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Commit 98b6bc78 authored by incardon's avatar incardon
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Branched for release 0.8.0

parent 2a805e31
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configure.ac
View file @ 98b6bc78
......@@ -4,7 +4,7 @@
## Take all the options with the exception of --enable-install-req
AC_PREREQ(2.59)
AC_INIT(FULL-PACKAGE-NAME, VERSION, BUG-REPORT-ADDRESS)
AC_INIT(OpenFPM_numerics, 0.8.0, BUG-REPORT-ADDRESS)
AC_CANONICAL_SYSTEM
AC_CONFIG_SRCDIR([src/main.cpp])
......
src/Draw/DrawParticles.hpp 0 → 100644
View file @ 98b6bc78
/*
* DrawParticles.hpp
*
* Created on: Jan 5, 2017
* Author: i-bird
*/
#ifndef OPENFPM_NUMERICS_SRC_DRAW_DRAWPARTICLES_HPP_
#define OPENFPM_NUMERICS_SRC_DRAW_DRAWPARTICLES_HPP_
#include "PointIterator.hpp"
#include "PointIteratorSkin.hpp"
#include "Vector/vector_dist.hpp"
class DrawParticles
{
public:
template<unsigned int dim, typename T, typename aggr, typename Decomposition> static PointIteratorSkin<dim,T,Decomposition>
DrawSkin(vector_dist<dim,T,aggr,Decomposition> & vd,
size_t (& sz)[dim],
Box<dim,T> & domain,
Box<dim,T> & sub_A,
Box<dim,T> & sub_B)
{
size_t bc[dim];
for (size_t i = 0 ; i < dim ; i++)
bc[i] = NON_PERIODIC;
return PointIteratorSkin<dim,T,Decomposition>(vd.getDecomposition(),sz,domain,sub_A, sub_B, bc);
}
template<unsigned int dim, typename T, typename aggr, typename Decomposition> static PointIteratorSkin<dim,T,Decomposition>
DrawSkin(vector_dist<dim,T,aggr,Decomposition> & vd,
size_t (& sz)[dim],
Box<dim,T> & domain,
openfpm::vector<Box<dim,T>> & sub_A,
Box<dim,T> & sub_B)
{
size_t bc[dim];
for (size_t i = 0 ; i < dim ; i++)
bc[i] = NON_PERIODIC;
PointIteratorSkin<dim,T,Decomposition> it(vd.getDecomposition(),sz,domain,sub_A.get(0), sub_B, bc);
for (size_t i = 1 ; i < sub_A.size() ; i++)
it.addBoxA(Box<dim,T>(sub_A.get(i)));
return it;
}
template<unsigned int dim, typename T, typename aggr, typename Decomposition> static PointIterator<dim,T,Decomposition>
DrawBox(vector_dist<dim,T,aggr,Decomposition> & vd,
size_t (& sz)[dim],
Box<dim,T> & domain,
Box<dim,T> & sub)
{
return PointIterator<dim,T,Decomposition>(vd.getDecomposition(),sz,domain,sub);
}
};
#endif /* OPENFPM_NUMERICS_SRC_DRAW_DRAWPARTICLES_HPP_ */
src/Draw/DrawParticlesGrid.hpp deleted 100644 → 0
View file @ 2a805e31
/*
* DrawParticlesGrid.hpp
*
* Created on: Jan 3, 2017
* Author: i-bird
*/
#ifndef OPENFPM_NUMERICS_SRC_DRAW_DRAWPARTICLESGRID_HPP_
#define OPENFPM_NUMERICS_SRC_DRAW_DRAWPARTICLESGRID_HPP_
/*! \brief this class draw particles on subset of grid-like position
*
\verbatim
Point B
| (0.6,0.6)
+ + + + + | + + + +
+---------------+
+ | + + + + | + + + +
| |
+ | + + + + | + + + +
| |
+ | + + + + | + + + +
| |
+ | + + + + | + + + +
| |
+ | + + + + | + + + +
| |
+ | + + + + | + + + +
| |
+ | + + + + | + + + +
+---------------+
+ + + + + ^ + + + +
(-1.0,-1.0) |
|
(Point A)
\endverbatim
*
*
* Suppose we have a grid 9x9 from (-1.0,-1.0 to 0.6,0.6)
*
* Defined a Box (-0.9,-0.9 to -0.1,0.5)
*
* This class will return the points
*
* (-0.8 -0.8)
* (-0.6 -0.8)
* (-0.4 -0.8)
* ...
* (-0.1,-0.8) Point A
* ...
* (-0.1,0.5) Point B
*
*/
template<unsigned int dim, typename T>
class DrawParticlesGrid
{
/*! \brief Draw Particles
*
* \param sp grid spacing
*
*/
DrawParticlesGrid(T (& sp)[dim], Box<dim,T> & domain)
{
}
PointIterator getPointIterator()
{
}
};
#endif /* OPENFPM_NUMERICS_SRC_DRAW_DRAWPARTICLESGRID_HPP_ */
src/Draw/DrawParticles_unit_tests.hpp
View file @ 98b6bc78
......@@ -9,15 +9,20 @@
#define OPENFPM_NUMERICS_SRC_DRAW_DRAWPARTICLES_UNIT_TESTS_HPP_
#include "PointIterator.hpp"
#include "PointIteratorSkin.hpp"
#include "DrawParticles.hpp"
BOOST_AUTO_TEST_SUITE( draw_particles )
BOOST_AUTO_TEST_CASE(point_iterator)
{
size_t sz[] = {30,17,28};
size_t sz[] = {23,27,20};
Box<3,double> domain({-1.2,0.5,-0.6},{1.0,3.1,1.312});
Box<3,double> sub_domain({-0.2,0.8,0.2},{1.0,1.1,1.0});
Box<3,double> domain({-1.2,0.5,-0.6},{1.0,3.1,1.3});
Box<3,double> sub_domain({-0.15,0.75,0.15},{1.05,1.15,1.05});
Box<3,double> sub_real({-0.1,0.80,0.2},{1.0,1.1,1.0});
size_t sz_sub[] = {12,4,9};
// Boundary conditions
size_t bc[3]={NON_PERIODIC,NON_PERIODIC,NON_PERIODIC};
......@@ -27,7 +32,7 @@ BOOST_AUTO_TEST_CASE(point_iterator)
vector_dist<3,double,aggregate<double>> vd(0,domain,bc,ghost);
PointIterator<3,double,CartDecomposition<3,double>> p(vd.getDecomposition(),sz,domain,sub_domain);
auto p = DrawParticles::DrawBox(vd,sz,domain,sub_domain);
size_t cnt = 0;
......@@ -50,8 +55,67 @@ BOOST_AUTO_TEST_CASE(point_iterator)
Vcluster & v_cl = create_vcluster();
v_cl.sum(cnt);
v_cl.execute();
BOOST_REQUIRE_EQUAL(cnt,sz_sub[0]*sz_sub[1]*sz_sub[2]);
BOOST_REQUIRE_EQUAL(good,true);
Box<3,double> marg = p.getBoxMargins();
BOOST_REQUIRE_CLOSE(marg.getLow(0), sub_real.getLow(0) ,0.0001);
BOOST_REQUIRE_CLOSE(marg.getLow(1), sub_real.getLow(1) ,0.0001);
BOOST_REQUIRE_CLOSE(marg.getLow(2), sub_real.getLow(2) ,0.0001);
BOOST_REQUIRE_CLOSE(marg.getHigh(0), sub_real.getHigh(0) ,0.0001);
BOOST_REQUIRE_CLOSE(marg.getHigh(1), sub_real.getHigh(1) ,0.0001);
BOOST_REQUIRE_CLOSE(marg.getHigh(2), sub_real.getHigh(2) ,0.0001);
}
BOOST_AUTO_TEST_CASE(point_iterator_skin)
{
size_t sz[] = {23,27,20};
Box<3,double> domain({-1.2,0.5,-0.6},{1.0,3.1,1.3});
Box<3,double> sub_domainA({-0.15,0.75,0.15},{1.05,1.15,1.05});
Box<3,double> sub_domainB({-0.25,0.65,0.05},{0.95,1.05,1.05});
// Boundary conditions
size_t bc[3]={NON_PERIODIC,NON_PERIODIC,NON_PERIODIC};
// ghost, big enough to contain the interaction radius
Ghost<3,float> ghost(0.01);
vector_dist<3,double,aggregate<double>> vd(0,domain,bc,ghost);
auto p = DrawParticles::DrawSkin(vd,sz,domain,sub_domainA, sub_domainB);
size_t cnt = 0;
bool good = true;
while (p.isNext())
{
vd.add();
vd.getLastPos()[0] = p.get().get(0);
vd.getLastPos()[1] = p.get().get(1);
vd.getLastPos()[2] = p.get().get(2);
if (!((p.get().get(0) > -0.21 && p.get().get(0) < -0.19) || (p.get().get(1) > 0.69 && p.get().get(1) < 0.71) || (p.get().get(2) > 0.09 && p.get().get(2) < 0.11)) )
good &= false;
if (sub_domainA.isInside(p.get()))
good &= false;
cnt++;
++p;
}
Vcluster & v_cl = create_vcluster();
v_cl.sum(cnt);
v_cl.execute();
BOOST_REQUIRE_EQUAL(cnt,sz[0]*sz[1]*sz[2]);
BOOST_REQUIRE_EQUAL(good,true);
}
......
src/Draw/PointIterator.hpp
View file @ 98b6bc78
......@@ -63,15 +63,17 @@ class PointIterator: protected grid_dist_id_iterator_dec<Decomposition>
//! sub_domain
Box<dim,T> sub_domain;
//! domain
Box<dim,T> domain;
//! Spacing
T sp[dim];
static grid_key_dx<dim> getStart(size_t (& gs)[dim], Box<dim,T> & dom, Box<dim,T> & sub_dom, T (& sp)[dim])
{
for (size_t i = 0 ; i < dim ; i++)
sp[i] = (dom.getHigh(i) - dom.getLow(i)) / gs[i];
sp[i] = (dom.getHigh(i) - dom.getLow(i)) / (gs[i] -1);
Point<dim,T> pstart = sub_dom.getP1();
grid_key_dx<dim> pkey;
for (size_t i = 0 ; i < dim ; i++)
......@@ -83,17 +85,24 @@ class PointIterator: protected grid_dist_id_iterator_dec<Decomposition>
static grid_key_dx<dim> getStop(size_t (& gs)[dim], Box<dim,T> & dom, Box<dim,T> & sub_dom, T (& sp)[dim])
{
for (size_t i = 0 ; i < dim ; i++)
sp[i] = (dom.getHigh(i) - dom.getLow(i)) / gs[i];
sp[i] = (dom.getHigh(i) - dom.getLow(i)) / (gs[i] - 1);
Point<dim,T> pstop = sub_dom.getP2();
grid_key_dx<dim> pkey;
for (size_t i = 0 ; i < dim ; i++)
pkey.set_d(i,std::ceil( (sub_dom.getLow(i) - dom.getLow(i)) / sp[i]));
pkey.set_d(i,std::floor( (sub_dom.getHigh(i) - dom.getLow(i)) / sp[i]));
return pkey;
}
void calculateAp()
{
grid_key_dx<dim> key = grid_dist_id_iterator_dec<Decomposition>::get();
for (size_t i = 0 ; i < dim ; i++)
ap.get(i) = key.get(i) * sp[i] + domain.getLow(i);
}
public:
/*! \brief Draw Particles
......@@ -102,11 +111,9 @@ public:
*
*/
PointIterator( Decomposition & dec, size_t (& sz)[dim], Box<dim,T> & domain, Box<dim,T> & sub_domain)
:grid_dist_id_iterator_dec<Decomposition>(dec, sz, getStart(sz,domain,sub_domain,sp), getStop(sz,domain,sub_domain,sp)),sub_domain(sub_domain)
:grid_dist_id_iterator_dec<Decomposition>(dec, sz, getStart(sz,domain,sub_domain,sp), getStop(sz,domain,sub_domain,sp)),sub_domain(sub_domain),domain(domain)
{
// Calculate the spacing
for (size_t i = 0 ; i < dim ; i++)
sp[i] = domain.getLow(i) / sz[i];
calculateAp();
}
/*! \Return the actual point
......@@ -126,10 +133,7 @@ public:
PointIterator & operator++()
{
grid_dist_id_iterator_dec<Decomposition>::operator++();
grid_key_dx<dim> key = grid_dist_id_iterator_dec<Decomposition>::get();
for (size_t i = 0 ; i < dim ; i++)
ap.get(i) = key.get(i) * sp[i] + sub_domain.getLow(i);
calculateAp();
return *this;
}
......@@ -138,6 +142,31 @@ public:
{
return grid_dist_id_iterator_dec<Decomposition>::isNext();
}
/*! \brief Return the real Margin of the box
*
* For example consider to have a domain (0.0,0.0) to (1.0,1.0)
* 11 points in each direction (spacing 0.1). if we have a sub-domain
* (0.15,0.15) to (0.55,0.55) getBoxMargins return the box (0.2,0.2) to
* (0.5,0.5). the smallest box that enclose the points that the point
* iterator is going to give
*
*/
Box<dim,T> getBoxMargins()
{
Box<dim,T> box;
grid_key_dx<dim> start = grid_dist_id_iterator_dec<Decomposition>::getStart();
grid_key_dx<dim> stop = grid_dist_id_iterator_dec<Decomposition>::getStop();
for (size_t i = 0 ; i < dim ; i++)
{
box.setLow(i, start.get(i)*sp[i] + domain.getLow(i));
box.setHigh(i, stop.get(i)*sp[i] + domain.getLow(i));
}
return box;
}
};
......
src/Draw/PointIteratorSkin.hpp 0 → 100644
View file @ 98b6bc78
/*
* PointIteratorSkin.hpp
*
* Created on: Jan 4, 2017
* Author: i-bird
*/
#ifndef OPENFPM_NUMERICS_SRC_DRAW_POINTITERATORSKIN_HPP_
#define OPENFPM_NUMERICS_SRC_DRAW_POINTITERATORSKIN_HPP_
#include "Grid/Iterators/grid_dist_id_iterator_dec_skin.hpp"
#define RETURN_A 1
#define RETURN_B 2
/*! \brief this class draw particles on subset of grid-like position
*
\verbatim
(Box B)
| (0.6,0.6)
+ + + + | + + + + +
+---+-------+---+
+ | * | + + | * | + + + +
| | |
+ | * | + + | * | + + + +
| | | |
+ | * | + + | * | + + + +
| | | |
+ | * | + + | * | + + + +
| | | |
+ | * | + + | * | + + + +
| | | |
+ | * | + + | * | + + + +
| +-------+ |
+ | * * * * | + + + +
+---------------+
+ + + + + | + + + +
(-1.0,-1.0) |
|
(Box A)
\endverbatim
*
*
* Suppose we have a grid 9x9 from (-1.0,-1.0 to 0.6,0.6)
*
* Defined a Box A (-0.9,-0.9 to -0.1,0.5) and a box B (-0.7, -0.7 to -0.3,0.5)
*
* This class will return the points indicated with *
*
*/
template<unsigned int dim, typename T, typename Decomposition>
class PointIteratorSkin: protected grid_dist_id_iterator_dec_skin<Decomposition>
{
//! Actual point
Point<dim,T> ap;
//! sub_domain (required to filter out points)
openfpm::vector<Box<dim,T>> sub_domainA;
//! domain
Box<dim,T> domain;
//! Spacing
T sp[dim];
static Box<dim,long int> getAB(size_t (& gs)[dim], const Box<dim,T> & dom, const Box<dim,T> & sub_domA , const Box<dim,T> & sub_domB, T (& sp)[dim], size_t AB)
{
for (size_t i = 0 ; i < dim ; i++)
sp[i] = (dom.getHigh(i) - dom.getLow(i)) / (gs[i] -1);
Box<dim,long int> box;
for (size_t i = 0 ; i < dim ; i++)
{
size_t Ast = std::ceil( (sub_domA.getLow(i) - dom.getLow(i)) / sp[i] ) - 1;
size_t Asp = std::floor( (sub_domA.getHigh(i) - dom.getLow(i)) / sp[i] ) + 1;
size_t Bst = std::ceil( (sub_domB.getLow(i) - dom.getLow(i)) / sp[i] );
size_t Bsp = std::floor( (sub_domB.getHigh(i) - dom.getLow(i)) / sp[i] );
// grid_dist_id_iterator_dec_skin only work if A is contained into B
Ast = (Ast < Bst)?Bst:Ast;
Asp = (Asp > Bsp)?Bsp:Asp;
if (AB == RETURN_A)
{
box.setLow(i,Ast);
box.setHigh(i,Asp);
}
else
{
box.setLow(i,Bst);
box.setHigh(i,Bsp);
}
}
return box;
}
void calculateAp()
{
grid_key_dx<dim> key = grid_dist_id_iterator_dec_skin<Decomposition>::get();
for (size_t i = 0 ; i < dim ; i++)
ap.get(i) = key.get(i) * sp[i] + domain.getLow(i);
}
/*! it check that the actual point is not inside B
*
* \return true if the point is not inside B
*
*/
bool isValidPoint()
{
bool valid = true;
for (size_t i = 0 ; i < sub_domainA.size() ; i++)
{
if (Box<dim,T>(sub_domainA.get(i)).isInside(ap) == true)
valid = false;
}
return valid;
}
public:
/*! \brief Draw Particles
*
* \param sp grid spacing
*
*/
PointIteratorSkin( Decomposition & dec, size_t (& sz)[dim], Box<dim,T> & domain, const Box<dim,T> & sub_A, const Box<dim,T> & sub_B, size_t (& bc)[dim])
:grid_dist_id_iterator_dec_skin<Decomposition>(dec, sz, getAB(sz,domain,sub_A,sub_B,sp,RETURN_A), getAB(sz,domain,sub_A,sub_B,sp,RETURN_B), bc),domain(domain)
{
sub_domainA.add(sub_A);
calculateAp();
}
/*! \Return the actual point
*
*
*/
Point<dim,T> & get()
{
return ap;
}
/*! \brief Next point
*
* \return itself
*
*/
PointIteratorSkin & operator++()
{
grid_dist_id_iterator_dec_skin<Decomposition>::operator++();
calculateAp();
while (grid_dist_id_iterator_dec_skin<Decomposition>::isNext() && isValidPoint() == false)
{
grid_dist_id_iterator_dec_skin<Decomposition>::operator++();
calculateAp();
}
return *this;
}
bool isNext()
{
return grid_dist_id_iterator_dec_skin<Decomposition>::isNext();
}
PointIteratorSkin<dim,T,Decomposition> & operator=(PointIteratorSkin<dim,T,Decomposition> & p)
{
grid_dist_id_iterator_dec_skin<Decomposition>::operator=(p);
ap = p.ap;
sub_domainA = p.sub_domainA;
domain = p.domain;
for (size_t i = 0 ; i < dim; i++)
sp[i] = p.sp[i];
return *this;
}
void addBoxA(const Box<dim,double> & BoxA)
{
sub_domainA.add(BoxA);
}
};
#endif /* OPENFPM_NUMERICS_SRC_DRAW_POINTITERATORSKIN_HPP_ */
src/Makefile.am
View file @ 98b6bc78
......@@ -11,7 +11,8 @@ Vector/Vector_eigen.hpp Vector/Vector_petsc.hpp Vector/Vector_util.hpp Vector/Ve
Solvers/umfpack_solver.hpp Solvers/petsc_solver.hpp \
util/petsc_util.hpp util/linalgebra_lib.hpp util/util_num.hpp util/grid_dist_testing.hpp \
FiniteDifference/Average.hpp FiniteDifference/Derivative.hpp FiniteDifference/eq.hpp FiniteDifference/FDScheme.hpp FiniteDifference/Laplacian.hpp FiniteDifference/mul.hpp FiniteDifference/sum.hpp FiniteDifference/util/common.hpp \
PSE/Kernels.hpp PSE/Kernels_test_util.hpp Operators/Vector/vector_dist_operators_extensions.hpp Operators/Vector/vector_dist_operators.hpp Operators/Vector/vector_dist_operators_apply_kernel.hpp Operators/Vector/vector_dist_operators_functions.hpp Operators/Vector/vector_dist_operator_assign.hpp
PSE/Kernels.hpp PSE/Kernels_test_util.hpp Operators/Vector/vector_dist_operators_extensions.hpp Operators/Vector/vector_dist_operators.hpp Operators/Vector/vector_dist_operators_apply_kernel.hpp Operators/Vector/vector_dist_operators_functions.hpp Operators/Vector/vector_dist_operator_assign.hpp \
Draw/DrawParticles.hpp Draw/PointIterator.hpp Draw/PointIteratorSkin.hpp
.cu.o :
$(NVCC) $(NVCCFLAGS) -o $@ -c $<
......
src/main.cpp
View file @ 98b6bc78
#include "config.h"
#define BOOST_TEST_MODULE "C++ test module for OpenFPM_numerics project"
#include <boost/test/included/unit_test.hpp>
#include "unit_test_init_cleanup.hpp"
#include "config.h"
#include "Vector/Vector_unit_tests.hpp"
#include "Matrix/SparseMatrix_unit_tests.hpp"
#include "FiniteDifference/FDScheme_unit_tests.hpp"
......
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