Skip to content
Snippets Groups Projects
Commit 59ec9fba authored by Pietro Incardona's avatar Pietro Incardona
Browse files

Adding Verlet and Celllist

parent 93e5f4a6
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
example/Vector/1_celllist/main.cpp 0 → 100644
+ 181
− 0
View file @ 59ec9fba
#include "Vector/vector_dist.hpp"
#include "Decomposition/CartDecomposition.hpp"
#include "data_type/aggregate.hpp"
/*
* ### WIKI 1 ###
*
* ## Simple example
*
* This example show cell lists for the distributed vector
*
* ### WIKI END ###
*
*/
int main(int argc, char* argv[])
{
//
// ### WIKI 2 ###
//
// Here we Initialize the library, we create a Box that define our domain, boundary conditions, ghost
// and the grid size
//
init_global_v_cluster(&argc,&argv);
Vcluster & v_cl = *global_v_cluster;
// we create a 128x128x128 Grid iterator
size_t sz[3] = {128,128,128};
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};
// ghost, big enough to contain the interaction radius
Ghost<3,float> ghost(1.0/(128-2));
//
// ### WIKI 3 ###
//
// Here we define a distributed vector in 3D, containing 3 properties, a
// scalar double, a vector double[3], and a tensor or rank 2 double[3][3].
// In this case the vector contain 0 particles in total
//
vector_dist<3,float, aggregate<double,double[3],double[3][3]>, CartDecomposition<3,float> > vd(0,box,bc,ghost);
//
// ### WIKI 4 ###
//
// We define a grid iterator, to create particles on a grid like way.
// An important note is that the grid iterator, iterator only on the
// local nodes for each processor for example suppose to have a domain like
// the one in figure
//
// +---------+
// |* * *|* *|
// | 2 | |
// |* * *|* *|
// | --- |
// |* *|* * *|
// | | |
// |* *|* * *|
// | | 1 |
// |* *|* * *|
// +---------+
//
// divided in 2 processors, the processor 1 will iterate only on the points
// inside the portion of space marked with one. A note grid iterator follow the
// boundary condition specified in vector. For a perdiodic 2D 5x5 grid we have
//
// +---------+
// * * * * * |
// | |
// * * * * * |
// | |
// * * * * * |
// | |
// * * * * * |
// | |
// *-*-*-*-*-+
//
// Because the right border is equivalent to the left border, while for a non periodic we have the
// following distribution of points
//
// *-*-*-*-*
// | |
// * * * * *
// | |
// * * * * *
// | |
// * * * * *
// | |
// *-*-*-*-*
//
// So in this loop each processor will place particles on a grid
//
auto it = vd.getGridIterator(sz);
while (it.isNext())
{
vd.add();
auto key = it.get();
vd.template getLastPos<0>()[0] = key.get(0) * it.getSpacing(0);
vd.template getLastPos<0>()[1] = key.get(1) * it.getSpacing(1);
vd.template getLastPos<0>()[2] = key.get(2) * it.getSpacing(2);
++it;
}
//
// ### WIKI 5 ###
//
// we synchronize the ghost, the scalar property, the vector, and the rank 2 tensor
// (just for fun)
vd.ghost_get<0,1,2>();
//
// ### WIKI 6 ###
//
// If the particle does not move, or does not move that much we can create a verlet list
// for each particle, it internally use CellList to find the neighborhood but it is still
// an expensive operation
//
float r_cut = 1.0/(128-2);
auto NN = vd.getCellList(r_cut);
auto it2 = vd.getDomainIterator();
while (it2.isNext())
{
auto p = it2.get();
Point<3,float> xp = vd.getPos<0>(p);
auto Np = NN.getIterator(NN.getCell(vd.getPos<0>(p)));
while (Np.isNext())
{
auto q = Np.get();
// repulsive
Point<3,float> xq = vd.getPos<0>(q);
Point<3,float> f = (xp - xq);
// we sum the distance of all the particles
vd.template getProp<0>(p) += f.norm();;
// we sum the distance of all the particles
vd.template getProp<1>(p)[0] += f.get(0);
vd.template getProp<1>(p)[1] += f.get(0);
vd.template getProp<1>(p.getKey())[2] += f.get(0);
vd.template getProp<2>(p)[0][0] += xp.get(0) - xq.get(0);
vd.template getProp<2>(p)[0][1] += xp.get(0) - xq.get(1);
vd.template getProp<2>(p)[0][2] += xp.get(0) - xq.get(2);
vd.template getProp<2>(p)[1][0] += xp.get(1) - xq.get(0);
vd.template getProp<2>(p)[1][1] += xp.get(1) - xq.get(1);
vd.template getProp<2>(p)[1][2] += xp.get(1) - xq.get(2);
vd.template getProp<2>(p)[2][0] += xp.get(2) - xq.get(0);
vd.template getProp<2>(p)[2][1] += xp.get(2) - xq.get(1);
vd.template getProp<2>(p)[2][2] += xp.get(2) - xq.get(2);
}
++it2;
}
//
// ### WIKI 10 ###
//
// Deinitialize the library
//
delete_global_v_cluster();
}
example/Vector/1_verlet/main.cpp 0 → 100644
+ 179
− 0
View file @ 59ec9fba
#include "Vector/vector_dist.hpp"
#include "Decomposition/CartDecomposition.hpp"
#include "data_type/aggregate.hpp"
/*
* ### WIKI 1 ###
*
* ## Simple example
*
* This example show cell and verlet list of the distributed vector
*
* ### WIKI END ###
*
*/
int main(int argc, char* argv[])
{
//
// ### WIKI 2 ###
//
// Here we Initialize the library, we create a Box that define our domain, boundary conditions, ghost
// and the grid size
//
init_global_v_cluster(&argc,&argv);
Vcluster & v_cl = *global_v_cluster;
// we create a 128x128x128 Grid iterator
size_t sz[3] = {128,128,128};
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};
// ghost, big enough to contain the interaction radius
Ghost<3,float> ghost(1.0/(128-2));
//
// ### WIKI 3 ###
//
// Here we define a distributed vector in 3D, containing 3 properties, a
// scalar double, a vector double[3], and a tensor or rank 2 double[3][3].
// In this case the vector contain 0 particles in total
//
vector_dist<3,float, aggregate<double,double[3],double[3][3]>, CartDecomposition<3,float> > vd(0,box,bc,ghost);
//
// ### WIKI 4 ###
//
// We define a grid iterator, to create particles on a grid like way.
// An important note is that the grid iterator, iterator only on the
// local nodes for each processor for example suppose to have a domain like
// the one in figure
//
// +---------+
// |* * *|* *|
// | 2 | |
// |* * *|* *|
// | --- |
// |* *|* * *|
// | | |
// |* *|* * *|
// | | 1 |
// |* *|* * *|
// +---------+
//
// divided in 2 processors, the processor 1 will iterate only on the points
// inside the portion of space marked with one. A note grid iterator follow the
// boundary condition specified in vector. For a perdiodic 2D 5x5 grid we have
//
// +---------+
// * * * * * |
// | |
// * * * * * |
// | |
// * * * * * |
// | |
// * * * * * |
// | |
// *-*-*-*-*-+
//
// Because the right border is equivalent to the left border, while for a non periodic we have the
// following distribution of points
//
// *-*-*-*-*
// | |
// * * * * *
// | |
// * * * * *
// | |
// * * * * *
// | |
// *-*-*-*-*
//
// So in this loop each processor will place particles on a grid
//
auto it = vd.getGridIterator(sz);
while (it.isNext())
{
vd.add();
auto key = it.get();
vd.template getLastPos<0>()[0] = key.get(0) * it.getSpacing(0);
vd.template getLastPos<0>()[1] = key.get(1) * it.getSpacing(1);
vd.template getLastPos<0>()[2] = key.get(2) * it.getSpacing(2);
++it;
}
//
// ### WIKI 5 ###
//
// we synchronize the ghost, the scalar property, the vector, and the rank 2 tensor
// (just for fun)
vd.ghost_get<0,1,2>();
//
// ### WIKI 6 ###
//
// If the particle does not move, or does not move that much we can create a verlet list
// for each particle, it internally use CellList to find the neighborhood but it is still
// an expensive operation
//
openfpm::vector<openfpm::vector<size_t>> verlet;
// cutting radius
float r_cut = 1.0/(128-2);
vd.getVerlet(verlet,r_cut);
//
// ### WIKI 7 ###
//
// for each particle we iterate across the neighborhoods particles and we
// do some demo calculation
//
for (size_t i = 0 ; i < verlet.size() ; i++)
{
Point<3,float> p = vd.getPos<0>(i);
// for each neighborhood particle
for (size_t j = 0 ; j < verlet.get(i).size() ; j++)
{
auto & NN = verlet.get(i);
Point<3,float> q = vd.getPos<0>(NN.get(j));
// some non-sense calculation as usage demo
// we sum the distance of all the particles
vd.template getProp<0>(i) += p.distance(q);
// we sum the distance of all the particles
vd.template getProp<1>(i)[0] += p.get(0) - q.get(0);
vd.template getProp<1>(i)[1] += p.get(0) - q.get(0);
vd.template getProp<1>(i)[2] += p.get(0) - q.get(0);
vd.template getProp<2>(i)[0][0] += p.get(0) - q.get(0);
vd.template getProp<2>(i)[0][1] += p.get(0) - q.get(1);
vd.template getProp<2>(i)[0][2] += p.get(0) - q.get(2);
vd.template getProp<2>(i)[1][0] += p.get(1) - q.get(0);
vd.template getProp<2>(i)[1][1] += p.get(1) - q.get(1);
vd.template getProp<2>(i)[1][2] += p.get(1) - q.get(2);
vd.template getProp<2>(i)[2][0] += p.get(2) - q.get(0);
vd.template getProp<2>(i)[2][1] += p.get(2) - q.get(1);
vd.template getProp<2>(i)[2][2] += p.get(2) - q.get(2);
}
}
//
// ### WIKI 8 ###
//
// Deinitialize the library
//
delete_global_v_cluster();
}
openfpm_io @ f8a9ae64
Subproject commit 45f102f913a9f721b76ab2338af52f1d451432a1
Subproject commit f8a9ae64e109fdcf542b3be5cb27c3b95e82b322
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment