpp
 numerics_CXXFLAGS = $(HDF5_CPPFLAGS) $(OPENMP_CFLAGS) $(LIBHILBERT_INCLUDE) $(AM_CXXFLAGS) $(INCLUDES_PATH) $(BOOST_CPPFLAGS) $(SUITESPARSE_INCLUDE) $(METIS_INCLUDE) $(PARMETIS_INCLUDE) $(EIGEN_INCLUDE) $(PETSC_INCLUDE) -Wno-deprecated-declarations -Wno-unused-local-typedefs
 numerics_CFLAGS = $(CUDA_CFLAGS)
 numerics_LDADD = $(LINKLIBS) -lparmetis -lmetis

src/Matrix/SparseMatrix_petsc.hpp

@@ -83,7 +83,7 @@ public:
 	triplet()	{};
 };
 
-/* ! \brief Sparse Matrix implementation, that map over Eigen
+/*! \brief Sparse Matrix implementation, that map over Eigen
  *
  * \tparam T Type of the sparse Matrix store on each row,colums
  * \tparam id_t type of id
@@ -194,6 +194,8 @@ private:
 
 		PETSC_SAFE_CALL(MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY));
 		PETSC_SAFE_CALL(MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY));
+
+		m_created = true;
 	}
 
 
@@ -207,7 +209,7 @@ public:
 	 *
 	 */
 	SparseMatrix(size_t N1, size_t N2, size_t n_row_local)
-	:l_row(n_row_local),l_col(n_row_local)
+	:g_row(N1),g_col(N2),l_row(n_row_local),l_col(n_row_local)
 	{
 		PETSC_SAFE_CALL(MatCreate(PETSC_COMM_WORLD,&mat));
 		PETSC_SAFE_CALL(MatSetType(mat,MATMPIAIJ));
@@ -230,6 +232,7 @@ public:
 	 *
 	 */
 	SparseMatrix()
+	:g_row(0),g_col(0),l_row(0l),l_col(0),start_row(0)
 	{
 		PETSC_SAFE_CALL(MatCreate(PETSC_COMM_WORLD,&mat));
 		PETSC_SAFE_CALL(MatSetType(mat,MATMPIAIJ));
@@ -251,6 +254,8 @@ public:
 	 */
 	openfpm::vector<triplet_type> & getMatrixTriplets()
 	{
+		m_created = false;
+
 		return this->trpl;
 	}
 
@@ -261,7 +266,8 @@ public:
 	 */
 	const Mat & getMat() const
 	{
-		fill_petsc();
+		if (m_created == false)
+		{fill_petsc();}
 
 		return mat;
 	}
@@ -273,7 +279,8 @@ public:
 	 */
 	Mat & getMat()
 	{
-		fill_petsc();
+		if (m_created == false)
+		{fill_petsc();}
 
 		return mat;
 	}

src/Solvers/umfpack_solver.hpp

@@ -46,11 +46,19 @@ class umfpack_solver<double>
 
 public:
 
-	/*! \brief No nothing
+	/*! \brief Here we invert the matrix and solve the system
+	 *
+	 *  \warning umfpack is not a parallel solver, this function work only with one processor
+	 *
+	 *  \note if you want to use umfpack in a NON parallel, but on a distributed data, use solve with triplet
 	 *
+	 *	\tparam impl Implementation of the SparseMatrix
 	 *
 	 */
-	void best_solve() {};
+	static Vector<double,EIGEN_BASE> try_solve(SparseMatrix<double,int,EIGEN_BASE> & A, const Vector<double,EIGEN_BASE> & b, size_t opt = UMFPACK_NONE)
+	{
+		return solve(A,b,opt);
+	}
 
 	/*! \brief Here we invert the matrix and solve the system
 	 *

src/Vector/Vector_petsc.hpp

@@ -9,6 +9,7 @@
 #define OPENFPM_NUMERICS_SRC_VECTOR_VECTOR_PETSC_HPP_
 
 #include "Vector/map_vector.hpp"
+#include "Vector/vector_def.hpp"
 #include <boost/mpl/int.hpp>
 #include <petscvec.h>
 #include "util/petsc_util.hpp"
@@ -32,18 +33,30 @@ public:
 	//! structure that store the data of the point
 	type data;
 
-	//! Property id of the point
+	//! Property id for the row
 	static const unsigned int row = 0;
+
+	//! Property id for the value
 	static const unsigned int value = 1;
+
+	//! This object has 2 properties
 	static const unsigned int max_prop = 2;
 
-	// Get the row
+	/*! \brief Get the row
+	 *
+	 * \return the row
+	 *
+	 */
 	long int & rw()
 	{
 		return boost::fusion::at_c<row>(data);
 	}
 
-	// Get the value
+	/*! \brief Get the value
+	 *
+	 * \return the value
+	 *
+	 */
 	T & val()
 	{
 		return boost::fusion::at_c<value>(data);
@@ -54,7 +67,7 @@ public:
 	 */
 	rval()	{}
 
-	/*! \brief Constructor from row, colum and value
+	/*! \brief Constructor from row, column and value
 	 *
 	 * \param i row
 	 * \param val value
@@ -70,28 +83,34 @@ public:
 constexpr unsigned int row_id = 0;
 constexpr unsigned int val_id = 1;
 
+
+/*! \brief PETSC vector for linear algebra
+ *
+ * This vector wrap the PETSC vector for solving linear systems
+ *
+ */
 template<typename T>
 class Vector<T,PETSC_BASE>
 {
-	// n_row
+	//! Number of row the petsc vector has
 	size_t n_row;
 
-	// Number of local rows
+	//! Number of local rows
 	size_t n_row_local;
 
-	// Indicate if v has been allocated
-	bool v_created = false;
+	//! Indicate if v has been allocated
+	mutable bool v_created = false;
 
-	// Mutable vector
+	//! Mutable vector
 	mutable Vec v;
 
-	// Mutable row value vector
+	//! Mutable row value vector
 	mutable openfpm::vector<rval<PetscScalar,PETSC_RVAL>,HeapMemory,typename memory_traits_inte<rval<PetscScalar,PETSC_RVAL>>::type > row_val;
 
-	// Global to local map
+	//! Global to local map
 	mutable std::unordered_map<size_t,size_t> map;
 
-	// invalid
+	//! invalid
 	T invalid;
 
 	/*! \brief Set the Eigen internal vector
@@ -112,7 +131,7 @@ class Vector<T,PETSC_BASE>
 		PETSC_SAFE_CALL(VecAssemblyBegin(v));
 		PETSC_SAFE_CALL(VecAssemblyEnd(v));
 
-
+		v_created = true;
 	}
 
 public:

src/util/petsc_util.hpp

@@ -15,7 +15,8 @@
 	if (err != 0) {\
 		std::string msg("Petsc error: ");\
 		msg += std::string(__FILE__) + std::string(" ") + std::to_string(__LINE__);\
-		PetscError(MPI_COMM_WORLD,__LINE__,__FUNCT__,__FILE__,err,PETSC_ERROR_INITIAL,"Error petsc");\
+		PetscInt ln = __LINE__;\
+		PetscError(MPI_COMM_WORLD,ln,__FUNCT__,__FILE__,err,PETSC_ERROR_INITIAL,"Error petsc");\
 	}\
 }