diff --git a/configure.ac b/configure.ac
index 51aaf839ee4d70f7fe299bdaf5bc0f9ef576e3a7..7675f169579547a69fce39b7f7f669e18afc66ea 100755
--- a/configure.ac
+++ b/configure.ac
@@ -136,8 +136,8 @@ AX_LIB_PETSC()
AC_LANG_PUSH([C++])
AC_CHECK_HEADER(quadmath.h, , [])
-AC_CHECK_LIB(quadmath, sinq, [ AC_CHECK_HEADER( quadmath.h ,[AC_DEFINE(HAVE_LIBQUADMATH,[],[Have quad math lib])
- LIBQUADMATH=" -lquadmath "],[])
+AC_CHECK_LIB(quadmath, sinq, [ AC_DEFINE(HAVE_LIBQUADMATH,[],[Have quad math lib])
+ LIBQUADMATH=" -lquadmath "
], [])
AC_LANG_POP([C++])
@@ -159,6 +159,14 @@ AX_LIB_HILBERT([],[echo "Cannot detect libhilbert, use the --with-libhilbert opt
INCLUDES_PATH+=" -I/usr/local/include -I. -I../../openfpm_devices/src -I../../openfpm_data/src -I../../openfpm_io/src -I../../openfpm_vcluster/src -I../../src"
+####### Detect OpenMP
+
+AX_OPENMP([CFLAGS="$OPENMP_CFLAGS"
+ LDFLAGS="$OPENMP_LDFLAGS"],[])
+
+AC_SUBST(OPENMP_CFLAGS)
+AC_SUBST(OPENMP_LDFLAGS)
+
###### Check for se-class1
AC_MSG_CHECKING(whether to build with security enhancement class1)
diff --git a/m4/ax_petsc_lib.m4 b/m4/ax_petsc_lib.m4
index ed14c831b4e230d19b4bd7c9b80b37fa7dd7a098..1bd159091052c10c40e9e9317a4cca0ec579c4ec 100755
--- a/m4/ax_petsc_lib.m4
+++ b/m4/ax_petsc_lib.m4
@@ -102,8 +102,10 @@ AC_DEFUN([AX_LIB_PETSC], [
old_CC=$CC
old_CFLAGS=$CFLAGS
old_LDFLAGS=$LDFLAGS
- CFLAGS="-I$with_petsc/include $HDF5_INCLUDE $METIS_INCLUDE "
- LDFLAGS="-L$with_petsc/lib $HDF5_LDFLAGS $HDF5_LIBS $METIS_LIB -lmetis "
+ AX_OPENMP([CFLAGS="$OPENMP_CFLAGS"
+ LDFLAGS="$OPENMP_LDFLAGS"],[])
+ CFLAGS="$CFLAGS -I$with_petsc/include $HDF5_INCLUDE $METIS_INCLUDE "
+ LDFLAGS="$LDFLAGS -L$with_petsc/lib $HDF5_LDFLAGS $HDF5_LIBS $METIS_LIB -lmetis "
CC=$CXX
AC_LANG_SAVE
diff --git a/run.sh b/run.sh
new file mode 100755
index 0000000000000000000000000000000000000000..00fd49ba09b02f9470f470d6caafe2d33353fac6
--- /dev/null
+++ b/run.sh
@@ -0,0 +1,14 @@
+#! /bin/bash
+
+echo "RUN numerics test"
+
+source $HOME/openfpm_vars
+
+mpirun -np $3 ./src/numerics
+if [ $? -ne 0 ]; then
+ curl -X POST --data "payload={\"icon_emoji\": \":jenkins:\", \"username\": \"jenkins\" , \"attachments\":[{ \"title\":\"Error:\", \"color\": \"#FF0000\", \"text\":\"$2 failed to complete the openfpm_numerics test \" }] }" https://hooks.slack.com/services/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
+ exit 1 ;
+fi
+
+curl -X POST --data "payload={\"icon_emoji\": \":jenkins:\", \"username\": \"jenkins\" , \"attachments\":[{ \"title\":\"Info:\", \"color\": \"#00FF00\", \"text\":\"$2 completed succeffuly the openfpm_numerics test \" }] }" https://hooks.slack.com/services/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
+
diff --git a/src/FiniteDifference/Average.hpp b/src/FiniteDifference/Average.hpp
index 8e92b279e85a5f1071675bb1bae0e0f7da66667a..45867c6c7f0ea9ff238d9033c9d4af82eb747734 100644
--- a/src/FiniteDifference/Average.hpp
+++ b/src/FiniteDifference/Average.hpp
@@ -45,7 +45,7 @@ class Avg
* In case of non staggered case this function just return a null grid_key, in case of staggered,
* it calculate how the operator shift the calculation in the cell
*
- * \param position where we are calculating the derivative
+ * \param pos position where we are calculating the derivative
* \param gs Grid info
* \param s_pos staggered position of the properties
*
@@ -77,7 +77,7 @@ class Avg<d,arg,Sys_eqs,CENTRAL>
* conditions it is a distributed map
*
* \param g_map It is the map explained in FDScheme
- * \param k_map position where the average is calculated
+ * \param kmap position where the average is calculated
* \param gs Grid info
* \param cols non-zero colums calculated by the function
* \param coeff coefficent (constant in front of the derivative)
@@ -113,7 +113,7 @@ class Avg<d,arg,Sys_eqs,CENTRAL>
*
* It follow the same concept of central derivative
*
- * \param position where we are calculating the derivative
+ * \param pos position where we are calculating the derivative
* \param gs Grid info
* \param s_pos staggered position of the properties
*
@@ -160,7 +160,7 @@ class Avg<d,arg,Sys_eqs,FORWARD>
* conditions it is a distributed map
*
* \param g_map It is the map explained in FDScheme
- * \param k_map position where the average is calculated
+ * \param kmap position where the average is calculated
* \param gs Grid info
* \param cols non-zero colums calculated by the function
* \param coeff coefficent (constant in front of the derivative)
@@ -188,7 +188,7 @@ class Avg<d,arg,Sys_eqs,FORWARD>
* In case of non staggered case this function just return a null grid_key, in case of staggered,
* the FORWARD scheme return the position of the staggered property
*
- * \param position where we are calculating the derivative
+ * \param pos position where we are calculating the derivative
* \param gs Grid info
* \param s_pos staggered position of the properties
*
@@ -220,7 +220,7 @@ class Avg<d,arg,Sys_eqs,BACKWARD>
* conditions it is a distributed map
*
* \param g_map It is the map explained in FDScheme
- * \param k_map position where the average is calculated
+ * \param kmap position where the average is calculated
* \param gs Grid info
* \param cols non-zero colums calculated by the function
* \param coeff coefficent (constant in front of the derivative)
@@ -247,7 +247,7 @@ class Avg<d,arg,Sys_eqs,BACKWARD>
* In case of non staggered case this function just return a null grid_key, in case of staggered,
* the BACKWARD scheme return the position of the staggered property
*
- * \param position where we are calculating the derivative
+ * \param pos position where we are calculating the derivative
* \param gs Grid info
* \param s_pos staggered position of the properties
*
diff --git a/src/FiniteDifference/eq_unit_test_3d.hpp b/src/FiniteDifference/eq_unit_test_3d.hpp
index 83ec81d88f61477d81b41e7221efd270b42b1e86..f8b4bc3d03e10b21498bb0d94f74846d85858a75 100644
--- a/src/FiniteDifference/eq_unit_test_3d.hpp
+++ b/src/FiniteDifference/eq_unit_test_3d.hpp
@@ -22,57 +22,56 @@
BOOST_AUTO_TEST_SUITE( eq_test_suite_3d )
-//!
-
+//! Specify the general caratteristic of system to solve
struct lid_nn_3d_eigen
{
- // dimensionaly of the equation ( 3D problem ...)
+ //! dimensionaly of the equation ( 3D problem ...)
static const unsigned int dims = 3;
- // number of fields in the system
+ //! number of fields in the system
static const unsigned int nvar = 4;
- // 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;
- // type of base grid
+ //! type of base grid
typedef grid_dist_id<3,float,aggregate<float[3],float>,CartDecomposition<3,float>> b_grid;
- // type of SparseMatrix for the linear solver
+ //! type of SparseMatrix for the linear solver
typedef SparseMatrix<double,int> SparseMatrix_type;
- // type of Vector for the linear solver
+ //! type of Vector for the linear solver
typedef Vector<double> Vector_type;
- // Define the underline grid is staggered
+ //! Define the underline grid is staggered
static const int grid_type = STAGGERED_GRID;
};
struct lid_nn_3d_petsc
{
- // dimensionaly of the equation ( 3D problem ...)
+ //! dimensionaly of the equation ( 3D problem ...)
static const unsigned int dims = 3;
- // number of fields in the system
+ //! number of fields in the system
static const unsigned int nvar = 4;
- // 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;
- // type of base grid
+ //! type of base grid
typedef grid_dist_id<3,float,aggregate<float[3],float>,CartDecomposition<3,float>> b_grid;
- // type of SparseMatrix for the linear solver
+ //! type of SparseMatrix for the linear solver
typedef SparseMatrix<double,int,PETSC_BASE> SparseMatrix_type;
- // type of Vector for the linear solver
+ //! type of Vector for the linear solver
typedef Vector<double,PETSC_BASE> Vector_type;
- // Define the underline grid is staggered
+ //! Define the underline grid is staggered
static const int grid_type = STAGGERED_GRID;
};
@@ -84,14 +83,13 @@ const bool lid_nn_3d_petsc::boundary[] = {NON_PERIODIC,NON_PERIODIC,NON_PERIODIC
// Constant Field
struct eta
{
+ //! define that eta is a constant field
typedef void const_field;
+ //! therutn the value of the constant
static float val() {return 1.0;}
};
-//#define SYSEQ_TYPE lid_nn_3d_eigen;
-//#include "Equations/stoke_flow_eq_3d.hpp"
-
template<typename solver_type,typename lid_nn_3d> void lid_driven_cavity_3d()
{
#include "Equations/stoke_flow_eq_3d.hpp"
diff --git a/src/Makefile.am b/src/Makefile.am
index 5b8f08cbb0171bbf37f466d111861903fbd74365..90ad2275f837baa87bb1a10154bd9869d37c2a94 100755
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -1,9 +1,9 @@
-LINKLIBS = $(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)
+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)
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_CXXFLAGS = $(AM_CXXFLAGS) $(HDF5_CPPFLAGS) $(INCLUDES_PATH) $(BOOST_CPPFLAGS) $(SUITESPARSE_INCLUDE) $(METIS_INCLUDE) $(PARMETIS_INCLUDE) $(EIGEN_INCLUDE) -I/usr/local/libhilbert/include -Wno-deprecated-declarations -Wno-unused-local-typedefs
+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
nobase_include_HEADERS = Matrix/SparseMatrix.hpp Matrix/SparseMatrix_Eigen.hpp Matrix/SparseMatrix_petsc.hpp \
diff --git a/src/Matrix/SparseMatrix_petsc.hpp b/src/Matrix/SparseMatrix_petsc.hpp
index d129624d286ba4340ffa62f3cfc1a98c23416889..78d352d1ab1d7d4a3921231173b26324edec3724 100644
--- a/src/Matrix/SparseMatrix_petsc.hpp
+++ b/src/Matrix/SparseMatrix_petsc.hpp
@@ -24,22 +24,42 @@
template<typename T>
class triplet<T,PETSC_BASE>
{
+ //! Row of the sparse matrix
PetscInt row_;
+
+ //! Colum of the sparse matrix
PetscInt col_;
+
+ //! Value of the Matrix
PetscScalar val_;
public:
+ /*! \brief Return the row of the triplet
+ *
+ * \return the row index
+ *
+ */
PetscInt & row()
{
return row_;
}
+ /*! \brief Return the colum of the triplet
+ *
+ * \return the colum index
+ *
+ */
PetscInt & col()
{
return col_;
}
+ /*! \brief Return the value of the triplet
+ *
+ * \return the value
+ *
+ */
PetscScalar & value()
{
return val_;
diff --git a/src/Operators/Vector/vector_dist_operators.hpp b/src/Operators/Vector/vector_dist_operators.hpp
index 7adb79008e4f184796bd44a2120bdc3ffc018b1a..21ec3c8271f2e5dfb8f8f8f60df7162a18523715 100644
--- a/src/Operators/Vector/vector_dist_operators.hpp
+++ b/src/Operators/Vector/vector_dist_operators.hpp
@@ -499,12 +499,15 @@ public:
template<unsigned int prp>
class vector_dist_expression<prp,float>
{
+ //! constant value
float d;
public:
+ //! type of object the structure return then evaluated
typedef float vtype;
+ //! constrictir from constant value
inline vector_dist_expression(const float & d)
:d(d)
{}
@@ -519,7 +522,9 @@ public:
/*! \brief Evaluate the expression
*
- * It just return the velue set in the constructor
+ * It just return the value set in the constructor
+ *
+ * \return the constant value set in the constructor
*
*/
inline float value(const vect_dist_key_dx & k) const
diff --git a/src/Operators/Vector/vector_dist_operators_functions.hpp b/src/Operators/Vector/vector_dist_operators_functions.hpp
index c0d9dfb3fd9079be6597c13515ca397619af21c9..ff7308e14a8ded59da50a283a9d731fb18e8edd2 100644
--- a/src/Operators/Vector/vector_dist_operators_functions.hpp
+++ b/src/Operators/Vector/vector_dist_operators_functions.hpp
@@ -49,14 +49,6 @@ fun_name(const vector_dist_expression_op<exp1,exp2_,op1> & va)\
return exp_sum;\
}\
\
-template<typename exp1, typename exp2_, unsigned int op1>\
-inline vector_dist_expression_op<vector_dist_expression<0,double>,void,OP_ID>\
-fun_name(double d)\
-{\
- vector_dist_expression_op<vector_dist_expression<0,double>,void,OP_ID> exp_sum( (vector_dist_expression<0,double>(d)) );\
-\
- return exp_sum;\
-}\
\
template<unsigned int prp1, typename v1>\
inline vector_dist_expression_op<vector_dist_expression<prp1,v1>,void,OP_ID>\