diff --git a/src/.deps/pdata-main.Po b/src/.deps/pdata-main.Po
index d2d126eb73dafc8573cf7700a17b3f27478b5b1d..1b92993c4fbb077028c03a2b06eb4db71ed44a34 100644
--- a/src/.deps/pdata-main.Po
+++ b/src/.deps/pdata-main.Po
@@ -1293,8 +1293,12 @@ pdata-main.o: main.cpp /usr/include/stdc-predef.h \
../../OpenFPM_data/src/Space/SpaceBox.hpp \
../../OpenFPM_data/src/Space/Shape/Point.hpp \
../../OpenFPM_data/src/Space/Shape/Box.hpp \
- ../../OpenFPM_data/src/Space/Ghost.hpp Grid/grid_dist_id_iterator.hpp \
- Grid/grid_dist_key.hpp ../../OpenFPM_data/src/Point_test.hpp \
+ ../../OpenFPM_data/src/Space/Ghost.hpp \
+ ../../OpenFPM_data/src/Space/SpaceBox.hpp Grid/grid_dist_id_iterator.hpp \
+ Grid/grid_dist_key.hpp \
+ ../../OpenFPM_data/src/NN/CellList/CellDecomposer.hpp \
+ ../../OpenFPM_data/src/Space/Matrix.hpp \
+ ../../OpenFPM_data/src/Point_test.hpp \
../../OpenFPM_data/src/base_type.hpp \
../../OpenFPM_data/src/Point_orig.hpp \
../../OpenFPM_data/src/Grid/Encap.hpp \
@@ -1367,8 +1371,6 @@ pdata-main.o: main.cpp /usr/include/stdc-predef.h \
/usr/include/boost/iostreams/detail/path.hpp \
/usr/include/boost/config/abi_prefix.hpp \
/usr/include/boost/config/abi_suffix.hpp dec_optimizer.hpp \
- ../../OpenFPM_data/src/NN/CellList/CellDecomposer.hpp \
- ../../OpenFPM_data/src/Space/Matrix.hpp \
/usr/include/c++/4.8.3/unordered_map \
/usr/include/c++/4.8.3/bits/hashtable.h \
/usr/include/c++/4.8.3/bits/hashtable_policy.h \
@@ -4254,10 +4256,16 @@ Grid/grid_dist_id.hpp:
../../OpenFPM_data/src/Space/Ghost.hpp:
+../../OpenFPM_data/src/Space/SpaceBox.hpp:
+
Grid/grid_dist_id_iterator.hpp:
Grid/grid_dist_key.hpp:
+../../OpenFPM_data/src/NN/CellList/CellDecomposer.hpp:
+
+../../OpenFPM_data/src/Space/Matrix.hpp:
+
../../OpenFPM_data/src/Point_test.hpp:
../../OpenFPM_data/src/base_type.hpp:
@@ -4414,10 +4422,6 @@ metis_util.hpp:
dec_optimizer.hpp:
-../../OpenFPM_data/src/NN/CellList/CellDecomposer.hpp:
-
-../../OpenFPM_data/src/Space/Matrix.hpp:
-
/usr/include/c++/4.8.3/unordered_map:
/usr/include/c++/4.8.3/bits/hashtable.h:
diff --git a/src/Decomposition/CartDecomposition.hpp b/src/Decomposition/CartDecomposition.hpp
index 1ff5b8951af2126f8ddcfced9e5db0197ba720fe..38cb2b1b5008edebc8103583c3ca5526bbcb597d 100644
--- a/src/Decomposition/CartDecomposition.hpp
+++ b/src/Decomposition/CartDecomposition.hpp
@@ -687,7 +687,7 @@ p1[0]<-----+ +----> p2[0]
{
if (ghost.template getLow(i) >= domain.template getHigh(i) / gr.size(i) || ghost.template getHigh(i) >= domain.template getHigh(i) / gr.size(i))
{
- std::cerr << "Error: Ghost are bigger that one domain" << "\n";
+ std::cerr << "Error " << __FILE__ << ":" << __LINE__ << " : Ghost are bigger than one domain" << "\n";
}
}
#endif
@@ -1186,6 +1186,7 @@ p1[0]<-----+ +----> p2[0]
* 1) p_sub_X.vtk domain for the processor X as union of sub-domain
* 2) sub_np_c_X.vtk sub-domain of the near processors contiguous to the processor X (Color encoded)
* 3) sub_X_inte_g_np.vtk Intersection between the ghosts of the near processors and the processors X sub-domains (Color encoded)
+ * 4) sub_X_ghost.vtk ghost for the processor X (Color encoded)
*
* where X is the processor number
*
@@ -1216,11 +1217,22 @@ p1[0]<-----+ +----> p2[0]
{
for (size_t s = 0 ; s < box_nn_processor_int.get(p).size() ; s++)
{
- auto & diocane = box_nn_processor_int.get(p).get(s).nbx;
- vtk_box3.add(diocane);
+ vtk_box3.add(box_nn_processor_int.get(p).get(s).nbx);
}
}
vtk_box3.write(std::string("sub_") + std::to_string(v_cl.getProcessUnitID()) + std::string("_inte_g_np") + std::string(".vtk"));
+
+
+ //! sub_X_ghost.vtk ghost for the processor X (Color encoded)
+ VTKWriter<openfpm::vector<::Box<dim,T>>,VECTOR_BOX> vtk_box4;
+ for (size_t p = 0 ; p < box_nn_processor_int.size() ; p++)
+ {
+ for (size_t s = 0 ; s < box_nn_processor_int.get(p).size() ; s++)
+ {
+ vtk_box4.add(box_nn_processor_int.get(p).get(s).bx);
+ }
+ }
+ vtk_box4.write(std::string("sub_") + std::to_string(v_cl.getProcessUnitID()) + std::string("_ghost") + std::string(".vtk"));
}
};
diff --git a/src/Grid/grid_dist_id.hpp b/src/Grid/grid_dist_id.hpp
index 5a786ab0e2d07e635c4239683385ebbb9621d235..ec62a10ca377eba1c97e0c35e64adb4a214ea0d1 100644
--- a/src/Grid/grid_dist_id.hpp
+++ b/src/Grid/grid_dist_id.hpp
@@ -8,36 +8,35 @@
#include "mathutil.hpp"
#include "grid_dist_id_iterator.hpp"
#include "grid_dist_key.hpp"
+#include "NN/CellList/CellDecomposer.hpp"
#define SUB_UNIT_FACTOR 64
/*! \brief This is a distributed grid
*
- * Implementation of a distributed grid with id decomposition. A distributed grid is a grid distributed
- * across processors. The decomposition is performed on the id of the elements
- *
- * [Examples]
+ * Implementation of a distributed grid with decomposition on the ids.
+ * A distributed grid is a grid distributed across processors.
+ * The decomposition is performed on the ids of the elements
*
- * on 1D where the id is from 1 to N
- * processor k take M contiguous elements
- *
- * on 3D where (for example)
- * processor k take M id-connected elements
*
* \param dim Dimensionality of the grid
- * \param T type of grid
+ * \param St Type of space where the grid is living
+ * \param T object the grid is storing
* \param Decomposition Class that decompose the grid for example CartDecomposition
* \param Mem Is the allocator
* \param device type of base structure is going to store the data
*
*/
-template<unsigned int dim, typename T, typename Decomposition,typename Memory=HeapMemory , typename device_grid=grid_cpu<dim,T> >
+template<unsigned int dim, typename St, typename T, typename Decomposition,typename Memory=HeapMemory , typename device_grid=grid_cpu<dim,T> >
class grid_dist_id
{
+ // Domain
+ Box<dim,St> domain;
+
// Ghost expansion
- Box<dim,size_t> ghost;
+ Ghost<dim,St> ghost;
//! Local grids
Vcluster_object_array<device_grid> loc_grid;
@@ -48,8 +47,10 @@ class grid_dist_id
//! Size of the grid on each dimension
size_t g_sz[dim];
- //! Communicator class
+ //! Structure that divide the space into cells
+ CellDecomposer_sm<dim,St> cd_sm;
+ //! Communicator class
Vcluster & v_cl;
/*! \brief Get the grid size
@@ -99,8 +100,8 @@ class grid_dist_id
public:
//! constructor
- grid_dist_id(Vcluster v_cl, Decomposition & dec, size_t (& g_sz)[dim], Box<dim,size_t> & ghost)
- :ghost(ghost),loc_grid(NULL),v_cl(v_cl),dec(dec)
+ grid_dist_id(Vcluster v_cl, Decomposition & dec, const size_t (& g_sz)[dim], const Box<dim,St> & domain, const Ghost<dim,T> & ghost)
+ :domain(domain),cd_sm(domain,g_sz,0),ghost(ghost),loc_grid(NULL),v_cl(v_cl),dec(dec)
{
// fill the global size of the grid
for (int i = 0 ; i < dim ; i++) {this->g_sz[i] = g_sz[i];}
@@ -123,9 +124,14 @@ public:
Create();
}
- //! constructor
- grid_dist_id(size_t (& g_sz)[dim])
- :dec(Decomposition(*global_v_cluster)),v_cl(*global_v_cluster)
+ /*! \brief Constrcuctor
+ *
+ * \param g_sz array with the grid size on each dimension
+ * \param domain
+ *
+ */
+ grid_dist_id(const size_t (& g_sz)[dim],const Box<dim,St> & domain)
+ :domain(domain),cd_sm(domain,g_sz,0),ghost(0),dec(Decomposition(*global_v_cluster)),v_cl(*global_v_cluster)
{
// fill the global size of the grid
for (int i = 0 ; i < dim ; i++) {this->g_sz[i] = g_sz[i];}
@@ -141,11 +147,8 @@ public:
for (int i = 0 ; i < dim ; i++)
{div[i] = openfpm::math::round_big_2(pow(n_sub,1.0/dim));}
- // Box
- Box<dim,size_t> b(g_sz);
-
// Create the sub-domains
- dec.setParameters(div,b);
+ dec.setParameters(div,domain);
// Create local grid
Create();
@@ -168,10 +171,13 @@ public:
void Create()
{
+ // Box used for rounding error
+ Box<dim,St> rnd_box;
+ for (size_t i = 0 ; i < dim ; i++) {rnd_box.setHigh(i,0.5); rnd_box.setLow(i,0.5);}
+
// ! Create an hyper-cube approximation.
// ! In order to work on grid_dist the decomposition
// ! has to be a set of hyper-cube
-
dec.hyperCube();
// Get the number of local grid needed
@@ -188,15 +194,34 @@ public:
for (size_t i = 0 ; i < n_grid ; i++)
{
// Get the local hyper-cube
+ SpaceBox<dim,St> sp = dec.getLocalHyperCube(i);
- SpaceBox<dim,size_t> sp = dec.getLocalHyperCube(i);
+ // Convert sp into grid units
+ sp /= cd_sm.getCellBox().getP2();
- // Calculate the local grid size
+ // enlarge by 0.5 for rounding
+ sp.enlarge(rnd_box);
- getGridSize(sp,l_res);
+ // Convert from SpaceBox<dim,float> to SpaceBox<dim,size_t>
+ SpaceBox<dim,size_t> sp_t = sp;
- // Set the dimensions of the local grid
+ // convert the ghost from space coordinate to grid units
+ Ghost<dim,St> g_int = ghost;
+ g_int /= cd_sm.getCellBox().getP2();
+
+ // enlarge by 0.5 for rounding
+ g_int.enlarge(rnd_box);
+
+ // convert from Ghost<dim,St> to Ghost<dim,size_t>
+ Ghost<dim,size_t> g_int_t = g_int;
+ // Enlarge sp with the Ghost size
+ sp_t.enlarge(g_int_t);
+
+ // Get the local size
+ for (size_t i = 0 ; i < dim ; i++) {l_res[i] = sp_t.getHigh(i) - sp_t.getLow(i);}
+
+ // Set the dimensions of the local grid
loc_grid.get(i).template resize<Memory>(l_res);
}
}
@@ -251,13 +276,7 @@ public:
* Implementation of a distributed grid with id decomposition. A distributed grid is a grid distributed
* across processors. The decomposition is performed on the id of the elements
*
- * [Examples]
- *
- * on 1D where the id is from 1 to N
- * processor k take M contiguous elements
- *
- * on 3D where (for example)
- * processor k take M id-connected elements
+ * 1D specialization
*
* \param dim Dimensionality of the grid
* \param T type of grid
@@ -270,8 +289,8 @@ public:
template<typename T, typename Decomposition,typename Memory , typename device_grid >
class grid_dist_id<1,T,Decomposition,Memory,device_grid>
{
- // Ghost expansion
- Box<1,size_t> ghost;
+ // Ghost
+ Ghost<1,T> ghost;
//! Local grids
Vcluster_object_array<device_grid> loc_grid;
@@ -327,7 +346,7 @@ class grid_dist_id<1,T,Decomposition,Memory,device_grid>
public:
//! constructor
- grid_dist_id(Vcluster v_cl, Decomposition & dec, size_t (& g_sz)[1], Box<1,size_t> & ghost)
+ grid_dist_id(Vcluster v_cl, Decomposition & dec, size_t (& g_sz)[1], Box<1,T> & ghost)
:ghost(ghost),loc_grid(NULL),v_cl(v_cl)
{
// fill the global size of the grid
@@ -339,7 +358,7 @@ public:
//! constructor
grid_dist_id(size_t (& g_sz)[1])
- :v_cl(*global_v_cluster)
+ :v_cl(*global_v_cluster),ghost(0)
{
// fill the global size of the grid
for (int i = 0 ; i < 1 ; i++) {this->g_sz[i] = g_sz[i];}
diff --git a/src/Grid/grid_dist_id_unit_test.hpp b/src/Grid/grid_dist_id_unit_test.hpp
index 7718e1d0b149dee76da8ad76b610be13f2fc6263..25a6f871b560a6d311307321e1c026fbe337b179 100644
--- a/src/Grid/grid_dist_id_unit_test.hpp
+++ b/src/Grid/grid_dist_id_unit_test.hpp
@@ -6,10 +6,10 @@
BOOST_AUTO_TEST_SUITE( grid_dist_id_test )
-template<typename iterator> void jacobi_iteration(iterator g_it, grid_dist_id<2, scalar<float>, CartDecomposition<2,size_t>> & g_dist)
+template<typename iterator> void jacobi_iteration(iterator g_it, grid_dist_id<2, float, scalar<float>, CartDecomposition<2,float>> & g_dist)
{
// scalar
- typedef scalar<size_t> S;
+ typedef scalar<float> S;
// iterator
@@ -30,6 +30,9 @@ template<typename iterator> void jacobi_iteration(iterator g_it, grid_dist_id<2,
BOOST_AUTO_TEST_CASE( grid_dist_id_iterator_test_use)
{
+ // Domain
+ Box<2,float> domain({0.0,0.0},{1.0,1.0});
+
// Initialize the global VCluster
init_global_v_cluster(&boost::unit_test::framework::master_test_suite().argc,&boost::unit_test::framework::master_test_suite().argv);
@@ -38,7 +41,7 @@ BOOST_AUTO_TEST_CASE( grid_dist_id_iterator_test_use)
// Distributed grid with id decomposition
- grid_dist_id<2, scalar<float>, CartDecomposition<2,size_t>> g_dist(sz);
+ grid_dist_id<2, float, scalar<float>, CartDecomposition<2,float>> g_dist(sz,domain);
// get the domain iterator
diff --git a/src/Vector/vector_dist_unit_test.hpp b/src/Vector/vector_dist_unit_test.hpp
index 9276a8a72bdaab5ac376768f1f106895652c73c9..145617e593abb24884cc99cc79cc61c3b744dbe1 100644
--- a/src/Vector/vector_dist_unit_test.hpp
+++ b/src/Vector/vector_dist_unit_test.hpp
@@ -94,9 +94,10 @@ BOOST_AUTO_TEST_CASE( vector_dist_ghost )
++it;
}
- // set the ghost based on the radius cut off
- Ghost<2,float> g(spacing.get(0));
+ // set the ghost based on the radius cut off (make just a little bit smaller than the spacing)
+ Ghost<2,float> g(spacing.get(0) - spacing .get(0) * 0.0001);
+ // set the ghost
vd.setGhost(g);
//! Output the decomposition
@@ -131,20 +132,30 @@ BOOST_AUTO_TEST_CASE( vector_dist_ghost )
bool is_in = false;
size_t b = 0;
+ size_t lb = 0;
// check if the received data is in one of the ghost boxes
for ( ; b < dec.getNGhostBox() ; b++)
{
if (dec.getGhostBox(b).isInside(vd.getPos<s::x>(key)) == true)
- {is_in = true; break;}
+ {
+ is_in = true;
+
+ // Add
+ vb.get(b)++;
+ lb = b;
+ }
}
BOOST_REQUIRE_EQUAL(is_in,true);
// Check that the particle come from the correct processor
- BOOST_REQUIRE_EQUAL(vd.getProp<p::v>(key)[0],dec.getGhostBoxProcessor(b));
+ BOOST_REQUIRE_EQUAL(vd.getProp<p::v>(key)[0],dec.getGhostBoxProcessor(lb));
- // Add
- vb.get(b)++;
+ if (b == 0)
+ {
+ int debug = 0;
+ debug++;
+ }
++g_it;
}