XGC1
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#include <species.hpp>
Public Types | |
enum | LaunchBounds { LaunchBounds::Default, LaunchBounds::Custom } |
Public Member Functions | |
Species (int idx_in, int nonadiabatic_idx_in, bool is_electron_in, bool is_adiabatic_in, KinType kintype_in, double mass_in, double charge_in, double charge_eu_in, int ncycles_in) | |
Species (NLReader::NamelistReader &nlr, const Grid< DeviceType > &grid, const MagneticField< DeviceType > &magnetic_field, const DomainDecomposition< DeviceType > &pol_decomp, int idx_in, int nonadiabatic_idx_in) | |
Species (SpeciesType sp_type, int n_ptl) | |
Species (int n_ptl_in) | |
void | resize_particles (int new_n_ptl) |
void | resize_host_particles_to_match_device () |
void | unassign_host_particles () |
void | resize_device_particles () |
void | resize_device_particles (int new_n_ptl) |
void | copy_particles_to_device () |
void | copy_particles_from_device () |
void | copy_particles_to_device_if_resident () |
void | copy_particles_from_device_if_resident () |
void | copy_particles_to_device_if_not_resident () |
void | copy_particles_from_device_if_not_resident () |
void | set_buffer_particles_d () |
void | set_buffer_phase0_d () |
template<typename F > | |
void | for_all_particles (const std::string label, F lambda_func) const |
void | back_up_SoA (Cabana::AoSoA< ParticleDataTypes, Device, VEC_LEN > &backup_SoA, int offset, int n) const |
void | restore_backup_SoA (Cabana::AoSoA< ParticleDataTypes, Device, VEC_LEN > &backup_SoA, int offset, int n) const |
template<typename F > | |
void | for_particle_range (int begin_idx, int end_idx, const std::string label, F lambda_func) const |
template<typename F > | |
void | for_all_particles (const std::string label, F lambda_func, const PtlMvmt mvmt, LaunchBounds launch_bounds=LaunchBounds::Default) |
KOKKOS_INLINE_FUNCTION VecParticles * | ptl () const |
KOKKOS_INLINE_FUNCTION VecPhase * | ph0 () const |
void | copy_to_phase0 (Species< Device > &species) |
void | save_backup_particles () |
void | restore_particles_from_backup () |
KOKKOS_INLINE_FUNCTION void | restore_phase_from_phase0 (const AoSoAIndices< Device > &inds, SimdParticles &part_one) const |
long long int | get_total_n_ptl () |
int | get_max_n_ptl () |
KOKKOS_INLINE_FUNCTION double | get_fg_gyro_radius (int inode, double smu_n, double bfield) const |
KOKKOS_INLINE_FUNCTION double | get_f0_eq_thermal_velocity (int inode) const |
KOKKOS_INLINE_FUNCTION double | get_f0_eq_thermal_velocity_lnode (int inode) const |
KOKKOS_INLINE_FUNCTION double | get_f0_eq_thermal_velocity_lnode_h (int inode) const |
KOKKOS_INLINE_FUNCTION double | get_f0_fg_unit_velocity_lnode_h (int inode) const |
KOKKOS_INLINE_FUNCTION void | get_particle_velocity_and_nearest_node (const Grid< DeviceType > &grid, const MagneticField< DeviceType > &magnetic_field, const DomainDecomposition< DeviceType > &pol_decomp, SimdParticles &part, Simd< double > &smu, Simd< double > &vp, Simd< int > &nearest_node, Simd< bool > ¬_in_triangle, Simd< bool > ¬_in_poloidal_domain) const |
void | update_decomposed_f0_calculations (const DomainDecomposition< DeviceType > &pol_decomp, const Grid< DeviceType > &grid, const MagneticField< DeviceType > &magnetic_field, const VelocityGrid &vgrid) |
void | calculate_global_f0_arrays (const Grid< DeviceType > &grid, const MagneticField< DeviceType > &magnetic_field) |
void | write_ptl_checkpoint_files (const DomainDecomposition< DeviceType > &pol_decomp, const XGC_IO_Stream &stream, std::string sp_name) |
void | write_f0_checkpoint_files (const DomainDecomposition< DeviceType > &pol_decomp, const XGC_IO_Stream &stream, std::string sp_name) |
void | read_f0_checkpoint_files (const DomainDecomposition< DeviceType > &pol_decomp, const XGC_IO_Stream &stream, std::string sp_name) |
void | read_ptl_checkpoint_files (const DomainDecomposition< DeviceType > &pol_decomp, const XGC_IO_Stream &stream, std::string sp_name, bool n_ranks_is_same, int version) |
long long int | get_max_gid () const |
void | get_ptl_write_total_and_offsets (const DomainDecomposition< DeviceType > &pol_decomp, long long int &inum_total, long long int &ioff) const |
Static Public Member Functions | |
static std::vector < MemoryPrediction > | estimate_memory_usage (NLReader::NamelistReader &nlr, const Grid< DeviceType > &grid, const DomainDecomposition< DeviceType > &pol_decomp, int species_idx) |
static int | get_initial_n_ptl (NLReader::NamelistReader &nlr, const Grid< DeviceType > &grid, const DomainDecomposition< DeviceType > &pol_decomp, int sml_special, int species_idx, bool verbose) |
Public Attributes | |
int | idx |
Index in all_species. More... | |
bool | is_electron |
Whether this species is the electrons. More... | |
bool | is_adiabatic |
Whether this species is adiabatic. More... | |
int | nonadiabatic_idx |
Index of species skipping adiabatic species (for compatibility with fortran arrays) More... | |
KinType | kintype |
Whether the species is gyrokinetic or drift kinetic. More... | |
double | mass |
Particle mass. More... | |
double | charge |
Particle charge. More... | |
double | charge_eu |
Particle charge in eu. More... | |
double | c_m |
c/m More... | |
double | c2_2m |
c2/2m More... | |
MarkerType | marker_type |
Marker type: reduced delta-f, total-f, full-f, or none (placeholder for adiabatic species) More... | |
FAnalyticShape | f_analytic_shape |
f_analytic_shape shape: Maxwellian, SlowingDown or None More... | |
WeightEvoEq | weight_evo_eq |
bool | dynamic_f0 |
Whether f0 can evolve in time. More... | |
int | ncycles |
Number of subcycles. More... | |
int | ncycles_between_sorts |
Number of subcycles between sorts. More... | |
int | minimum_ptl_reservation |
The minimum reservation size for particles. More... | |
int | n_ptl |
Number of particles. More... | |
Cabana::AoSoA < ParticleDataTypes, HostType, VEC_LEN > | particles |
Particles. More... | |
Cabana::AoSoA < ParticleDataTypes, Device, VEC_LEN > | particles_d |
Particles on device. More... | |
bool | owns_particles_d |
Whether the species owns the device particle allocation right now. More... | |
bool | particles_resident_on_device |
Whether the particles can reside on device. More... | |
bool | stream_particles |
Whether to stream particles between host and device if possible. More... | |
RKRestorationMethod | RK_restoration_method |
Currently, electrons must use first method and ions must use second. More... | |
bool | particles_are_backed_up |
Whether particles are currently backed up. More... | |
Cabana::AoSoA< PhaseDataTypes, HostType, VEC_LEN > | phase0 |
Cabana::AoSoA< PhaseDataTypes, Device, VEC_LEN > | phase0_d |
Cabana::AoSoA < ParticleDataTypes, HostType, VEC_LEN > | backup_particles |
Copy of particles to be restored for RK2. More... | |
int | n_backup_particles |
Distribution< Device > | f0 |
Species distribution in velocity space on local mesh nodes. More... | |
int | collision_grid_index |
Which collision grid to use. More... | |
Eq::Profile< Device > | eq_temp |
Eq::Profile< Device > | eq_den |
Eq::Profile< Device > | eq_flow |
int | eq_flow_type |
Eq::Profile< Device > | eq_fg_temp |
Eq::Profile< Device > | eq_fg_den |
Eq::Profile< Device > | eq_fg_flow |
int | eq_fg_flow_type |
Eq::Profile< Device > | eq_mk_temp |
Eq::Profile< Device > | eq_mk_den |
Eq::Profile< Device > | eq_mk_flow |
int | eq_mk_flow_type |
GyroAverageMatrices< HostType > | gyro_avg_matrices |
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Species< Device >::Species | ( | int | idx_in, |
int | nonadiabatic_idx_in, | ||
bool | is_electron_in, | ||
bool | is_adiabatic_in, | ||
KinType | kintype_in, | ||
double | mass_in, | ||
double | charge_in, | ||
double | charge_eu_in, | ||
int | ncycles_in | ||
) |
Constructor for species class used in collisions kernel
Species< Device >::Species | ( | NLReader::NamelistReader & | nlr, |
const Grid< DeviceType > & | grid, | ||
const MagneticField< DeviceType > & | magnetic_field, | ||
const DomainDecomposition< DeviceType > & | pol_decomp, | ||
int | idx_in, | ||
int | nonadiabatic_idx_in | ||
) |
Constructor for species class
< Upper cutoff of the gyroradius grid (should be the gyroradius of the fastest ions of interest)
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void Species< Device >::calculate_global_f0_arrays | ( | const Grid< DeviceType > & | grid, |
const MagneticField< DeviceType > & | magnetic_field | ||
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Loops over particles and calls a parallel_for, with no particle movement
[in] | label | is the label of the parallel_for used for debugging |
[in] | lambda_func | is the lambda function. Must be copy [=] not by reference |
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Loops over particles and calls a parallel_for, with particle being moved where requested
[in] | label | is the label of the parallel_for used for debugging |
[in] | lambda_func | is the lambda function. Must be copy [=] not by reference |
[in] | mvmt | specifies whether particles need to be sent to device or host |
[in] | launch_bounds | specifies whether to use default launch bounds or custom |
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Loops over a subset of particles and calls a parallel_for, with no particle movement
[in] | label | is the label of the parallel_for used for debugging |
[in] | lambda_func | is the lambda function. Must be copy [=] not by reference |
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long long int Species< Device >::get_max_gid | ( | ) | const |
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void Species< Device >::get_ptl_write_total_and_offsets | ( | const DomainDecomposition< DeviceType > & | pol_decomp, |
long long int & | inum_total, | ||
long long int & | ioff | ||
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void Species< Device >::read_f0_checkpoint_files | ( | const DomainDecomposition< DeviceType > & | pol_decomp, |
const XGC_IO_Stream & | stream, | ||
std::string | sp_name | ||
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void Species< Device >::read_ptl_checkpoint_files | ( | const DomainDecomposition< DeviceType > & | pol_decomp, |
const XGC_IO_Stream & | stream, | ||
std::string | sp_name, | ||
bool | n_ranks_is_same, | ||
int | version | ||
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Fills the remainder of the last AoSoA vector with realistic-looking particles (clones of the final particle). Since gid is set to -1, they will basically act as tracers in the kernel. Ideally garbage data in this buffer doesn't affect anything, but better to be safe here
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Fills the remainder of the last AoSoA phase0 vector with realistic-looking particles (clones of the final particle). Since gid is set to -1, they will basically act as tracers in the kernel. Ideally garbage data in this buffer doesn't affect anything, but better to be safe here
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void Species< Device >::update_decomposed_f0_calculations | ( | const DomainDecomposition< DeviceType > & | pol_decomp, |
const Grid< DeviceType > & | grid, | ||
const MagneticField< DeviceType > & | magnetic_field, | ||
const VelocityGrid & | vgrid | ||
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void Species< Device >::write_f0_checkpoint_files | ( | const DomainDecomposition< DeviceType > & | pol_decomp, |
const XGC_IO_Stream & | stream, | ||
std::string | sp_name | ||
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void Species< Device >::write_ptl_checkpoint_files | ( | const DomainDecomposition< DeviceType > & | pol_decomp, |
const XGC_IO_Stream & | stream, | ||
std::string | sp_name | ||
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Cabana::AoSoA<ParticleDataTypes,HostType,VEC_LEN> Species< Device >::backup_particles |
Copy of particles to be restored for RK2.
double Species< Device >::c2_2m |
c2/2m
double Species< Device >::c_m |
c/m
double Species< Device >::charge |
Particle charge.
double Species< Device >::charge_eu |
Particle charge in eu.
int Species< Device >::collision_grid_index |
Which collision grid to use.
bool Species< Device >::dynamic_f0 |
Whether f0 can evolve in time.
Eq::Profile<Device> Species< Device >::eq_den |
Eq::Profile<Device> Species< Device >::eq_fg_den |
Eq::Profile<Device> Species< Device >::eq_fg_flow |
int Species< Device >::eq_fg_flow_type |
Eq::Profile<Device> Species< Device >::eq_fg_temp |
Eq::Profile<Device> Species< Device >::eq_flow |
int Species< Device >::eq_flow_type |
Eq::Profile<Device> Species< Device >::eq_mk_den |
Eq::Profile<Device> Species< Device >::eq_mk_flow |
int Species< Device >::eq_mk_flow_type |
Eq::Profile<Device> Species< Device >::eq_mk_temp |
Eq::Profile<Device> Species< Device >::eq_temp |
Distribution<Device> Species< Device >::f0 |
Species distribution in velocity space on local mesh nodes.
FAnalyticShape Species< Device >::f_analytic_shape |
f_analytic_shape shape: Maxwellian, SlowingDown or None
GyroAverageMatrices<HostType> Species< Device >::gyro_avg_matrices |
int Species< Device >::idx |
Index in all_species.
bool Species< Device >::is_adiabatic |
Whether this species is adiabatic.
bool Species< Device >::is_electron |
Whether this species is the electrons.
Whether the species is gyrokinetic or drift kinetic.
MarkerType Species< Device >::marker_type |
Marker type: reduced delta-f, total-f, full-f, or none (placeholder for adiabatic species)
double Species< Device >::mass |
Particle mass.
int Species< Device >::minimum_ptl_reservation |
The minimum reservation size for particles.
int Species< Device >::n_backup_particles |
int Species< Device >::n_ptl |
Number of particles.
int Species< Device >::ncycles |
Number of subcycles.
int Species< Device >::ncycles_between_sorts |
Number of subcycles between sorts.
int Species< Device >::nonadiabatic_idx |
Index of species skipping adiabatic species (for compatibility with fortran arrays)
bool Species< Device >::owns_particles_d |
Whether the species owns the device particle allocation right now.
Cabana::AoSoA<ParticleDataTypes,HostType,VEC_LEN> Species< Device >::particles |
Particles.
bool Species< Device >::particles_are_backed_up |
Whether particles are currently backed up.
Cabana::AoSoA<ParticleDataTypes,Device,VEC_LEN> Species< Device >::particles_d |
Particles on device.
bool Species< Device >::particles_resident_on_device |
Whether the particles can reside on device.
Cabana::AoSoA<PhaseDataTypes,HostType,VEC_LEN> Species< Device >::phase0 |
Cabana::AoSoA<PhaseDataTypes,Device,VEC_LEN> Species< Device >::phase0_d |
RKRestorationMethod Species< Device >::RK_restoration_method |
Currently, electrons must use first method and ions must use second.
Whether to restore particles on original rank, or to carry phase0 to new rank and restore there.
bool Species< Device >::stream_particles |
Whether to stream particles between host and device if possible.
WeightEvoEq Species< Device >::weight_evo_eq |
Specifies the weight evolution equation method: Direct, PDE, or None.