Species< Device > Class Template Reference

#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 > &not_in_triangle, Simd< bool > &not_in_poloidal_domain) const
KOKKOS_INLINE_FUNCTION double	eq_flow_ms (const MagneticField< DeviceType > &magnetic_field, double psi_in, double r, double z, double bphi_over_b) const
void	update_decomposed_f0_calculations (const DomainDecomposition< DeviceType > &pol_decomp, const Grid< DeviceType > &grid, const MagneticField< DeviceType > &magnetic_field, const VelocityGrid &vgrid)
void	initialize_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)
void	read_initial_distribution (NLReader::NamelistReader &nlr, const DomainDecomposition< DeviceType > &pol_decomp)
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 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...
bool	maxwellian_init
	whether initial distribution is maxwellian 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_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< Device >	gyro_avg_matrices

Member Enumeration Documentation

template<class Device>

enum Species::LaunchBounds

strong

Enumerator
Default
Custom

Constructor & Destructor Documentation

template<class Device >

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

template<class Device >

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

< Specifies the weight evolution equation method: Direct, PDE, or None.

< - Direct integration: Is used in the Total-F method, where the source term and particle contributions are evaluated separately. Refer to Section II C of Hager et al., Phys. Plasmas 29, 112308 (2022) for more details.

• PDE: The PDE (Partial Differential Equation) method, where the source term and particle contributions are evaluated together (delta-f).
• None: No weight evolution is applied.

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template<class Device>

Species< Device >::Species ( SpeciesType  sp_type, int  n_ptl  )

inline

template<class Device>

Species< Device >::Species ( int  n_ptl_in )

inline

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Member Function Documentation

template<class Device>

void Species< Device >::back_up_SoA ( Cabana::AoSoA< ParticleDataTypes, Device, VEC_LEN > &  backup_SoA, int  offset, int  n  ) const

inline

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template<class Device>

void Species< Device >::copy_particles_from_device ( )

inline

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template<class Device>

void Species< Device >::copy_particles_from_device_if_not_resident ( )

inline

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template<class Device>

void Species< Device >::copy_particles_from_device_if_resident ( )

inline

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template<class Device>

void Species< Device >::copy_particles_to_device ( )

inline

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template<class Device>

void Species< Device >::copy_particles_to_device_if_not_resident ( )

inline

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template<class Device>

void Species< Device >::copy_particles_to_device_if_resident ( )

inline

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template<class Device>

void Species< Device >::copy_to_phase0 ( Species< Device > &  species )

inline

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template<class Device>

KOKKOS_INLINE_FUNCTION double Species< Device >::eq_flow_ms ( const MagneticField< DeviceType > &  magnetic_field, double  psi_in, double  r, double  z, double  bphi_over_b  ) const

inline

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template<class Device >

std::vector< MemoryPrediction > Species< Device >::estimate_memory_usage ( NLReader::NamelistReader &  nlr, const Grid< DeviceType > &  grid, const DomainDecomposition< DeviceType > &  pol_decomp, int  species_idx  )

static

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template<class Device>

template<typename F >

void Species< Device >::for_all_particles ( const std::string  label, F  lambda_func  ) const

inline

Loops over particles and calls a parallel_for, with no particle movement

Parameters

[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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template<class Device>

template<typename F >

void Species< Device >::for_all_particles ( const std::string  label, F  lambda_func, const PtlMvmt  mvmt, LaunchBounds  launch_bounds = LaunchBounds::Default  )

inline

Loops over particles and calls a parallel_for, with particle being moved where requested

Parameters

[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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template<class Device>

template<typename F >

void Species< Device >::for_particle_range ( int  begin_idx, int  end_idx, const std::string  label, F  lambda_func  ) const

inline

Loops over a subset of particles and calls a parallel_for, with no particle movement

Parameters

[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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template<class Device>

KOKKOS_INLINE_FUNCTION double Species< Device >::get_f0_eq_thermal_velocity ( int  inode ) const

inline

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template<class Device>

KOKKOS_INLINE_FUNCTION double Species< Device >::get_f0_eq_thermal_velocity_lnode ( int  inode ) const

inline

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template<class Device>

KOKKOS_INLINE_FUNCTION double Species< Device >::get_f0_eq_thermal_velocity_lnode_h ( int  inode ) const

inline

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template<class Device>

KOKKOS_INLINE_FUNCTION double Species< Device >::get_f0_fg_unit_velocity_lnode_h ( int  inode ) const

inline

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template<class Device>

KOKKOS_INLINE_FUNCTION double Species< Device >::get_fg_gyro_radius ( int  inode, double  smu_n, double  bfield  ) const

inline

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template<class Device >

int Species< Device >::get_initial_n_ptl ( NLReader::NamelistReader &  nlr, const Grid< DeviceType > &  grid, const DomainDecomposition< DeviceType > &  pol_decomp, int  species_idx, bool  verbose  )

static

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template<class Device >

long long int Species< Device >::get_max_gid

(

)

const

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template<class Device>

int Species< Device >::get_max_n_ptl ( )

inline

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template<class Device>

KOKKOS_INLINE_FUNCTION void Species< Device >::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 > &  not_in_triangle, Simd< bool > &  not_in_poloidal_domain  ) const

inline

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template<class Device >

void Species< Device >::get_ptl_write_total_and_offsets	(	const DomainDecomposition< DeviceType > &	pol_decomp,
		long long int &	inum_total,
		long long int &	ioff
	)		const

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template<class Device>

long long int Species< Device >::get_total_n_ptl ( )

inline

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template<class Device >

void Species< Device >::initialize_global_f0_arrays	(	const Grid< DeviceType > &	grid,
		const MagneticField< DeviceType > &	magnetic_field
	)

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template<class Device>

KOKKOS_INLINE_FUNCTION VecPhase* Species< Device >::ph0 ( ) const

inline

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template<class Device>

KOKKOS_INLINE_FUNCTION VecParticles* Species< Device >::ptl ( ) const

inline

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template<class Device >

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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template<class Device >

void Species< Device >::read_initial_distribution	(	NLReader::NamelistReader &	nlr,
		const DomainDecomposition< DeviceType > &	pol_decomp
	)

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template<class Device >

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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template<class Device>

void Species< Device >::resize_device_particles ( )

inline

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template<class Device>

void Species< Device >::resize_device_particles ( int  new_n_ptl )

inline

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template<class Device>

void Species< Device >::resize_host_particles_to_match_device ( )

inline

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template<class Device>

void Species< Device >::resize_particles ( int  new_n_ptl )

inline

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template<class Device>

void Species< Device >::restore_backup_SoA ( Cabana::AoSoA< ParticleDataTypes, Device, VEC_LEN > &  backup_SoA, int  offset, int  n  ) const

inline

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template<class Device>

void Species< Device >::restore_particles_from_backup ( )

inline

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template<class Device>

KOKKOS_INLINE_FUNCTION void Species< Device >::restore_phase_from_phase0 ( const AoSoAIndices< Device > &  inds, SimdParticles &  part_one  ) const

inline

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template<class Device>

void Species< Device >::save_backup_particles ( )

inline

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template<class Device>

void Species< Device >::set_buffer_particles_d ( )

inline

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

Returns

void

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template<class Device>

void Species< Device >::set_buffer_phase0_d ( )

inline

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

Returns

void

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template<class Device>

void Species< Device >::unassign_host_particles ( )

inline

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template<class Device >

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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template<class Device >

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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template<class Device >

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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Member Data Documentation

template<class Device>

Cabana::AoSoA<ParticleDataTypes,HostType,VEC_LEN> Species< Device >::backup_particles

Copy of particles to be restored for RK2.

template<class Device>

double Species< Device >::c2_2m

c2/2m

template<class Device>

double Species< Device >::c_m

c/m

template<class Device>

double Species< Device >::charge

Particle charge.

template<class Device>

double Species< Device >::charge_eu

Particle charge in eu.

template<class Device>

int Species< Device >::collision_grid_index

Which collision grid to use.

template<class Device>

bool Species< Device >::dynamic_f0

Whether f0 can evolve in time.

template<class Device>

Eq::Profile<Device> Species< Device >::eq_den

template<class Device>

Eq::Profile<Device> Species< Device >::eq_fg_flow

template<class Device>

int Species< Device >::eq_fg_flow_type

template<class Device>

Eq::Profile<Device> Species< Device >::eq_fg_temp

template<class Device>

Eq::Profile<Device> Species< Device >::eq_flow

template<class Device>

int Species< Device >::eq_flow_type

template<class Device>

Eq::Profile<Device> Species< Device >::eq_mk_den

template<class Device>

Eq::Profile<Device> Species< Device >::eq_mk_flow

template<class Device>

int Species< Device >::eq_mk_flow_type

template<class Device>

Eq::Profile<Device> Species< Device >::eq_mk_temp

template<class Device>

Eq::Profile<Device> Species< Device >::eq_temp

template<class Device>

Distribution<Device> Species< Device >::f0

Species distribution in velocity space on local mesh nodes.

template<class Device>

FAnalyticShape Species< Device >::f_analytic_shape

f_analytic_shape shape: Maxwellian, SlowingDown or None

template<class Device>

GyroAverageMatrices<Device> Species< Device >::gyro_avg_matrices

template<class Device>

int Species< Device >::idx

Index in all_species.

template<class Device>

bool Species< Device >::is_adiabatic

Whether this species is adiabatic.

template<class Device>

bool Species< Device >::is_electron

Whether this species is the electrons.

template<class Device>

KinType Species< Device >::kintype

Whether the species is gyrokinetic or drift kinetic.

template<class Device>

MarkerType Species< Device >::marker_type

Marker type: reduced delta-f, total-f, full-f, or none (placeholder for adiabatic species)

template<class Device>

double Species< Device >::mass

Particle mass.

template<class Device>

bool Species< Device >::maxwellian_init

whether initial distribution is maxwellian

template<class Device>

int Species< Device >::minimum_ptl_reservation

The minimum reservation size for particles.

template<class Device>

int Species< Device >::n_backup_particles

template<class Device>

int Species< Device >::n_ptl

Number of particles.

template<class Device>

int Species< Device >::ncycles

Number of subcycles.

template<class Device>

int Species< Device >::ncycles_between_sorts

Number of subcycles between sorts.

template<class Device>

int Species< Device >::nonadiabatic_idx

Index of species skipping adiabatic species (for compatibility with fortran arrays)

template<class Device>

bool Species< Device >::owns_particles_d

Whether the species owns the device particle allocation right now.

template<class Device>

Cabana::AoSoA<ParticleDataTypes,HostType,VEC_LEN> Species< Device >::particles

Particles.

template<class Device>

bool Species< Device >::particles_are_backed_up

Whether particles are currently backed up.

template<class Device>

Cabana::AoSoA<ParticleDataTypes,Device,VEC_LEN> Species< Device >::particles_d

Particles on device.

template<class Device>

bool Species< Device >::particles_resident_on_device

Whether the particles can reside on device.

template<class Device>

Cabana::AoSoA<PhaseDataTypes,HostType,VEC_LEN> Species< Device >::phase0

template<class Device>

Cabana::AoSoA<PhaseDataTypes,Device,VEC_LEN> Species< Device >::phase0_d

template<class Device>

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.

template<class Device>

bool Species< Device >::stream_particles

Whether to stream particles between host and device if possible.

template<class Device>

WeightEvoEq Species< Device >::weight_evo_eq

Specifies the weight evolution equation method: Direct, PDE, or None.

• Direct integration: Is used in the Total-F method, where the source term and particle contributions are evaluated separately. Refer to Section II C of Hager et al., Phys. Plasmas 29, 112308 (2022) for more details.
• PDE: The PDE (Partial Differential Equation) method, where the source term and particle contributions are evaluated together (delta-f).
• None: No weight evolution is applied.

---

The documentation for this class was generated from the following files:

• /u/gitlab-xgc/builds/YGMz2TJ8/0/xgc/XGC-Devel/XGC_core/cpp/species.hpp
• /u/gitlab-xgc/builds/YGMz2TJ8/0/xgc/XGC-Devel/XGC_core/cpp/species.cpp