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Add neighbor skin distance to delay neighbor build #177

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Add neighbor skin distance to delay neighbor build #177

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8f18626
Add neighbor skin distance to delay neighbor build
streeve Jan 17, 2025
4e61ae6
Fix neighbor rebuild delay: displacement since last build
streeve Jan 21, 2025
ca95a98
fixup: remove unused delta from Hertzian model
streeve Jan 29, 2025
7794e31
fixup: huge mistake in slice
streeve Jan 29, 2025
2bd96b5
fixup: contact radius naming
streeve Jan 29, 2025
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2 changes: 1 addition & 1 deletion examples/mechanics/fragmenting_cylinder.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -139,7 +139,7 @@ void fragmentingCylinderExample( const std::string filename )
{
double r_c = inputs["contact_horizon_factor"];
r_c *= dx[0];
CabanaPD::NormalRepulsionModel contact_model( delta, r_c, K );
CabanaPD::NormalRepulsionModel contact_model( delta, r_c, r_c, K );

auto cabana_pd = CabanaPD::createSolver<memory_space>(
inputs, particles, force_model, contact_model );
Expand Down
14 changes: 12 additions & 2 deletions src/CabanaPD_Force.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -179,6 +179,12 @@ class Force<MemorySpace, BaseForceModel>
{
}

// FIXME: should it be possible to update this list?
template <class ParticleType>
void update( const ParticleType&, const double, const bool = false )
{
}

unsigned getMaxLocalNeighbors()
{
auto neigh = _neigh_list;
Expand Down Expand Up @@ -234,6 +240,7 @@ class Force<MemorySpace, BaseForceModel>

auto time() { return _timer.time(); };
auto timeEnergy() { return _energy_timer.time(); };
auto timeNeighbor() { return 0.0; };
};

template <class MemorySpace>
Expand Down Expand Up @@ -276,6 +283,7 @@ class BaseFracture
******************************************************************************/
template <class ForceType, class ParticleType, class ParallelType>
void computeForce( ForceType& force, ParticleType& particles,
const double max_displacement,
const ParallelType& neigh_op_tag, const bool reset = true )
{
auto x = particles.sliceReferencePosition();
Expand All @@ -294,9 +302,11 @@ void computeForce( ForceType& force, ParticleType& particles,

// Forces only atomic if using team threading.
if ( std::is_same<decltype( neigh_op_tag ), Cabana::TeamOpTag>::value )
force.computeForceFull( f_a, x, u, particles, neigh_op_tag );
force.computeForceFull( f_a, x, u, particles, max_displacement,
neigh_op_tag );
else
force.computeForceFull( f, x, u, particles, neigh_op_tag );
force.computeForceFull( f, x, u, particles, max_displacement,
neigh_op_tag );
Kokkos::fence();
}

Expand Down
22 changes: 18 additions & 4 deletions src/CabanaPD_Integrate.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -85,18 +85,19 @@ class Integrator
~Integrator() {}

template <class ParticlesType>
void initialHalfStep( ParticlesType& p )
double initialHalfStep( ParticlesType& p )
{
_timer.start();

auto u = p.sliceDisplacement();
auto v = p.sliceVelocity();
auto f = p.sliceForce();
auto rho = p.sliceDensity();
auto u_neigh = p.sliceDisplacementNeighborBuild();

auto dt = _dt;
auto half_dt = _half_dt;
auto init_func = KOKKOS_LAMBDA( const int i )
auto init_func = KOKKOS_LAMBDA( const int i, double& max_u )
{
const double half_dt_m = half_dt / rho( i );
v( i, 0 ) += half_dt_m * f( i, 0 );
Expand All @@ -105,13 +106,26 @@ class Integrator
u( i, 0 ) += dt * v( i, 0 );
u( i, 1 ) += dt * v( i, 1 );
u( i, 2 ) += dt * v( i, 2 );

// FIXME: only used for contact: get displacement since last
// neighbor update.
u_neigh( i, 0 ) += u( i, 0 );
u_neigh( i, 1 ) += u( i, 1 );
u_neigh( i, 2 ) += u( i, 2 );
auto u_mag = Kokkos::hypot( u_neigh( i, 0 ), u_neigh( i, 1 ),
u_neigh( i, 2 ) );
if ( u_mag > max_u )
max_u = u_mag;
};
Kokkos::RangePolicy<exec_space> policy( p.frozenOffset(),
p.localOffset() );
Kokkos::parallel_for( "CabanaPD::Integrator::Initial", policy,
init_func );
double max_displacement;
Kokkos::parallel_reduce( "CabanaPD::Integrator::Initial", policy,
init_func,
Kokkos::Max<double>( max_displacement ) );

_timer.stop();
return max_displacement;
}

template <class ParticlesType>
Expand Down
68 changes: 57 additions & 11 deletions src/CabanaPD_Particles.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -108,14 +108,15 @@ class Particles<MemorySpace, PMB, TemperatureIndependent, BaseOutput, Dimension>
// no-fail.
using int_type = Cabana::MemberTypes<int>;
// v, rho, type.
using other_types = Cabana::MemberTypes<double[dim], double, int>;
using other_types = Cabana::MemberTypes<double[dim], double>;

// FIXME: add vector length.
// FIXME: enable variable aosoa.
using aosoa_u_type = Cabana::AoSoA<vector_type, memory_space, 1>;
using aosoa_y_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>;
using aosoa_u_neigh_type = Cabana::AoSoA<vector_type, memory_space, 1>;
using aosoa_other_type = Cabana::AoSoA<other_types, memory_space>;
// Using grid here for the particle init.
using plist_x_type =
Expand Down Expand Up @@ -284,11 +285,11 @@ class Particles<MemorySpace, PMB, TemperatureIndependent, BaseOutput, Dimension>
auto x = sliceReferencePosition();
auto v = sliceVelocity();
auto f = sliceForce();
auto type = sliceType();
// auto type = sliceType();
auto rho = sliceDensity();
auto u = sliceDisplacement();
auto vol = sliceVolume();
auto nofail = sliceNoFail();
auto u_neigh = sliceDisplacementNeighborBuild();

// Initialize particles.
auto create_functor =
Expand All @@ -307,15 +308,15 @@ class Particles<MemorySpace, PMB, TemperatureIndependent, BaseOutput, Dimension>
Cabana::get( particle, CabanaPD::Field::ReferencePosition(),
d ) = px[d];
u( pid, d ) = 0.0;
u_neigh( pid, d ) = 0;
v( pid, d ) = 0.0;
f( pid, d ) = 0.0;
}
// Get the volume of the cell.
vol( pid ) = pv;

// FIXME: hardcoded.
type( pid ) = 0;
nofail( pid ) = 0;
// type( pid ) = 0;
rho( pid ) = 1.0;

return create;
Expand Down Expand Up @@ -353,10 +354,10 @@ class Particles<MemorySpace, PMB, TemperatureIndependent, BaseOutput, Dimension>
auto p_vol = sliceVolume();
auto v = sliceVelocity();
auto f = sliceForce();
auto type = sliceType();
// auto type = sliceType();
auto rho = sliceDensity();
auto u = sliceDisplacement();
auto nofail = sliceNoFail();
auto u_neigh = sliceDisplacementNeighborBuild();

static_assert(
Cabana::is_accessible_from<
Expand All @@ -374,11 +375,11 @@ class Particles<MemorySpace, PMB, TemperatureIndependent, BaseOutput, Dimension>
{
p_x( pid, d ) = x( pid_offset, d );
u( pid, d ) = 0.0;
u_neigh( pid, d ) = 0;
v( pid, d ) = 0.0;
f( pid, d ) = 0.0;
}
type( pid ) = 0;
nofail( pid ) = 0;
// type( pid ) = 0;
rho( pid ) = 1.0;
} );

Expand Down Expand Up @@ -447,6 +448,14 @@ class Particles<MemorySpace, PMB, TemperatureIndependent, BaseOutput, Dimension>
{
return Cabana::slice<0>( _aosoa_u, "displacements" );
}
auto sliceDisplacementNeighborBuild()
{
return Cabana::slice<0>( _aosoa_u_neigh, "displacement_since_rebuild" );
}
auto sliceDisplacementNeighborBuild() const
{
return Cabana::slice<0>( _aosoa_u_neigh, "displacement_since_rebuild" );
}
auto sliceForce() { return _plist_f.slice( CabanaPD::Field::Force() ); }
auto sliceForceAtomic()
{
Expand Down Expand Up @@ -474,8 +483,9 @@ class Particles<MemorySpace, PMB, TemperatureIndependent, BaseOutput, Dimension>
{
return Cabana::slice<1>( _aosoa_other, "density" );
}
auto sliceType() { return Cabana::slice<2>( _aosoa_other, "type" ); }
auto sliceType() const { return Cabana::slice<2>( _aosoa_other, "type" ); }
// auto sliceType() { return Cabana::slice<2>( _aosoa_other, "type" ); }
// auto sliceType() const { return Cabana::slice<2>( _aosoa_other, "type" );
// }

auto sliceNoFail()
{
Expand Down Expand Up @@ -524,10 +534,45 @@ class Particles<MemorySpace, PMB, TemperatureIndependent, BaseOutput, Dimension>
_plist_f.aosoa().resize( localOffset() );
_aosoa_other.resize( localOffset() );
_aosoa_nofail.resize( referenceOffset() );
_aosoa_u_neigh.resize( localOffset() );

size = _plist_x.size();
_timer.stop();
};

void shrink()
{
_timer.start();
_plist_x.aosoa().shrinkToFit();
_aosoa_u.shrinkToFit();
_aosoa_y.shrinkToFit();
_aosoa_vol.shrinkToFit();
_plist_f.aosoa().shrinkToFit();
_aosoa_other.shrinkToFit();
_aosoa_u_neigh.shrinkToFit();
_timer.stop();
};

template <typename KeepType>
void remove( const int num_keep, const KeepType& keep )
{
Cabana::remove( execution_space(), num_keep, keep, _plist_x.aosoa(),
numFrozen() );
Cabana::remove( execution_space(), num_keep, keep, _plist_f.aosoa(),
numFrozen() );
Cabana::remove( execution_space(), num_keep, keep, _aosoa_u,
numFrozen() );
Cabana::remove( execution_space(), num_keep, keep, _aosoa_vol,
numFrozen() );
Cabana::remove( execution_space(), num_keep, keep, _aosoa_y,
numFrozen() );
Cabana::remove( execution_space(), num_keep, keep, _aosoa_other,
numFrozen() );
Cabana::remove( execution_space(), num_keep, keep, _aosoa_u_neigh,
numFrozen() );
resize( frozen_offset + num_keep, 0 );
}

auto getPosition( const bool use_reference )
{
if ( use_reference )
Expand Down Expand Up @@ -577,6 +622,7 @@ class Particles<MemorySpace, PMB, TemperatureIndependent, BaseOutput, Dimension>

protected:
aosoa_u_type _aosoa_u;
aosoa_u_neigh_type _aosoa_u_neigh;
aosoa_y_type _aosoa_y;
aosoa_vol_type _aosoa_vol;
aosoa_nofail_type _aosoa_nofail;
Expand Down
25 changes: 15 additions & 10 deletions src/CabanaPD_Solver.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -217,7 +217,7 @@ class Solver
comm->gatherWeightedVolume();
}
// Compute initial internal forces and energy.
updateForce();
updateForce( 0.0 );
computeEnergy( *force, *particles, neigh_iter_tag() );

if ( initial_output )
Expand Down Expand Up @@ -266,6 +266,8 @@ class Solver
init( boundary_condition, initial_output );
}

void updateNeighbors() { force->update( *particles, 0.0, true ); }

template <typename BoundaryType>
void run( BoundaryType boundary_condition )
{
Expand All @@ -277,7 +279,7 @@ class Solver
_step_timer.start();

// Integrate - velocity Verlet first half.
integrator->initialHalfStep( *particles );
auto max_displacement = integrator->initialHalfStep( *particles );

// Update ghost particles.
comm->gatherDisplacement();
Expand All @@ -300,10 +302,11 @@ class Solver
comm->gatherTemperature();

// Compute internal forces.
updateForce();
updateForce( max_displacement );

if constexpr ( is_contact<contact_model_type>::value )
computeForce( *contact, *particles, neigh_iter_tag{}, false );
computeForce( *contact, *particles, max_displacement,
neigh_iter_tag{}, false );

// Add force boundary condition.
if ( boundary_condition.forceUpdate() )
Expand All @@ -329,16 +332,17 @@ class Solver
_step_timer.start();

// Integrate - velocity Verlet first half.
integrator->initialHalfStep( *particles );
auto max_displacement = integrator->initialHalfStep( *particles );

// Update ghost particles.
comm->gatherDisplacement();

// Compute internal forces.
updateForce();
updateForce( max_displacement );

if constexpr ( is_contact<contact_model_type>::value )
computeForce( *contact, *particles, neigh_iter_tag{}, false );
computeForce( *contact, *particles, max_displacement,
neigh_iter_tag{}, false );

if constexpr ( is_temperature_dependent<
typename force_model_type::thermal_type>::value )
Expand All @@ -356,7 +360,7 @@ class Solver

// Compute and communicate fields needed for force computation and update
// forces.
void updateForce()
void updateForce( const double max_displacement )
{
// Compute and communicate weighted volume for LPS (does nothing for
// PMB). Only computed once without fracture.
Expand All @@ -371,7 +375,7 @@ class Solver
comm->gatherDilatation();

// Compute internal forces.
computeForce( *force, *particles, neigh_iter_tag{} );
computeForce( *force, *particles, max_displacement, neigh_iter_tag{} );
}

void output( const int step )
Expand Down Expand Up @@ -419,6 +423,7 @@ class Solver
double integrate_time = integrator->time();
double force_time = force->time();
double energy_time = force->timeEnergy();
double neigh_time = force->timeNeighbor();
double output_time = particles->timeOutput();
_total_time += step_time;
auto rate = static_cast<double>( particles->numGlobal() *
Expand All @@ -428,7 +433,7 @@ class Solver
" ", std::scientific, std::setprecision( 2 ), step * dt, " ",
W, " ", std::fixed, _total_time, " ", force_time, " ",
comm_time, " ", integrate_time, " ", energy_time, " ",
output_time, " ", std::scientific, rate );
neigh_time, " ", output_time, " ", std::scientific, rate );
out.close();
}
}
Expand Down
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