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CHANGELOG.md
View file @ 5fdb12a6
# 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)
example/Vector/0_simple/main.cpp
View file @ 5fdb12a6
......@@ -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
*
......
example/Vector/4_multiphase_celllist_verlet/Makefile
View file @ 5fdb12a6
......@@ -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
example/Vector/4_multiphase_celllist_verlet/main.cpp
View file @ 5fdb12a6
......@@ -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 ##
*