Fixing change name in VCluster

src/Makefile.am

@@ -2,7 +2,7 @@
 LINKLIBS = $(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) $(HDF5_LDFLAGS)  $(HDF5_LIBS) $(LIBQUADMATH) $(OPENMP_LDFLAGS) $(LIBIFCORE)
 
 noinst_PROGRAMS = numerics
-numerics_SOURCES = main.cpp ../../openfpm_vcluster/src/VCluster.cpp ../../openfpm_devices/src/memory/HeapMemory.cpp ../../openfpm_devices/src/memory/PtrMemory.cpp ../../openfpm_devices/src/Memleak_check.cpp
+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_CXXFLAGS = $(OPENMP_CFLAGS) $(LIBHILBERT_INCLUDE) $(AM_CXXFLAGS) $(HDF5_CPPFLAGS) $(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_Eigen.hpp

@@ -10,7 +10,7 @@
 
 #include "Vector/map_vector.hpp"
 #include <boost/mpl/int.hpp>
-#include "VCluster.hpp"
+#include "VCluster/VCluster.hpp"
 
 #define EIGEN_TRIPLET 1
 

src/Operators/Vector/vector_dist_operators_apply_kernel.hpp

@@ -199,15 +199,27 @@ struct apply_kernel_is_number_or_expression_gen
 template <typename exp1,typename vector_type>
 class vector_dist_expression_op<exp1,vector_type,VECT_APPLYKER_IN>
 {
+	//! Type of neighborhood
 	typedef typename boost::mpl::at<vector_type,boost::mpl::int_<0>>::type NN;
+	//! Type of kernel
 	typedef typename boost::mpl::at<vector_type,boost::mpl::int_<1>>::type Kernel;
+
+	// Type of the vector containing the particles
 	typedef typename boost::mpl::at<vector_type,boost::mpl::int_<2>>::type vector_orig;
 
+	//! expression
 	const exp1 o1;
+
+	//! neighborhood list
 	NN & cl;
+
+	//! kernel
 	Kernel & ker;
+
+	//! Vector of particles
 	const vector_orig & vd;
 
+	//! Return type of the expression
 	typedef typename apply_kernel_rtype<decltype(o1.value(vect_dist_key_dx(0)))>::rtype rtype;
 
 public:
@@ -246,14 +258,25 @@ public:
 template <typename exp1,typename vector_type>
 class vector_dist_expression_op<exp1,vector_type,VECT_APPLYKER_IN_SIM>
 {
+	//! Type of neighborhood list
 	typedef typename boost::mpl::at<vector_type,boost::mpl::int_<0>>::type NN;
+
+	//! Type of the kernel
 	typedef typename boost::mpl::at<vector_type,boost::mpl::int_<1>>::type Kernel;
+
+	//! Type that store the particles
 	typedef typename boost::mpl::at<vector_type,boost::mpl::int_<2>>::type vector_orig;
 
+	//! Neighborhood list
 	NN & cl;
+
+	//! kernel
 	Kernel & ker;
+
+	//! vector of particles
 	const vector_orig & vd;
 
+	//! return type of the expression
 	typedef typename apply_kernel_rtype<decltype(std::declval<Kernel>().value(Point<vector_orig::dims,typename vector_orig::stype>(0.0), Point<vector_orig::dims,typename vector_orig::stype>(0.0) ) )>::rtype rtype;
 
 
@@ -268,6 +291,13 @@ public:
 	{
 	}
 
+	/*! \brief Constructor
+	 *
+	 * \param cl neighborhood-list
+	 * \param ker kernel to apply
+	 * \param vd particle set to which apply the kernel
+	 *
+	 */
 	vector_dist_expression_op(NN & cl, Kernel & ker, const vector_orig & vd)
 	:cl(cl),ker(ker),vd(vd)
 	{}
@@ -293,15 +323,28 @@ public:
 template <typename exp1,typename vector_type>
 class vector_dist_expression_op<exp1,vector_type,VECT_APPLYKER_IN_GEN>
 {
+	//! Type of nearest neighborhood
 	typedef typename boost::mpl::at<vector_type,boost::mpl::int_<0>>::type NN;
+
+	//! Type of kernel
 	typedef typename boost::mpl::at<vector_type,boost::mpl::int_<1>>::type Kernel;
+
+	//! Type of vector
 	typedef typename boost::mpl::at<vector_type,boost::mpl::int_<2>>::type vector_orig;
 
+	//! expression 1
 	const exp1 o1;
+
+	//! nearest neighborhood
 	NN & cl;
+
+	//! kernel
 	Kernel & ker;
+
+	//! Vector containing the particles
 	const vector_orig & vd;
 
+	//! Return type of the kernel
 	typedef typename apply_kernel_rtype<decltype(o1.value(vect_dist_key_dx(0)))>::rtype rtype;
 
 public:
@@ -316,6 +359,14 @@ public:
 		o1.init();
 	}
 
+	/*! \brief Constructor from expression
+	 *
+	 * \param o1 first expression
+	 * \param NN neighborhood
+	 * \param kernel
+	 * \param vd vector with particles
+	 *
+	 */
 	vector_dist_expression_op(const exp1 & o1, NN & cl, Kernel & ker, const vector_orig & vd)
 	:o1(o1),cl(cl),ker(ker),vd(vd)
 	{}

src/Operators/Vector/vector_dist_operators_functions.hpp

@@ -208,24 +208,34 @@ CREATE_VDIST_ARG2_FUNC(pmul,pmul,VECT_PMUL)
 ////////// Special function reduce /////////////////////////
 
 
+/*! \brief expression that encapsulate a vector reduction expression
+ *
+ * \tparam exp1 expression 1
+ * \tparam vector_type type of vector on which the expression is acting
+ *
+ */
 template <typename exp1, typename vector_type>
 class vector_dist_expression_op<exp1,vector_type,VECT_SUM_REDUCE>
 {
+	//! expression 1
 	const exp1 o1;
 
+	//! return type comming from the expression
 	typedef typename apply_kernel_rtype<decltype(o1.value(vect_dist_key_dx(0)))>::rtype rtype;
 
-	// calculated value
+	//! r_type without reference
 	mutable typename std::remove_reference<rtype>::type val;
 
 	const vector_type & vd;
 
 public:
 
+	//! constructor from an epxression exp1 and a vector vd
 	vector_dist_expression_op(const exp1 & o1, const vector_type & vd)
 	:o1(o1), vd(vd)
 	{}
 
+	//! initialize the expression
 	inline void init() const
 	{
 		o1.init();
@@ -244,19 +254,21 @@ public:
 		}
 	}
 
+	//! Get the value of the expression
 	inline typename std::remove_reference<rtype>::type get()
 	{
 		init();
 		return value(vect_dist_key_dx(0));
 	}
 
+	//! Get the value  of the expression
 	template<typename r_type= typename std::remove_reference<rtype>::type > inline r_type value(const vect_dist_key_dx & key) const
 	{
 		return val;
 	}
 };
 
-
+//! Reduce function (it generate an expression)
 template<typename exp1, typename exp2_, unsigned int op1, typename vector_type>
 inline vector_dist_expression_op<vector_dist_expression_op<exp1,exp2_,op1>,vector_type,VECT_SUM_REDUCE>
 rsum(const vector_dist_expression_op<exp1,exp2_,op1> & va, const vector_type & vd)
@@ -266,6 +278,7 @@ rsum(const vector_dist_expression_op<exp1,exp2_,op1> & va, const vector_type & v
 	return exp_sum;
 }
 
+//! Reduce function (It generate an expression)
 template<unsigned int prp1, typename v1, typename vector_type>
 inline vector_dist_expression_op<vector_dist_expression<prp1,v1>,vector_type,VECT_SUM_REDUCE>
 rsum(const vector_dist_expression<prp1,v1> & va, const vector_type & vd)

src/Operators/Vector/vector_dist_operators_unit_tests.hpp

@@ -652,12 +652,16 @@ typedef vector_dist<3,float,aggregate<float,float,float,VectorS<3,float>,VectorS
 //! Exponential kernel
 struct exp_kernel
 {
+	//! variance of the exponential kernel
 	float var;
 
+	//! Exponential kernel giving variance
 	exp_kernel(float var)
 	:var(var)
 	{}
 
+	//! Calculate the value of the exponential kernel given two points p and q
+	// pA is the property on p pB is the property on B
 	inline float value(const Point<3,float> & p, const Point<3,float> & q,float pA,float pB)
 	{
 		float dist = norm(p-q);
@@ -665,6 +669,8 @@ struct exp_kernel
 		return (pA + pB) * exp(dist * dist / var);
 	}
 
+	//! Calculate the value of the exponential kernel given two points p and q
+	// pA is the value of the property on pA and pB is the value of the property on pB
 	inline Point<3,float> value(const Point<3,float> & p, const Point<3,float> & q,const Point<3,float> & pA, const Point<3,float> & pB)
 	{
 		float dist = norm(p-q);
@@ -672,6 +678,9 @@ struct exp_kernel
 		return (pA + pB) * exp(dist * dist / var);
 	}
 
+	//! Calculate the value of the exponential kernel given two points p and q
+	// pA is the value of the property on pA and pB is the value of the property on pB
+	// vd1 is the set of particles
 	inline float value(size_t p, size_t q, float pA, float pB, const vector_type & vd1)
 	{
 		Point<3,float> pp = vd1.getPos(p);
@@ -682,6 +691,9 @@ struct exp_kernel
 		return (pA + pB) * exp(dist * dist / var);
 	}
 
+	//! Calculate the value of the exponential kernel given two points p and q
+	// pA is the value of the property on pA and pB is the value of the property on pB
+	// vd1 is the set of particles
 	inline Point<3,float> value(size_t p, size_t q, const Point<3,float> & pA, const Point<3,float> & pB , const vector_type & vd1)
 	{
 		Point<3,float> pp = vd1.getPos(p);
@@ -692,6 +704,7 @@ struct exp_kernel
 		return (pA + pB) * exp(dist * dist / var);
 	}
 
+	//! Calculate the value of the exponential kernel given two points p and q
 	inline Point<2,float> value(const Point<3,float> & p, const Point<3,float> & q)
 	{
 		float dist = norm(p-q);

src/unit_test_init_cleanup.hpp

@@ -8,7 +8,7 @@
 #ifndef UNIT_TEST_INIT_CLEANUP_HPP_
 #define UNIT_TEST_INIT_CLEANUP_HPP_
 
-#include "VCluster.hpp"
+#include "VCluster/VCluster.hpp"
 
 struct ut_start {
     ut_start()   {