From 5fdb12a668508333a2dbea2ebb159082c7c022d3 Mon Sep 17 00:00:00 2001
From: Pietro Incardona <incardon@mpi-cbg.de>
Date: Thu, 20 Oct 2016 13:45:01 +0200
Subject: [PATCH] Adding missing files
---
CHANGELOG.md | 27 +-
example/Vector/0_simple/main.cpp | 2 +-
.../4_multiphase_celllist_verlet/Makefile | 8 +-
.../4_multiphase_celllist_verlet/main.cpp | 448 +++++++++++++++---
src/Grid/staggered_dist_grid_util.hpp | 22 +
src/Makefile.am | 2 +-
src/Vector/vector_dist_MP_unit_tests.hpp | 377 +++++++++++++++
.../vector_dist_multiphase_functions.hpp | 126 +++++
src/Vector/vector_dist_unit_test.hpp | 36 +-
9 files changed, 978 insertions(+), 70 deletions(-)
create mode 100644 src/Vector/vector_dist_MP_unit_tests.hpp
create mode 100644 src/Vector/vector_dist_multiphase_functions.hpp
diff --git a/CHANGELOG.md b/CHANGELOG.md
index bfc246e8c..7c8573692 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,12 +1,30 @@
# Change Log
All notable changes to this project will be documented in this file.
+## [0.6.0] - End October 2016
+
+### Added
+- Symmetric cell-list/verlet list
+- Multi-phase cell-list and Multi-phase cell-list
+- Added ghost_get that keep properties
+- Examples: 1_ghost_get_put it show how to use ghost_get and put with the new options
+ 4_multiphase_celllist_verlet completely rewritten for new Cell-list and multiphase verlet
+ 5_molecular_dynamic use case of symmetric cell-list and verlet list with ghost put
+ 6_complex_usage It show how the flexibility of openfpm can be used to debug your program
+
+### Fixed
+- Option NO_POSITION was untested
+
+### Changes
+
+
## [0.5.1] - 27 September 2016
### Added
- ghost_put support for particles
- Full-Support for complex property on vector_dist (Serialization)
- Added examples for serialization of complex properties 4_Vector
+- improved speed of the iterators
### Fixed
- Installation PETSC installation fail in case of preinstalled MPI
@@ -131,17 +149,14 @@ All notable changes to this project will be documented in this file.
- Algebraic Multigrid solver
- Parallel VTK, improved visualization
+- Asynchronous communication
-## [0.6.0] - Middle of October
+## [0.7.0] - December of October
### Added
+- Asynchronous communication
-- Symmetric Cell list and Verlet (15 days)
-- Semantic communication (??)
-- Improved Finite difference interface (15 days)
-## [0.6.0] - Beginning of September
-- Complex properties and serialization interface (15 days)
diff --git a/example/Vector/0_simple/main.cpp b/example/Vector/0_simple/main.cpp
index aeba11f0a..0e6a33447 100644
--- a/example/Vector/0_simple/main.cpp
+++ b/example/Vector/0_simple/main.cpp
@@ -348,7 +348,7 @@ int main(int argc, char* argv[])
*
* ## Finalize ## {#finalize_e0_sim}
*
- * At the very end of the program we have always to de-initialize the library
+ * At the very end of the program we have always de-initialize the library
*
* \snippet Vector/0_simple/main.cpp finalize
*
diff --git a/example/Vector/4_multiphase_celllist_verlet/Makefile b/example/Vector/4_multiphase_celllist_verlet/Makefile
index 16168a458..6043bb602 100644
--- a/example/Vector/4_multiphase_celllist_verlet/Makefile
+++ b/example/Vector/4_multiphase_celllist_verlet/Makefile
@@ -9,16 +9,16 @@ OBJ = main.o
%.o: %.cpp
$(CC) -fext-numeric-literals -O3 -g -c --std=c++11 -o $@ $< $(INCLUDE_PATH)
-cell: $(OBJ)
+multip: $(OBJ)
$(CC) -o $@ $^ $(CFLAGS) $(LIBS_PATH) $(LIBS)
-all: cell
+all: multip
run: all
- source $$HOME/openfpm_vars; mpirun -np 2 ./cell
+ source $$HOME/openfpm_vars; mpirun -np 2 ./multip
.PHONY: clean all run
clean:
- rm -f *.o *~ core cell
+ rm -f *.o *~ core multip
diff --git a/example/Vector/4_multiphase_celllist_verlet/main.cpp b/example/Vector/4_multiphase_celllist_verlet/main.cpp
index c353f0d8d..bf6223ca4 100644
--- a/example/Vector/4_multiphase_celllist_verlet/main.cpp
+++ b/example/Vector/4_multiphase_celllist_verlet/main.cpp
@@ -3,16 +3,18 @@
#include "Decomposition/CartDecomposition.hpp"
#include "data_type/aggregate.hpp"
#include "NN/CellList/CellListM.hpp"
+#include "Vector/vector_dist_multiphase_functions.hpp"
/*!
- * \page Vector_4_mp_cl Vector 4 Multi Phase cell-list
+ * \page Vector_4_mp_cl Vector 4 Multi Phase cell-list and verlet
*
* [TOC]
*
*
- * # Vector Multi Phase cell-list # {#e4_ph_cl}
+ * # Vector Multi Phase cell-list and Verlet # {#e4_ph_cl}
*
- * This example show multi-phase cell lists for the distributed vector
+ * This example show how to use multi-phase cell lists and Verlet-list.More in general
+ * it show how to construct Verlet and Cell-list between multiple vector_dist.
*
*
*/
@@ -25,19 +27,23 @@ int main(int argc, char* argv[])
* ## Initialization ##
*
* Here we Initialize the library, and we create a set of distributed vectors all forced to have the same
- * decomposition. Each vector identify one phase
+ * decomposition. Each vector identify one phase.
*
- * \snippet Vector/4_multiphase_celllist/main.cpp Initialization and parameters
+ * \note Be carefull on how you initialize the other phases. All the other phases
+ * must be forced to use the same decomposition. In order to do this we have
+ * to use the special constructor where we pass the decomposition from the first
+ * phase. The second parameter is just the the number of particles
+ *
+ * \snippet Vector/4_multiphase_celllist_verlet/main.cpp Initialization and parameters
*
*/
//! \cond [Initialization and parameters] \endcond
openfpm_init(&argc,&argv);
- Vcluster & v_cl = create_vcluster();
- // we will place the particles on a grid like way with 128 particles on each direction
- size_t sz[3] = {128,128,128};
+ // Vcluster for general usage
+ Vcluster & v_cl = create_vcluster();
// The domain
Box<3,float> box({0.0,0.0,0.0},{1.0,1.0,1.0});
@@ -45,11 +51,13 @@ int main(int argc, char* argv[])
// Boundary conditions
size_t bc[3]={PERIODIC,PERIODIC,PERIODIC};
+ // cut-off radius
float r_cut = 0.05;
// ghost, big enough to contain the interaction radius
Ghost<3,float> ghost(r_cut);
+ // The set of phases
openfpm::vector< vector_dist<3,float, aggregate<double,double>> > phases;
// first phase
@@ -67,108 +75,431 @@ int main(int argc, char* argv[])
/*!
* \page Vector_4_mp_cl Vector 4 Multi Phase cell-list
*
- * ## Initialization ##
+ * ## Create phases ##
+ *
+ * We initialize all the phases with particle randomly positioned in the space. Completed this
+ * iteration we redistribute the particles using the classical map, and we synchronize the ghost
*
- * We initialize all the phases with particle randomly positioned in the space
+ * \warning we cannot use the same iterator for all the phases even if the number of particles for
+ * each phase is the same. Consider that the number of particles (per-processor) can be
+ * different. The case of the initialization ("before map") is the only case where we are
+ * sure that the number of particles per processor is the same for each phase
*
- * \snippet Vector/4_multiphase_celllist/main.cpp rand dist
+ * \snippet Vector/4_multiphase_celllist_verlet/main.cpp rand dist
*
*/
//! \cond [rand dist] \endcond
+ // An iterator over the particles of the phase0
auto it = phases.get(0).getDomainIterator();
- // For all the particles
+ // For all the particles of phase0
while (it.isNext())
{
- // for all phases
- for (size_t i = 0 ; i < phases.size() ; i++)
- {
- auto key = it.get();
+ // particle p
+ auto p = it.get();
- phases.get(i).getPos(key)[0] = (float)rand() / RAND_MAX;
- phases.get(i).getPos(key)[1] = (float)rand() / RAND_MAX;
- phases.get(i).getPos(key)[2] = (float)rand() / RAND_MAX;
+ // Assign the position of the particles to each phase
+ for (size_t i = 0 ; i < phases.size(); i++)
+ {
+ // Assign random position
+ phases.get(i).getPos(p)[0] = (float)rand() / RAND_MAX;
+ phases.get(i).getPos(p)[1] = (float)rand() / RAND_MAX;
+ phases.get(i).getPos(p)[2] = (float)rand() / RAND_MAX;
}
- // next point
+
+ // Next particle
++it;
}
- // Redistribute all the phases in the mean while also take the iterators of all the phases
- typedef decltype(phases.get(0).getIterator()) iterator;
- openfpm::vector<iterator> phase_it;
-
- for (size_t i = 0 ; i < phases.size() ; i++)
+ // Redistribute and sync all the phases
+ for (size_t i = 0 ; i < 4 ; i++)
+ {
phases.get(i).map();
+ phases.get(i).ghost_get<>();
+ }
//! \cond [rand dist] \endcond
/*!
* \page Vector_4_mp_cl Vector 4 Multi Phase cell-list
*
- * ## Multi-phase cell-list construction ##
+ * ## Multi phase Verlet-list ##
+ *
+ * In general verlet-list can be constructed from the vector itself using **getVerlerList()**
+ *
+ * \see \ref Vector_3_md_vl
+ *
+ * In the multi-phase case if we use such function on phase0 such function
+ * produce a Verlet list where for each particle of the phase0 we get the neighborhood
+ * particles within the phase0. Most of time we also want to construct Verlet-list across
+ * phases, for example between phase0 and phase1. Let suppose now that we want to construct
+ * a verlet-list that given the particles of the phase0 it return the neighborhood particles
+ * in phase1. In order to do this we can create a Cell-list from phase1. Once we have the
+ * Cell-list for phase 1 we give to **createVerlet()**
+ * the particle set of phase0, the Cell-list of phase1 and the cut-off radius.
+ * The function return a VerletList between phase0 and 1 that can be used to do computation.
+ *
+ *
+ * \snippet Vector/4_multiphase_celllist_verlet/main.cpp create multi-phase verlet
+ *
+ */
+
+ //! \cond [create multi-phase verlet] \endcond
+
+ // Get the cell list of the phase1
+ auto CL_phase1 = phases.get(1).getCellList(r_cut);
+
+ // This function create a Verlet-list between phases 0 and 1
+ auto NN_ver01 = createVerlet(phases.get(0),CL_phase1,r_cut);
+
+ //! \cond [create multi-phase verlet] \endcond
+
+ /*!
+ * \page Vector_4_mp_cl Vector 4 Multi Phase cell-list
+ *
+ * Once we have a Verlet-list, we can do easily computation with that. We can use
+ * the function **getNNIterator()** to get an iterator of the neighborhood particles
+ * for a specified particle. In this case for each particle of the phase0 we count
+ * the neighborhood particles in phase1
+ *
+ * \snippet Vector/4_multiphase_celllist_verlet/main.cpp count part from phase0 to 1
+ *
+ */
+
+ //! \cond [count part from phase0 to 1] \endcond
+
+ // Get an iterator of the particles of the phase0
+ auto it = phases.get(0).getDomainIterator();
+
+ // For each particle of the phase0
+ while (it.isNext())
+ {
+ // Get the particle p
+ auto p = it.get();
+
+ // reset the counter
+ phases.get(0).getProp<0>(p) = 0;
+
+ // Get an iterator over the neighborhood particles for the particle p
+ auto Np = NN_ver01.template getNNIterator<NO_CHECK>(p.getKey());
+
+ // For each neighborhood of the particle p
+ while (Np.isNext())
+ {
+ // Neighborhood particle q
+ auto q = Np.get();
+
+ // Count the number of particles
+ // Here in general we can do our computation
+ phases.get(0).getProp<0>(p)++;
+
+ // Next particle
+ ++Np;
+ }
+
+ // Next particle
+ ++it;
+ }
+
+ //! \cond [count part from phase0 to 1] \endcond
+
+ /*!
+ * \page Vector_4_mp_cl Vector 4 Multi Phase cell-list
+ *
+ * ## From one phase to all ##
+ *
+ * It is also possible to construct a Verlet-list from one phase to all the other phases.
+ * To do this we use the function **createCellListM<2>()** to first create a
+ * multi-phase cell-list. The template parameter is required to indicate how many bit
+ * to reserve for the phase information.
+ *
+ * \note In case of
+ * * 2 bit mean that you can store up to 4 phases (2^62 number of particles for each phase)
+ * * 3 bit mean that you can store up to 8 phases (2^61 number of particles for each phase)
*
- * In this part we construct the Multi-phase cell list. The multiphase cell list has 3 parameters
- * * one is the dimensionality (3)
- * * The precision of the coordinates (float),
- * * How many bit to use for the phase.
- * Multi-phase cell-list try to pack into a 64bit number information about the particle id and the
- * the phase id.
+ * Once created the multiphase-cell list from the phases. We can use the function
+ * **createVerletM()** to create a verlet-list from one phase to all the others.
+ * The function requires the particle for which we are constructing the verlet list, in this case
+ * the phase0, the Cell-list containing all the other phases and the cut-off radius.
*
- * \snippet Vector/4_multiphase_celllist/main.cpp cl construction
+ *
+ * \snippet Vector/4_multiphase_celllist_verlet/main.cpp create multi-phase multi verlet
*
*/
- //! \cond [cl construction] \endcond
+ //! \cond [create multi-phase multi verlet] \endcond
+
+ // This function create an "Empty" Multiphase Cell List from all the phases
+ auto CL_all = createCellListM<2>(phases,r_cut);
+
+ // This create a Verlet-list between phase0 and all the other phases
+ auto NNver0_all = createVerletM<2>(phases.get(0),CL_all,r_cut);
- // Construct one single Multi-phase cell list to use in the computation
- // in 3d, precision float, 2 bit dedicated to the phase for a maximum of 2^2 = 4 (Maximum number of phase)
- //
- //
-
- size_t div[3];
- Box<3,float> box_cl;
- phases.get(0).getCellListParams(r_cut,div,box_cl);
+ //! \cond [create multi-phase multi verlet] \endcond
- CellListM<3,float,2> NN;
- NN.Initialize(box_cl,div);
+ /*!
+ * \page Vector_4_mp_cl Vector 4 Multi Phase cell-list
+ *
+ * Compute on a multiphase verlet-list is very similar to a non multi-phase.
+ * The only difference is that the function **get()** is substituted by two
+ * other functions **getP()** and **getV()** The first return the phase from where
+ * it come the particle the second it return the particle-id
+ *
+ * \snippet Vector/4_multiphase_celllist_verlet/main.cpp compute multi-phase multi verlet
+ *
+ */
+ //! \cond [compute multi-phase multi verlet] \endcond
+ // Get an iterator for the phase0 particles
+ it = phases.get(0).getDomainIterator();
- // for all the phases i
- for (size_t i = 0; i < phases.size() ; i++)
+ while (it.isNext())
{
- // iterate across all the particle of the phase i
- auto it = phases.get(i).getDomainIterator();
+ // Get the particle p
+ auto p = it.get();
+
+ // Get an interator over the neighborhood of the particle p
+ auto Np = NNver0_all.template getNNIterator<NO_CHECK>(p.getKey());
+
+ // reset the counter
+ phases.get(0).getProp<0>(p) = 0;
+
+ // For each neighborhood of the particle p
+ while (Np.isNext())
+ {
+ // Get the particle q near to p
+ auto q = Np.getP();
+
+ // Get from which phase it come from
+ auto ph_q = Np.getV();
+
+ // count
+ phases.get(0).getProp<0>(p)++;
+
+ // Next particle
+ ++Np;
+ }
+
+ // Next particle
+ ++it;
+ }
+
+ //! \cond [compute multi-phase multi verlet] \endcond
+
+ /*!
+ * \page Vector_4_mp_cl Vector 4 Multi Phase cell-list
+ *
+ * ## Symmetric interaction case ##
+ *
+ * The same functions exist also in the case we want to construct
+ * symmetric-verlet list.
+ *
+ * \see \ref Vector_5_md_vl_sym For more details on how to use symmetric
+ * verlet-list in a real case.
+ *
+ * In general the main differences can be summarized in
+ * * we have to reset the **forces** or **interaction** variable(s)
+ * * calculate the interaction p-q and apply the result to p and q at the same time
+ * * merge with ghost_put the result is stored in the ghost part with the
+ * real particles
+ *
+ * \snippet Vector/4_multiphase_celllist_verlet/main.cpp compute sym multi-phase two phase
+ *
+ */
+
+ //! \cond [compute sym multi-phase two phase] \endcond
+
+ // Get the cell list of the phase1
+ auto CL_phase1 = phases.get(1).getCellListSym(r_cut);
+
+ // This function create a Verlet-list between phases 0 and 1
+ auto NN_ver01 = createVerletSym(phases.get(0),CL_phase1,r_cut);
+
+ // Get an iterator over the real and ghost particles
+ auto it = phases.get(0).getDomainAndGhostIterator();
+
+ // For each particles
+ while (it.isNext())
+ {
+ // Get the particle p
+ auto p = it.get();
+
+ // Reset the counter
+ phases.get(0).getProp<0>(p) = 0;
+
+ // Next particle
+ ++it;
+ }
+
+ // Compute interaction from phase0 to phase1
+
+ // Get an iterator over the real particles of phase0
+ auto it = phases.get(0).getDomainIterator();
+
+ // For each particle of the phase0
+ while (it.isNext())
+ {
+ // get particle p
+ auto p = it.get();
+
+ // Get the neighborhood of particle p
+ auto Np = NN_ver01.template getNNIterator<NO_CHECK>(p.getKey());
+
+ // For each neighborhood of the particle p
+ while (Np.isNext())
+ {
+ // Neighborhood particle q of p
+ auto q = Np.get();
+
+ // increment the counter for the phase 0 and 1
+ phases.get(0).getProp<0>(p)++;
+ phases.get(1).getProp<0>(q)++;
+
+ // Next particle
+ ++Np;
+ }
+
+ // Next particle
+ ++it;
+ }
+
+ // Merge the information of the ghost with the real particles
+ phases.get(0).ghost_put<add_,0>();
+ phases.get(1).ghost_put<add_,0>();
+
+ //! \cond [compute sym multi-phase two phase] \endcond
+
+ /*!
+ * \page Vector_4_mp_cl Vector 4 Multi Phase cell-list
+ *
+ * For the case of a Verlet-list between the phase0 and all the other phases.
+ * The code remain very similar to the previous one the only differences is that
+ * we have to create a Multi-phase cell list from the vector of the phases.
+ * When we compute with the verlet-list list now the simple function **get**
+ * is substituted by the function **getP** and **getV**. In this example we are
+ * creating 4 multiphase symmetric verlet-list
+ *
+ * * 0 to all
+ * * 1 to all
+ * * 2 to all
+ * * 3 to all
+ *
+ * The computation is an all to all
+ *
+ * \snippet Vector/4_multiphase_celllist_verlet/main.cpp create sym multi-phase multi verlet
+ *
+ */
+
+ //! \cond [create sym multi-phase multi verlet] \endcond
+
+ // Get an iterator over the phase0
+ auto it = phases.get(0).getDomainAndGhostIterator();
+
+ // For each particle of the phase 0
+ while (it.isNext())
+ {
+ // get the particle p
+ auto p = it.get();
+
+ // Reset the counter for the domain and ghost particles
+ phases.get(0).getProp<0>(p) = 0;
+ phases.get(1).getProp<0>(p) = 0;
+ phases.get(2).getProp<0>(p) = 0;
+ phases.get(3).getProp<0>(p) = 0;
+
+ // next particle
+ ++it;
+ }
+
+ // This function create an "Empty" Multiphase Cell List
+ auto CL_all = createCellListSymM<2>(phases,r_cut);
+
+ // Type of the multiphase Verlet-list
+ typedef decltype(createVerletSymM<2>(phases.get(0),CL_all,r_cut)) verlet_type;
+
+ // for each phase we create one Verlet-list that contain the neighborhood
+ // from all the phases
+ verlet_type NNver_all[4];
+
+ // Here we create a Verlet-list between each phases
+
+ // 0 to all
+ NNver_all[0] = createVerletSymM<2>(phases.get(0),CL_all,r_cut);
+
+ // 1 to all
+ NNver_all[1] = createVerletSymM<2>(phases.get(1),CL_all,r_cut);
+
+ // 2 to all
+ NNver_all[2] = createVerletSymM<2>(phases.get(2),CL_all,r_cut);
+
+ // 3 to all
+ NNver_all[3] = createVerletSymM<2>(phases.get(3),CL_all,r_cut);
+
+ // For each phase
+ for (size_t i = 0 ; i < phases.size() ; i++)
+ {
+ // Get an iterator over the particles of that phase
+ it = phases.get(i).getDomainIterator();
+
+ // for each particle of the phase
while (it.isNext())
{
- auto key = it.get();
+ // Get the particle p
+ auto p = it.get();
+
+ // Get an iterator for neighborhood of the particle p
+ auto Np = NNver_all[i].template getNNIterator<NO_CHECK>(p.getKey());
+
+ // For each neighborhood particle
+ while (Np.isNext())
+ {
+ // Get the particle q near to p
+ auto q = Np.getP();
- // Add the particle of the phase i to the cell list
- NN.add(phases.get(i).getPos(key), key.getKey(), i);
+ // Get from which phase it come from
+ auto ph_q = Np.getV();
+ // increment the counter on both p and q
+ phases.get(i).getProp<0>(p)++;
+ phases.get(ph_q).getProp<0>(q)++;
+
+ // Next particle
+ ++Np;
+ }
+
+ // Next particle
++it;
}
}
- //! \cond [cl construction] \endcond
+ // Merge the ghost part with the real particles
+ phases.get(0).ghost_put<add_,0>();
+ phases.get(1).ghost_put<add_,0>();
+ phases.get(2).ghost_put<add_,0>();
+ phases.get(3).ghost_put<add_,0>();
+
+ //! \cond [create sym multi-phase multi verlet] \endcond
/*!
* \page Vector_4_mp_cl Vector 4 Multi Phase cell-list
*
* ## Multi-phase cell-list usage ##
*
- * After construction we show how to use the Cell-list. In this case we accumulate on the property
+ * The multiphase cell-list that we constructed before to create a Verlet-list can be also used
+ * directly. In this case we accumulate on the property
* 0 of the phase 0 the distance of the near particles from all the phases
*
- * \snippet Vector/4_multiphase_celllist/main.cpp cl usage
+ * \snippet Vector/4_multiphase_celllist_verlet/main.cpp cl usage
*
*/
//! \cond [cl usage] \endcond
+ // we create a reference to phase0 particle for convenience
vector_dist<3,float, aggregate<double,double> > & current_phase = phases.get(0);
// Get the iterator of the particles of phase 0
@@ -183,8 +514,11 @@ int main(int argc, char* argv[])
// Get the position of the particle p
Point<3,float> xp = current_phase.getPos(p);
+ // Reset to zero the propety 0
+ current_phase.getProp<0>(p) = 0.0;
+
// Get an iterator of all the particles neighborhood of p
- auto Np = NN.getNNIterator(NN.getCell(current_phase.getPos(p)));
+ auto Np = CL_all.getNNIterator(NN.getCell(current_phase.getPos(p)));
// For each particle near p
while (Np.isNext())
@@ -216,7 +550,7 @@ int main(int argc, char* argv[])
*
* At the very end of the program we have always de-initialize the library
*
- * \snippet Vector/4_multiphase_celllist/main.cpp finalize
+ * \snippet Vector/4_multiphase_celllist_verlet/main.cpp finalize
*
*/
@@ -231,7 +565,7 @@ int main(int argc, char* argv[])
*
* # Full code # {#code}
*
- * \include Vector/4_multiphase_celllist/main.cpp
+ * \include Vector/4_multiphase_celllist_verlet/main.cpp
*
*/
}
diff --git a/src/Grid/staggered_dist_grid_util.hpp b/src/Grid/staggered_dist_grid_util.hpp
index c7d20ec6a..938f1d9ab 100644
--- a/src/Grid/staggered_dist_grid_util.hpp
+++ b/src/Grid/staggered_dist_grid_util.hpp
@@ -66,11 +66,13 @@ struct vtk_write<ele,vtk,false>
template<typename T>
struct extends
{
+ //! number of elements
static inline size_t mul()
{
return 1;
}
+ //! number of indexes
static inline size_t dim()
{
return 0;
@@ -81,11 +83,13 @@ struct extends
template<typename T,size_t N1>
struct extends<T[N1]>
{
+ //! number of elements
static inline size_t mul()
{
return N1;
}
+ //! number of indexes
static inline size_t dim()
{
return 1;
@@ -96,11 +100,13 @@ struct extends<T[N1]>
template<typename T,size_t N1,size_t N2>
struct extends<T[N1][N2]>
{
+ //! number of elements
static inline size_t mul()
{
return N1 * N2;
}
+ //! number of indexes
static inline size_t dim()
{
return 2;
@@ -111,11 +117,13 @@ struct extends<T[N1][N2]>
template<typename T,size_t N1,size_t N2,size_t N3>
struct extends<T[N1][N2][N3]>
{
+ //! number of elements
static inline size_t mul()
{
return N1 * N2 * N3;
}
+ //! number of indexes
static inline size_t dim()
{
return 3;
@@ -126,11 +134,13 @@ struct extends<T[N1][N2][N3]>
template<typename T,size_t N1,size_t N2,size_t N3,size_t N4>
struct extends<T[N1][N2][N3][N4]>
{
+ //! number of elements
static inline size_t mul()
{
return N1 * N2 * N3 * N4;
}
+ //! number of indexes
static inline size_t dim()
{
return 4;
@@ -141,11 +151,13 @@ struct extends<T[N1][N2][N3][N4]>
template<typename T,size_t N1,size_t N2,size_t N3,size_t N4,size_t N5>
struct extends<T[N1][N2][N3][N4][N5]>
{
+ //! number of elements
static inline size_t mul()
{
return N1 * N2 * N3 * N4 * N5;
}
+ //! number of indexes
static inline size_t dim()
{
return 5;
@@ -156,11 +168,13 @@ struct extends<T[N1][N2][N3][N4][N5]>
template<typename T,size_t N1,size_t N2,size_t N3,size_t N4,size_t N5, size_t N6>
struct extends<T[N1][N2][N3][N4][N5][N6]>
{
+ //! number of elements
static inline size_t mul()
{
return N1 * N2 * N3 * N4 * N5 * N6;
}
+ //! number of indexes
static inline size_t dim()
{
return 6;
@@ -171,11 +185,13 @@ struct extends<T[N1][N2][N3][N4][N5][N6]>
template<typename T,size_t N1,size_t N2,size_t N3,size_t N4,size_t N5, size_t N6, size_t N7>
struct extends<T[N1][N2][N3][N4][N5][N6][N7]>
{
+ //! number of elements
static inline size_t mul()
{
return N1 * N2 * N3 * N4 * N5 * N6 * N7;
}
+ //! number of indexes
static inline size_t dim()
{
return 7;
@@ -186,11 +202,13 @@ struct extends<T[N1][N2][N3][N4][N5][N6][N7]>
template<typename T,size_t N1,size_t N2,size_t N3,size_t N4,size_t N5, size_t N6, size_t N7, size_t N8>
struct extends<T[N1][N2][N3][N4][N5][N6][N7][N8]>
{
+ //! number of elements
static inline size_t mul()
{
return N1 * N2 * N3 * N4 * N5 * N6 * N7 * N8;
}
+ //! number of indexes
static inline size_t dim()
{
return 8;
@@ -201,11 +219,13 @@ struct extends<T[N1][N2][N3][N4][N5][N6][N7][N8]>
template<typename T,size_t N1,size_t N2,size_t N3,size_t N4,size_t N5, size_t N6, size_t N7, size_t N8, size_t N9>
struct extends<T[N1][N2][N3][N4][N5][N6][N7][N8][N9]>
{
+ //! number of elements
static inline size_t mul()
{
return N1 * N2 * N3 * N4 * N5 * N6 * N7 * N8 * N9;
}
+ //! number of indexes
static inline size_t dim()
{
return 9;
@@ -216,11 +236,13 @@ struct extends<T[N1][N2][N3][N4][N5][N6][N7][N8][N9]>
template<typename T,size_t N1,size_t N2,size_t N3,size_t N4,size_t N5, size_t N6, size_t N7, size_t N8, size_t N9, size_t N10>
struct extends<T[N1][N2][N3][N4][N5][N6][N7][N8][N9][N10]>
{
+ //! number of elements
static inline size_t mul()
{
return N1 * N2 * N3 * N4 * N5 * N6 * N7 * N8 * N9 * N10;
}
+ //! number of indexes
static inline size_t dim()
{
return 10;
diff --git a/src/Makefile.am b/src/Makefile.am
index fff4127b0..3ba89adcd 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -9,7 +9,7 @@ nobase_include_HEADERS = Decomposition/CartDecomposition.hpp Decomposition/CartD
Decomposition/nn_processor.hpp Decomposition/ie_loc_ghost.hpp Decomposition/ORB.hpp \
Graph/CartesianGraphFactory.hpp \
Grid/grid_dist_id.hpp Grid/grid_dist_id_iterator_dec.hpp Grid/grid_dist_util.hpp Grid/grid_dist_id_iterator_sub.hpp Grid/grid_dist_id_iterator.hpp Grid/grid_dist_key.hpp Grid/staggered_dist_grid.hpp Grid/staggered_dist_grid_util.hpp Grid/staggered_dist_grid_copy.hpp \
- Vector/vector_dist_comm.hpp Vector/vector_dist.hpp Vector/vector_dist_ofb.hpp Vector/vector_dist_iterator.hpp Vector/vector_dist_key.hpp \
+ Vector/vector_dist_multiphase_functions.hpp Vector/vector_dist_comm.hpp Vector/vector_dist.hpp Vector/vector_dist_ofb.hpp Vector/vector_dist_iterator.hpp Vector/vector_dist_key.hpp \
config/config.h \
example.mk \
Decomposition/Distribution/metis_util.hpp Decomposition/Distribution/parmetis_dist_util.hpp Decomposition/Distribution/parmetis_util.hpp Decomposition/Distribution/MetisDistribution.hpp Decomposition/Distribution/ParMetisDistribution.hpp Decomposition/Distribution/DistParMetisDistribution.hpp dec_optimizer.hpp SubdomainGraphNodes.hpp \
diff --git a/src/Vector/vector_dist_MP_unit_tests.hpp b/src/Vector/vector_dist_MP_unit_tests.hpp
new file mode 100644
index 000000000..7d9eff81e
--- /dev/null
+++ b/src/Vector/vector_dist_MP_unit_tests.hpp
@@ -0,0 +1,377 @@
+/*
+ * vector_dist_MP_unit_tests.hpp
+ *
+ * Created on: Oct 14, 2016
+ * Author: i-bird
+ */
+
+#ifndef SRC_VECTOR_VECTOR_DIST_MP_UNIT_TESTS_HPP_
+#define SRC_VECTOR_VECTOR_DIST_MP_UNIT_TESTS_HPP_
+
+#include "Vector/vector_dist_multiphase_functions.hpp"
+
+BOOST_AUTO_TEST_SUITE( vector_dist_multiphase_test )
+
+BOOST_AUTO_TEST_CASE( vector_dist_multiphase_cell_list_test )
+{
+ if (create_vcluster().getProcessingUnits() > 24)
+ return;
+
+ size_t sz[3] = {60,60,40};
+
+ // The domain
+ Box<3,float> box({-1000.0,-1000.0,-1000.0},{2000.0,2000.0,1000.0});
+
+ // Boundary conditions
+ size_t bc[3]={PERIODIC,PERIODIC,PERIODIC};
+
+ float r_cut = 51.0;
+
+ // ghost, big enough to contain the interaction radius
+ Ghost<3,float> ghost(r_cut);
+
+ openfpm::vector< vector_dist<3,float, aggregate<double,double>> > phases;
+
+ // first phase
+ phases.add( vector_dist<3,float, aggregate<double,double>>(0,box,bc,ghost) );
+
+ // The other 3 phases
+ phases.add( vector_dist<3,float, aggregate<double,double>>(phases.get(0).getDecomposition(),0) );
+ phases.add( vector_dist<3,float, aggregate<double,double>>(phases.get(0).getDecomposition(),0) );
+ phases.add( vector_dist<3,float, aggregate<double,double>>(phases.get(0).getDecomposition(),0) );
+
+ // Fill the phases with particles
+
+ auto g_it = phases.get(0).getGridIterator(sz);
+
+ while (g_it.isNext())
+ {
+ auto key = g_it.get();
+
+ // Add a particle to all the phases
+ phases.get(0).add();
+ phases.get(1).add();
+ phases.get(2).add();
+ phases.get(3).add();
+
+ phases.get(0).getLastPos()[0] = key.get(0) * g_it.getSpacing(0) + box.getLow(0);
+ phases.get(0).getLastPos()[1] = key.get(1) * g_it.getSpacing(1) + box.getLow(1);
+ phases.get(0).getLastPos()[2] = key.get(2) * g_it.getSpacing(2) + box.getLow(2);
+
+ phases.get(1).getLastPos()[0] = key.get(0) * g_it.getSpacing(0) + box.getLow(0);
+ phases.get(1).getLastPos()[1] = key.get(1) * g_it.getSpacing(1) + box.getLow(1);
+ phases.get(1).getLastPos()[2] = key.get(2) * g_it.getSpacing(2) + box.getLow(2);
+
+ phases.get(2).getLastPos()[0] = key.get(0) * g_it.getSpacing(0) + box.getLow(0);
+ phases.get(2).getLastPos()[1] = key.get(1) * g_it.getSpacing(1) + box.getLow(1);
+ phases.get(2).getLastPos()[2] = key.get(2) * g_it.getSpacing(2) + box.getLow(2);
+
+ phases.get(3).getLastPos()[0] = key.get(0) * g_it.getSpacing(0) + box.getLow(0);
+ phases.get(3).getLastPos()[1] = key.get(1) * g_it.getSpacing(1) + box.getLow(1);
+ phases.get(3).getLastPos()[2] = key.get(2) * g_it.getSpacing(2) + box.getLow(2);
+
+ ++g_it;
+ }
+
+ // Sync all phases
+ for (size_t i = 0 ; i < 4 ; i++)
+ {
+ phases.get(i).map();
+ phases.get(i).ghost_get<>();
+ }
+
+ // Get the cell list of the phase 0 and 1
+ auto CL_phase0 = phases.get(0).getCellList(r_cut);
+ auto CL_phase1 = phases.get(1).getCellList(r_cut);
+
+ // This function create a Verlet-list between phases 0 and 1
+ auto NN_ver01 = createVerlet(phases.get(0),CL_phase1,r_cut);
+
+ // Check NNver0_1
+
+ bool ret = true;
+ auto it = phases.get(0).getDomainIterator();
+
+ while (it.isNext())
+ {
+ auto p = it.get();
+ auto Np = NN_ver01.template getNNIterator<NO_CHECK>(p.getKey());
+
+ size_t nn_count = 0;
+
+ // For each neighborhood of the particle p
+ while (Np.isNext())
+ {
+ // Neighborhood particle q
+ auto q = Np.get();
+
+ // Count the number of particles
+ nn_count++;
+
+ ++Np;
+ }
+
+ ret &= nn_count == 7ul;
+
+ ++it;
+ }
+
+ BOOST_REQUIRE_EQUAL(ret,true);
+
+ // Sync all phases
+ for (size_t i = 0 ; i < 4 ; i++)
+ {
+ phases.get(i).map();
+ phases.get(i).ghost_get<>();
+ }
+
+ // NN_ver0_all
+
+ // This function create an "Empty" Multiphase Cell List
+ auto CL_all = createCellListM<2>(phases,r_cut);
+
+ // This create a Verlet-list between phase 0 and all the other phases
+ auto NNver0_all = createVerletM<2>(phases.get(0),CL_all,r_cut);
+
+ it = phases.get(0).getDomainIterator();
+
+ while (it.isNext())
+ {
+ auto p = it.get();
+ auto Np = NNver0_all.template getNNIterator<NO_CHECK>(p.getKey());
+
+ size_t nn_cout[4] = {0,0,0,0};
+
+ // For each neighborhood of the particle p
+ while (Np.isNext())
+ {
+ // Get the particle q near to p
+ auto q = Np.getP();
+
+ // Get from which phase it come from
+ auto ph_q = Np.getV();
+
+ nn_cout[ph_q]++;
+
+ ++Np;
+ }
+
+ ret &= nn_cout[0] == 7;
+ ret &= nn_cout[1] == 7;
+ ret &= nn_cout[2] == 7;
+ ret &= nn_cout[3] == 7;
+
+ ++it;
+ }
+
+ BOOST_REQUIRE_EQUAL(ret,true);
+}
+
+
+BOOST_AUTO_TEST_CASE( vector_dist_multiphase_cell_list_sym_test )
+{
+ if (create_vcluster().getProcessingUnits() > 24)
+ return;
+
+ size_t sz[3] = {60,60,40};
+
+ // The domain
+ Box<3,float> box({-1000.0,-1000.0,-1000.0},{2000.0,2000.0,1000.0});
+
+ // Boundary conditions
+ size_t bc[3]={PERIODIC,PERIODIC,PERIODIC};
+
+ float r_cut = 51.0;
+
+ // ghost, big enough to contain the interaction radius
+ Ghost<3,float> ghost(r_cut);
+
+ openfpm::vector< vector_dist<3,float, aggregate<size_t>> > phases;
+
+ // first phase
+ phases.add( vector_dist<3,float, aggregate<size_t>>(0,box,bc,ghost) );
+
+ // The other 3 phases
+ phases.add( vector_dist<3,float, aggregate<size_t>>(phases.get(0).getDecomposition(),0) );
+ phases.add( vector_dist<3,float, aggregate<size_t>>(phases.get(0).getDecomposition(),0) );
+ phases.add( vector_dist<3,float, aggregate<size_t>>(phases.get(0).getDecomposition(),0) );
+
+ // Fill the phases with particles
+
+ auto g_it = phases.get(0).getGridIterator(sz);
+
+ while (g_it.isNext())
+ {
+ auto key = g_it.get();
+
+ // Add a particle to all the phases
+ phases.get(0).add();
+ phases.get(1).add();
+ phases.get(2).add();
+ phases.get(3).add();
+
+ phases.get(0).getLastPos()[0] = key.get(0) * g_it.getSpacing(0) + box.getLow(0);
+ phases.get(0).getLastPos()[1] = key.get(1) * g_it.getSpacing(1) + box.getLow(1);
+ phases.get(0).getLastPos()[2] = key.get(2) * g_it.getSpacing(2) + box.getLow(2);
+
+ phases.get(1).getLastPos()[0] = key.get(0) * g_it.getSpacing(0) + box.getLow(0);
+ phases.get(1).getLastPos()[1] = key.get(1) * g_it.getSpacing(1) + box.getLow(1);
+ phases.get(1).getLastPos()[2] = key.get(2) * g_it.getSpacing(2) + box.getLow(2);
+
+ phases.get(2).getLastPos()[0] = key.get(0) * g_it.getSpacing(0) + box.getLow(0);
+ phases.get(2).getLastPos()[1] = key.get(1) * g_it.getSpacing(1) + box.getLow(1);
+ phases.get(2).getLastPos()[2] = key.get(2) * g_it.getSpacing(2) + box.getLow(2);
+
+ phases.get(3).getLastPos()[0] = key.get(0) * g_it.getSpacing(0) + box.getLow(0);
+ phases.get(3).getLastPos()[1] = key.get(1) * g_it.getSpacing(1) + box.getLow(1);
+ phases.get(3).getLastPos()[2] = key.get(2) * g_it.getSpacing(2) + box.getLow(2);
+
+ ++g_it;
+ }
+
+ // Sync all phases
+ for (size_t i = 0 ; i < 4 ; i++)
+ {
+ phases.get(i).map();
+ phases.get(i).ghost_get<>();
+ }
+
+ // Get the cell list of the phase 0 and 1
+ auto CL_phase0 = phases.get(0).getCellListSym(r_cut);
+ auto CL_phase1 = phases.get(1).getCellListSym(r_cut);
+
+ // This function create a Verlet-list between phases 0 and 1
+ auto NN_ver01 = createVerletSym(phases.get(0),CL_phase1,r_cut);
+
+ // Check NNver0_1
+
+ bool ret = true;
+ auto it = phases.get(0).getDomainIterator();
+
+ while (it.isNext())
+ {
+ auto p = it.get();
+ auto Np = NN_ver01.template getNNIterator<NO_CHECK>(p.getKey());
+
+ // For each neighborhood of the particle p
+ while (Np.isNext())
+ {
+ // Neighborhood particle q
+ auto q = Np.get();
+
+ phases.get(0).getProp<0>(p)++;
+ phases.get(1).getProp<0>(q)++;
+
+ ++Np;
+ }
+
+ ++it;
+ }
+
+ phases.get(0).ghost_put<add_,0>();
+ phases.get(1).ghost_put<add_,0>();
+
+ it = phases.get(0).getDomainIterator();
+ while (it.isNext())
+ {
+ auto p = it.get();
+
+ ret &= phases.get(0).getProp<0>(p) == 7;
+ ret &= phases.get(1).getProp<0>(p) == 7;
+
+ ++it;
+ }
+
+ BOOST_REQUIRE_EQUAL(ret,true);
+
+ // Sync all phases
+ for (size_t i = 0 ; i < 4 ; i++)
+ {
+ phases.get(i).map();
+ phases.get(i).ghost_get<>();
+ }
+
+ // Reset counter on all phases
+
+ for (size_t i = 0 ; i < phases.size() ; i++)
+ {
+ it = phases.get(i).getDomainAndGhostIterator();
+ while (it.isNext())
+ {
+ auto p = it.get();
+
+ phases.get(i).getProp<0>(p) = 0;
+
+ ++it;
+ }
+ }
+
+ // NN_ver0_all
+
+ // This function create an "Empty" Multiphase Cell List
+ auto CL_all = createCellListSymM<2>(phases,r_cut);
+
+ typedef decltype(createVerletSymM<2>(phases.get(0),CL_all,r_cut)) verlet_type;
+
+ verlet_type NNver_all[4];
+
+ // This create a Verlet-list between phase all phases to all the other phases
+ NNver_all[0] = createVerletSymM<2>(phases.get(0),CL_all,r_cut);
+ NNver_all[1] = createVerletSymM<2>(phases.get(1),CL_all,r_cut);
+ NNver_all[2] = createVerletSymM<2>(phases.get(2),CL_all,r_cut);
+ NNver_all[3] = createVerletSymM<2>(phases.get(3),CL_all,r_cut);
+
+ // all phases to all phases
+
+ for (size_t i = 0 ; i < phases.size() ; i++)
+ {
+ it = phases.get(i).getDomainIterator();
+
+ while (it.isNext())
+ {
+ auto p = it.get();
+ auto Np = NNver_all[i].template getNNIterator<NO_CHECK>(p.getKey());
+
+ // For each neighborhood of the particle p
+ while (Np.isNext())
+ {
+ // Get the particle q near to p
+ auto q = Np.getP();
+
+ // Get from which phase it come from
+ auto ph_q = Np.getV();
+
+ phases.get(i).getProp<0>(p)++;
+ phases.get(ph_q).getProp<0>(q)++;
+
+ ++Np;
+ }
+
+ ++it;
+ }
+ }
+
+ phases.get(0).ghost_put<add_,0>();
+ phases.get(1).ghost_put<add_,0>();
+ phases.get(2).ghost_put<add_,0>();
+ phases.get(3).ghost_put<add_,0>();
+
+ it = phases.get(0).getDomainIterator();
+ while (it.isNext())
+ {
+ auto p = it.get();
+
+ ret &= phases.get(0).getProp<0>(p) == 32;
+ ret &= phases.get(1).getProp<0>(p) == 32;
+ ret &= phases.get(2).getProp<0>(p) == 32;
+ ret &= phases.get(3).getProp<0>(p) == 32;
+
+ ++it;
+ }
+
+ BOOST_REQUIRE_EQUAL(ret,true);
+}
+
+BOOST_AUTO_TEST_SUITE_END()
+
+#endif /* SRC_VECTOR_VECTOR_DIST_MP_UNIT_TESTS_HPP_ */
diff --git a/src/Vector/vector_dist_multiphase_functions.hpp b/src/Vector/vector_dist_multiphase_functions.hpp
new file mode 100644
index 000000000..4a3c6e32b
--- /dev/null
+++ b/src/Vector/vector_dist_multiphase_functions.hpp
@@ -0,0 +1,126 @@
+/*
+ * vector_dist_multiphase_functions.hpp
+ *
+ * Created on: Oct 14, 2016
+ * Author: i-bird
+ */
+
+#ifndef SRC_VECTOR_VECTOR_DIST_MULTIPHASE_FUNCTIONS_HPP_
+#define SRC_VECTOR_VECTOR_DIST_MULTIPHASE_FUNCTIONS_HPP_
+
+#include "NN/CellList/CellListM.hpp"
+#include "NN/VerletList/VerletListM.hpp"
+
+template<typename Vector,typename CL, typename T> VerletList<Vector::dims,typename Vector::stype,FAST,shift<Vector::dims,typename Vector::stype>> createVerlet(Vector & v, CL & cl, T r_cut)
+{
+ VerletList<Vector::dims,typename Vector::stype,FAST,shift<Vector::dims,typename Vector::stype>> ver;
+
+ ver.Initialize(cl,r_cut,v.getPosVector(),v.size_local());
+
+ return ver;
+}
+
+template<unsigned int sh_byte, typename Vector,typename CL, typename T> VerletListM<Vector::dims,typename Vector::stype,sh_byte,shift<Vector::dims,typename Vector::stype>> createVerletM(Vector & v, CL & cl, T r_cut)
+{
+ VerletListM<Vector::dims,typename Vector::stype,sh_byte,shift<Vector::dims,typename Vector::stype>> ver;
+
+ ver.Initialize(cl,r_cut,v.getPosVector(),v.size_local());
+
+ return ver;
+}
+
+template<unsigned int nbit, typename Vector, typename T> CellListM<Vector::dims,typename Vector::stype,nbit> createCellListM(openfpm::vector<Vector> & phases, T r_cut)
+{
+ size_t div[3];
+ Box<Vector::dims,typename Vector::stype> box_cl;
+
+ CellListM<Vector::dims,typename Vector::stype,nbit> NN;
+ if (phases.size() == 0)
+ return NN;
+
+ box_cl = phases.get(0).getDecomposition().getProcessorBounds();
+ phases.get(0).getCellListParams(r_cut,div,box_cl);
+
+ NN.Initialize(box_cl,div);
+
+ // for all the phases i
+ for (size_t i = 0; i < phases.size() ; i++)
+ {
+ // iterate across all the particle of the phase i
+ auto it = phases.get(i).getDomainAndGhostIterator();
+ while (it.isNext())
+ {
+ auto key = it.get();
+
+ // Add the particle of the phase i to the cell list
+ NN.add(phases.get(i).getPos(key), key.getKey(), i);
+
+ ++it;
+ }
+ }
+
+ return NN;
+}
+
+
+/////// Symmetric version
+
+template<typename Vector,typename CL, typename T> VerletList<Vector::dims,typename Vector::stype,FAST,shift<Vector::dims,typename Vector::stype>> createVerletSym(Vector & v, CL & cl, T r_cut)
+{
+ VerletList<Vector::dims,typename Vector::stype,FAST,shift<Vector::dims,typename Vector::stype>> ver;
+
+ ver.Initialize(cl,r_cut,v.getPosVector(),v.size_local());
+
+ return ver;
+}
+
+template<unsigned int sh_byte, typename Vector,typename CL, typename T> VerletListM<Vector::dims,typename Vector::stype,sh_byte,shift<Vector::dims,typename Vector::stype>> createVerletSymM(Vector & v, CL & cl, T r_cut)
+{
+ VerletListM<Vector::dims,typename Vector::stype,sh_byte,shift<Vector::dims,typename Vector::stype>> ver;
+
+ ver.Initialize(cl,r_cut,v.getPosVector(),v.size_local(),VL_SYMMETRIC);
+
+ return ver;
+}
+
+template<unsigned int nbit, typename Vector, typename T> CellListM<Vector::dims,typename Vector::stype,nbit> createCellListSymM(openfpm::vector<Vector> & phases, T r_cut)
+{
+ Box<Vector::dims,typename Vector::stype> box_cl;
+
+ CellListM<Vector::dims,typename Vector::stype,nbit> NN;
+ if (phases.size() == 0)
+ return NN;
+
+ // Calculate the Cell list division for this CellList
+ CellDecomposer_sm<Vector::dims,typename Vector::stype,shift<Vector::dims,typename Vector::stype>> cd_sm;
+
+ size_t pad = 0;
+ cl_param_calculateSym(phases.get(0).getDecomposition().getDomain(),cd_sm,phases.get(0).getDecomposition().getGhost(),r_cut,pad);
+
+ // Processor bounding box
+ Box<Vector::dims, typename Vector::stype> pbox = phases.get(0).getDecomposition().getProcessorBounds();
+
+ // Ghost padding extension
+ Ghost<Vector::dims,size_t> g_ext(0);
+ NN.Initialize(cd_sm,pbox,pad);
+
+ // for all the phases i
+ for (size_t i = 0; i < phases.size() ; i++)
+ {
+ // iterate across all the particle of the phase i
+ auto it = phases.get(i).getDomainAndGhostIterator();
+ while (it.isNext())
+ {
+ auto key = it.get();
+
+ // Add the particle of the phase i to the cell list
+ NN.add(phases.get(i).getPos(key), key.getKey(), i);
+
+ ++it;
+ }
+ }
+
+ return NN;
+}
+
+#endif /* SRC_VECTOR_VECTOR_DIST_MULTIPHASE_FUNCTIONS_HPP_ */
diff --git a/src/Vector/vector_dist_unit_test.hpp b/src/Vector/vector_dist_unit_test.hpp
index 8c3c800e3..866868b36 100644
--- a/src/Vector/vector_dist_unit_test.hpp
+++ b/src/Vector/vector_dist_unit_test.hpp
@@ -1523,6 +1523,24 @@ BOOST_AUTO_TEST_CASE( vector_dist_ghost_with_ghost_buffering )
vd.map();
vd.ghost_get<0,1,2>();
+ // shift the particle position by 1.0
+
+ it = vd.getGhostIterator();
+ while (it.isNext())
+ {
+ // Particle p
+ auto p = it.get();
+
+ // we shift down he particles
+ vd.getPos(p)[0] = 10.0;
+
+ // we shift
+ vd.getPos(p)[1] = 17.0;
+
+ // next particle
+ ++it;
+ }
+
for (size_t i = 0 ; i < 10 ; i++)
{
auto it = vd.getDomainIterator();
@@ -1543,7 +1561,7 @@ BOOST_AUTO_TEST_CASE( vector_dist_ghost_with_ghost_buffering )
++it;
}
- vd.ghost_get<0>(SKIP_LABELLING);
+ vd.ghost_get<0>(SKIP_LABELLING | NO_POSITION);
auto it2 = vd.getGhostIterator();
bool ret = true;
@@ -1560,6 +1578,22 @@ BOOST_AUTO_TEST_CASE( vector_dist_ghost_with_ghost_buffering )
++it2;
}
+ it2 = vd.getGhostIterator();
+ while (it2.isNext())
+ {
+ // Particle p
+ auto p = it.get();
+
+ // we shift down he particles
+ ret &= vd.getPos(p)[0] == 10.0;
+
+ // we shift
+ ret &= vd.getPos(p)[1] == 17.0;
+
+ // next particle
+ ++it2;
+ }
+
BOOST_REQUIRE_EQUAL(ret,true);
}
}
--
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