Procedures

Procedure	Location	Procedure Type	Description
absb	equilibrium_storage_m	Function	Computes absolute value of magnetic field from stured quantities
add_fields_to_averaged_internal_fields	iol_source_m	Interface
advance	multistep_m	Interface
advance	runge_kutta_m	Interface
alloc_state_template	state_template_m	Subroutine	Allocates memory for state fields
allocate_diags	diagnostics_group_m	Subroutine	Initialize diagnostic
allocate_managed_memory_double	allocate_data_cuda	Interface
allocate_managed_memory_int	allocate_data_cuda	Interface
allocate_memory_double	allocate_data_cuda	Subroutine
allocate_memory_int	allocate_data_cuda	Subroutine
apar_solve	ohm_electromagnetic_braginskii_m	Subroutine	Solves for parallel electromagnetic potential if co_inert presents, \f[ \beta A_\parallel -\frac{mu}{n}\nabla_\perp^2A_\parallel= \psi_\parallel \f] otherwise, \f[ -\nabla_\perp^2A_\parallel= \psi_\parallel \f]
apply_boundaries	timestep_template_m	Subroutine	Applies boundaries
apply_dissipation_inplane	inplane_operators_m	Interface
apply_immersed_sources	immersed_template_m	Subroutine	Applies immersed sources, related with parallel (Sheath) boundary conditions
apply_mms_boundaries	timestep_template_m	Interface
apply_mms_sources	timestep_template_m	Interface
apply_pardiff	timestep_template_m	Interface
apply_partransp	timestep_template_m	Interface
apply_perptransp	timestep_template_m	Interface
apply_taylor_parbnds	taylor_template_m	Subroutine	Applies parallel (Sheath) boundary conditions with Taylor's method
arakawa	inplane_operators_m	Interface
arakawa_loc	inplane_operators_m	Interface
buffer_write_netcdf	create_buffer_m	Subroutine	Writes cf_buffer to netcdf file
build_adjacency	polygon_in_mesh_m	Interface
build_braginskii_initial_state	init_braginskii_m	Subroutine	Builds initial state
build_cuda_struct	parallel_map_m	Interface
build_derived_operators	parallel_map_m	Interface
build_initial_state	init_diffusion_m	Subroutine	Builds initial state
build_mask_data	mask_data_m	Subroutine	Builds mask arrays
build_neutrals_initial_state	init_neutrals_m	Subroutine	Builds initial state
build_parallel_map	parallel_map_m	Interface
build_pen_inds	penalisation_m	Interface
build_penalisation	penalisation_m	Interface
build_polars	polars_m	Interface
build_ranking	polygon_in_mesh_m	Interface
build_segmentation	polygon_in_mesh_m	Interface
build_target_markers	parallel_target_flux_m	Interface
build_via_in_vessel	penalisation_m	Interface
build_via_rho	penalisation_m	Interface
build_via_stable_trace	penalisation_m	Interface
build_via_subtrace	penalisation_m	Interface
build_via_trace	penalisation_m	Interface
build_vtk_mesh	static_data_m	Interface
build_wip3d_penalisation	penalisation_m	Interface
build_zhdanov_initial_state	init_zhdanov_m	Subroutine	Builds initial state
checksum_braginskii	checksum_braginskii_m	Subroutine	Computes and writes checksum of a plasma state The checksum does not have any physical meaning, but is used e.g in CI/CD to ensure code integrity
compute_diagnostics_packet	diagnostics_packet_m	Subroutine	Compute diagnostics Only work for tratio=1
compute_diffusive_flux	perp_bnd_flux_m	Subroutine	Computes the diffusive flux through a perpendicular boundary polygon, i.e. \int_S v \nabla u dS, where nabla is gradient within plane Sign convention is that flux out of inner domain is positive
compute_drift_flux	perp_bnd_flux_m	Subroutine	Computes fluxes due to drift through a toroidally extended polygon \int_S v * (B/B^2 \times \nabla u) dS The integrand can be expressed via a derivative along the polygon \int v * 1/Btor du/dl J dl dphi where l measures the length along the polygon $omp parallel default(none) & $omp private(iseg, ks, ks_glob, l, lfwd, x, y, xfwd, yfwd, & $omp jac_av, btor_av, v_av) & $omp shared(equi, equi_storage, mesh, dphi, polygon, phi, nexclude_last, & $omp u, v, drift_flux) $omp do $omp end do $omp end parallel
compute_electron_density	compute_electron_density_m	Subroutine	Computes electron density via reduction of ion charge density
compute_jpar	ohm_electromagnetic_braginskii_m	Subroutine	Computes parallel current from parallel electromagnetic potential \f[ j_\parallel = -\nabla_\perp^2 A_\parallel \f]
compute_recycling_source	recycling_m	Subroutine	Compute source contribution from recycling
compute_rhs_explicit	timestep_template_m	Subroutine	Computes explicit changerate at time tau
compute_target_flux	parallel_target_flux_m	Interface
compute_target_flux_single	parallel_target_flux_m	Interface
compute_vorticity	polarisation_braginskii_m	Subroutine	Computes generalised vorticity \f[ \nabla\cdot\left[co\nabla_\perp\left(swpot\nabla_\perp\phi+swdia\tau\frac{\nabla_\perp p_i}{n}\right)\right] \f]
convert_descriptor_char_int	descriptors_braginskii_m	Subroutine	Extends PARALLAX subroutine of the same name converts character, e.g. as specified in parameter files, into actual (integer) descriptor Dirichlet boundary condition zeroth order Dirichlet boundary condition first order Neumann boundary condition first order nothing applied for boundary conditions
convert_descriptor_char_int	descriptors_neutrals_m	Subroutine	Extends PARALLAX subroutine of the same name converts character, e.g. as specified in parameter files, into actual (integer) descriptor Dirichlet boundary condition zeroth order Neumann boundary condition first order Nothing applied for boundary conditions
convert_descriptor_int_char	descriptors_braginskii_m	Subroutine	Converts integer descriptor into character descriptor
convert_logical_integer	test_type_conversion_m	Subroutine	Tests logical <-> integer conversion
create_buffer	create_buffer_m	Subroutine	Creates buffer function
create_halos	variable_m	Interface
create_radrate_table	coronal_impurities_m	Subroutine	Create rate coefficient object from data file
create_rate_coeff	rate_coeff_neutrals_m	Subroutine	Create rate coefficient object with fit coefficients taken from data file
curvature_btor_based	inplane_operators_m	Interface
curvature_ddy_based	inplane_operators_m	Interface
curvature_interface	inplane_operators_m	Interface
curvature_sqrd_btor_based	inplane_operators_m	Interface
curvature_sqrd_ddy_based	inplane_operators_m	Interface
cxx_timestep	timestep_template_m	Interface
ddx	inplane_operators_m	Interface
ddy	inplane_operators_m	Interface
destructor	polars_m	Interface
destructor	perp_bnd_flux_m	Interface
destructor	parallel_target_flux_m	Interface
destructor	polygon_in_mesh_m	Interface
destructor	penalisation_m	Interface
destructor	runge_kutta_m	Interface
destructor	inplane_operators_m	Interface
destructor	equilibrium_storage_m	Subroutine	Destructor
destructor	sources_external_m	Subroutine	Destructor
destructor	gyroviscosity_m	Subroutine	Destructor
destructor	boundaries_braginskii_m	Subroutine	Frees memory associated with boundaries_braginskii
destructor	diagnostics_group_m	Subroutine
destructor	diagnostics_packet_m	Subroutine
destructor	boundaries_neutrals_m	Subroutine	Frees memory associated with boundaries_neutrals
destructor	comm_handler_m	Subroutine
destructor	snapshot_m	Subroutine	Destructor
destructor	diagnostic_variable_m	Subroutine	Frees memory associated with variable
destructor	variable_m	Interface
destructor_cuda_map_t	parallel_map_m	Interface
destructor_iol	iol_source_m	Subroutine	Deallocates stuff related with iol source
destructor_karniadakis	multistep_m	Interface
destructor_mask_data_t	mask_data_m	Subroutine
destructor_parallel_map_t	parallel_map_m	Interface
destructor_storage	multistep_m	Interface
diagnostics_helpers	test_diagnostics_helpers_m	Subroutine	Test of diagnostics helper functions
diagnostics_template	diagnostics_template_m	Subroutine	Diagnostics for template model Yet just the L1, L2 global minimum and global maximum values of dynamical fields are computed
direction_order	polygon_in_mesh_m	Interface
display_build_static	static_data_m	Subroutine	Writes control build parameters of static data parameters to screen
display_iol_source	iol_source_m	Interface
display_karniadakis	multistep_m	Interface
display_mms_params_template	mms_template_m	Subroutine	Displays MMS parameters for template model
display_parallel_map	parallel_map_m	Interface
display_params_template_features	params_template_m	Interface
display_params_template_model	params_template_m	Interface
display_params_template_parbnd	params_template_m	Interface
display_params_template_paths	params_template_m	Interface
display_params_template_tstep	params_template_m	Interface
display_penalisation	penalisation_m	Interface
display_polars	polars_m	Interface
display_polygon_in_mesh	polygon_in_mesh_m	Subroutine	Displays information on polygon_in_mesh
display_runge_kutta	runge_kutta_m	Interface
display_snapshot	snapshot_m	Subroutine	Displays information
display_source_constantrate	sources_external_m	Subroutine	Displays constantrate source parameters
display_source_gaussian	sources_external_m	Subroutine	Display parameters related to the gas puff module
display_source_individual	sources_external_m	Interface
display_source_none	sources_external_m	Subroutine	Displays source_none parameters
display_source_zonal	sources_external_m	Subroutine	Displays zonal source parameters
display_zhdanov_params	params_zhdanov_species_m	Subroutine	Displays parameters for zhdanov model
display_zhdanov_params	params_zhdanov_general_m	Subroutine	Displays parameters for zhdanov model
doubled_arakawa	inplane_operators_m	Interface
doubled_arakawa_loc	inplane_operators_m	Interface
drift_surface_integral	polar_operators_m	Subroutine	Computes surface integral of flux in drift form, i.e. \int dS v/B^2 B\times\nabla u via integration along flux surface, i.e. = \int v/B du/d\theta J dphi d\theta
drive	checkpoint_monitor_m	Subroutine	Check if time aligns with cycle and set according checkpoint flag
drive_diagnostics	diagnostics_braginskii_m	Interface
drive_gyroviscosity	gyroviscosity_m	Subroutine	Performs auxiliary precomputations necessary to evaluate guroviscosity - Precomputes viscosities - Communicates uB^3/2 and qiparB^(3/2)
driver_iol	iol_source_m	Interface
equilibrium_storage_cerfons	test_equilibrium_storage_m	Subroutine	Test of inplane operators in cerfons geometry
error_ananum	commons_misc_m	Subroutine	Computes the norm and difference between two fields, useful for MMS-analysis
eta_neo_flow	gyroviscosity_m	Function	Computes ion flow viscosity with "beyond Braginskii extensions" according to parameters
eval_curvature	gyroviscosity_m	Subroutine	Evaluates curvature of ion stress function. This routine is present, because there is an issue if one simply evaluated the curvature of gstress obtained via ion_stress_function. Squared curvature operators appear that would imply chequerboarding. Therefore the evaluation of squared curvature operators has to be performed numerically careful and explicit.
eval_diff_coeff	diff_coeff_neutrals_m	Subroutine	Evaluate the normalized pressure diffusion coefficient
eval_gstress	gyroviscosity_m	Subroutine	Computation of ion stress function G = G_flow + G_heat with "beyond Braginskii extensions" according to parameters
eval_pargrad_b32	gyroviscosity_m	Subroutine	Evaluates B^(3/2)par_grad(G/B^(3/2)) of ion stress function. Used for the parallel momentum equation
eval_radrate	coronal_impurities_m	Function	Evaluate the normalized rate coefficient through interpolation
eval_rate_coeff	rate_coeff_neutrals_m	Function	Evaluate the normalized rate coefficient from a double polynomial fit
eval_source_constantrate	sources_external_m	Subroutine	Evaluates constantrate source
eval_source_gaussian	sources_external_m	Subroutine	Compute neutrals density source from contributions of gaussian centers
eval_source_zonal	sources_external_m	Subroutine	Evaluates zonal source
eval_sources_external	sources_external_m	Subroutine	Evaluates external sources
eval_sources_neutrals	neutrals_module_m	Subroutine	Evaluate source terms to pass to Braginskii model
evaluate_apar_fluct	model_apar_shift_m	Subroutine	Evaluate the fluctuating part of parallel electromagnetic potential
execute_sort	polygon_in_mesh_m	Interface
fill_storage	equilibrium_storage_m	Subroutine	Fills storage with values on mesh points
finalize_comm_halos	variable_m	Interface
finalize_comm_planes	communication_planes_m	Subroutine	Finalises communication
finalize_static	static_data_m	Subroutine	Cleans up temporary data, that was used during initialization stage, and sets static_data_is_initialized to true
find_neighbor_inds	mesh_index_helpers_m	Subroutine	Scan points in 3x3 vicinity and return their index only
flat_stag_to_cano	parallel_map_m	Interface
flat_stag_to_cano_single	parallel_map_m	Interface
flip	iol_source_m	Interface
flutter_div	inplane_operators_m	Interface
flutter_grad	inplane_operators_m	Interface
flux_surface_average	polar_operators_m	Subroutine	Computes zonal average of quantity
fortran_timestep	timestep_template_m	Function
func_hermite_aux	penalisation_m	Interface
get_charfun_at_target	penalisation_m	Function	Contourvalue of characteristic function at target plate
get_charfun_parwidth	penalisation_m	Function	Returns parallel decay length of characteristic penalisation function
get_charfun_radlimwidth	penalisation_m	Function	Radial radial decay length (only for limiter geometry)
get_charfun_val	penalisation_m	Function	Returns value of characteristic function
get_comm_cart	comm_handler_m	Function
get_comm_planes	comm_handler_m	Function
get_comm_species	comm_handler_m	Function
get_current_order	multistep_m	Interface
get_diffusive_flux_local	perp_bnd_flux_m	Function	Computes local flux through polygon point (area associated with polygon point) diff_flux array has to be computed previously via compute_diffusive_flux
get_diffusive_flux_total	perp_bnd_flux_m	Function	Computes total flux through polygon segment from diff_flux array, which has to be computed previously via compute_diffusive_flux.
get_dirindfun_parwidth	penalisation_m	Function	Returns parallel decay length of direction indicator function
get_dirindfun_val	penalisation_m	Function	Returns value of direction indicator function
get_dphi	penalisation_m	Function	Toroidal grid distance
get_dphi	parallel_map_m	Function	Returns toroidal grid distance used for map
get_dphi_max	penalisation_m	Function	Maximum angle to be traced for building penalisation
get_drift_flux_local	perp_bnd_flux_m	Function	Computes local flux through polygon point (area associated with polygon point) drift_flux array has to be computed previously via compute_drift_flux
get_drift_flux_total	perp_bnd_flux_m	Function	Computes total flux through polygon segment from drift_flux array, which has to be computed previously via compute_drift_flux. $omp parallel default(none) private(is, ks, ks_glob) & $omp shared(polygon, iseg_start, iseg_end, nexclude_last, drift_flux, res) $omp do reduction(+ : res) $omp end do $omp end parallel
get_dtau	multistep_m	Interface
get_dtau_bdf	multistep_m	Interface
get_halo	variable_m	Interface
get_hermite_order	penalisation_m	Function	Returns order of Hermite polynomial used as penalisation function
get_ind_on_mesh	polygon_in_mesh_m	Function	Returns mesh index of point of segement
get_init_continue	iol_source_m	Function	Getter routine
get_intorder	parallel_map_m	Function	Returns interpolation order used for map
get_iplane	parallel_map_m	Function	Returns index of poloidal plane (0 to nplanes-1)
get_major_tally	checkpoint_monitor_m	Function	Return current tally for the major cycle
get_mat_entry_cartbased	helpers_grillix_m	Function	Returns a specifig entry of csr matrix based on Cartesian indexing i.e. row lt corresponds to point (it, jt) and columnd lg to point (ig, jg)
get_minor_tally_bwd	checkpoint_monitor_m	Function	Return current bwd tally for the minor cycle
get_minor_tally_fwd	checkpoint_monitor_m	Function	Return current fwd tally for the minor cycle
get_ncart	comm_handler_m	Function
get_ncount	multistep_m	Interface
get_ncount	runge_kutta_m	Interface
get_ndim	multistep_m	Interface
get_ndim	runge_kutta_m	Interface
get_ndim	diagnostic_variable_m	Function	Returns dimension of variable
get_ndim	variable_m	Interface
get_nfields	multistep_m	Interface
get_np_total	polygon_in_mesh_m	Function	Returns total number of polygon points
get_nplanes	parallel_map_m	Function	Returns number of poloidal planes used for map
get_nplanes	comm_handler_m	Function
get_nps	polygon_in_mesh_m	Function	Returns number of points of segment
get_nsegs	polygon_in_mesh_m	Function	Returns number of segements
get_nspecies	comm_handler_m	Function
get_nstorage	multistep_m	Interface
get_order	multistep_m	Interface
get_order	runge_kutta_m	Interface
get_penfuns_type	penalisation_m	Function	Returns type of penalisation function
get_phi_cano	parallel_map_m	Function	Returns phi coordinate of current plane
get_phi_stag	parallel_map_m	Function	Returns phi coordinate of current staggered plane
get_plane	comm_handler_m	Function
get_rank	comm_handler_m	Function
get_species	comm_handler_m	Function
get_xorder	parallel_map_m	Function	Returns order of subcell splitting used for map
gradient_3D_staggered	nonaligned_operators_m	Subroutine	Computes gradient (dudx, dudy, dudphi = dudz) at 3D staggered positions Gradient is computed according to symmetric formulation of Guenter's scheme Staggered point is at northeast-forward position w.r.t. its considered grid point on full grid Second and fourth order are implemented
grid_init	iol_source_m	Interface
grillix_banner	startups_m	Subroutine	Prints banner for grillix code
handle_error	error_handling_grillix_m	Subroutine	Logs an error to stderr and stops the program. If status_code is GRILLIX_SUCCESS, this subroutine will do nothing. Read more…
handle_error_netcdf	error_handling_grillix_m	Subroutine	Wrapper of handle error for calls of NetCDF functions. Checks for NetCDF errors and prints a standardized error message.
heat_flux_braginskii	heat_flux_m	Subroutine	Computes heat flux according to Braginskii model with free streaming limter
heat_flux_free_streaming	heat_flux_m	Subroutine	Computes heat flux according to free streaming model
heat_flux_landau	heat_flux_m	Subroutine	Contains a routine that calculates the heat flux according to the landau heat flux model Ref.: J.G. Chen, X.Q. Xu, Y.A. Lei, Extension of Landau-fluid closure to weakly collisional plasma regime, Computer Physics Communications, Volume 236, 2019, Pages 128-134, ISSN 0010-4655, https://doi.org/10.1016/j.cpc.2018.10.024.
init	comm_handler_m	Subroutine	Initialises MPI topology and communicators
init_boundaries_braginskii	boundaries_braginskii_m	Subroutine	Sets boundary types and values according to parameters
init_boundaries_neutrals	boundaries_neutrals_m	Subroutine	Sets boundary types and values according to parameters
init_braginskii_halos	init_braginskii_m	Subroutine	Allocates halo points of Braginskii fields
init_diagnostic_variable	diagnostic_variable_m	Subroutine	Writes variable to netcdf file
init_diagnostics	diagnostics_braginskii_m	Interface
init_diagnostics_group	diagnostics_group_m	Subroutine	Initialize diagnostic
init_gyroviscosity	gyroviscosity_m	Subroutine	Initialise gyroviscosity
init_inplane_operators	inplane_operators_m	Interface
init_iol	iol_source_m	Interface
init_karniadakis	multistep_m	Interface
init_lineout	diagnostics_lineout_m	Subroutine	Initialize lineout diagnostic
init_mms_template	mms_template_m	Subroutine	Initializes MMS parameters for template model
init_monitor	checkpoint_monitor_m	Subroutine	Initialize checkpoint monitor
init_neutrals	neutrals_module_m	Subroutine	Setup data structures for neutrals timestepping
init_neutrals_halos	init_neutrals_m	Subroutine	Allocates halo points of Neutrals fields
init_next_diagnostic	diagnostics_group_m	Subroutine	Initialize single diagnostic and provide pointer to its vals field
init_perp_bnd_flux	perp_bnd_flux_m	Interface
init_polygon_in_mesh	polygon_in_mesh_m	Interface
init_runge_kutta	runge_kutta_m	Interface
init_snapshot	snapshot_m	Subroutine	Initialises snapshots, creates dirpath
init_source_constantrate	sources_external_m	Subroutine	Initialises constantrate source
init_source_gaussian	sources_external_m	Subroutine	Initialize gaussian source from input file
init_source_individual	sources_external_m	Interface
init_source_none	sources_external_m	Subroutine	Initialises source=none
init_source_zonal	sources_external_m	Subroutine	Initialises zonal source
init_sources_external	sources_external_m	Subroutine	Initialises (reads parameters) sources_external
init_state_profile	init_braginskii_m	Interface
init_storage	multistep_m	Interface
init_template	init_template_m	Subroutine	Creates an initial state depending on init_type
init_variable	variable_m	Interface
init_zhdanov_state_profile	init_zhdanov_m	Interface
initialise_apar_shift	model_apar_shift_m	Subroutine	Initialise apar shift variable, snapshot, and timestepper
initialise_neutrals_timesteppers	init_neutrals_m	Subroutine	Initialises the timesteppers. This automatically will use a lower-order method for the first few timesteps to fill the storage
initialise_timesteppers	init_zhdanov_m	Subroutine	Initialises the timesteppers
initialise_timesteppers	init_braginskii_m	Subroutine	Initialises the timesteppers. This automatically will use a lower-order method for the first few timesteps to fill the storage
initialise_timesteppers_with_mms	init_braginskii_m	Subroutine	Initialise the timesteppers, and fills their storage with the MMS solution and derivative at previous "timesteps" (which have t < 0)
inner_product	diagnostics_helpers_m	Function	Compute inner product of u*v over all volume elements Only accepts input arrays of lengths n_points or n_points_inner
integer_to_logical	type_conversion_m	Function	Returns true if input = 1, otherwise 0
interpolate_lineout	diagnostics_helpers_m	Subroutine	Compute interpolation along a lineout within poloidal plane
is_fixed_stencil	parallel_map_m	Function	Returns if fixed stencil is used for interpolation
is_gauss_quadrature	parallel_map_m	Function	Returns if gauss-quadrature or midpoint rule is used for integration
is_periodic	polygon_in_mesh_m	Function	Returns tru if polygon is closed (periodic)
karniadakis	test_timestepping_m	Subroutine	Test of module karniadakis_m integrates - dy_1/dtau = y --> y_1(tau) = exp(tau) - dy_2/dtau = 2tauy --> y_2(tau) = exp(tau^2) until tau = 2 Analytic result of y_1(2) = exp(2) ~ 7.38905609893 Analytic result of y_2(2) = exp(4) ~ 54.5981500331
lift_cano_to_stag	parallel_map_m	Interface
lift_cano_to_stag_single	parallel_map_m	Interface
log_bnd	boundaries_braginskii_m	Function	Sets bnd value to the logarithm of the prescribed value if the descrpitor is "DIRICHLET". Necessary for ne, te and ti
logical_to_integer	type_conversion_m	Function	Returns 1 if input = true, otherwise 0
logne_penalisation	penalisation_braginskii_m	Subroutine	Sets the logarithmic-density penalisation values.
logte_penalisation	penalisation_braginskii_m	Subroutine	Sets the logarithmic electron temperature penalisation values.
logti_penalisation	penalisation_braginskii_m	Subroutine	Sets the logarithmic ion temperature penalisation values.
map_cart_to_polar	polar_operators_m	Subroutine	Maps quantity from Cartesian mesh to polar grid
map_polar_to_cart	polar_operators_m	Subroutine	Maps quantity from polar grid to Cartesian mesh
mesh_index_helpers	test_mesh_index_helpers_m	Subroutine	Test of mesh index helper functions
mesh_sample_cerfons	helpers_mesh_sample_m	Subroutine
mesh_sample_circular	helpers_mesh_sample_m	Subroutine
mirrorset_polyperpbnd_points	perp_bnd_flux_m	Subroutine	Sets points of field u on boundary-polygon to the value of its connected inner points, according to connectivity matrix conn.
mms_diagnostics_braginskii	mms_braginskii_m	Subroutine	Prints information on numerical errors of numerical solutions
mms_diagnostics_diffusion	mms_diffusion_m	Subroutine	Prints information on numerical errors of numerical solution
mms_diagnostics_neutrals	mms_neutrals_m	Subroutine	Prints information on numerical errors of numerical solutions
mms_diagnostics_template	mms_template_m	Subroutine	Prints information on numerical errors of numerical solution
mms_diagnostics_zhdanov	mms_zhdanov_m	Subroutine	Prints information on numerical errors of numerical solution
mms_sol_braginskii_apar	mms_braginskii_m	Function	MMS solution for parallel electromagnetic potential
mms_sol_braginskii_circular_apar	mms_braginskii_circular_m	Function	MMS solution for parallel electromagnetic potential
mms_sol_braginskii_circular_jpar	mms_braginskii_circular_m	Function	MMS solution for parallel current
mms_sol_braginskii_circular_ne	mms_braginskii_circular_m	Function	MMS solution for electron density
mms_sol_braginskii_circular_pot	mms_braginskii_circular_m	Function	MMS solution for electrostatic potential
mms_sol_braginskii_circular_te	mms_braginskii_circular_m	Function	MMS solution for electron temperature
mms_sol_braginskii_circular_ti	mms_braginskii_circular_m	Function	MMS solution for ion temperature
mms_sol_braginskii_circular_upar	mms_braginskii_circular_m	Function	MMS solution for parallel ion velocity
mms_sol_braginskii_circular_vort	mms_braginskii_circular_m	Function	MMS solution for generalised vorticity TODO: Boussinesq version
mms_sol_braginskii_jpar	mms_braginskii_m	Function	MMS solution for parallel current
mms_sol_braginskii_ne	mms_braginskii_m	Function	MMS solution for electron density
mms_sol_braginskii_pot	mms_braginskii_m	Function	MMS solution for electrostatic potential
mms_sol_braginskii_psipar	mms_braginskii_m	Function	MMS solution for generalised electromagnetic potential (aixiliary)
mms_sol_braginskii_qe	mms_braginskii_m	Function	MMS solution for electron heat flux
mms_sol_braginskii_qi	mms_braginskii_m	Function	MMS solution for ion heat flux
mms_sol_braginskii_slab_apar	mms_braginskii_slab_m	Function	MMS solution for parallel electromagnetic potential
mms_sol_braginskii_slab_jpar	mms_braginskii_slab_m	Function	MMS solution for parallel current
mms_sol_braginskii_slab_ne	mms_braginskii_slab_m	Function	MMS solution for electron density
mms_sol_braginskii_slab_pot	mms_braginskii_slab_m	Function	MMS solution for electrostatic potential
mms_sol_braginskii_slab_qe	mms_braginskii_slab_m	Function	MMS solution for ion heat flux
mms_sol_braginskii_slab_qi	mms_braginskii_slab_m	Function	MMS solution for ion heat flux
mms_sol_braginskii_slab_te	mms_braginskii_slab_m	Function	MMS solution for electron temperature
mms_sol_braginskii_slab_ti	mms_braginskii_slab_m	Function	MMS solution for ion temperature
mms_sol_braginskii_slab_upar	mms_braginskii_slab_m	Function	MMS solution for parallel ion velocity
mms_sol_braginskii_slab_vort	mms_braginskii_slab_m	Function	MMS solution for generalised vorticity
mms_sol_braginskii_slab_vortbsq	mms_braginskii_slab_m	Function	MMS solution for Boussinesq vorticity
mms_sol_braginskii_te	mms_braginskii_m	Function	MMS solution for electron temperature
mms_sol_braginskii_ti	mms_braginskii_m	Function	MMS solution for ion temperature
mms_sol_braginskii_upar	mms_braginskii_m	Function	MMS solution for parallel ion velocity
mms_sol_braginskii_vort	mms_braginskii_m	Function	MMS solution for generalised vorticity
mms_sol_circular_neutrals_dens	mms_neutrals_circular_m	Function	MMS solution for neutrals density
mms_sol_circular_neutrals_parmom	mms_neutrals_circular_m	Function	MMS solution for neutrals parallel momentum
mms_sol_circular_neutrals_pressure	mms_neutrals_circular_m	Function	MMS solution for neutrals temperature
mms_sol_diffusion	mms_diffusion_m	Function	MMS solution
mms_sol_diffusion_circular	mms_diffusion_circular_m	Function	MMS solution
mms_sol_diffusion_slab	mms_diffusion_slab_m	Function	MMS solution
mms_sol_neutrals_dens	mms_neutrals_m	Function	MMS solution for neutrals density
mms_sol_neutrals_parmom	mms_neutrals_m	Function	MMS solution for neutrals parallel momentum
mms_sol_neutrals_pressure	mms_neutrals_m	Function	MMS solution for neutrals temperature
mms_sol_slab_neutrals_dens	mms_neutrals_slab_m	Function	MMS solution for neutrals density
mms_sol_slab_neutrals_parmom	mms_neutrals_slab_m	Function	MMS solution for neutrals parallel momentum
mms_sol_slab_neutrals_pressure	mms_neutrals_slab_m	Function	MMS solution for neutrals temperature
mms_source_braginskii_circular_continuity	mms_braginskii_circular_m	Function	MMS source for continuity equation
mms_source_braginskii_circular_etemp	mms_braginskii_circular_m	Function	MMS source for electron temperature equation
mms_source_braginskii_circular_itemp	mms_braginskii_circular_m	Function	MMS source for ion temperature equation
mms_source_braginskii_circular_ohm	mms_braginskii_circular_m	Function	MMS source for parallel momentum equation
mms_source_braginskii_circular_parmomentum	mms_braginskii_circular_m	Function	MMS source for parallel momentum equation
mms_source_braginskii_circular_vorticity	mms_braginskii_circular_m	Function	MMS source for continuity equation
mms_source_braginskii_continuity	mms_braginskii_m	Function	MMS source for continuity equation
mms_source_braginskii_etemp	mms_braginskii_m	Function	MMS source for electron temperature equation
mms_source_braginskii_itemp	mms_braginskii_m	Function	MMS source for ion temperature equation
mms_source_braginskii_landau_e	mms_braginskii_m	Function	MMS source for elliptic Landau heat flux equation
mms_source_braginskii_landau_i	mms_braginskii_m	Function	MMS source for elliptic Landau heat flux equation
mms_source_braginskii_ohm	mms_braginskii_m	Function	MMS source for Ohm's law
mms_source_braginskii_parmomentum	mms_braginskii_m	Function	MMS source for parallel momentum equation
mms_source_braginskii_slab_continuity	mms_braginskii_slab_m	Function	MMS source for continuity equation
mms_source_braginskii_slab_etemp	mms_braginskii_slab_m	Function	MMS source for electron temperature equation
mms_source_braginskii_slab_itemp	mms_braginskii_slab_m	Function	MMS source for ion temperature equation
mms_source_braginskii_slab_landau_e	mms_braginskii_slab_m	Function	MMS source for elliptic Landau heat flux equation
mms_source_braginskii_slab_landau_i	mms_braginskii_slab_m	Function	MMS source for elliptic Landau heat flux equation
mms_source_braginskii_slab_ohm	mms_braginskii_slab_m	Function	MMS source for parallel momentum equation
mms_source_braginskii_slab_parmomentum	mms_braginskii_slab_m	Function	MMS source for parallel momentum equation
mms_source_braginskii_slab_vorticity	mms_braginskii_slab_m	Function	MMS source for continuity equation
mms_source_braginskii_slab_vorticitybsq	mms_braginskii_slab_m	Function	MMS source for continuity equation
mms_source_braginskii_vorticity	mms_braginskii_m	Function	MMS source for continuity equation
mms_source_circular_neutrals_dens	mms_neutrals_circular_m	Function	MMS source for neutral density equation
mms_source_circular_neutrals_parmom	mms_neutrals_circular_m	Function	MMS source for neutral parallel momentum equation
mms_source_circular_neutrals_pressure	mms_neutrals_circular_m	Function	MMS source for neutral temperature equation
mms_source_diffusion	mms_diffusion_m	Function	Source corresponding to MMS solution
mms_source_diffusion_circular	mms_diffusion_circular_m	Function	Source corresponding to MMS solution
mms_source_diffusion_slab	mms_diffusion_slab_m	Function	Source corresponding to MMS solution
mms_source_neutrals_dens	mms_neutrals_m	Function	MMS source for Neutrals density equation
mms_source_neutrals_parmom	mms_neutrals_m	Function	MMS source for Neutrals parallel momentum equation
mms_source_neutrals_pressure	mms_neutrals_m	Function	MMS source for Neutrals temperature equation
mms_source_slab_neutrals_dens	mms_neutrals_slab_m	Function	MMS source for neutrals density equation
mms_source_slab_neutrals_parmom	mms_neutrals_slab_m	Function	MMS source for neutrals parallel momentum equation
mms_source_slab_neutrals_pressure	mms_neutrals_slab_m	Function	MMS source for neutrals temperature equation
MmsSolDens	mms_zhdanov_m	Function	MMS solution of density for specific species
MmsSourceDens	mms_zhdanov_m	Function	MMS solution of density for specific species
model_braginskii	model_braginskii_m	Subroutine	Boundary conditions for the braginskii model Boundary conditions for the neutrals model
model_diffusion	model_diffusion_m	Subroutine
model_template	model_template_m	Subroutine	Model template subroutine
model_zhdanov	model_zhdanov_m	Subroutine	Runs Zhdanov model
multistep_storage	test_timestepping_m	Subroutine	Test of multistep_storage_m
nabla_pol_sqrd	inplane_operators_m	Interface
neumann_mirror	neutrals_module_m	Subroutine	Apply "neumann mirroring", i.e. perpendicular neumann zero boundary condition in preparation for implicit solve of a neutrals equation
neutrals_dens_penalisation	penalisation_neutrals_m	Subroutine	Sets the penalisation values for neutrals density
neutrals_parmom_penalisation	penalisation_neutrals_m	Subroutine	Sets the penalisation values for neutrals parallel momentum
neutrals_pressure_penalisation	penalisation_neutrals_m	Subroutine	Sets the penalisation values for neutrals pressure
ohm_advance	ohm_electromagnetic_braginskii_m	Subroutine	Advances Ohm's law in time and solves for parallel elctromagnetic potential and parallel current
on_major_checkpoint	checkpoint_monitor_m	Function	Return current checkpoint state for the major cycle
on_minor_checkpoint	checkpoint_monitor_m	Function	Return current checkpoint state for the minor cycle
par_divb	parallel_map_m	Interface
par_divb_cuda	parallel_map_m	Interface
par_divb_single	parallel_map_m	Interface
par_grad	parallel_map_m	Interface
par_grad_cuda	parallel_map_m	Interface
par_grad_single	parallel_map_m	Interface
parallel_divergence_nonaligned	nonaligned_operators_m	Subroutine	Computes parallel divergence from parallel flux defined at 3D staggered positions Result (pardivu) is defined on full grid Based on symmetric formulation of Guenter's scheme (2nd and 4th order available)
parallel_gradient_nonaligned	nonaligned_operators_m	Subroutine	Computes parallel gradient at 3D staggered positions Based on gradient_3D_staggered
parallel_map_cerfons	test_parallel_map_m	Subroutine	test parallel_map for cerfons equilibrium
parallel_map_circular	test_parallel_map_m	Subroutine	Test of parallel map for circular geometry
parallel_map_dommaschk	test_parallel_map3d_m	Subroutine
parallel_polarisation_advection	polarisation_braginskii_m	Subroutine	Computes the parallel advection part in the vorticity equation
parallel_target_flux_cerfons	test_parallel_target_flux_m	Subroutine	Tests parallel target flux in CERFONS geometry
parallel_target_flux_circular	test_parallel_target_flux_m	Subroutine	Tests parallel target flux in CIRCULAR geometry
parallelisation_finalize	parallelisation_setup_m	Subroutine	Finalises MPI-environment
parallelisation_init	parallelisation_setup_m	Subroutine	Initialises MPI-environment and prints some general information
parse_cmd_filename	startups_m	Subroutine	Parses a filepath from command line
pen_ind_checksum	test_penalisation_m	Function	Compute sum of indices
penalisation_cerfons	test_penalisation_m	Subroutine	Tests penalisation in CIRCULAR geometry
penalisation_circular	test_penalisation_m	Subroutine	Tests penalisation in CIRCULAR geometry
penalisation_circular_stable_trace	test_penalisation_m	Subroutine	Tests penalisation in CIRCULAR geometry via the stable trace method
penalisation_dommaschk	test_penalisation_m	Subroutine	Tests penalisation in DOMMASCHK geometry only VIA_IN_VESSEL and NONE methods
planes_reduction	checksum_braginskii_m	Subroutine	Performs reduction over planes with plane dependent factor
polar_operators_cerfons	test_polar_operators_m	Subroutine	Test of polar operators in circular geometry
polar_operators_circular	test_polar_operators_m	Subroutine	Test of polar operators in circular geometry
polarisation_advance	polarisation_braginskii_m	Subroutine	Advances vorticity in time and solves for pential
polarisation_advection	inplane_operators_m	Interface
poly8_eval	rate_coeff_neutrals_m	Function	Returns polynomial of degree 8, with coefficients pc(0:8), evaluated at x.
poly8x8_eval	rate_coeff_neutrals_m	Function	Returns double polynomial of degree 8x8, with coefficients pc(x,y), evaluated at x and y.
pot_penalisation	penalisation_braginskii_m	Subroutine	Sets the electrostatic potential penalisation values. The boundary condition BND_BRAGTYPE_FLOATING_POTENTIAL_LOCAL should always be combined with a zero-current boundary condition
process_to_file	diagnostics_lineout_m	Subroutine	Main diagnostics computation routine
process_to_file	diagnostics_zonal_m	Subroutine	Main diagnostics computation routine
process_to_file	diagnostics_field_m	Subroutine	Main diagnostics computation routine
process_to_file	diagnostics_scalar_m	Subroutine	Main diagnostics computation routine
project_lineout	diagnostics_lineout_m	Subroutine	Project input onto lineout diagnostic dimension nrho
project_scalar	diagnostics_scalar_m	Subroutine	Project input onto scalar diagnostic dimension nrho
project_zonal	diagnostics_zonal_m	Subroutine	Project input onto zonal diagnostic dimension nrho
psipar_penalisation	penalisation_braginskii_m	Subroutine	Sets the penalisation values for the modified electromagnetic potential. Currently, the only option is to set a dirichelet-zero value, which penalised jpar and apar to zero at the boundary
read_all_params_braginskii	facade_params_m	Subroutine	Reads all parameters related with Braginskii model
read_all_params_diffusion	params_diffusion_m	Subroutine	Reads all parameters related with diffusion model
read_all_params_neutrals	facade_params_m	Subroutine	Reads all parameters related with Neutrals model
read_all_params_template	params_template_m	Subroutine	Initializes all parameters of template model (except for paths)
read_build_static	static_data_m	Subroutine	Reads parameters that control build of static data
read_netcdf_equilibrium_storage	equilibrium_storage_m	Interface
read_netcdf_iol_source	iol_source_m	Interface
read_netcdf_mask_data	mask_data_m	Interface
read_netcdf_parallel_map	parallel_map_m	Interface
read_netcdf_penalisation	penalisation_m	Interface
read_netcdf_perp_bnd_flux	perp_bnd_flux_m	Interface
read_netcdf_polars	polars_m	Interface
read_netcdf_polygon_in_mesh	polygon_in_mesh_m	Interface
read_netcdf_target_markers	parallel_target_flux_m	Interface
read_netcdf_variable	variable_m	Interface
read_params_boundaries_parpen	params_diffusion_boundaries_parpen_m	Subroutine	Reads parameters related with boundaries_parpen
read_params_boundaries_perp	params_diffusion_boundaries_perp_m	Subroutine	Reads parameters related with boundaries_perp
read_params_brag_boundaries_parpen	params_brag_boundaries_parpen_m	Subroutine	Reads parameters related with brag_boundaries_parpen
read_params_brag_boundaries_perp	params_brag_boundaries_perp_m	Subroutine	Reads parameters related with brag_boundaries_perp
read_params_brag_buffer	params_brag_buffer_m	Subroutine	Reads parameters related with brag_buffer
read_params_brag_floors	params_brag_floors_m	Subroutine	Reads parameters related with brag_floors
read_params_brag_init_select	params_brag_init_select_m	Subroutine	Reads parameters related with brag_init_select
read_params_brag_model	params_brag_model_m	Subroutine	Reads parameters related with brag_model
read_params_brag_numdiss	params_brag_numdiss_m	Subroutine	Reads parameters related with brag_numdiss
read_params_brag_pardiss_model	params_brag_pardiss_model_m	Subroutine	Reads parameters related with brag_pardiss_model
read_params_brag_sources_external_select	params_brag_sources_external_select_m	Subroutine	Reads parameters related with brag_sources_external_select
read_params_brag_switches	params_brag_switches_m	Subroutine	Reads parameters related with brag_switches
read_params_evol_apar_shift	params_apar_shift_m	Subroutine	Reads parameters related to apar_shift model
read_params_feature_selection	params_feature_selection_m	Subroutine	Reads parameters related with feature_selection
read_params_hsolver	params_hsolver_m	Subroutine	Reads parameters related with hsolver
read_params_impy_coronal	params_impy_coronal_m	Subroutine	Reads parameters related with impy_coronal
read_params_init_select	params_diffusion_init_select_m	Subroutine	Reads parameters related with selection of initial state in diffusion model
read_params_iol	iol_source_m	Interface
read_params_lineout	diagnostics_lineout_m	Interface
read_params_mms	params_diffusion_mms_m	Subroutine	Reads parameters related with mms in diffusion model
read_params_model	params_diffusion_model_m	Subroutine	Reads parameters related with diffusion model
read_params_neut_boundaries_parpen	params_neut_boundaries_parpen_m	Subroutine	Reads parameters related with neut_boundaries_parpen
read_params_neut_boundaries_perp	params_neut_boundaries_perp_m	Subroutine	Reads parameters related with neut_boundaries_perp
read_params_neut_data_paths	params_neut_data_paths_m	Subroutine	Reads parameters related with neut_data_paths_m
read_params_neut_floors	params_neut_floors_m	Subroutine	Reads parameters related with neut_floors
read_params_neut_init_select	params_neut_init_select_m	Subroutine	Reads parameters related with neut_init_select
read_params_neut_model	params_neut_model_m	Subroutine	Reads parameters related with neutrals model
read_params_neut_switches	params_neut_switches_m	Subroutine	Reads parameters related with neut_switches
read_params_template_features	params_template_m	Interface
read_params_template_model	params_template_m	Interface
read_params_template_parbnd	params_template_m	Interface
read_params_template_paths	params_template_m	Interface
read_params_template_tstep	params_template_m	Interface
read_params_timestep	params_zhdanov_general_m	Subroutine	Reads parameters related with timestepping
read_params_tstep	params_diffusion_tstep_m	Subroutine	Reads parameters related with timestepping in diffusion model
read_params_tstep	params_tstep_m	Subroutine	Reads parameters related with timestepping in Braginskii model
read_paths	params_diffusion_m	Subroutine	Reads paths to parameter files
read_paths	facade_params_m	Subroutine	Reads paths to parameter files
read_snaps	snapshot_m	Subroutine	Reads snapshot
read_snaps_last	snapshot_m	Subroutine	Reads last available snapshot
read_template_state_netcdf	state_template_m	Interface
read_zhdanov_controls	params_zhdanov_general_m	Subroutine	Reads parameters related with control of Zhdanov model
read_zhdanov_params	params_zhdanov_species_m	Subroutine	Reads parameters related with physical model
read_zhdanov_params	params_zhdanov_general_m	Subroutine	Reads parameters related with physical model
rhs_fun_for_rk	timestep_template_m	Subroutine	Evaluates right hand side (explicit terms) for use in Runge-Kutta time-step integrator Be aware, that this function changes the state of the template model. For interface, see the corresponding Runge-Kutta module
runge_kutta	test_timestepping_m	Subroutine	Test of module runge_kutta_m integrates - dy_1/dtau = y --> y_1(tau) = exp(tau) - dy_2/dtau = 2tauy --> y_2(tau) = exp(tau^2) until tau = 2 Analytic result of y_1(2) = exp(2) ~ 7.38905609893 Analytic result of y_2(2) = exp(4) ~ 54.5981500331
say_hello	comm_handler_m	Subroutine
set_blob_aligned	variable_m	Interface
set_blob_toroidal	variable_m	Interface
set_coeffs	sources_external_m	Subroutine	Compute the coefficient that matches the total input rate
set_intorder	parallel_map_m	Subroutine	Set interpolation order
set_parameters_map	parallel_map_m	Interface
set_parameters_penalisation	penalisation_m	Interface
set_parameters_polars	polars_m	Interface
set_rank_info_writer	parallelisation_setup_m	Subroutine	Sets rank_info_writer as rank that performs info output within GRILLIX
set_toroidal_location	parallel_map_m	Interface
set_xorder	parallel_map_m	Subroutine	Set order of subcell splitting
setup_implicit_solve	neutrals_module_m	Subroutine	Setup equation system for a neutrals diffusion equation on target variable u by setting lambda, xi, co, rhs coefficients in the helmholtz operator
shift_storage	multistep_m	Interface
snaps_average	snapshots_helpers_m	Subroutine	Averages an variable in the snapshots from nsnaps_start until nsnaps_end
solve_aligned3d	solver_aligned3d_m	Interface
solve_aligned3d_adjoint	solver_aligned3d_m	Interface
spline_grid_init	iol_source_m	Interface
start_comm_halos	variable_m	Interface
start_comm_planes	communication_planes_m	Subroutine	Starts communication among two planes
static_all_components_init	static_data_m	Subroutine	Initializes a complete static data set with all components
static_bnd_flux_init	static_data_m	Interface
static_equi_init	static_data_m	Interface
static_equi_on_mesh_init	static_data_m	Interface
static_field_solver_init	static_data_m	Interface
static_map_init	static_data_m	Interface
static_masks_init	static_data_m	Interface
static_multigrid_init	static_data_m	Interface
static_parbnd_immersed_init	static_data_m	Interface
static_parbnd_taylor_init	static_data_m	Interface
static_polars_init	static_data_m	Interface
surface_average	polar_operators_m	Subroutine	Computes zonal average of quantity
test_apar_fluct_evaluate	test_apar_fluct_evaluate_m	Subroutine	Tests evaluate_apar_fluct function in CIRCULAR geometry
test_apar_shift	test_apar_shift_m	Subroutine	Tests apar_shift module in CIRCULAR geometry
test_checkpoint_monitor	test_checkpoint_monitor_m	Subroutine	Test of checkpoint monitor
test_comm_handler	test_comm_handler_m	Subroutine	test of communication handler
test_communication_planes	test_communication_planes_m	Subroutine	Tests communiacationa among planes with varying dimensions
test_masked_data_cerfons	test_masked_data_m	Subroutine	Test of masked data in cerfons geometry
test_parallel_map_operators_cerfons	test_parallel_map_operators_m	Subroutine	Test of parallel operators in CERFONS geometry
test_parallel_map_operators_circular	test_parallel_map_operators_m	Subroutine	Test of parallel operators in circular geometry
test_parallel_map_operators_dommaschk	test_parallel_map_operators_m	Subroutine	Test of parallel operators in DOMMASCHK geometry
test_params_diffusion_boundaries_parpen	test_params_diffusion_m	Subroutine	Tests params_diffusion_boundaries_parpen
test_params_diffusion_boundaries_perp	test_params_diffusion_m	Subroutine	Tests params_diffusion_boundaries_perp
test_params_diffusion_init_select	test_params_diffusion_m	Subroutine	Tests params_diffusion_boundaries_parpen
test_params_diffusion_mms	test_params_diffusion_m	Subroutine	Tests params_diffusion_mms
test_params_diffusion_model	test_params_diffusion_m	Subroutine	Tests params_diffusion_model
test_params_diffusion_parsolver	test_params_diffusion_m	Subroutine	Tests params_diffusion_parsolver
test_params_diffusion_tstep	test_params_diffusion_m	Subroutine	Tests params_diffusion_tstep
test_polygon_in_mesh_cerfons	test_polygon_in_mesh_m	Subroutine	Tests polygon on mesh in CERFONS geometry
test_variable	test_variable_m	Subroutine	Tests variable data structure
test_variable_set	test_variable_m	Subroutine	Tests set_blob_toroidal and set_blob_aligned of variables
timestep_apar_shift	model_apar_shift_m	Subroutine	Advances apar_shift from t to t+1
timestep_braginskii	timestep_braginskii_m	Subroutine	Evolves variables a single time-step according to BRAGINSKII model ... parallel mappings - map to canonical
timestep_diffusion	timestep_diffusion_m	Subroutine	Evolves variable a single time-step according to anisotropic diffusion model
timestep_neutrals	neutrals_module_m	Subroutine	Advances neutrals quantities from t to t+1
timestep_template	timestep_template_m	Subroutine	Model template subroutine Yet a simple in-plane diffusion equation with first order explicit Euler scheme is implemented
timestep_zhdanov	timestep_zhdanov_m	Subroutine	Evolves variable a single time-step according to zhdanov model
total_volume	diagnostics_helpers_m	Function	Compute total volume over all mesh points
upar_penalisation	penalisation_braginskii_m	Subroutine	Sets the parallel velocity penalisation values.
update_derived_fields	state_template_m	Subroutine	Updates derived fields upar = parmom /dens_(stag) tion = pion / dens_(cano)
update_iol_source	iol_source_m	Interface
upstream_cano_from_cano_bwd	parallel_map_m	Interface
upstream_cano_from_cano_bwd2	parallel_map_m	Interface
upstream_cano_from_cano_bwd2_single	parallel_map_m	Interface
upstream_cano_from_cano_bwd_single	parallel_map_m	Interface
upstream_cano_from_cano_fwd	parallel_map_m	Interface
upstream_cano_from_cano_fwd2	parallel_map_m	Interface
upstream_cano_from_cano_fwd2_single	parallel_map_m	Interface
upstream_cano_from_cano_fwd_single	parallel_map_m	Interface
upstream_stag_from_stag_bwd	parallel_map_m	Interface
upstream_stag_from_stag_bwd_single	parallel_map_m	Interface
upstream_stag_from_stag_fwd	parallel_map_m	Interface
upstream_stag_from_stag_fwd_single	parallel_map_m	Interface
vort_penalisation	penalisation_braginskii_m	Subroutine	Sets the vorticity penalisation values.
write_all_params_braginskii	facade_params_m	Subroutine	Writes all parameters related with Braginskii model
write_all_params_diffusion	params_diffusion_m	Subroutine	Writes all parameters related with diffusion model
write_all_params_neutrals	facade_params_m	Subroutine	Writes all parameters related with Neutrals model
write_ascii_iol_source	iol_source_m	Interface
write_diagnostics	diagnostics_group_m	Subroutine	Write all diagnostics
write_netcdf_diagnostic_variable	diagnostic_variable_m	Subroutine	Writes variable to netcdf file
write_netcdf_equilibrium_storage	equilibrium_storage_m	Interface
write_netcdf_iol_source	iol_source_m	Interface
write_netcdf_mask_data	mask_data_m	Interface
write_netcdf_parallel_map	parallel_map_m	Interface
write_netcdf_penalisation	penalisation_m	Interface
write_netcdf_perp_bnd_flux	perp_bnd_flux_m	Interface
write_netcdf_polars	polars_m	Interface
write_netcdf_polygon_in_mesh	polygon_in_mesh_m	Interface
write_netcdf_target_markers	parallel_target_flux_m	Interface
write_netcdf_variable	variable_m	Interface
write_params_apar_shift	params_apar_shift_m	Subroutine	Writes parameters related to mshift
write_params_boundaries_parpen	params_diffusion_boundaries_parpen_m	Subroutine	Writes parameters related with boundaries_parpen
write_params_boundaries_perp	params_diffusion_boundaries_perp_m	Subroutine	Writes parameters related with boundaries_perp
write_params_brag_boundaries_parpen	params_brag_boundaries_parpen_m	Subroutine	Reads parameters related with brag_boundaries_parpen
write_params_brag_boundaries_perp	params_brag_boundaries_perp_m	Subroutine	Reads parameters related with brag_boundaries_perp
write_params_brag_buffer	params_brag_buffer_m	Subroutine	Reads parameters related with brag_buffer
write_params_brag_floors	params_brag_floors_m	Subroutine	Reads parameters related with brag_floors
write_params_brag_init_select	params_brag_init_select_m	Subroutine	Reads parameters related with brag_init_select
write_params_brag_model	params_brag_model_m	Subroutine	Reads parameters related with brag_model
write_params_brag_numdiss	params_brag_numdiss_m	Subroutine	Reads parameters related with brag_numdiss
write_params_brag_pardiss_model	params_brag_pardiss_model_m	Subroutine	Reads parameters related with brag_pardiss_model
write_params_brag_sources_external_select	params_brag_sources_external_select_m	Subroutine	Reads parameters related with brag_sources_external_select
write_params_brag_switches	params_brag_switches_m	Subroutine	Reads parameters related with switches
write_params_feature_selection	params_feature_selection_m	Subroutine	Reads parameters related with feature_selection
write_params_hsolver	params_hsolver_m	Subroutine	Writes parameters related with hsolver
write_params_impy_coronal	params_impy_coronal_m	Subroutine	Reads parameters related with impy_coronal
write_params_init_select	params_diffusion_init_select_m	Subroutine	Reads parameters related with selection of initial state in diffusion model
write_params_lineout	diagnostics_lineout_m	Interface
write_params_mms	params_diffusion_mms_m	Subroutine	Reads parameters related with mms in diffusion model
write_params_model	params_diffusion_model_m	Subroutine	Reads parameters related with diffusion model
write_params_neut_boundaries_parpen	params_neut_boundaries_parpen_m	Subroutine	Reads parameters related with neut_boundaries_parpen
write_params_neut_boundaries_perp	params_neut_boundaries_perp_m	Subroutine	Reads parameters related with neutral neut_boundaries_perp
write_params_neut_data_paths	params_neut_data_paths_m	Subroutine	Reads parameters related with neut_data_paths_m
write_params_neut_floors	params_neut_floors_m	Subroutine	Reads parameters related with neut_floors
write_params_neut_init_select	params_neut_init_select_m	Subroutine	Reads parameters related with neut_init_select
write_params_neut_model	params_neut_model_m	Subroutine	Reads parameters related with neutrals model
write_params_neut_switches	params_neut_switches_m	Subroutine	Reads parameters related with neut_switches
write_params_tstep	params_diffusion_tstep_m	Subroutine	Reads parameters related with timestepping in diffusion model
write_params_tstep	params_tstep_m	Subroutine	Reads parameters related with timestepping in Braginskii model
write_paths	params_diffusion_m	Subroutine	WWrites paths to parameter files
write_paths	facade_params_m	Subroutine	WWrites paths to parameter files
write_snaps	model_apar_shift_m	Subroutine	Writes apar_shift to snapshots
write_snaps	snapshot_m	Subroutine	Writes snapshot
write_template_state_netcdf	state_template_m	Interface
xplane_init	iol_source_m	Interface
zonal_neumann_core	boundaries_braginskii_m	Subroutine	Sets Zonal Neumann boundary conditions on u (or v), u_b = , after local Neumann b.c. d/dr u_b_N = 0 had been applied to u. u is flux-surface averaged and the core value is used as a Dirichlet b.c.. For data handling reasons, in- and output can be separated with variable v = .