File list

• File adas_carbon.hxx
  • ADAS_CARBON_H
  • carbon_ionisation_energy
  • carbon_species_name
  • carbon_species_name< 1 >
  • carbon_species_name< 0 >
  • ADASCarbonIonisation
    • ADASCarbonIonisation()
    • transform_impl()
  • ADASCarbonRecombination
    • ADASCarbonRecombination()
    • transform_impl()
  • ADASCarbonCX
    • ADASCarbonCX()
    • transform_impl()
• File adas_lithium.hxx
  • ADAS_LITHIUM_H
  • lithium_ionisation_energy
  • lithium_species_name
  • lithium_species_name< 3 >
  • lithium_species_name< 1 >
  • lithium_species_name< 0 >
  • ADASLithiumIonisation
    • ADASLithiumIonisation()
    • transform_impl()
  • ADASLithiumRecombination
    • ADASLithiumRecombination()
    • transform_impl()
  • ADASLithiumCX
    • ADASLithiumCX()
    • transform_impl()
• File adas_neon.hxx
  • ADAS_NEON_H
  • neon_ionisation_energy
  • neon_species_name
  • neon_species_name< 10 >
  • neon_species_name< 1 >
  • neon_species_name< 0 >
  • ADASNeonIonisation
    • ADASNeonIonisation()
    • transform_impl()
  • ADASNeonRecombination
    • ADASNeonRecombination()
    • transform_impl()
  • ADASNeonCX
    • ADASNeonCX()
    • transform_impl()
• File adas_reaction.cxx
• File adas_reaction.hxx
  • ADAS_REACTION_H
  • OpenADASRateCoefficient
    • OpenADASRateCoefficient()
    • evaluate()
    • log_coeff
    • log_temperature
    • log_density
    • Tmin
    • Tmax
    • nmin
    • nmax
  • OpenADAS
    • OpenADAS()
    • calculate_rates()
    • rate_coef
    • radiation_coef
    • electron_heating
    • Tnorm
    • Nnorm
    • FreqNorm
  • OpenADASChargeExchange
    • OpenADASChargeExchange()
    • calculate_rates()
    • rate_coef
    • Tnorm
    • Nnorm
    • FreqNorm
• File amjuel_data.cxx
  • hermes
    • eval_amjuel_nT_fit()
    • eval_amjuel_T_fit()
• File amjuel_data.hxx
  • AMJUEL_DATA_H
  • hermes
    • hermes::AmjuelData
      • AmjuelData()
      • eval_sigma_vE_nT_impl()
      • eval_sigma_v_ET_impl()
      • eval_sigma_v_nT_impl()
      • eval_sigma_v_T_impl()
• File anomalous_diffusion.cxx
• File anomalous_diffusion.hxx
  • ANOMALOUS_DIFFUSION_H
  • AnomalousDiffusion
    • AnomalousDiffusion()
    • outputVars()
    • transform_impl()
    • name
    • diagnose
    • include_D
    • include_chi
    • include_nu
    • anomalous_D
    • anomalous_chi
    • anomalous_nu
    • anomalous_sheath_flux
• File binormal_stpm.cxx
• File binormal_stpm.hxx
  • BINORMAL_STPM_H
  • BinormalSTPM
    • BinormalSTPM()
    • outputVars()
    • transform_impl()
    • name
    • diagnose
    • Theta
    • chi
    • D
    • nu
    • nu_Theta
    • chi_Theta
    • D_Theta
    • Theta_inv
• File braginskii_collisions.cxx
• File braginskii_collisions.hxx
  • COLLISIONS_H
  • BraginskiiCollisions
    • BraginskiiCollisions()
    • outputVars()
    • transform_impl()
    • collide()
    • Tnorm
    • Nnorm
    • rho_s0
    • Omega_ci
    • electron_electron
    • electron_ion
    • electron_neutral
    • ion_ion
    • ion_neutral
    • neutral_neutral
    • ei_multiplier
    • collision_rates
    • diagnose
• File braginskii_conduction.cxx
• File braginskii_conduction.hxx
  • BRAGINSKII_CONDUCTION_H
  • BraginskiiConduction
    • BraginskiiConduction()
    • outputVars()
    • transform_impl()
    • all_nu
    • all_kappa_par
    • all_conduction_collisions_mode
    • all_collision_names
    • all_kappa_coefficient
    • all_kappa_limit_alpha
    • all_flow_ylow_conduction
    • all_diagnose
• File braginskii_electron_viscosity.cxx
• File braginskii_electron_viscosity.hxx
  • BRAGINSKII_ELECTRON_VISCOSITY_H
  • BraginskiiElectronViscosity
    • BraginskiiElectronViscosity()
    • outputVars()
    • transform_impl()
    • eta_limit_alpha
    • diagnose
    • viscosity
• File braginskii_friction.cxx
  • momentumCoefficient()
  • momentumCoefficient()
• File braginskii_friction.hxx
  • BRAGINSKII_FRICTION_H
  • BraginskiiFriction
    • BraginskiiFriction()
    • outputVars()
    • transform_impl()
    • frictional_heating
    • friction_energy_channels
    • momentum_channels
    • diagnose
• File braginskii_heat_exchange.cxx
• File braginskii_heat_exchange.hxx
  • BRAGINSKII_HEAT_EXCHANGE_H
  • BraginskiiHeatExchange
    • BraginskiiHeatExchange()
    • outputVars()
    • transform_impl()
    • energy_channels
    • diagnose
• File braginskii_ion_viscosity.cxx
• File braginskii_ion_viscosity.hxx
  • ION_VISCOSITY_H
  • BraginskiiIonViscosity
    • BraginskiiIonViscosity()
    • outputVars()
    • transform_impl()
    • eta_limit_alpha
    • parallel
    • perpendicular
    • collision_names
    • viscosity_collisions_mode
    • nu
    • Curlb_B
    • bounce_frequency
    • bounce_frequency_q95
    • bounce_frequency_epsilon
    • bounce_frequency_R
    • density_floor
    • diagnose
    • diagnostics
    • BraginskiiIonViscosity::Diagnostics
      • Pi_ciperp
      • Pi_cipar
      • DivJ
      • bounce_factor
      • nu_star
• File braginskii_thermal_force.cxx
• File braginskii_thermal_force.hxx
  • BRAGINSKII_THERMAL_FORCE_H
  • BraginskiiThermalForce
    • BraginskiiThermalForce()
    • transform_impl()
    • electron_ion
    • ion_ion
    • override_ion_mass_restrictions
    • first_time
• File classical_diffusion.cxx
• File classical_diffusion.hxx
  • CLASSICAL_DIFFUSION_H
  • ClassicalDiffusion
    • ClassicalDiffusion()
    • outputVars()
    • transform_impl()
    • Bsq
    • diagnose
    • Dn
    • custom_D
    • cls_pf_perp_xlow
    • cls_pf_perp_ylow
    • cls_mf_perp_xlow
    • cls_mf_perp_ylow
    • cls_nef_perp_xlow
    • cls_nef_perp_ylow
    • cls_tef_perp_xlow
    • cls_tef_perp_ylow
• File component.cxx
  • isSetFinal()
  • isSetFinal()
  • isSetFinalNoBoundary()
  • isSetFinalNoBoundary()
• File component.hxx
  • HERMES_COMPONENT_H
  • TOSTRING_
  • TOSTRING
  • IS_SET
  • IS_SET_NOBOUNDARY
  • GET_VALUE
  • GET_NOBOUNDARY
  • RegisterComponent
  • getNonFinal()
  • getNonFinal()
  • get()
  • get()
  • isSetFinal()
  • isSetFinal()
  • isSetFinalNoBoundary()
  • isSetFinalNoBoundary()
  • getNoBoundary()
  • getNoBoundary()
  • hermesDataInvalid()
  • hermesDataInvalid()
  • hermesDataInvalid()
  • set()
  • set()
  • setBoundary()
  • setBoundary()
  • add()
  • add()
  • subtract()
  • subtract()
  • set_with_attrs()
  • set_with_attrs()
  • SpeciesInformation
    • SpeciesInformation()
    • SpeciesInformation()
    • electrons
    • neutrals
    • positive_ions
    • negative_ions
    • ions
    • charged
    • non_electrons
    • all_species
    • finish_construction()
  • Component
    • Component()
    • ~Component()
    • transform()
    • finally()
    • outputVars()
    • restartVars()
    • precon()
    • declareAllSpecies()
    • create()
    • setPermissions()
    • setPermissions()
    • substitutePermissions()
    • transform_impl()
    • state_variable_access
  • ComponentFactory
    • type_name
    • section_name
    • option_name
    • default_type
  • hermes
    • EnableIfGuardedOption
• File component_scheduler.cxx
• File component_scheduler.hxx
  • COMPONENT_SCHEDULER_H
  • ComponentScheduler
    • ComponentScheduler()
    • transform()
    • outputVars()
    • restartVars()
    • precon()
    • create()
    • components
• File cx_reaction.cxx
  • hermes
• File cx_reaction.hxx
  • CX_REACTION_H
  • hermes
    • hermes::CXReaction
      • CXReaction()
      • CXReaction()
      • set_species_and_validate()
      • transform_additional()
      • has_neutral_reactant
      • no_neutral_cx_mom_gain
      • r1
      • r2
      • p1
      • p2
• File detachment_controller.cxx
  • calculateGradient()
• File detachment_controller.hxx
  • detachment_controller_H
  • DetachmentController
    • DetachmentController()
    • outputVars()
    • restartVars()
    • transform_impl()
    • connection_length
    • detachment_front_setpoint
    • min_time_for_change
    • min_error_for_change
    • species_for_source_shape
    • neutral_species
    • actuator
    • ignore_restart
    • velocity_form
    • reset_integral_on_first_crossing
    • response_sign
    • controller_gain
    • integral_time
    • derivative_time
    • species_list
    • scaling_factors_list
    • source_shape
    • source_units
    • source_conversion
    • diagnose
    • minval_for_source_multiplier
    • maxval_for_source_multiplier
    • control_offset
    • settling_time
    • debug
    • control_mode
    • control_power
    • control_particles
    • detachment_source_feedback
    • detachment_front_location
    • control
    • change_in_error
    • change_in_time
    • proportional_term
    • integral_term
    • derivative_term
    • time
    • error
    • derivative
    • change_in_derivative
    • change_in_control
    • error_integral
    • previous_time
    • previous_error
    • previous_control
    • previous_derivative
    • time_normalisation
    • initialise
    • first_step
    • number_of_crossings
    • buffer_size
    • time_buffer
    • error_buffer
• File diamagnetic_drift.cxx
• File diamagnetic_drift.hxx
  • DIAMAGNETIC_DRIFT_H
  • DiamagneticDrift
    • DiamagneticDrift()
    • transform_impl()
    • Curlb_B
    • bndry_flux
    • diamag_form
• File div_ops.cxx
  • Div_par_diffusion_index()
  • minmod()
  • MC()
  • Div_n_bxGrad_f_B_XPPM()
  • Div_Perp_Lap_FV_Index()
  • Div_Z_FV_Index()
  • D4DX4_FV_Index()
  • D4DZ4_Index()
  • Laplace_FV()
  • Div_a_Grad_perp_flows()
  • Div_a_Grad_perp_upwind()
  • Div_a_Grad_perp_nonorthog()
  • Div_a_Grad_perp_upwind_flows()
  • Div_n_g_bxGrad_f_B_XZ()
  • Div_par_K_Grad_par_mod()
  • Stencil1D
    • c
    • m
    • p
    • mm
    • pp
    • L
    • R
• File div_ops.hxx
  • Div_par_diffusion_index()
  • Div_n_bxGrad_f_B_XPPM()
  • Div_n_g_bxGrad_f_B_XZ()
  • Div_Perp_Lap_FV_Index()
  • Div_Z_FV_Index()
  • D4DX4_FV_Index()
  • D4DZ4_Index()
  • Laplace_FV()
  • Div_a_Grad_perp_flows()
  • Div_a_Grad_perp_upwind()
  • Div_a_Grad_perp_upwind_flows()
  • Div_par_K_Grad_par_mod()
  • Div_a_Grad_perp_nonorthog()
  • FV
    • Div_par_fvv()
    • Div_par_fvv_heating()
    • Div_par_mod()
    • Div_a_Grad_perp_limit()
    • FV::Superbee
      • operator()()
• File electromagnetic.cxx
• File electromagnetic.hxx
  • ELECTROMAGNETIC_H
  • Electromagnetic
    • Electromagnetic()
    • restartVars()
    • outputVars()
    • transform_impl()
    • Apar
    • Ajpar
    • alpha_em
    • beta_em
    • aparSolver
    • const_gradient
    • apar_boundary_timescale
    • last_time
    • magnetic_flutter
    • Apar_flutter
    • diagnose
• File electron_force_balance.cxx
• File electron_force_balance.hxx
  • ELECTRON_FORCE_BALANCE
  • ElectronForceBalance
    • ElectronForceBalance()
    • outputVars()
    • transform_impl()
    • diagnose
    • Epar
• File evolve_density.cxx
• File evolve_density.hxx
  • EVOLVE_DENSITY_H
  • EvolveDensity
    • EvolveDensity()
    • finally()
    • outputVars()
    • updateSource()
    • transform_impl()
    • name
    • charge
    • AA
    • N
    • bndry_flux
    • poloidal_flows
    • neumann_boundary_average_z
    • density_floor
    • low_n_diffuse
    • low_n_diffuse_perp
    • pressure_floor
    • low_p_diffuse_perp
    • hyper_z
    • evolve_log
    • logN
    • source
    • final_source
    • Sn
    • source_only_in_core
    • source_time_dependent
    • source_normalisation
    • time_normalisation
    • source_prefactor_function
    • diagnose
    • flow_xlow
    • flow_ylow
• File evolve_energy.cxx
• File evolve_energy.hxx
  • EVOLVE_ENERGY_H
  • EvolveEnergy
    • EvolveEnergy()
    • finally()
    • outputVars()
    • precon()
    • transform_impl()
    • name
    • E
    • P
    • T
    • N
    • adiabatic_index
    • Cv
    • bndry_flux
    • neumann_boundary_average_z
    • poloidal_flows
    • thermal_conduction
    • nu
    • evolve_log
    • logE
    • density_floor
    • source
    • Se
    • hyper_z
    • diagnose
    • enable_precon
    • flow_xlow
    • flow_ylow
• File evolve_momentum.cxx
• File evolve_momentum.hxx
  • EVOLVE_MOMENTUM_H
  • EvolveMomentum
    • EvolveMomentum()
    • finally()
    • outputVars()
    • transform_impl()
    • name
    • NV
    • NV_err
    • NV_solver
    • V
    • momentum_source
    • bndry_flux
    • poloidal_flows
    • density_floor
    • low_n_diffuse_perp
    • pressure_floor
    • low_p_diffuse_perp
    • hyper_z
    • diagnose
    • fix_momentum_boundary_flux
    • flow_xlow
    • flow_ylow
• File evolve_pressure.cxx
• File evolve_pressure.hxx
  • EVOLVE_PRESSURE_H
  • EvolvePressure
    • EvolvePressure()
    • finally()
    • outputVars()
    • precon()
    • transform_impl()
    • name
    • P
    • T
    • N
    • bndry_flux
    • neumann_boundary_average_z
    • poloidal_flows
    • thermal_conduction
    • p_div_v
    • evolve_log
    • logP
    • density_floor
    • low_n_diffuse_perp
    • temperature_floor
    • low_T_diffuse_perp
    • pressure_floor
    • low_p_diffuse_perp
    • damp_p_nt
    • source
    • final_source
    • Sp
    • source_prefactor_function
    • hyper_z
    • hyper_z_T
    • diagnose
    • enable_precon
    • source_normalisation
    • time_normalisation
    • source_time_dependent
    • flow_xlow
    • flow_ylow
    • flow_ylow_advection
    • flow_ylow_viscous_heating
    • numerical_viscous_heating
    • fix_momentum_boundary_flux
    • Sp_nvh
    • E_PdivV
    • E_VgradP
• File fixed_density.hxx
  • FIXED_DENSITY_H
  • FixedDensity
    • FixedDensity()
    • outputVars()
    • transform_impl()
    • name
    • charge
    • AA
    • N
• File fixed_fraction_ions.cxx
• File fixed_fraction_ions.hxx
  • FIXED_FRACTION_IONS_H
  • FixedFractionIons
    • FixedFractionIons()
    • transform_impl()
    • fractions
• File fixed_fraction_radiation.hxx
  • FIXED_FRACTION_RADIATION_H
  • FixedFractionRadiation
    • FixedFractionRadiation()
    • outputVars()
    • transform_impl()
    • name
    • cooling
    • fraction
    • diagnose
    • no_core_radiation
    • radiation_multiplier
    • radiation
    • Tnorm
    • Nnorm
    • FreqNorm
• File fixed_temperature.hxx
  • FIXED_TEMPERATURE_H
  • FixedTemperature
    • FixedTemperature()
    • outputVars()
    • transform_impl()
    • name
    • T
    • P
    • diagnose
• File fixed_velocity.hxx
  • FIXED_VELOCITY_H
  • FixedVelocity
    • FixedVelocity()
    • outputVars()
    • transform_impl()
    • name
    • V
• File guarded_options.cxx
  • isSetRecursive()
  • updateAccessRecords()
• File guarded_options.hxx
  • GuardedOptions
    • GuardedOptions()
    • GuardedOptions()
    • operator[]()
    • operator[]()
    • getChildren()
    • isSection()
    • isSection()
    • isSection()
    • isSet()
    • isSet()
    • isSet()
    • name()
    • get()
    • GetRef()
    • getWritable()
    • unreadItems()
    • unwrittenItems()
    • operator==()
    • operator!=()
    • getHighestPermission()
    • GuardedOptions()
    • options
    • permissions
    • unread_variables
    • unwritten_variables
• File hermes_utils.hxx
  • HERMES_UTILS_H
  • floor()
  • softFloor()
  • softFloor()
  • clamp()
  • str_keys()
  • BOUT_ENUM_CLASS()
  • identifySpeciesType()
  • indexAt()
  • containsAnySubstring()
  • collisionSpeciesMatch()
• File integrate.hxx
  • INTEGRATE_H
  • firstArg()
  • threePointStencil()
  • cellLeft()
  • cellRight()
  • cellAverage()
• File ionisation.cxx
• File ionisation.hxx
  • IONISATION_H
  • Ionisation
    • Ionisation()
    • transform_impl()
    • Eionize
    • Tnorm
    • Nnorm
    • FreqNorm
• File isothermal.cxx
• File isothermal.hxx
  • ISOTHERMAL_H
  • Isothermal
    • Isothermal()
    • outputVars()
    • transform_impl()
    • name
    • T
    • P
    • diagnose
• File izn_rec_reaction.cxx
  • hermes
• File izn_rec_reaction.hxx
  • IZN_REC_REACTION_H
  • hermes
    • hermes::IznRecReaction
      • IznRecReaction()
      • transform_additional()
      • heavy_reactant
      • heavy_product
      • heavy_collfreq_species
      • short_reaction_type
      • e_energy_loss_data
    • hermes::IznReaction
      • IznReaction()
      • IznReaction()
    • hermes::RecReaction
      • RecReaction()
      • RecReaction()
• File neutral_boundary.cxx
• File neutral_boundary.hxx
  • NEUTRAL_BOUNDARY_H
  • NeutralBoundary
    • NeutralBoundary()
    • outputVars()
    • transform_impl()
    • name
    • Tnorm
    • target_energy_refl_factor
    • sol_energy_refl_factor
    • pfr_energy_refl_factor
    • target_fast_refl_fraction
    • sol_fast_refl_fraction
    • pfr_fast_refl_fraction
    • target_energy_source
    • wall_energy_source
    • diagnose
    • lower_y
    • upper_y
    • sol
    • pfr
• File neutral_full_velocity.cxx
• File neutral_full_velocity.hxx
  • NEUTRAL_FULL_VELOCITY_H
  • NeutralFullVelocity
    • NeutralFullVelocity()
    • finally()
    • outputVars()
    • transform_impl()
    • coord
    • name
    • AA
    • density_floor
    • temperature_floor
    • pressure_floor
    • Nn2D
    • Pn2D
    • Vn2D
    • Vn2D_contravariant
    • Tn2D
    • Rxy
    • sigma_Bp
    • Txr
    • Txz
    • Tyr
    • Tyz
    • Urx
    • Ury
    • Uzx
    • Uzy
    • adiabatic_index
    • neutral_viscosity
    • neutral_conduction
    • neutral_gamma
    • collision_names
    • diffusion_collisions_mode
    • nu
    • Dnn
    • kappa_n
    • eta_n
    • flux_limit
    • neutral_lmax
    • diffusion_limit
    • toroidal_flow
    • momentum_advection
    • curved_torus
    • constant_transport_coef
    • zero_timederivs
    • output_ddt
    • diagnose
    • Vnpar
    • density_source
    • pressure_source
    • Sn
    • Sp
    • Snv
• File neutral_mixed.cxx
  • ParLimiter
• File neutral_mixed.hxx
  • NEUTRAL_MIXED_H
  • NeutralMixed
    • NeutralMixed()
    • finally()
    • outputVars()
    • precon()
    • transform_impl()
    • name
    • Nn
    • Pn
    • NVn
    • Vn
    • Tn
    • Nnlim
    • Pnlim
    • logPnlim
    • AA
    • collision_names
    • diffusion_collisions_mode
    • nu
    • Dnn
    • DnnNn
    • DnnPn
    • DnnTn
    • DnnNVn
    • flux_limit
    • diffusion_limit
    • neutral_lmax
    • sheath_ydown
    • sheath_yup
    • density_floor
    • temperature_floor
    • pressure_floor
    • freeze_low_density
    • collisionality_override
    • density_norm
    • pressure_norm
    • momentum_norm
    • neutral_viscosity
    • neutral_conduction
    • evolve_momentum
    • normalise_sources
    • kappa_n
    • eta_n
    • nonorthogonal_operators
    • precondition
    • precon_laplacexy
    • lax_flux
    • inv
    • density_source
    • pressure_source
    • momentum_source
    • Sn
    • Sp
    • Snv
    • sound_speed
    • output_ddt
    • diagnose
    • pf_adv_perp_xlow
    • pf_adv_perp_ylow
    • pf_adv_par_ylow
    • mf_adv_perp_xlow
    • mf_adv_perp_ylow
    • mf_adv_par_ylow
    • mf_visc_perp_xlow
    • mf_visc_perp_ylow
    • mf_visc_par_ylow
    • ef_adv_perp_xlow
    • ef_adv_perp_ylow
    • ef_adv_par_ylow
    • ef_cond_perp_xlow
    • ef_cond_perp_ylow
    • ef_cond_par_ylow
• File neutral_parallel_diffusion.cxx
• File neutral_parallel_diffusion.hxx
  • NEUTRAL_PARALLEL_DIFFUSION_H
  • NeutralParallelDiffusion
    • NeutralParallelDiffusion()
    • outputVars()
    • transform_impl()
    • dneut
    • diagnose
    • collision_names
    • diffusion_collisions_mode
    • nu
    • equation_fix
    • perpendicular_conduction
    • perpendicular_viscosity
    • diagnostics
    • NeutralParallelDiffusion::Diagnostics
      • Dn
      • S
      • E
      • F
• File noflow_boundary.cxx
• File noflow_boundary.hxx
  • NOFLOW_BOUNDARY_H
  • NoFlowBoundary
    • NoFlowBoundary()
    • transform_impl()
    • name
    • noflow_lower_y
    • noflow_upper_y
• File permissions.cxx
  • applyLowerPermissions()
  • replaceAll()
  • operator<<()
  • operator>>()
• File permissions.hxx
  • PermissionTypes
    • None
    • ReadIfSet
    • Read
    • Write
    • Final
    • END
  • Regions
    • Nowhere
    • Interior
    • Boundaries
    • All
  • operator&()
  • operator|()
  • operator~()
  • format_as()
  • readIfSet()
  • readOnly()
  • readWrite()
  • writeFinal()
  • writeBoundary()
  • writeBoundaryIfSet()
  • writeBoundaryReadInteriorIfSet()
  • operator<<()
  • operator>>()
  • Permissions
    • AccessRights
    • Permissions()
    • Permissions()
    • Permissions()
    • operator=()
    • operator=()
    • Permissions()
    • setAccess()
    • setAccess()
    • substitute()
    • checkNoRemainingSubstitutions()
    • canAccess()
    • getHighestPermission()
    • getVariablesWithPermission()
    • regionNames()
    • fundamental_regions
    • bestMatchRights()
    • variable_permissions
    • LABEL_RE
    • operator<<
    • operator>>
    • Permissions::VarRights
      • name
      • rights
  • fmt::formatter< Permissions >
    • format()
• File polarisation_drift.cxx
• File polarisation_drift.hxx
  • POLARISATION_DRIFT_H
  • PolarisationDrift
    • PolarisationDrift()
    • outputVars()
    • calcDivJ()
    • diamagneticCompression()
    • calcMassDensity()
    • calcPolFlowPotential()
    • polarisationAdvection()
    • transform_impl()
    • phiSolver
    • Bsq
    • diagnose
    • DivJ
    • phi_pol
    • diagnostics
    • boussinesq
    • average_atomic_mass
    • density_floor
    • advection
    • diamagnetic_polarisation
• File quasineutral.cxx
• File quasineutral.hxx
  • QUASINEUTRAL
  • Quasineutral
    • Quasineutral()
    • finally()
    • outputVars()
    • transform_impl()
    • name
    • charge
    • AA
    • density
• File rate_helper.hxx
  • RATE_HELPER_H
  • hermes
    • OneDRateFunc
    • TwoDRateFunc
    • RateFuncVariant
    • dependent_false
    • Teff_name
    • hermes::CellData
      • CellData()
      • CellData()
      • centre
      • left
      • right
    • hermes::RateData
      • coll_freq()
      • rate
      • collision_frequencies
    • hermes::RateHelper
      • RateHelper()
      • calc_rates()
      • add_rate_param()
      • calc_Teff()
      • compute_collision_freq_density()
      • compute_mass_actions()
      • compute_rate_param()
      • num_reactants
      • rate_calc_func
      • reactant_densities
      • reactant_names
      • region
      • rate_params
      • Teff_storage
• File reaction.cxx
  • hermes
• File reaction.hxx
  • REACTION_H
  • hermes
    • OPTYPE
    • hermes::ReactionBase
      • ReactionBase()
      • incremented_instance_num()
      • reset_instance_counter()
      • inst_num
      • instance_num_ref()
    • hermes::Reaction
      • Reaction()
      • outputVars()
      • add_diagnostic()
      • init_channel_weights()
      • set_energy_channel_weight()
      • set_momentum_channel_weight()
      • transform_additional()
      • update_source()
      • update_source()
      • parser
      • rate_data
      • units
      • Tnorm
      • Nnorm
      • FreqNorm
      • rate_multiplier
      • radiation_multiplier
      • diagnose
      • diagnostics
      • do_parallel_averaging
      • get_reaction_settings()
      • transform_impl()
      • zero_diagnostics()
      • energy_channels
      • momentum_channels
      • name
      • pfactors
• File reaction_data.cxx
  • get_json_db_dir()
• File reaction_data.hxx
  • REACTION_DATA_H
  • RegisterReactionData
  • get_json_db_dir()
  • ReactionData
    • ~ReactionData()
    • ReactionData()
    • get_coeffs()
    • get_fit_type()
    • eval_sigma_v_ET()
    • eval_sigma_v_T()
    • eval_sigma_v_nT()
    • eval_sigma_vE_nT()
    • get_metadata()
    • get_type()
    • src_str()
    • eval_sigma_v_ET_impl()
    • eval_sigma_v_T_impl()
    • eval_sigma_v_nT_impl()
    • eval_sigma_vE_nT_impl()
    • set_metadata()
    • fit_type
    • type
    • data_label
    • metadata_keys
    • metadata
  • ReactionDataWithCoeffs
    • ReactionDataWithCoeffs()
    • get_coeffs()
    • coeffs
  • ReactionDataFactory
    • type_name
    • section_name
    • option_name
    • default_type
• File reaction_diagnostic.hxx
  • REACTION_DIAGNOSTIC_H
  • DiagnosticTransformerType
  • BOUT_ENUM_CLASS()
  • toString()
  • identity()
  • negate()
  • sp_data_keys
  • ReactionDiagnostic
    • ReactionDiagnostic()
    • ReactionDiagnostic()
    • ReactionDiagnostic()
    • operator=()
    • operator=()
    • ReactionDiagnostic()
    • ~ReactionDiagnostic()
    • add_to_state()
    • get_name()
    • set_data()
    • transform()
    • default_std_name()
    • conversion
    • data
    • long_name
    • name
    • source
    • standard_name
    • transformer
    • type
    • units
• File reaction_parser.cxx
• File reaction_parser.hxx
  • REACTION_PARSER_H
  • species_filter
    • consumed
    • electron
    • ion
    • neutral
    • reactants
    • produced
    • products
    • heavy
  • count_species()
  • ReactionParser
    • ReactionParser()
    • get_reaction_str()
    • get_single_species()
    • get_single_species()
    • get_species()
    • get_species()
    • get_species()
    • get_species()
    • get_species()
    • get_mom_energy_pop_changes()
    • get_reactant_by_position()
    • get_product_by_position()
    • is_symmetric()
    • pop_change()
    • pop_change_product()
    • pop_change_reactant()
    • diff_reactants_products()
    • reaction_str
    • reactants
    • products
    • stoich
    • mom_energy_stoich
    • ordered_reactants
    • ordered_products
    • symmetric
• File reaction_settings.hxx
  • get_default_data_id()
  • add_default_id()
  • generate_default_data_ids_map()
  • get_default_data_ids_str()
  • split_csv_str()
  • split_csv_str()
  • NO_DATA_ID_DEFAULT_FOUND
  • default_data_ids
• File recalculate_metric.cxx
  • recalculate_metric()
• File recalculate_metric.hxx
  • recalculate_metric()
• File recycling.cxx
• File recycling.hxx
  • RECYCLING_H
  • Recycling
    • Recycling()
    • outputVars()
    • transform_impl()
    • channels
    • target_recycle
    • sol_recycle
    • pfr_recycle
    • neutral_pump
    • diagnose
    • has_sheath_boundary_simple
    • density_floor
    • pressure_floor
    • gamma_i
    • density_source
    • energy_source
    • energy_flow_xlow
    • particle_flow_xlow
    • is_pump
    • Recycling::RecycleChannel
      • from
      • to
      • target_multiplier
      • sol_multiplier
      • pfr_multiplier
      • pump_multiplier
      • target_energy
      • sol_energy
      • pfr_energy
      • target_fast_recycle_fraction
      • pfr_fast_recycle_fraction
      • sol_fast_recycle_fraction
      • target_fast_recycle_energy_factor
      • sol_fast_recycle_energy_factor
      • pfr_fast_recycle_energy_factor
      • target_recycle_density_source
      • target_recycle_energy_source
      • wall_recycle_density_source
      • wall_recycle_energy_source
      • pump_density_source
      • pump_energy_source
• File relax_potential.cxx
• File relax_potential.hxx
  • RELAX_POTENTIAL_H
  • RelaxPotential
    • RelaxPotential()
    • finally()
    • outputVars()
    • transform_impl()
    • Vort
    • phi1
    • phi
    • Pi_hat
    • exb_advection
    • exb_advection_simplified
    • diamagnetic
    • diamagnetic_polarisation
    • boussinesq
    • average_atomic_mass
    • poloidal_flows
    • bndry_flux
    • collisional_friction
    • sheath_boundary
    • vort_dissipation
    • phi_dissipation
    • phi_sheath_dissipation
    • damp_core_vorticity
    • phi_boundary_relax
    • phi_boundary_timescale
    • phi_boundary_last_update
    • phi_core_averagey
    • Bsq
    • Curlb_B
    • hyper_z
    • viscosity
    • viscosity_par
    • lambda_1
    • lambda_2
    • DivJdia
    • DivJcol
    • diagnose
• File scale_timederivs.hxx
  • SCALE_TIMEDERIVS_H
  • ScaleTimeDerivs
    • ScaleTimeDerivs()
    • outputVars()
    • transform_impl()
    • scaling
• File set_temperature.hxx
  • SET_TEMPERATURE_H
  • SetTemperature
    • SetTemperature()
    • outputVars()
    • transform_impl()
    • name
    • temperature_from
    • T
    • diagnose
• File sheath_boundary.cxx
• File sheath_boundary.hxx
  • SHEATH_BOUNDARY_H
  • SheathBoundary
    • SheathBoundary()
    • ionSecondaryElectronEmissionGamma()
    • transform_impl()
    • Ge
    • sin_alpha
    • lower_y
    • upper_y
    • always_set_phi
    • wall_potential
    • floor_potential
    • ion_ee_gamma_max
    • ion_ee_E_th
    • ion_ee_E_max
    • ion_ee_p
• File sheath_boundary_insulating.cxx
• File sheath_boundary_insulating.hxx
  • SHEATH_BOUNDARY_INSULATING_H
  • SheathBoundaryInsulating
    • SheathBoundaryInsulating()
    • transform_impl()
    • Ge
    • sin_alpha
    • lower_y
    • upper_y
    • gamma_e
• File sheath_boundary_simple.cxx
• File sheath_boundary_simple.hxx
  • SHEATH_BOUNDARY_SIMPLE_H
  • SheathBoundarySimple
    • SheathBoundarySimple()
    • outputVars()
    • transform_impl()
    • Ge
    • sin_alpha
    • gamma_e
    • gamma_i
    • sheath_ion_polytropic
    • lower_y
    • upper_y
    • always_set_phi
    • wall_potential
    • hflux_e
    • phi
    • ion_sum
    • diagnose
    • diagnostics
    • no_flow
    • density_boundary_mode
    • pressure_boundary_mode
    • temperature_boundary_mode
• File sheath_closure.cxx
• File sheath_closure.hxx
  • SHEATH_CLOSURE_H
  • SheathClosure
    • SheathClosure()
    • transform_impl()
    • L_par
    • sheath_gamma
    • sheath_gamma_ions
    • offset
    • sinks
• File simple_conduction.hxx
  • SIMPLE_CONDUCTION_H
  • SimpleConduction
    • SimpleConduction()
    • transform_impl()
    • name
    • kappa0
    • Nnorm
    • Tnorm
    • temperature
    • density
    • boundary_flux
• File simple_pump.hxx
  • simple_pump_H
  • SimplePump
    • SimplePump()
    • outputVars()
    • transform_impl()
    • name
    • sink_shape
    • pumping_sink
    • Nnorm
    • Omega_ci
    • residence_time
    • diagnose
• File snb_conduction.cxx
• File snb_conduction.hxx
  • SNB_CONDUCTION_H
  • SNBConduction
    • SNBConduction()
    • outputVars()
    • transform_impl()
    • snb
    • rho_s0
    • Tnorm
    • Nnorm
    • Omega_ci
    • Div_Q_SH
    • Div_Q_SNB
    • diagnose
• File solkit_hydrogen_charge_exchange.cxx
• File solkit_hydrogen_charge_exchange.hxx
  • SOLKIT_HYDROGEN_CHARGE_EXCHANGE_H
  • SOLKITHydrogenChargeExchange
    • SOLKITHydrogenChargeExchange()
    • calculate_rates()
    • Nnorm
    • rho_s0
  • SOLKITHydrogenChargeExchangeIsotope
    • SOLKITHydrogenChargeExchangeIsotope()
    • transform_impl()
• File solkit_neutral_parallel_diffusion.cxx
• File solkit_neutral_parallel_diffusion.hxx
  • SOLKIT_NEUTRAL_PARALLEL_DIFFUSION_H
  • SOLKITNeutralParallelDiffusion
    • SOLKITNeutralParallelDiffusion()
    • transform_impl()
    • neutral_temperature
    • area_norm
• File sound_speed.cxx
• File sound_speed.hxx
  • SOUND_SPEED_H
  • SoundSpeed
    • SoundSpeed()
    • transform_impl()
    • electron_dynamics
    • alfven_wave
    • beta_norm
    • temperature_floor
    • fastest_wave_factor
• File species_parser.cxx
• File species_parser.hxx
  • SPECIES_PARSER_H
  • SpeciesParser
    • SpeciesParser()
    • get_charge()
    • get_element()
    • get_str()
    • long_name()
    • ionised()
    • recombined()
    • SpeciesParser()
    • species_str
    • element
    • charge
• File temperature_feedback.cxx
• File temperature_feedback.hxx
  • temperature_feedback_H
  • TemperatureFeedback
    • TemperatureFeedback()
    • outputVars()
    • restartVars()
    • transform_impl()
    • name
    • species_list
    • scaling_factors_list
    • temperature_setpoint
    • temperature_controller_p
    • temperature_controller_i
    • error
    • temperature_error_integral
    • control_target_temperature
    • temperature_integral_positive
    • temperature_source_positive
    • temperature_error_lasttime
    • temperature_error_last
    • source_shape
    • source_multiplier
    • proportional_term
    • integral_term
    • diagnose
• File transform.cxx
• File transform.hxx
  • TRANSFORM_H
  • Transform
    • Transform()
    • transform_impl()
    • transforms
• File upstream_density_feedback.cxx
• File upstream_density_feedback.hxx
  • UPSTREAM_DENSITY_FEEDBACK_H
  • UpstreamDensityFeedback
    • UpstreamDensityFeedback()
    • outputVars()
    • restartVars()
    • transform_impl()
    • name
    • density_upstream
    • density_controller_p
    • density_controller_i
    • error
    • density_error_integral
    • density_integral_positive
    • density_source_positive
    • density_error_lasttime
    • density_error_last
    • density_source_shape
    • source_multiplier
    • proportional_term
    • integral_term
    • diagnose
• File vorticity.cxx
• File vorticity.hxx
  • VORTICITY_H
  • Vorticity
    • Vorticity()
    • finally()
    • outputVars()
    • restartVars()
    • calculatePihat()
    • calculateDivJdia()
    • transform_impl()
    • Vort
    • phi
    • phiSolver
    • Pi_hat
    • exb_advection
    • exb_advection_simplified
    • diamagnetic
    • diamagnetic_polarisation
    • average_atomic_mass
    • poloidal_flows
    • bndry_flux
    • collisional_friction
    • sheath_boundary
    • vort_dissipation
    • phi_dissipation
    • phi_sheath_dissipation
    • damp_core_vorticity
    • phi_boundary_relax
    • phi_boundary_timescale
    • phi_boundary_last_update
    • phi_core_averagey
    • split_n0
    • laplacexy
    • Bsq
    • Curlb_B
    • hyper_z
    • viscosity
    • viscous_heating
    • include_viscosity
    • DivJdia
    • DivJcol
    • diagnose
• File zero_current.cxx
• File zero_current.hxx
  • ZERO_CURRENT
  • ZeroCurrent
    • ZeroCurrent()
    • finally()
    • outputVars()
    • transform_impl()
    • name
    • charge
    • velocity