From f4a04798e369d4d958863a95600ef6035feaf6f6 Mon Sep 17 00:00:00 2001
From: Pietro Incardona <incardon@mpi-cbg.de>
Date: Tue, 25 Jul 2017 01:42:01 +0200
Subject: [PATCH] Fixing run for numerics
---
run.sh | 3 +-
src/FiniteDifference/FDScheme.hpp | 35 +++++++-
src/FiniteDifference/Laplacian.hpp | 69 +++++-----------
src/Vector/Vector.hpp | 128 +++++++++++++++++++++++++++--
src/Vector/Vector_petsc.hpp | 4 +-
5 files changed, 177 insertions(+), 62 deletions(-)
diff --git a/run.sh b/run.sh
index 6485943..935d4c4 100755
--- a/run.sh
+++ b/run.sh
@@ -2,7 +2,8 @@
echo "RUN numerics test"
-source $HOME/openfpm_vars
+branch=$(git ls-remote --heads origin | grep $(git rev-parse HEAD) | cut -d / -f 3)
+source $HOME/openfpm_vars_$branch
mpirun -np $3 ./src/numerics
if [ $? -ne 0 ]; then
diff --git a/src/FiniteDifference/FDScheme.hpp b/src/FiniteDifference/FDScheme.hpp
index ff669b8..9f50ef2 100644
--- a/src/FiniteDifference/FDScheme.hpp
+++ b/src/FiniteDifference/FDScheme.hpp
@@ -134,32 +134,60 @@ public:
private:
- // Encapsulation of the b term as constant
+ //! Encapsulation of the b term as constant
struct constant_b
{
+ //! scalar
typename Sys_eqs::stype scal;
+ /*! \brief Constrictor from a scalar
+ *
+ * \param scal scalar
+ *
+ */
constant_b(typename Sys_eqs::stype scal)
{
this->scal = scal;
}
+ /*! \brief Get the b term on a grid point
+ *
+ * \note It does not matter the grid point it is a scalar
+ *
+ * \param key grid position (unused because it is a constant)
+ *
+ * \return the scalar
+ *
+ */
typename Sys_eqs::stype get(grid_dist_key_dx<Sys_eqs::dims> & key)
{
return scal;
}
};
- // Encapsulation of the b term as grid
+ //! Encapsulation of the b term as grid
template<typename grid, unsigned int prp>
struct grid_b
{
+ //! b term fo the grid
grid & gr;
+ /*! \brief gr grid that encapsulate
+ *
+ * \param gr grid
+ *
+ */
grid_b(grid & gr)
:gr(gr)
{}
+ /*! \brief Get the value of the b term on a grid point
+ *
+ * \param key grid point
+ *
+ * \return the value
+ *
+ */
typename Sys_eqs::stype get(grid_dist_key_dx<Sys_eqs::dims> & key)
{
return gr.template get<prp>(key);
@@ -439,7 +467,7 @@ private:
auto it = it_d;
grid_sm<Sys_eqs::dims,void> gs = g_map.getGridInfoVoid();
- std::unordered_map<long int,float> cols;
+ std::unordered_map<long int,typename Sys_eqs::stype> cols;
// iterate all the grid points
while (it.isNext())
@@ -699,7 +727,6 @@ public:
*
* The periodicity is given by the grid b_g
*
- * \param pd Padding, how many points out of boundary are present
* \param stencil maximum extension of the stencil on each directions
* \param domain the domain
* \param b_g object grid that will store the solution
diff --git a/src/FiniteDifference/Laplacian.hpp b/src/FiniteDifference/Laplacian.hpp
index 5736add..05f6317 100644
--- a/src/FiniteDifference/Laplacian.hpp
+++ b/src/FiniteDifference/Laplacian.hpp
@@ -26,7 +26,9 @@ class Lap
* stub_or_real it is just for change the argument type when testing, in normal
* conditions it is a distributed map
*
- * \param pos position where the laplacian is calculated
+ * \param g_map map grid
+ * \param kmap position in the grid
+ * \param spacing of the grid
* \param gs Grid info
* \param cols non-zero colums calculated by the function
* \param coeff coefficent (constant in front of the derivative)
@@ -36,19 +38,11 @@ class Lap
* \snippet FDScheme_unit_tests.hpp Laplacian usage
*
*/
- inline static void value(const typename stub_or_real<Sys_eqs,Sys_eqs::dims,typename Sys_eqs::stype,typename Sys_eqs::b_grid::decomposition::extended_type>::type & g_map, grid_dist_key_dx<Sys_eqs::dims> & kmap , const grid_sm<Sys_eqs::dims,void> & gs, std::unordered_map<long int,typename Sys_eqs::stype > & cols, typename Sys_eqs::stype coeff)
- {
- std::cerr << "Error " << __FILE__ << ":" << __LINE__ << " only CENTRAL, FORWARD, BACKWARD derivative are defined";
- }
-
- /*! \brief Calculate the position where the derivative is calculated
- *
- * \param position where we are calculating the derivative
- * \param gs Grid info
- * \param s_pos staggered position of the properties
- *
- */
- inline static grid_key_dx<Sys_eqs::dims> position(grid_key_dx<Sys_eqs::dims> & pos, const grid_sm<Sys_eqs::dims,void> & gs)
+ inline static void value(const typename stub_or_real<Sys_eqs,Sys_eqs::dims,typename Sys_eqs::stype,typename Sys_eqs::b_grid::decomposition::extended_type>::type & g_map,
+ grid_dist_key_dx<Sys_eqs::dims> & kmap ,
+ const grid_sm<Sys_eqs::dims,void> & gs,
+ std::unordered_map<long int,typename Sys_eqs::stype > & cols,
+ typename Sys_eqs::stype coeff)
{
std::cerr << "Error " << __FILE__ << ":" << __LINE__ << " only CENTRAL, FORWARD, BACKWARD derivative are defined";
}
@@ -81,7 +75,9 @@ public:
* stub_or_real it is just for change the argument type when testing, in normal
* conditions it is a distributed map
*
- * \param pos position where the laplacian is calculated
+ * \param g_map map grid
+ * \param kmap position in the grid
+ * \param spacing of the grid
* \param gs Grid info
* \param cols non-zero colums calculated by the function
* \param coeff coefficent (constant in front of the derivative)
@@ -91,7 +87,12 @@ public:
* \snippet FDScheme_unit_tests.hpp Laplacian usage
*
*/
- inline static void value(const typename stub_or_real<Sys_eqs,Sys_eqs::dims,typename Sys_eqs::stype,typename Sys_eqs::b_grid::decomposition::extended_type>::type & g_map, grid_dist_key_dx<Sys_eqs::dims> & kmap , const grid_sm<Sys_eqs::dims,void> & gs, typename Sys_eqs::stype (& spacing )[Sys_eqs::dims] , std::unordered_map<long int,typename Sys_eqs::stype > & cols, typename Sys_eqs::stype coeff)
+ inline static void value(const typename stub_or_real<Sys_eqs,Sys_eqs::dims,typename Sys_eqs::stype,typename Sys_eqs::b_grid::decomposition::extended_type>::type & g_map,
+ grid_dist_key_dx<Sys_eqs::dims> & kmap ,
+ const grid_sm<Sys_eqs::dims,void> & gs,
+ typename Sys_eqs::stype (& spacing )[Sys_eqs::dims] ,
+ std::unordered_map<long int,typename Sys_eqs::stype > & cols,
+ typename Sys_eqs::stype coeff)
{
// for each dimension
for (size_t i = 0 ; i < Sys_eqs::dims ; i++)
@@ -109,22 +110,6 @@ public:
arg::value(g_map,kmap,gs,spacing,cols, - 2.0 * coeff/spacing[i]/spacing[i]);
}
}
-
-
- /*! \brief Calculate the position where the derivative is calculated
- *
- * In case of non staggered case this function just return a null grid_key, in case of staggered,
- * the CENTRAL Laplacian scheme return the position of the staggered property
- *
- * \param position where we are calculating the derivative
- * \param gs Grid info
- * \param s_pos staggered position of the properties
- *
- */
- inline static grid_key_dx<Sys_eqs::dims> position(grid_key_dx<Sys_eqs::dims> & pos, const grid_sm<Sys_eqs::dims,void> & gs, const comb<Sys_eqs::dims> (& s_pos)[Sys_eqs::nvar])
- {
- return arg::position(pos,gs,s_pos);
- }
};
@@ -155,7 +140,9 @@ public:
* stub_or_real it is just for change the argument type when testing, in normal
* conditions it is a distributed map
*
- * \param pos position where the laplacian is calculated
+ * \param g_map map grid
+ * \param kmap position in the grid
+ * \param spacing of the grid
* \param gs Grid info
* \param cols non-zero colums calculated by the function
* \param coeff coefficent (constant in front of the derivative)
@@ -183,22 +170,6 @@ public:
arg::value(g_map,kmap,gs,spacing,cols, - 2.0 * coeff/spacing[i]/spacing[i]/4.0);
}
}
-
-
- /*! \brief Calculate the position where the derivative is calculated
- *
- * In case of non staggered case this function just return a null grid_key, in case of staggered,
- * the CENTRAL Laplacian scheme return the position of the staggered property
- *
- * \param position where we are calculating the derivative
- * \param gs Grid info
- * \param s_pos staggered position of the properties
- *
- */
- inline static grid_key_dx<Sys_eqs::dims> position(grid_key_dx<Sys_eqs::dims> & pos, const grid_sm<Sys_eqs::dims,void> & gs, const comb<Sys_eqs::dims> (& s_pos)[Sys_eqs::nvar])
- {
- return arg::position(pos,gs,s_pos);
- }
};
#endif /* OPENFPM_NUMERICS_SRC_FINITEDIFFERENCE_LAPLACIAN_HPP_ */
diff --git a/src/Vector/Vector.hpp b/src/Vector/Vector.hpp
index 24ef44f..66c5eec 100644
--- a/src/Vector/Vector.hpp
+++ b/src/Vector/Vector.hpp
@@ -32,32 +32,148 @@ class rval
#define DEFAULT_VECTOR = 0
#endif
-/* ! \brief Sparse Matrix implementation stub object when OpenFPM is compiled with no linear algebra support
+/*! \brief Sparse Matrix implementation stub object when OpenFPM is compiled with no linear algebra support
*
*/
template<typename T,unsigned int impl DEFAULT_VECTOR >
class Vector
{
+ //! stub
T stub;
+
+ //! stub
int stub_i;
public:
- Vector(const Vector<T> & v) {std::cerr << __FILE__ << ":" << __LINE__ << " Error in order to use this class you must compile OpenFPM with linear algebra support" << std::endl;}
- Vector(Vector<T> && v) {std::cerr << __FILE__ << ":" << __LINE__ << " Error in order to use this class you must compile OpenFPM with linear algebra support" << std::endl;}
- Vector(size_t n) {std::cerr << __FILE__ << ":" << __LINE__ << " Error in order to use this class you must compile OpenFPM with linear algebra support" << std::endl;}
- Vector() {std::cerr << __FILE__ << ":" << __LINE__ << " Error in order to use this class you must compile OpenFPM with linear algebra support" << std::endl;}
- Vector(size_t n, size_t n_row_local) {std::cerr << __FILE__ << ":" << __LINE__ << " Error in order to use this class you must compile OpenFPM with linear algebra support" << std::endl;}
+ /*! \brief stub copy constructor
+ *
+ * \param v stub
+ *
+ */
+ Vector(const Vector<T> & v)
+ :stub(0),stub_i(0)
+ {std::cerr << __FILE__ << ":" << __LINE__ << " Error in order to use this class you must compile OpenFPM with linear algebra support" << std::endl;}
+
+ /*! \brief stub copy constructor
+ *
+ * \param v vector to copy
+ *
+ */
+ Vector(Vector<T> && v)
+ :stub(0),stub_i(0)
+ {std::cerr << __FILE__ << ":" << __LINE__ << " Error in order to use this class you must compile OpenFPM with linear algebra support" << std::endl;}
+
+ /*! \brief stub constructor from number of rows
+ *
+ * \param n stub
+ *
+ */
+ Vector(size_t n)
+ :stub(0),stub_i(0)
+ {std::cerr << __FILE__ << ":" << __LINE__ << " Error in order to use this class you must compile OpenFPM with linear algebra support" << std::endl;}
+
+ //! stub default constructor
+ Vector()
+ :stub(0),stub_i(0)
+ {std::cerr << __FILE__ << ":" << __LINE__ << " Error in order to use this class you must compile OpenFPM with linear algebra support" << std::endl;}
+
+ /*! \brief stub constructor
+ *
+ * \param n global number of row
+ * \param n_row_local local number of rows
+ *
+ */
+ Vector(size_t n, size_t n_row_local)
+ :stub(0),stub_i(0)
+ {std::cerr << __FILE__ << ":" << __LINE__ << " Error in order to use this class you must compile OpenFPM with linear algebra support" << std::endl;}
+
+ /*! \brief stub resize
+ *
+ * \param row stub
+ * \param row_n stub
+ *
+ */
void resize(size_t row, size_t row_n) {std::cerr << __FILE__ << ":" << __LINE__ << " Error in order to use this class you must compile OpenFPM with linear algebra support" << std::endl;}
+
+ /*! \brief stub insert
+ *
+ * \param i stub
+ * \param val stub
+ *
+ */
void insert(size_t i, T val) {std::cerr << __FILE__ << ":" << __LINE__ << " Error in order to use this class you must compile OpenFPM with linear algebra support" << std::endl;}
+
+ /*! \brief stub insert
+ *
+ * \param i stub
+ *
+ * \return stub
+ *
+ */
inline T & insert(size_t i) {std::cerr << __FILE__ << ":" << __LINE__ << " Error in order to use this class you must compile OpenFPM with linear algebra support" << std::endl;return stub;}
+
+ /*! \brief stub insert
+ *
+ * \param i stub
+ *
+ */
inline const T & insert(size_t i) const {std::cerr << __FILE__ << ":" << __LINE__ << " Error in order to use this class you must compile OpenFPM with linear algebra support" << std::endl; return stub;}
+
+ /*! \brief stub
+ *
+ * \param i stub
+ *
+ * \return stub
+ *
+ */
const T & operator()(size_t i) const {std::cerr << __FILE__ << ":" << __LINE__ << " Error in order to use this class you must compile OpenFPM with linear algebra support" << std::endl;return stub;}
+
+ /*! \brief stub
+ *
+ * \param i stub
+ *
+ * \return stub
+ *
+ */
T & operator()(size_t i) {std::cerr << __FILE__ << ":" << __LINE__ << " Error in order to use this class you must compile OpenFPM with linear algebra support" << std::endl;return stub;}
+
+ /*! \brief scatter
+ *
+ */
void scatter() {std::cerr << __FILE__ << ":" << __LINE__ << " Error in order to use this class you must compile OpenFPM with linear algebra support" << std::endl;}
+
+ /*! \brief fromFile
+ *
+ * \param file stub
+ *
+ */
void fromFile(std::string file) {std::cerr << __FILE__ << ":" << __LINE__ << " Error in order to use this class you must compile OpenFPM with linear algebra support" << std::endl;}
+
+
+ /*! \brief stub operator=
+ *
+ * \param v stub
+ *
+ * \return itself
+ *
+ */
Vector<T> & operator=(const Vector<T> & v) {std::cerr << __FILE__ << ":" << __LINE__ << " Error in order to use this class you must compile OpenFPM with linear algebra support" << std::endl; return *this;}
+
+ /*! \brief stub operator=
+ *
+ * \param v stub
+ *
+ * \return itself
+ *
+ */
Vector<T> & operator=(Vector<T> && v) {std::cerr << __FILE__ << ":" << __LINE__ << " Error in order to use this class you must compile OpenFPM with linear algebra support" << std::endl; return *this;}
+
+ /*! \brief stub getVec
+ *
+ * \return stub
+ *
+ */
int & getVec() {std::cerr << __FILE__ << ":" << __LINE__ << " Error in order to use this class you must compile OpenFPM with linear algebra support" << std::endl; return stub_i;}
};
diff --git a/src/Vector/Vector_petsc.hpp b/src/Vector/Vector_petsc.hpp
index 1f3a2cb..2ea14c7 100644
--- a/src/Vector/Vector_petsc.hpp
+++ b/src/Vector/Vector_petsc.hpp
@@ -168,8 +168,8 @@ public:
/*! \brief Create a vector with n elements
*
- * \param n number of elements in the vector
- * \param n_row_loc number
+ * \param n global number of elements in the vector
+ * \param n_row_local number
*
*/
Vector(size_t n, size_t n_row_local)
--
GitLab