From 6794c24bc6fe9c474496f9b5908b97a823214ded Mon Sep 17 00:00:00 2001
From: Pietro Incardona <incardon@mpi-cbg.de>
Date: Tue, 13 Dec 2016 18:30:20 +0100
Subject: [PATCH] Fixing change name in VCluster
---
src/Makefile.am | 2 +-
src/Matrix/SparseMatrix_Eigen.hpp | 2 +-
.../vector_dist_operators_apply_kernel.hpp | 51 +++++++++++++++++++
.../vector_dist_operators_functions.hpp | 17 ++++++-
.../vector_dist_operators_unit_tests.hpp | 13 +++++
src/unit_test_init_cleanup.hpp | 2 +-
6 files changed, 82 insertions(+), 5 deletions(-)
diff --git a/src/Makefile.am b/src/Makefile.am
index 7aa6946c..d631e1b8 100755
--- a/src/Makefile.am
+++ b/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
diff --git a/src/Matrix/SparseMatrix_Eigen.hpp b/src/Matrix/SparseMatrix_Eigen.hpp
index 9a5fc42a..ce655797 100644
--- a/src/Matrix/SparseMatrix_Eigen.hpp
+++ b/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
diff --git a/src/Operators/Vector/vector_dist_operators_apply_kernel.hpp b/src/Operators/Vector/vector_dist_operators_apply_kernel.hpp
index 59bbc478..f80da3ac 100644
--- a/src/Operators/Vector/vector_dist_operators_apply_kernel.hpp
+++ b/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)
{}
diff --git a/src/Operators/Vector/vector_dist_operators_functions.hpp b/src/Operators/Vector/vector_dist_operators_functions.hpp
index ff7308e1..53d28f9c 100644
--- a/src/Operators/Vector/vector_dist_operators_functions.hpp
+++ b/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)
diff --git a/src/Operators/Vector/vector_dist_operators_unit_tests.hpp b/src/Operators/Vector/vector_dist_operators_unit_tests.hpp
index 372bde70..7ec35c5d 100644
--- a/src/Operators/Vector/vector_dist_operators_unit_tests.hpp
+++ b/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);
diff --git a/src/unit_test_init_cleanup.hpp b/src/unit_test_init_cleanup.hpp
index 51288040..7cf89f01 100644
--- a/src/unit_test_init_cleanup.hpp
+++ b/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() {
--
GitLab