orb5x::Diagnostics Class Reference

Owns diagnostic accumulation, MPI reduction, normalization, and HDF5 output. More...

#include "diagnostics.hpp"

Collaboration diagram for orb5x::Diagnostics:

Classes
struct	PlaceholderEntry

Public Member Functions
	Diagnostics ()
	Constructor - initializes all static member defaults.

Static Public Member Functions
static void	accumulate_diagnostics (int isp, Real wt, Real w3t, Real pt, Real pvolgc, Real ze, Real zf0, Real sigmat, Real q_vgc_dot_genelec, Real q_dvpadt0_dot_gyroapar)
	Accumulate weights, entropy, and energy-transfer scalars for one marker.
static void	accumulate_displacements (int isp, bool in_ksieta, Real chit_cos, Real chit_sin, Real sigmat, const std::array< Real, 3 > &tempd, const std::array< Real, 3 > &vgc, const std::array< Real, 3 > &vexb, Real dvpadt1, Real dvpadt0, Real rhs, bool nl_directdf)
	Accumulate total and E x B marker-displacement statistics.
static void	accumulate_flux1d_f0 (int isp, int irloc, Real zf0, Real dPsidt1, Real dPsidt0, Real ze, Real ut, Real rt2, const std::vector< Real > &vpar)
	Accumulate equilibrium-distribution radial flux channels.
static void	accumulate_flux1d_w (int isp, int irloc, Real wt, Real dPsidt1, Real dPsidt0, Real ze, Real ut, Real rt2, const std::vector< Real > &vpar)
	Accumulate marker-weighted radial particle, heat, and momentum flux.
static void	accumulate_moment1d_f (int isp, int irloc, Real zf0, Real wt, Real ut, Real ut2, Real vpt2)
	Accumulate total-distribution one-dimensional velocity moments.
static void	accumulate_moment1d_f0 (int isp, int irloc, Real zf0, Real ut, Real ut2, Real vpt2, Real rt2, const std::vector< Real > &vpar, const std::vector< Real > &vexb, Real b)
	Accumulate equilibrium-distribution one-dimensional moments.
static void	accumulate_moment1d_w (int isp, int irloc, Real zf0, Real wt, Real ut, Real ut2, Real vpt2, Real rt2, const std::vector< Real > &vpar, const std::vector< Real > &vexb, Real b, Real jdote_tot)
	Accumulate perturbation-weighted one-dimensional moments.
static void	add_efield (int isp, int component, Real value)
static void	add_efield_av (int isp, int component, Real value)
static void	add_to_0d_vexbnavg (int isp, Real to_add)
	Accumulate mean thermal-normalized E x B speed.
static void	add_to_entropy_fluct (int isp, int idiag, Real value)
static void	add_to_jdote_bg (int isp, int idiag, Real value)
static void	add_to_jdote_fluct (int isp, int idiag, Real value)
static void	add_trap_frac (int isp, int type, Real value)
static void	append_placeholder_slices (int step, Real time)
	Append zero-filled compatibility slices for one output sample.
static void	append_scalar (const std::string &path, const Real *values, size_t count)
	Append scalar values to an extensible HDF5 dataset.
static void	append_stat_int (const std::string &path, const int *array, size_t count)
	Matching Fortran append_stat (util.F90:473-511): Appends integer array data to an extensible HDF5 dataset.
static void	clear_diagnostics (int isp)
	Clear per-step accumulators for one species.
static void	clear_entropy_diag (int isp)
static void	clear_jdote (int isp)
static void	clear_jdote_fluct (int isp)
static void	createg_1D (const std::string &name, const std::string &description, const std::vector< Real > &coord1, const std::string &coord1_name)
	Create generic 1D dataset group (matching Fortran createg_1D, diagnostics.F90:2663-2674) Creates /data/var1d/generic/{name} with coord1, time, data datasets and attaches PlotOrder attribute.
static void	createg_1Dms (const std::string &species_name, const std::string &name, const std::string &description, const std::vector< Real > &coord1, const std::string &coord1_name)
	Create species 1D dataset group (matching Fortran createg_1Dms, diagnostics.F90:2746-2759) Creates /data/var1d/{species_name}/{name} with coord1, time, data datasets and attaches PlotOrder attribute.
static void	createg_2D (const std::string &name, const std::string &description, const std::vector< Real > &coord1, const std::string &coord1_name, const std::vector< Real > &coord2, const std::string &coord2_name)
	Create generic 2D dataset group (matching Fortran createg_2D, diagnostics.F90:2647-2659) Creates /data/var2d/generic/{name} with coord1, coord2, time, data datasets and attaches PlotOrder attribute.
static void	createg_2Dms (const std::string &species_name, const std::string &name, const std::string &description, const std::vector< Real > &coord1, const std::string &coord1_name, const std::vector< Real > &coord2, const std::string &coord2_name)
	Create species 2D dataset group (matching Fortran createg_2Dms, diagnostics.F90:2678-2701) Creates /data/var2d/{species_name}/{name} with coord1, coord2, time, data datasets and attaches PlotOrder attribute.
static void	createg_3D (const std::string &name, const std::string &description, const std::vector< Real > &coord1, const std::string &coord1_name, const std::vector< Real > &coord2, const std::string &coord2_name, const std::vector< Real > &coord3, const std::string &coord3_name)
	Create generic 3D dataset group (matching Fortran createg_3D, diagnostics.F90:2608-2622) Creates /data/var3d/generic/{name} with coord1, coord2, coord3, time, data datasets and attaches PlotOrder attribute.
static void	createg_3Dms (const std::string &species_name, const std::string &name, const std::string &description, const std::vector< Real > &coord1, const std::string &coord1_name, const std::vector< Real > &coord2, const std::string &coord2_name, const std::vector< Real > &coord3, const std::string &coord3_name, const std::vector< std::vector< int > > *mmin_f=nullptr)
	Create species 3D dataset group (matching Fortran createg_3Dms, diagnostics.F90:2705-2720) Creates /data/var3d/{species_name}/{name} with coord1, coord2, coord3, time, data datasets and attaches PlotOrder attribute.
static void	createg_3Dz (const std::string &name, const std::string &description, const std::vector< Real > &coord1, const std::string &coord1_name, const std::vector< Real > &coord2, const std::string &coord2_name, const std::vector< Real > &coord3, const std::string &coord3_name, const std::vector< std::vector< int > > *mmin_f=nullptr)
	Create generic 3D complex dataset group (matching Fortran createg_3Dz, diagnostics.F90:2626-2643) Creates /data/var3d/generic/{name} with coord1, coord2, coord3, time, data (complex) datasets Optionally creates mmin dataset if mmin_f is provided.
static void	createg_3Dzms (const std::string &species_name, const std::string &name, const std::string &description, const std::vector< Real > &coord1, const std::string &coord1_name, const std::vector< Real > &coord2, const std::string &coord2_name, const std::vector< Real > &coord3, const std::string &coord3_name, const std::vector< std::vector< int > > *mmin_f=nullptr)
	Create species 3D complex dataset group (matching Fortran createg_3Dzms, diagnostics.F90:2724-2742) Creates /data/var3d/{species_name}/{name} with coord1, coord2, coord3, time, data (complex) datasets Optionally creates mmin dataset if mmin_f is provided.
static void	destroyStaticViews ()
	Release static Kokkos Views before Kokkos::finalize()
static void	diag3d_on_fluid_moments (int isp)
	Derive vorticity, potential, temperature, and spectra from fluid moments.
static void	diag3d_spectrum (const std::vector< std::vector< std::vector< Real > > > &field, std::vector< std::vector< Real > > &spectrum_out, int nmax)
	Compute a toroidal-mode spectrum from a real three-dimensional field.
static void	diag_fields_torpol (int fieldnum, Real time)
	Write toroidal and poloidal Fourier spectra.
static void	diag_fields_torpol_init ()
	=============================================================================
static void	diag_fulltorus (int fieldnum, Real time)
	Write selected full-torus plane cuts.
static void	diag_fulltorus_init ()
	=============================================================================
static void	diagnose (int step, int step_tot, Real time)
	Run diagnostics scheduled for the current integration step.
static void	diagnose_phasespace (int isp, Real s, Real vpar, Real mu, Real B, Real pvol, Real w, Real zf0)
	Accumulate the (psi,v_parallel,v_perp) phase-space histogram.
static void	diagnose_sampling (int isp, Real s, Real en, Real pvol, Real w, Real zf0)
	Accumulate the (s,v^2) marker-sampling histogram.
static void	diagnostics_after_loop (int isp)
	Reduce and normalize diagnostics after one species push loop.
static std::vector< std::vector< Real > > &	displacement_avg_ref ()
static std::vector< std::vector< Real > > &	displacement_exb_avg_ref ()
static std::vector< std::vector< Real > > &	displacement_exb_max_ref ()
static std::vector< std::vector< Real > > &	displacement_max_ref ()
static void	electron_fluxes_moments (int isp, int irloc, Real zf0, Real dPsidt1, Real dPsidt0, Real ze, Real wt, Real ffinit_tmp1, Real ffinit_tmp2, Real ffinit_tmp3, Real ffinit_tmp4, bool is_trapped)
	Accumulate passing/trapped electron fluxes and moments.
static std::vector< std::vector< Real > > &	entropy_fluct_avg_ref ()
static std::vector< std::vector< std::vector< std::vector< std::vector< Real > > > > > &	fluid_moments_ref ()
static void	flush0d ()
	Flush 0D diagnostics buffer to file Writes accumulated 0D diagnostic data to HDF5.
static std::vector< std::vector< std::vector< Real > > > &	flux1d_f0_ref ()
static std::vector< std::vector< std::vector< Real > > > &	flux1d_w_ref ()
static Real	get_adiab (int isp)
static Kokkos::View< Real ** > &	get_buf ()
static Kokkos::View< Real *** > &	get_buf_pic ()
static int	get_cum_non_cg_bins (int isp)
static int	get_cum_non_cg_markers (int isp)
static Real	get_dSdt_heat (int isp)
static Real	get_dSdt_nc (int isp)
static Real	get_dSdt_nc_corr (int isp)
static Real	get_efield (int isp, int component)
static Real	get_efield_av (int isp, int component)
static Real	get_efield_fft (int isp, int component)
static Real	get_entropy_fluct_avg (int isp, int idiag)
static Real	get_flux0d_f0 (int isp, int idiag)
static Real	get_flux0d_w (int isp, int idiag)
static Kokkos::View< Real * >	get_generic_signoise_avg ()
static int	get_generic_signoise_size ()
static Real	get_generic_spectrum2d_avg (int idiag, int i, int j)
static int	get_ibuf ()
static Real	get_inner_edge_losses (int isp, int component)
static int	get_irloc_in ()
static Real	get_jdote_bg (int isp, int idiag)
static Real	get_jdote_fluct (int isp, int idiag)
static Real	get_misc_avg (int isp, int idiag)
static Kokkos::View< Real ** > &	get_noise_2d_all ()
static int	get_nsbound_in (int isp)
static int	get_nsbound_out (int isp)
static Real	get_outer_edge_losses (int isp, int component)
static Kokkos::View< Real ** > &	get_signal_2d_all ()
static Real	get_spectrum2d_avg (int isp, int idiag, int i, int j)
static int	get_tot_cg_bins (int isp)
static int	get_tot_cg_markers (int isp)
static Real	get_trap_frac (int isp, int type)
static Real	get_variance (int isp, int index)
static Real	get_vexbnavg (int isp, int idiag)
static Real	get_vthmax2_cached (int isp)
static Real	get_vthmax_cached (int isp)
static Real	get_wsqreduced (int isp)
static Real	getpot_fieldnum (Real s, Real theta, Real phi, int fieldnum)
	Interpolate a selected field in magnetic coordinates.
static void	init_generic_signoise ()
	Allocate and clear generic signal-to-noise accumulators.
static void	init_phase1_diagnostics ()
	Initialize Phase 1 diagnostic arrays and flags Called from initialize_diagnostics()
static void	init_test_diagnostic_arrays (int nspecies)
	Allocate deterministic in-memory diagnostic storage for tests.
static void	init_variance (int nspecies)
	Size and zero variance storage.
static void	initialize_diagnostics ()
	Initialize diagnostics system Sets up all diagnostic structures, grids, and output files.
static void	initialize_phasespace_diags ()
	Initialize phase space diagnostics.
static void	initialize_source_3d_diags ()
	Initialize source 3D diagnostics.
static Real	jdote (int isp, Real ut2, Real vpt2, const std::vector< Real > &vpar, const std::vector< Real > &genelec, const std::vector< Real > &elec_par, Real wt, Real bstar_inv, const std::vector< Real > &bgrb, const std::vector< Real > &vgb, const std::vector< Real > &vpressure, const std::vector< Real > &veb_f, const std::vector< Real > &vexb, Real expt_back, Real eypt_back, Real dvpadt0, Real gyroapar)
	Compute and accumulate one marker's j dot E power transfer.
static std::vector< std::vector< Real > > &	jdote_bg_ref ()
static std::vector< std::vector< Real > > &	jdote_fluct_ref ()
static void	max_of_0d (int isp, int i, Real to_add)
	Update a maximum-valued zero-dimensional channel.
static void	max_of_0d_vexbnmax (int isp, Real to_add)
	Update maximum thermal-normalized E x B speed.
static void	max_of_0d_vmax (int isp, Real to_add)
	Update maximum normalized marker speed.
static void	max_of_0d_wmax (int isp, Real to_add)
	Update maximum absolute marker weight.
static std::vector< std::vector< Real > > &	misc_avg_ref ()
static void	mmin_f_serialize ()
	Serializes mmin_f array across MPI ranks for 3D output.
static std::vector< std::vector< std::vector< Real > > > &	moment1d_f0_ref ()
static std::vector< std::vector< std::vector< Real > > > &	moment1d_f_ref ()
static std::vector< std::vector< std::vector< Real > > > &	moment1d_w_ref ()
static std::vector< std::vector< std::vector< std::vector< Real > > > > &	moment2d_avg_ref ()
static std::vector< std::vector< std::vector< std::vector< Real > > > > &	mpr_2d_ref ()
static void	mpr_es_calc (int isp, int iuloc, int imuloc, Real sigmat, Real thetat, Real wt, Real ut2, Real vpt2, Real bstar_inv, const std::vector< Real > &vpar, const std::vector< Real > &genelec, const std::vector< Real > &bgrb, const std::vector< Real > &vgb, const std::vector< Real > &vpressure, const std::vector< Real > &veb_f)
	Accumulate electrostatic mode-particle-resonance power transfer.
static bool	nl_do_diag (int step_tot, int nfreq)
	Test a diagnostic cadence.
static void	normalize_flux1d (int isp)
	Normalize radial fluxes and form zero-dimensional integrals.
static void	normalize_moment1d_f (int isp)
	Normalize total-distribution radial moments.
static void	normalize_moment1d_f0 (int isp)
	Normalize equilibrium-distribution radial moments.
static void	normalize_moment1d_w (int isp)
	Normalize perturbation-weighted radial moments.
static void	normalize_moment2d (int isp)
	Normalize two-dimensional averaged moments.
static void	normalize_poloidal1d (int isp)
	Normalize one-dimensional poloidal moments.
template<typename T >
static void	omp_reduce_diag (T &data, bool use_max=false)
	Generic diagnostic reduction interface (matches Fortran omp_reduce_diag)
static void	omp_reduce_diag0d (Real &data, bool use_max=false)
	=============================================================================
static void	omp_reduce_diag1d (std::vector< Real > &data, bool use_max=false)
	Reduce 1D diagnostic array.
static void	omp_reduce_diag2d (std::vector< std::vector< Real > > &data, bool use_max=false)
	Reduce 2D diagnostic array.
static void	omp_reduce_diag3d (std::vector< std::vector< std::vector< Real > > > &data, bool use_max=false)
	Reduce 3D diagnostic array.
static std::vector< std::vector< std::vector< std::vector< std::vector< Real > > > > > &	phasespace_3d_ref ()
static void	polarisation_fieldcalc (int isp)
	Compute polarization-field diagnostic channels after reduction.
static std::vector< std::vector< std::vector< Real > > > &	poloidal1d_f_ref ()
static std::vector< std::vector< std::vector< Real > > > &	poloidal1d_w_ref ()
static void	profsphi (Real theta, int fieldnum, std::vector< std::vector< Real > > &pot_sp)
	Sample a selected field on an (s,phi) plane.
static void	profsth (Real phi, int fieldnum, int ns0, std::vector< std::vector< Real > > &pot_st, std::vector< std::vector< Real > > *xc=nullptr, std::vector< std::vector< Real > > *zc=nullptr)
	Sample a selected field on an (s,theta) plane.
static void	put3d_dens (Real time, bool do_moments=false)
	Write three-dimensional density and optional moment diagnostics.
static void	put3d_h5s (Real time, int diag_select, int field_select, int isp=-1)
	Write one three-dimensional field/density diagnostic.
static void	putarr (const std::string &path, const Real *array, size_t length, const std::string &title="")
	Write a one-dimensional real array and optional title.
static void	putarr_attime_1d (const std::string &path, const Real *array, size_t length, Real time)
	Append a one-dimensional real slice at a simulation time.
static void	putarr_attime_2d (const std::string &path, const Real *array, size_t dim1, size_t dim2, Real time)
	Append a two-dimensional real slice at a simulation time.
static void	read_restart_state (int datn)
static void	rhs_f_serialize (const std::vector< std::vector< std::complex< Real > > > &rhs_f_ptr)
	Gather distributed Fourier RHS coefficients for three-dimensional output.
static std::vector< std::vector< std::vector< std::vector< Real > > > > &	sampling_2d_ref ()
static void	set_buf (Kokkos::View< Real ** > v)
static void	set_buf_pic (Kokkos::View< Real *** > v)
static void	set_dSdt_heat (int isp, Real value)
static void	set_dSdt_nc (int isp, Real value)
static void	set_dSdt_nc_corr (int isp, Real value)
static void	set_efield (int isp, int component, Real value)
static void	set_efield_av (int isp, int component, Real value)
static void	set_efield_fft (int isp, int component, Real value)
static void	set_generic_spectrum2d_avg (int idiag, int i, int j, Real value)
static void	set_ibuf (int val)
static void	set_inner_edge_losses (int isp, int component, Real value)
static void	set_misc_avg (int isp, int idx, Real val)
static void	set_nsbound_in (int isp, int value)
static void	set_nsbound_out (int isp, int value)
static void	set_outer_edge_losses (int isp, int component, Real value)
static void	set_signal2noise (Real sn, Real sn_nozf)
static void	set_signal2noise_em (Real sn, Real sn_nozf)
static void	set_spectrum2d_avg (int isp, int idiag, int i, int j, Real value)
static void	set_variance (int isp, int index, Real value)
static void	snapshot_variance (int isp)
static std::vector< std::vector< std::vector< Real > > > &	source_diag1d_avg_ref ()
static void	strong_diagnostic_output (int isp, int ip, Real psi0t, Real temp2, Real ze, Real vecrossb_f2, Real pot_equil, Real zf0, Real zvth2_inv, Real dpotdpsi, Real vdr, Real rhs)
	Record one marker's strong-flow parity diagnostics.
static void	sum_entropy_fluctuation (int isp, Real wt, Real zf0, Real q_vgc_dot_genelec, Real zvth2_inv, Real df0_dpsi_prof, Real df0_dchi_prof, Real dpsi_prof_dt)
	Accumulate one marker's fluctuation-entropy balance.
static void	sum_fluid_moments (int isp, Real sigmat, Real chit, Real phit, Real wt, Real ut, Real ut2, Real vpt2)
	Deposit one marker into three-dimensional fluid moments.
static void	sum_in_radial_bins_island (int isp, int irloc, int ipol, Real ut, const std::vector< Real > &gradpsi0, Real htildex, Real htildey, Real ze, Real zf0, Real wt, Real dPsidt1, Real ffinit_tmp1, Real ffinit_tmp2, Real ffinit_tmp3, Real ffinit_tmp4)
	Accumulate magnetic-island radial/poloidal diagnostics.
static void	sum_moment2d (int isp, int irloc, int ithetaloc, Real wt, Real ffinit_tmp1, Real ffinit_tmp2, Real ffinit_tmp3, Real ffinit_tmp4)
	Accumulate (s,theta) initial-distribution moments.
static void	sum_particles_in_poloidal_bins (int isp, int ithetaloc, Real wt, Real ffinit_tmp1, Real ffinit_tmp2, Real ffinit_tmp3, Real ffinit_tmp4, Real wt_tmp1, Real wt_tmp2, Real wt_tmp3)
	Accumulate poloidal moments at the configured radial surface.
static void	sum_particles_in_radial_bins (int isp, int ip, int irloc, Real zf0, Real dPsidt1, Real dPsidt0, Real ze, Real wt, Real ut, Real ut2, Real vpt2, Real rt2, const std::vector< Real > &vpar, Real zf0_tmp1, Real zf0_tmp2, Real zf0_tmp3, Real sigmat, Real zf0_local, Real grsigma2, Real grsigmagrchi, Real b, const std::vector< Real > &exh, Real wt_tmp1, Real wt_tmp2, Real wt_tmp3, const std::vector< Real > &vexb, Real ffinit_tmp1, Real ffinit_tmp2, Real ffinit_tmp3, Real ffinit_tmp4, Real ffinit_tmp5, Real jdote_tot, const std::vector< Real > &eloc)
	Accumulate all configured radial-bin diagnostics for one marker.
static Real	sum_spectrum2d_avg (int isp, int idiag, int ndim, int mdim)
static void	sum_velocities (int isp, int iuloc, int imuloc, Real wt, Real zf0, Real pvol)
	Accumulate one- and two-dimensional velocity-space diagnostics.
static void	test_particle_output (int isp, int ip, Real psi0t, Real ze, Real pot_equil, Real wt, Real zvth2, Real nval, Real pvol_updated, Real zf0)
	Store one selected test-particle record.
static std::vector< std::vector< std::vector< Real > > > &	vel1d_avg_ref ()
static std::vector< std::vector< std::vector< std::vector< Real > > > > &	vel2d_avg_ref ()
static void	velocity_space_diag_init ()
	Initialize velocity space diagnostics Sets up velocity space grids and output structures.
static std::vector< Real > &	vmax_ref ()
static std::vector< Real > &	wmax_ref ()
static void	write_output (int step, Real time)
	Write the standard scalar, profile, and spectrum output set.
static void	write_restart_state (int datn)
static void	zero_generic_spectrum2d_avg (int idiag, int ndim, int mdim)
	Zero one generic (m,n) spectrum slice.
static void	zero_spectrum2d_avg (int isp, int idiag, int ndim, int mdim)
	Zero one per-species (m,n) spectrum slice.

Static Public Attributes
static std::vector< Real >	apaloc
	Local \(A_\parallel(s,0,0)\) radial cut.
static constexpr int	FIELD_APAR = 2
	Select total parallel vector potential.
static constexpr int	FIELD_APAR_HAM = 3
	Select Hamiltonian \(A_\parallel\).
static constexpr int	FIELD_APAR_SYMPL = 4
	Select symplectic \(A_\parallel\).
static constexpr int	FIELD_DENS = 5
	Select density field.
static constexpr int	FIELD_PHI = 1
	=============================================================================
static constexpr int	FIELD_USER = 6
	Select user-defined external field.
static std::vector< std::vector< std::vector< Real > > >	moment1d_w
	moment1d_w: 1D moment diagnostics weighted by w (matching Fortran moment1d_w) [nspecies][nbin_flux+2][14 diagnostic types] - matching moment1d_w structure
static std::vector< bool >	out
	Species output flags (matching Fortran out(0:NSPECIES_MAX)) out[0] = true for pure fluid model, out[isp] = true if species isp has diagnostic output.
static std::array< int, 3 >	pe_phi_cuts = {0, 0, 0}
	MPI ranks responsible for phi cuts (matching Fortran pe_phi_cuts(0:2)) Stores the PE rank that owns each of the 3 phi cut positions for output.
static std::vector< Real >	phi00
	Public diagnostic arrays (accessed by FieldsModule in solve_fem, matching Fortran pde_solver) Potential diagnostic arrays (matching Fortran diagnostics.F90)
static std::vector< Real >	phi0_chi
	Poloidal potential cut at the configured diagnostic radius.
static std::vector< Real >	phibar
	Flux-surface-averaged electrostatic potential.
static std::vector< Real >	philoc
	\(\phi(s,\theta=0,\varphi=0)\) radial cut.
static std::vector< Real >	philoc_hfs
	High-field-side cut \(\phi(s,\theta=\pi,\varphi=0)\).
static std::vector< std::vector< Real > >	rho00
	Flux-surface-averaged charge density by radius and species.

Detailed Description

Owns diagnostic accumulation, MPI reduction, normalization, and HDF5 output.

Particle pushers accumulate weighted fluxes, moments, entropy transfer, and phase-space statistics through this static service. After each species loop, Diagnostics reduces rank-local data, applies physical bin-volume and distribution normalizations, stages field and three-dimensional products, and appends them to the configured output datasets. Species arguments use zero-based C++ indexing unless a function explicitly states otherwise; physical values are in ORB5X normalization and angles are in radians.

Constructor & Destructor Documentation

Diagnostics()

orb5x::Diagnostics::Diagnostics ( )

inline

Constructor - initializes all static member defaults.

Scalar members

References pe_phi_cuts.

Member Function Documentation

accumulate_diagnostics()

static void orb5x::Diagnostics::accumulate_diagnostics ( int  isp, Real  wt, Real  w3t, Real  pt, Real  pvolgc, Real  ze, Real  zf0, Real  sigmat, Real  q_vgc_dot_genelec, Real  q_dvpadt0_dot_gyroapar  )

static

Accumulate weights, entropy, and energy-transfer scalars for one marker.

Parameters

[in]	isp	Zero-based species index.
[in]	wt	Perturbation weight.
[in]	w3t	Third weight/control-variate channel.
[in]	pt	Total marker weight used by the selected formulation.
[in]	pvolgc	Guiding-centre phase-space volume.
[in]	ze	Normalized kinetic energy.
[in]	zf0	Equilibrium distribution value.
[in]	sigmat	Radial coordinate s=sqrt(psi).
[in]	q_vgc_dot_genelec	Charge-weighted electric energy transfer.
[in]	q_dvpadt0_dot_gyroapar	Equilibrium-acceleration/vector-potential transfer.

Note

Matches sum_of_weights_and_energy_transfer in part.F90.

accumulate_displacements()

static void orb5x::Diagnostics::accumulate_displacements ( int  isp, bool  in_ksieta, Real  chit_cos, Real  chit_sin, Real  sigmat, const std::array< Real, 3 > &  tempd, const std::array< Real, 3 > &  vgc, const std::array< Real, 3 > &  vexb, Real  dvpadt1, Real  dvpadt0, Real  rhs, bool  nl_directdf  )

static

Accumulate total and E x B marker-displacement statistics.

Parameters

[in]	isp	Zero-based species index.
[in]	in_ksieta	Whether coordinates use the (ksi,eta) representation.
[in]	chit_cos	Cosine of marker poloidal angle.
[in]	chit_sin	Sine of marker poloidal angle.
[in]	sigmat	Radial marker coordinate.
[in]	tempd	Three-component displacement increment.
[in]	vgc	Three-component guiding-centre velocity.
[in]	vexb	Three-component E x B velocity.
[in]	dvpadt1	Perturbed parallel acceleration.
[in]	dvpadt0	Equilibrium parallel acceleration.
[in]	rhs	Weight-equation right-hand side.
[in]	nl_directdf	Direct-delta-f formulation flag.

accumulate_flux1d_f0()

static void orb5x::Diagnostics::accumulate_flux1d_f0 ( int  isp, int  irloc, Real  zf0, Real  dPsidt1, Real  dPsidt0, Real  ze, Real  ut, Real  rt2, const std::vector< Real > &  vpar  )

static

Accumulate equilibrium-distribution radial flux channels.

Parameters

[in]	isp	Zero-based species index.
[in]	irloc	Zero-based radial diagnostic bin.
[in]	zf0	Equilibrium distribution value.
[in]	dPsidt1	Perturbed radial/canonical-flux characteristic.
[in]	dPsidt0	Equilibrium radial/canonical-flux characteristic.
[in]	ze	Normalized kinetic energy.
[in]	ut	Normalized parallel marker coordinate.
[in]	rt2	Squared cylindrical major radius.
[in]	vpar	Three-component parallel velocity.

accumulate_flux1d_w()

static void orb5x::Diagnostics::accumulate_flux1d_w ( int  isp, int  irloc, Real  wt, Real  dPsidt1, Real  dPsidt0, Real  ze, Real  ut, Real  rt2, const std::vector< Real > &  vpar  )

static

Accumulate marker-weighted radial particle, heat, and momentum flux.

Parameters

[in]	isp	Zero-based species index.
[in]	irloc	Zero-based radial diagnostic bin.
[in]	wt	Perturbation weight.
[in]	dPsidt1	Perturbed flux characteristic.
[in]	dPsidt0	Equilibrium flux characteristic.
[in]	ze	Normalized kinetic energy.
[in]	ut	Normalized parallel marker coordinate.
[in]	rt2	Squared cylindrical major radius.
[in]	vpar	Three-component parallel velocity.

accumulate_moment1d_f()

static void orb5x::Diagnostics::accumulate_moment1d_f ( int  isp, int  irloc, Real  zf0, Real  wt, Real  ut, Real  ut2, Real  vpt2  )

static

Accumulate total-distribution one-dimensional velocity moments.

Parameters

[in]	isp	Zero-based species index.
[in]	irloc	Zero-based radial bin.
[in]	zf0	Equilibrium distribution value.
[in]	wt	Perturbation weight.
[in]	ut	Parallel velocity.
[in]	ut2	Squared parallel velocity.
[in]	vpt2	Squared perpendicular velocity.

accumulate_moment1d_f0()

static void orb5x::Diagnostics::accumulate_moment1d_f0 ( int  isp, int  irloc, Real  zf0, Real  ut, Real  ut2, Real  vpt2, Real  rt2, const std::vector< Real > &  vpar, const std::vector< Real > &  vexb, Real  b  )

static

Accumulate equilibrium-distribution one-dimensional moments.

Parameters

[in]	isp	Zero-based species index.
[in]	irloc	Zero-based radial bin.
[in]	zf0	Equilibrium distribution value.
[in]	ut	Parallel velocity.
[in]	ut2	Squared parallel velocity.
[in]	vpt2	Squared perpendicular velocity.
[in]	rt2	Squared cylindrical major radius.
[in]	vpar	Three-component parallel velocity.
[in]	vexb	Three-component E x B velocity.
[in]	b	Normalized magnetic-field magnitude.

accumulate_moment1d_w()

static void orb5x::Diagnostics::accumulate_moment1d_w ( int  isp, int  irloc, Real  zf0, Real  wt, Real  ut, Real  ut2, Real  vpt2, Real  rt2, const std::vector< Real > &  vpar, const std::vector< Real > &  vexb, Real  b, Real  jdote_tot  )

static

Accumulate perturbation-weighted one-dimensional moments.

Parameters

[in]	isp	Zero-based species index.
[in]	irloc	Zero-based radial bin.
[in]	zf0	Equilibrium distribution value.
[in]	wt	Perturbation weight.
[in]	ut	Parallel velocity.
[in]	ut2	Squared parallel velocity.
[in]	vpt2	Squared perpendicular velocity.
[in]	rt2	Squared cylindrical major radius.
[in]	vpar	Three-component parallel velocity.
[in]	vexb	Three-component E x B velocity.
[in]	b	Normalized magnetic-field magnitude.
[in]	jdote_tot	Marker contribution to j dot E.

add_efield()

static void orb5x::Diagnostics::add_efield ( int  isp, int  component, Real  value  )

static

Parameters

[in]	isp	Zero-based species index.
[in]	component	Zero-based total-energy component.
[in]	value	Normalized contribution to add.

add_efield_av()

static void orb5x::Diagnostics::add_efield_av ( int  isp, int  component, Real  value  )

static

Parameters

[in]	isp	Zero-based species index.
[in]	component	Zero-based averaged component.
[in]	value	Normalized contribution to add.

add_to_0d_vexbnavg()

static void orb5x::Diagnostics::add_to_0d_vexbnavg ( int  isp, Real  to_add  )

static

Accumulate mean thermal-normalized E x B speed.

Parameters

[in]	isp	Zero-based species index.
[in]	to_add	Marker contribution.

add_to_entropy_fluct()

static void orb5x::Diagnostics::add_to_entropy_fluct ( int  isp, int  idiag, Real  value  )

static

Parameters

[in]	isp	Zero-based species index.
[in]	idiag	Entropy channel index.
[in]	value	Normalized contribution.

add_to_jdote_bg()

static void orb5x::Diagnostics::add_to_jdote_bg ( int  isp, int  idiag, Real  value  )

static

Parameters

[in]	isp	Zero-based species index.
[in]	idiag	Channel index.
[in]	value	Normalized contribution to add.

add_to_jdote_fluct()

static void orb5x::Diagnostics::add_to_jdote_fluct ( int  isp, int  idiag, Real  value  )

static

Parameters

[in]	isp	Zero-based species index.
[in]	idiag	Channel index.
[in]	value	Normalized contribution to add.

add_trap_frac()

static void orb5x::Diagnostics::add_trap_frac ( int  isp, int  type, Real  value  )

static

Parameters

[in]	isp	Zero-based species index.
[in]	type	Orbit-transition selector.
[in]	value	Fraction contribution to add.

append_placeholder_slices()

static void orb5x::Diagnostics::append_placeholder_slices ( int  step, Real  time  )

static

Append zero-filled compatibility slices for one output sample.

Parameters

[in]	step	Current global timestep index.
[in]	time	Current normalized simulation time.

append_scalar()

static void orb5x::Diagnostics::append_scalar ( const std::string &  path, const Real *  values, size_t  count  )

static

Append scalar values to an extensible HDF5 dataset.

Parameters

[in]	path	Absolute dataset path.
[in]	values	Contiguous scalar values.
[in]	count	Number of appended values.

append_stat_int()

static void orb5x::Diagnostics::append_stat_int ( const std::string &  path, const int *  array, size_t  count  )

static

Matching Fortran append_stat (util.F90:473-511): Appends integer array data to an extensible HDF5 dataset.

Called from rank 0 after data has been gathered.

Parameters

[in]	path	Absolute dataset path.
[in]	array	Contiguous integer values.
[in]	count	Number of appended values.

clear_diagnostics()

static void orb5x::Diagnostics::clear_diagnostics ( int  isp )

static

Clear per-step accumulators for one species.

Parameters

[in]

isp

Zero-based species index.

clear_entropy_diag()

static void orb5x::Diagnostics::clear_entropy_diag ( int  isp )

static

Parameters

[in]

isp

Zero-based species index.

clear_jdote()

static void orb5x::Diagnostics::clear_jdote ( int  isp )

static

Parameters

[in]

isp

Zero-based species index.

clear_jdote_fluct()

static void orb5x::Diagnostics::clear_jdote_fluct ( int  isp )

static

Parameters

[in]

isp

Zero-based species index.

createg_1D()

static void orb5x::Diagnostics::createg_1D ( const std::string &  name, const std::string &  description, const std::vector< Real > &  coord1, const std::string &  coord1_name  )

static

Create generic 1D dataset group (matching Fortran createg_1D, diagnostics.F90:2663-2674) Creates /data/var1d/generic/{name} with coord1, time, data datasets and attaches PlotOrder attribute.

Parameters

[in]	name	Dataset-group name.
[in]	description	Human-readable physical quantity and units.
[in]	coord1	Coordinate values.
[in]	coord1_name	Coordinate label.

createg_1Dms()

static void orb5x::Diagnostics::createg_1Dms ( const std::string &  species_name, const std::string &  name, const std::string &  description, const std::vector< Real > &  coord1, const std::string &  coord1_name  )

static

Create species 1D dataset group (matching Fortran createg_1Dms, diagnostics.F90:2746-2759) Creates /data/var1d/{species_name}/{name} with coord1, time, data datasets and attaches PlotOrder attribute.

Parameters

[in]	species_name	Species output-group label.
[in]	name	Dataset-group name.
[in]	description	Human-readable physical quantity and units.
[in]	coord1	Coordinate values.
[in]	coord1_name	Coordinate label.

createg_2D()

static void orb5x::Diagnostics::createg_2D ( const std::string &  name, const std::string &  description, const std::vector< Real > &  coord1, const std::string &  coord1_name, const std::vector< Real > &  coord2, const std::string &  coord2_name  )

static

Create generic 2D dataset group (matching Fortran createg_2D, diagnostics.F90:2647-2659) Creates /data/var2d/generic/{name} with coord1, coord2, time, data datasets and attaches PlotOrder attribute.

Parameters

[in]	name	Dataset-group name.
[in]	description	Human-readable physical quantity and units.
[in]	coord1	First coordinate values.
[in]	coord1_name	First-coordinate label.
[in]	coord2	Second coordinate values.
[in]	coord2_name	Second-coordinate label.

createg_2Dms()

static void orb5x::Diagnostics::createg_2Dms ( const std::string &  species_name, const std::string &  name, const std::string &  description, const std::vector< Real > &  coord1, const std::string &  coord1_name, const std::vector< Real > &  coord2, const std::string &  coord2_name  )

static

Create species 2D dataset group (matching Fortran createg_2Dms, diagnostics.F90:2678-2701) Creates /data/var2d/{species_name}/{name} with coord1, coord2, time, data datasets and attaches PlotOrder attribute.

Parameters

[in]	species_name	Species output-group label.
[in]	name	Dataset-group name.
[in]	description	Human-readable physical quantity and units.
[in]	coord1	First coordinate values.
[in]	coord1_name	First-coordinate label.
[in]	coord2	Second coordinate values.
[in]	coord2_name	Second-coordinate label.

createg_3D()

static void orb5x::Diagnostics::createg_3D ( const std::string &  name, const std::string &  description, const std::vector< Real > &  coord1, const std::string &  coord1_name, const std::vector< Real > &  coord2, const std::string &  coord2_name, const std::vector< Real > &  coord3, const std::string &  coord3_name  )

static

Create generic 3D dataset group (matching Fortran createg_3D, diagnostics.F90:2608-2622) Creates /data/var3d/generic/{name} with coord1, coord2, coord3, time, data datasets and attaches PlotOrder attribute.

Parameters

[in]	name	Dataset-group name.
[in]	description	Human-readable physical quantity and units.
[in]	coord1	First coordinate values.
[in]	coord1_name	First-coordinate label.
[in]	coord2	Second coordinate values.
[in]	coord2_name	Second-coordinate label.
[in]	coord3	Third coordinate values.
[in]	coord3_name	Third-coordinate label.

createg_3Dms()

static void orb5x::Diagnostics::createg_3Dms ( const std::string &  species_name, const std::string &  name, const std::string &  description, const std::vector< Real > &  coord1, const std::string &  coord1_name, const std::vector< Real > &  coord2, const std::string &  coord2_name, const std::vector< Real > &  coord3, const std::string &  coord3_name, const std::vector< std::vector< int > > *  mmin_f = nullptr  )

static

Create species 3D dataset group (matching Fortran createg_3Dms, diagnostics.F90:2705-2720) Creates /data/var3d/{species_name}/{name} with coord1, coord2, coord3, time, data datasets and attaches PlotOrder attribute.

Parameters

[in]	species_name	Species output-group label.
[in]	name	Dataset-group name.
[in]	description	Human-readable physical quantity and units.
[in]	coord1	First coordinate values.
[in]	coord1_name	First-coordinate label.
[in]	coord2	Second coordinate values.
[in]	coord2_name	Second-coordinate label.
[in]	coord3	Third coordinate values.
[in]	coord3_name	Third-coordinate label.
[in]	mmin_f	Optional minimum-poloidal-mode metadata.

createg_3Dz()

static void orb5x::Diagnostics::createg_3Dz ( const std::string &  name, const std::string &  description, const std::vector< Real > &  coord1, const std::string &  coord1_name, const std::vector< Real > &  coord2, const std::string &  coord2_name, const std::vector< Real > &  coord3, const std::string &  coord3_name, const std::vector< std::vector< int > > *  mmin_f = nullptr  )

static

Create generic 3D complex dataset group (matching Fortran createg_3Dz, diagnostics.F90:2626-2643) Creates /data/var3d/generic/{name} with coord1, coord2, coord3, time, data (complex) datasets Optionally creates mmin dataset if mmin_f is provided.

Parameters

[in]	name	Dataset-group name.
[in]	description	Human-readable physical quantity and units.
[in]	coord1	First coordinate values.
[in]	coord1_name	First-coordinate label.
[in]	coord2	Second coordinate values.
[in]	coord2_name	Second-coordinate label.
[in]	coord3	Third coordinate values.
[in]	coord3_name	Third-coordinate label.
[in]	mmin_f	Optional minimum-poloidal-mode metadata.

createg_3Dzms()

static void orb5x::Diagnostics::createg_3Dzms ( const std::string &  species_name, const std::string &  name, const std::string &  description, const std::vector< Real > &  coord1, const std::string &  coord1_name, const std::vector< Real > &  coord2, const std::string &  coord2_name, const std::vector< Real > &  coord3, const std::string &  coord3_name, const std::vector< std::vector< int > > *  mmin_f = nullptr  )

static

Create species 3D complex dataset group (matching Fortran createg_3Dzms, diagnostics.F90:2724-2742) Creates /data/var3d/{species_name}/{name} with coord1, coord2, coord3, time, data (complex) datasets Optionally creates mmin dataset if mmin_f is provided.

Parameters

[in]	species_name	Species output-group label.
[in]	name	Dataset-group name.
[in]	description	Human-readable physical quantity and units.
[in]	coord1	First coordinate values.
[in]	coord1_name	First-coordinate label.
[in]	coord2	Second coordinate values.
[in]	coord2_name	Second-coordinate label.
[in]	coord3	Third coordinate values.
[in]	coord3_name	Third-coordinate label.
[in]	mmin_f	Optional minimum-poloidal-mode metadata.

destroyStaticViews()

static void orb5x::Diagnostics::destroyStaticViews ( )

static

Release static Kokkos Views before Kokkos::finalize()

diag3d_on_fluid_moments()

static void orb5x::Diagnostics::diag3d_on_fluid_moments ( int  isp )

static

Derive vorticity, potential, temperature, and spectra from fluid moments.

Parameters

[in]

isp

Zero-based species index.

diag3d_spectrum()

static void orb5x::Diagnostics::diag3d_spectrum ( const std::vector< std::vector< std::vector< Real > > > &  field, std::vector< std::vector< Real > > &  spectrum_out, int  nmax  )

static

Compute a toroidal-mode spectrum from a real three-dimensional field.

Parameters

[in]	field	Real samples indexed by radial, poloidal, and toroidal bins.
[out]	spectrum_out	Mode power by radial/poloidal index.
[in]	nmax	Maximum retained toroidal mode.

diag_fields_torpol()

static void orb5x::Diagnostics::diag_fields_torpol ( int  fieldnum, Real  time  )

static

Write toroidal and poloidal Fourier spectra.

Parameters

[in]	fieldnum	Field selector.
[in]	time	Normalized simulation time.

diag_fields_torpol_init()

static void orb5x::Diagnostics::diag_fields_torpol_init ( )

static

=============================================================================

PHASE 2 IMPLEMENTATIONS (Toroidal/Poloidal Spectrum Diagnostics)

Initialize torpol diagnostics - creates fields_torpol.hdf5 with proper structure Matches Fortran diag_fields_torpol_init() subroutine (diagnostics.F90:1987-2103) Creates HDF5 file and datasets for poloidal (m) and toroidal (n) mode spectra Called once during initialization if nfreq_torpol > 0

diag_fulltorus()

static void orb5x::Diagnostics::diag_fulltorus ( int  fieldnum, Real  time  )

static

Write selected full-torus plane cuts.

Parameters

[in]	fieldnum	Field selector.
[in]	time	Normalized simulation time.

diag_fulltorus_init()

static void orb5x::Diagnostics::diag_fulltorus_init ( )

static

=============================================================================

PHASE 3 IMPLEMENTATIONS (Full Torus Diagnostics)

Initialize fulltorus diagnostics - creates fulltorus.hdf5 with proper structure Matches Fortran diag_fulltorus_init() subroutine (diagnostics.F90:1631-1762) Creates HDF5 file and datasets for (R,Z) plane cuts and (s,theta) plane cuts Called once during initialization if nfreq_fulltorus > 0

diagnose()

static void orb5x::Diagnostics::diagnose ( int  step, int  step_tot, Real  time  )

static

Run diagnostics scheduled for the current integration step.

Parameters

[in]	step	Step index within the current run/restart segment.
[in]	step_tot	Global step index including previous segments.
[in]	time	Current normalized simulation time.

diagnose_phasespace()

static void orb5x::Diagnostics::diagnose_phasespace ( int  isp, Real  s, Real  vpar, Real  mu, Real  B, Real  pvol, Real  w, Real  zf0  )

static

Accumulate the (psi,v_parallel,v_perp) phase-space histogram.

Parameters

[in]	isp	Zero-based species index.
[in]	s	Radial coordinate s=sqrt(psi).
[in]	vpar	Normalized parallel velocity.
[in]	mu	Normalized magnetic moment.
[in]	B	Normalized magnetic-field magnitude.
[in]	pvol	Marker phase-space volume.
[in]	w	Perturbation weight.
[in]	zf0	Equilibrium distribution value.

diagnose_sampling()

static void orb5x::Diagnostics::diagnose_sampling ( int  isp, Real  s, Real  en, Real  pvol, Real  w, Real  zf0  )

static

Accumulate the (s,v^2) marker-sampling histogram.

Parameters

[in]	isp	Zero-based species index.
[in]	s	Radial coordinate s=sqrt(psi).
[in]	en	Normalized kinetic energy.
[in]	pvol	Marker phase-space volume.
[in]	w	Perturbation weight.
[in]	zf0	Equilibrium distribution value.

Note

Matches diagnose_sampling in part.F90.

diagnostics_after_loop()

static void orb5x::Diagnostics::diagnostics_after_loop ( int  isp )

static

Reduce and normalize diagnostics after one species push loop.

Parameters

[in]

isp

Zero-based species index.

Note

Matches diagnostics_after_loop in part.F90.

displacement_avg_ref()

static std::vector< std::vector< Real > > & orb5x::Diagnostics::displacement_avg_ref ( )

static

Returns

Mutable displacement-average accumulator by species/channel.

displacement_exb_avg_ref()

static std::vector< std::vector< Real > > & orb5x::Diagnostics::displacement_exb_avg_ref ( )

static

Returns

Mutable E x B displacement-average accumulator.

displacement_exb_max_ref()

static std::vector< std::vector< Real > > & orb5x::Diagnostics::displacement_exb_max_ref ( )

static

Returns

Mutable maximum E x B displacement accumulator.

displacement_max_ref()

static std::vector< std::vector< Real > > & orb5x::Diagnostics::displacement_max_ref ( )

static

Returns

Mutable maximum-displacement accumulator.

electron_fluxes_moments()

static void orb5x::Diagnostics::electron_fluxes_moments ( int  isp, int  irloc, Real  zf0, Real  dPsidt1, Real  dPsidt0, Real  ze, Real  wt, Real  ffinit_tmp1, Real  ffinit_tmp2, Real  ffinit_tmp3, Real  ffinit_tmp4, bool  is_trapped  )

static

Accumulate passing/trapped electron fluxes and moments.

Parameters

[in]	isp	Zero-based electron-species index.
[in]	irloc	Zero-based radial bin.
[in]	zf0	Equilibrium distribution value.
[in]	dPsidt1	Perturbed flux characteristic.
[in]	dPsidt0	Equilibrium flux characteristic.
[in]	ze	Normalized kinetic energy.
[in]	wt	Perturbation weight.
[in]	ffinit_tmp1	First initial-distribution moment.
[in]	ffinit_tmp2	Second initial-distribution moment.
[in]	ffinit_tmp3	Third initial-distribution moment.
[in]	ffinit_tmp4	Fourth initial-distribution moment.
[in]	is_trapped	Trapped-orbit classification.

entropy_fluct_avg_ref()

static std::vector< std::vector< Real > > & orb5x::Diagnostics::entropy_fluct_avg_ref ( )

static

Returns

Mutable fluctuation-entropy accumulator.

fluid_moments_ref()

static std::vector< std::vector< std::vector< std::vector< std::vector< Real > > > > > & orb5x::Diagnostics::fluid_moments_ref ( )

static

Returns

Mutable three-dimensional fluid-moment accumulator.

flush0d()

static void orb5x::Diagnostics::flush0d ( )

static

Flush 0D diagnostics buffer to file Writes accumulated 0D diagnostic data to HDF5.

flux1d_f0_ref()

static std::vector< std::vector< std::vector< Real > > > & orb5x::Diagnostics::flux1d_f0_ref ( )

static

Returns

Mutable equilibrium-distribution radial-flux accumulator.

flux1d_w_ref()

static std::vector< std::vector< std::vector< Real > > > & orb5x::Diagnostics::flux1d_w_ref ( )

static

Returns

Mutable perturbation-weighted radial-flux accumulator.

get_adiab()

static Real orb5x::Diagnostics::get_adiab ( int  isp )

static

Parameters

[in]

isp

Zero-based species index.

Returns

Normalized adiabatic-response diagnostic.

get_buf()

static Kokkos::View< Real ** > & orb5x::Diagnostics::get_buf ( )

inlinestatic

Returns

Mutable generic zero-dimensional output buffer.

get_buf_pic()

static Kokkos::View< Real *** > & orb5x::Diagnostics::get_buf_pic ( )

inlinestatic

Returns

Mutable per-species zero-dimensional output buffer.

get_cum_non_cg_bins()

static int orb5x::Diagnostics::get_cum_non_cg_bins ( int  isp )

static

Parameters

[in]

isp

Zero-based species index.

Returns

Cumulative non-coarse-grained bin count.

get_cum_non_cg_markers()

static int orb5x::Diagnostics::get_cum_non_cg_markers ( int  isp )

static

Parameters

[in]

isp

Zero-based species index.

Returns

Cumulative non-coarse-grained marker count.

get_dSdt_heat()

static Real orb5x::Diagnostics::get_dSdt_heat ( int  isp )

static

Parameters

[in]

isp

Zero-based species index.

Returns

Entropy rate from the heating operator.

get_dSdt_nc()

static Real orb5x::Diagnostics::get_dSdt_nc ( int  isp )

static

Parameters

[in]

isp

Zero-based species index.

Returns

Entropy rate from the naive Krook operator.

get_dSdt_nc_corr()

static Real orb5x::Diagnostics::get_dSdt_nc_corr ( int  isp )

static

Parameters

[in]

isp

Zero-based species index.

Returns

Entropy rate from the conserving Krook correction.

get_efield()

static Real orb5x::Diagnostics::get_efield ( int  isp, int  component  )

static

Parameters

[in]	isp	Zero-based species index.
[in]	component	Field-energy component selector.

Returns

Normalized total field-energy component.

get_efield_av()

static Real orb5x::Diagnostics::get_efield_av ( int  isp, int  component  )

static

Parameters

[in]	isp	Zero-based species index.
[in]	component	Flux-averaged component selector.

Returns

Normalized flux-averaged field energy.

get_efield_fft()

static Real orb5x::Diagnostics::get_efield_fft ( int  isp, int  component  )

static

Parameters

[in]	isp	Zero-based species index.
[in]	component	Spectral component selector.

Returns

Normalized spectrally evaluated field energy.

get_entropy_fluct_avg()

static Real orb5x::Diagnostics::get_entropy_fluct_avg ( int  isp, int  idiag  )

static

Parameters

[in]	isp	Zero-based species index.
[in]	idiag	Entropy channel index.

Returns

Normalized fluctuation-entropy channel.

get_flux0d_f0()

static Real orb5x::Diagnostics::get_flux0d_f0 ( int  isp, int  idiag  )

static

Parameters

[in]	isp	Zero-based species index.
[in]	idiag	Flux-channel index.

Returns

Equilibrium-distribution flux integrated over radius.

get_flux0d_w()

static Real orb5x::Diagnostics::get_flux0d_w ( int  isp, int  idiag  )

static

Parameters

[in]	isp	Zero-based species index.
[in]	idiag	Flux-channel index.

Returns

Marker-weighted flux integrated over radius.

get_generic_signoise_avg()

static Kokkos::View< Real * > orb5x::Diagnostics::get_generic_signoise_avg ( )

static

Returns

View of generic signal-to-noise averaged channels.

get_generic_signoise_size()

static int orb5x::Diagnostics::get_generic_signoise_size ( )

static

Returns

Number of generic signal-to-noise channels.

get_generic_spectrum2d_avg()

static Real orb5x::Diagnostics::get_generic_spectrum2d_avg ( int  idiag, int  i, int  j  )

static

Parameters

[in]	idiag	Generic spectrum selector.
[in]	i	Toroidal-mode storage index.
[in]	j	Poloidal-mode storage index.

Returns

Stored spectral power/value.

get_ibuf()

static int orb5x::Diagnostics::get_ibuf ( )

inlinestatic

Returns

Next sample slot in the zero-dimensional output buffer.

get_inner_edge_losses()

static Real orb5x::Diagnostics::get_inner_edge_losses ( int  isp, int  component  )

static

Parameters

[in]	isp	Zero-based species index.
[in]	component	Density, energy, or parallel-momentum selector.

Returns

Normalized inner-edge loss.

get_irloc_in()

static int orb5x::Diagnostics::get_irloc_in ( )

static

Returns

Radial bin used by one-dimensional poloidal diagnostics.

get_jdote_bg()

static Real orb5x::Diagnostics::get_jdote_bg ( int  isp, int  idiag  )

static

Parameters

[in]	isp	Zero-based species index.
[in]	idiag	j dot E channel index.

Returns

Background-field power-transfer channel.

get_jdote_fluct()

static Real orb5x::Diagnostics::get_jdote_fluct ( int  isp, int  idiag  )

static

Parameters

[in]	isp	Zero-based species index.
[in]	idiag	j dot E channel index.

Returns

Fluctuating-field power-transfer channel.

get_misc_avg()

static Real orb5x::Diagnostics::get_misc_avg ( int  isp, int  idiag  )

static

Parameters

[in]	isp	Zero-based species index.
[in]	idiag	Zero-based miscellaneous channel.

Returns

Accumulated normalized channel value.

get_noise_2d_all()

static Kokkos::View< Real ** > & orb5x::Diagnostics::get_noise_2d_all ( )

static

Returns

Mutable two-dimensional noise spectrum.

get_nsbound_in()

static int orb5x::Diagnostics::get_nsbound_in ( int  isp )

static

Parameters

[in]

isp

Zero-based species index.

Returns

Number of markers lost through the inner boundary.

get_nsbound_out()

static int orb5x::Diagnostics::get_nsbound_out ( int  isp )

static

Parameters

[in]

isp

Zero-based species index.

Returns

Number of markers lost through the outer boundary.

get_outer_edge_losses()

static Real orb5x::Diagnostics::get_outer_edge_losses ( int  isp, int  component  )

static

Parameters

[in]	isp	Zero-based species index.
[in]	component	Density, energy, or parallel-momentum selector.

Returns

Normalized outer-edge loss.

get_signal_2d_all()

static Kokkos::View< Real ** > & orb5x::Diagnostics::get_signal_2d_all ( )

static

Returns

Mutable two-dimensional signal spectrum.

get_spectrum2d_avg()

static Real orb5x::Diagnostics::get_spectrum2d_avg ( int  isp, int  idiag, int  i, int  j  )

static

Parameters

[in]	isp	Zero-based species index.
[in]	idiag	Spectrum selector.
[in]	i	Toroidal-mode storage index.
[in]	j	Poloidal-mode storage index.

Returns

Stored spectral power/value.

get_tot_cg_bins()

static int orb5x::Diagnostics::get_tot_cg_bins ( int  isp )

static

Parameters

[in]

isp

Zero-based species index.

Returns

Total coarse-grained bin count.

get_tot_cg_markers()

static int orb5x::Diagnostics::get_tot_cg_markers ( int  isp )

static

Parameters

[in]

isp

Zero-based species index.

Returns

Total coarse-grained marker count.

get_trap_frac()

static Real orb5x::Diagnostics::get_trap_frac ( int  isp, int  type  )

static

Parameters

[in]	isp	Zero-based species index.
[in]	type	Orbit-transition selector (FR_PASS through FR_RETRAP).

Returns

Accumulated orbit-class fraction.

get_variance()

static Real orb5x::Diagnostics::get_variance ( int  isp, int  index  )

static

Parameters

[in]	isp	Zero-based species index.
[in]	index	Weight-moment/variance channel.

Returns

Stored weight moment or variance.

get_vexbnavg()

static Real orb5x::Diagnostics::get_vexbnavg ( int  isp, int  idiag  )

static

Parameters

[in]	isp	Zero-based species index.
[in]	idiag	Velocity-channel index.

Returns

Thermal-normalized E x B statistic.

get_vthmax2_cached()

static Real orb5x::Diagnostics::get_vthmax2_cached ( int  isp )

static

Parameters

[in]

isp

Zero-based species index.

Returns

Cached squared maximum thermal speed.

get_vthmax_cached()

static Real orb5x::Diagnostics::get_vthmax_cached ( int  isp )

static

Parameters

[in]

isp

Zero-based species index.

Returns

Cached maximum thermal speed.

get_wsqreduced()

static Real orb5x::Diagnostics::get_wsqreduced ( int  isp )

static

Parameters

[in]

isp

Zero-based species index.

Returns

Reduced squared-weight/noise measure.

getpot_fieldnum()

static Real orb5x::Diagnostics::getpot_fieldnum ( Real  s, Real  theta, Real  phi, int  fieldnum  )

static

Interpolate a selected field in magnetic coordinates.

Parameters

[in]	s	Radial coordinate s=sqrt(psi).
[in]	theta	Poloidal angle [rad].
[in]	phi	Toroidal angle [rad].
[in]	fieldnum	One of FIELD_PHI through FIELD_USER.

Returns

Interpolated normalized field value.

init_generic_signoise()

static void orb5x::Diagnostics::init_generic_signoise ( )

static

Allocate and clear generic signal-to-noise accumulators.

Referenced by init_test_diagnostic_arrays().

init_phase1_diagnostics()

static void orb5x::Diagnostics::init_phase1_diagnostics ( )

static

Initialize Phase 1 diagnostic arrays and flags Called from initialize_diagnostics()

init_test_diagnostic_arrays()

static void orb5x::Diagnostics::init_test_diagnostic_arrays ( int  nspecies )

inlinestatic

Allocate deterministic in-memory diagnostic storage for tests.

Parameters

[in]

nspecies

Number of species to allocate.

References init_generic_signoise(), and moment1d_w.

init_variance()

static void orb5x::Diagnostics::init_variance ( int  nspecies )

inlinestatic

Size and zero variance storage.

Parameters

[in]

nspecies

Number of species.

initialize_diagnostics()

static void orb5x::Diagnostics::initialize_diagnostics ( )

static

Initialize diagnostics system Sets up all diagnostic structures, grids, and output files.

initialize_phasespace_diags()

static void orb5x::Diagnostics::initialize_phasespace_diags ( )

static

Initialize phase space diagnostics.

initialize_source_3d_diags()

static void orb5x::Diagnostics::initialize_source_3d_diags ( )

static

Initialize source 3D diagnostics.

jdote()

static Real orb5x::Diagnostics::jdote ( int  isp, Real  ut2, Real  vpt2, const std::vector< Real > &  vpar, const std::vector< Real > &  genelec, const std::vector< Real > &  elec_par, Real  wt, Real  bstar_inv, const std::vector< Real > &  bgrb, const std::vector< Real > &  vgb, const std::vector< Real > &  vpressure, const std::vector< Real > &  veb_f, const std::vector< Real > &  vexb, Real  expt_back, Real  eypt_back, Real  dvpadt0, Real  gyroapar  )

static

Compute and accumulate one marker's j dot E power transfer.

Parameters

[in]	isp	Zero-based species index.
[in]	ut2	Squared parallel velocity.
[in]	vpt2	Squared perpendicular velocity.
[in]	vpar	Parallel-velocity vector.
[in]	genelec	Electric-gradient vector.
[in]	elec_par	Parallel electric-field vector.
[in]	wt	Perturbation weight.
[in]	bstar_inv	Inverse guiding-centre B* denominator.
[in]	bgrb	Magnetic-gradient vector.
[in]	vgb	Magnetic-drift vector.
[in]	vpressure	Pressure-gradient drift vector.
[in]	veb_f	Fluctuating E x B vector.
[in]	vexb	Total E x B vector.
[in]	expt_back	Radial equilibrium electric field.
[in]	eypt_back	Poloidal equilibrium electric field.
[in]	dvpadt0	Equilibrium parallel acceleration.
[in]	gyroapar	Gyroaveraged parallel vector potential.

Returns

Total normalized marker power-transfer contribution.

jdote_bg_ref()

static std::vector< std::vector< Real > > & orb5x::Diagnostics::jdote_bg_ref ( )

static

Returns

Mutable background j dot E accumulator.

jdote_fluct_ref()

static std::vector< std::vector< Real > > & orb5x::Diagnostics::jdote_fluct_ref ( )

static

Returns

Mutable fluctuating j dot E accumulator.

max_of_0d()

static void orb5x::Diagnostics::max_of_0d ( int  isp, int  i, Real  to_add  )

static

Update a maximum-valued zero-dimensional channel.

Parameters

[in]	isp	Zero-based species index.
[in]	i	Zero-based channel index.
[in]	to_add	Candidate normalized value.

max_of_0d_vexbnmax()

static void orb5x::Diagnostics::max_of_0d_vexbnmax ( int  isp, Real  to_add  )

static

Update maximum thermal-normalized E x B speed.

Parameters

[in]	isp	Zero-based species index.
[in]	to_add	Candidate normalized speed.

max_of_0d_vmax()

static void orb5x::Diagnostics::max_of_0d_vmax ( int  isp, Real  to_add  )

static

Update maximum normalized marker speed.

Parameters

[in]	isp	Zero-based species index.
[in]	to_add	Candidate speed.

max_of_0d_wmax()

static void orb5x::Diagnostics::max_of_0d_wmax ( int  isp, Real  to_add  )

static

Update maximum absolute marker weight.

Parameters

[in]	isp	Zero-based species index.
[in]	to_add	Candidate absolute weight.

misc_avg_ref()

static std::vector< std::vector< Real > > & orb5x::Diagnostics::misc_avg_ref ( )

static

Returns

Mutable miscellaneous scalar accumulator.

mmin_f_serialize()

static void orb5x::Diagnostics::mmin_f_serialize ( )

static

Serializes mmin_f array across MPI ranks for 3D output.

moment1d_f0_ref()

static std::vector< std::vector< std::vector< Real > > > & orb5x::Diagnostics::moment1d_f0_ref ( )

static

Returns

Mutable equilibrium-distribution radial-moment accumulator.

moment1d_f_ref()

static std::vector< std::vector< std::vector< Real > > > & orb5x::Diagnostics::moment1d_f_ref ( )

static

Returns

Mutable total-distribution radial-moment accumulator.

moment1d_w_ref()

static std::vector< std::vector< std::vector< Real > > > & orb5x::Diagnostics::moment1d_w_ref ( )

static

Returns

Mutable perturbation-weighted radial-moment accumulator.

moment2d_avg_ref()

static std::vector< std::vector< std::vector< std::vector< Real > > > > & orb5x::Diagnostics::moment2d_avg_ref ( )

static

Returns

Mutable two-dimensional averaged-moment accumulator.

mpr_2d_ref()

static std::vector< std::vector< std::vector< std::vector< Real > > > > & orb5x::Diagnostics::mpr_2d_ref ( )

static

Returns

Mutable mode-particle-resonance accumulator.

mpr_es_calc()

static void orb5x::Diagnostics::mpr_es_calc ( int  isp, int  iuloc, int  imuloc, Real  sigmat, Real  thetat, Real  wt, Real  ut2, Real  vpt2, Real  bstar_inv, const std::vector< Real > &  vpar, const std::vector< Real > &  genelec, const std::vector< Real > &  bgrb, const std::vector< Real > &  vgb, const std::vector< Real > &  vpressure, const std::vector< Real > &  veb_f  )

static

Accumulate electrostatic mode-particle-resonance power transfer.

Parameters

[in]	isp	Zero-based species index.
[in]	iuloc	Parallel-velocity bin.
[in]	imuloc	Magnetic-moment bin.
[in]	sigmat	Radial coordinate.
[in]	thetat	Diagnostic poloidal angle [rad].
[in]	wt	Perturbation weight.
[in]	ut2	Squared parallel velocity.
[in]	vpt2	Squared perpendicular velocity.
[in]	bstar_inv	Inverse guiding-centre B* denominator.
[in]	vpar	Parallel-velocity vector.
[in]	genelec	Electric-gradient vector.
[in]	bgrb	Magnetic-gradient vector.
[in]	vgb	Magnetic-drift vector.
[in]	vpressure	Pressure-gradient drift vector.
[in]	veb_f	Fluctuating E x B vector.

nl_do_diag()

static bool orb5x::Diagnostics::nl_do_diag ( int  step_tot, int  nfreq  )

static

Test a diagnostic cadence.

Parameters

[in]	step_tot	Global timestep index.
[in]	nfreq	Requested frequency in timesteps; nonpositive disables output.

Returns

true when this step is on the requested cadence.

normalize_flux1d()

static void orb5x::Diagnostics::normalize_flux1d ( int  isp )

static

Normalize radial fluxes and form zero-dimensional integrals.

Parameters

[in]

isp

Zero-based species index.

normalize_moment1d_f()

static void orb5x::Diagnostics::normalize_moment1d_f ( int  isp )

static

Normalize total-distribution radial moments.

Parameters

[in]

isp

Zero-based species index.

normalize_moment1d_f0()

static void orb5x::Diagnostics::normalize_moment1d_f0 ( int  isp )

static

Normalize equilibrium-distribution radial moments.

Parameters

[in]

isp

Zero-based species index.

normalize_moment1d_w()

static void orb5x::Diagnostics::normalize_moment1d_w ( int  isp )

static

Normalize perturbation-weighted radial moments.

Parameters

[in]

isp

Zero-based species index.

normalize_moment2d()

static void orb5x::Diagnostics::normalize_moment2d ( int  isp )

static

Normalize two-dimensional averaged moments.

Parameters

[in]

isp

Zero-based species index.

normalize_poloidal1d()

static void orb5x::Diagnostics::normalize_poloidal1d ( int  isp )

static

Normalize one-dimensional poloidal moments.

Parameters

[in]

isp

Zero-based species index.

omp_reduce_diag()

template<typename T >

static void orb5x::Diagnostics::omp_reduce_diag ( T &  data, bool  use_max = false  )

static

Generic diagnostic reduction interface (matches Fortran omp_reduce_diag)

In C++ with Kokkos, this is primarily a documentation marker since reductions are handled differently than in Fortran OpenMP.

Template Parameters

T	Diagnostic array type (Real, vector<Real>, etc.)

Parameters

data	Reference to diagnostic data
use_max	If true, compute max; otherwise sum

omp_reduce_diag0d()

static void orb5x::Diagnostics::omp_reduce_diag0d ( Real &  data, bool  use_max = false  )

static

=============================================================================

OMP_REDUCE_DIAG FUNCTIONS (Kokkos adaptation of Fortran OpenMP reduction)

In Fortran, omp_reduce_diag() reduces per-thread diagnostic arrays to thread 0. The Fortran code uses OpenMP with thread-local storage (diag0d, diag1d, etc.).

In C++ with Kokkos:

• Diagnostic arrays are std::vector<> (not thread-local)
• Kokkos uses atomic updates or parallel_reduce during accumulation
• MPI reductions are done directly in diagnostics_after_loop()

These functions are provided for API compatibility and documentation. They perform in-place reduction (sum or max) on the diagnostic array. For single-rank scenarios, these are essentially no-ops.

Matching Fortran part.F90 lines 5198-5282 (omp_reduce_diag interface)

Reduce 0D diagnostic array (single value per species)

Parameters

data	Reference to diagnostic value
use_max	If true, compute max; otherwise sum

omp_reduce_diag1d()

static void orb5x::Diagnostics::omp_reduce_diag1d ( std::vector< Real > &  data, bool  use_max = false  )

static

Reduce 1D diagnostic array.

Parameters

data	Reference to 1D vector
use_max	If true, compute max; otherwise sum

omp_reduce_diag2d()

static void orb5x::Diagnostics::omp_reduce_diag2d ( std::vector< std::vector< Real > > &  data, bool  use_max = false  )

static

Reduce 2D diagnostic array.

Parameters

data	Reference to 2D vector
use_max	If true, compute max; otherwise sum

omp_reduce_diag3d()

static void orb5x::Diagnostics::omp_reduce_diag3d ( std::vector< std::vector< std::vector< Real > > > &  data, bool  use_max = false  )

static

Reduce 3D diagnostic array.

Parameters

data	Reference to 3D vector
use_max	If true, compute max; otherwise sum

phasespace_3d_ref()

static std::vector< std::vector< std::vector< std::vector< std::vector< Real > > > > > & orb5x::Diagnostics::phasespace_3d_ref ( )

static

Returns

Mutable (psi,v_parallel,v_perp) phase-space histogram.

polarisation_fieldcalc()

static void orb5x::Diagnostics::polarisation_fieldcalc ( int  isp )

static

Compute polarization-field diagnostic channels after reduction.

Parameters

[in]

isp

Zero-based species index.

poloidal1d_f_ref()

static std::vector< std::vector< std::vector< Real > > > & orb5x::Diagnostics::poloidal1d_f_ref ( )

static

Returns

Mutable total-distribution poloidal-moment accumulator.

poloidal1d_w_ref()

static std::vector< std::vector< std::vector< Real > > > & orb5x::Diagnostics::poloidal1d_w_ref ( )

static

Returns

Mutable perturbation-weighted poloidal-moment accumulator.

profsphi()

static void orb5x::Diagnostics::profsphi ( Real  theta, int  fieldnum, std::vector< std::vector< Real > > &  pot_sp  )

static

Sample a selected field on an (s,phi) plane.

Parameters

[in]	theta	Fixed poloidal angle [rad].
[in]	fieldnum	Field selector.
[out]	pot_sp	Globally reduced samples shaped [ns][nphi].

profsth()

static void orb5x::Diagnostics::profsth ( Real  phi, int  fieldnum, int  ns0, std::vector< std::vector< Real > > &  pot_st, std::vector< std::vector< Real > > *  xc = nullptr, std::vector< std::vector< Real > > *  zc = nullptr  )

static

Sample a selected field on an (s,theta) plane.

Parameters

[in]	phi	Fixed toroidal angle [rad].
[in]	fieldnum	Field selector.
[in]	ns0	Number of radial samples.
[out]	pot_st	Samples shaped [ns0][ntheta].
[out]	xc	Optional cylindrical R coordinates.
[out]	zc	Optional cylindrical Z coordinates.

put3d_dens()

static void orb5x::Diagnostics::put3d_dens ( Real  time, bool  do_moments = false  )

static

Write three-dimensional density and optional moment diagnostics.

Parameters

[in]	time	Normalized simulation time.
[in]	do_moments	Also write fluid moments when true.

put3d_h5s()

static void orb5x::Diagnostics::put3d_h5s ( Real  time, int  diag_select, int  field_select, int  isp = -1  )

static

Write one three-dimensional field/density diagnostic.

Parameters

[in]	time	Normalized simulation time.
[in]	diag_select	Diagnostic dataset selector.
[in]	field_select	Field selector.
[in]	isp	Optional zero-based species index.

putarr()

static void orb5x::Diagnostics::putarr ( const std::string &  path, const Real *  array, size_t  length, const std::string &  title = ""  )

static

Write a one-dimensional real array and optional title.

Parameters

[in]	path	Absolute HDF5 dataset path.
[in]	array	Contiguous values.
[in]	length	Number of values.
[in]	title	Optional human-readable quantity/units title.

putarr_attime_1d()

static void orb5x::Diagnostics::putarr_attime_1d ( const std::string &  path, const Real *  array, size_t  length, Real  time  )

static

Append a one-dimensional real slice at a simulation time.

Parameters

[in]	path	Absolute HDF5 dataset path.
[in]	array	Contiguous values.
[in]	length	Number of values.
[in]	time	Normalized simulation time.

putarr_attime_2d()

static void orb5x::Diagnostics::putarr_attime_2d ( const std::string &  path, const Real *  array, size_t  dim1, size_t  dim2, Real  time  )

static

Append a two-dimensional real slice at a simulation time.

Parameters

[in]	path	Absolute HDF5 dataset path.
[in]	array	Contiguous row-major values.
[in]	dim1	First dimension.
[in]	dim2	Second dimension.
[in]	time	Normalized simulation time.

read_restart_state()

static void orb5x::Diagnostics::read_restart_state ( int  datn )

static

Parameters

[in]

datn

Alternating restart generation, normally 0 or 1.

rhs_f_serialize()

static void orb5x::Diagnostics::rhs_f_serialize ( const std::vector< std::vector< std::complex< Real > > > &  rhs_f_ptr )

static

Gather distributed Fourier RHS coefficients for three-dimensional output.

Parameters

[in]

rhs_f_ptr

Rank-local coefficients converted from the Kokkos field view.

sampling_2d_ref()

static std::vector< std::vector< std::vector< std::vector< Real > > > > & orb5x::Diagnostics::sampling_2d_ref ( )

static

Returns

Mutable (s,v^2) sampling histogram.

set_buf()

static void orb5x::Diagnostics::set_buf ( Kokkos::View< Real ** >  v )

inlinestatic

Parameters

[in]

v

Generic buffer view to bind and mirror.

set_buf_pic()

static void orb5x::Diagnostics::set_buf_pic ( Kokkos::View< Real *** >  v )

inlinestatic

Parameters

[in]

v

Per-species buffer view to bind and mirror.

set_dSdt_heat()

static void orb5x::Diagnostics::set_dSdt_heat ( int  isp, Real  value  )

static

Parameters

[in]	isp	Zero-based species index.
[in]	value	Normalized heating entropy rate.

set_dSdt_nc()

static void orb5x::Diagnostics::set_dSdt_nc ( int  isp, Real  value  )

static

Parameters

[in]	isp	Zero-based species index.
[in]	value	Normalized entropy rate.

set_dSdt_nc_corr()

static void orb5x::Diagnostics::set_dSdt_nc_corr ( int  isp, Real  value  )

static

Parameters

[in]	isp	Zero-based species index.
[in]	value	Normalized corrected entropy rate.

set_efield()

static void orb5x::Diagnostics::set_efield ( int  isp, int  component, Real  value  )

static

Parameters

[in]	isp	Zero-based species index.
[in]	component	Zero-based total-energy component.
[in]	value	Normalized field energy.

set_efield_av()

static void orb5x::Diagnostics::set_efield_av ( int  isp, int  component, Real  value  )

static

Parameters

[in]	isp	Zero-based species index.
[in]	component	Zero-based averaged component.
[in]	value	Normalized averaged field energy.

set_efield_fft()

static void orb5x::Diagnostics::set_efield_fft ( int  isp, int  component, Real  value  )

static

Parameters

[in]	isp	Zero-based species index.
[in]	component	Zero-based spectral component.
[in]	value	Normalized spectral field energy.

set_generic_spectrum2d_avg()

static void orb5x::Diagnostics::set_generic_spectrum2d_avg ( int  idiag, int  i, int  j, Real  value  )

static

Parameters

[in]	idiag	Generic spectrum selector.
[in]	i	Toroidal-mode storage index.
[in]	j	Poloidal-mode storage index.
[in]	value	Spectral power/value to store.

set_ibuf()

static void orb5x::Diagnostics::set_ibuf ( int  val )

inlinestatic

Parameters

[in]

val

Next sample slot in the output buffer.

set_inner_edge_losses()

static void orb5x::Diagnostics::set_inner_edge_losses ( int  isp, int  component, Real  value  )

static

Parameters

[in]	isp	Zero-based species index.
[in]	component	Density, energy, or parallel-momentum selector.
[in]	value	Normalized inner-edge loss.

set_misc_avg()

static void orb5x::Diagnostics::set_misc_avg ( int  isp, int  idx, Real  val  )

inlinestatic

Parameters

[in]	isp	Zero-based species index.
[in]	idx	Zero-based miscellaneous channel.
[in]	val	Normalized value; invalid indices are ignored.

set_nsbound_in()

static void orb5x::Diagnostics::set_nsbound_in ( int  isp, int  value  )

static

Parameters

[in]	isp	Zero-based species index.
[in]	value	Inner-boundary marker-loss count.

set_nsbound_out()

static void orb5x::Diagnostics::set_nsbound_out ( int  isp, int  value  )

static

Parameters

[in]	isp	Zero-based species index.
[in]	value	Outer-boundary marker-loss count.

set_outer_edge_losses()

static void orb5x::Diagnostics::set_outer_edge_losses ( int  isp, int  component, Real  value  )

static

Parameters

[in]	isp	Zero-based species index.
[in]	component	Density, energy, or parallel-momentum selector.
[in]	value	Normalized outer-edge loss.

set_signal2noise()

static void orb5x::Diagnostics::set_signal2noise ( Real  sn, Real  sn_nozf  )

static

Parameters

[in]	sn	Total electrostatic signal-to-noise ratio.
[in]	sn_nozf	Non-zonal electrostatic signal-to-noise ratio.

set_signal2noise_em()

static void orb5x::Diagnostics::set_signal2noise_em ( Real  sn, Real  sn_nozf  )

static

Parameters

[in]	sn	Total electromagnetic signal-to-noise ratio.
[in]	sn_nozf	Non-zonal electromagnetic signal-to-noise ratio.

set_spectrum2d_avg()

static void orb5x::Diagnostics::set_spectrum2d_avg ( int  isp, int  idiag, int  i, int  j, Real  value  )

static

Parameters

[in]	isp	Zero-based species index.
[in]	idiag	Spectrum selector.
[in]	i	Toroidal-mode storage index.
[in]	j	Poloidal-mode storage index.
[in]	value	Spectral power/value to store.

set_variance()

static void orb5x::Diagnostics::set_variance ( int  isp, int  index, Real  value  )

static

Parameters

[in]	isp	Zero-based species index.
[in]	index	Weight-moment channel.
[in]	value	Normalized moment value.

snapshot_variance()

static void orb5x::Diagnostics::snapshot_variance ( int  isp )

static

Parameters

[in]

isp

Zero-based species index.

source_diag1d_avg_ref()

static std::vector< std::vector< std::vector< Real > > > & orb5x::Diagnostics::source_diag1d_avg_ref ( )

static

Returns

Mutable one-dimensional source-diagnostic accumulator.

strong_diagnostic_output()

static void orb5x::Diagnostics::strong_diagnostic_output ( int  isp, int  ip, Real  psi0t, Real  temp2, Real  ze, Real  vecrossb_f2, Real  pot_equil, Real  zf0, Real  zvth2_inv, Real  dpotdpsi, Real  vdr, Real  rhs  )

static

Record one marker's strong-flow parity diagnostics.

Parameters

[in]	isp	Zero-based species index.
[in]	ip	Zero-based local marker index.
[in]	psi0t	Canonical/profile flux coordinate.
[in]	temp2	Squared thermal-speed scale.
[in]	ze	Normalized kinetic energy.
[in]	vecrossb_f2	Squared equilibrium E x B contribution.
[in]	pot_equil	Equilibrium potential.
[in]	zf0	Equilibrium distribution value.
[in]	zvth2_inv	Inverse squared thermal-speed scale.
[in]	dpotdpsi	Radial potential derivative.
[in]	vdr	Radial characteristic.
[in]	rhs	Weight-equation right-hand side.

sum_entropy_fluctuation()

static void orb5x::Diagnostics::sum_entropy_fluctuation ( int  isp, Real  wt, Real  zf0, Real  q_vgc_dot_genelec, Real  zvth2_inv, Real  df0_dpsi_prof, Real  df0_dchi_prof, Real  dpsi_prof_dt  )

static

Accumulate one marker's fluctuation-entropy balance.

Parameters

[in]	isp	Zero-based species index.
[in]	wt	Perturbation weight.
[in]	zf0	Equilibrium distribution value.
[in]	q_vgc_dot_genelec	Electric energy-transfer term.
[in]	zvth2_inv	Inverse squared thermal speed.
[in]	df0_dpsi_prof	Radial profile derivative of f0.
[in]	df0_dchi_prof	Poloidal profile derivative of f0.
[in]	dpsi_prof_dt	Profile-flux characteristic.

sum_fluid_moments()

static void orb5x::Diagnostics::sum_fluid_moments ( int  isp, Real  sigmat, Real  chit, Real  phit, Real  wt, Real  ut, Real  ut2, Real  vpt2  )

static

Deposit one marker into three-dimensional fluid moments.

Parameters

[in]	isp	Zero-based species index.
[in]	sigmat	Radial coordinate s=sqrt(psi).
[in]	chit	Poloidal angle [rad].
[in]	phit	Toroidal angle [rad].
[in]	wt	Perturbation weight.
[in]	ut	Parallel velocity.
[in]	ut2	Squared parallel velocity.
[in]	vpt2	Squared perpendicular velocity.

sum_in_radial_bins_island()

static void orb5x::Diagnostics::sum_in_radial_bins_island ( int  isp, int  irloc, int  ipol, Real  ut, const std::vector< Real > &  gradpsi0, Real  htildex, Real  htildey, Real  ze, Real  zf0, Real  wt, Real  dPsidt1, Real  ffinit_tmp1, Real  ffinit_tmp2, Real  ffinit_tmp3, Real  ffinit_tmp4  )

static

Accumulate magnetic-island radial/poloidal diagnostics.

Parameters

[in]	isp	Zero-based species index.
[in]	irloc	Island radial bin.
[in]	ipol	Island poloidal bin.
[in]	ut	Parallel velocity.
[in]	gradpsi0	Equilibrium-flux gradient vector.
[in]	htildex	Radial island perturbation component.
[in]	htildey	Poloidal island perturbation component.
[in]	ze	Normalized kinetic energy.
[in]	zf0	Equilibrium distribution value.
[in]	wt	Perturbation weight.
[in]	dPsidt1	Perturbed flux characteristic.
[in]	ffinit_tmp1	First initial-distribution moment.
[in]	ffinit_tmp2	Second initial-distribution moment.
[in]	ffinit_tmp3	Third initial-distribution moment.
[in]	ffinit_tmp4	Fourth initial-distribution moment.

sum_moment2d()

static void orb5x::Diagnostics::sum_moment2d ( int  isp, int  irloc, int  ithetaloc, Real  wt, Real  ffinit_tmp1, Real  ffinit_tmp2, Real  ffinit_tmp3, Real  ffinit_tmp4  )

static

Accumulate (s,theta) initial-distribution moments.

Parameters

[in]	isp	Zero-based species index.
[in]	irloc	Radial bin.
[in]	ithetaloc	Poloidal-angle bin.
[in]	wt	Perturbation weight.
[in]	ffinit_tmp1	First initial-distribution moment.
[in]	ffinit_tmp2	Second initial-distribution moment.
[in]	ffinit_tmp3	Third initial-distribution moment.
[in]	ffinit_tmp4	Fourth initial-distribution moment.

sum_particles_in_poloidal_bins()

static void orb5x::Diagnostics::sum_particles_in_poloidal_bins ( int  isp, int  ithetaloc, Real  wt, Real  ffinit_tmp1, Real  ffinit_tmp2, Real  ffinit_tmp3, Real  ffinit_tmp4, Real  wt_tmp1, Real  wt_tmp2, Real  wt_tmp3  )

static

Accumulate poloidal moments at the configured radial surface.

Parameters

[in]	isp	Zero-based species index.
[in]	ithetaloc	Poloidal-angle bin.
[in]	wt	Perturbation weight.
[in]	ffinit_tmp1	First initial-distribution moment.
[in]	ffinit_tmp2	Second initial-distribution moment.
[in]	ffinit_tmp3	Third initial-distribution moment.
[in]	ffinit_tmp4	Fourth initial-distribution moment.
[in]	wt_tmp1	First perturbation-weight moment.
[in]	wt_tmp2	Second perturbation-weight moment.
[in]	wt_tmp3	Third perturbation-weight moment.

sum_particles_in_radial_bins()

static void orb5x::Diagnostics::sum_particles_in_radial_bins ( int  isp, int  ip, int  irloc, Real  zf0, Real  dPsidt1, Real  dPsidt0, Real  ze, Real  wt, Real  ut, Real  ut2, Real  vpt2, Real  rt2, const std::vector< Real > &  vpar, Real  zf0_tmp1, Real  zf0_tmp2, Real  zf0_tmp3, Real  sigmat, Real  zf0_local, Real  grsigma2, Real  grsigmagrchi, Real  b, const std::vector< Real > &  exh, Real  wt_tmp1, Real  wt_tmp2, Real  wt_tmp3, const std::vector< Real > &  vexb, Real  ffinit_tmp1, Real  ffinit_tmp2, Real  ffinit_tmp3, Real  ffinit_tmp4, Real  ffinit_tmp5, Real  jdote_tot, const std::vector< Real > &  eloc  )

static

Accumulate all configured radial-bin diagnostics for one marker.

Parameters

[in]	isp	Zero-based species index.
[in]	ip	Zero-based local marker index.
[in]	irloc	Zero-based radial bin.
[in]	zf0	Equilibrium distribution value.
[in]	dPsidt1	Perturbed flux characteristic.
[in]	dPsidt0	Equilibrium flux characteristic.
[in]	ze	Normalized kinetic energy.
[in]	wt	Perturbation weight.
[in]	ut	Parallel velocity.
[in]	ut2	Squared parallel velocity.
[in]	vpt2	Squared perpendicular velocity.
[in]	rt2	Squared cylindrical major radius.
[in]	vpar	Three-component parallel velocity.
[in]	zf0_tmp1	First equilibrium-distribution moment weight.
[in]	zf0_tmp2	Second equilibrium-distribution moment weight.
[in]	zf0_tmp3	Third equilibrium-distribution moment weight.
[in]	sigmat	Radial coordinate s=sqrt(psi).
[in]	zf0_local	Local Maxwellian/equilibrium reference value.
[in]	grsigma2	Squared radial metric coefficient.
[in]	grsigmagrchi	Radial-poloidal metric cross coefficient.
[in]	b	Normalized magnetic-field magnitude.
[in]	exh	Three-component electric-field cross product.
[in]	wt_tmp1	First perturbation-weight moment.
[in]	wt_tmp2	Second perturbation-weight moment.
[in]	wt_tmp3	Third perturbation-weight moment.
[in]	vexb	Three-component E x B velocity.
[in]	ffinit_tmp1	First initial-distribution moment weight.
[in]	ffinit_tmp2	Second initial-distribution moment weight.
[in]	ffinit_tmp3	Third initial-distribution moment weight.
[in]	ffinit_tmp4	Fourth initial-distribution moment weight.
[in]	ffinit_tmp5	Fifth initial-distribution moment weight.
[in]	jdote_tot	Marker contribution to j dot E.
[in]	eloc	Three-component local electric-field gradient.

Note

Matches sum_particles_in_radial_bins in part.F90.

sum_spectrum2d_avg()

static Real orb5x::Diagnostics::sum_spectrum2d_avg ( int  isp, int  idiag, int  ndim, int  mdim  )

static

Parameters

[in]	isp	Zero-based species index.
[in]	idiag	Spectrum selector.
[in]	ndim	Toroidal spectrum dimension.
[in]	mdim	Poloidal spectrum dimension.

Returns

Sum over the requested spectral slice.

sum_velocities()

static void orb5x::Diagnostics::sum_velocities ( int  isp, int  iuloc, int  imuloc, Real  wt, Real  zf0, Real  pvol  )

static

Accumulate one- and two-dimensional velocity-space diagnostics.

Parameters

[in]	isp	Zero-based species index.
[in]	iuloc	Parallel-velocity bin.
[in]	imuloc	Magnetic-moment/perpendicular-velocity bin.
[in]	wt	Perturbation weight.
[in]	zf0	Equilibrium distribution value.
[in]	pvol	Marker phase-space volume.

test_particle_output()

static void orb5x::Diagnostics::test_particle_output ( int  isp, int  ip, Real  psi0t, Real  ze, Real  pot_equil, Real  wt, Real  zvth2, Real  nval, Real  pvol_updated, Real  zf0  )

static

Store one selected test-particle record.

Parameters

[in]	isp	Zero-based species index.
[in]	ip	Zero-based local marker index.
[in]	psi0t	Canonical/profile flux coordinate.
[in]	ze	Normalized kinetic energy.
[in]	pot_equil	Equilibrium potential.
[in]	wt	Perturbation weight.
[in]	zvth2	Squared thermal-speed scale.
[in]	nval	Normalized density.
[in]	pvol_updated	Updated phase-space volume.
[in]	zf0	Equilibrium distribution value.

vel1d_avg_ref()

static std::vector< std::vector< std::vector< Real > > > & orb5x::Diagnostics::vel1d_avg_ref ( )

static

Returns

Mutable one-dimensional velocity-space accumulator.

vel2d_avg_ref()

static std::vector< std::vector< std::vector< std::vector< Real > > > > & orb5x::Diagnostics::vel2d_avg_ref ( )

static

Returns

Mutable two-dimensional velocity-space accumulator.

velocity_space_diag_init()

static void orb5x::Diagnostics::velocity_space_diag_init ( )

static

Initialize velocity space diagnostics Sets up velocity space grids and output structures.

vmax_ref()

static std::vector< Real > & orb5x::Diagnostics::vmax_ref ( )

static

Returns

Mutable per-species maximum-speed accumulator.

wmax_ref()

static std::vector< Real > & orb5x::Diagnostics::wmax_ref ( )

static

Returns

Mutable per-species maximum-weight accumulator.

write_output()

static void orb5x::Diagnostics::write_output ( int  step, Real  time  )

static

Write the standard scalar, profile, and spectrum output set.

Parameters

[in]	step	Current global timestep index.
[in]	time	Current normalized simulation time.

Note

Matches write_output(step,time) in diagnostics.F90.

write_restart_state()

static void orb5x::Diagnostics::write_restart_state ( int  datn )

static

Parameters

[in]

datn

Alternating restart generation, normally 0 or 1.

zero_generic_spectrum2d_avg()

static void orb5x::Diagnostics::zero_generic_spectrum2d_avg ( int  idiag, int  ndim, int  mdim  )

static

Zero one generic (m,n) spectrum slice.

Parameters

[in]	idiag	Potential/vector-potential spectrum selector.
[in]	ndim	Toroidal spectrum dimension.
[in]	mdim	Poloidal spectrum dimension.

zero_spectrum2d_avg()

static void orb5x::Diagnostics::zero_spectrum2d_avg ( int  isp, int  idiag, int  ndim, int  mdim  )

static

Zero one per-species (m,n) spectrum slice.

Parameters

[in]	isp	Zero-based species index.
[in]	idiag	Field/density/current spectrum selector.
[in]	ndim	Toroidal spectrum dimension.
[in]	mdim	Poloidal spectrum dimension.

Member Data Documentation

apaloc

std::vector<Real> orb5x::Diagnostics::apaloc

inlinestatic

Local \(A_\parallel(s,0,0)\) radial cut.

FIELD_APAR

constexpr int orb5x::Diagnostics::FIELD_APAR = 2

staticconstexpr

Select total parallel vector potential.

FIELD_APAR_HAM

constexpr int orb5x::Diagnostics::FIELD_APAR_HAM = 3

staticconstexpr

Select Hamiltonian \(A_\parallel\).

FIELD_APAR_SYMPL

constexpr int orb5x::Diagnostics::FIELD_APAR_SYMPL = 4

staticconstexpr

Select symplectic \(A_\parallel\).

FIELD_DENS

constexpr int orb5x::Diagnostics::FIELD_DENS = 5

staticconstexpr

Select density field.

FIELD_PHI

constexpr int orb5x::Diagnostics::FIELD_PHI = 1

staticconstexpr

=============================================================================

PHASE 1 IMPLEMENTATIONS (Core Dependencies for field diagnostics)

Field type constants (matching Fortran names.F90 lines 162-167) Used to select which field to retrieve in getpot_fieldnum() Select electrostatic potential \(\phi\).

FIELD_USER

constexpr int orb5x::Diagnostics::FIELD_USER = 6

staticconstexpr

Select user-defined external field.

moment1d_w

std::vector<std::vector<std::vector<Real> > > orb5x::Diagnostics::moment1d_w

inlinestatic

moment1d_w: 1D moment diagnostics weighted by w (matching Fortran moment1d_w) [nspecies][nbin_flux+2][14 diagnostic types] - matching moment1d_w structure

Referenced by init_test_diagnostic_arrays().

out

std::vector<bool> orb5x::Diagnostics::out

inlinestatic

Species output flags (matching Fortran out(0:NSPECIES_MAX)) out[0] = true for pure fluid model, out[isp] = true if species isp has diagnostic output.

pe_phi_cuts

std::array<int, 3> orb5x::Diagnostics::pe_phi_cuts = {0, 0, 0}

inlinestatic

MPI ranks responsible for phi cuts (matching Fortran pe_phi_cuts(0:2)) Stores the PE rank that owns each of the 3 phi cut positions for output.

Referenced by Diagnostics().

phi00

std::vector<Real> orb5x::Diagnostics::phi00

inlinestatic

Public diagnostic arrays (accessed by FieldsModule in solve_fem, matching Fortran pde_solver) Potential diagnostic arrays (matching Fortran diagnostics.F90)

Flux-surface average of \(\phi\) on the radial spline grid.

phi0_chi

std::vector<Real> orb5x::Diagnostics::phi0_chi

inlinestatic

Poloidal potential cut at the configured diagnostic radius.

phibar

std::vector<Real> orb5x::Diagnostics::phibar

inlinestatic

Flux-surface-averaged electrostatic potential.

philoc

std::vector<Real> orb5x::Diagnostics::philoc

inlinestatic

\(\phi(s,\theta=0,\varphi=0)\) radial cut.

philoc_hfs

std::vector<Real> orb5x::Diagnostics::philoc_hfs

inlinestatic

High-field-side cut \(\phi(s,\theta=\pi,\varphi=0)\).

rho00

std::vector<std::vector<Real> > orb5x::Diagnostics::rho00

inlinestatic

Flux-surface-averaged charge density by radius and species.

---

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

• diagnostics.hpp