Procedures

Procedure	Location	Procedure Type	Description
add_bmatrix_terms	mod_matrix_manager	Interface
add_conduction_matrix_terms	mod_matrix_manager	Interface
add_conduction_matrix_terms_bfield	smod_conduction_matrix	Subroutine
add_element	mod_matrix_structure	Subroutine	Adds a given element at a certain (row, column) position to the matrix datastructure. Elements that are zero are not added, sanity checks are done on the row and column indices.
add_flow_matrix_terms	mod_matrix_manager	Interface
add_hall_bmatrix_terms	mod_matrix_manager	Interface
add_hall_matrix_terms	mod_matrix_manager	Interface
add_heatloss_matrix_terms	mod_matrix_manager	Interface
add_natural_conduction_terms	mod_natural_boundaries	Interface
add_natural_conduction_terms_bfield	smod_natural_bounds_conduction	Subroutine
add_natural_flow_terms	mod_natural_boundaries	Interface
add_natural_hall_Bterms	mod_natural_boundaries	Interface
add_natural_hall_terms	mod_natural_boundaries	Interface
add_natural_regular_terms	mod_natural_boundaries	Interface
add_natural_resistive_terms	mod_natural_boundaries	Interface
add_natural_viscosity_terms	mod_natural_boundaries	Interface
add_node	mod_matrix_elements	Subroutine
add_node	mod_matrix_row	Subroutine	Adds a new node to the linked list with a given column index and value.
add_regular_matrix_terms	mod_matrix_manager	Interface
add_resistive_matrix_terms	mod_matrix_manager	Interface
add_to_node_element	mod_matrix_node	Subroutine	Adds a given element to the node element, does type-checking of the polymorphic element given. Allowed types are complex, real, integer.
add_to_quadblock	mod_build_quadblock	Subroutine	This routine builds the quadblock at one particular grid point in the Gaussian grid and for one particular Gaussian weight. For a 2x2 block at index $(i, j)$ in the top-left block we have $(2i, 2j)$ as index of the bottom-right corner of the 2x2 block. The other corners are then filled by subtracting one from an index.
add_viscosity_matrix_terms	mod_matrix_manager	Interface
adiabatic_homo_eq	mod_equilibrium	Interface	interface to the different equilibrium submodules
append_node	mod_matrix_row	Subroutine	Subroutine to append a new node to an already existing list of nodes. A new node is created, appended, and the tail is updated.
apply_boundary_conditions	mod_boundary_manager	Subroutine
apply_essential_boundaries_left	mod_essential_boundaries	Subroutine
apply_essential_boundaries_right	mod_essential_boundaries	Subroutine
apply_natural_boundaries_left	mod_natural_boundaries	Subroutine
apply_natural_boundaries_right	mod_natural_boundaries	Subroutine
are_set	mod_units	Function
arnoldi	mod_solvers	Interface	interface to the different solution methods implemented in submodules
array_to_banded	mod_transform_matrix	Interface
array_to_complex_banded	mod_transform_matrix	Subroutine	Converts a given array to a banded datastructure.
array_to_complex_hermitian_banded	mod_transform_matrix	Subroutine	Converts a given array to a Hermitian banded datastructure.
array_to_hermitian_banded	mod_transform_matrix	Interface
array_to_matrix	mod_transform_matrix	Interface
assemble	mod_base_efs	Subroutine
assemble	mod_eigenfunctions	Subroutine
assemble	mod_derived_efs	Subroutine
assemble	mod_state_vector	Subroutine
assemble_eigenfunction	mod_ef_assembly	Function
assert	mod_assert	Subroutine	Utility function used by assert.fpp's `assert` macro. Read more…
ax_values	mod_solar_atmosphere	Function
B0	smod_equil_resistive_homo	Function
B0	smod_equil_harris_sheet	Function
B0	smod_equil_resistive_tearing_flow	Function
B0	smod_equil_resistive_tearing	Function
B01_and_cylindrical	mod_inspections	Function
B02	smod_equil_MRI	Function
B02	smod_equil_kelvin_helmholtz_cd	Function
B02	smod_equil_interchange_modes	Function
B02	smod_equil_resonant_absorption	Function
B02	smod_equil_flow_driven_instabilities	Function
B02	smod_equil_resistive_homo	Function
B02	smod_equil_rotating_plasma_cylinder	Function
B02	smod_equil_adiabatic_homo	Function
B02	smod_equil_harris_sheet	Function
B02	smod_equil_suydam_cluster	Function
B02	smod_equil_resistive_tearing_flow	Function
B02	smod_numerical	Function
B02	mod_solar_atmosphere	Function
B02	smod_equil_magnetothermal_instabilities	Function
B02	smod_equil_isothermal_atmosphere	Function
B02	smod_equil_resistive_tearing	Function
B02	smod_equil_discrete_alfven	Function
B02	smod_equil_tc_pinch	Function
B02	smod_equil_gold_hoyle	Function
B02	smod_equil_constant_current	Function
B02	smod_equil_internal_kink_instability	Function
B03	smod_equil_RTI_theta_pinch	Function
B03	smod_equil_MRI	Function
B03	smod_equil_kelvin_helmholtz_cd	Function
B03	smod_equil_coronal_flux_tube	Function
B03	smod_equil_interchange_modes	Function
B03	smod_equil_resonant_absorption	Function
B03	smod_equil_flow_driven_instabilities	Function
B03	smod_equil_photospheric_flux_tube	Function
B03	smod_equil_resistive_homo	Function
B03	smod_equil_rotating_plasma_cylinder	Function
B03	smod_equil_adiabatic_homo	Function
B03	smod_equil_harris_sheet	Function
B03	smod_equil_suydam_cluster	Function
B03	smod_equil_gravito_mhd	Function
B03	smod_equil_resistive_tearing_flow	Function
B03	smod_numerical	Function
B03	smod_user_defined	Function
B03	mod_solar_atmosphere	Function
B03	smod_equil_isothermal_atmosphere	Function
B03	smod_equil_resistive_tearing	Function
B03	smod_equil_discrete_alfven	Function
B03	smod_equil_gold_hoyle	Function
B03	smod_equil_constant_current	Function
B03	smod_equil_internal_kink_instability	Function
banded_matrix_x_vector	mod_banded_operations	Function	Calculates the matrix-vector product of a general complex banded matrix and a complex vector. Uses the level 2 BLAS routine `zgbmv`.
banded_to_array	mod_transform_matrix	Interface
banded_to_complex_array	mod_transform_matrix	Function	Converts a banded datastructure to a full complex array.
basis_function	mod_basis_functions	Interface
build_matrices	mod_matrix_manager	Subroutine	The quadblock is shifted along the main (tri)diagonal. We add `dim_subblock` instead of `dim_quadblock` to the indices, due to overlapping of the bottom-right part of the quadblock with the top-left part of the next grid interval. Read more…
bx_values	mod_solar_atmosphere	Function
can_calculate_pp_quantities	mod_derived_ef_names	Function
can_get_B1	mod_derived_ef_names	Function
can_get_B2	mod_derived_ef_names	Function
can_get_B3	mod_derived_ef_names	Function
can_get_B_pp	mod_derived_ef_names	Function
can_get_curl_B_i	mod_derived_ef_names	Function
can_get_curl_B_pp	mod_derived_ef_names	Function
can_get_curl_v_1	mod_derived_ef_names	Function
can_get_curl_v_2	mod_derived_ef_names	Function
can_get_curl_v_3	mod_derived_ef_names	Function
can_get_curl_v_pp	mod_derived_ef_names	Function
can_get_dB1	mod_derived_ef_names	Function
can_get_div_B	mod_derived_ef_names	Function
can_get_div_v	mod_derived_ef_names	Function
can_get_entropy	mod_derived_ef_names	Function
can_get_v_pp	mod_derived_ef_names	Function
cast_node_element_to_complex	mod_matrix_elements	Function
character_array_tostring	mod_logging	Function
check_bfield	mod_settings	Subroutine
check_eigenfunction_subset_params	mod_input	Subroutine	Called when the eigenfunction subset selection is enabled, this checks if the global variables are properly set.
check_if_thermal_balance_needs_enforcing	mod_heatloss	Subroutine
cleanup	legolas	Subroutine	Deallocates all main variables, then calls the cleanup routines of all relevant subroutines to do the same thing.
complex_is_equal	mod_check_values	Function	Equality check between complex values
complex_is_zero	mod_check_values	Function	Checks if complex values are zero
complex_tostring	mod_logging	Function
constant_current_eq	mod_equilibrium	Interface	interface to the different equilibrium submodules
contains_inf_complex	mod_check_values	Function	checks a given complex value/array/matrix for infinity.
contains_inf_real	mod_check_values	Function	checks a given real value/array/matrix for infinity.
contains_NaN	mod_inspections	Function
contains_NaN_complex	mod_check_values	Function	Checks a given complex value/array/matrix for NaN.
contains_NaN_real	mod_check_values	Function	Checks a given real value/array/matrix for NaN.
contains_negative	mod_inspections	Function
contains_on_component	mod_state_vector	Function
contains_on_name	mod_state_vector	Function
continuity_condition	mod_inspections	Function
copy	mod_matrix_structure	Function	Dedicated function to copy a matrix structure into a new matrix structure. The datastructure contains pointers, such that simply setting matrix1 = matrix2 may result in pointer target losses (and wrong results). Read more…
coronal_flux_tube_eq	mod_equilibrium	Interface	interface to the different equilibrium submodules
couette_flow_eq	mod_equilibrium	Interface	interface to the different equilibrium submodules
cputic	mod_timing	Subroutine	Subroutine to start a CPU timer. Read more…
cputoc	mod_timing	Subroutine	Subroutine to end a CPU timer. Read more…
create_and_set_derived_state_vector	mod_derived_ef_names	Function
create_atmosphere_curves	mod_solar_atmosphere	Subroutine	Interpolates the atmospheric tables to the desired resolution. The temperature derivative is obtained numerically.
create_datfile	mod_output	Subroutine
create_first_node	mod_matrix_row	Subroutine	Subroutine to add the first node to the linked list. Allocates a new node and sets both the head and tail to this node.
dB02	smod_equil_MRI	Function
dB02	smod_equil_kelvin_helmholtz_cd	Function
dB02	smod_equil_interchange_modes	Function
dB02	smod_equil_flow_driven_instabilities	Function
dB02	smod_equil_rotating_plasma_cylinder	Function
dB02	smod_equil_harris_sheet	Function
dB02	smod_equil_suydam_cluster	Function
dB02	smod_equil_resistive_tearing_flow	Function
dB02	smod_numerical	Function
dB02	mod_solar_atmosphere	Function
dB02	smod_equil_magnetothermal_instabilities	Function
dB02	smod_equil_resistive_tearing	Function
dB02	smod_equil_discrete_alfven	Function
dB02	smod_equil_tc_pinch	Function
dB02	smod_equil_gold_hoyle	Function
dB02	smod_equil_constant_current	Function
dB02	smod_equil_internal_kink_instability	Function
dB03	smod_equil_RTI_theta_pinch	Function
dB03	smod_equil_MRI	Function
dB03	smod_equil_interchange_modes	Function
dB03	smod_equil_flow_driven_instabilities	Function
dB03	smod_equil_harris_sheet	Function
dB03	smod_equil_suydam_cluster	Function
dB03	smod_equil_gravito_mhd	Function
dB03	smod_equil_resistive_tearing_flow	Function
dB03	smod_numerical	Function
dB03	mod_solar_atmosphere	Function
dB03	smod_equil_resistive_tearing	Function
dB03	smod_equil_gold_hoyle	Function
dB03	smod_equil_internal_kink_instability	Function
ddB02	smod_equil_harris_sheet	Function
ddB02	smod_equil_resistive_tearing_flow	Function
ddB02	smod_numerical	Function
ddB02	smod_equil_resistive_tearing	Function
ddB02	smod_equil_tc_pinch	Function
ddB03	smod_equil_harris_sheet	Function
ddB03	smod_equil_resistive_tearing_flow	Function
ddB03	smod_numerical	Function
ddB03	smod_equil_resistive_tearing	Function
ddhcubic	mod_basis_functions	Function
ddspline	mod_state_vector_component	Subroutine
ddT0	smod_numerical	Function
ddv02	smod_numerical	Function
ddv02	smod_user_defined	Function
ddv02	smod_equil_taylor_couette	Function
ddv02	smod_equil_tc_pinch	Function
ddv03	smod_numerical	Function
deallocate_cooling_curves	mod_cooling_curves	Subroutine
deallocate_derived_ef_module_variables	mod_derived_efs	Subroutine
deallocate_input	mod_arrays	Subroutine	Deallocates this module's arrays. Called in main as part of cleanup.
debug	mod_logging	Subroutine
delete	mod_equilibrium_settings	Subroutine
delete	mod_state_vector_component	Subroutine
delete	mod_thermal_conduction	Subroutine
delete	mod_matrix_elements	Subroutine
delete	mod_gravity	Subroutine
delete	mod_grid_settings	Subroutine
delete	mod_background	Subroutine
delete	mod_io_settings	Subroutine
delete	mod_bg_temperature	Subroutine
delete	mod_bg_velocity	Subroutine
delete	mod_settings	Subroutine
delete	mod_matrix_node	Subroutine	Destructor, deallocates the node attributes.
delete	mod_hall	Subroutine
delete	mod_base_efs	Subroutine
delete	mod_bg_density	Subroutine
delete	mod_radiative_cooling	Subroutine
delete	mod_grid	Subroutine
delete	mod_resistivity	Subroutine
delete	mod_solver_settings	Subroutine
delete	mod_eigenfunctions	Subroutine
delete	mod_matrix_element_node	Subroutine
delete	mod_derived_efs	Subroutine
delete	mod_heating	Subroutine
delete	mod_state_vector	Subroutine
delete	mod_heatloss	Subroutine
delete	mod_physics	Subroutine
delete	mod_bg_magnetic	Subroutine
delete_matrix	mod_matrix_structure	Subroutine	Deallocates the matrix datastructure, nullifies all corresponding pointers and deallocates the various nodes in the rows.
delete_node_from_row	mod_matrix_row	Subroutine	Deletes a given node from the current row.
delete_row	mod_matrix_row	Subroutine	Deletes a given linked list row by recursively iterating over all nodes. Nullifies the pointers and deallocates the elements.
derived_ef_func	mod_derived_efs	Interface
derived_state_vector_is_set	mod_settings	Function
destroy	mod_banded_matrix	Subroutine	Destructor, deallocates the datastructure.
destroy	mod_banded_matrix_hermitian	Subroutine	Destructor, deallocates the datastructure.
destroy	mod_arpack_type	Subroutine	Destructor, deallocates variables.
dfx	smod_equil_RTI_theta_pinch	Function
dhcubic	mod_basis_functions	Function
dhquad	mod_basis_functions	Function
dimensions_are_valid	mod_banded_matrix	Function	Checks if the given matrix dimensions are valid. For now, we only accept square matrices. Returns `.true.` if `rows` equals `cols`, `.false.` otherwise.
disable	mod_conduction_settings	Subroutine
disable	mod_viscosity_settings	Subroutine
disable	mod_resistivity_settings	Subroutine
disable	mod_cooling_settings	Subroutine
disable	mod_hall_settings	Subroutine
disable	mod_gravity_settings	Subroutine
disable	mod_flow_settings	Subroutine
disable	mod_heating_settings	Subroutine
disable_prefix	mod_logging	Subroutine
discrete_alfven_eq	mod_equilibrium	Interface	interface to the different equilibrium submodules
DJ0	smod_equil_suydam_cluster	Function
dJ0	smod_equil_internal_kink_instability	Function
DJ1	smod_equil_suydam_cluster	Function
dJ1	smod_equil_internal_kink_instability	Function
do_eigenvalue_problem_allocations	legolas	Subroutine
do_equilibrium_inspections	mod_inspections	Subroutine
dp0	smod_equil_MRI	Function
dp0	smod_equil_discrete_alfven	Function
dp0	smod_equil_constant_current	Function
dp_func	mod_inspections	Interface
drho0	smod_equil_RTI_theta_pinch	Function
drho0	smod_equil_MRI	Function
drho0	smod_equil_interchange_modes	Function
drho0	smod_equil_resonant_absorption	Function
drho0	smod_equil_flow_driven_instabilities	Function
drho0	smod_equil_gravito_mhd	Function
drho0	smod_numerical	Function
drho0	smod_equil_gravito_acoustic	Function
drho0	smod_user_defined	Function
drho0	mod_solar_atmosphere	Function	Sets density derivative using the differential equation to ensure force balance, instead of relying on numerical differentiation.
drho0	smod_equil_magnetothermal_instabilities	Function
drho0	smod_equil_isothermal_atmosphere	Function
drho0	smod_equil_discrete_alfven	Function
drho0	smod_equil_internal_kink_instability	Function
dspline	mod_state_vector_component	Subroutine
dT0	smod_equil_MRI	Function
dT0	smod_equil_kelvin_helmholtz_cd	Function
dT0	smod_equil_flow_driven_instabilities	Function
dT0	smod_equil_rotating_plasma_cylinder	Function
dT0	smod_equil_harris_sheet	Function
dT0	smod_equil_suydam_cluster	Function
dT0	smod_numerical	Function
dT0	mod_solar_atmosphere	Function
dT0	smod_equil_discrete_alfven	Function
dT0	smod_equil_taylor_couette	Function
dT0	smod_equil_tc_pinch	Function
dT0	smod_equil_constant_current	Function
dT0	smod_equil_internal_kink_instability	Function
dv02	smod_equil_RTI_theta_pinch	Function
dv02	smod_equil_MRI	Function
dv02	smod_equil_flow_driven_instabilities	Function
dv02	smod_equil_rotating_plasma_cylinder	Function
dv02	smod_equil_resistive_tearing_flow	Function
dv02	smod_numerical	Function
dv02	smod_user_defined	Function
dv02	smod_equil_couette_flow	Function
dv02	smod_equil_taylor_couette	Function
dv02	smod_equil_tc_pinch	Function
dv03	smod_equil_kelvin_helmholtz_cd	Function
dv03	smod_equil_flow_driven_instabilities	Function
dv03	smod_equil_suydam_cluster	Function
dv03	smod_numerical	Function
dv03	smod_equil_couette_flow	Function
dv03	smod_equil_internal_kink_instability	Function
dx_func_i	mod_grid	Interface
eigenvalue_is_inside_subset_radius	mod_eigenfunctions	Function
enable	mod_resistivity_settings	Subroutine
enable	mod_cooling_settings	Subroutine
enable	mod_hall_settings	Subroutine
enable	mod_gravity_settings	Subroutine
enable	mod_flow_settings	Subroutine
enable	mod_heating_settings	Subroutine
enable_cooling	mod_physics_settings	Subroutine
enable_electron_inertia	mod_hall_settings	Subroutine
enable_flow	mod_physics_settings	Subroutine
enable_gravity	mod_physics_settings	Subroutine
enable_hall	mod_physics_settings	Subroutine
enable_heating	mod_physics_settings	Subroutine
enable_para_conduction	mod_conduction_settings	Subroutine
enable_parallel_conduction	mod_physics_settings	Subroutine
enable_perp_conduction	mod_conduction_settings	Subroutine
enable_perpendicular_conduction	mod_physics_settings	Subroutine
enable_prefix	mod_logging	Subroutine
enable_resistivity	mod_physics_settings	Subroutine
enable_viscosity	mod_physics_settings	Subroutine
enable_viscous_heating	mod_viscosity_settings	Subroutine
end_timer	mod_timing	Function
energy_balance_condition	mod_inspections	Function
error	mod_logging	Subroutine
fetch_boundary_quadblock	mod_natural_boundaries	Subroutine
find_index_in_character_array	mod_get_indices	Function	Function to locate the index of a given character in a character array. Iterates over the elements and returns on the first hit, if no match was found zero is returned.
find_indices_in_character_array	mod_get_indices	Function	Function to locate the indices of an array of characters in another character array. Returns the indices of the first hit, it no match was found zero is returned.
flow_driven_instabilities_eq	mod_equilibrium	Interface	interface to the different equilibrium submodules
force_balance_1_condition	mod_inspections	Function
force_balance_2_condition	mod_inspections	Function
force_balance_3_condition	mod_inspections	Function
from_function	mod_function_utils	Function
func	mod_integration	Interface
fx	smod_equil_RTI_theta_pinch	Function
g0	smod_equil_MRI	Function
g0	smod_equil_interchange_modes	Function
g0	smod_equil_flow_driven_instabilities	Function
g0	smod_equil_gravito_mhd	Function
g0	smod_equil_gravito_acoustic	Function
g0	smod_user_defined	Function
g0	mod_solar_atmosphere	Function	Default profile for the solar gravitational field $g(x) = g_\odot \left(\frac{R_\odot}{(R_\odot + x)}\right)^2$
g0	smod_equil_isothermal_atmosphere	Function
general_array_to_matrix	mod_transform_matrix	Function	Converts a given 2D array to the linked-list matrix datastructure.
generate_grid	mod_grid	Subroutine
get_arpack_mode	mod_solver_settings	Function
get_array_element	mod_transform_matrix	Function	Retrieves the element at index (i, j) for an array of general type. Returns the element as a (casted) complex type.
get_B0	mod_bg_magnetic	Function
get_B1	mod_derived_efs	Function
get_B2	mod_derived_efs	Function
get_B3	mod_derived_efs	Function
get_B_para	mod_derived_efs	Function
get_B_perp	mod_derived_efs	Function
get_base_eigenfunction	mod_derived_efs	Function
get_basename_datfile	mod_io_settings	Function
get_basis_function_name	mod_state_vector_component	Function
get_basis_functions	mod_state_vector	Function
get_block_index_for_single_component	mod_essential_boundaries	Function
get_block_indices	mod_essential_boundaries	Function
get_bmat	mod_arpack_type	Function	Getter for kind of B-matrix in eigenvalue problem.
get_boundary_type	mod_equilibrium_settings	Function
get_combined_value_from_eigenvector	mod_ef_assembly	Function
get_complex_element	mod_matrix_structure	Function	Returns the complex element associated with the linked-list node at position (row, column) in the matrix datastructure. Non-existing nodes correspond to zero values, so when a node at (row, column) is not found this function returns (complex) zero.
get_components_from_basis_function	mod_state_vector	Function
get_cooling_curve	mod_cooling_settings	Function
get_cooling_table	mod_cooling_curves	Subroutine
get_curl_B_1	mod_derived_efs	Function
get_curl_B_2	mod_derived_efs	Function
get_curl_B_3	mod_derived_efs	Function
get_curl_B_para	mod_derived_efs	Function
get_curl_B_perp	mod_derived_efs	Function
get_curl_v_1	mod_derived_efs	Function
get_curl_v_2	mod_derived_efs	Function
get_curl_v_3	mod_derived_efs	Function
get_curl_v_para	mod_derived_efs	Function
get_curl_v_perp	mod_derived_efs	Function
get_datfile_path	mod_output	Function
get_dB0	mod_bg_magnetic	Function
get_dB1	mod_derived_efs	Function
get_default_basis_function	mod_state_vector_component	Function
get_deps	mod_grid	Function
get_derived_state_vector	mod_settings	Function
get_diagonal_factor	mod_essential_boundaries	Function
get_dim_integralblock	mod_dims	Function
get_dim_matrix	mod_dims	Function
get_dim_quadblock	mod_dims	Function
get_dim_subblock	mod_dims	Function
get_div_B	mod_derived_efs	Function
get_div_v	mod_derived_efs	Function
get_dlambdadT	mod_radiative_cooling	Function
get_dLdrho	mod_heatloss	Function
get_dLdT	mod_heatloss	Function
get_dropoff	mod_physics_utils	Function
get_dropoff_dr	mod_physics_utils	Function
get_dtcparadr	mod_thermal_conduction	Function
get_dtcparadT	mod_thermal_conduction	Function
get_dtcperpdB2	mod_thermal_conduction	Function
get_dtcperpdr	mod_thermal_conduction	Function
get_dtcperpdrho	mod_thermal_conduction	Function
get_dtcperpdT	mod_thermal_conduction	Function
get_dtcprefactordr	mod_thermal_conduction	Function
get_ef_gridpts	mod_grid_settings	Function
get_eigenfunctions	legolas	Subroutine	Initialises and calculates the eigenfunctions if requested.
get_electron_fraction	mod_hall_settings	Function
get_element	mod_banded_matrix	Function	Retrieves the element at position (row, col) of the original matrix. See the LAPACK documentation, element $a_{ij}$ of the original matrix is stored at position $(ku + 1 + i - j, j)$ (with $ku$ the number of superdiagonals).
get_element	mod_banded_matrix_hermitian	Function	Retrieves the element at position (row, col) of the original matrix. See the LAPACK documentation, element $a_{ij}$ of the original matrix is stored at position $(kd + 1 + i - j, j)$ if `uplo = "U"` and at position $(1 + i - j, j)$ if `uplo = "L"` in the banded storage.
get_element	mod_matrix_element_node	Function
get_elements	mod_matrix_elements	Function
get_entropy	mod_derived_efs	Function
get_eps	mod_grid	Function
get_equilibrium_type	mod_equilibrium_settings	Function
get_evpdim	mod_arpack_type	Function	Getter for dimension of eigenvalue problem.
get_fixed_resistivity	mod_resistivity_settings	Function
get_fixed_tc_para	mod_conduction_settings	Function
get_fixed_tc_perp	mod_conduction_settings	Function
get_gamma	mod_physics_settings	Function
get_gamma_1	mod_physics_settings	Function
get_gauss_gridpts	mod_grid_settings	Function
get_geometry	mod_grid_settings	Function
get_grid_end	mod_grid_settings	Function
get_grid_start	mod_grid_settings	Function
get_gridpts	mod_grid_settings	Function
get_hallfactor	mod_hall	Function	Retrieves the normalised Hall factor as described by Porth et al. (2014).
get_index	mod_get_indices	Interface	interface to retrieve the index of an element in an array. Read more…
get_inertiafactor	mod_hall	Function
get_interpolated_dlambdadT	mod_cooling_curves	Function
get_interpolated_lambdaT	mod_cooling_curves	Function
get_interpolation_points	mod_cooling_settings	Function
get_L0	mod_heatloss	Function
get_label	mod_matrix_structure	Function	Returns the current label.
get_lambdaT	mod_radiative_cooling	Function
get_logging_level	mod_logging	Function
get_LU_factorisation_banded	mod_linear_systems	Subroutine	Calculates the LU factorisation of a complex banded matrix $A$ . Uses the LAPACK routine zgbtrf.
get_lworkl	mod_arpack_type	Function	Getter for length of workl array, returns 3 * ncv*2 + 5 ncv
get_maxiter	mod_arpack_type	Function	Getter for maximum number of iterations.
get_mean_molecular_weight	mod_units	Function
get_name	mod_state_vector_component	Function
get_names	mod_state_vector	Function
get_nb_diagonals	mod_matrix_structure	Subroutine	Subroutine to get the number of super- and sub-diagonals in the matrix.
get_nb_elements	mod_matrix_elements	Function
get_nb_eqs	mod_settings	Function
get_ncv	mod_arpack_type	Function	Getter for number of Arnoldi basis vectors that should be calculated.
get_nev	mod_arpack_type	Function	Getter for number of eigenvalues to calculate.
get_node	mod_matrix_elements	Function
get_node	mod_matrix_row	Function	Returns a pointer to the node corresponding to the given column. Returns a nullified pointer if no node containing the given column index was found.
get_node_element	mod_matrix_node	Function	Returns the node element.
get_numerical_derivative	mod_interpolation	Subroutine	Calculates the numerical derivative of a given array. A sixth-order accurate central difference stencil is used to calculate the derivative. Near the edges a sixth-order accurate forward and backward difference stencil is used for the left and right boundary, respectively. It is assumed that the x values are all equally spaced. If this is not the case, a polynomial interpolation on a uniform grid can be done and that one can be differentiated instead. The stencils are as follows: Read more…
get_odd_parity_from_basis_function_name	mod_essential_boundaries	Function	This relies on the behaviour of the basis functions. If a variable needs to be zero, then this is done by forcing the basis functions on that edge to zero. For both left and right edges the quadratic basis functions have a non-zero entry in their even rows/columns, whereas the cubic basis functions have a non-zero entry in their odd rows/columns. Concrete: - cubic, left: C2 is non-zero, zero out elements with spline(2) - cubic, right: C1 is non-zero, zero out elements with spline(1) - quad, left: Q4 is non-zero, zero out elements with spline(4) - quad, right: Q3 is non-zero, zero out elements with spline(3) See also ordening of a quadblock in `mod_build_quadblock`.
get_output_folder	mod_io_settings	Function
get_parfile	mod_input	Subroutine	Parses the command line arguments and retrieves the parfile passed. Read more…
get_physics_type	mod_settings	Function
get_position	mod_matrix_element_node	Function
get_positions	mod_matrix_elements	Function
get_residual	mod_output	Function
get_rosner_dlambdadT	mod_cooling_curves	Function
get_rosner_index	mod_cooling_curves	Function
get_rosner_lambdaT	mod_cooling_curves	Function
get_second_numerical_derivative	mod_interpolation	Subroutine	Calculates the second numerical derivative of a given array. A sixth-order accurate central difference stencil is used to calculate the derivative. Near the edges a sixth-order accurate forward and backward difference stencil is used for the left and right boundary, respectively. It is assumed that the x values are all equally spaced. If this is not the case, a polynomial interpolation on a uniform grid can be done and that one can be differentiated instead. Read more…
get_solver	mod_solver_settings	Function
get_spline_function	mod_state_vector_component	Subroutine
get_state_vector	mod_settings	Function
get_tcpara	mod_thermal_conduction	Function
get_tcperp	mod_thermal_conduction	Function
get_tcprefactor	mod_thermal_conduction	Function
get_tolerance	mod_arpack_type	Function	Getter for tolerance (relative accuracy) to indicate eigenvalue convergence.
get_total_nb_elements	mod_banded_matrix	Function	Returns the total number of elements inside the banded matrix.
get_total_nb_elements	mod_banded_matrix_hermitian	Function	Returns the total number of elements inside the banded matrix
get_total_nb_elements	mod_matrix_structure	Function	Returns the total number of elements (nodes) across the various rows.
get_total_nb_nonzero_elements	mod_banded_matrix	Function	Returns the total number of nonzero elements inside the banded matrix.
get_total_time	mod_timing	Function
get_unit_conduction	mod_units	Function
get_unit_density	mod_units	Function
get_unit_gravity	mod_units	Function
get_unit_lambdaT	mod_units	Function
get_unit_length	mod_units	Function
get_unit_magneticfield	mod_units	Function
get_unit_mass	mod_units	Function
get_unit_numberdensity	mod_units	Function
get_unit_pressure	mod_units	Function
get_unit_resistivity	mod_units	Function
get_unit_temperature	mod_units	Function
get_unit_time	mod_units	Function
get_unit_velocity	mod_units	Function
get_updated_number_of_gridpoints	mod_grid	Function
get_v0	mod_bg_velocity	Function
get_v_para	mod_derived_efs	Function
get_v_perp	mod_derived_efs	Function
get_viscosity_value	mod_viscosity_settings	Function
get_which	mod_arpack_type	Function	Getter for which eigenvalues to return.
gold_hoyle_eq	mod_equilibrium	Interface	interface to the different equilibrium submodules
gravito_acoustic_eq	mod_equilibrium	Interface	interface to the different equilibrium submodules
gravito_mhd_eq	mod_equilibrium	Interface	interface to the different equilibrium submodules
H_for_thermal_balance	mod_heatloss	Function
harris_sheet_eq	mod_equilibrium	Interface	interface to the different equilibrium submodules
has_bfield	mod_settings	Function
has_electron_inertia	mod_hall_settings	Function
has_fixed_resistivity	mod_resistivity_settings	Function
has_fixed_tc_para	mod_conduction_settings	Function
has_fixed_tc_perp	mod_conduction_settings	Function
has_parallel_conduction	mod_conduction_settings	Function
has_perpendicular_conduction	mod_conduction_settings	Function
has_viscous_heating	mod_viscosity_settings	Function
hcubic	mod_basis_functions	Function
hermitian_banded_to_array	mod_transform_matrix	Interface
hermitian_banded_to_complex_array	mod_transform_matrix	Function	Converts a Hermitian banded datastructure to a full complex array.
hquad	mod_basis_functions	Function
import_equilibrium_data	mod_arrays	Subroutine	Imports arrays from the file specified by the parfile parameter input_file. To be called in the equilibrium submodule.
in_cgs	mod_units	Function
increment_nb_elements	mod_matrix_elements	Subroutine
induction_1_condition	mod_inspections	Function
induction_2_condition	mod_inspections	Function
info	mod_logging	Subroutine
init_equilibrium_params	mod_equilibrium_params	Subroutine	Initialises all variables defined at module scope to NaN, including the wave numbers. This ensures that these have to be explicitly set.
initialise	mod_base_efs	Subroutine
initialise	mod_radiative_cooling	Subroutine
initialise	mod_grid	Subroutine
initialise	mod_logging	Subroutine
initialise	mod_eigenfunctions	Subroutine
initialise	mod_derived_efs	Subroutine
initialise_exceptions	mod_exceptions	Subroutine	Private subroutine, sets the pointer to the default method to be used when raising exceptions.
initialise_globals	mod_global_variables	Subroutine
initialise_sv_components	mod_state_vector	Subroutine
integer_array_tostring	mod_logging	Function
integer_tostring	mod_logging	Function
integrate_ode_rk45	mod_integration	Subroutine	Numerically integrates the differential equation $y'(x) = A(x)y(x) + B(x)$ using a fifth-order Runge-Kutta method. The functions A(x) and B(x) are passed as arguments and should be conform to the given interface, that is, these should be `real(dp)` functions which take a single `real(dp), intent(in)` argument. The integration is performed on the interval [x0, x1] with a stepsize of `dh = (x1 - x0) / (nbpoints - 1)`.
interchange_modes_eq	mod_equilibrium	Interface	interface to the different equilibrium submodules
internal_kink_eq	mod_equilibrium	Interface	interface to the different equilibrium submodules
interpolate_and_derive	mod_arrays	Subroutine
interpolate_array_on_ef_grid	mod_derived_efs	Function
interpolate_cooling_curves	mod_cooling_curves	Subroutine	The cooling tables contain dimensionfull values on a logarithmic scale. To avoid resampling the table on an unequally spaced temperature grid by doing 10**T, we interpolate the logarithmic table values on an equally spaced T grid in log scale, so we get log10(lambda(T)) and log10(T) values. Read more…
interpolate_table	mod_interpolation	Subroutine	Interpolates a given set of tables (x, y(x)) into a smooth curve. Assumes that x_table is an array with a monotone increase in values. Interpolation is done using `n_interp` points, in general a second order polynomial approximation is used except near sharp jumps. Read more…
inverse_iteration	mod_solvers	Interface	interface to the different solution methods implemented in submodules
is_adiabatic	mod_heatloss	Function
is_compatible_with	mod_banded_matrix	Function	Checks if a banded matrix is compatibe with another banded matrix. This implies that the following attributes should be equal: - dimensions of the original matrices - number of superdiagonals and subdiagonals - dimensions of the banded matrices themselves Returns `.true.` if these three criteria are satisfied, `.false.` otherwise.
is_compatible_with	mod_banded_matrix_hermitian	Function	Checks if a Hermitian band matrix is compatible with another Hermitian band matrix. This implies that the following attributes should be equal: - number of rows/columns - number of sub/superdiagonals - storage of upper or lower triangular part - dimensions of the banded matrices themselves Returns `.true.` if all criteria are satisfied, `.false.` otherwise.
is_compatible_with	mod_state_vector	Function
is_constant	mod_check_values	Interface	interface to check if an array is constant
is_enabled	mod_conduction_settings	Function
is_enabled	mod_viscosity_settings	Function
is_enabled	mod_resistivity_settings	Function
is_enabled	mod_cooling_settings	Function
is_enabled	mod_hall_settings	Function
is_enabled	mod_gravity_settings	Function
is_enabled	mod_flow_settings	Function
is_enabled	mod_heating_settings	Function
is_equal	mod_check_values	Interface	interface to check equality between values/arrays
is_in_state_vector	mod_derived_ef_names	Function
is_inf_element	mod_matrix_elements	Function
is_infinite	mod_check_values	Interface	interface to check for inf values
is_NaN	mod_check_values	Interface	interface to check for NaN values
is_NaN_element	mod_matrix_elements	Function
is_negative	mod_check_values	Interface	interface to check for negative values
is_using_substitution	mod_hall_settings	Function
is_valid_cooling_curve	mod_cooling_curves	Function
is_valid_custom_base_grid	mod_grid	Function
is_valid_dx	mod_grid	Function
is_valid_element	mod_matrix_structure	Function	Checks if a given element is valid in order to add it to the matrix. Returns `.true.` if the element is of type real or complex, `.false.` otherwise.
is_valid_index	mod_matrix_structure	Function	Checks if a given index is valid for the current matrix datastructure. Returns `.true.` if the index (either row or column) is larger than 0 and smaller than the dimension of the matrix. Returns `.false.` otherwise.
is_valid_position	mod_matrix_elements	Function
is_within_band	mod_banded_matrix	Function	Checks if a given position (row, col) is within the banded structure, i.e. $max(1, col - ku) \leq row \leq min(m, col + kl)$ with $ku$ the number of superdiagonals and $kl$ the number of subdiagonals.
is_within_band	mod_banded_matrix_hermitian	Function	Checks if a given position (row, col) is within the banded structure. For `uplo = "U"` the position is within the band if $max(1, col - kd) \leq row \leq col,$ for `uplo = "L"` the position is within the band if $col \leq row \leq min(n, col + kd)$ with $kd$ the number of sub/superdiagonals and $n$ the number of rows/columns.
is_zero	mod_check_values	Interface	interface to check if values/arrays are zero
isothermal_atmosphere_eq	mod_equilibrium	Interface	interface to the different equilibrium submodules
J0	smod_equil_suydam_cluster	Function
J0	smod_equil_internal_kink_instability	Function
J1	smod_equil_suydam_cluster	Function
J1	smod_equil_internal_kink_instability	Function
J2	smod_equil_internal_kink_instability	Function
kh_cd_instability_eq	mod_equilibrium	Interface	interface to the different equilibrium submodules
KHI_eq	mod_equilibrium	Interface	interface to the different equilibrium submodules
log_equilibrium_info	mod_console	Subroutine
log_function_warning	mod_physics	Subroutine
log_grid_info	mod_console	Subroutine
log_io_info	mod_console	Subroutine
log_msg_by_gridpoint_change	mod_grid	Subroutine
log_physics_info	mod_console	Subroutine
log_solver_info	mod_console	Subroutine
log_usr_H_func_warning	mod_heatloss	Subroutine
logical_tostring	mod_logging	Function
lookup_equilibrium_value	mod_arrays	Subroutine	Looks up the equilibrium value for given quantity and position.
lookup_table_value	mod_interpolation	Function	Function for fast table-lookup, returns the corresponding y-value in `y_values` based on a given based on a given $x0$ . If the `allow_outside` flag is given as `.true.` then values on the edge of the table are returned when the lookup value is outside the array. Uses simple linear interpolation.
magnetothermal_instability_eq	mod_equilibrium	Interface	interface to the different equilibrium submodules
matrix_to_array	mod_transform_matrix	Interface
matrix_to_banded	mod_transform_matrix	Interface
matrix_to_complex_array	mod_transform_matrix	Subroutine	Converts a given matrix data structure with complex nodes to a 2D complex array.
matrix_to_complex_banded	mod_transform_matrix	Subroutine	Converts a matrix data structure into a complex banded matrix.
matrix_to_complex_hermitian_banded	mod_transform_matrix	Subroutine	Converts a matrix data structure into a complex Hermitian banded matrix.
matrix_to_hermitian_banded	mod_transform_matrix	Interface
MRI_accretion_eq	mod_equilibrium	Interface	interface to the different equilibrium submodules
multiply	mod_banded_operations	Interface
nan_values_present	mod_inspections	Function
needs_noslip_left	mod_essential_boundaries	Function	Check if we need a no-slip condition on the left-hand side (i.e. viscosity). Does not apply on-axis for cylindrical unless two coaxial wall are present.
needs_noslip_right	mod_essential_boundaries	Function	Check if we need a no-slip condition on the right-hand side (i.e. viscosity).
needs_T_bounds	mod_essential_boundaries	Function	Checks if we need regularity conditions on temperature, this is the case if we have perpendicular thermal conduction.
negative_values_present	mod_inspections	Function
new_arpack_config	mod_arpack_type	Function	Constructor for a new ARPACK configuration based on the dimension of the eigenvalue problem, mode of the solver and type of the B-matrix. Initialises required variables and allocates work arrays to be used when calling the solvers.
new_background	mod_background	Function
new_banded_matrix	mod_banded_matrix	Function	Constructor for a new banded matrix with a given number of rows, columns, subdiagonals and superdiagonals. Allocates and initialises the datatype.
new_bg_density	mod_bg_density	Function
new_bg_magnetic	mod_bg_magnetic	Function
new_bg_temperature	mod_bg_temperature	Function
new_bg_velocity	mod_bg_velocity	Function
new_block_dims	mod_dims	Function
new_conduction	mod_thermal_conduction	Function
new_conduction_settings	mod_conduction_settings	Function
new_cooling	mod_radiative_cooling	Function
new_cooling_settings	mod_cooling_settings	Function
new_eigenfunctions	mod_eigenfunctions	Function
new_equilibrium_settings	mod_equilibrium_settings	Function
new_flow_settings	mod_flow_settings	Function
new_gravity	mod_gravity	Function
new_gravity_settings	mod_gravity_settings	Function
new_grid	mod_grid	Function
new_grid_settings	mod_grid_settings	Function
new_hall	mod_hall	Function
new_hall_settings	mod_hall_settings	Function
new_heating	mod_heating	Function
new_heating_settings	mod_heating_settings	Function
new_heatloss	mod_heatloss	Function
new_hermitian_banded_matrix	mod_banded_matrix_hermitian	Function	Constructor for a new Hermitian banded matrix with a given number of rows and diagonals. Allocates and initialises the datatype. initialise all to zero
new_io_settings	mod_io_settings	Function
new_matrix	mod_matrix_structure	Function	Constructor for a new matrix matrix with a given number of rows. Allocates and initialises the matrix datatype.
new_matrix_element_node	mod_matrix_element_node	Function
new_matrix_elements	mod_matrix_elements	Function
new_node	mod_matrix_node	Function	Constructor for a new node, sets the column and element attributes. The element passed is polymorphic, but will be cast to complex in the node itself. No nodes are linked yet; the pointer to the next node is initialised to `null()`.
new_physics	mod_physics	Function
new_physics_settings	mod_physics_settings	Function
new_resistivity	mod_resistivity	Function
new_resistivity_settings	mod_resistivity_settings	Function
new_row	mod_matrix_row	Function	Constructor for a new row, initialises the linked list datastructure and sets the current head and tail pointers to `null()`.
new_settings	mod_settings	Function
new_solver_settings	mod_solver_settings	Function
new_sv_component	mod_state_vector_component	Function
new_timer	mod_timing	Function
new_unit_system	mod_units	Function
new_viscosity_settings	mod_viscosity_settings	Function
node_has_spline	mod_build_quadblock	Function
numerical_eq	mod_equilibrium	Interface	interface to the different equilibrium submodules
on_exception_raised	mod_exceptions	Subroutine	Workflow that is executed by default when an exception is raised. The argument `message` is printed to the console and program execution is terminated.
open_file	mod_output	Subroutine
p0	smod_equil_MRI	Function
p0	smod_equil_coronal_flux_tube	Function
p0	smod_equil_magnetothermal_instabilities	Function
p0	smod_equil_discrete_alfven	Function
p0	smod_equil_constant_current	Function
p_prof	smod_equil_flow_driven_instabilities	Function
paint_string	mod_painting	Function	Subroutine to paint a given string to the desired colour, returns a new string with ANSI escape sequences prepended and appended. If the 'colour' argument is not known, simply returns the string itself.
parse_finished_stats	mod_arpack_type	Subroutine	Parses the statistics that come out of ARPACK when the run is finished. Displays the number of OPX and BX operations and the number of re-orthogonalisation steps that were needed.
parse_io_info	mod_input	Subroutine
parse_znaupd_info	mod_arpack_type	Subroutine	Parses the info parameter that comes out of ARPACK's `znaupd` method. If info = 0, everything behaved nicely and the reverse communication subroutines exited properly. If info is any other value something went wrong and we handle it accordingly.
parse_zneupd_info	mod_arpack_type	Subroutine	Parses the info parameter that comes out of ARPACK's `zneupd` method. If info = 0, the eigenvalues extraction routines exited properly, if info is any other value something went wrong and we handle it accordingly.
phi_prof	smod_equil_flow_driven_instabilities	Function
photospheric_flux_tube_eq	mod_equilibrium	Interface	interface to the different equilibrium submodules
print_console_info	mod_console	Subroutine	Prints various console messages showing geometry, grid parameters, equilibrium parameters etc. Only for logging level "info" or above.
print_logo	mod_console	Subroutine	Prints the Legolas logo to the console. The logo is wrapped in 1 whitespace at the top and two at the bottom. Only for logging level 'warning' (1) and above
print_startup_info	mod_console	Subroutine
print_timelog	legolas	Subroutine
print_whitespace	mod_console	Subroutine	Prints an empty line to the console. Only if logging level is 'warning' or above.
qr_cholesky	mod_solvers	Interface	interface to the different solution methods implemented in submodules
qr_invert	mod_solvers	Interface	interface to the different solution methods implemented in submodules
qz_direct	mod_solvers	Interface	interface to the different solution methods implemented in submodules
raise_exception	mod_exceptions	Subroutine	Raises an exception with a given message. By default, exceptions terminate program execution. Calls the initialisation routine if not already done.
read_equilibriumlist	mod_input	Subroutine
read_gridlist	mod_input	Subroutine
read_paramlist	mod_input	Subroutine
read_parfile	mod_input	Subroutine
read_physicslist	mod_input	Subroutine
read_savelist	mod_input	Subroutine
read_solvelist	mod_input	Subroutine
read_unitlist	mod_input	Subroutine
read_user_parfile	legolas	Subroutine
real_array_is_constant	mod_check_values	Function	Check if an array has constant values
real_is_equal	mod_check_values	Function	Equality check between real values
real_is_negative	mod_check_values	Function	Check if values are or contain negative numbers
real_is_zero	mod_check_values	Function	Checks if real values are zero
real_tostring	mod_logging	Function
resistive_homo_eq	mod_equilibrium	Interface	interface to the different equilibrium submodules
resistive_tearing_modes_eq	mod_equilibrium	Interface	interface to the different equilibrium submodules
resistive_tearing_modes_flow_eq	mod_equilibrium	Interface	interface to the different equilibrium submodules
resonant_absorption_eq	mod_equilibrium	Interface	interface to the different equilibrium submodules
retransform_eigenfunction	mod_ef_assembly	Function
rho0	smod_equil_RTI_theta_pinch	Function
rho0	smod_equil_MRI	Function
rho0	smod_equil_kelvin_helmholtz_cd	Function
rho0	smod_equil_coronal_flux_tube	Function
rho0	smod_equil_interchange_modes	Function
rho0	smod_equil_resonant_absorption	Function
rho0	smod_equil_flow_driven_instabilities	Function
rho0	smod_equil_photospheric_flux_tube	Function
rho0	smod_equil_resistive_homo	Function
rho0	smod_equil_rotating_plasma_cylinder	Function
rho0	smod_equil_adiabatic_homo	Function
rho0	smod_equil_harris_sheet	Function
rho0	smod_equil_suydam_cluster	Function
rho0	smod_equil_gravito_mhd	Function
rho0	smod_equil_resistive_tearing_flow	Function
rho0	smod_numerical	Function
rho0	smod_equil_gravito_acoustic	Function
rho0	smod_user_defined	Function
rho0	mod_solar_atmosphere	Function
rho0	smod_equil_couette_flow	Function
rho0	smod_equil_magnetothermal_instabilities	Function
rho0	smod_equil_isothermal_atmosphere	Function
rho0	smod_equil_resistive_tearing	Function
rho0	smod_equil_discrete_alfven	Function
rho0	smod_equil_taylor_couette	Function
rho0	smod_equil_tc_pinch	Function
rho0	smod_equil_gold_hoyle	Function
rho0	smod_equil_constant_current	Function
rho0	smod_equil_internal_kink_instability	Function
rk45	mod_integration	Subroutine	Calculates the Runge-Kutta coefficients and calculates the fourth and fifth order solutions for step i+1 based on the values at step i.
rotating_plasma_cyl_eq	mod_equilibrium	Interface	interface to the different equilibrium submodules
RTI_eq	mod_equilibrium	Interface	interface to the different equilibrium submodules
RTI_KHI_eq	mod_equilibrium	Interface	interface to the different equilibrium submodules
RTI_theta_pinch_eq	mod_equilibrium	Interface	interface to the different equilibrium submodules
select_eigenfunctions_to_save	mod_eigenfunctions	Subroutine
set_all_io_to_false	mod_io_settings	Subroutine
set_arpack_mode	mod_solver_settings	Subroutine
set_base_grid	mod_grid	Subroutine
set_based_on_to_false	mod_units	Subroutine
set_basename_datfile	mod_io_settings	Subroutine
set_basis_function	mod_state_vector_component	Subroutine
set_basis_functions	mod_state_vector	Subroutine
set_block_dims	mod_dims	Subroutine
set_bmat	mod_arpack_type	Subroutine	Sets the type of B-matrix.
set_boundary_type	mod_equilibrium_settings	Subroutine
set_cooling_curve	mod_cooling_settings	Subroutine
set_cooling_funcs	mod_physics	Subroutine
set_custom_grid	mod_grid	Subroutine
set_custom_spline	mod_state_vector_component	Subroutine
set_default_basis_functions	mod_state_vector	Subroutine
set_density_funcs	mod_background	Subroutine
set_derived_state_vector	mod_settings	Subroutine
set_ef_grid	mod_grid	Subroutine
set_electron_fraction	mod_hall_settings	Subroutine
set_element	mod_banded_matrix	Subroutine	Sets the element $a_{ij}$ of the original array into the banded structure. The `row` and `col` arguments refer to the row and column indices of the element in the original array. This routine has no effect if the location falls outside of the banded structure.
set_element	mod_banded_matrix_hermitian	Subroutine	Sets the element $a_{ij}$ of the original array into the banded structure. The `row` and `col` arguments refer to the row and column indices of the element in the original array. This routine has no effect if the location falls outside of the banded structure.
set_equilibrium	mod_equilibrium	Subroutine	Calls the routine to set the equilibrium pointer, then calls the correct submodule. Performs some sanity checks (negative values, NaNs etc.) when the equilibrium is set, then calls additional physics modules if needed. Read more…
set_equilibrium_arrays_on_ef_grid	mod_derived_efs	Subroutine
set_equilibrium_pointer	mod_equilibrium	Subroutine	Selects the submodule based on the specified equilibrium in the parfile. Works on a case-select basis. Read more…
set_equilibrium_type	mod_equilibrium_settings	Subroutine
set_fixed_resistivity	mod_resistivity_settings	Subroutine
set_fixed_tc_para	mod_conduction_settings	Subroutine
set_fixed_tc_perp	mod_conduction_settings	Subroutine
set_function_pointer	mod_derived_efs	Subroutine
set_gamma	mod_physics_settings	Subroutine
set_gaussian_grid	mod_grid	Subroutine
set_geometry	mod_grid_settings	Subroutine
set_gravity_funcs	mod_physics	Subroutine
set_grid_boundaries	mod_grid_settings	Subroutine
set_gridpts	mod_grid_settings	Subroutine
set_heating_funcs	mod_physics	Subroutine
set_incompressible	mod_physics_settings	Subroutine
set_interpolation_points	mod_cooling_settings	Subroutine
set_label	mod_matrix_structure	Subroutine	Sets the label of the current matrix.
set_logging_level	mod_logging	Subroutine
set_magnetic_1_funcs	mod_background	Subroutine
set_magnetic_2_funcs	mod_background	Subroutine
set_magnetic_3_funcs	mod_background	Subroutine
set_maxiter	mod_arpack_type	Subroutine	Sets the maximum number of iterations that ARPACK is allowed to take, defaults to max(100, 10 * k) with k the number of eigenvalues. Read more…
set_mean_molecular_weight	mod_units	Subroutine
set_mode	mod_arpack_type	Subroutine	Sets the mode for the solver.
set_module_pointers	mod_heatloss	Subroutine
set_nb_eqs	mod_settings	Subroutine
set_ncv	mod_arpack_type	Subroutine	Setter for ncv, the number of Arnoldi basis vectors to calculate. This should satisfy 1 <= ncv - nev and ncv <= evpdim, with recommended value ncv = 2 * nev (see arpack docs).
set_nev	mod_arpack_type	Subroutine	Setter for number of eigenvalues to calculate.
set_output_folder	mod_io_settings	Subroutine
set_parallel_conduction_funcs	mod_physics	Subroutine
set_perpendicular_conduction_funcs	mod_physics	Subroutine
set_raise_method	mod_exceptions	Subroutine	Subroutine meant to be publicly called, sets the routine to be used when raising exceptions. Calls the initialisation routine if not already done.
set_residual	mod_arpack_type	Subroutine	Setter for the residual vector, allocates and manually initialises the residual (= starting) vector using a uniform distribution on (-1, 1) for both the real and imaginary parts. Relies on the LAPACK routine `zlarnv`.
set_resistivity_funcs	mod_physics	Subroutine
set_small_values_to_zero	mod_check_values	Interface	interface to check for small values
set_solar_atmosphere	mod_solar_atmosphere	Subroutine	Sets the density, temperature, gravity and magnetic field attributes of the respective fields to a realistic solar atmosphere profile. This routine first interpolates the temperature and numberdensity table at `n_interp` resolution, then solves the following ODE for the density: $\rho'(x) = -\frac{T'(x) + g(x)}{T(x)}\rho(x) - \frac{B_{02}(x)B'_{02}(x) + B_{03}(x)B'_{03}(x)}{T(x)}$ using a fifth order Runge-Kutta method. If the optional argument `save_to` is provided then the density profiles are saved to that file, which can be loaded back in on subsequent runs through the optional argument `load_from`. The integration is done over the entire table, the curve is sampled on the Gaussian grid, meaning that grid variations can all use the same result. Read more…
set_solver	mod_solver_settings	Subroutine
set_spacing_function	mod_grid	Subroutine
set_state_vector	mod_settings	Subroutine
set_temperature_funcs	mod_background	Subroutine
set_units_from_density	mod_units	Subroutine
set_units_from_numberdensity	mod_units	Subroutine
set_units_from_temperature	mod_units	Subroutine
set_velocity_1_funcs	mod_background	Subroutine
set_velocity_2_funcs	mod_background	Subroutine
set_velocity_3_funcs	mod_background	Subroutine
set_viscosity_value	mod_viscosity_settings	Subroutine
set_which	mod_arpack_type	Subroutine	Setter for the "which" argument of ARPACK routines.
should_compute_eigenvectors	mod_io_settings	Function
small_values_complex	mod_check_values	Subroutine	Small value checks for a complex variable/array/matrix, with the real and imaginary parts checked separately. Values that are smaller than the specified tolerance `tol` are set to zero. If `tol` is not present, `DP_LIMIT` is used as tolerance.
small_values_real	mod_check_values	Subroutine	Small value checks for a real variable/array/matrix. Values that are smaller than the specified tolerance `tol` are set to zero. If `tol` is not present, `DP_LIMIT` is used as tolerance.
solar_atmosphere_dealloc	mod_solar_atmosphere	Subroutine
solve_arpack_general	smod_arpack_main	Interface
solve_arpack_shift_invert	smod_arpack_main	Interface
solve_evp	mod_solvers	Subroutine	Main subroutine to solve the eigenvalue problem. Depending on the solvelist passed in the parfile, different solvers are called. Read more…
solve_linear_system_complex_banded	mod_linear_systems	Function	Calculates the solution $X$ to a system of linear equations $AX = B$ where $A$ is a complex banded matrix and $B$ is a complex vector.
solve_linear_system_complex_banded_LU	mod_linear_systems	Function	Calculates the solution $X$ to a system of linear equations $AX = B$ where $A$ is a complex banded matrix and $B$ is a complex vector. Uses the LU factorisation of $A$ and pivoting information from zgbtrf.
spitzer_detadr	mod_resistivity	Function	Default profile for the derivative of the resistivity $\eta$ with respect to position. Returns zero unless a dropoff profile was chosen.
spitzer_detadT	mod_resistivity	Function	Default profile for the derivative of the resistivity $\eta$ with respect to the temperature $T$. Returns one of the following: - zero (if resistivity is disabled or for fixed resistivity) - derivative of Spitzer resistivity with respect to T Values are normalised on return.
spitzer_eta	mod_resistivity	Function	Default profile for the resistivity $\eta$. Returns one of the following: - The Spitzer resistivity based on the equilibrium temperature profile - a fixed resistivity value - zero (if resistivity is disabled) Values are normalised on return.
spline	mod_state_vector_component	Subroutine
start_timer	mod_timing	Subroutine
state_vector_is_set	mod_settings	Function
str	mod_logging	Interface
suydam_cluster_eq	mod_equilibrium	Interface	interface to the different equilibrium submodules
T0	smod_equil_RTI_theta_pinch	Function
T0	smod_equil_MRI	Function
T0	smod_equil_kelvin_helmholtz_cd	Function
T0	smod_equil_coronal_flux_tube	Function
T0	smod_equil_interchange_modes	Function
T0	smod_equil_resonant_absorption	Function
T0	smod_equil_flow_driven_instabilities	Function
T0	smod_equil_photospheric_flux_tube	Function
T0	smod_equil_resistive_homo	Function
T0	smod_equil_rotating_plasma_cylinder	Function
T0	smod_equil_adiabatic_homo	Function
T0	smod_equil_harris_sheet	Function
T0	smod_equil_suydam_cluster	Function
T0	smod_equil_gravito_mhd	Function
T0	smod_equil_resistive_tearing_flow	Function
T0	smod_numerical	Function
T0	smod_equil_gravito_acoustic	Function
T0	smod_user_defined	Function
T0	mod_solar_atmosphere	Function
T0	smod_equil_couette_flow	Function
T0	smod_equil_magnetothermal_instabilities	Function
T0	smod_equil_isothermal_atmosphere	Function
T0	smod_equil_resistive_tearing	Function
T0	smod_equil_discrete_alfven	Function
T0	smod_equil_taylor_couette	Function
T0	smod_equil_tc_pinch	Function
T0	smod_equil_gold_hoyle	Function
T0	smod_equil_constant_current	Function
T0	smod_equil_internal_kink_instability	Function
tag_to_index	mod_arrays	Subroutine	Translates equilibrium name to index.
taylor_couette_eq	mod_equilibrium	Interface	interface to the different equilibrium submodules
tc_pinch_eq	mod_equilibrium	Interface	interface to the different equilibrium submodules
throw_info_nonzero_warning	mod_linear_systems	Subroutine
tic	mod_timing	Subroutine	Subroutine to start a wall clock timer. Read more…
toc	mod_timing	Subroutine	Subroutine to end a wall clock timer. Read more…
update_block_dimensions	mod_settings	Subroutine
update_dependent_units	mod_units	Subroutine
uplo_is_valid	mod_banded_matrix_hermitian	Function	Checks whether the given `uplo` parameter is valid.
user_defined_eq	mod_equilibrium	Interface	interface to the different equilibrium submodules
v02	smod_equil_RTI_theta_pinch	Function
v02	smod_equil_MRI	Function
v02	smod_equil_flow_driven_instabilities	Function
v02	smod_equil_rotating_plasma_cylinder	Function
v02	smod_equil_suydam_cluster	Function
v02	smod_equil_resistive_tearing_flow	Function
v02	smod_numerical	Function
v02	smod_user_defined	Function
v02	smod_equil_couette_flow	Function
v02	smod_equil_taylor_couette	Function
v02	smod_equil_tc_pinch	Function
v03	smod_equil_kelvin_helmholtz_cd	Function
v03	smod_equil_flow_driven_instabilities	Function
v03	smod_equil_rotating_plasma_cylinder	Function
v03	smod_equil_suydam_cluster	Function
v03	smod_numerical	Function
v03	smod_equil_couette_flow	Function
v03	smod_equil_internal_kink_instability	Function
v_prof	smod_equil_flow_driven_instabilities	Function
validate_equilibrium_conditions	mod_inspections	Subroutine
validate_grid_start	mod_grid_settings	Subroutine
validate_on_axis_values	mod_inspections	Subroutine
validate_scale_ratio	mod_hall	Subroutine
warning	mod_logging	Subroutine
wave_numbers_are_valid	mod_inspections	Function
write_background_data	mod_output	Subroutine
write_background_names	mod_output	Subroutine
write_base_eigenfunction_data	mod_output	Subroutine
write_derived_eigenfunction_data	mod_output	Subroutine
write_eigenvector_data	mod_output	Subroutine
write_equilibrium_info	mod_output	Subroutine
write_grid_info	mod_output	Subroutine
write_header	mod_output	Subroutine
write_io_info	mod_output	Subroutine
write_matrix_data	mod_output	Subroutine
write_parameters	mod_output	Subroutine
write_physics_info	mod_output	Subroutine
write_physics_type_info	mod_output	Subroutine
write_residual_data	mod_output	Subroutine
write_solver_info	mod_output	Subroutine
write_units_info	mod_output	Subroutine
zero_func	mod_function_utils	Function
zero_out_row_and_col	mod_essential_boundaries	Subroutine	Zeroes out the row and column corresponding to the given indices. Afterwards `diagonal_factor` is introduced in that row/column on the main diagonal.