diff --git a/CHANGELOG.md b/CHANGELOG.md
index fa176d72caa6e413dfae2d4b3d235b46d689bf4d..c8ca27d71ea95a3649d1ca76b85fccd1d413ab33 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,15 @@
# Change Log
All notable changes to this project will be documented in this file.
+## [0.9.0]
+
+### Added
+- Introduced getDomainIterator for Cell-list
+
+### Fixed
+- Installation of PETSC in case with MUMPS try without MUMPS
+- In case of miss compilation ignore system wide installation
+
## [0.8.0] 28 February 2016
### Added
diff --git a/openfpm_data b/openfpm_data
index 1152e735515f48cd9d6734f2d1a7b6d6dd0a4b91..dde50897665d36fc2723aabb0917291c9573c065 160000
--- a/openfpm_data
+++ b/openfpm_data
@@ -1 +1 @@
-Subproject commit 1152e735515f48cd9d6734f2d1a7b6d6dd0a4b91
+Subproject commit dde50897665d36fc2723aabb0917291c9573c065
diff --git a/src/Decomposition/CartDecomposition.hpp b/src/Decomposition/CartDecomposition.hpp
index cf3c91a1b194fc0115bbd9baa2ef267889e4bb0a..2ea88a1234e956a855dc043891e384de3e2d2e3f 100755
--- a/src/Decomposition/CartDecomposition.hpp
+++ b/src/Decomposition/CartDecomposition.hpp
@@ -1288,7 +1288,22 @@ public:
return domain_nn_calculator_cart<dim>::getDomainCells(shift,cell_shift,gs,proc_box,loc_box);
}
- /*! \brief Get the anomalous cells
+ /*! \brief Get the CRS domain Cells
+ *
+ * It perform a linearization of the domain cells using the extension provided in gs
+ *
+ *
+ * \param shift Cell padding
+ * \param cell_shift where the domain cell start
+ * \param gs grid extension
+ *
+ */
+ openfpm::vector<size_t> & getCRSDomainCells(grid_key_dx<dim> & shift, grid_key_dx<dim> & cell_shift, grid_sm<dim,void> & gs)
+ {
+ return domain_nn_calculator_cart<dim>::getCRSDomainCells(shift,cell_shift,gs,proc_box,loc_box);
+ }
+
+ /*! \brief Get the CRS anomalous cells
*
* This function include also a linearization of the indexes
*
@@ -1301,9 +1316,9 @@ public:
* \return the anomalous cells with neighborhood
*
*/
- openfpm::vector<subsub_lin<dim>> & getAnomDomainCells(grid_key_dx<dim> & shift, grid_key_dx<dim> & cell_shift, grid_sm<dim,void> & gs)
+ openfpm::vector<subsub_lin<dim>> & getCRSAnomDomainCells(grid_key_dx<dim> & shift, grid_key_dx<dim> & cell_shift, grid_sm<dim,void> & gs)
{
- return domain_nn_calculator_cart<dim>::getAnomDomainCells(shift,cell_shift,gs,proc_box,loc_box);
+ return domain_nn_calculator_cart<dim>::getCRSAnomDomainCells(shift,cell_shift,gs,proc_box,loc_box);
}
/*! \brief Check if the particle is local considering boundary conditions
diff --git a/src/Decomposition/Distribution/SpaceDistribution.hpp b/src/Decomposition/Distribution/SpaceDistribution.hpp
index c7b2d9ac1197c1bf963a257bc32fd00897a0ffe4..346008d5acb726620f0e1ee5a3d827f7b064a39e 100644
--- a/src/Decomposition/Distribution/SpaceDistribution.hpp
+++ b/src/Decomposition/Distribution/SpaceDistribution.hpp
@@ -371,6 +371,18 @@ public:
return *this;
}
+
+ /*! \brief It return the decomposition id
+ *
+ * It just return 0
+ *
+ * \return 0
+ *
+ */
+ size_t get_ndec()
+ {
+ return 0;
+ }
};
diff --git a/src/Decomposition/Domain_NN_calculator_cart.hpp b/src/Decomposition/Domain_NN_calculator_cart.hpp
index b4571fad5afe836c81673677b96ef18be3d6b8e2..e0889bc25ffe0f236c6d81530ca51ed6334db061 100644
--- a/src/Decomposition/Domain_NN_calculator_cart.hpp
+++ b/src/Decomposition/Domain_NN_calculator_cart.hpp
@@ -20,18 +20,24 @@ class domain_nn_calculator_cart
//! True if domain and anomalous domain cells are computed
bool are_domain_anom_computed;
- //! Are linearized the domain cell
+ //! Are linearized the domain cells
+ bool are_dom_cells_lin;
+
+ //! Are linearized the CRS domain cell
bool are_dom_lin;
- //! are linearized the anomalous cells
+ //! are linearized the CRS anomalous cells
bool are_anom_lin;
- //! anomalous cell neighborhood
+ //! anomalous cell neighborhood for CRS
openfpm::vector<subsub<dim>> anom;
- //! Set of normal domain cells
+ //! Set of normal domain cells for CRS
openfpm::vector<grid_key_dx<dim>> dom;
+ //! Set of domain cells
+ openfpm::vector<grid_key_dx<dim>> dom_cells;
+
//! Linearization is calculated out of a shift and grid dimension this is the shift
grid_key_dx<dim> shift_calc_dom;
@@ -45,12 +51,15 @@ class domain_nn_calculator_cart
grid_sm<dim,void> gs_calc_anom;
- //! Set of normal domain cells linearized
+ //! Set of normal CRS domain cells linearized
openfpm::vector<size_t> dom_lin;
- //! Set of normal domain cells linearized
+ //! Set of anomalous CRS domain cells linearized
openfpm::vector<subsub_lin<dim>> anom_lin;
+ //! Set of linearized domain cells
+ openfpm::vector<size_t> dom_cells_lin;
+
//! Processor box
Box<dim,long int> proc_box;
@@ -103,6 +112,7 @@ class domain_nn_calculator_cart
*/
void CalculateDomAndAnomCells(openfpm::vector<subsub<dim>> & sub_keys,
openfpm::vector<grid_key_dx<dim>> & dom_subsub,
+ openfpm::vector<grid_key_dx<dim>> & dom_cells,
const ::Box<dim,long int> & proc_box,
grid_key_dx<dim> & shift,
const openfpm::vector<::Box<dim, size_t>> & loc_box)
@@ -149,6 +159,8 @@ class domain_nn_calculator_cart
g.template get<0>(src).add(dst + shift);
}
+ dom_cells.add(key + shift);
+
++sub;
}
}
@@ -183,7 +195,7 @@ class domain_nn_calculator_cart
public:
domain_nn_calculator_cart()
- :are_domain_anom_computed(false),are_dom_lin(false),are_anom_lin(false)
+ :are_domain_anom_computed(false),are_dom_cells_lin(false),are_dom_lin(false),are_anom_lin(false)
{}
/*! \brief Get the domain Cells
@@ -200,7 +212,39 @@ public:
{
if (are_domain_anom_computed == false)
{
- CalculateDomAndAnomCells(anom,dom,proc_box,shift,loc_box);
+ CalculateDomAndAnomCells(anom,dom,dom_cells,proc_box,shift,loc_box);
+ are_domain_anom_computed = true;
+ }
+
+ if (are_dom_cells_lin == false)
+ {
+ dom_cells_lin.clear();
+ shift_calc_dom = shift;
+ gs_calc_dom = gs;
+ for (size_t i = 0 ; i < dom_cells.size() ; i++)
+ dom_cells_lin.add(gs.LinId(dom_cells.get(i) - cell_shift));
+
+ are_dom_cells_lin = true;
+ }
+
+ return dom_cells_lin;
+ }
+
+ /*! \brief Get the domain Cells
+ *
+ * \param shift Shifting point
+ * \param gs grid extension
+ * \param proc_box processor bounding box
+ * \param loc_box set of local sub-domains
+ *
+ * \return The set of domain cells
+ *
+ */
+ openfpm::vector<size_t> & getCRSDomainCells(grid_key_dx<dim> & shift, grid_key_dx<dim> & cell_shift, grid_sm<dim,void> & gs, Box<dim,size_t> & proc_box, openfpm::vector<::Box<dim, size_t>> & loc_box)
+ {
+ if (are_domain_anom_computed == false)
+ {
+ CalculateDomAndAnomCells(anom,dom,dom_cells,proc_box,shift,loc_box);
are_domain_anom_computed = true;
}
@@ -228,12 +272,12 @@ public:
* \return The set of anomalous cells
*
*/
- openfpm::vector<subsub_lin<dim>> & getAnomDomainCells(grid_key_dx<dim> & shift, grid_key_dx<dim> & cell_shift, grid_sm<dim,void> & gs, Box<dim,size_t> & proc_box, openfpm::vector<::Box<dim, size_t>> & loc_box)
+ openfpm::vector<subsub_lin<dim>> & getCRSAnomDomainCells(grid_key_dx<dim> & shift, grid_key_dx<dim> & cell_shift, grid_sm<dim,void> & gs, Box<dim,size_t> & proc_box, openfpm::vector<::Box<dim, size_t>> & loc_box)
{
// if the neighborhood of each sub-sub-domains has not been calculated, calculate it
if (are_domain_anom_computed == false)
{
- CalculateDomAndAnomCells(anom,dom,proc_box,shift,loc_box);
+ CalculateDomAndAnomCells(anom,dom,dom_cells,proc_box,shift,loc_box);
are_domain_anom_computed = true;
}
diff --git a/src/Vector/vector_dist.hpp b/src/Vector/vector_dist.hpp
index 4ddfc2cac16206b04ec639f68a6a656c3ddd079a..8a715c74c2988d8a8bb6825947604ecebf78ffa4 100644
--- a/src/Vector/vector_dist.hpp
+++ b/src/Vector/vector_dist.hpp
@@ -938,7 +938,9 @@ public:
grid_sm<dim,void> gs = NN.getInternalGrid();
- ver.createVerletCrs(r_cut,g_m,v_pos,getDecomposition().getDomainCells(shift,cell_shift,gs),getDecomposition().getAnomDomainCells(shift,cell_shift,gs));
+ ver.createVerletCrs(r_cut,g_m,v_pos,
+ getDecomposition().getCRSDomainCells(shift,cell_shift,gs),
+ getDecomposition().getCRSAnomDomainCells(shift,cell_shift,gs));
ver.set_ndec(getDecomposition().get_ndec());
@@ -1031,7 +1033,9 @@ public:
grid_sm<dim,void> gs = NN.getInternalGrid();
- ver.updateCrs(getDecomposition().getDomain(),r_cut,v_pos,g_m,getDecomposition().getDomainCells(shift,cell_shift,gs),getDecomposition().getAnomDomainCells(shift,cell_shift,gs));
+ ver.updateCrs(getDecomposition().getDomain(),r_cut,v_pos,g_m,
+ getDecomposition().getCRSDomainCells(shift,cell_shift,gs),
+ getDecomposition().getCRSAnomDomainCells(shift,cell_shift,gs));
}
else
{
@@ -1061,60 +1065,6 @@ public:
}
}
-#if 0
-
-/* void getVerletDeprecated(openfpm::vector<openfpm::vector<size_t>> & verlet, St r_cut)
- {
- // resize verlet to store the number of particles
- verlet.resize(size_local());
-
- // get the cell-list
- auto cl = getCellList(r_cut);
-
- // square of the cutting radius
- St r_cut2 = r_cut * r_cut;
-
- // iterate the particles
- auto it_p = this->getDomainIterator();
- while (it_p.isNext())
- {
- // key
- vect_dist_key_dx key = it_p.get();
-
- // Get the position of the particles
- Point<dim, St> p = this->getPos(key);
-
- // Clear the neighborhood of the particle
- verlet.get(key.getKey()).clear();
-
- // Get the neighborhood of the particle
- auto NN = cl.template getNNIterator<NO_CHECK>(cl.getCell(p));
- while (NN.isNext())
- {
- auto nnp = NN.get();
-
- // p != q
- if (nnp == key.getKey())
- {
- ++NN;
- continue;
- }
-
- Point<dim, St> q = this->getPos(nnp);
-
- if (p.distance2(q) < r_cut2)
- verlet.get(key.getKey()).add(nnp);
-
- // Next particle
- ++NN;
- }
-
- // next particle
- ++it_p;
- }
- }*/
-
-#endif
/*! \brief Construct a cell list starting from the stored particles and reorder a vector according to the Hilberts curve
*
@@ -1322,6 +1272,32 @@ public:
return vector_dist_iterator(g_m, v_pos.size());
}
+ /*! \brief Get an iterator that traverse the particles in the domain
+ *
+ * \return an iterator
+ *
+ */
+ template<typename CellList> ParticleIt_Cells<dim,CellList> getDomainIteratorCells(CellList & NN)
+ {
+#ifdef SE_CLASS3
+ se3.getIterator();
+#endif
+
+ // Shift
+ grid_key_dx<dim> cell_shift = NN.getShift();
+
+ // Shift
+ grid_key_dx<dim> shift = NN.getShift();
+
+ // Add padding
+ for (size_t i = 0 ; i < dim ; i++)
+ shift.set_d(i,shift.get(i) + NN.getPadding(i));
+
+ grid_sm<dim,void> gs = NN.getInternalGrid();
+
+ return ParticleIt_Cells<dim,CellList>(NN,getDecomposition().getDomainCells(shift,cell_shift,gs));
+ }
+
/*! \brief Get an iterator that traverse the particles in the domain
*
* \return an iterator
@@ -1768,7 +1744,9 @@ public:
grid_sm<dim,void> gs = NN.getInternalGrid();
// First we check that
- return ParticleItCRS_Cells<dim,cli>(NN,getDecomposition().getDomainCells(shift,cell_shift,gs),getDecomposition().getAnomDomainCells(shift,cell_shift,gs),NN.getNNc_sym());
+ return ParticleItCRS_Cells<dim,cli>(NN,getDecomposition().getCRSDomainCells(shift,cell_shift,gs),
+ getDecomposition().getCRSAnomDomainCells(shift,cell_shift,gs),
+ NN.getNNc_sym());
}
/*! \brief Return from which cell we have to start in case of CRS interation
diff --git a/src/Vector/vector_dist_NN_tests.hpp b/src/Vector/vector_dist_NN_tests.hpp
index a750bc95b6bfc5e915ef7e9f46268a9a8b96b5d0..c893c741e2dba2bf097e70dce8fd722cb232dae9 100644
--- a/src/Vector/vector_dist_NN_tests.hpp
+++ b/src/Vector/vector_dist_NN_tests.hpp
@@ -217,5 +217,90 @@ BOOST_AUTO_TEST_CASE( vector_dist_full_NN )
}
}
+BOOST_AUTO_TEST_CASE( vector_dist_particle_iteration )
+{
+ Vcluster & v_cl = create_vcluster();
+
+ if (v_cl.getProcessingUnits() > 12)
+ return;
+
+ // set the seed
+ // create the random generator engine
+ std::srand(v_cl.getProcessUnitID());
+ std::default_random_engine eg;
+ std::uniform_real_distribution<float> ud(0.0f, 1.0f);
+
+ long int k = 750 * v_cl.getProcessingUnits();
+
+ print_test("Testing 3D particle cell iterator=",k);
+ BOOST_TEST_CHECKPOINT( "Testing 3D full NN search k=" << k );
+
+ Box<3,float> box({0.0,0.0,0.0},{1.0,1.0,1.0});
+
+ // Boundary conditions
+ size_t bc[3]={PERIODIC,PERIODIC,PERIODIC};
+
+ float r_cut = 0.01;
+
+ // ghost
+ Ghost<3,float> ghost(r_cut);
+
+ typedef aggregate<float> part_prop;
+
+ // Distributed vector
+ vector_dist<3,float, part_prop > vd(k,box,bc,ghost,BIND_DEC_TO_GHOST);
+
+ auto it = vd.getIterator();
+
+ while (it.isNext())
+ {
+ auto key = it.get();
+
+ vd.getPos(key)[0] = ud(eg);
+ vd.getPos(key)[1] = ud(eg);
+ vd.getPos(key)[2] = ud(eg);
+
+ // Fill some properties randomly
+
+ vd.getProp<0>(key) = 0.0;
+
+ ++it;
+ }
+
+ vd.map();
+
+ // sync the ghost
+ vd.ghost_get<0>();
+
+ openfpm::vector<size_t> ids;
+ ids.resize(vd.size_local());
+
+ auto NN = vd.getCellListSym(r_cut);
+
+ auto it_pcell = vd.getDomainIteratorCells(NN);
+
+ size_t count = 0;
+ while (it_pcell.isNext())
+ {
+ count++;
+
+ size_t id = it_pcell.get();
+ ids.get(id) = 1;
+
+ BOOST_REQUIRE(id < vd.size_local());
+
+ ++it_pcell;
+ }
+
+ v_cl.sum(count);
+ v_cl.execute();
+
+ for (size_t i = 0 ; i < ids.size() ; i++)
+ {
+ std::cout << "OUTPUT: " << i << " " << ids.get(i) << create_vcluster().getProcessUnitID() << std::endl;
+ }
+
+ BOOST_REQUIRE_EQUAL((long int)count,k);
+}
#endif /* SRC_VECTOR_VECTOR_DIST_NN_TESTS_HPP_ */