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Merge pull request #32 from pabloseleson/current_positions
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add particle property to store current positions
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@streeve
streeve committed Oct 4, 2023
2 parents fdc5596 + fc61746 commit 3dbc754
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Showing 13 changed files with 102 additions and 50 deletions.
5 changes: 3 additions & 2 deletions examples/crack_branching.cpp
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Expand Up @@ -49,6 +49,7 @@ int main( int argc, char* argv[] )
double t_final = 43e-6;
double dt = 5e-8;
double output_frequency = 5;
bool output_reference = true;

// Material constants
double E = 72e+9; // [Pa]
Expand Down Expand Up @@ -79,7 +80,7 @@ int main( int argc, char* argv[] )
CabanaPD::ForceModel<CabanaPD::PMB, CabanaPD::Fracture>;
model_type force_model( delta, K, G0 );
CabanaPD::Inputs<3> inputs( num_cell, low_corner, high_corner, t_final,
dt, output_frequency );
dt, output_frequency, output_reference );
inputs.read_args( argc, argv );

// Create particles from mesh.
Expand All @@ -91,7 +92,7 @@ int main( int argc, char* argv[] )
inputs.num_cells, halo_width );

// Define particle initialization.
auto x = particles->sliceRefPosition();
auto x = particles->sliceReferencePosition();
auto v = particles->sliceVelocity();
auto f = particles->sliceForce();
auto rho = particles->sliceDensity();
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7 changes: 4 additions & 3 deletions examples/elastic_wave.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -35,6 +35,7 @@ int main( int argc, char* argv[] )
double t_final = 0.6;
double dt = 0.01;
int output_frequency = 5;
bool output_reference = true;
double K = 1.0;
double G = 0.5;
double delta = 0.075;
Expand All @@ -51,7 +52,7 @@ int main( int argc, char* argv[] )
model_type force_model( delta, K, G );

CabanaPD::Inputs<3> inputs( num_cell, low_corner, high_corner, t_final,
dt, output_frequency );
dt, output_frequency, output_reference );
inputs.read_args( argc, argv );

// Create particles from mesh.
Expand All @@ -64,7 +65,7 @@ int main( int argc, char* argv[] )
inputs.num_cells, halo_width );

// Define particle initialization.
auto x = particles->sliceRefPosition();
auto x = particles->sliceReferencePosition();
auto u = particles->sliceDisplacement();
auto v = particles->sliceVelocity();
auto rho = particles->sliceDensity();
Expand Down Expand Up @@ -96,7 +97,7 @@ int main( int argc, char* argv[] )
cabana_pd->init_force();
cabana_pd->run();

x = particles->sliceRefPosition();
x = particles->sliceReferencePosition();
u = particles->sliceDisplacement();
double num_cell_x = inputs.num_cells[0];
auto profile = Kokkos::View<double* [2], memory_space>(
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5 changes: 3 additions & 2 deletions examples/kalthoff_winkler.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -46,6 +46,7 @@ int main( int argc, char* argv[] )
double t_final = 70e-6;
double dt = 0.133e-6;
int output_frequency = 10;
bool output_reference = true;

// Material constants
double E = 191e+9; // [Pa]
Expand Down Expand Up @@ -82,7 +83,7 @@ int main( int argc, char* argv[] )
// CabanaPD::ForceModel<CabanaPD::LPS, CabanaPD::Fracture>;
// model_type force_model( delta, K, G, G0 );
CabanaPD::Inputs<3> inputs( num_cell, low_corner, high_corner, t_final,
dt, output_frequency );
dt, output_frequency, output_reference );
inputs.read_args( argc, argv );

// Create particles from mesh.
Expand All @@ -95,7 +96,7 @@ int main( int argc, char* argv[] )
inputs.num_cells, halo_width );

// Define particle initialization.
auto x = particles->sliceRefPosition();
auto x = particles->sliceReferencePosition();
auto v = particles->sliceVelocity();
auto f = particles->sliceForce();
auto rho = particles->sliceDensity();
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6 changes: 3 additions & 3 deletions src/CabanaPD_Boundary.hpp
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Expand Up @@ -87,7 +87,7 @@ struct BoundaryIndexSpace<MemorySpace, RegionBoundary>

auto index_space = _view;
auto count = _count;
auto x = particles.sliceRefPosition();
auto x = particles.sliceReferencePosition();
Kokkos::RangePolicy<ExecSpace> policy( 0, particles.n_local );
auto index_functor = KOKKOS_LAMBDA( const std::size_t pid )
{
Expand Down Expand Up @@ -163,7 +163,7 @@ struct BoundaryCondition<BCIndexSpace, ForceValueBCTag>
void apply( ExecSpace, ParticleType& particles )
{
auto f = particles.sliceForce();
auto x = particles.sliceRefPosition();
auto x = particles.sliceReferencePosition();
auto index_space = _index_space._view;
Kokkos::RangePolicy<ExecSpace> policy( 0, index_space.size() );
auto value = _value;
Expand Down Expand Up @@ -234,7 +234,7 @@ struct BoundaryCondition<BCIndexSpace, ForceCrackBranchBCTag>
void apply( ExecSpace, ParticleType& particles )
{
auto f = particles.sliceForce();
auto x = particles.sliceRefPosition();
auto x = particles.sliceReferencePosition();
auto index_space = _index_space._view;
Kokkos::RangePolicy<ExecSpace> policy( 0, index_space.size() );
auto value = _value;
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2 changes: 1 addition & 1 deletion src/CabanaPD_Comm.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -251,7 +251,7 @@ class Comm<ParticleType, PMB>
MPI_Comm_size( local_grid->globalGrid().comm(), &mpi_size );
MPI_Comm_rank( local_grid->globalGrid().comm(), &mpi_rank );

auto positions = particles.sliceRefPosition();
auto positions = particles.sliceReferencePosition();
// Get all 26 neighbor ranks.
auto halo_width = local_grid->haloCellWidth();
auto topology = Cajita::getTopology( *local_grid );
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16 changes: 8 additions & 8 deletions src/CabanaPD_Force.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -402,7 +402,7 @@ class Force<ExecutionSpace, ForceModel<LPS, Elastic>>
const ParallelType neigh_op_tag )
{
auto n_local = particles.n_local;
auto x = particles.sliceRefPosition();
auto x = particles.sliceReferencePosition();
auto u = particles.sliceDisplacement();
const auto vol = particles.sliceVolume();
auto m = particles.sliceWeightedVolume();
Expand Down Expand Up @@ -430,7 +430,7 @@ class Force<ExecutionSpace, ForceModel<LPS, Elastic>>
const ParallelType neigh_op_tag ) const
{
auto n_local = particles.n_local;
const auto x = particles.sliceRefPosition();
const auto x = particles.sliceReferencePosition();
auto u = particles.sliceDisplacement();
const auto vol = particles.sliceVolume();
auto m = particles.sliceWeightedVolume();
Expand Down Expand Up @@ -567,7 +567,7 @@ class Force<ExecutionSpace, ForceModel<LPS, Fracture>>
const MuView& mu )
{
auto n_local = particles.n_local;
auto x = particles.sliceRefPosition();
auto x = particles.sliceReferencePosition();
auto u = particles.sliceDisplacement();
const auto vol = particles.sliceVolume();
auto m = particles.sliceWeightedVolume();
Expand Down Expand Up @@ -606,7 +606,7 @@ class Force<ExecutionSpace, ForceModel<LPS, Fracture>>
const MuView& mu ) const
{
auto n_local = particles.n_local;
const auto x = particles.sliceRefPosition();
const auto x = particles.sliceReferencePosition();
auto u = particles.sliceDisplacement();
const auto vol = particles.sliceVolume();
auto m = particles.sliceWeightedVolume();
Expand Down Expand Up @@ -1210,7 +1210,7 @@ void computeForce( const ForceType& force, ParticleType& particles,
const ParallelType& neigh_op_tag )
{
auto n_local = particles.n_local;
auto x = particles.sliceRefPosition();
auto x = particles.sliceReferencePosition();
auto u = particles.sliceDisplacement();
auto f = particles.sliceForce();
auto f_a = particles.sliceForceAtomic();
Expand Down Expand Up @@ -1240,7 +1240,7 @@ double computeEnergy( const ForceType force, ParticleType& particles,
const ParallelType& neigh_op_tag )
{
auto n_local = particles.n_local;
auto x = particles.sliceRefPosition();
auto x = particles.sliceReferencePosition();
auto u = particles.sliceDisplacement();
auto f = particles.sliceForce();
auto W = particles.sliceStrainEnergy();
Expand Down Expand Up @@ -1269,7 +1269,7 @@ void computeForce( const ForceType& force, ParticleType& particles,
const ParallelType& neigh_op_tag )
{
auto n_local = particles.n_local;
auto x = particles.sliceRefPosition();
auto x = particles.sliceReferencePosition();
auto u = particles.sliceDisplacement();
auto f = particles.sliceForce();
auto f_a = particles.sliceForceAtomic();
Expand Down Expand Up @@ -1300,7 +1300,7 @@ double computeEnergy( const ForceType force, ParticleType& particles,
const ParallelType& neigh_op_tag )
{
auto n_local = particles.n_local;
auto x = particles.sliceRefPosition();
auto x = particles.sliceReferencePosition();
auto u = particles.sliceDisplacement();
auto f = particles.sliceForce();
auto W = particles.sliceStrainEnergy();
Expand Down
4 changes: 3 additions & 1 deletion src/CabanaPD_Input.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -34,18 +34,20 @@ class Inputs
double final_time;
double timestep;
int output_frequency;
bool output_reference;

bool half_neigh = false;

Inputs( const std::array<int, Dim> nc, std::array<double, Dim> lc,
std::array<double, Dim> hc, const double t_f, const double dt,
const int of )
const int of, const bool output_ref )
: num_cells( nc )
, low_corner( lc )
, high_corner( hc )
, final_time( t_f )
, timestep( dt )
, output_frequency( of )
, output_reference( output_ref )
{
num_steps = final_time / timestep;
}
Expand Down
78 changes: 61 additions & 17 deletions src/CabanaPD_Particles.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -88,6 +88,7 @@ class Particles<DeviceType, PMB, Dimension>
using self_type = Particles<DeviceType, PMB, Dimension>;
using device_type = DeviceType;
using memory_space = typename device_type::memory_space;
using execution_space = typename memory_space::execution_space;
static constexpr int dim = Dimension;

// Per particle.
Expand All @@ -111,6 +112,7 @@ class Particles<DeviceType, PMB, Dimension>
// FIXME: enable variable aosoa.
using aosoa_x_type = Cabana::AoSoA<vector_type, memory_space, 1>;
using aosoa_u_type = Cabana::AoSoA<vector_type, memory_space, 1>;
using aosoa_y_type = Cabana::AoSoA<vector_type, memory_space, 1>;
using aosoa_f_type = Cabana::AoSoA<vector_type, memory_space, 1>;
using aosoa_vol_type = Cabana::AoSoA<scalar_type, memory_space, 1>;
using aosoa_nofail_type = Cabana::AoSoA<int_type, memory_space, 1>;
Expand Down Expand Up @@ -213,12 +215,13 @@ class Particles<DeviceType, PMB, Dimension>
int num_particles = particles_per_cell * owned_cells.size();
resize( num_particles, 0 );

auto x = sliceRefPosition();
auto x = sliceReferencePosition();
auto v = sliceVelocity();
auto f = sliceForce();
auto type = sliceType();
auto rho = sliceDensity();
auto u = sliceDisplacement();
auto y = sliceCurrentPosition();
auto vol = sliceVolume();
auto nofail = sliceNoFail();

Expand Down Expand Up @@ -253,6 +256,7 @@ class Particles<DeviceType, PMB, Dimension>
{
x( pid, d ) = cell_coord[d];
u( pid, d ) = 0.0;
y( pid, d ) = 0.0;
v( pid, d ) = 0.0;
f( pid, d ) = 0.0;
}
Expand Down Expand Up @@ -295,13 +299,25 @@ class Particles<DeviceType, PMB, Dimension>
KOKKOS_LAMBDA( const int pid ) { init_functor( pid ); } );
}

auto sliceRefPosition()
auto sliceReferencePosition()
{
return Cabana::slice<0>( _aosoa_x, "positions" );
return Cabana::slice<0>( _aosoa_x, "reference_positions" );
}
auto sliceRefPosition() const
auto sliceReferencePosition() const
{
return Cabana::slice<0>( _aosoa_x, "positions" );
return Cabana::slice<0>( _aosoa_x, "reference_positions" );
}
auto sliceCurrentPosition()
{
// Update before returning data.
updateCurrentPosition();
return Cabana::slice<0>( _aosoa_y, "current_positions" );
}
auto sliceCurrentPosition() const
{
// Update before returning data.
updateCurrentPosition();
return Cabana::slice<0>( _aosoa_y, "current_positions" );
}
auto sliceDisplacement()
{
Expand Down Expand Up @@ -362,36 +378,62 @@ class Particles<DeviceType, PMB, Dimension>
return Cabana::slice<0>( _aosoa_nofail, "no_fail_region" );
}

void updateCurrentPosition()
{
// Not using slice function because this is called inside.
auto y = Cabana::slice<0>( _aosoa_y, "current_positions" );
auto x = sliceReferencePosition();
auto u = sliceDisplacement();
Kokkos::RangePolicy<execution_space> policy( 0, n_local + n_ghost );
auto sum_x_u = KOKKOS_LAMBDA( const std::size_t pid )
{
for ( int d = 0; d < 3; d++ )
y( pid, d ) = x( pid, d ) + u( pid, d );
};
Kokkos::parallel_for( "CabanaPD::CalculateCurrentPositions", policy,
sum_x_u );
}

void resize( int new_local, int new_ghost )
{
n_local = new_local;
n_ghost = new_ghost;

_aosoa_x.resize( new_local + new_ghost );
_aosoa_u.resize( new_local + new_ghost );
_aosoa_y.resize( new_local + new_ghost );
_aosoa_vol.resize( new_local + new_ghost );
_aosoa_f.resize( new_local );
_aosoa_other.resize( new_local );
_aosoa_nofail.resize( new_local + new_ghost );
size = _aosoa_x.size();
};

void output( const int output_step, const double output_time )
auto getPosition( const bool use_reference )
{
if ( use_reference )
return sliceReferencePosition();
else
return sliceCurrentPosition();
}

void output( [[maybe_unused]] const int output_step,
[[maybe_unused]] const double output_time,
[[maybe_unused]] const bool use_reference = true )
{
#ifdef Cabana_ENABLE_HDF5
Cabana::Experimental::HDF5ParticleOutput::writeTimeStep(
h5_config, "particles", MPI_COMM_WORLD, output_step, output_time,
n_local, sliceRefPosition(), sliceStrainEnergy(), sliceForce(),
sliceDisplacement(), sliceVelocity(), sliceDamage() );
n_local, getPosition( use_reference ), sliceStrainEnergy(),
sliceForce(), sliceDisplacement(), sliceVelocity(), sliceDamage() );
#else
#ifdef Cabana_ENABLE_SILO
Cajita::Experimental::SiloParticleOutput::writePartialRangeTimeStep(
"particles", local_grid->globalGrid(), output_step, output_time, 0,
n_local, sliceRefPosition(), sliceStrainEnergy(), sliceForce(),
sliceDisplacement(), sliceVelocity(), sliceDamage() );
n_local, getPosition( use_reference ), sliceStrainEnergy(),
sliceForce(), sliceDisplacement(), sliceVelocity(), sliceDamage() );
#else
log( std::cout, "No particle output enabled for step ", output_step,
" (", output_time, ")" );
log( std::cout, "No particle output enabled." );
#endif
#endif
}
Expand All @@ -401,6 +443,7 @@ class Particles<DeviceType, PMB, Dimension>
protected:
aosoa_x_type _aosoa_x;
aosoa_u_type _aosoa_u;
aosoa_y_type _aosoa_y;
aosoa_f_type _aosoa_f;
aosoa_vol_type _aosoa_vol;
aosoa_nofail_type _aosoa_nofail;
Expand Down Expand Up @@ -505,12 +548,14 @@ class Particles<DeviceType, LPS, Dimension>
_aosoa_m.resize( new_local + new_ghost );
}

void output( const int output_step, const double output_time )
void output( [[maybe_unused]] const int output_step,
[[maybe_unused]] const double output_time,
[[maybe_unused]] const bool use_reference = true )
{
#ifdef Cabana_ENABLE_HDF5
Cabana::Experimental::HDF5ParticleOutput::writeTimeStep(
h5_config, "particles", MPI_COMM_WORLD, output_step, output_time,
n_local, base_type::sliceRefPosition(),
n_local, base_type::getPosition( use_reference ),
base_type::sliceStrainEnergy(), base_type::sliceForce(),
base_type::sliceDisplacement(), base_type::sliceVelocity(),
base_type::sliceDamage(), sliceWeightedVolume(),
Expand All @@ -519,14 +564,13 @@ class Particles<DeviceType, LPS, Dimension>
#ifdef Cabana_ENABLE_SILO
Cajita::Experimental::SiloParticleOutput::writePartialRangeTimeStep(
"particles", local_grid->globalGrid(), output_step, output_time, 0,
n_local, base_type::sliceRefPosition(),
n_local, base_type::getPosition( use_reference ),
base_type::sliceStrainEnergy(), base_type::sliceForce(),
base_type::sliceDisplacement(), base_type::sliceVelocity(),
base_type::sliceDamage(), sliceWeightedVolume(),
sliceDilatation() );
#else
log( std::cout, "No particle output enabled for ", output_step, "(",
output_time, ")" );
log( std::cout, "No particle output enabled." );
#endif
#endif
}
Expand Down
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