From 4e9909f5aa6ba293c2ae466f117183c3ba54e84e Mon Sep 17 00:00:00 2001
From: Pietro Incardona <i-bird@linux.fritz.box>
Date: Tue, 9 Aug 2016 10:25:08 +0200
Subject: [PATCH] Adding some example
---
example/Vector/0_simple/main.cpp | 7 +-
example/Vector/1_celllist/main.cpp | 7 +-
example/Vector/3_molecular_dynamic/main.cpp | 12 +-
example/Vector/4_reorder/no_reorder.html | 3023 +++++++++++++++++++
example/Vector/4_reorder/reorder_10000.html | 3021 ++++++++++++++++++
example/Vector/4_reorder/reorder_200.html | 3021 ++++++++++++++++++
openfpm_data | 2 +-
openfpm_devices | 2 +-
src/Decomposition/ie_ghost.hpp | 2 +-
src/Grid/grid_dist_id.hpp | 2 +
src/Grid/grid_dist_id_iterator.hpp | 24 +
src/Grid/grid_dist_id_unit_test.cpp | 24 +-
src/Makefile.am | 2 +-
src/Vector/vector_dist.hpp | 83 +-
src/Vector/vector_dist_performance_util.hpp | 53 +
src/Vector/vector_dist_unit_test.hpp | 74 +
16 files changed, 9321 insertions(+), 38 deletions(-)
create mode 100644 example/Vector/4_reorder/no_reorder.html
create mode 100644 example/Vector/4_reorder/reorder_10000.html
create mode 100644 example/Vector/4_reorder/reorder_200.html
diff --git a/example/Vector/0_simple/main.cpp b/example/Vector/0_simple/main.cpp
index b18d4650f..0b7a3364b 100644
--- a/example/Vector/0_simple/main.cpp
+++ b/example/Vector/0_simple/main.cpp
@@ -4,6 +4,9 @@
* \subpage Vector_1_celllist
* \subpage Vector_2_expression
* \subpage Vector_3_md
+ * \subpage Vector_4_reo
+ * \subpage Vector_4_comp_reo
+ * \subpage Vector_4_complex_prop
*
*/
@@ -179,10 +182,10 @@ int main(int argc, char* argv[])
auto key = it.get();
// we define x, assign a random position between 0.0 and 1.0
- vd.getPos(key)[0] = rand() / RAND_MAX;
+ vd.getPos(key)[0] = (float)rand() / RAND_MAX;
// we define y, assign a random position between 0.0 and 1.0
- vd.getPos(key)[1] = rand() / RAND_MAX;
+ vd.getPos(key)[1] = (float)rand() / RAND_MAX;
// next particle
++it;
diff --git a/example/Vector/1_celllist/main.cpp b/example/Vector/1_celllist/main.cpp
index 8bda5b858..c6197f421 100644
--- a/example/Vector/1_celllist/main.cpp
+++ b/example/Vector/1_celllist/main.cpp
@@ -306,9 +306,6 @@ int main(int argc, char* argv[])
//! \cond [verletlist] \endcond
openfpm::vector<openfpm::vector<size_t>> verlet;
-
- // interaction radius
- float r_cut = 1.0/(128-2);
vd.getVerlet(verlet,r_cut);
// For each particle i verlet.size() == Number of particles
@@ -324,8 +321,10 @@ int main(int argc, char* argv[])
// for each neighborhood j of particle to i
for (size_t j = 0 ; j < NN.size() ; j++)
{
+ size_t p = NN.get(j);
+
// Get the position of the particle neighborhood if i
- Point<3,float> xq = vd.getPos(NN.get(j));
+ Point<3,float> xq = vd.getPos(p);
// Calculate the distance vector between p and q
Point<3,float> f = (xp - xq);
diff --git a/example/Vector/3_molecular_dynamic/main.cpp b/example/Vector/3_molecular_dynamic/main.cpp
index 86dd675c1..ac62885fb 100644
--- a/example/Vector/3_molecular_dynamic/main.cpp
+++ b/example/Vector/3_molecular_dynamic/main.cpp
@@ -33,7 +33,7 @@ constexpr int force = 1;
*
* \page Vector_3_md Vector 3 molecular dynamic
*
- * ## Calculate forces ##
+ * ## Calculate forces ## {#e3_md_cf}
*
* In this function we calculate the forces between particles. It require the vector of particles
* Cell list and scaling factor for the Lennard-Jhones potential.
@@ -154,7 +154,7 @@ void calc_forces(vector_dist<3,double, aggregate<double[3],double[3]> > & vd, Ce
/*!
* \page Vector_3_md Vector 3 molecular dynamic
*
- * ## Calculate energy ##
+ * ## Calculate energy ## {#e3_md_ce}
*
* We also need a function to calculate energy, this function require the same parameter as calculate forces
*
@@ -272,7 +272,7 @@ int main(int argc, char* argv[])
/*!
* \page Vector_3_md Vector 3 molecular dynamic
*
- * ## Initialization ##
+ * ## Initialization ## {#e3_md_init}
*
* After we defined the two main function calc forces and calc energy, we define
* important parameters of the simulation, time step integration,
@@ -347,7 +347,7 @@ int main(int argc, char* argv[])
/*!
* \page Vector_3_md Vector 3 molecular dynamic
*
- * ## Particles on a grid like position ##
+ * ## Particles on a grid like position ## {#e3_md_gl}
*
* We define a grid iterator, to create particles on a grid like way. In the same cycle we also reset
* force and velocity
@@ -388,7 +388,7 @@ int main(int argc, char* argv[])
/*!
* \page Vector_3_md Vector 3 molecular dynamic
*
- * ## Molecular dynamic steps ##
+ * ## Molecular dynamic steps ## {#e3_md_vi}
*
* Here we do 10000 MD steps using verlet integrator
*
@@ -509,7 +509,7 @@ int main(int argc, char* argv[])
/*!
* \page Vector_3_md Vector 3 molecular dynamic
*
- * ## Plotting graphs ##
+ * ## Plotting graphs ## {#e3_md_pg}
*
* After we terminate the MD steps our vector x contains at which iteration we calculated the energy
* while y contains the energy value at that time-step. We can produce a graph X Y
diff --git a/example/Vector/4_reorder/no_reorder.html b/example/Vector/4_reorder/no_reorder.html
new file mode 100644
index 000000000..ea901c139
--- /dev/null
+++ b/example/Vector/4_reorder/no_reorder.html
@@ -0,0 +1,3023 @@
+ <script type="text/javascript" src="https://www.gstatic.com/charts/loader.js"></script>
+ <script type="text/javascript">
+ google.charts.load('current', {'packages':['corechart']});
+ google.charts.setOnLoadCallback(drawVisualization);
+
+
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+[27370,0.067627],
+[27380,0.0679012],
+[27390,0.068008],
+[27400,0.0615957],
+[27410,0.0662527],
+[27420,0.0663246],
+[27430,0.0665131],
+[27440,0.0664668],
+[27450,0.066576],
+[27460,0.0666348],
+[27470,0.0667531],
+[27480,0.066585],
+[27490,0.0670569],
+[27500,0.0668247],
+[27510,0.0672195],
+[27520,0.066988],
+[27530,0.0754134],
+[27540,0.0670947],
+[27550,0.0671704],
+[27560,0.0671648],
+[27570,0.0674943],
+[27580,0.0674597],
+[27590,0.0676229],
+[27600,0.061417],
+[27610,0.0661571],
+[27620,0.066179],
+[27630,0.0664136],
+[27640,0.0664521],
+[27650,0.0663764],
+[27660,0.0665172],
+[27670,0.0665489],
+[27680,0.0667355],
+[27690,0.0666544],
+[27700,0.0668166],
+[27710,0.0669402],
+[27720,0.0669557],
+[27730,0.0676617],
+[27740,0.0670829],
+[27750,0.0672079],
+[27760,0.0690708],
+[27770,0.0672863],
+[27780,0.0672775],
+[27790,0.0675224],
+[27800,0.0616887],
+[27810,0.066388],
+[27820,0.0661582],
+[27830,0.070088],
+[27840,0.0662411],
+[27850,0.0663081],
+[27860,0.0665059],
+[27870,0.0664487],
+[27880,0.0669701],
+[27890,0.0666719],
+[27900,0.0666063],
+[27910,0.0689808],
+[27920,0.0669706],
+[27930,0.0669238],
+[27940,0.0673359],
+[27950,0.067171],
+[27960,0.0670581],
+[27970,0.0673313],
+[27980,0.0676458],
+[27990,0.0672082],
+[28000,0.0613572],
+[28010,0.0660919],
+[28020,0.0662571],
+[28030,0.0662212],
+[28040,0.066396],
+[28050,0.0663594],
+[28060,0.0665996],
+[28070,0.0664796],
+[28080,0.0665605],
+[28090,0.0664925],
+[28100,0.0665098],
+[28110,0.0667828],
+[28120,0.0669367],
+[28130,0.0673012],
+[28140,0.0670155],
+[28150,0.0670136],
+[28160,0.0672305],
+[28170,0.0671933],
+[28180,0.0671339],
+[28190,0.0672318],
+[28200,0.0618736],
+[28210,0.0751749],
+[28220,0.06593],
+[28230,0.0661386],
+[28240,0.0664151],
+[28250,0.0661881],
+[28260,0.0666777],
+[28270,0.0663621],
+[28280,0.0663062],
+[28290,0.0664607],
+[28300,0.0664408],
+[28310,0.0666982],
+[28320,0.0666156],
+[28330,0.0667925],
+[28340,0.0667224],
+[28350,0.0668073],
+[28360,0.06689],
+[28370,0.0670645],
+[28380,0.0671938],
+[28390,0.067238],
+[28400,0.0629119],
+[28410,0.065768],
+[28420,0.0657286],
+[28430,0.065887],
+[28440,0.0659172],
+[28450,0.0732268],
+[28460,0.0729568],
+[28470,0.0760136],
+[28480,0.0663306],
+[28490,0.0664434],
+[28500,0.0669928],
+[28510,0.0775773],
+[28520,0.068647],
+[28530,0.0668149],
+[28540,0.0667469],
+[28550,0.0668856],
+[28560,0.0668441],
+[28570,0.0669857],
+[28580,0.0669495],
+[28590,0.0669466],
+[28600,0.0617759],
+[28610,0.0657715],
+[28620,0.0659094],
+[28630,0.0659811],
+[28640,0.066059],
+[28650,0.0659247],
+[28660,0.0660815],
+[28670,0.0665136],
+[28680,0.0662522],
+[28690,0.0662991],
+[28700,0.0670135],
+[28710,0.0664842],
+[28720,0.066507],
+[28730,0.0664852],
+[28740,0.0666016],
+[28750,0.0687182],
+[28760,0.0668687],
+[28770,0.0670036],
+[28780,0.0669777],
+[28790,0.0670478],
+[28800,0.0608617],
+[28810,0.0666932],
+[28820,0.0657153],
+[28830,0.0657676],
+[28840,0.0658071],
+[28850,0.0658753],
+[28860,0.0662504],
+[28870,0.066423],
+[28880,0.0660712],
+[28890,0.0744867],
+[28900,0.0662039],
+[28910,0.0663565],
+[28920,0.0663546],
+[28930,0.0664407],
+[28940,0.0666461],
+[28950,0.0666672],
+[28960,0.066744],
+[28970,0.0668414],
+[28980,0.0668137],
+[28990,0.0668328],
+[29000,0.0610747],
+[29010,0.0656692],
+[29020,0.065617],
+[29030,0.0656931],
+[29040,0.0675438],
+[29050,0.0657247],
+[29060,0.0658678],
+[29070,0.065822],
+[29080,0.0658516],
+[29090,0.0666068],
+[29100,0.0660199],
+[29110,0.0662744],
+[29120,0.0663334],
+[29130,0.0665079],
+[29140,0.0666716],
+[29150,0.0666633],
+[29160,0.0666534],
+[29170,0.0670362],
+[29180,0.0669711],
+[29190,0.0671669],
+[29200,0.0617813],
+[29210,0.0656473],
+[29220,0.0657926],
+[29230,0.0658049],
+[29240,0.0658103],
+[29250,0.0659391],
+[29260,0.0659811],
+[29270,0.0662582],
+[29280,0.0662709],
+[29290,0.0662952],
+[29300,0.0662956],
+[29310,0.0665375],
+[29320,0.0667662],
+[29330,0.0666507],
+[29340,0.0667729],
+[29350,0.0671904],
+[29360,0.0669527],
+[29370,0.0676529],
+[29380,0.066941],
+[29390,0.0671373],
+[29400,0.0609652],
+[29410,0.0678232],
+[29420,0.0659643],
+[29430,0.0659679],
+[29440,0.0660097],
+[29450,0.0661144],
+[29460,0.0663559],
+[29470,0.0660932],
+[29480,0.0662008],
+[29490,0.066305],
+[29500,0.0720171],
+[29510,0.0666074],
+[29520,0.0668451],
+[29530,0.0666018],
+[29540,0.0667379],
+[29550,0.0666789],
+[29560,0.0665507],
+[29570,0.0669804],
+[29580,0.0668747],
+[29590,0.0668949],
+[29600,0.0607842],
+[29610,0.0654884],
+[29620,0.065859],
+[29630,0.0659515],
+[29640,0.0656517],
+[29650,0.0660389],
+[29660,0.0670411],
+[29670,0.0662775],
+[29680,0.0663648],
+[29690,0.0659095],
+[29700,0.0671183],
+[29710,0.0662409],
+[29720,0.0667549],
+[29730,0.0662609],
+[29740,0.0664278],
+[29750,0.0664463],
+[29760,0.0664993],
+[29770,0.0665851],
+[29780,0.0667814],
+[29790,0.0665125],
+[29800,0.0603979],
+[29810,0.0653865],
+[29820,0.0653331],
+[29830,0.0659518],
+[29840,0.0655267],
+[29850,0.0663368],
+[29860,0.0655432],
+[29870,0.0657105],
+[29880,0.0656853],
+[29890,0.0671827],
+[29900,0.0667766],
+[29910,0.0668508],
+[29920,0.0661257],
+[29930,0.0662415],
+[29940,0.0662618],
+[29950,0.0663139],
+[29960,0.0665374],
+[29970,0.0664781],
+[29980,0.0667351],
+[29990,0.0666235],
+]);
+var options0= {
+title : 'Force calculation time',
+vAxis: {title: 'Time'},
+hAxis: {title: 'iteration'},
+curveType: 'function',
+lineWidth: 1,
+intervals: { 'style':'area' },
+explorer: {actions: ['dragToZoom', 'rightClickToReset'],axis: 'horizontal,vertical',keepInBounds: true, maxZoomIn: 128.0},hAxis: { logscale: true },vAxis: { logscale: true }};
+var chart = new google.visualization.ComboChart(document.getElementById('chart_div3'));chart.draw(data0, options0);
+}</script>
+<div id="chart_div3" style="width: 900px; height: 500px;"></div>
diff --git a/openfpm_data b/openfpm_data
index 24469b200..e2d9725f7 160000
--- a/openfpm_data
+++ b/openfpm_data
@@ -1 +1 @@
-Subproject commit 24469b20034a8513d205e46db2aa058b824725be
+Subproject commit e2d9725f7101cf273213f69a6f91655c9112c17a
diff --git a/openfpm_devices b/openfpm_devices
index 36227626f..95ed584d3 160000
--- a/openfpm_devices
+++ b/openfpm_devices
@@ -1 +1 @@
-Subproject commit 36227626f5a6020d8f4ecd7d26a9261b37e9101b
+Subproject commit 95ed584d33c976f3e13568ec8fd9c391de95db07
diff --git a/src/Decomposition/ie_ghost.hpp b/src/Decomposition/ie_ghost.hpp
index 8b1923b68..36648c136 100755
--- a/src/Decomposition/ie_ghost.hpp
+++ b/src/Decomposition/ie_ghost.hpp
@@ -455,7 +455,7 @@ public:
proc_int_box = ie.proc_int_box;
vb_ext = ie.vb_ext;
vb_int = ie.vb_int;
- geo_cell = geo_cell;
+ geo_cell = ie.geo_cell;
shifts = ie.shifts;
ids_p = ie.ids_p;
ids = ie.ids;
diff --git a/src/Grid/grid_dist_id.hpp b/src/Grid/grid_dist_id.hpp
index b9d3df791..452fcc657 100644
--- a/src/Grid/grid_dist_id.hpp
+++ b/src/Grid/grid_dist_id.hpp
@@ -135,6 +135,8 @@ class grid_dist_id
/*! \brief flip box just convert and internal ghost box into an external ghost box
*
+ * \param box to convert
+ * \param cmb sector position of the box
*
*/
Box<dim,long int> flip_box(const Box<dim,long int> & box, const comb<dim> & cmb)
diff --git a/src/Grid/grid_dist_id_iterator.hpp b/src/Grid/grid_dist_id_iterator.hpp
index 571b6d6ac..84b2cd8db 100644
--- a/src/Grid/grid_dist_id_iterator.hpp
+++ b/src/Grid/grid_dist_id_iterator.hpp
@@ -208,6 +208,18 @@ class grid_dist_iterator<dim,device_grid,FREE>
return start;
}
+
+ /*! \brief Get the boxes
+ *
+ * Get the boxes that define the local grids
+ *
+ * \return Vector of local boxes
+ *
+ */
+ inline const openfpm::vector<GBoxes<device_grid::dims>> & getGBoxes()
+ {
+ return gdb_ext;
+ }
};
@@ -333,6 +345,18 @@ class grid_dist_iterator<dim,device_grid,FIXED>
{
return grid_dist_key_dx<dim>(g_c,a_it.get());
}
+
+ /*! \brief Get the boxes
+ *
+ * Get the boxes that define the local grids
+ *
+ * \return Vector of local boxes
+ *
+ */
+ inline const openfpm::vector<GBoxes<device_grid::dims>> & getGBoxes()
+ {
+ return gdb_ext;
+ }
};
#endif /* GRID_DIST_ID_ITERATOR_SUB_HPP_ */
diff --git a/src/Grid/grid_dist_id_unit_test.cpp b/src/Grid/grid_dist_id_unit_test.cpp
index 06f69aa4c..c557db317 100644
--- a/src/Grid/grid_dist_id_unit_test.cpp
+++ b/src/Grid/grid_dist_id_unit_test.cpp
@@ -1451,6 +1451,9 @@ void Test3D_periodic(const Box<3,float> & domain, long int k)
auto key = dom_gi.get();
auto key_g = g_dist.getGKey(key);
+ // Return the external boxes
+ auto & gb = dom_gi.getGBoxes();
+
// transform the key to be periodic
for (size_t i = 0 ; i < 3 ; i++)
{
@@ -1463,8 +1466,25 @@ void Test3D_periodic(const Box<3,float> & domain, long int k)
if (g_dist.template get<0>(key) != -1 && out_p == true)
out_cnt++;
- if ( g_dist.template get<0>(key) != -1 && info.LinId(key_g) != g_dist.template get<0>(key) )
- match &= false;
+ // The last points can be invalid because of rounding off problems
+ bool can_invalid = false;
+ if (key.getKey().get(0) == 0 || key.getKey().get(1) == 0 || key.getKey().get(2) == 0)
+ can_invalid = true;
+ else if (key.getKey().get(0) == gb.get(key.getSub()).GDbox.getHigh(0) ||
+ key.getKey().get(1) == gb.get(key.getSub()).GDbox.getHigh(1) ||
+ key.getKey().get(2) == gb.get(key.getSub()).GDbox.getHigh(2))
+ can_invalid = true;
+
+ if (can_invalid == true)
+ {
+ if ( g_dist.template get<0>(key) != -1 && info.LinId(key_g) != g_dist.template get<0>(key) )
+ match &= false;
+ }
+ else
+ {
+ if (info.LinId(key_g) != g_dist.template get<0>(key) )
+ match &= false;
+ }
++dom_gi;
}
diff --git a/src/Makefile.am b/src/Makefile.am
index a052e4db5..d61146d9d 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -5,7 +5,7 @@ pdata_SOURCES = main.cpp Grid/grid_dist_id_unit_test.cpp lib/pdata.cpp test_mul
pdata_CXXFLAGS = $(LIBHILBERT_INCLUDE) $(PETSC_INCLUDE) $(HDF5_CPPFLAGS) $(CUDA_CFLAGS) $(INCLUDES_PATH) $(PARMETIS_INCLUDE) $(METIS_INCLUDE) $(BOOST_CPPFLAGS) $(H5PART_INCLUDE) -DPARALLEL_IO -Wno-unused-local-typedefs
pdata_CFLAGS = $(CUDA_CFLAGS)
pdata_LDADD = $(LINKLIBS) -lparmetis -lmetis
-nobase_include_HEADERS = Decomposition/CartDecomposition.hpp Decomposition/common.hpp Decomposition/Decomposition.hpp Decomposition/ie_ghost.hpp \
+nobase_include_HEADERS = Decomposition/CartDecomposition.hpp Decomposition/CartDecomposition_ext.hpp Decomposition/common.hpp Decomposition/Decomposition.hpp Decomposition/ie_ghost.hpp \
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 \
diff --git a/src/Vector/vector_dist.hpp b/src/Vector/vector_dist.hpp
index 33ad138a7..93005267e 100644
--- a/src/Vector/vector_dist.hpp
+++ b/src/Vector/vector_dist.hpp
@@ -795,29 +795,13 @@ private:
return pbox;
}
-public:
-
- //! space type
- typedef St stype;
-
- //! dimensions of space
- static const unsigned int dims = dim;
-
- /*! \brief Constructor
+ /*! \brief Initialize the structures
*
- * \param np number of elements
- * \param box domain where the vector of elements live
- * \param boundary conditions
- * \param g Ghost margins
+ * \param np number of particles
*
*/
- vector_dist(size_t np, Box<dim, St> box, const size_t (&bc)[dim], const Ghost<dim, St> & g) :
- dec(create_vcluster()), v_cl(create_vcluster())
+ void init_structures(size_t np)
{
-#ifdef SE_CLASS2
- check_new(this,8,VECTOR_DIST_EVENT,4);
-#endif
-
// convert to a local number of elements
size_t p_np = np / v_cl.getProcessingUnits();
@@ -835,7 +819,17 @@ public:
v_prp.resize(p_np);
g_m = p_np;
+ }
+ /*! \brief Initialize the decomposition
+ *
+ * \param box domain
+ * \param bc boundary conditions
+ * \param g ghost extension
+ *
+ */
+ void init_decomposition(Box<dim,St> & box, const size_t (& bc)[dim],const Ghost<dim,St> & g)
+ {
// Create a valid decomposition of the space
// Get the number of processor and calculate the number of sub-domain
// for decomposition
@@ -855,6 +849,53 @@ public:
dec.decompose();
}
+public:
+
+ //! space type
+ typedef St stype;
+
+ //! dimensions of space
+ static const unsigned int dims = dim;
+
+
+ /*! \brief Constructor
+ *
+ * \param np number of elements
+ * \param box domain where the vector of elements live
+ * \param boundary conditions
+ * \param g Ghost margins
+ *
+ */
+ vector_dist(const Decomposition & dec, size_t np) :
+ dec(dec), v_cl(create_vcluster())
+ {
+#ifdef SE_CLASS2
+ check_new(this,8,VECTOR_DIST_EVENT,4);
+#endif
+
+ init_structures(np);
+ }
+
+
+ /*! \brief Constructor
+ *
+ * \param np number of elements
+ * \param box domain where the vector of elements live
+ * \param boundary conditions
+ * \param g Ghost margins
+ *
+ */
+ vector_dist(size_t np, Box<dim, St> box, const size_t (&bc)[dim], const Ghost<dim, St> & g) :
+ dec(create_vcluster()), v_cl(create_vcluster())
+ {
+#ifdef SE_CLASS2
+ check_new(this,8,VECTOR_DIST_EVENT,4);
+#endif
+
+ init_structures(np);
+ init_decomposition(box,bc,g);
+ }
+
~vector_dist()
{
#ifdef SE_CLASS2
@@ -1296,7 +1337,7 @@ public:
{
// Get ghost and anlarge by 1%
Ghost<dim,St> g = dec.getGhost();
- g.magnify(1.01);
+ g.magnify(1.013);
return getCellList_hilb(r_cut, g);
}
@@ -1325,6 +1366,8 @@ public:
++it;
}
+
+ cell_list.set_gm(g_m);
}
/*! \brief Construct a cell list starting from the stored particles
diff --git a/src/Vector/vector_dist_performance_util.hpp b/src/Vector/vector_dist_performance_util.hpp
index ae373d23c..ef9bbdbb4 100644
--- a/src/Vector/vector_dist_performance_util.hpp
+++ b/src/Vector/vector_dist_performance_util.hpp
@@ -155,6 +155,59 @@ template<unsigned int dim, size_t prp = 0, typename T, typename V> void calc_for
}
}
+
+/*! \brief For each particle of vd calculate the accumulation of the distances of the neighborhood
+ * particles inside vd2
+ *
+ *
+ * \param NN Cell list vd
+ * \param NN2 Cell list vd2
+ * \param vd Distributed vector
+ * \param vd2 Distributed vector 2
+ * \param r_cut Cut-off radius
+ *
+ */
+template<unsigned int dim, unsigned int prp, typename T, typename V> void cross_calc(T & NN, T & NN2, V & vd, V & vd2)
+{
+ auto it_v = vd.getDomainIterator();
+
+ float sum[dim];
+
+ for (size_t i = 0; i < dim; i++)
+ sum[i] = 0;
+
+ while (it_v.isNext())
+ {
+ //key
+ vect_dist_key_dx key = it_v.get();
+
+ // Get the position of the particles
+ Point<dim,float> p = vd.getPos(key);
+
+ // Get the neighborhood of the particle
+ auto cell_it = NN2.template getNNIterator<NO_CHECK>(NN2.getCell(p));
+
+ double sum = 0.0;
+
+ while(cell_it.isNext())
+ {
+ auto nnp = cell_it.get();
+
+ Point<dim,float> q = vd2.getPos(nnp);
+
+ sum += norm(p - q);
+
+ //Next particle in a cell
+ ++cell_it;
+ }
+
+ vd.template getProp<prp>(key) = sum;
+
+ //Next particle in cell list
+ ++it_v;
+ }
+}
+
/*! \brief Benchmark particles' forces time
*
* \param NN Cell list
diff --git a/src/Vector/vector_dist_unit_test.hpp b/src/Vector/vector_dist_unit_test.hpp
index b726fe0ae..b589959c3 100644
--- a/src/Vector/vector_dist_unit_test.hpp
+++ b/src/Vector/vector_dist_unit_test.hpp
@@ -431,6 +431,80 @@ BOOST_AUTO_TEST_CASE( vector_dist_iterator_test_use_3d )
}
}
+
+BOOST_AUTO_TEST_CASE( vector_dist_iterator_fixed_dec_3d )
+{
+ Vcluster & v_cl = create_vcluster();
+
+ // 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 = 52428 * v_cl.getProcessingUnits();
+
+ long int big_step = k / 4;
+ big_step = (big_step == 0)?1:big_step;
+
+ print_test_v( "Testing 3D vector copy decomposition k<=",k);
+
+ // 3D test
+ for ( ; k >= 2 ; k-= decrement(k,big_step) )
+ {
+ BOOST_TEST_CHECKPOINT( "Testing 3D vector copy decomposition k=" << k );
+
+ 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};
+
+ vector_dist<3,float, aggregate<double,double> > vd(k,box,bc,Ghost<3,float>(0.05));
+ vector_dist<3,float, aggregate<double,double> > vd2(vd.getDecomposition(),k);
+
+ 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);
+
+ vd2.getPos(key)[0] = vd.getPos(key)[0];
+ vd2.getPos(key)[1] = vd.getPos(key)[1];
+ vd2.getPos(key)[2] = vd.getPos(key)[2];
+
+ ++it;
+ }
+
+ vd.map();
+ vd2.map();
+
+ vd.ghost_get();
+ vd2.ghost_get();
+
+ auto NN = vd.getCellList(0.05);
+ auto NN2 = vd2.getCellList(0.05);
+
+ cross_calc<3,0>(NN,NN2,vd,vd2);
+ cross_calc<3,1>(NN,NN,vd,vd);
+
+
+ auto it3 = vd.getIterator();
+
+ while (it3.isNext())
+ {
+ auto key = it3.get();
+
+ BOOST_REQUIRE_EQUAL(vd.getProp<0>(key),vd.getProp<1>(key));
+
+ ++it3;
+ }
+ }
+}
+
BOOST_AUTO_TEST_CASE( vector_dist_periodic_test_use_2d )
{
Vcluster & v_cl = create_vcluster();
--
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