From 25dda0296b3c4620d6dab40c5a6c9d6c989aca67 Mon Sep 17 00:00:00 2001
From: Pietro Incardona <i-bird@private-incardon-3.mpi-cbg.de>
Date: Wed, 13 Jan 2016 07:54:03 -0500
Subject: [PATCH] Actual numerics branch
---
configure.ac | 2 +-
install | 4 +-
src/Decomposition/CartDecomposition.hpp | 10 ++--
.../CartDecomposition_unit_test.hpp | 2 -
src/Decomposition/ie_ghost.hpp | 45 +++++++++++++++++
src/Vector/vector_dist.hpp | 44 ++++++++++++++--
src/Vector/vector_dist_unit_test.hpp | 50 +++++++++++++++++++
7 files changed, 142 insertions(+), 15 deletions(-)
diff --git a/configure.ac b/configure.ac
index 3e1da5c5..1012cfa6 100755
--- a/configure.ac
+++ b/configure.ac
@@ -7,7 +7,7 @@ AC_PREREQ(2.59)
AC_INIT(FULL-PACKAGE-NAME, VERSION, BUG-REPORT-ADDRESS)
AC_CANONICAL_SYSTEM
AC_CONFIG_SRCDIR([src/main.cpp])
-AC_CONFIG_SUBDIRS([openfpm_data openfpm_devices openfpm_vcluster openfpm_io])
+AC_CONFIG_SUBDIRS([openfpm_data openfpm_devices openfpm_vcluster openfpm_io openfpm_numerics])
#### Adding --with-pdata option and openfpm_pdata to prefix folder
diff --git a/install b/install
index c2a82f79..12822e8f 100755
--- a/install
+++ b/install
@@ -210,8 +210,8 @@ fi
### Create example.mk
install_base=$(cat install_dir)
-echo "INCLUDE_PATH=-I. -I$install_base/openfpm_pdata/include/config -I$install_base/openfpm_pdata/include -I$install_base/openfpm_data/include -I$install_base/openfpm_vcluster/include -I$install_base/openfpm_io/include -I$install_base/openfpm_devices/include -I$i_dir/METIS/include -I$i_dir/BOOST/include" > example.mk
-echo "LIBS_PATH=-L$install_base/openfpm_devices/lib -L$install_base/openfpm_vcluster/lib -L$i_dir/METIS/lib -L$i_dir/BOOST/lib " >> example.mk
+echo "INCLUDE_PATH=-I. -I$install_base/openfpm_numerics/include -I$install_base/openfpm_pdata/include/config -I$install_base/openfpm_pdata/include -I$install_base/openfpm_data/include -I$install_base/openfpm_vcluster/include -I$install_base/openfpm_io/include -I$install_base/openfpm_devices/include -I$i_dir/METIS/include -I$i_dir/BOOST/include" > example.mk
+echo "LIBS_PATH= -L$install_base/openfpm_devices/lib -L$install_base/openfpm_vcluster/lib -L$i_dir/METIS/lib -L$i_dir/BOOST/lib " >> example.mk
echo "LIBS=-lvcluster -lofpmmemory -lmetis -lboost_iostreams" >> example.mk
echo "LIBS_SE2=-lvcluster -lofpmmemory_se2 -lmetis -lboost_iostreams" >> example.mk
cp example.mk src/example.mk
diff --git a/src/Decomposition/CartDecomposition.hpp b/src/Decomposition/CartDecomposition.hpp
index 11d72f5b..64416216 100644
--- a/src/Decomposition/CartDecomposition.hpp
+++ b/src/Decomposition/CartDecomposition.hpp
@@ -505,7 +505,7 @@ public:
* \param p Point to apply the boundary condition
*
*/
- void applyPointBC(Point<dim,T> & pt) const
+ bool applyPointBC(Point<dim,T> & pt) const
{
for (size_t i = 0 ; i < dim ; i++)
{
@@ -802,9 +802,9 @@ p1[0]<-----+ +----> p2[0]
* \return processorID
*
*/
- template<typename Mem> size_t inline processorID(encapc<1, Point<dim,T>, Mem> p)
+ template<typename Mem, typename ofb> size_t inline processorID(encapc<1, Point<dim,T>, Mem> p)
{
- return fine_s.get(cd.getCell(p));
+ return fine_s.get(cd.template getCell<ofb>(p));
}
/*! \brief Given a point return in which processor the particle should go
@@ -849,7 +849,7 @@ p1[0]<-----+ +----> p2[0]
* \return processorID
*
*/
- size_t inline processorIDBC(const Point<dim,T> &p) const
+ template<typename ofb> size_t inline processorIDBC(const Point<dim,T> &p) const
{
Point<dim,T> pt = p;
applyPointBC(pt);
@@ -864,7 +864,7 @@ p1[0]<-----+ +----> p2[0]
* \return processorID
*
*/
- size_t inline processorIDBC(const T (&p)[dim]) const
+ template<typename ofb> size_t inline processorIDBC(const T (&p)[dim]) const
{
Point<dim,T> pt = p;
applyPointBC(pt);
diff --git a/src/Decomposition/CartDecomposition_unit_test.hpp b/src/Decomposition/CartDecomposition_unit_test.hpp
index 86da4299..834cad13 100644
--- a/src/Decomposition/CartDecomposition_unit_test.hpp
+++ b/src/Decomposition/CartDecomposition_unit_test.hpp
@@ -100,8 +100,6 @@ BOOST_AUTO_TEST_CASE( CartDecomposition_non_periodic_test)
ret = dec3.check_consistency();
BOOST_REQUIRE_EQUAL(ret,true);
- dec3.write("output_dec3_1.vtk");
-
// Check that dec3 is equal to dec2 with the exception of the ghost part
ret = dec3.is_equal_ng(dec2);
BOOST_REQUIRE_EQUAL(ret,true);
diff --git a/src/Decomposition/ie_ghost.hpp b/src/Decomposition/ie_ghost.hpp
index f40f83d9..333e12e1 100644
--- a/src/Decomposition/ie_ghost.hpp
+++ b/src/Decomposition/ie_ghost.hpp
@@ -393,6 +393,51 @@ protected:
public:
+ //! Default constructor
+ ie_ghost() {};
+
+ //! Copy constructor
+ ie_ghost(const ie_ghost<dim,T> & ie)
+ {
+ this->operator =(ie);
+ }
+
+ //! Copy constructor
+ ie_ghost(ie_ghost<dim,T> && ie)
+ {
+ this->operator=(ie);
+ }
+
+ //! Copy operator
+ inline ie_ghost<dim,T> & operator=(ie_ghost<dim,T> && ie)
+ {
+ box_nn_processor_int.swap(ie.box_nn_processor_int);
+ proc_int_box.swap(ie.proc_int_box);
+ vb_ext.swap(ie.vb_ext);
+ vb_int.swap(ie.vb_int);
+ geo_cell.swap(ie.geo_cell);
+ shifts.swap(ie.shifts);
+ ids_p.swap(ie.ids_p);
+ ids.swap(ie.ids);
+
+ return *this;
+ }
+
+ //! Copy operator
+ inline ie_ghost<dim,T> & operator=(const ie_ghost<dim,T> & ie)
+ {
+ box_nn_processor_int = ie.box_nn_processor_int;
+ proc_int_box = ie.proc_int_box;
+ vb_ext = ie.vb_ext;
+ vb_int = ie.vb_int;
+ geo_cell = geo_cell;
+ shifts = ie.shifts;
+ ids_p = ie.ids_p;
+ ids = ie.ids;
+
+ return *this;
+ }
+
/*! It return the shift vector
*
* Consider a domain with some ghost, at the border of the domain the
diff --git a/src/Vector/vector_dist.hpp b/src/Vector/vector_dist.hpp
index f45d61a1..5cb96f0d 100644
--- a/src/Vector/vector_dist.hpp
+++ b/src/Vector/vector_dist.hpp
@@ -21,6 +21,7 @@
#include "memory/ExtPreAlloc.hpp"
#include "CSVWriter.hpp"
#include "Decomposition/common.hpp"
+#include "Vector/vector_dist_ofb.hpp"
#define V_SUB_UNIT_FACTOR 64
@@ -138,7 +139,7 @@ private:
* \param opart id of the particles to send
*
*/
- void labelParticleProcessor(openfpm::vector<openfpm::vector<size_t>> & lbl_p, openfpm::vector<size_t> & prc_sz, openfpm::vector<size_t> & opart)
+ template<typename obp> void labelParticleProcessor(openfpm::vector<openfpm::vector<size_t>> & lbl_p, openfpm::vector<size_t> & prc_sz, openfpm::vector<size_t> & opart)
{
// reset lbl_p
lbl_p.resize(v_cl.getProcessingUnits());
@@ -158,7 +159,14 @@ private:
// Apply the boundary conditions
dec.applyPointBC(v_pos.get(key));
- size_t p_id = dec.processorIDBC(v_pos.get(key));
+ size_t p_id = 0;
+
+ // Check if the particle is inside the domain
+// if (dec.getDomain().isInside(v_pos.get(key)) == true)
+ p_id = dec.processorIDBC(v_pos.get(key));
+// else
+// p_id = obp::out(key,v_cl.getProcessUnitID());
+
// Particle to move
if (p_id != v_cl.getProcessUnitID())
@@ -674,7 +682,7 @@ public:
*/
size_t size_local()
{
- return v_pos.get(0).size();
+ return g_m;
}
/*! \brief Get the position of an element
@@ -707,13 +715,15 @@ public:
}
/*! \brief It move all the particles that does not belong to the local processor to the respective processor
+ *
+ * \tparam out of bound policy it specify what to do when the particles are detected out of bound
*
* In general this function is called after moving the particles to move the
* elements out the local processor. Or just after initialization if each processor
* contain non local particles
*
*/
- void map()
+ template<typename obp=KillParticle> void map()
{
// outgoing particles-id
openfpm::vector<size_t> out_part;
@@ -729,7 +739,7 @@ public:
v_prp.resize(g_m);
// Contain the processor id of each particle (basically where they have to go)
- labelParticleProcessor(opart,prc_sz,out_part);
+ labelParticleProcessor<obp>(opart,prc_sz,out_part);
// Calculate the sending buffer size for each processor, put this information in
// a contiguous buffer
@@ -907,6 +917,30 @@ public:
return vd->recv_mem_gm.get(i).getPointer();
}
+ /*! \brief Construct a cell list starting from the stored particles
+ *
+ * \tparam CellL CellList type to construct
+ *
+ */
+ template<typename CellL=CellList<dim,St,FAST>> CellL getCellList()
+ {
+ CellL cell_list;
+
+ // for each particle add the particle to the cell list
+
+ auto it = getDomainIterator();
+
+ while (it.isNext())
+ {
+ auto key = it.get();
+
+ cell_list.add(this->template getPos<0>(key),key.getKey());
+
+ ++it;
+ }
+
+ return cell_list;
+ }
/*! \brief Get the iterator across the position of the particles
*
diff --git a/src/Vector/vector_dist_unit_test.hpp b/src/Vector/vector_dist_unit_test.hpp
index 738e3e93..9d810f51 100644
--- a/src/Vector/vector_dist_unit_test.hpp
+++ b/src/Vector/vector_dist_unit_test.hpp
@@ -822,6 +822,56 @@ BOOST_AUTO_TEST_CASE( vector_dist_not_periodic_map )
}
}
+BOOST_AUTO_TEST_CASE( vector_dist_out_of_bound_policy )
+{
+/* Vcluster & v_cl = *global_v_cluster;
+
+ if (v_cl.getProcessingUnits() > 8)
+ return;
+
+ typedef Point<3,float> s;
+
+ Box<3,float> box({0.0,0.0,0.0},{1.0,1.0,1.0});
+
+ // Boundary conditions
+ size_t bc[3]={NON_PERIODIC,NON_PERIODIC,NON_PERIODIC};
+
+ // factor
+ float factor = pow(global_v_cluster->getProcessingUnits()/2.0f,1.0f/3.0f);
+
+ // ghost
+ Ghost<3,float> ghost(0.05 / factor);
+
+ // Distributed vector
+ vector_dist<3,float, Point_test<float>, CartDecomposition<3,float> > vd(100,box,bc,ghost);
+
+ // put particles at out of the boundary, they must be detected and and killed
+
+ auto it = vd.getIterator();
+
+ while (it.isNext())
+ {
+ auto key = it.get();
+
+ vd.template getPos<s::x>(key)[0] = -0.06;
+ vd.template getPos<s::x>(key)[1] = -0.06;
+ vd.template getPos<s::x>(key)[2] = -0.06;
+
+ ++it;
+ }
+
+ vd.map();
+
+ // Particles out of the boundary are killed
+
+ size_t cnt = vd.size_local();
+
+ v_cl.sum(cnt);
+ v_cl.execute();
+
+ BOOST_REQUIRE_EQUAL(cnt,0);*/
+}
+
BOOST_AUTO_TEST_SUITE_END()
#endif /* VECTOR_DIST_UNIT_TEST_HPP_ */
--
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