Procedure | Location | Procedure Type | Description |
---|---|---|---|
a_ext_data | antenna | Subroutine | FIXME : Add documentation |
a_minor | geo_utils | Subroutine | FIXME : Add documentation | Designed for eeq/gs2deq only |
aaaa | quadpack | Subroutine | AAAA is a dummy subroutine with QUADPACK documentation in its comments. |
aborter | convert | Subroutine | ABORTS A PROGRAM AFTER A FATAL ERROR CONDITION IS DETECTED. |
add_eigenpair_to_file | gs2_save | Subroutine | Add an eigenpairs data to file |
add_explicit | nonlinear_terms | Subroutine | FIXME : Add documentation |
add_explicit_terms | nonlinear_terms | Subroutine | FIXME : Add documentation |
add_nl | nonlinear_terms | Subroutine | Calculate the nonlinear term and part of the corresponding CFL condition |
adjust_abserr | quadpack | Function | Adjust estimate of absolute error |
adjust_time_norm | gs2_time | Subroutine | FIXME : Add documentation |
adjust_vnmult | collisions | Subroutine | Given estimates of the velocity space integration errors adjust the collision frequency scaling factor vnmult. |
advance | fields | Subroutine | FIXME : Add documentation |
advance_gf_local | fields_gf_local | Subroutine | This routine advances the solution by one full time step DD>TAGGED: Should we only this is fapar>0 as well? |
advance_implicit | fields_implicit | Subroutine | FIXME : Add documentation |
advance_local | fields_local | Subroutine | This routine advances the solution by one full time step DD>TAGGED: Should we only this is fapar>0 as well? |
advance_nonlinear_term | split_nonlinear_terms | Subroutine | Advances dg/dt = NL(g,chi) from g_state, chi from t -> t+dt by calling specific requested method. On output g_state contains new g at next step, chi is left unchanged |
advance_nonlinear_term_ab3 | split_nonlinear_terms | Subroutine | Advances dg/dt = NL(g,chi) from current g_state, chi from t -> t+dt by using AB scheme of orders up to 3rd. |
advance_nonlinear_term_beuler | split_nonlinear_terms | Subroutine | Advances dg/dt = NL(g,chi) from current g_state, chi from t -> t+dt by using backwards Euler with fixed-point iteration. |
advance_nonlinear_term_picard | split_nonlinear_terms | Subroutine | Advances dg/dt = NL(g,chi) from current g_state, chi from t -> t+dt by using a simple Picard iteration scheme |
advance_nonlinear_term_rk | split_nonlinear_terms | Subroutine | Advances dg/dt = NL(g,chi) from current g_state, chi from t -> t+dt by using an Runge-Kutta scheme with embedded error estimate for error control. This method is a wrapper to the true generic RK implementation. |
advance_nonlinear_term_rk_implementation | split_nonlinear_terms | Subroutine | Advances dg/dt = NL(g,chi) from current g_state, chi from t -> t+dt by using an Runge-Kutta scheme with embedded error estimate for error control |
advance_test | fields_test | Subroutine | FIXME : Add documentation |
agrees_with | unit_tests | Interface | |
agrees_with_complex_1d_array | unit_tests | Function | |
agrees_with_integer | unit_tests | Function | |
agrees_with_real | unit_tests | Function | |
agrees_with_real_1d_array | unit_tests | Function | |
all_to_group | mp | Interface | |
all_to_group_real | mp | Subroutine | FIXME : Add documentation |
all_to_group_real_array | mp | Subroutine | FIXME : Add documentation |
allgather | mp | Interface | |
allgather_integer_array_1to1 | mp | Subroutine | A subroutine to do a allgatherv operation, sending recvcnts(iproc) data from the iproc'th processor to all others starting at arr(start). |
allgatherv | mp | Interface | |
allgatherv_complex_array_1to1 | mp | Subroutine | A subroutine to do a allgatherv operation, sending recvcnts(iproc) data from the iproc'th processor to all others starting at arr(start). |
allgatherv_complex_array_1to1_sub | mp | Subroutine | A subroutine to do a allgatherv operation, sending recvcnts(iproc) data from the iproc'th processor to all others starting at arr(start). |
allgatherv_complex_array_1to3 | mp | Subroutine | A subroutine to do a allgatherv operation, sending recvcnts(iproc) data from the iproc'th processor to all others starting at arr(start). |
allgatherv_complex_array_1to3_sub | mp | Subroutine | A subroutine to do a allgatherv operation, sending recvcnts(iproc) data from the iproc'th processor to all others starting at arr(start). |
alloc_arrays | geo_utils | Subroutine | |
alloc_common_arrays | geo_utils | Subroutine | |
alloc_response_objects | fields_implicit | Subroutine | A subroutine to allocate the response matrix storage objects |
alloc_special_arrays_null | geo_utils | Subroutine | |
allocate_arrays | dist_fn | Subroutine | FIXME : Add documentation |
allocate_arrays | fields | Subroutine | FIXME : Add documentation |
allocate_arrays | theta_grid | Subroutine | FIXME : Add documentation |
allocate_arrays | hyper | Subroutine | FIXME : Add documentation |
allocate_arrays | kt_grids | Subroutine | FIXME : Add documentation |
allocate_arrays | rungridgen | Subroutine | FIXME : Add documentation |
allocate_arrays_3d | rungridgen | Subroutine | FIXME : Add documentation |
allocate_current_results | diagnostics_config | Subroutine | |
allocate_geom | geometry | Subroutine | Allocate the geom instance to the correct type |
allocate_outputs | gs2_main | Subroutine | FIXME : Add documentation |
allocate_target_arrays | parameter_scan | Subroutine | FIXME : Add documentation |
almost_equal | warning_helpers | Interface | Are two numbers almost equal within some tolerance |
almost_equal_r128 | warning_helpers | Function | Are two numbers almost equal |
almost_equal_r32 | warning_helpers | Function | Are two numbers almost equal |
almost_equal_r64 | warning_helpers | Function | Are two numbers almost equal |
almost_zero | warning_helpers | Interface | Is the argument almost zero |
almost_zero_r128 | warning_helpers | Function | |
almost_zero_r32 | warning_helpers | Function | Is a scalar almost zero |
almost_zero_r64 | warning_helpers | Function | |
announce_check | unit_tests | Subroutine | |
announce_functional_test | functional_tests | Subroutine | FIXME : Add documentation |
announce_module_test | unit_tests | Subroutine | |
announce_test | unit_tests | Subroutine | |
antenna_amplitudes | antenna | Subroutine | FIXME : Add documentation |
antenna_apar | antenna | Subroutine | FIXME : Add documentation |
antenna_w | antenna | Function | FIXME : Add documentation |
append_output_file | file_utils | Subroutine | Open an output file to write (appending if existing) whose name is
|
apply_linked_boundary_conditions | dist_fn | Subroutine | Applies linked (twist-shift) boundary conditions to passed distribution function DD>Note these fill routines are often equivalent to an all-to-all type |
apply_new_defaults | diagnostics_config | Subroutine | Set values according to the new diagnostics defaults. |
apply_old_defaults | gs2_diagnostics | Subroutine | Set values according to the old diagnostics defaults. |
apply_parallel_boundary_conditions | dist_fn | Subroutine | Apply one of the "end of the grid" parallel boundary conditions |
arclength | geometry | Subroutine | Given an initial theta and gradpar (=dtheta/dl) compute a new theta grid, returned in arcl, which has gradpar = dg/dl = constant. |
average_all | volume_averages | Interface | |
average_all_2_complex_txy | volume_averages | Subroutine | FIXME : Add documentation |
average_all_2_complex_xy | volume_averages | Subroutine | FIXME : Add documentation |
average_all_complex_xy | volume_averages | Subroutine | FIXME : Add documentation |
average_all_real_xy | volume_averages | Subroutine | FIXME : Add documentation |
average_all_real_xys | volume_averages | Subroutine | FIXME : Add documentation |
average_all_txy | volume_averages | Subroutine | FIXME : Add documentation |
average_kx | volume_averages | Interface | |
average_kx_xy | volume_averages | Subroutine | FIXME : Add documentation |
average_kx_xys | volume_averages | Subroutine | FIXME : Add documentation |
average_ky | volume_averages | Interface | |
average_ky_2_complex_xy | volume_averages | Subroutine | FIXME : Add documentation |
average_ky_complex_xy | volume_averages | Subroutine | FIXME : Add documentation |
average_ky_xy | volume_averages | Subroutine | FIXME : Add documentation |
average_ky_xys | volume_averages | Subroutine | FIXME : Add documentation |
average_theta | volume_averages | Interface | |
average_theta_1_real_txy | volume_averages | Subroutine | FIXME : Add documentation |
average_theta_2_complex_txy | volume_averages | Subroutine | FIXME : Add documentation |
average_theta_complex_complex_complex_t | volume_averages | Subroutine | FIXME : Add documentation |
average_theta_complex_complex_real_t | volume_averages | Subroutine | FIXME : Add documentation |
average_theta_complex_complex_t | volume_averages | Subroutine | FIXME : Add documentation |
average_theta_complex_complex_txys | volume_averages | Subroutine | FIXME : Add documentation |
average_theta_real_real_t | volume_averages | Subroutine | FIXME : Add documentation |
average_theta_txy | volume_averages | Subroutine | FIXME : Add documentation |
average_theta_txys | volume_averages | Subroutine | FIXME : Add documentation |
avg_dv | gs2_heating | Subroutine | FIXME : Add documentation |
avg_dvk | gs2_heating | Subroutine | FIXME : Add documentation |
avg_h | gs2_heating | Subroutine | Calculate the average of various heating quantities |
avg_hk | gs2_heating | Subroutine | Calculate the average of various heating quantities as a function of |
B_mod | geometry | Subroutine | FIXME : Add documentation |
B_pol | geometry | Subroutine | FIXME : Add documentation |
barrier | mp | Interface | |
barrier_comm | mp | Subroutine | |
barrier_nocomm | mp | Subroutine | FIXME : Add documentation |
basic_init | fft_work | Subroutine | Does some common initialisation for fft_type |
bcast_scan_parameter | gs2_diagnostics | Subroutine | Broadcast one of the input parameters according to target_parameter_switch |
bcastfrom_character | mp | Subroutine | FIXME : Add documentation |
bcastfrom_complex | mp | Subroutine | FIXME : Add documentation |
bcastfrom_complex_2array | mp | Subroutine | FIXME : Add documentation |
bcastfrom_complex_2array_sub | mp | Subroutine | FIXME : Add documentation |
bcastfrom_complex_3array | mp | Subroutine | FIXME : Add documentation |
bcastfrom_complex_3array_sub | mp | Subroutine | FIXME : Add documentation |
bcastfrom_complex_4array_sub | mp | Subroutine | FIXME : Add documentation |
bcastfrom_complex_array | mp | Subroutine | FIXME : Add documentation |
bcastfrom_complex_array_sub | mp | Subroutine | FIXME : Add documentation |
bcastfrom_integer | mp | Subroutine | FIXME : Add documentation |
bcastfrom_integer_array | mp | Subroutine | FIXME : Add documentation |
bcastfrom_logical | mp | Subroutine | FIXME : Add documentation |
bcastfrom_logical_array | mp | Subroutine | FIXME : Add documentation |
bcastfrom_real | mp | Subroutine | FIXME : Add documentation |
bcastfrom_real_array | mp | Subroutine | FIXME : Add documentation |
benchmark_identifier | benchmarks | Function | A string which is used as an extension for timing files and which identifies the time when and system on which the benchmark was carried out |
beta_loop | ball | Subroutine | |
beta_prime_range_high | ingen_mod | Subroutine | FIXME : Add documentation |
beta_prime_range_low | ingen_mod | Subroutine | FIXME : Add documentation |
beta_range_high | ingen_mod | Subroutine | FIXME : Add documentation |
beta_range_low | ingen_mod | Subroutine | FIXME : Add documentation |
betafun | leq | Function | FIXME : Add documentation |
betafun_eqfile | geo_utils | Function | |
bilinear_interpolate | geo_utils | Function | use opposite area stencil to interpolate to point bound by [istar,istar+1] and [jstar, jstar + 1]. |
bishop_gradB | geometry | Subroutine | FIXME : Add documentation |
bits_to_human_readable | memory_usage | Function | Converts the passed number of bits into a slightly more human readable form. |
bound_eqfile_cart | geo_utils | Function | Find the value of the major radius on the plasma boundary at given geometric theta. |
box_get_grids | kt_grids_box | Subroutine | Calculate the grid of wavenumbers for box mode |
box_get_sizes | kt_grids_box | Subroutine | Get the various grid sizes |
box_set_overrides | kt_grids_box | Subroutine | FIXME : Add documentation |
broadcast | mp | Interface | |
broadcast_ballstab_config | ballstab | Subroutine | Broadcasts all config parameters so object is populated identically on all processors |
broadcast_character | mp | Subroutine | FIXME : Add documentation |
broadcast_character_array | mp | Subroutine | FIXME : Add documentation |
broadcast_collisions_config | collisions | Subroutine | Broadcasts all config parameters so object is populated identically on all processors |
broadcast_complex | mp | Subroutine | FIXME : Add documentation |
broadcast_complex8_array | mp | Subroutine | FIXME : Add documentation |
broadcast_complex_2array | mp | Subroutine | FIXME : Add documentation |
broadcast_complex_3array | mp | Subroutine | FIXME : Add documentation |
broadcast_complex_4array | mp | Subroutine | FIXME : Add documentation |
broadcast_complex_array | mp | Subroutine | FIXME : Add documentation |
broadcast_diagnostics_base_config | diagnostics_base_configuration | Subroutine | Broadcasts all config parameters so object is populated identically on all processors |
broadcast_dist_fn_config | dist_fn | Subroutine | Broadcasts all config parameters so object is populated identically on all processors |
broadcast_dist_fn_species_config | dist_fn | Subroutine | Broadcasts all config parameters so object is populated identically on all processors |
broadcast_driver_config | antenna | Subroutine | Broadcasts all config parameters so object is populated identically on all processors |
broadcast_fields_config | fields | Subroutine | Broadcasts all config parameters so object is populated identically on all processors |
broadcast_hyper_config | hyper | Subroutine | Broadcasts all config parameters so object is populated identically on all processors |
broadcast_ingen_config | ingen_mod | Subroutine | Broadcasts all config parameters so object is populated identically on all processors |
broadcast_init_g_config | init_g | Subroutine | Broadcasts all config parameters so object is populated identically on all processors |
broadcast_integer | mp | Subroutine | FIXME : Add documentation |
broadcast_integer_2array | mp | Subroutine | FIXME : Add documentation |
broadcast_integer_array | mp | Subroutine | FIXME : Add documentation |
broadcast_interface | abstract_config | Interface | |
broadcast_knobs_config | run_parameters | Subroutine | Broadcasts all config parameters so object is populated identically on all processors |
broadcast_kt_grids_box_config | kt_grids_box | Subroutine | Broadcasts all config parameters so object is populated identically on all processors |
broadcast_kt_grids_config | kt_grids | Subroutine | Broadcasts all config parameters so object is populated identically on all processors |
broadcast_kt_grids_range_config | kt_grids_range | Subroutine | Broadcasts all config parameters so object is populated identically on all processors |
broadcast_kt_grids_single_config | kt_grids_single | Subroutine | Broadcasts all config parameters so object is populated identically on all processors |
broadcast_kt_grids_specified_config | kt_grids_specified | Subroutine | Broadcasts all config parameters so object is populated identically on all processors |
broadcast_kt_grids_specified_element_config | kt_grids_specified | Subroutine | Broadcasts all config parameters so object is populated identically on all processors |
broadcast_layouts_config | gs2_layouts | Subroutine | Broadcasts all config parameters so object is populated identically on all processors |
broadcast_le_grids_config | le_grids | Subroutine | Broadcasts all config parameters so object is populated identically on all processors |
broadcast_logical | mp | Subroutine | FIXME : Add documentation |
broadcast_logical_2array | mp | Subroutine | FIXME : Add documentation |
broadcast_logical_array | mp | Subroutine | FIXME : Add documentation |
broadcast_nonlinear_terms_config | nonlinear_terms | Subroutine | Broadcasts all config parameters so object is populated identically on all processors |
broadcast_normalisations_config | normalisations | Subroutine | Broadcasts all config parameters so object is populated identically on all processors |
broadcast_optimisation_config | optimisation_configuration | Subroutine | Broadcasts all config parameters so object is populated identically on all processors |
broadcast_parameter_scan_config | parameter_scan | Subroutine | Broadcasts all config parameters so object is populated identically on all processors |
broadcast_real | mp | Subroutine | FIAME : Add documentation |
broadcast_real_2array | mp | Subroutine | FIXME : Add documentation |
broadcast_real_3array | mp | Subroutine | FIAME : Add documentation |
broadcast_real_4array | mp | Subroutine | FIXME : Add documentation |
broadcast_real_5array | mp | Subroutine | FIXME : Add documentation |
broadcast_real_array | mp | Subroutine | FIAME : Add documentation |
broadcast_reinit_config | gs2_reinit | Subroutine | Broadcasts all config parameters so object is populated identically on all processors |
broadcast_results | theta_grid | Subroutine | FIXME : Add documentation |
broadcast_results | le_grids | Subroutine | FIXME : Add documentation |
broadcast_source_config | dist_fn | Subroutine | Broadcasts all config parameters so object is populated identically on all processors |
broadcast_species_config | species | Subroutine | Broadcasts all config parameters so object is populated identically on all processors |
broadcast_species_element_config | species | Subroutine | Broadcasts all config parameters so object is populated identically on all processors |
broadcast_split_nonlinear_terms_config | split_nonlinear_terms | Subroutine | Broadcasts all config parameters so object is populated identically on all processors |
broadcast_stir_config | antenna | Subroutine | Broadcasts all config parameters so object is populated identically on all processors |
broadcast_sub | mp | Interface | |
broadcast_theta_grid_config | theta_grid | Subroutine | Broadcasts all config parameters so object is populated identically on all processors |
broadcast_theta_grid_eik_config | theta_grid_eik | Subroutine | Broadcasts all config parameters so object is populated identically on all processors |
broadcast_theta_grid_file_config | theta_grid_file | Subroutine | Broadcasts all config parameters so object is populated identically on all processors |
broadcast_theta_grid_gridgen_config | theta_grid_gridgen | Subroutine | Broadcasts all config parameters so object is populated identically on all processors |
broadcast_theta_grid_parameters_config | theta_grid_params | Subroutine | Broadcasts all config parameters so object is populated identically on all processors |
broadcast_theta_grid_salpha_config | theta_grid_salpha | Subroutine | Broadcasts all config parameters so object is populated identically on all processors |
btori | leq | Function | FIXME : Add documentation |
btori_eqfile | geo_utils | Function | |
build_identifier | runtime_tests | Function | This function is just a call of build_identifier_runtime_info and is provided for backwards compatibility. |
build_identifier_runtime_info | runtime_tests | Function | Returns an identifier of the system and build: "system.compiler.githash". |
bvectortgrid | geometry | Subroutine | FIXME : Add documentation |
c2r | convert | Interface | |
c_allocate | fields_local | Subroutine | Allocate storage space |
c_allocate | fields_gf_local | Subroutine | Allocate storage space |
c_deallocate | fields_local | Subroutine | Deallocate storage space |
c_deallocate | fields_gf_local | Subroutine | Deallocate storage space |
c_debug_print | fields_local | Subroutine | Debug printing |
c_debug_print | fields_gf_local | Subroutine | Debug printing |
c_fill_2 | redistribute | Subroutine | FIXME : Add documentation |
c_fill_3 | redistribute | Subroutine | FIXME : Add documentation |
c_fill_3_mpi_copy | redistribute | Subroutine | FIXME : Add documentation |
c_fill_3_mpi_copy_nonblock | redistribute | Subroutine | Non-blocking version of mpi copy |
c_fill_4 | redistribute | Subroutine | FIXME : Add documentation |
c_get_field_update | fields_local | Subroutine | Get the field update for this cells data Note still need to reduce across other cells in this supercell. |
c_get_field_update | fields_gf_local | Subroutine | Get the field update for this cells data Note still need to reduce across other cells in this supercell. |
c_has_row | fields_local | Function | Test if a given row belongs to the current cell |
c_has_row | fields_gf_local | Function | Test if a given row belongs to the current cell |
c_init | fields_local | Subroutine | Initialise the members of the cell instance |
c_init | fields_gf_local | Subroutine | Initialise the members of the cell instance |
c_mv_mult_rb | fields_local | Subroutine | Do matrix vector multiplication at rowblock level |
c_mv_mult_rb | fields_gf_local | Subroutine | Do matrix vector multiplication at rowblock level |
c_redist_12 | redistribute | Subroutine | FIXME : Add documentation |
c_redist_22 | redistribute | Subroutine | FIXME : Add documentation |
c_redist_22_inv | redistribute | Subroutine | FIXME : Add documentation |
c_redist_22_inv_mpi_copy | redistribute | Subroutine | FIXME : Add documentation |
c_redist_22_inv_mpi_copy_nonblock | redistribute | Subroutine | This routine does redistributes using entirely non-blocking comms. |
c_redist_22_inv_mpi_copy_persist_end | redistribute | Subroutine | Finish persistent communications associated with redistribute. Unpacks receive buffer. |
c_redist_22_inv_mpi_copy_persist_start | redistribute | Subroutine | Launch persistent communications associated with redistribute. Packs send buffer. |
c_redist_22_inv_new_copy | redistribute | Subroutine | FIXME : Add documentation |
c_redist_22_inv_old_copy | redistribute | Subroutine | FIXME : Add documentation |
c_redist_22_mpi_copy | redistribute | Subroutine | FIXME : Add documentation |
c_redist_22_mpi_copy_nonblock | redistribute | Subroutine | This routine does redistributes using entirely non-blocking comms. |
c_redist_22_mpi_copy_persist_end | redistribute | Subroutine | Finish persistent communications associated with redistribute. Unpacks receive buffer. |
c_redist_22_mpi_copy_persist_start | redistribute | Subroutine | Launch persistent communications associated with redistribute. Packs send buffer. |
c_redist_22_new_copy | redistribute | Subroutine | FIXME : Add documentation |
c_redist_22_old_copy | redistribute | Subroutine | FIXME : Add documentation |
c_redist_23 | redistribute | Subroutine | FIXME : Add documentation |
c_redist_32 | redistribute | Subroutine | FIXME : Add documentation |
c_redist_32_inv | redistribute | Subroutine | FIXME : Add documentation |
c_redist_32_inv_mpi_copy | redistribute | Subroutine | FIXME : Add documentation |
c_redist_32_inv_mpi_copy_nonblock | redistribute | Subroutine | This routine does redistributes using entirely non-blocking comms. |
c_redist_32_inv_mpi_copy_persist_end | redistribute | Subroutine | Finish persistent communications associated with redistribute. Unpacks receive buffer. |
c_redist_32_inv_mpi_copy_persist_start | redistribute | Subroutine | Launch persistent communications associated with redistribute. Packs send buffer. |
c_redist_32_inv_new_copy | redistribute | Subroutine | FIXME : Add documentation |
c_redist_32_inv_new_opt_copy | redistribute | Subroutine | FIXME : Add documentation |
c_redist_32_inv_old_copy | redistribute | Subroutine | FIXME : Add documentation |
c_redist_32_mpi_copy | redistribute | Subroutine | FIXME : Add documentation |
c_redist_32_mpi_copy_nonblock | redistribute | Subroutine | This routine does redistributes using entirely non-blocking comms. |
c_redist_32_mpi_copy_persist_end | redistribute | Subroutine | Finish persistent communications associated with redistribute. Unpacks receive buffer. |
c_redist_32_mpi_copy_persist_start | redistribute | Subroutine | Launch persistent communications associated with redistribute. Packs send buffer. |
c_redist_32_new_copy | redistribute | Subroutine | FIXME : Add documentation |
c_redist_32_new_opt_copy | redistribute | Subroutine | FIXME : Add documentation |
c_redist_32_old_copy | redistribute | Subroutine | FIXME : Add documentation |
c_redist_33 | redistribute | Subroutine | FIXME : Add documentation DD> |
c_redist_33_inv | redistribute | Subroutine | FIXME : Add documentation |
c_redist_33_inv_mpi_copy | redistribute | Subroutine | FIXME : Add documentation |
c_redist_33_inv_mpi_copy_nonblock | redistribute | Subroutine | This routine does redistributes using entirely non-blocking comms. |
c_redist_33_inv_mpi_copy_persist_end | redistribute | Subroutine | Finish persistent communications associated with redistribute. Unpacks receive buffer. |
c_redist_33_inv_mpi_copy_persist_start | redistribute | Subroutine | Launch persistent communications associated with redistribute. Packs send buffer. |
c_redist_33_mpi_copy | redistribute | Subroutine | FIXME : Add documentation |
c_redist_33_mpi_copy_nonblock | redistribute | Subroutine | This routine does redistributes using entirely non-blocking comms. |
c_redist_33_mpi_copy_persist_end | redistribute | Subroutine | Finish persistent communications associated with redistribute. Unpacks receive buffer. |
c_redist_33_mpi_copy_persist_start | redistribute | Subroutine | Launch persistent communications associated with redistribute. Packs send buffer. |
c_redist_34 | redistribute | Subroutine | FIXME : Add documentation |
c_redist_36 | redistribute | Subroutine | FIXME : Add documentation |
c_redist_36_inv | redistribute | Subroutine | FIXME : Add documentation DD> |
c_redist_36_inv_mpi_copy | redistribute | Subroutine | FIXME : Add documentation |
c_redist_36_inv_mpi_copy_nonblock | redistribute | Subroutine | FIXME : Add documentation |
c_redist_36_mpi_copy | redistribute | Subroutine | FIXME : Add documentation |
c_redist_36_mpi_copy_nonblock | redistribute | Subroutine | FIXME : Add documentation |
c_redist_42 | redistribute | Subroutine | FIXME : Add documentation |
c_redist_42_inv | redistribute | Subroutine | FIXME : Add documentation |
c_reset | fields_local | Subroutine | A routine to reset the object |
c_reset | fields_gf_local | Subroutine | A routine to reset the object |
c_set_locality | fields_local | Subroutine | Set the locality of each object |
c_set_locality | fields_gf_local | Subroutine | Set the locality of each object |
c_signed_char_to_hex | uuid_mod | Function | Convert a 1-byte integer into hexadecimal |
calc_jext | gs2_diagnostics | Subroutine | Calculate the time-averaged antenna current |
calc_jext | diagnostics_antenna | Subroutine | A subroutine to calculate the time-averaged antenna current j_ext = kperp^2 A_antenna. |
calculate_and_broadcast_species_properties | species | Subroutine | FIXME : Add documentation |
calculate_block_breakdown | gs2_layouts | Subroutine | This subroutine (calculate_block_breakdown) is used in the code to create unbalanced xxf and yxf layouts to address 1 communication overheads in the redistribution of data for the FFTs used in the nonlinear calculations to move from Fourier space to real space and back again. |
calculate_block_size | gs2_layouts | Subroutine | This subroutine (calculate_block_size) is used in the code to create unbalanced xxf and yxf layouts to address 1 communication overheads in the redistribution of data for the FFTs used in the nonlinear calculations to move from Fourier space to real space and back again. |
calculate_bounce_points | le_grids | Subroutine | Determine which theta grid points correspond to bounce points for each pitch angle. |
calculate_bracket | nonlinear_terms | Subroutine | Calculate (d Chi /dx).(d g_wesson/dy) and store in bracket if is_first_term = .true. else calculate (d Chi /dy).(d g_wesson/dx) and subtract from bracket |
calculate_collisional | collisional_heating | Subroutine | FIXME : Add documentation |
calculate_current_nl_source_and_cfl_limit | nonlinear_terms | Subroutine | Calculates the current nonlinear source term by calling add_nl and the associated cfl limit. |
calculate_f0_arrays | species | Subroutine | FIXME : Add documentation |
calculate_f0_arrays_tabulated | species | Subroutine | This subroutine calculates f0 on the grid from an external input file. The grid on the input file can differ from that of gs2. A cubic spline is used to interpolate between the two. The user can either specify df0/dE or it can be estimated internally. The radial derivative of f0 as a function of energy should also be given. |
calculate_fields | split_nonlinear_terms | Subroutine | Calculates the fields consistent with the passed distribution function |
calculate_flux_surface_average | dist_fn | Subroutine | Calculate the flux surface average term for the adiabatic response. |
calculate_fluxes | diagnostics_fluxes | Subroutine | Calculate and possibly write fluxes. |
calculate_forbidden_region | le_grids | Subroutine | Determine which lambda grid points are forbidden at each theta/bmag value. |
calculate_gradients | geo_utils | Subroutine | Given theta, R, Z, B and psi on 2D grids calculate the index space derivatives in the two grid dimensions and use these to find gradients in cartesian and Bishop space. |
calculate_heating | diagnostics_heating | Subroutine | FIXME : Add documentation |
calculate_idle_processes | gs2_layouts | Subroutine | This subroutine (calculate_idle_processes) is used to calculate the difference between the number of processes used in the xxf and yxf data layouts. This is important as it can affect the amount of communication that the code has to undertake when moving between linear and non-linear calculations. |
calculate_instantaneous_omega | gs2_diagnostics | Function | Calculates the instantaneous omega from chinew = chi * exp(-i * omega * dt) with chi = phi + apar + bpar. This gives omega = log(chinew/chi) * i / dt. |
calculate_ittp | le_grids | Subroutine | Determine which lambda grid point is totally trapped at this theta grid point. |
calculate_jend | le_grids | Subroutine | Determine which lambda grid point bounces at this theta/bmag value. |
calculate_kinetic_energy_transfer | diagnostics_kinetic_energy_transfer | Subroutine | |
calculate_kinetic_energy_transfer_this_theta | diagnostics_kinetic_energy_transfer | Subroutine | |
calculate_metric_terms | geometry | Subroutine | |
calculate_omega | diagnostics_omega | Subroutine | Calculates omega and stores it in omegahist. Calculates omega_average, the average of omega over navg timesteps DD>The logic below was originally |
calculate_outputs | gs2_main | Subroutine | FIXME : Add documentation |
calculate_potentials_from_nonadiabatic_dfn | dist_fn | Subroutine | Calculates the potentials consistent with the passed nonadiabatic
distribution function, |
calculate_simple_quasilinear_flux_metric_by_k | gs2_diagnostics | Function | Calculates a simple gamma/kperp2 QL flux metric |
calculate_slowingdown_parameters | species | Subroutine | FIXME : Add documentation |
calculate_standard_flux_properties | diagnostics_fluxes | Subroutine | Writes a range of different summed and averaged properties of the given flux... e.g. the flux summed over kx as a function of ky, species and time |
calculate_supercell_labels | dist_fn | Subroutine | Assigns a label to each {it, ik} point denoting which unique supercell the point belongs to. |
calculate_surface_area | geometry | Subroutine | |
calculate_unbalanced_decomposition | gs2_layouts | Subroutine | This subroutine (calculate_unbalanced_decomposition) is used in the code to create unbalanced xxf and yxf layouts to address 1 communication overheads in the redistribution of data for the FFTs used in the nonlinear calculations to move from Fourier space to real space and back again. |
calculate_unbalanced_x | gs2_layouts | Subroutine | This subroutine (calculate_unbalanced_x) wraps up all the functionality required to calculate the xxf blocksizes and work out if and unbalanced decomposition should be used, and if so the size of the unbalanced blocks. |
calculate_unbalanced_y | gs2_layouts | Subroutine | FIXME : Add documentation |
calculate_zonal_transfer | diagnostics_zonal_transfer | Subroutine | FIXME : Add documentation |
cgemm | lapack_wrapper | Interface | |
cgemv | lapack_wrapper | Interface | |
cgetrf | lapack_wrapper | Interface | |
cgetri | lapack_wrapper | Interface | |
change_level_specific_interface | gs2_init | Interface | |
chease_chi_index | ceq | Function | Convert from theta-index which is |
check | geometry | Subroutine | Perform minor checks on consistency of flags |
check_accel | gs2_layouts | Subroutine | FIXME : Add documentation |
check_antenna | antenna | Subroutine | FIXME : Add documentation |
check_are_bouncepoint_values_consistent | dist_fn_arrays | Subroutine | Check if the passed distribution function shaped array has the same value at bounce points for both signs of v||. This provides similar functionality to check_g_bouncepoints but is intended to offer a quieter approach which could be used more routinely (i.e. throughout a run). |
check_collisions | collisions | Subroutine | FIXME : Add documentation |
check_dist_fn | dist_fn | Subroutine | FIXME : Add documentation |
check_fields | fields | Subroutine | FIXME : Add documentation |
check_frequency | functional_tests | Function | FIXME : Add documentation |
check_g2gf | le_grids | Subroutine | FIXME : Add documentation |
check_g2le | le_grids | Subroutine | FIXME : Add documentation |
check_g_bouncepoints | dist_fn_arrays | Subroutine | This routine checks trapped particle bounce conditions: g(thetab,1:ik,it,il,ie,is)=g(thetab,2:ik,it,il,ie,is) and flags fractional errors exceeding a threshold tolerance, tol. CMR, 3/10/2013: |
check_getan | dist_fn | Subroutine | FIXME : Add documentation |
check_growth_rate | functional_tests | Function | FIXME : Add documentation |
check_growth_rates_equal_in_list | functional_tests | Function | FIXME : Add documentation |
check_gs2_diagnostics | gs2_diagnostics | Subroutine | Perform some basic checking of the diagnostic input parameters, and write the results to file |
check_hyper | hyper | Subroutine | FIXME : Add documentation |
check_increment_condition_satisfied | parameter_scan | Subroutine | FIXME : Add documentation |
check_init_g | init_g | Subroutine | FIXME : Add documentation |
check_is_zero_in_forbidden_region | dist_fn_arrays | Subroutine | Check if the passed distribution function shaped array is non-zero in the forbidden region. If it is then trigger an abort. |
check_kt_grids | kt_grids | Subroutine | FIXME : Add documentation |
check_kt_grids_box | kt_grids_box | Subroutine | FIXME : Add documentation |
check_kt_grids_range | kt_grids_range | Subroutine | FIXME : Add documentation DD>Calculate the kt grids |
check_kt_grids_single | kt_grids_single | Subroutine | FIXME : Add documentation |
check_kt_grids_specified | kt_grids_specified | Subroutine | |
check_laguerre_weights | gauss_quad | Subroutine | FIXME : Add documentation |
check_laguerre_zeros | gauss_quad | Subroutine | FIXME : Add documentation |
check_legendre_weights | gauss_quad | Subroutine | FIXME : Add documentation |
check_legendre_zero | gauss_quad | Subroutine | FIXME : Add documentation |
check_linked_boundaries_are_satisfied | dist_fn | Subroutine | Check if the passed distribution function shaped array has the same value at the duplicate theta points arising from the linked boundary conditions. |
check_llocal | gs2_layouts | Subroutine | FIXME : Add documentation |
check_netcdf_file_precision | netcdf_utils | Subroutine | Check that an existing netCDF file uses the same |
check_nonlin_convergence | gs2_diagnostics | Subroutine | Trinity convergence condition - simple and experimental look for the averaged differential of the summed averaged heat flux to drop below a threshold |
check_nonlin_convergence | diagnostics_nonlinear_convergence | Subroutine | Trinity convergence condition - simple and experimental look for the averaged differential of the summed averaged heat flux to drop below a threshold |
check_nonlinear_terms | nonlinear_terms | Subroutine | FIXME : Add documentation |
check_normalisations | normalisations | Subroutine | FIXME : Add documentation |
check_parameters | gs2_diagnostics_new | Subroutine | FIXME : Add documentation |
check_restart_file_writeable | gs2_diagnostics | Subroutine | Check if we can write the restart files |
check_run_parameters | run_parameters | Subroutine | FIXME : Add documentation |
check_species | species | Subroutine | FIXME : Add documentation |
check_stability | ballstab | Subroutine | Test if given shat/beta is unstable |
check_target_reached | parameter_scan | Subroutine | FIXME : Add documentation |
check_theta_grid | theta_grid | Subroutine | FIXME : Add documentation |
check_theta_grid_eik | theta_grid_eik | Subroutine | FIXME : Add documentation |
check_theta_grid_file | theta_grid_file | Subroutine | FIXME : Add documentation |
check_theta_grid_file_nc | theta_grid_file | Subroutine | FIXME : Add documentation |
check_theta_grid_salpha | theta_grid_salpha | Subroutine | FIXME : Add documentation |
check_time_step | gs2_reinit | Subroutine | FIXME : Add documentation |
check_time_step_too_large | gs2_time | Subroutine | Check if the current time step is too big |
check_unique_integers | gs2_layouts | Subroutine | Checks that the given array contains unique integers 1 to (array size) (in any order), aborts if not. |
checklogic_theta_grid_eik | theta_grid_eik | Subroutine | FIXME : Add documentation |
checkstop | job_manage | Subroutine | Check whether the stop file |
checktime | job_manage | Subroutine | Check whether elapsed run time is within a 5 minutes of exceeding the available CPU time, and if so trigger the code exit. |
close_files | gs2_diagnostics | Subroutine | Close various text output files |
close_functional_test | functional_tests | Subroutine | FIXME : Add documentation |
close_module_test | unit_tests | Subroutine | |
close_output_file | file_utils | Subroutine | Close the file associated with |
code_matches_instance | exit_codes | Function | Determines if a passed |
code_matches_integer | exit_codes | Function | Determines if a passed |
collision_error | diagnostics_velocity_space | Subroutine | Calculate the collision error and write to text file |
collisions_advance | dist_fn | Subroutine | Advance collision term one timestep by implicit Euler. |
common_calculate_fluxes | diagnostics_fluxes | Subroutine | Calculate heat, particle, and momentum fluxes |
compiler_pgi | runtime_tests | Function | This function is just a call of compiler_pgi_runtime_info and is provided for backwards compatibility. |
compiler_pgi_runtime_info | runtime_tests | Function | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Tests for compilers !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Returns whether a PGI compiler was used |
complex_local_sum | integration | Function | A wrapper routine to perform a sum. Used to provide a single point at which we choose a summation method |
complex_rectangular_integration | integration | Function | Apply the (left) rectangular rule to integrate y over the domain of x. |
complex_sq_mod | warning_helpers | Interface | Returns , the square modulus of a complex number |
complex_sq_mod_r128 | warning_helpers | Function | |
complex_sq_mod_r32 | warning_helpers | Function | |
complex_sq_mod_r64 | warning_helpers | Function | |
complex_trapezoidal_integration | integration | Function | Apply the trapezium rule to integrate y over the domain of x. |
compute_connections | dist_fn | Subroutine | Look up and store the iglo index and responsible processor for connections to the left and right of each local iglo index. Note this is only interested in passing particles and the non-trapped wfb. Trapped particles are considered to have no connections. |
compute_itleft_and_itright | dist_fn | Subroutine | For the passed jshift0 value determine the it (kx) indices to the left and right of each {it, ik} index pair. Used to construct the connected boundary conditions. |
compute_jshift0 | dist_fn | Function | Compute the spacing in kx indices between connected kx domains (cells) for the lowest non-zonal ky. |
conserve_diffuse | collisions | Interface | |
conserve_diffuse_le_layout | collisions | Subroutine | FIXME : Add documentation !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! First get v0y0 and then y1 = y0 - v0y0 * z0 / (1 + v0z0) $OMP PARALLEL DO DEFAULT(none) & $OMP PRIVATE(ile, it, ik, is, ie, ig, ixi, vnE, v0y0) & $OMP SHARED(le_lo, kwork_filter, negrid, nxi_lim, w, wxi, ieqzip, bz0le, vnmult, vnew_E, aj0le, gle) & $OMP SCHEDULE(static) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Now get v1y1 and then y2 = y1 - v1y1 * s1 / (1 + v1s1) $OMP PARALLEL DO DEFAULT(none) & $OMP PRIVATE(ile, it, ik, is, ig, delnu, ie, ixi, v1y1) & $OMP SHARED(le_lo, kwork_filter, negrid, vnmult, delvnew, nxi_lim, & $OMP bs0le, vpa_aj0_le, gle, w, wxi, ieqzip) & $OMP SCHEDULE(static) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Now get v2y2 and then get x = y2 - v2y2 * w2 / (1 + v2w2) $OMP PARALLEL DO DEFAULT(none) & $OMP PRIVATE(ile, it, ik, is, ie, ig, ixi, delnu, v2y2) & $OMP SHARED(le_lo, kwork_filter, negrid, nxi_lim, ieqzip, & $OMP bw0le, delvnew, vperp_aj1le, gle, vnmult, w, wxi) & $OMP SCHEDULE(static) |
conserve_diffuse_standard_layout | collisions | Subroutine | FIXME : Add documentation !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! First get v0y0 $OMP PARALLEL DO DEFAULT(none) & $OMP PRIVATE(iglo, it, ik, ie, is, isgn) & $OMP SHARED(g_lo, kwork_filter, gtmp, vnmult, vnew_E, aj0, g) & $OMP SCHEDULE(static) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Get y1 = y0 - v0y0 * z0 / (1 + v0z0) $OMP PARALLEL DO DEFAULT(none) & $OMP PRIVATE(iglo, it, ik, is, isgn) & $OMP SHARED(g_lo, kwork_filter, g1, g, ieqzip, v0y0, bz0) & $OMP SCHEDULE(static) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Now get v1y1 $OMP PARALLEL DO DEFAULT(none) & $OMP PRIVATE(iglo, it, ik, ie, is, isgn) & $OMP SHARED(g_lo, kwork_filter, gtmp, vns, vpa, aj0, g1) & $OMP SCHEDULE(static) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Get y2 = y1 - v1y1 * s1 / (1 + v1s1) $OMP PARALLEL DO DEFAULT(none) & $OMP PRIVATE(iglo, it, ik, is, isgn) & $OMP SHARED(g_lo, kwork_filter, g1, ieqzip, v1y1, bs0) & $OMP SCHEDULE(static) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Now get v2y2 $OMP PARALLEL DO DEFAULT(none) & $OMP PRIVATE(iglo, it, ik, ie, il, is, isgn) & $OMP SHARED(g_lo, kwork_filter, gtmp, vns, energy, al, aj1, g1) & $OMP SCHEDULE(static) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Finally get x = y2 - v2y2 * w2 / (1 + v2w2) $OMP PARALLEL DO DEFAULT(none) & $OMP PRIVATE(iglo, it, ik, is, isgn) & $OMP SHARED(g_lo, kwork_filter, g, g1, ieqzip, v2y2, bw0) & $OMP SCHEDULE(static) |
conserve_lorentz | collisions | Interface | |
conserve_lorentz_le_layout | collisions | Subroutine | FIXME : Add documentation !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! First get v0y0 and y1 = y0 - v0y0 * z0 / (1 + v0z0) v0 = vpa J0 f0, y0 = gle $OMP PARALLEL DO DEFAULT(none) & $OMP PRIVATE(ile, it, ik, ixi, ie, is, ig, v0y0) & $OMP SHARED(le_lo, kwork_filter, ieqzip, negrid, nxi_lim, & $OMP z0le, w, wxi, vpa_aj0_le, gle) & $OMP SCHEDULE(static) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Now get v1y1 and y2 = y1 - v1y1 * s1 / (1 + v1s1) v1 = nud vpa J0 f0, y1 = gle |
conserve_lorentz_standard_layout | collisions | Subroutine | FIXME : Add documentation !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! First get v0y0 $OMP PARALLEL DO DEFAULT(none) & $OMP PRIVATE(iglo, it, ik, isgn) & $OMP SHARED(g_lo, kwork_filter, gtmp, vpa, aj0, g) & $OMP SCHEDULE(static) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Get y1 = y0 - v0y0 * z0 / (1 + v0z0) $OMP PARALLEL DO DEFAULT(none) & $OMP PRIVATE(iglo, it, ik, is, isgn) & $OMP SHARED(g_lo, kwork_filter, g1, g, ieqzip, v0y0, z0) & $OMP SCHEDULE(static) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Now get v1y1 $OMP PARALLEL DO DEFAULT(none) & $OMP PRIVATE(iglo, it, ik, il, ie, is, isgn) & $OMP SHARED(g_lo, kwork_filter, conservative, gtmp, vns, speed, vpdiff, aj0, g1, vpa) & $OMP SCHEDULE(static) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Get y2 = y1 - v1y1 * s1 / (1 + v1s1) $OMP PARALLEL DO DEFAULT(none) & $OMP PRIVATE(iglo, it, ik, is, isgn) & $OMP SHARED(g_lo, kwork_filter, g1, ieqzip, v1y1, s0) & $OMP SCHEDULE(static) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Now get v2y2 $OMP PARALLEL DO DEFAULT(none) & $OMP PRIVATE(iglo, it, ik, ie, il, is, isgn) & $OMP SHARED(g_lo, kwork_filter, gtmp, vns, energy, al, aj1, g1) & $OMP SCHEDULE(static) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Finally get x = y2 - v2y2 * w2 / (1 + v2w2) $OMP PARALLEL DO DEFAULT(none) & $OMP PRIVATE(iglo, it, ik, is, isgn) & $OMP SHARED(g_lo, kwork_filter, g, g1, ieqzip, v2y2, w0) & $OMP SCHEDULE(static) |
copy | array_utils | Interface | Interface to helper subroutines for copying one array into another. |
copy_complex_array_3 | array_utils | Subroutine | Copy 3D complex arrays |
copy_complex_array_4 | array_utils | Subroutine | Copy 4D complex arrays |
copy_real_array_3 | array_utils | Subroutine | Copy 3D real arrays |
copy_real_array_4 | array_utils | Subroutine | Copy 4D real arrays |
coredump | shmem | Subroutine | FIXME : Add documentation |
correlation | gs2_diagnostics | Subroutine | Calculate the correlation function on the physical domain |
correlation_extend | gs2_diagnostics | Subroutine | Calculate the correlation function over the extended domain |
coshm_fun | splines | Function | Calculate coshm(x) = cosh(x) - 1 |
coshmm_fun | splines | Function | Calculate coshmm(x) = (cosh(x) - 1 - x * x / 2) / (x * x) |
count_links | dist_fn | Subroutine | Count the links to the left and right of each {it, ik} point and work out how many values are required to set the bc. |
count_links_one_side | dist_fn | Subroutine | Count how many links are to the left/right of each {it,ik} point |
create_message | exit_codes | Function | Make a string containing the error code and exit reason. This is kept minimal to make it easier for tests to parse. |
create_metadata | gs2_metadata | Subroutine | Add some standard metadata as global attributes to the file: |
create_seed_from_single_integer | ran | Function | Returns an array of integers to use as a seed to the random number generator given a single integer as input. |
crosstgrid | geometry | Subroutine | Calculate the cross product c = a x b on the |
cubgcv | rungridgen | Subroutine | FIXME : Add documentation |
date_iso8601 | standard_header | Function | Return the current date and time in ISO8601 format: YYYY-MM-DDThh:mm:ss.ssssZhh:mm |
dbtori | leq | Function | FIXME : Add documentation |
dbtori_eqfile | geo_utils | Function | at the given normalised |
dealiasing | gs2_layouts | Function | FIXME : Add documentation |
dealloc_arrays | ballstab | Subroutine | Deallocate arrays |
dealloc_arrays | geo_utils | Subroutine | |
dealloc_common_arrays | geo_utils | Subroutine | |
dealloc_special_arrays | eeq | Subroutine | FIXME : Add documentation |
dealloc_special_arrays | deq | Subroutine | FIXME : Add documentation |
dealloc_special_arrays_null | geo_utils | Subroutine | |
deallocate_arrays | theta_grid | Subroutine | FIXME : Add documentation |
deallocate_arrays | gs2_diagnostics | Subroutine | Deallocate the gs2_diagnostics module-level arrays |
deallocate_arrays | gs2_save | Subroutine | Deallocate all module level arrays |
deallocate_current_results | diagnostics_config | Subroutine | |
deallocate_g_layout | layouts_type | Subroutine | Deallocate g_layout's arrays |
deallocate_layout | layouts_type | Interface | |
deallocate_outputs | gs2_main | Subroutine | FIXME : Add documentation |
deallocate_target_arrays | parameter_scan | Subroutine | FIXME : Add documentation |
debug_message | unit_tests | Subroutine | |
define_dims | gs2_io | Subroutine | Ensure the netCDF file contains all the dimensions and grids, creating them if necessary |
define_kinetic_energy_transfer_dims | diagnostics_kinetic_energy_transfer | Subroutine | |
define_vars | gs2_io | Subroutine | Create (but don't fill) the various diagnostics variables in the output netCDF file DD>Added protective if statement as theta_extended_dim is only defined if io_write_corr_extend |
del_dvtype | gs2_heating | Interface | |
del_dvtype_0 | gs2_heating | Subroutine | FIXME : Add documentation |
del_dvtype_1 | gs2_heating | Subroutine | FIXME : Add documentation |
del_dvtype_2 | gs2_heating | Subroutine | FIXME : Add documentation |
del_dvtype_3 | gs2_heating | Subroutine | FIXME : Add documentation |
del_htype | gs2_heating | Interface | |
del_htype_0 | gs2_heating | Subroutine | FIXME : Add documentation |
del_htype_1 | gs2_heating | Subroutine | FIXME : Add documentation |
del_htype_2 | gs2_heating | Subroutine | FIXME : Add documentation |
del_htype_3 | gs2_heating | Subroutine | FIXME : Add documentation |
delete_fft | fft_work | Subroutine | Destroy 42 plan |
delete_list | redistribute | Subroutine | FIXME : Add documentation |
delete_periodic_spline | splines | Subroutine | Reset and deallocate variables in passed periodic spline |
delete_redist | redistribute | Subroutine | FIXME : Add documentation |
delete_special_splines | eeq | Subroutine | |
delete_special_splines | deq | Subroutine | |
delete_special_splines_eqfile_null | geo_utils | Subroutine | |
delete_spline | splines | Subroutine | Reset and deallocate variables in passed spline |
delete_splines_eqfile | geo_utils | Subroutine | |
derf_ext | spfunc | Function | FIXME : Add documentation |
derm | geo_utils | Subroutine | Calculate the derivative of f w.r.t to the radial and poloidal indexes (i.e. calculate the finite differences without dividing by delta psi and delta theta). - dfm(:,:,1) is the psi derivative - dfm(:,:,2) is the theta derivative - char specifies the periodicity in theta - 'E', 'O' mean continuous at theta = +/- pi - 'T' means a jump of 2 pi at theta = +/- pi |
derm_cart | geo_utils | Subroutine | Calculate the derivative of f w.r.t. R, Z - dfm(:,:,1) is deriv w.r.t. R - dfm(:,:,2) is deriv w.r.t. Z |
diameter | geometry | Function | Returns the diameter of the surface labelled by rp. |
diameter | leq | Function | FIXME : Add documentation |
diameter_eqfile | geo_utils | Function | Return the diameter of the flux surface at a given major radius |
diameter_eqfile_cart | geo_utils | Function | |
diffusivity | gs2_diagnostics | Function | A linear estimate of the diffusivity, used for Trinity testing |
dj0 | spfunc | Function | FIXME : Add documentation |
dj1 | spfunc | Function | FIXME : Add documentation |
dlgamma_ext | spfunc | Function | FIXME : Add documentation |
do_dump_fields_periodically | gs2_diagnostics | Subroutine | Write out to text file |
do_get_omega | gs2_diagnostics | Subroutine | Calculate gs2_diagnostics_knobs for linear simulations or if run_parameters_knobs is on; otherwise set gs2_diagnostics_knobs and gs2_diagnostics_knobs to zero |
do_print_line | gs2_diagnostics | Subroutine | Print estimated frequencies and growth rates to screen/stdout |
do_smoothing | rungridgen | Subroutine | FIXME : Add documentation |
do_write_avg_moments | gs2_diagnostics | Subroutine | Calculate flux surfgace averaged low-order moments of and write to netCDF |
do_write_correlation | gs2_diagnostics | Subroutine | Calculate the correlation function over the physical domain and write to netCDF |
do_write_correlation_extend | gs2_diagnostics | Subroutine | Calculate the correlation function over the extended domain and write to netCDF |
do_write_crossphase | gs2_diagnostics | Subroutine | Calculate the cross-phase (see get_cross_phase) and write to the phase_unit file |
do_write_dump_1 | gs2_diagnostics | Subroutine | Calculate the field-line average of and write to dump_check1_unit |
do_write_dump_2 | gs2_diagnostics | Subroutine | Calculate at |
do_write_eigenfunc | gs2_diagnostics | Subroutine | Write normalised to the value of at the outboard midplane |
do_write_f | gs2_diagnostics | Subroutine | Write at |
do_write_final_antot | diagnostics_final_routines | Subroutine | Write the right-hand sides of the field equations, overwriting existing values |
do_write_final_db | diagnostics_final_routines | Subroutine | Calculate and write , overwriting existing values |
do_write_final_epar | diagnostics_final_routines | Subroutine | Calculate and write , overwriting existing values |
do_write_final_fields | diagnostics_final_routines | Subroutine | Write , overwriting existing values |
do_write_final_moments | diagnostics_final_routines | Subroutine | Calculate and write the various low-order moments, overwriting existing values |
do_write_full_moments_notgc | gs2_diagnostics | Subroutine | Calculate moments (density, parallel flow, and parallel and perpendicular temperatures) in non-guiding centre coordinates and write to netCDF |
do_write_fyx | gs2_diagnostics | Subroutine | Write distribution function ( or possibly ?) in real space to text file
" |
do_write_geom | gs2_diagnostics | Subroutine | Write some geometry information to text file |
do_write_gs | diagnostics_final_routines | Subroutine | FIXME : Add documentation |
do_write_heating | gs2_diagnostics | Subroutine | Write the (total) heating diagnostics to heat_unit and heat_unit2 (per-species) |
do_write_jext | gs2_diagnostics | Subroutine | Calculate and write the time-averaged antenna current to jext_unit |
do_write_kinetic_energy_transfer | gs2_diagnostics | Subroutine | |
do_write_kpar | diagnostics_final_routines | Subroutine | Write the parallel spectrum of , overwriting existing values |
do_write_line | gs2_diagnostics | Subroutine | Write estimated frequency and growth rates to out_unit for an individual point |
do_write_moments | gs2_diagnostics | Subroutine | Write various moments to netCDF |
do_write_movie | gs2_diagnostics | Subroutine | Transform to real space, then write to netCDF |
do_write_ncloop | gs2_diagnostics | Subroutine | Compute volume averages of the fields and write the fields, field averages, heating and frequency to the netCDF files |
do_write_nl_flux_dist | gs2_diagnostics | Subroutine | Calculate the poloidal distributions of the fluxes of particles, parallel momentum, perpendicular momentum, and energy (see section 3.1 and appendix A of Ball et al. PPCF 58 (2016) 045023 as well as section 5 of "GS2 analytic geometry specification") |
do_write_omavg | gs2_diagnostics | Subroutine | Write time-averaged growth rate and frequency to out_unit for an individual point |
do_write_omega | gs2_diagnostics | Subroutine | Write instantaneous growth rate and frequency to out_unit for an individual point |
do_write_parity | gs2_diagnostics | Subroutine | Calculate average parity of distribution function under , and write to parity_unit |
do_write_symmetry | gs2_diagnostics | Subroutine | Calculate the momentum flux as a function of and write to netCDF |
do_write_verr | gs2_diagnostics | Subroutine | Write some error estimates. |
dot | gs2_heating | Subroutine | Get a theta-centered and time-centered estimate of the time derivative of a field. |
dottgridf | geometry | Subroutine | Calculate the dot product c = a.b where a, b and c are on the |
dpfun | leq | Function | FIXME : Add documentation |
dpfun_eqfile | geo_utils | Function | |
drho_drhod | geometry | Function | FIXME : Add documentation | Only used for writelots output and if irho=1 |
drho_drp | geometry | Function | Calculate the derivative of the flux label rho with respect to the internal flux label rp (the normalised poloidal flux) |
drift | geometry | Subroutine | FIXME : Add documentation |
dsplint | splines | Function | FIXME : Add documentation |
dsteqr | lapack_wrapper | Interface | |
dump_ant_amp | antenna | Subroutine | Write antenna amplitudes to out_unit |
dump_current_source_term | dist_fn | Subroutine | Routine to dump the current source term used in invert_rhs. |
dump_homogeneous_solution | dist_fn | Subroutine | Routine to dump the homogeneous solution |
dump_response_to_file | fields | Subroutine | Force the current response matrices to be written to file |
dump_response_to_file_gf_local | fields_gf_local | Subroutine | Routine to dump the current response matrix data to file. One file per connected domain. Each written by the head of the supercell. |
dump_response_to_file_imp | fields_implicit | Subroutine | A routine to dump the current response matrix to file |
dump_response_to_file_local | fields_local | Subroutine | Routine to dump the current response matrix data to file. One file per connected domain. Each written by the head of the supercell. |
eexchange | diagnostics_fluxes | Subroutine | Calculate energy exchange diagnostic that numerically guarantees that the total energy exchange (summed over species) is zero |
efit_read_and_set | eeq | Subroutine | This subroutine reads an EFIT output file containing the axisymmetric magnetic field geometry on a rectangular domain defined by the coordinates (R,Z). It reads and stores the following quantities (among others). |
eigval_functional | eigval | Function | Returns true if GS2 was compiled with WITH_EIG defined -- here forced to .false. as compiled without SLEPc support |
eigval_functional | fields_eigval | Function | Returns true if GS2 was compiled with WITH_EIG defined -- here forced to .false. as compiled without SLEPc support |
eik_get_grids | theta_grid_eik | Subroutine | FIXME : Add documentation |
eik_get_sizes | theta_grid_eik | Subroutine | FIXME : Add documentation |
eikcoefs | geometry | Subroutine | FIXME : Add documentation |
eikonal | geometry | Subroutine | FIXME : Add documentation |
eint_error | le_grids | Subroutine | FIXME : Add documentation |
enforce_linked_boundary_conditions | dist_fn | Subroutine | A shorthand for apply_linked_boundary_conditions passing the regular module level instances of each of the required arguments. Primarily intended for testing to avoid having to expose additional data arrays. |
enforce_parity | dist_fn | Subroutine | Enforce requested parity |
ensemble_average | gs2_diagnostics | Subroutine | FIXME : Add documentation |
ensure_netcdf_att_exists | netcdf_utils | Interface | Add an attribute to an existing netCDF variable |
ensure_netcdf_att_exists_text | netcdf_utils | Subroutine | Add an attribute to an existing netCDF variable. Aborts if any errors are detected. |
ensure_netcdf_dim_exists | netcdf_utils | Subroutine | Get the netCDF ID for a dimension, creating it if it doesn't exist already. Aborts if any errors are detected. |
ensure_netcdf_var_exists | netcdf_utils | Interface | Get the netCDF ID for a variable, creating it if it doesn't exist already |
ensure_netcdf_var_exists_manydims | netcdf_utils | Subroutine | Get the netCDF ID for a variable, creating it if it doesn't exist already. Aborts if any errors are detected. |
ensure_netcdf_var_exists_onedim | netcdf_utils | Subroutine | Get the netCDF ID for a variable, creating it if it doesn't exist already. Aborts if any errors are detected. |
ensure_netcdf_var_exists_scalar | netcdf_utils | Subroutine | Get the netCDF ID for a variable, creating it if it doesn't exist already. Aborts if any errors are detected. |
ensure_redist_persist_consistency | gs2_layouts | Subroutine | Disable opt_redist_persist and opt_redist_persist_overlap if dependent settings not set |
ensure_single_val_fields_pass | dist_fn | Subroutine | Ensure that linked boundary values of passed complex field are single valued (e.g. kperp2(ntgrid,ikx,iky) is equal to kperp2(-ntgrid,ikx_link,iky) as these correspond to the same location). |
ensure_single_val_fields_pass_r | dist_fn | Subroutine | Ensure that linked boundary values of passed real field are single valued (e.g. kperp2(ntgrid,ikx,iky) is equal to kperp2(-ntgrid,ikx_link,iky) as these correspond to the same location). |
eqdbish | geo_utils | Subroutine | Convert gradients of a function f w.r.t. R,Z into bishop form.
Note that |
eqdcart | geo_utils | Subroutine | Converts derivatives w.r.t. (psi_index,theta_index) to derivatives
w.r.t. (R,Z). Note that |
eqitem | leq | Function | Calculates |
eqitem_cart | geo_utils | Function | fstar is f(R,Z) interpolated at the values (r,thetain). The parameter r is the distance to the magnetic axis. |
eqitem_eqfile | geo_utils | Function | Calculates fstar which is f interpolated at the location (r,theta). Here r is the normalised poloidal flux coordinate rp (= psi_pN + psi_0N) and theta_in is theta. f is a grid of values of f as a function of psi_p,theta First we find the radial and theta indices bounding our requested point and we then interpolate within the bound rectangle. |
eqitem_interface | geo_utils | Interface | |
erf_ext | spfunc | Interface | |
error | shmem | Subroutine | FIXME : Add documentation |
error_abort | shm_mpi3 | Subroutine | FIXME : Add documentation |
error_unit | file_utils | Function | Returns the file unit number associated with the error file |
estimate_error | nonlinear_terms | Function | Get an estimate of the error on the NL source term by comparing 2nd and 3rd order calculations of the source term. |
estimate_error | diagnostics_velocity_space | Subroutine | FIXME : Add documentation |
eval_f0 | species | Function | FIXME : Add documentation |
eval_f0_sdanalytic | species | Subroutine | FIXME : Add documentation |
evolve_equations | gs2_main | Subroutine | Run the initial value solver. nstep_run must
be less than or equal to |
exactly_equal | warning_helpers | Interface | Are two numbers exactly equal to each other |
exactly_equal_r128 | warning_helpers | Function | |
exactly_equal_r32 | warning_helpers | Function | |
exactly_equal_r64 | warning_helpers | Function | |
exb_shear | dist_fn | Subroutine | FIXME : Add documentation |
execute_c2c | fft_work | Subroutine | Small wrapper to bind execute c2c to fft_type |
execute_c2r | fft_work | Subroutine | Small wrapper to bind execute c2r to fft_type |
execute_r2c | fft_work | Subroutine | Small wrapper to bind execute r2c to fft_type |
exit_reason_unit | file_utils | Function | Returns the file unit number associated with the exit_reason file |
extend_ky | diagnostics_kinetic_energy_transfer | Subroutine | extend ky to negative values and return in "shifted" format. due to reality condition only ky >= 0 is used in GS2. |
f_trap | geometry | Function | FIXME : Add documentation |
factors | gs2_layouts | Subroutine | Get the factors of an integer n |
favg | gs2_heating | Function | Construct time and space-centered quantities (should use actual bakdif and fexpr values?) |
favg_x | gs2_heating | Function | FIXME : Add documentation |
fdot | gs2_heating | Function | FIXME : Add documentation |
fdot_t | gs2_heating | Function | FIXME : Add documentation |
fftshift | diagnostics_kinetic_energy_transfer | Interface | |
fftshift1D_real | diagnostics_kinetic_energy_transfer | Subroutine | similar to numpy.fft.fftshift in Python shift data such that the element for kx=0 or ky=0 is in the center of the array |
fftshift2D_complex | diagnostics_kinetic_energy_transfer | Subroutine | similar to numpy.fft.fftshift in Python shift data such that the element for kx=0 and ky=0 is in the center of the matrix |
ffttest | ffttest_helper | Subroutine | FIXME : Add documentation |
fftw_flags | fft_work | Function | Set flags for FFTW3 |
field_k_local | fields_parallelization | Function | FIXME : Add documentation |
field_line_average | theta_grid | Interface | |
field_line_average_complex | theta_grid | Function | Calculates the field line / theta average of a passed quantity |
field_line_average_real | theta_grid | Function | Calculates the field line / theta average of a passed quantity |
fieldline_average_phi | fields_implicit | Subroutine | This generates a field line average of phi_in and writes it to phi_average. If ik_only is supplied, it will only calculate the field line average for that ky, leaving the rest of phi_avg unchanged. EGH |
fields_gf_local_functional | fields_gf_local | Function | Returns true if GS2 was built in such a way as to allow this module to work. Currently does not work with PGI compilers. See online discussions. |
fields_init_response | fields | Subroutine | FIXME : Add documentation |
fields_local_functional | fields_local | Function | Returns true if GS2 was built in such a way as to allow this module to work. Currently does not work with PGI compilers. See online discussions. |
fields_pre_init | fields | Subroutine | Calls all initialisations required for init_fields_implicit/local, reads parameters and allocates field arrays |
file_and_line_id | dist_fn_arrays | Function | A small helper function which constructs and returns the string
' |
file_get_grids | theta_grid_file | Subroutine | FIXME : Add documentation DD> Should jacob also be provided by this routine? |
file_get_sizes | theta_grid_file | Subroutine | FIXME : Add documentation |
file_nc_get_grids | theta_grid_file | Subroutine | FIXME : Add documentation |
file_nc_get_sizes | theta_grid_file | Subroutine | FIXME : Add documentation |
fill | redistribute | Interface | |
finalise | leq | Subroutine | Finalise leq module |
finalise_eqfile | geo_utils | Subroutine | |
finalize_diagnostics | gs2_main | Subroutine | FIXME : Add documentation |
finalize_equations | gs2_main | Subroutine | FIXME : Add documentation |
finalize_gs2 | gs2_main | Subroutine | FIXME : Add documentation |
finalize_gs2_optimisation | gs2_optimisation | Subroutine | FIXME : Add documentation |
finalize_overrides | gs2_main | Subroutine | FIXME : Add documentation |
find_leftmost_link | dist_fn | Subroutine | FIXME : Add documentation |
find_lower_bound | geo_utils | Function | |
find_rightmost_link | dist_fn | Subroutine | FIXME : Add documentation |
find_zero | gauss_quad | Subroutine | FIXME : Add documentation |
find_zero_bisect_newton | gauss_quad | Subroutine | FIXME : Add documentation |
find_zero_bisect_newton_radau | gauss_quad | Subroutine | FIXME : Add documentation |
finish_antenna | antenna | Subroutine | FIXME : Add documentation |
finish_antenna_data | antenna_data | Subroutine | FIXME : Add documentation |
finish_ballstab | ballstab | Subroutine | Finalise this module Deallocate |
finish_collisional | collisional_heating | Subroutine | FIXME : Add documentation |
finish_collisions | collisions | Subroutine | Forces recalculation of coefficients in collision operator when timestep changes. |
finish_constant_random | constant_random | Subroutine | |
finish_diagnostics_antenna | diagnostics_antenna | Subroutine | FIXME : Add documentation |
finish_diagnostics_config | diagnostics_config | Subroutine | |
finish_diagnostics_fluxes | diagnostics_fluxes | Subroutine | Clean up module, deallocate module-level arrays |
finish_diagnostics_heating | diagnostics_heating | Subroutine | FIXME : Add documentation |
finish_diagnostics_kinetic_energy_transfer | diagnostics_kinetic_energy_transfer | Subroutine | |
finish_diagnostics_omega | diagnostics_omega | Subroutine | FIXME : Add documentation |
finish_diagnostics_velocity_space | diagnostics_velocity_space | Subroutine | FIXME : Add documentation |
finish_dist_fn | dist_fn | Subroutine | FIXME : Add documentation |
finish_dist_fn_arrays | dist_fn | Subroutine | |
finish_dist_fn_layouts | gs2_layouts | Subroutine | FIXME : Add documentation |
finish_dist_fn_level_1 | dist_fn | Subroutine | |
finish_dist_fn_level_2 | dist_fn | Subroutine | FIXME : Add documentation |
finish_dist_fn_level_3 | dist_fn | Subroutine | FIXME : Add documentation |
finish_dist_fn_parameters | dist_fn | Subroutine | FIXME : Add documentation |
finish_dump_response | dump_response | Subroutine | Call the finialise routines for any module we have initialised. |
finish_eigenfunc_file | gs2_save | Subroutine | Close the eigenfunction file |
finish_fft_work | fft_work | Subroutine | Restore FFTW to pristine state |
finish_fields | fields | Subroutine | FIXME : Add documentation |
finish_fields_gf_local | fields_gf_local | Subroutine | Finish the fields_gf_local module |
finish_fields_layouts | fields_implicit | Subroutine | FIXME : Add documentation |
finish_fields_layouts | gs2_layouts | Subroutine | FIXME : Add documentation |
finish_fields_level_1 | fields | Subroutine | FIXME : Add documentation |
finish_fields_level_2 | fields | Subroutine | FIXME : Add documentation |
finish_fields_local | fields_local | Subroutine | Finish the fields_local module |
finish_fields_parameters | fields | Subroutine | FIXME : Add documentation |
finish_file_utils | file_utils | Subroutine | Close any files opened by init_file_utils |
finish_geometry | geometry | Subroutine | FIXME : Add documentation |
finish_gs2 | gs2_main | Subroutine | Finish and cleanup a complete simulation |
finish_gs2_diagnostics | gs2_diagnostics | Subroutine | Finalise the diagnostics module, writing final timestep diagnostics and closing any open files |
finish_gs2_diagnostics_new | gs2_diagnostics_new | Subroutine | Close the output file and deallocate arrays |
finish_gs2_init | gs2_init | Subroutine | Finish this module |
finish_gs2_layouts | gs2_layouts | Subroutine | FIXME : Add documentation |
finish_gs2_reinit | gs2_reinit | Subroutine | FIXME : Add documentation |
finish_gs2_save | gs2_save | Subroutine | FIXME : Add documentation |
finish_gs2_time | gs2_time | Subroutine | Finalise the gs2_time module |
finish_hyper | hyper | Subroutine | FIXME : Add documentation |
finish_ingen | ingen_mod | Subroutine | FIXME : Add documentation |
finish_init | nonlinear_terms | Subroutine | FIXME : Add documentation |
finish_init | theta_grid | Subroutine | FIXME : Add documentation |
finish_init_g | init_g | Subroutine | FIXME : Add documentation |
finish_jfields_layouts | gs2_layouts | Subroutine | FIXME : Add documentation |
finish_kt_grids | kt_grids | Subroutine | FIXME : Add documentation |
finish_kt_grids_parameters | kt_grids | Subroutine | FIXME : Add documentation |
finish_layouts | gs2_layouts | Subroutine | FIXME : Add documentation |
finish_le_grids | le_grids | Subroutine | FIXME : Add documentation |
finish_mp | mp | Subroutine | Finalise 1 library if it hasn't been finalised already |
finish_nonblocking_max_vel_reduction | nonlinear_terms | Subroutine | Finish nonblocking calculation of the maximum velocity |
finish_nonlinear_convergence | diagnostics_nonlinear_convergence | Subroutine | FIXME : Add documentation |
finish_nonlinear_terms | nonlinear_terms | Subroutine | FIXME : Add documentation |
finish_normalisations | normalisations | Subroutine | Free memory etc. associated with normalisations |
finish_optimisation_config | optimisation_configuration | Subroutine | |
finish_parameter_scan | parameter_scan | Subroutine | FIXME : Add documentation |
finish_parameters_box | kt_grids_box | Subroutine | FIXME : Add documentation |
finish_parameters_range | kt_grids_range | Subroutine | FIXME : Add documentation |
finish_parameters_single | kt_grids_single | Subroutine | FIXME : Add documentation |
finish_parameters_specified | kt_grids_specified | Subroutine | FIXME : Add documentation |
finish_run_parameters | run_parameters | Subroutine | FIXME : Add documentation |
finish_setup | leq | Subroutine | Finish the leq setup |
finish_setup_eqfile | geo_utils | Subroutine | |
finish_species | species | Subroutine | FIXME : Add documentation |
finish_split_nonlinear_terms | split_nonlinear_terms | Subroutine | Reset the module, freeing memory etc. |
finish_theta_grid | theta_grid | Subroutine | FIXME : Add documentation |
finish_theta_grid_eik | theta_grid_eik | Subroutine | |
finish_theta_grid_file | theta_grid_file | Subroutine | FIXME : Add documentation |
finish_theta_grid_gridgen | theta_grid_gridgen | Subroutine | FIXME : Add documentation |
finish_theta_grid_params | theta_grid_params | Subroutine | FIXME : Add documentation |
finish_theta_grid_salpha | theta_grid_salpha | Subroutine | FIXME : Add documentation |
finish_transforms | gs2_transforms | Subroutine | FIXME : Add documentation |
finish_weights | le_grids | Subroutine | Deallocate the weights used to provide error estimates |
fitp_ceez | splines | Subroutine | FIXME : Add documentation |
fitp_curv1 | splines | Subroutine | FIXME : Add documentation (or tidyup above) |
fitp_curv2 | splines | Function | FIXME : Add documentation |
fitp_curvd | splines | Function | FIXME : Add documentation |
fitp_curvi | splines | Function | FIXME : Add documentation |
fitp_curvp1 | splines | Subroutine | FIXME : Add documentation |
fitp_curvp2 | splines | Function | FIXME : Add documentation |
fitp_curvpd | splines | Function | FIXME : Add documentation |
fitp_curvpi | splines | Function | FIXME : Add documentation |
fitp_intrv_helper | splines | Function | |
fitp_intrvl | splines | Function | FIXME : Add documentation |
fitp_intrvp | splines | Function | FIXME : Add documentation |
fitp_periodic_wrap_value | splines | Function | Given a value t, and stating value of abscissae, x, periodic with period p map t to the equivalent value in the range of x (i.e. between x(1) and x(1) + p) |
fitp_surf1 | splines | Subroutine | FIXME : Add documentation |
fitp_surf2 | splines | Function | FIXME : Add documentation |
fitp_terms | splines | Subroutine | FIXME : Add documentation |
flae | init_g | Subroutine | FIXME : Add documentation |
flush_files | gs2_diagnostics | Subroutine | Flush text files (only out_unit, res_unit, lpc_unit, and parity_unit) |
flux | diagnostics_fluxes | Subroutine | Calculate various fluxes |
flux_dist | diagnostics_fluxes | Subroutine | Diagnose the poloidal distribution of the particle, angular momentum, and energy fluxes |
flux_surface_type | geo_utils | Interface | |
flux_tube_field_like_to_ballooning_space | dist_fn | Subroutine | Extracts the field like data corresponding to the supercell with the {it, ik} wavenumber pair as a member and constructs the ballooning space form. By default includes duplicate theta points but can drop these on request. |
flux_vs_e | diagnostics_fluxes | Subroutine | FIXME : Add documentation |
flux_vs_theta_vs_vpa | diagnostics_fluxes | Subroutine | Calculate the momentum flux as a function of |
fluxavg | geometry | Function | FIXME : Add documentation |
fm_allocate | fields_local | Subroutine | Allocate storage space |
fm_allocate | fields_gf_local | Subroutine | Allocate storage space |
fm_calc_sc_heads | fields_local | Subroutine | |
fm_calc_sc_heads | fields_gf_local | Subroutine | Record the process that is the supercell head associated with a given ik,it point Supercells have a single ik but may have many it points so a given supercell head may be responsible for a range of points |
fm_check_an | fields_local | Subroutine | |
fm_count_subcom | fields_local | Subroutine | Count how many subcommunicators will be created |
fm_count_subcom | fields_gf_local | Subroutine | Count how many subcommunicators will be created |
fm_deallocate | fields_local | Subroutine | Deallocate storage space |
fm_deallocate | fields_gf_local | Subroutine | Deallocate storage space |
fm_debug_print | fields_local | Subroutine | Debug printing |
fm_debug_print | fields_gf_local | Subroutine | Debug printing |
fm_gather_fields | fields_local | Subroutine | Gather all the fields to proc0/all for diagnostics etc. DD>TAGGED:Worth looking at improving this bad memory pattern |
fm_gather_fields | fields_gf_local | Subroutine | Redistribute fields from gf_lo to g_lo. This first involves unpacking the calculated fields from tmpsum on the supercell heads to the field arrays and then sending them back to the processes that calculated them in gf_lo and the processes that need them in g_lo. DD>TAGGED:Worth looking at improving this bad memory pattern |
fm_gather_init_fields | fields_gf_local | Subroutine | Redistribute initial fields from gf_lo to g_lo. These are fields that have not been reduced to the supercell heads, just calculated on each process that owns gf_lo points |
fm_get_condition_numbers | fields_local | Subroutine | Fetch all condition numbers to proc0 and report on worrying values as required. |
fm_get_field_update | fields_local | Subroutine | A routine to calculate the update to the fields DD>Could improve performance by using a "smart" routine which only operates on local/not empty data |
fm_get_field_update | fields_gf_local | Subroutine | A routine to calculate the update to the fields |
fm_getfieldeq1_nogath | fields_local | Subroutine | |
fm_getfieldeq1_nogath | fields_gf_local | Subroutine | FIXME : Add documentation |
fm_getfieldeq_nogath | fields_local | Subroutine | |
fm_getfieldeq_nogath | fields_gf_local | Subroutine | FIXME : Add documentation |
fm_init | fields_local | Subroutine | Initialise the field objects |
fm_init | fields_gf_local | Subroutine | Initialise the field objects |
fm_init_next_field_points | fields_local | Subroutine | Initialise the next set of delta functions, find the response and store in the appropriate rows. DD>Could improve performance by using a "smart" routine which only operates on local/not empty data |
fm_init_next_field_points | fields_gf_local | Subroutine | Initialise the next set of delta functions, find the response and store in the appropriate rows. |
fm_make_subcom_1 | fields_local | Subroutine | Create all the necessary subcommunicators |
fm_make_subcom_1 | fields_gf_local | Subroutine | Create all the necessary subcommunicators |
fm_make_subcom_2 | fields_local | Subroutine | Create the secondary subcommunicators |
fm_make_subcom_2 | fields_gf_local | Subroutine | Create the secondary subcommunicators |
fm_populate | fields_local | Subroutine | Find the response of g to delta-fn field perturbations and store at the row level |
fm_populate | fields_gf_local | Subroutine | Find the response of g to delta-fn field perturbations and store at the row level |
fm_prepare | fields_local | Subroutine | Prepare the field matrix for calculating field updates |
fm_prepare | fields_gf_local | Subroutine | Prepare the field matrix for calculating field updates |
fm_reduce_an_head_send_broadcast | fields_local | Subroutine | |
fm_reset | fields_local | Subroutine | A routine to reset the object |
fm_reset | fields_gf_local | Subroutine | A routine to reset the object |
fm_scatter_fields | fields_gf_local | Subroutine | Redistribute the fields from g_lo to gf_lo This is used to take the initial fields that are calculated in initialisation using the fields_implicit functionality, and therefore in g_lo, and distribute them to gf_lo layout as well so that we can start the advance_gf_local routine with the correct field data in both formats. |
fm_set_is_local | fields_local | Subroutine | Just work out the locality (also sets is_empty etc. but is not intended for this) |
fm_set_is_local | fields_gf_local | Subroutine | Just work out the locality (also sets is_empty etc. but is not intended for this) |
fm_unpack_to_field | fields_local | Subroutine | A routine to unpack the supercell tmp_sum vectors to full field arrays |
fm_unpack_to_field | fields_gf_local | Subroutine | A routine to unpack the supercell tmp_sum vectors to full field arrays |
fm_update_fields | fields_local | Subroutine | Update the fields using calculated update |
fm_update_fields | fields_gf_local | Subroutine | Update the fields using calculated update We update both the g_lo (phi,apar,bpar) and gf_lo (gf_phi,gf_apar,gf_bpar) fields as these are needed to make sure we can progress the fields in g_lo and gf_lo both times and thereby not have to transfer the full fields for all processes every iteration, only the required updates. With some refactoring it should be possible to do all the work on a single set of field arrays as they are the same size regardless of the layout being used. |
fm_update_fields_newstep | fields_local | Subroutine | Update the fields using the new fields |
fm_update_fields_newstep | fields_gf_local | Subroutine | Update the fields using the new fields |
fm_write_debug_data | fields_local | Subroutine | Write some debug data to file |
fm_write_debug_data | fields_gf_local | Subroutine | Write some debug data to file |
format_key | abstract_config | Function | Takes a given key and formats it in a consistent style.
Currently that style is left justified in a character variable
of minimum length |
format_uuid | uuid_mod | Function | Convert an array of 1-byte integers into UUID format: "xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx" |
formatted_build_config | build_config | Function | |
free_comm | mp | Interface | |
free_comm_id | mp | Subroutine | A routine to free the communicator with id comm |
free_comm_type | mp | Subroutine | A routine to free the communicator represented by comm |
free_handle_persist | mp | Subroutine | Frees a single persistent request handle |
free_handles_persist | mp | Subroutine | Frees multiple persistent request handles |
free_request | mp | Interface | |
g_adjust | dist_fn_arrays | Interface | g_adjust transforms between representations of perturbed dist'n func'n.
|
g_adjust_direction | dist_fn_arrays | Subroutine | Transform between g_gs2 and g_wesson with direction indicated by passed logical [to_g_gs2]. |
g_adjust_floats | dist_fn_arrays | Subroutine | Transform between g_gs2 and g_wesson with direction indicated by passed floats [facphi] and [facbpar]. |
gather | redistribute | Interface | |
gemm | lapack_wrapper | Interface | |
gemv | lapack_wrapper | Interface | |
generate | mt19937 | Function | Generate a random number from a mt19937_type |
generate_grids | rungridgen | Subroutine | FIXME : Add documentation |
generate_uuid | uuid_mod | Function | Generate a version 4 UUID using either the libuuid library, or our own random number generator wrapper |
geo_FourierSeries | leq | Subroutine | Calculate the cylindrical at for the Fourier model |
geo_generalizedElongation | leq | Subroutine | Calculate the cylindrical at for the generalised elongation model |
geo_global | leq | Subroutine | Calculate the cylindrical at for the global MHD model |
geo_Miller | leq | Subroutine | Calculate the cylindrical (r, \theta) for the generalised Miller model |
geo_MillerExtendedHarmonic | leq | Subroutine | Calculate the cylindrical at for the Miller Extended Harmonic model |
geofax | eiktest | Subroutine | FIXME : Add documentation DD>WARNING : Rinnr has not been defined on first loop through DD>WARNING : Routr has not been defined on first loop through |
get_adams_bashforth_coefficients | gs2_time | Function | Returns the current set of Adams Bashforth coefficients. The order is determined by how much time history we have available up to a maximum of 3rd order. The coefficients are generalised for variable timestep. |
get_adjust | dist_fn_arrays | Function | Return the offset between g and h at a specific set of indices |
get_arg | multigs2 | Subroutine | |
get_ballstab_config | ballstab | Function | Get the module level config instance |
get_beta_prime | ballstab | Subroutine | Gets the current value of beta_prime (or equivalent var) Really just gets the variable that we can use to control the pressure gradient. |
get_choice | ingen_mod | Subroutine | FIXME : Add documentation |
get_collisions_config | collisions | Function | Get the module level config instance |
get_compiler_name | runtime_tests | Function | Returns the name of the compiler used |
get_configs | config_collection | Subroutine | Copy all the module-level configs into \p self. |
get_cross_phase | gs2_diagnostics | Subroutine | This is a highly simplified synthetic diagnostic which
calculates the cross phase between the electron density and the
perpendicular electron temperature for comparisons with DIII-D. |
get_cross_phase | diagnostics_turbulence | Subroutine | This is a highly simplified synthetic diagnostic which
calculates the cross phase between the electron density and the
perpendicular electron temperature for comparisons with DIII-D. |
get_default_name_ballstab_config | ballstab | Function | Gets the default name for this namelist |
get_default_name_collisions_config | collisions | Function | Gets the default name for this namelist |
get_default_name_diagnostics_base_config | diagnostics_base_configuration | Function | Gets the default name for this namelist |
get_default_name_dist_fn_config | dist_fn | Function | Gets the default name for this namelist |
get_default_name_dist_fn_species_config | dist_fn | Function | Gets the default name for this namelist |
get_default_name_driver_config | antenna | Function | Gets the default name for this namelist |
get_default_name_fields_config | fields | Function | Gets the default name for this namelist |
get_default_name_hyper_config | hyper | Function | Gets the default name for this namelist |
get_default_name_ingen_config | ingen_mod | Function | Gets the default name for this namelist |
get_default_name_init_g_config | init_g | Function | Gets the default name for this namelist |
get_default_name_interface | abstract_config | Interface | |
get_default_name_knobs_config | run_parameters | Function | Gets the default name for this namelist |
get_default_name_kt_grids_box_config | kt_grids_box | Function | Gets the default name for this namelist |
get_default_name_kt_grids_config | kt_grids | Function | Gets the default name for this namelist |
get_default_name_kt_grids_range_config | kt_grids_range | Function | Gets the default name for this namelist |
get_default_name_kt_grids_single_config | kt_grids_single | Function | Gets the default name for this namelist |
get_default_name_kt_grids_specified_config | kt_grids_specified | Function | Gets the default name for this namelist |
get_default_name_kt_grids_specified_element_config | kt_grids_specified | Function | Gets the default name for this namelist |
get_default_name_layouts_config | gs2_layouts | Function | Gets the default name for this namelist |
get_default_name_le_grids_config | le_grids | Function | Gets the default name for this namelist |
get_default_name_nonlinear_terms_config | nonlinear_terms | Function | Gets the default name for this namelist |
get_default_name_normalisations_config | normalisations | Function | Gets the default name for this namelist |
get_default_name_optimisation_config | optimisation_configuration | Function | Gets the default name for this namelist |
get_default_name_parameter_scan_config | parameter_scan | Function | Gets the default name for this namelist |
get_default_name_reinit_config | gs2_reinit | Function | Gets the default name for this namelist |
get_default_name_source_config | dist_fn | Function | Gets the default name for this namelist |
get_default_name_species_config | species | Function | Gets the default name for this namelist |
get_default_name_species_element_config | species | Function | Gets the default name for this namelist |
get_default_name_split_nonlinear_terms_config | split_nonlinear_terms | Function | Gets the default name for this namelist |
get_default_name_stir_config | antenna | Function | Gets the default name for this namelist |
get_default_name_theta_grid_config | theta_grid | Function | Gets the default name for this namelist |
get_default_name_theta_grid_eik_config | theta_grid_eik | Function | Gets the default name for this namelist |
get_default_name_theta_grid_file_config | theta_grid_file | Function | Gets the default name for this namelist |
get_default_name_theta_grid_gridgen_config | theta_grid_gridgen | Function | Gets the default name for this namelist |
get_default_name_theta_grid_parameters_config | theta_grid_params | Function | Gets the default name for this namelist |
get_default_name_theta_grid_salpha_config | theta_grid_salpha | Function | Gets the default name for this namelist |
get_default_netcdf_compression | netcdf_utils | Function | Returns the current value of use_compression_default |
get_default_netcdf_compression_level | netcdf_utils | Function | Returns the current value of deflate_level_default |
get_default_requires_index_ballstab_config | ballstab | Function | Gets the default requires index for this namelist |
get_default_requires_index_collisions_config | collisions | Function | Gets the default requires index for this namelist |
get_default_requires_index_diagnostics_base_config | diagnostics_base_configuration | Function | Gets the default requires index for this namelist |
get_default_requires_index_dist_fn_config | dist_fn | Function | Gets the default requires index for this namelist |
get_default_requires_index_dist_fn_species_config | dist_fn | Function | Gets the default requires index for this namelist |
get_default_requires_index_driver_config | antenna | Function | Gets the default requires index for this namelist |
get_default_requires_index_fields_config | fields | Function | Gets the default requires index for this namelist |
get_default_requires_index_hyper_config | hyper | Function | Gets the default requires index for this namelist |
get_default_requires_index_ingen_config | ingen_mod | Function | Gets the default requires index for this namelist |
get_default_requires_index_init_g_config | init_g | Function | Gets the default requires index for this namelist |
get_default_requires_index_interface | abstract_config | Interface | |
get_default_requires_index_knobs_config | run_parameters | Function | Gets the default requires index for this namelist |
get_default_requires_index_kt_grids_box_config | kt_grids_box | Function | Gets the default requires index for this namelist |
get_default_requires_index_kt_grids_config | kt_grids | Function | Gets the default requires index for this namelist |
get_default_requires_index_kt_grids_range_config | kt_grids_range | Function | Gets the default requires index for this namelist |
get_default_requires_index_kt_grids_single_config | kt_grids_single | Function | Gets the default requires index for this namelist |
get_default_requires_index_kt_grids_specified_config | kt_grids_specified | Function | Gets the default requires index for this namelist |
get_default_requires_index_kt_grids_specified_element_config | kt_grids_specified | Function | Gets the default requires index for this namelist |
get_default_requires_index_layouts_config | gs2_layouts | Function | Gets the default requires index for this namelist |
get_default_requires_index_le_grids_config | le_grids | Function | Gets the default requires index for this namelist |
get_default_requires_index_nonlinear_terms_config | nonlinear_terms | Function | Gets the default requires index for this namelist |
get_default_requires_index_normalisations_config | normalisations | Function | Gets the default requires index for this namelist |
get_default_requires_index_optimisation_config | optimisation_configuration | Function | Gets the default requires index for this namelist |
get_default_requires_index_parameter_scan_config | parameter_scan | Function | Gets the default requires index for this namelist |
get_default_requires_index_reinit_config | gs2_reinit | Function | Gets the default requires index for this namelist |
get_default_requires_index_source_config | dist_fn | Function | Gets the default requires index for this namelist |
get_default_requires_index_species_config | species | Function | Gets the default requires index for this namelist |
get_default_requires_index_species_element_config | species | Function | Gets the default requires index for this namelist |
get_default_requires_index_split_nonlinear_terms_config | split_nonlinear_terms | Function | Gets the default requires index for this namelist |
get_default_requires_index_stir_config | antenna | Function | Gets the default requires index for this namelist |
get_default_requires_index_theta_grid_config | theta_grid | Function | Gets the default requires index for this namelist |
get_default_requires_index_theta_grid_eik_config | theta_grid_eik | Function | Gets the default requires index for this namelist |
get_default_requires_index_theta_grid_file_config | theta_grid_file | Function | Gets the default requires index for this namelist |
get_default_requires_index_theta_grid_gridgen_config | theta_grid_gridgen | Function | Gets the default requires index for this namelist |
get_default_requires_index_theta_grid_parameters_config | theta_grid_params | Function | Gets the default requires index for this namelist |
get_default_requires_index_theta_grid_salpha_config | theta_grid_salpha | Function | Gets the default requires index for this namelist |
get_diagnostics_base_config | diagnostics_base_configuration | Function | Get the module level config instance |
get_diagnostics_config_config | diagnostics_config | Function | Get the module level config instance |
get_dim_length | gs2_io | Function | Wrapper around |
get_dist_fn_config | dist_fn | Function | Get the module level config instance |
get_dist_fn_species_config | dist_fn | Function | Get the array of module level config instances. If it isn't allocated, then return a zero-length array |
get_driver_config | antenna | Function | Get the module level config instance |
get_ediffuse_matrix | collisions | Subroutine | FIXME : Add documentation |
get_epar | diagnostics_final_routines | Subroutine | Calculate |
get_field_inconsistency | dist_fn | Subroutine | Calculates the potentials directly from the passed distribution function and compares the result to the passed potentials. Returns the maximum relative error for each potential. |
get_field_solution | fields_implicit | Subroutine | FIXME : Add documentation |
get_field_vector | fields_implicit | Subroutine | FIXME : Add documentation |
get_field_weighted_average_kperp2 | gs2_diagnostics | Function | Calculates <|field|2 kperp2>_theta / <|field|2>_theta. Useful for simple quasilinear metric |
get_fields_config | fields | Function | Get the module level config instance |
get_fields_direct_from_dfn | dist_fn | Subroutine | Inverts the field equations: gamtot * phi - gamtot1 * bpar = antot kperp2 * apar = antota beta/2 * gamtot1 * phi + (beta * gamtot2 + 1) * bpar = - beta * antotp |
get_file_proc | gs2_save | Function | Returns the file corresponding to restart file in current setup |
get_fldline_avg | gs2_diagnostics | Interface | Calculate the field-line average |
get_fldline_avg_c | gs2_diagnostics | Subroutine | Calculate the field-line average (complex values) |
get_fldline_avg_r | gs2_diagnostics | Subroutine | Calculate the field-line average (real values) |
get_flux | diagnostics_fluxes | Subroutine | Calculate the flux of a field |
get_flux_dist | diagnostics_fluxes | Subroutine | Identical to get_flux except don't integrate over poloidal angle ! JRB |
get_flux_vs_e | diagnostics_fluxes | Subroutine | FIXME : Add documentation |
get_flux_vs_theta_vs_vpa | diagnostics_fluxes | Subroutine | Calculates and returns toroidal momentum flux as a function of vpar and theta |
get_full | diagnostics_kinetic_energy_transfer | Subroutine | extend a 2D data array to negative ky-values with the original "unshifted" order |
get_git_hash | git_hash.fpp | Function | Returns the git hash of the current commit |
get_git_hash | git_version_mod | Interface | |
get_git_hash | runtime_tests | Function | This function is just a call of get_git_hash_runtime_info and is provided for backwards compatibility. |
get_git_hash_runtime_info | runtime_tests | Function | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Tests for git info !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Returns the git hash |
get_git_modified | runtime_tests | Function | This function is just a call of get_git_modified_runtime_info and is provided for backwards compatibility. |
get_git_modified_runtime_info | runtime_tests | Function | Returns whether the source code has been modified relative to the repository version |
get_git_state | git_hash.fpp | Function | Return "-dirty" if the repository has modifications to tracked files, or the empty string otherwise |
get_git_state | git_version_mod | Interface | |
get_git_version | git_hash.fpp | Function | Returns the git version from |
get_git_version | git_version_mod | Interface | |
get_gk_system | runtime_tests | Function | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! System info !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Returns the value of the "fedora" environment variable |
get_grids | theta_grid | Subroutine | FIXME : Add documentation |
get_grids | kt_grids | Subroutine | FIXME : Add documentation |
get_gs2_diagnostics_config | gs2_diagnostics | Function | Get the module level config instance |
get_gtran | diagnostics_velocity_space | Subroutine | Error estimate based on monitoring amplitudes of legendre polynomial coefficients. |
get_heat | gs2_heating | Subroutine | Calculate some heating quantities: - ion/electron heating - antenna power and B-field contributions to E and E_dot - gradient contributions to heating - hyperviscosity - hyperresistivity |
get_hermite_polynomials | diagnostics_fluxes | Interface | |
get_hermite_polynomials_1d | diagnostics_fluxes | Subroutine | Returns Gn = Hn / sqrt(2^n n!) / pi^(1/4), where Hn are the hermite polynomials i.e. int dx Gm * Gn exp(-x^2) = 1 |
get_hermite_polynomials_4d | diagnostics_fluxes | Subroutine | Returns Gn = Hn / sqrt(2^n n!) / pi^(1/4), where Hn are the hermite polynomials i.e. int dx Gm * Gn exp(-x^2) = 1 |
get_hyper_config | hyper | Function | Get the module level config instance |
get_idle_processes | ingen_mod | Subroutine | This subroutine is used to return the idle processes from the xxf and yxf layouts. Idle processes sometimes occur, dependent on the process count used, because the data domain does not evenly divide by the total number of processes available. These can cause high communications overheads for the non-linear calculations for large numbers of processes so it is useful to print this data out in ingen to let users know which process counts this can happen at for a given input file We currently use an arbitrary cutoff of 10% difference in idle processes to suggest that the unbalanced decomposition functionality should be used to mitigate the impact of this difference. |
get_ikm | diagnostics_kinetic_energy_transfer | Function | return the mediator index for either kx or ky |
get_indexed_namelist_unit | file_utils | Subroutine | Copy namelist, |
get_ingen_config | ingen_mod | Function | Get the module level config instance |
get_init_field | dist_fn | Subroutine | Calls get_fields_direct_from_dfn to solve for fields consistent with current gnew |
get_init_g_config | init_g | Function | Get the module level config instance |
get_initial_grids | rungridgen | Subroutine | FIXME : Add documentation |
get_initial_grids_3d | rungridgen | Subroutine | FIXME : Add documentation |
get_input_filename | file_utils | Function | Return the input filename as set by the command line |
get_input_unit | file_utils | Subroutine | Returns the file unit number associated with the input file |
get_intrvl_weights | le_grids | Subroutine | Used by get_weights to find the Lagrange quadrature weights for the given grid. |
get_inverse_error | split_nonlinear_terms | Function | Returns the normalised inverse error estimate. In other words the error tolerance, rtol*errors(2) + atol, divided by the error estimate (plus a small number to avoid divide by zero). |
get_jext | antenna | Subroutine | Calculate the external current in the antenna |
get_knobs_config | run_parameters | Function | Get the module level config instance |
get_kt_grids_box_config | kt_grids_box | Function | Get the module level config instance |
get_kt_grids_config | kt_grids | Function | Get the module level config instance |
get_kt_grids_range_config | kt_grids_range | Function | Get the module level config instance |
get_kt_grids_single_config | kt_grids_single | Function | Get the module level config instance |
get_kt_grids_specified_config | kt_grids_specified | Function | Get the module level config instance |
get_kt_grids_specified_element_config | kt_grids_specified | Function | Get the array of module level config instances. If it isn't allocated, then return a zero-length array |
get_laguerre_grids | gauss_quad | Subroutine | Returns Laguerre zeros and weights. The order is determined from the size of the array 'zero'. |
get_layouts_config | gs2_layouts | Function | Get the module level config instance |
get_le_grids_config | le_grids | Function | Get the module level config instance |
get_left_connection | dist_fn | Subroutine | FIXME : Add documentation |
get_leftmost_it | dist_fn | Function | Helper function for finding the leftmost it of supercell |
get_legendre_grids_from_cheb | gauss_quad | Subroutine | returns Legendre zeros and weights in the given interval [x1,x2]. The order is determined from the size of the array 'zero'. $ if (abs(sum(wgt)/abs(x2-x1)) - 1.0 > epsilon(wgt)) then $ print *, 'roundoff correction occurred' |
get_lorentz_matrix | collisions | Subroutine | FIXME : Add documentation |
get_max_vel | nonlinear_terms | Function | Given the max_vel_components array return the limiting max_vel |
get_mediator_helpers | diagnostics_kinetic_energy_transfer | Subroutine | create a boolean lookup for the valid mediator attribute of a pair of target wavevector and source wavevector |
get_mp_times | mp | Subroutine | Returns current requested timer values |
get_name_generic | abstract_config | Function | Returns the namelist name. Not very useful at the moment but may want to do more interesting things in the future |
get_namelists | ingen_mod | Subroutine | FIXME : Add documentation |
get_netcdf_code_precision | netcdf_utils | Function | Returns the correct netCDF constant for the |
get_netcdf_dim_length | netcdf_utils | Function | Wrapper around |
get_netcdf_file_id | gs2_io | Function | Provides read-only access to the netCDF file ID |
get_netcdf_movie_file_id | gs2_io | Function | Provides read-only access to the netCDF movie file ID |
get_nonlinear_terms_config | nonlinear_terms | Function | Get the module level config instance |
get_normalisations_config | normalisations | Function | Get the module level config instance |
get_omegaavg | gs2_diagnostics | Subroutine | Calculate the time-averaged complex frequency, check convergence criterion, and numerical instability criterion. |
get_optimisation_config | optimisation_configuration | Function | Get the module level config instance |
get_option_value | text_options | Subroutine | FIXME : Add documentation |
get_option_with_default | optionals | Interface | |
get_option_with_default_character | optionals | Function | Returns |
get_option_with_default_complex128 | optionals | Function | Returns |
get_option_with_default_complex32 | optionals | Function | Returns |
get_option_with_default_complex64 | optionals | Function | Returns |
get_option_with_default_integer | optionals | Function | Returns |
get_option_with_default_logical | optionals | Function | Returns |
get_option_with_default_real128 | optionals | Function | Returns |
get_option_with_default_real32 | optionals | Function | Returns |
get_option_with_default_real64 | optionals | Function | Returns |
get_parallel_statistics | gs2_main | Subroutine | Gets statistics of passed real value across all processes. Intended for use with our timers. |
get_parameter_scan_config | parameter_scan | Function | Get the module level config instance |
get_parameters_as_surf | theta_grid_params | Function | Packs all relevant parameters into a flux_surface_type instance. Note we can't fully populate the surface instance as we don't hold delrho |
get_parity_conn | dist_fn | Subroutine | Return the iglo corresponding to the part of the domain given by iglo reflected in theta=theta0 |
get_phi0 | diagnostics_fields | Function | Calculate the |
get_phi_mediator | diagnostics_kinetic_energy_transfer | Subroutine | calculate the mediator mode for all possible pairs of source and target wavevectors |
get_plotdata | rungridgen | Subroutine | |
get_proc_name | mp | Subroutine | FIXME : Add documentation |
get_quadrature_rule | genquad | Subroutine | Accepts a weighting function (with only one argument), defined as external, calculates the modified moments, and returns the abscissae and weights for a new scheme based on polynomials orthogonal to the given weight function. The method is that of Wheeler. Also described in Numerical Recipes, 3rd ed. section 4.6.2 and 4.6.3. Input: Suitable integration weights as a single-argument function. Defined as "external" in calling routine! Input: The number of integration points desired Input: The left boundary of the integration domain Input: The right boundary of the integration domain Output: The abscissae (quadrature points) for integration Output: The integration weights Optional: Set to true to make lower bound -inf Optional: Set to true to make upper bound +inf |
get_radau_gauss_grids | gauss_quad | Subroutine | returns radau zeros and weights in the given interval [x1,x2]. The order is determined from the size of the array 'zero'. Note that the last element of 'zero' and 'wgt' are the fixed lower endpoint -1 in (1,-1] Note also that 'zero'(i) contains the zeros in descending order 1 -> -1 with increasing i |
get_random_seed | uuid_mod | Function | Uses a method for getting a nice seed for the PRNG taken from gfortran documentation |
get_redist_times | redistribute | Subroutine | Returns current requested timer values |
get_redistname | redistribute | Function | Get redistname |
get_reinit_config | gs2_reinit | Function | Get the module level config instance |
get_requires_index_generic | abstract_config | Function | Returns the requires_index value. Allows access whilst keeping the variable private |
get_restart_dir | init_g | Function | Returns the value of restart_dir |
get_right_connection | dist_fn | Subroutine | FIXME : Add documentation |
get_rightmost_it | dist_fn | Function | Helper function for finding the rightmost it of supercell |
get_rk_scheme | rk_schemes | Function | Returns an rk_scheme instance describing the scheme represented by the passed variant type. |
get_rk_scheme_by_id | rk_schemes | Function | Returns an rk_scheme instance describing the scheme with id matching the passed id value. |
get_rk_schemes_as_text_options | rk_schemes | Function | Returns an array of text_option values representing the known rk schemes, mapping names to integer ids |
get_rnd_seed | ran | Subroutine | Returns the current value of the generator seed. This is not currently supported by the Mersenne generator so in this case we return 0. |
get_rnd_seed_length | ran | Function | Gets the length of the integer vector for the random number generator seed. This is always 1 for the Mersenne case but otherwise depends on the compiler version. |
get_shat | ballstab | Subroutine | Gets the current value of shat |
get_sizes | theta_grid | Subroutine | FIXME : Add documentation |
get_sizes | kt_grids | Subroutine | FIXME : Add documentation |
get_source_config | dist_fn | Function | Get the module level config instance |
get_source_term | dist_fn | Subroutine | FIXME : Add documentation !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Default choice: solve self-consistent equations !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Solve self-consistent terms + include external i omega_d * F_0 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Do matrix multiplications !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! special source term for totally trapped particles !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CMR, 13/10/2014: Upper limit of following loops setting source changed from ntgrid to ntgrid-1 Source is allocated as: source(-ntgrid:ntgrid-1), so ntgrid is out of bounds. |
get_source_term_on_local_domain | dist_fn | Subroutine | Calculates the regular source term on the entire local
domain and stores in the output |
get_source_term_opt | dist_fn | Subroutine | This is a version of get_source_term which does both sign (sigma) together and uses precalculated constant terms. Leads to more memory usage than original version but can be significantly faster (~50%) |
get_species_config | species | Function | Get the module level config instance |
get_species_element_config | species | Function | Get the array of module level config instances. If it isn't allocated, then return a zero-length array |
get_specific_response_file_name | fields_arrays | Function | This function returns the response file name when given characteristic data. |
get_split_nonlinear_terms_config | split_nonlinear_terms | Function | Get the module level config instance |
get_status_entry | memory_usage | Function | Try to read an integer from /proc/self/status. Returns negative if not possible to open file. |
get_stir_config | antenna | Function | Get the array of module level config instances. If it isn't allocated, then return a zero-length array |
get_surf_average | gs2_diagnostics | Subroutine | FIXME : Add documentation |
get_theta_grid_config | theta_grid | Function | Get the module level config instance |
get_theta_grid_eik_config | theta_grid_eik | Function | Get the module level config instance |
get_theta_grid_file_config | theta_grid_file | Function | Get the module level config instance |
get_theta_grid_gridgen_config | theta_grid_gridgen | Function | Get the module level config instance |
get_theta_grid_parameters_config | theta_grid_params | Function | Get the module level config instance |
get_theta_grid_salpha_config | theta_grid_salpha | Function | Get the module level config instance |
get_trapped_lambda_grid_error_estimate_weights | le_grids | Subroutine | Routine for getting the weights used in estimating the error on trapped particle integrals as a part of trap_error |
get_unbalanced_suggestions | ingen_mod | Subroutine | This subroutine is used to return the unbalanced suggestions for a given process count (npe). The calculation is performed using the calculate_unbalanced_x and calculate_unbalanced_y subroutines from gs2_layouts. These return the unbalanced decomposition size (difference between the suggested small and large block size for the decomposition) and from this a logical is set to recommend whether the unbalanced decomposition should be used or not. |
get_unused_unit | file_utils | Subroutine | Get an unused unit number for I/O. |
get_verbosity | runtime_tests | Function | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Testing the runtime environment !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! This function interrogates the environment variable GK_VERBOSITY and returns its integer value. This is used to control the level of debug output (not diagnostic/physics output). Normal levels range from 0 to 5, with output getting heavier as the value increases. Values higher than 5 can be used for specialised/very heavy output. |
get_verr | diagnostics_velocity_space | Subroutine | Error estimate obtained by comparing standard integral with less-accurate integral |
get_vol_average | gs2_diagnostics | Interface | |
get_vol_average_all | gs2_diagnostics | Subroutine | FIXME : Add documentation |
get_vol_average_one | gs2_diagnostics | Subroutine | FIXME : Add documentation |
get_vol_int | gs2_diagnostics | Interface | |
get_vol_int_all | gs2_diagnostics | Subroutine | FIXME : Add documentation |
get_vol_int_one | gs2_diagnostics | Subroutine | FIXME : Add documentation |
get_volume_average | gs2_diagnostics | Subroutine | FIXME : Add documentation |
get_volume_int | gs2_diagnostics | Subroutine | FIXME : Add documentation |
get_weights | le_grids | Subroutine | The get_weights subroutine determines how to divide up the integral into subintervals and how many grid points should be in each subinterval |
get_wisdom_file | gs2_layouts | Subroutine | Set the fft_wisdom_file based on the value set in the namelist (if any) and the value in the GK_FFTW3_WISDOM environment variable |
get_z_factor | diagnostics_kinetic_energy_transfer | Subroutine | where the second term, , is unique for kinetic energy transfer and does not appear for internal energy transfer or entropy transfer |
getan | dist_fn | Subroutine | Compute velocity space integrals over : |
getan_from_dfn | dist_fn | Subroutine | Compute velocity space integrals over : |
getan_nogath | dist_fn | Subroutine | Calls getan_nogath_from_dfn to calculate antot arrays for current gnew value |
getan_nogath_from_dfn | dist_fn | Subroutine | Getan_nogath has been substantially changed to enable gf_lo field calculations, it can now operate in 2 modes; using the standard integrate_species (integrate_species_sub in le_grids) when called from fields_local and gf_lo_integrate is false (which is teh default, or doing the integrate in place when called from fields_gf_local or from fields_local when gf_lo_integrate is true. Note, if this is called from fields_local and gf_lo_integrate is true then the calculation will be done locally but there is a function called after this has finished in fields_local that sends the data back (from gf_lo to g_lo layouts). When call with gf_lo_integrate = .true. this routine does a gather that converts the gnew array from g_lo data distribution to gf_lo data distribution and stores the result in gfarray. With gf_lo_integrate = .false. g_in is used instead and this is in g_lo data distribution. |
getemoms | diagnostics_moments | Subroutine | Returns electron density and Tperp moment integrals to PE 0 |
getfield | fields_implicit | Subroutine | FIXME : Add documentation |
getfield_gf_local | fields_gf_local | Subroutine | Calculate the update to the fields |
getfield_local | fields_local | Subroutine | Calculate the update to the fields |
getfieldeq | dist_fn | Subroutine | FIXME : Add documentation |
getfieldeq1 | dist_fn | Subroutine | FIXME : Add documentation |
getfieldeq1_nogath | dist_fn | Subroutine | FIXME : Add documentation |
getfieldeq_nogath | dist_fn | Subroutine | FIXME : Add documentation |
getmoms | diagnostics_moments | Subroutine | Calculate various moments of the distribution function
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
integrate moments over the nonadiabatic part of |
getmoms_notgc | diagnostics_moments | Subroutine | Calculates moments at not guiding center coordinate |
getrf | lapack_wrapper | Interface | |
getri | lapack_wrapper | Interface | |
ginit | init_g | Subroutine | FIXME : Add documentation |
ginit_alf | init_g | Subroutine | FIXME : Add documentation |
ginit_all_modes_equal | init_g | Subroutine | Initialize with every parallel and perpendicular mode having equal amplitude. Only makes sense in a linear calculation. k_parallel is specified with kpar_init or with ikpar_init when periodic boundary conditions are used. EGH doc> reality condition for ky = 0 component: |
ginit_cgyro | init_g | Subroutine | Sets g to a constant value everywhere except zonal component which is 0 Default initial conditions for CGYRO |
ginit_constant | init_g | Subroutine | Initialise the distribution function to a constant but satisfying forbidden regions. Can scale the zonal component separately as usual. |
ginit_convect | init_g | Subroutine | FIXME : Add documentation |
ginit_default | init_g | Subroutine | Set initial condition to gaussian in |
ginit_default_odd | init_g | Subroutine | Set initial condition to gaussian in |
ginit_gs | init_g | Subroutine | FIXME : Add documentation |
ginit_harris | init_g | Subroutine | FIXME : Add documentation |
ginit_kpar | init_g | Subroutine | FIXME : Add documentation |
ginit_kz0 | init_g | Subroutine | Initialise with only the kparallel = 0 mode. |
ginit_nl | init_g | Subroutine | "nl": Two modes set to constant amplitude. Controlled by: |
ginit_nl2 | init_g | Subroutine | "nl2": Two modes proportional to . Controlled by: |
ginit_nl3 | init_g | Subroutine | "nl3": Two modes with a Gaussian envelope, and perturbation in fields of form , except for parallel velocity which uses is 90 degrees out of phase and uses . Density, parallel velocity, and perpendicular and parallel temperatures can all be controlled independently. Controlled by: |
ginit_nl3r | init_g | Subroutine | FIXME : Add documentation |
ginit_nl4 | init_g | Subroutine | FIXME : Add documentation |
ginit_nl5 | init_g | Subroutine | FIXME : Add documentation |
ginit_nl6 | init_g | Subroutine | FIXME : Add documentation |
ginit_nl7 | init_g | Subroutine | FIXME : Add documentation |
ginit_noise | init_g | Subroutine | Initialise the distribution function with random noise. This is the recommended initialisation option. Each different mode is given a random amplitude between zero and one. |
ginit_ot | init_g | Subroutine | Orszag-Tang 2D vortex problem phi, jpar are local !! $ phi(:,1,2) = phiinit * cmplx(2.0, 0.0) ! 2 cos(y) $ phi(:,2,1) = phiinit * cmplx(1.0, 0.0) ! 2 cos(x) $ jpar(:,1,2) = apar0 * cmplx(2.0, 0.0) ! 2 cos(y) $ jpar(:,3,1) = apar0 * cmplx(2.0, 0.0) ! 4 cos(2x) |
ginit_random_sine | init_g | Subroutine | Construct the initial condition from a sum of sine waves scaled with random amplitude up to phiinit (ky > 0) or zf_init (ky == 0). Use mode numbers up to minimum of max_mode or last resolved wave (i.e. ntheta/8). |
ginit_recon | init_g | Subroutine | FIXME : Add documentation |
ginit_recon3 | init_g | Subroutine | FIXME : Add documentation |
ginit_restart_eig | init_g | Subroutine | Uses the restart files written by the eigensolver. File to read is set by restart_eig_id |
ginit_restart_many | init_g | Subroutine | Restore |
ginit_restart_no_zonal | init_g | Subroutine | Restart but remove the zonal flow (ky = 0) component upon restarting. |
ginit_restart_small | init_g | Subroutine | Restores |
ginit_restart_smallflat | init_g | Subroutine | Similar to |
ginit_restart_zonal_only | init_g | Subroutine | Restart but set all non-zonal components of the potential and the distribution function to 0. Noise can be added to these other components by setting phiinit > 0. The size of the zonal flows can be adjusted using zf_init. |
ginit_rh | init_g | Subroutine | FIXME : Add documentation |
ginit_single_parallel_mode | init_g | Subroutine | Initialise only with a single parallel mode specified by either ikpar_init for periodic boundary conditions or kpar_init for linked boundary conditions. Only makes sense for linear calculations. doc> reality condition for ky = 0 component: |
ginit_stationary_mode | init_g | Subroutine | The stationary mode test case is a method of testing the geometry implementation by initializing the distribution function in a particular way For collisionless runs with ky=0, we expect the solution to be time-independent (see section 3.3.1 of Ball MIT Masters thesis) |
ginit_test3 | init_g | Subroutine | FIXME : Add documentation |
ginit_xi | init_g | Subroutine | FIXME : Add documentation |
ginit_xi2 | init_g | Subroutine | FIXME : Add documentation |
ginit_zero | init_g | Subroutine | FIXME : Add documentation |
gradient | geo_utils | Subroutine | |
gradl | geometry | Subroutine | Compute df / dltheta using a periodic central difference. The
input |
gradstottgrid | geometry | Subroutine | FIXME : Add documentation |
grid_has_trapped_particles | le_grids | Function | Returns true if there are trapped particles on the current pitch angle grid. |
gridgen4_1 | gridgen4mod | Subroutine | FIXME : Add documentation |
gridgen4_2 | gridgen4mod | Subroutine | FIXME : Add documentation |
gridgen_get_grids | theta_grid_gridgen | Subroutine | FIXME : Add documentation DD>NOTE: Regrid assumes nnew<nold but doesn't check it. Do we need to? |
grnd | mt19937 | Function | Generate a random number from the module-level mt19937_type instance |
group_to_all | mp | Interface | |
group_to_all_real | mp | Subroutine | FIXME : Add documentation |
group_to_all_real_array | mp | Subroutine | FIXME : Add documentation |
gs2_abs | array_utils | Interface | Interface to helper functions for finding magnitude of an array |
gs2_abs_complex_array_2 | array_utils | Function | Return absolute of 2D array |
gs2_abs_complex_array_3 | array_utils | Function | Return absolute of 3D array |
gs2_abs_real_array_2 | array_utils | Function | Return absolute of 2D array |
gs2_abs_real_array_3 | array_utils | Function | Return absolute of 3D array |
gs2_max_abs | array_utils | Interface | Interface to helper functions for finding maxval of magnitude of an array |
gs2_max_abs_complex_array_2 | array_utils | Function | Find maximum of abs 2D array |
gs2_max_abs_complex_array_3 | array_utils | Function | Find maximum of abs 3D array |
gs2_max_abs_real_array_2 | array_utils | Function | Find maximum of abs 2D array |
gs2_max_abs_real_array_3 | array_utils | Function | Find maximum of abs 3D array |
gs2_maxval | array_utils | Interface | Interface to helper functions for finding the maximum in an array |
gs2_maxval_real_array_2 | array_utils | Function | Find maximum in 2D array |
gs2_maxval_real_array_3 | array_utils | Function | Find maximum in 3D array |
gs2_restore | gs2_save | Interface | |
gs2_restore_many | gs2_save | Subroutine | FIXME : Add documentation |
gs2_restore_response | gs2_save | Subroutine | This routine reads a square complex array from a file with passed name |
gs2_save_for_restart | gs2_save | Subroutine | Create and fill the restart files |
gs2_save_response | gs2_save | Subroutine | This routine writes a passed square complex array to a file with passed name |
gs2_save_slice | gs2_save | Subroutine | Save g slices |
gs2d_read_and_set | eeq | Subroutine | This subroutine reads a GS2D output file containing the axisymmetric magnetic field geometry on a rectangular domain defined by the coordinates (R,Z). |
hahm_burrell | geo_utils | Subroutine | FIXME : Add documentation |
handle_processor_request | gs2_layouts | Function | Handle nproc values outside valid range (i.e. <= 0 or > nproc_total). Values outside of this range are replaced with nproc_total |
handle_spline_error | splines | Interface | |
handle_spline_error_logical | splines | Subroutine | If not valid abort with error noting invalid spline and which method was invoked |
has_electron_species | species | Function | Determine if any of the known species are electron like |
has_hybrid_electron_species | species | Function | Determine if any of the known species are hybrid electrons |
has_ion_species | species | Function | Determine if any of the known species are ion like |
has_linked_boundary | dist_fn | Function | Returns true if we're using linked boundary conditions and false otherwise |
has_nonmaxw_species | species | Function | Determine if any of the known species are non-Maxwellian |
hdf_finish | hdf_wrapper | Subroutine | FIXME : Add documentation |
hdf_init | hdf_wrapper | Subroutine | FIXME : Add documentation |
heating | gs2_diagnostics | Subroutine | Calculate some heating diagnostics, and update their time history |
hk_repack | gs2_heating | Subroutine | FIXME : Add documentation |
hsg_func | collisions | Function | FIXME : Add documentation |
hyper_diff | hyper | Subroutine | FIXME : Add documentation |
i_1_insertsort | sorting | Subroutine | Sorts integer arrays |
i_1_quicksort | sorting | Subroutine | Sort an integer array based on integer KEY |
i_2_insertsort | sorting | Subroutine | Sorts integer arrays |
i_2_quicksort | sorting | Subroutine | Sort two integer arrays based on integer KEY |
i_3_insertsort | sorting | Subroutine | Sorts integer arrays |
i_3_quicksort | sorting | Subroutine | Sort three integer arrays based on integer KEY |
i_fill_2 | redistribute | Subroutine | FIXME : Add documentation |
i_fill_3 | redistribute | Subroutine | FIXME : Add documentation |
i_fill_4 | redistribute | Subroutine | FIXME : Add documentation |
i_insertsort | sorting | Subroutine | Sorts integer array |
i_quicksort | sorting | Subroutine | Sort an integer array based on integer KEY |
i_redist_12 | redistribute | Subroutine | FIXME : Add documentation |
i_redist_22 | redistribute | Subroutine | FIXME : Add documentation |
i_redist_22_inv | redistribute | Subroutine | FIXME : Add documentation |
i_redist_32 | redistribute | Subroutine | FIXME : Add documentation |
i_redist_32_inv | redistribute | Subroutine | FIXME : Add documentation |
i_redist_42 | redistribute | Subroutine | FIXME : Add documentation |
i_redist_42_inv | redistribute | Subroutine | FIXME : Add documentation |
i_swap_elem | sorting | Subroutine | Swaps element at |
idx | gs2_layouts | Interface | |
idx_accelx | gs2_layouts | Function | FIXME : Add documentation |
idx_e | gs2_layouts | Function | FIXME : Add documentation |
idx_f | gs2_layouts | Function | FIXME : Add documentation |
idx_g | gs2_layouts | Function | Return the global index in the g_lo layout given the dimensional indices |
idx_gf | gs2_layouts | Function | FIXME : Add documentation |
idx_jf | gs2_layouts | Function | FIXME : Add documentation |
idx_le | gs2_layouts | Function | FIXME : Add documentation |
idx_local | gs2_layouts | Interface | |
idx_local_accelx | gs2_layouts | Function | FIXME : Add documentation |
idx_local_e | gs2_layouts | Function | FIXME : Add documentation |
idx_local_f | gs2_layouts | Function | FIXME : Add documentation |
idx_local_g | gs2_layouts | Function | Return whether a point is local to a processor given the dimensional indices |
idx_local_gf | gs2_layouts | Function | FIXME : Add documentation |
idx_local_jf | gs2_layouts | Function | FIXME : Add documentation |
idx_local_le | gs2_layouts | Function | FIXME : Add documentation |
idx_local_lz | gs2_layouts | Function | FIXME : Add documentation |
idx_local_parity | gs2_layouts | Function | FIXME : Add documentation |
idx_local_xxf | gs2_layouts | Function | Return whether a point is local to a processor given the dimensional indices |
idx_local_yxf | gs2_layouts | Function | Return whether a point is local to a processor given the dimensional indices |
idx_lz | gs2_layouts | Function | FIXME : Add documentation |
idx_parity | gs2_layouts | Function | FIXME : Add documentation |
idx_xxf | gs2_layouts | Function | Return the global index in the xxf_lo layout given the dimensional indices |
idx_yxf | gs2_layouts | Function | Return the global index in the yxf_lo layout given the dimensional indices |
ie_idx | gs2_layouts | Interface | |
ie_idx_accelx | gs2_layouts | Function | FIXME : Add documentation |
ie_idx_g | gs2_layouts | Function | Return the energy index, given g-layout and a global index |
ie_idx_lz | gs2_layouts | Function | FIXME : Add documentation |
ie_idx_parity | gs2_layouts | Function | FIXME : Add documentation |
ie_idx_xxf | gs2_layouts | Function | Return the energy index, given xxf-layout and a global index |
ie_idx_yxf | gs2_layouts | Function | Return the energy index, given yxf-layout and a global index |
if_idx | gs2_layouts | Interface | |
if_idx_f | gs2_layouts | Function | FIXME : Add documentation |
if_idx_jf | gs2_layouts | Function | FIXME : Add documentation |
ifield_idx | gs2_layouts | Interface | |
ifield_idx_f | gs2_layouts | Function | FIXME : Add documentation |
ifield_idx_jf | gs2_layouts | Function | FIXME : Add documentation |
ig_idx | gs2_layouts | Interface | |
ig_idx_e | gs2_layouts | Function | FIXME : Add documentation |
ig_idx_f | gs2_layouts | Function | FIXME : Add documentation |
ig_idx_jf | gs2_layouts | Function | FIXME : Add documentation |
ig_idx_le | gs2_layouts | Function | FIXME : Add documentation |
ig_idx_lz | gs2_layouts | Function | FIXME : Add documentation |
ig_idx_xxf | gs2_layouts | Function | Return the theta index, given xxf-layout and a global index |
ig_idx_yxf | gs2_layouts | Function | Return the theta index, given yxf-layout and a global index of a point on this proc |
ig_local_accelx | gs2_layouts | Function | FIXME : Add documentation |
ig_local_e | gs2_layouts | Function | FIXME : Add documentation |
ig_local_f | gs2_layouts | Function | FIXME : Add documentation |
ig_local_g | gs2_layouts | Function | Return whether a point is local to a processor given the global index |
ig_local_gf | gs2_layouts | Function | FIXME : Add documentation |
ig_local_jf | gs2_layouts | Function | FIXME : Add documentation |
ig_local_le | gs2_layouts | Function | FIXME : Add documentation |
ig_local_lz | gs2_layouts | Function | FIXME : Add documentation |
ig_local_parity | gs2_layouts | Function | FIXME : Add documentation |
ig_local_xxf | gs2_layouts | Function | Return whether a point is local to a processor given the global index |
ig_local_yxf | gs2_layouts | Function | Return whether a point is local to a processor given the global index |
ij_idx | gs2_layouts | Interface | |
ij_idx_f | gs2_layouts | Function | FIXME : Add documentation |
ij_idx_jf | gs2_layouts | Function | FIXME : Add documentation |
ik_idx | gs2_layouts | Interface | |
ik_idx_accel | gs2_layouts | Function | FIXME : Add documentation |
ik_idx_accelx | gs2_layouts | Function | FIXME : Add documentation |
ik_idx_e | gs2_layouts | Function | FIXME : Add documentation |
ik_idx_f | gs2_layouts | Function | FIXME : Add documentation |
ik_idx_g | gs2_layouts | Function | Return the ky index, given g-layout and a global index |
ik_idx_gf | gs2_layouts | Function | FIXME : Add documentation |
ik_idx_jf | gs2_layouts | Function | FIXME : Add documentation |
ik_idx_le | gs2_layouts | Function | FIXME : Add documentation |
ik_idx_lz | gs2_layouts | Function | FIXME : Add documentation |
ik_idx_parity | gs2_layouts | Function | FIXME : Add documentation |
ik_idx_xxf | gs2_layouts | Function | Return the ky index, given xxf-layout and a global index |
il_idx | gs2_layouts | Interface | |
il_idx_accelx | gs2_layouts | Function | FIXME : Add documentation |
il_idx_e | gs2_layouts | Function | FIXME : Add documentation |
il_idx_g | gs2_layouts | Function | Return the lambda index, given g-layout and a global index |
il_idx_parity | gs2_layouts | Function | FIXME : Add documentation |
il_idx_xxf | gs2_layouts | Function | Return the lambda index, given xxf-layout and a global index |
il_idx_yxf | gs2_layouts | Function | Return the lambda index, given yxf-layout and a global index |
il_is_passing | le_grids | Function | Returns true if the passed pitch angle grid point is considered passing. |
il_is_trapped | le_grids | Function | Returns true if the passed pitch angle grid point is considered trapped. |
il_is_wfb | le_grids | Function | Returns true if the passed pitch angle grid point is considered the wfb. |
im_idx | gs2_layouts | Interface | |
im_idx_f | gs2_layouts | Function | FIXME : Add documentation |
in_idx | gs2_layouts | Interface | |
in_idx_f | gs2_layouts | Function | FIXME : Add documentation |
increase_time_step | gs2_reinit | Subroutine | Increases the time step by a factor |
increment_scan_parameter | parameter_scan | Subroutine | FIXME : Add documentation |
init | gs2_init | Interface | |
init_3d | gs2_transforms | Subroutine | FIXME : Add documentation |
init_accel_fft | gs2_transforms | Subroutine | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Setup accelerated 2D or SHMEM 42(s) |
init_accel_transform_layouts | gs2_layouts | Subroutine | Setup the module level accelx_lo and accel_lo instances |
init_allfields_gf_local | fields_gf_local | Subroutine | Initialise the fields from the initial g, just uses the fields_implicit routine |
init_allfields_implicit | fields_implicit | Subroutine | FIXME : Add documentation |
init_allfields_local | fields_local | Subroutine | Initialise the fields from the initial g, just uses the fields_implicit routine |
init_and_dump | dump_response | Subroutine | Initialise the response matrices and write to file |
init_ant_amp | gs2_save | Subroutine | FIXME : Add documentation |
init_antenna | antenna | Subroutine | FIXME : Add documentation |
init_antenna_data | antenna_data | Subroutine | FIXME : Add documentation |
init_arrays | collisions | Subroutine | FIXME : Add documentation |
init_ballstab | ballstab | Subroutine | Initialise grids, other modules etc. |
init_bc | dist_fn | Subroutine | FIXME : Add documentation |
init_bessel | dist_fn | Subroutine | Compute and store the Bessel functions required for future usage, aj0 and aj1. |
init_ccfftw | fft_work | Subroutine | Create an FFTW plan for complex-to-complex transforms |
init_checktime | job_manage | Subroutine | FIXME : Add documentation |
init_collisional | collisional_heating | Subroutine | FIXME : Add documentation |
init_collisions | collisions | Subroutine | FIXME : Add documentation |
init_comm | mp | Subroutine | Initialise a communicator and associated variables |
init_connected_bc | dist_fn | Subroutine | Coordinates the calculation of all data required for later application of linked boundary conditions. Deals with identifying the communication pattern and creating the associated redistributes used to perform the required communication. |
init_constant_random | constant_random | Subroutine | |
init_crfftw | fft_work | Interface | |
init_crfftw_1d | fft_work | Subroutine | Create FFTW plan suitable for 1D complex to real transformation |
init_crfftw_2d | fft_work | Subroutine | Create FFTW plan suitable for 2D complex to real transformation |
init_delt | gs2_time | Subroutine | Set the full timestep history. Inputs set the current, previous and last but one timesteps |
init_diagnostics_antenna | diagnostics_antenna | Subroutine | FIXME : Add documentation |
init_diagnostics_config | diagnostics_config | Subroutine | |
init_diagnostics_fluxes | diagnostics_fluxes | Subroutine | Allocate and zero module-level arrays |
init_diagnostics_heating | diagnostics_heating | Subroutine | FIXME : Add documentation |
init_diagnostics_kinetic_energy_transfer | diagnostics_kinetic_energy_transfer | Subroutine | |
init_diagnostics_omega | diagnostics_omega | Subroutine | Allocate arrays for storing omega history and averages |
init_diagnostics_transfer | diagnostics_zonal_transfer | Subroutine | FIXME : Add documentation initialize zonal_transfer to zero |
init_diagnostics_velocity_space | diagnostics_velocity_space | Subroutine | FIXME : Add documentation |
init_diffuse_conserve | collisions | Subroutine | Precompute three quantities needed for momentum and energy conservation: bz0, bw0, bs0 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Now get z0 (first form) $OMP PARALLEL DO DEFAULT(none) & $OMP PRIVATE(iglo, ik, it, ie, il, is, isgn, ig) & $OMP SHARED(g_lo, ntgrid, forbid, bz0tmp, code_dt, vnmult, vnew_E, & $OMP aj0, duinv, conserve_forbid_zero) & $OMP SCHEDULE(static) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Now get v0z0 $OMP PARALLEL DO DEFAULT(none) & $OMP PRIVATE(iglo, ik, ie, is, isgn) & $OMP SHARED(g_lo, gtmp, vnmult, vnew_E, aj0, bz0tmp) & $OMP SCHEDULE(static) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Redefine z0 = z0 / (1 + v0z0) $OMP PARALLEL DO DEFAULT(none) & $OMP PRIVATE(iglo, ik, it, is, isgn) & $OMP SHARED(g_lo, bz0tmp, dtmp) & $OMP SCHEDULE(static) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! redefine dq = du (for momentum-conserving terms) du == int (E nu_s f_0); du = du(z, kx, ky, s) duinv = 1/du $OMP PARALLEL DO DEFAULT(none) & $OMP PRIVATE(iglo, ik, ie, is, isgn) & $OMP SHARED(g_lo, gtmp, vns, vpa) & $OMP SCHEDULE(static) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Now get s0 (first form) $OMP PARALLEL DO DEFAULT(none) & $OMP PRIVATE(iglo, ik, it, ie, is, isgn) & $OMP SHARED(g_lo, bs0tmp, vns, vpa, aj0, code_dt, duinv) & $OMP SCHEDULE(static) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Now get v0s0 $OMP PARALLEL DO DEFAULT(none) & $OMP PRIVATE(iglo, ik, ie, is, isgn) & $OMP SHARED(g_lo, gtmp, vnmult, vnew_E, aj0, bs0tmp) & $OMP SCHEDULE(static) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Redefine s0 = s0 - v0s0 * z0 / (1 + v0z0) $OMP PARALLEL DO DEFAULT(none) & $OMP PRIVATE(iglo, ik, it, is, isgn) & $OMP SHARED(g_lo, bs0tmp, dtmp, bz0tmp) & $OMP SCHEDULE(static) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Now get v1s0 $OMP PARALLEL DO DEFAULT(none) & $OMP PRIVATE(iglo, ik, ie, is, isgn) & $OMP SHARED(g_lo, gtmp, vns, vpa, aj0, bs0tmp) & $OMP SCHEDULE(static) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Redefine s0 = s0 / (1 + v0s0) $OMP PARALLEL DO DEFAULT(none) & $OMP PRIVATE(iglo, ik, it, is, isgn) & $OMP SHARED(g_lo, bs0tmp, dtmp) & $OMP SCHEDULE(static) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Now get w0 $OMP PARALLEL DO DEFAULT(none) & $OMP PRIVATE(iglo, ik, it, ie, il, is, isgn, ig) & $OMP SHARED(g_lo, ntgrid, forbid, bw0tmp, vns, energy, al, aj1, code_dt, & $OMP spec, kperp2, duinv, bmag, conserve_forbid_zero) & $OMP SCHEDULE(static) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Now get v0w0 $OMP PARALLEL DO DEFAULT(none) & $OMP PRIVATE(iglo, ik, ie, is, isgn) & $OMP SHARED(g_lo, gtmp, vnmult, vnew_E, aj0, bw0tmp) & $OMP SCHEDULE(static) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Redefine w0 = w0 - v0w0 * z0 / (1 + v0z0) (this is w1 from MAB notes) $OMP PARALLEL DO DEFAULT(none) & $OMP PRIVATE(iglo, ik, it, is, isgn) & $OMP SHARED(g_lo, bw0tmp, bz0tmp, dtmp) & $OMP SCHEDULE(static) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Get v1w1 $OMP PARALLEL DO DEFAULT(none) & $OMP PRIVATE(iglo, ik, ie, is, isgn) & $OMP SHARED(g_lo, gtmp, vns, vpa, aj0, bw0tmp) & $OMP SCHEDULE(static) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Redefine w0 = w1 - v1w1 * s1 / (1 + v1s1) (this is w2 from MAB notes) $OMP PARALLEL DO DEFAULT(none) & $OMP PRIVATE(iglo, ik, it, is, isgn) & $OMP SHARED(g_lo, bw0tmp, bs0tmp, dtmp) & $OMP SCHEDULE(static) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Get v2w2 $OMP PARALLEL DO DEFAULT(none) & $OMP PRIVATE(iglo, ik, ie, il, is, isgn) & $OMP SHARED(g_lo, gtmp, vns, energy, al, aj1, bw0tmp) & $OMP SCHEDULE(static) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Redefine w0 = w2 / (1 + v2w2) $OMP PARALLEL DO DEFAULT(none) & $OMP PRIVATE(iglo, ik, it, is, isgn) & $OMP SHARED(g_lo, bw0tmp, dtmp) & $OMP SCHEDULE(static) |
init_dist_fn | dist_fn | Subroutine | FIXME : Add documentation |
init_dist_fn_arrays | dist_fn | Subroutine | FIXME : Add documentation |
init_dist_fn_layouts | gs2_layouts | Subroutine | Construct the work decomposition for the g_layout and store it in the module level g_lo instance. |
init_dist_fn_level_1 | dist_fn | Subroutine | FIXME : Add documentation |
init_dist_fn_level_2 | dist_fn | Subroutine | FIXME : Add documentation |
init_dist_fn_level_3 | dist_fn | Subroutine | FIXME : Add documentation |
init_dist_fn_parameters | dist_fn | Subroutine | FIXME : Add documentation |
init_dt | gs2_save | Subroutine | FIXME : Add documentation |
init_dvtype | gs2_heating | Interface | |
init_dvtype_0 | gs2_heating | Subroutine | FIXME : Add documentation |
init_dvtype_1 | gs2_heating | Subroutine | FIXME : Add documentation |
init_dvtype_2 | gs2_heating | Subroutine | FIXME : Add documentation |
init_dvtype_3 | gs2_heating | Subroutine | FIXME : Add documentation |
init_ediffuse | collisions | Subroutine | FIXME : Add documentation |
init_eigenfunc_file | gs2_save | Subroutine | Initialises a file for saving output of eigensolver to netcdf |
init_energy_layouts | gs2_layouts | Subroutine | Setup the module level energy layout. |
init_energy_redistribute_local | le_grids | Subroutine | Constructs the redistribute mapping from the global g_lo data decomposition to the global e_lo decomposition |
init_enforce_parity | dist_fn | Subroutine | Subroutine to setup a redistribute object to be used in enforcing parity |
init_error_unit | file_utils | Subroutine | Open error file and record associated lun/unit |
init_exit_reason_unit | file_utils | Subroutine | Open exit_reason file and record associated lun/unit |
init_fft_work | fft_work | Subroutine | Perform any one off setup of the fft library. This is currently mostly only needed for builds with OpenMP for threaded transforms. |
init_fieldeq | dist_fn | Subroutine | FIXME : Add documentation |
init_fields | fields | Subroutine | FIXME : Add documentation |
init_fields_gf_local | fields_gf_local | Subroutine | Routine to initialise |
init_fields_implicit | fields_implicit | Subroutine | FIXME : Add documentation |
init_fields_layouts | gs2_layouts | Subroutine | Construct the module level fields_layout instance |
init_fields_level_1 | fields | Subroutine | FIXME : Add documentation |
init_fields_level_2 | fields | Subroutine | FIXME : Add documentation |
init_fields_local | fields_local | Subroutine | Routine to initialise |
init_fields_matrixlocal | fields_local | Subroutine | Routine use to initialise field matrix data !!!!!!!! NOTE: All of the above should be a one off setup cost unless something fundamental changes with the parallel layout (a change in nproc/layout etc.) The remaining two tasks (populate+prepare) must be repeated each time the relevant physics and numerical parameters change. In practice this just means when the time step changes. !!!!!!!! |
init_fields_matrixlocal | fields_gf_local | Subroutine | Routine use to initialise field matrix data !!!!!!!! NOTE: All of the above should be a one off setup cost unless something fundamental changes with the parallel layout (a change in nproc/layout etc.) The remaining two tasks (populate+prepare) must be repeated each time the relevant physics and numerical parameters change. In practice this just means when the time step changes. !!!!!!!! |
init_fields_parameters | fields | Subroutine | FIXME : Add documentation |
init_fields_test | fields_test | Subroutine | FIXME : Add documentation |
init_file_utils | file_utils | Subroutine | Read the run_name from the command line (if not given), and determine from the extension whether this is a list run (i.e. a list of runs has been given). If so or if this is a run with multiple ensembles, open the list description. If not, open the error file and call init_input_unit |
init_fill | redistribute | Subroutine | FIXME : Add documentation |
init_g2gf | le_grids | Subroutine | FIXME : Add documentation |
init_g2gf_redistribute | le_grids | Subroutine | Setup the module level g2gf instance describing the transformation from global g_lo to global gf_lo. |
init_g2le_redistribute_local | le_grids | Subroutine | Constructs the redistribute mapping from the global g_lo data decomposition to the le_lo decomposition. |
init_generic | abstract_config | Subroutine | Fully initialise the config object |
init_gf_layouts | gs2_layouts | Subroutine | Setup the module level gf_lo instance. |
init_gs2_diagnostics | gs2_diagnostics | Subroutine | Initialise this module and all its dependencies, including defining NetCDF vars, call real_init, which calls read_parameters; broadcast all the different write flags. |
init_gs2_diagnostics_new | gs2_diagnostics_new | Subroutine | Read namelist diagnostics_config, initialise submodules, open output file 'run_name.cdf' and create dimensions. !!!!!!!!!!!!!!!!!!!!! Adjust other modules !!!!!!!!!!!!!!!!!!!!! |
init_gs2_init | gs2_init | Subroutine | Initialise this module. As we pass in the initialisation state object (current), we could/should consider making this set the level to basic, e.g. current%level = init_level_list%basic |
init_gs2_io | gs2_io | Subroutine | Create and initialise the output netCDF files |
init_gs2_layouts | gs2_layouts | Subroutine | FIXME : Add documentation |
init_gs2_reinit | gs2_reinit | Subroutine | FIXME : Add documentation |
init_gs2_save | gs2_save | Subroutine | FIXME : Add documentation |
init_gs2_time | gs2_time | Subroutine | Initialise the gs2_time module |
init_homogeneous_g | dist_fn | Subroutine | Calculates the homogeneous solution |
init_htype | gs2_heating | Interface | Allocate the array components of heating_diagnostics |
init_htype_0 | gs2_heating | Subroutine | FIXME : Add documentation |
init_htype_1 | gs2_heating | Subroutine | FIXME : Add documentation |
init_htype_2 | gs2_heating | Subroutine | FIXME : Add documentation |
init_htype_3 | gs2_heating | Subroutine | FIXME : Add documentation |
init_hyper | hyper | Subroutine | FIXME : Add documentation |
init_ingen | ingen_mod | Subroutine | FIXME : Add documentation |
init_init_g | init_g | Subroutine | FIXME : Add documentation |
init_input_unit | file_utils | Subroutine | Opens the input file, strip out any comments and write them into the file
|
init_integrations | le_grids | Subroutine | FIXME : Add documentation |
init_inverse_matrix | fields_implicit | Subroutine | FIXME : Add documentation |
init_invert_rhs | dist_fn | Subroutine | FIXME : Add documentation |
init_jfields_layouts | gs2_layouts | Subroutine | Setup the module level jfields instance |
init_job_name | file_utils | Subroutine | Set run_name and job_name to |
init_jobs | mp | Subroutine | FIXME : Add documentation |
init_kperp2 | kt_grids | Subroutine | FIXME : Add documentation |
init_kt_grids | kt_grids | Subroutine | FIXME : Add documentation |
init_kt_grids_box | kt_grids_box | Subroutine | FIXME : Add documentation |
init_kt_grids_parameters | kt_grids | Subroutine | FIXME : Add documentation |
init_kt_grids_range | kt_grids_range | Subroutine | FIXME : Add documentation |
init_kt_grids_single | kt_grids_single | Subroutine | FIXME : Add documentation |
init_kt_grids_specified | kt_grids_specified | Subroutine | FIXME : Add documentation |
init_lambda_layouts | gs2_layouts | Subroutine | Setup the module level lz_lo instance |
init_lambda_redistribute_local | le_grids | Subroutine | Computes the redistribute mapping from the global g_lo data decomposition to the global lz_lo decomposition |
init_le_bessel | collisions | Subroutine | Communicate Bessel functions from g_lo to le_lo Currently just aj1 |
init_le_grids | le_grids | Subroutine | FIXME : Add documentation |
init_le_layouts | gs2_layouts | Subroutine | Setup the module level le_lo |
init_level_change_level | gs2_init | Function | General wrapper to the init_level instance's specific change level method. |
init_level_generate_debug_message | gs2_init | Subroutine | Produce the debug message associated with this level |
init_level_report_time | gs2_init | Subroutine | Report the time spent in init for this level |
init_lorentz | collisions | Subroutine | FIXME : Add documentation |
init_lorentz_conserve | collisions | Subroutine | Precompute three quantities needed for momentum and energy conservation: z0, w0, s0 (z0le, w0le, s0le if use_le_layout chosen in the input file defined) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Now get z0 (first form) $OMP PARALLEL DO DEFAULT(none) & $OMP PRIVATE(iglo, ik, ie, il, is, isgn) & $OMP SHARED(g_lo, conservative, z0tmp, code_dt, vns, vpdiff, speed, aj0, vpa) & $OMP SCHEDULE(static) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Now get v0z0 $OMP PARALLEL DO DEFAULT(none) & $OMP PRIVATE(iglo, isgn) & $OMP SHARED(g_lo, vpa, gtmp, aj0, z0tmp) & $OMP COLLAPSE(2) & $OMP SCHEDULE(static) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Redefine z0 = z0 / (1 + v0z0) $OMP PARALLEL DO DEFAULT(none) & $OMP PRIVATE(iglo, ik, it, is, isgn) & $OMP SHARED(g_lo, z0tmp, dtmp) & $OMP SCHEDULE(static) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! du == int (E nu_s f_0); du = du(z, kx, ky, s) duinv = 1/du |
init_lorentz_error | collisions | Subroutine | FIXME : Add documentation |
init_map | le_grids | Subroutine | FIXME : Add documentation |
init_mom_coeff | diagnostics_moments | Subroutine | FIXME : Add documentation |
init_mp | mp | Subroutine | Initialise the 1 library, communicators, and related variables |
init_nonlinear_convergence | diagnostics_nonlinear_convergence | Subroutine | FIXME : Add documentation |
init_nonlinear_terms | nonlinear_terms | Subroutine | FIXME : Add documentation |
init_normalisations | normalisations | Subroutine | Read input file and populate the norms object |
init_optimisation_config | optimisation_configuration | Subroutine | |
init_par_filter | diagnostics_final_routines | Subroutine | Setup the FFTs for calculating the parallel spectrum |
init_parameter_scan | parameter_scan | Subroutine | FIXME : Add documentation |
init_parity_layouts | gs2_layouts | Subroutine | Setup the module level p_lo instance |
init_pass_ends | dist_fn | Subroutine | Copy of CMR's init_pass_right (revision 2085) but in customisable direction to aid code reuse and with optional range in theta (i.e. so can pass more than just boundary points) An example use is: call init_pass_ends(pass_right,'r',1,'c',3) call fill(pass_right,gnew,gnew) This will pass gnew(ntgrid-2:ntgrid,1,iglo) to gnew(-ntgrid-2:-ntgrid,1,iglo_linked) |
init_pass_int | gs2_init | Subroutine | Initialize gs2 to the level of target_level. The init_type current contains info about the current initialization level. At the end of the subroutine, current%level is set to target_level |
init_pass_type | gs2_init | Subroutine | Small wrapper to allow init_level_type to be passed instead of the level integer. |
init_phi_test | fields_test | Subroutine | FIXME : Add documentation |
init_ranf | ran | Subroutine | Seed the choosen random number generator.
If randomize=T, a random seed based on date and time is used.
(this randomizing procedure is proposed in GNU gfortran manual.)
Otherwise, it sets the seed using init_seed
In either case, it sets |
init_rcfftw | fft_work | Interface | |
init_rcfftw_1d | fft_work | Subroutine | Create FFTW plan suitable for 1D real to complex transformation |
init_rcfftw_2d | fft_work | Subroutine | Create FFTW plan suitable for 2D real to complex transformation |
init_redist | redistribute | Interface | |
init_redist_agk | redistribute | Subroutine | FIXME : Add documentation |
init_redist_gs2 | redistribute | Subroutine | FIXME : Add documentation |
init_reinit | gs2_reinit | Subroutine | FIXME : Add documentation |
init_response_matrix | fields_implicit | Subroutine | FIXME : Add documentation |
init_response_row | fields_implicit | Subroutine | FIXME : Add documentation |
init_run_name | file_utils | Subroutine | This is called for a non Trinity or list run - it checks that the input
file name ends in |
init_run_parameters | run_parameters | Subroutine | FIXME : Add documentation |
init_source_term | dist_fn | Subroutine | FIXME : Add documentation |
init_species | species | Subroutine | FIXME : Add documentation |
init_split_nonlinear_terms | split_nonlinear_terms | Subroutine | Initialises the split_nonlinear_terms module. Primarily just reading input |
init_theta_grid | theta_grid | Subroutine | FIXME : Add documentation |
init_theta_grid_eik | theta_grid_eik | Subroutine | FIXME : Add documentation |
init_theta_grid_file | theta_grid_file | Subroutine | FIXME : Add documentation |
init_theta_grid_params | theta_grid_params | Subroutine | FIXME : Add documentation |
init_theta_grid_salpha | theta_grid_salpha | Subroutine | FIXME : Add documentation |
init_transforms | gs2_transforms | Subroutine | FIXME : Add documentation |
init_tstart | gs2_time | Subroutine | FIXME : Add documentation |
init_uniform_theta_grid | geometry | Subroutine | Initialse geometry to a uniform grid with |
init_vnew | collisions | Subroutine | FIXME : Add documentation MAB MAB |
init_vnm | gs2_save | Subroutine | FIXME : Add documentation |
init_vnmult | init_g | Subroutine | FIXME : Add documentation |
init_vpa_vpac | dist_fn | Subroutine | Initialised the on grid v|| (vpa) and grid-centred v|| (vpac) arrays |
init_vpar | dist_fn | Subroutine | FIXME : Add documentation |
init_vpdiff | collisions | Subroutine | FIXME : Add documentation |
init_vperp2 | dist_fn | Subroutine | FIXME : Add documentation |
init_wdrift | dist_fn | Subroutine | FIXME : Add documentation |
init_weights | le_grids | Subroutine | Calculates energy grid and (untrapped) pitch angle weights for integrals which drop a point from the energy/lambda dimensions. These are only used for estimating the velocity space error in [[dist_fn::get_verr]] as a part of the adaptive collisionality algorithm. |
init_wstar | dist_fn | Subroutine | FIXME : Add documentation |
init_x_redist_local | gs2_transforms | Subroutine | Setup global xxf_lo and redistribute between global g_lo -> xxf_lo |
init_x_transform_layouts | gs2_layouts | Subroutine | Setup the module level xxf_lo instance |
init_xy_fft | gs2_transforms | Subroutine | Setup non-accelerated separate x and y FFTs |
init_y_redist_local | gs2_transforms | Subroutine | Setup the module level xxf -> yxf redistribute. Note this also calls init_x_redist_local in order to setup the mapping for g_lo to xxf_lo as well. |
init_y_transform_layouts | gs2_layouts | Subroutine | Setup the module level yxf_lo instance. |
init_z | fft_work | Subroutine | FIXME : Add documentation |
init_zf | gs2_transforms | Subroutine | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! FIXME : Add documentation |
initialise | geo_utils | Subroutine | |
initialise_requests | mp | Subroutine | A Routine to initialise request arrays properly so they can have null requests in them and still work problems with waitall and waitany |
initialize_diagnostics | gs2_main | Subroutine | Initialize the diagostics modules. This function can only be called when the init level is 'full', i.e., after calling initialize_equations. However, gs2 can be partially uninitialized without finalizing the diagnostics, for example to change parameters such as the timestep. |
initialize_equations | gs2_main | Subroutine | Initialize all the modules which are used to evolve the
equations. After calling this function, gs2 reaches |
initialize_gs2 | gs2_main | Subroutine | Initialise message passing, open the input file, split the communicator if running in list mode or if nensembles > 1, initialize the timers. After calling this function, gs2 reaches init\%level = basic. If it is desired to provide an external commuicator or set the input file name externally, these should be set before calling this function. |
initialize_gs2_optimisation | gs2_optimisation | Subroutine | FIXME : Add documentation |
initialize_wall_clock_timer | gs2_main | Subroutine | Starts the global wall clock timer used by check time. This is useful if you have multiple copies of gs2 running but you don't want to start them all at the same time, but you want them all to respect avail_cpu_time |
input_unit | file_utils | Function | Rewind the input file to start of namelist |
input_unit_exist | file_utils | Function | Similar to input_unit but set |
insertsort | sorting | Interface | |
integrate | geometry | Subroutine | Integrates arg(grid) from i = 0 (generally theta = 0) to either
ends of the grid (usually +/- pi) storing the cumulative integral
in the output |
integrate_kysum | le_grids | Subroutine | FIXME : Add documentation |
integrate_moment | le_grids | Interface | |
integrate_moment_c34 | le_grids | Subroutine | FIXME : Add documentation |
integrate_moment_lec | le_grids | Subroutine | Perform an integral over velocity space whilst in the LE_LAYOUT in which we have ensured that all of velocity space is local. As such we don't need any calls to MPI reduction routines. Note that this means the processors for different distributed spatial points (x,y) don't know the results at other points. |
integrate_moment_r33 | le_grids | Subroutine | FIXME : Add documentation |
integrate_moment_r34 | le_grids | Subroutine | Takes f = f(theta, sigma ; x, y, z, lambda, E, species) and returns int f, where the integral is over all velocity space returns results to PE 0 [or to all processors if 'all' is present in input arg list] |
integrate_species | le_grids | Interface | |
integrate_species_gf | le_grids | Subroutine | Integrate species using gf_lo data format |
integrate_species_gf_nogather | le_grids | Subroutine | Integrate species using gf_lo data format assuming that gf has already been gathered prior to being passed to this routine. Currently this routine isn't being used as the functionality has been directly added to getan_nogath in dist_fn. |
integrate_species_master | le_grids | Subroutine | Integrate_species on subcommunicator with gather Falls back to original method if not using xyblock sub comm |
integrate_species_original | le_grids | Subroutine | FIXME : Add documentation |
integrate_species_sub | le_grids | Subroutine | Integrate species on xy subcommunicator - NO GATHER |
integrate_volume | le_grids | Interface | |
integrate_volume_c | le_grids | Subroutine | FIXME : Add documentation |
integrate_volume_r | le_grids | Subroutine | FIXME : Add documentation |
inter_cspl | splines | Subroutine | FIXME : Add documentation |
inter_d_cspl | splines | Subroutine | FIXME : Add documentation |
interactive | ingen_mod | Subroutine | FIXME : Add documentation |
inv_Rpol | geometry | Subroutine | General calculation of the poloidal magnetic field radius of curvature (see section 2.3 of "GS2 analytic geometry specification") ! JRB |
inverse2 | gs2_transforms | Interface | |
inverse2_2d | gs2_transforms | Subroutine | FIXME : Add documentation DD>Reinstating after discussion with RN, if this causes anyone an issue |
inverse2_3d | gs2_transforms | Subroutine | FIXME : Add documentation |
inverse2_5d | gs2_transforms | Subroutine | FIXME : Add documentation |
inverse2_5d_accel | gs2_transforms | Subroutine | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! FIXME : Add documentation |
inverse_x | gs2_transforms | Interface | |
inverse_x5d | gs2_transforms | Subroutine | FIXME : Add documentation |
inverse_y | gs2_transforms | Interface | |
inverse_y5d | gs2_transforms | Subroutine | FIXME : Add documentation |
invert_block | mat_inv | Subroutine | Serial Block inverse |
invert_field_func | split_nonlinear_terms | Interface | Interface to describe the call signatures for routines to calculate the field from gnew (invert_field_func) and to calculate the source term used in the advance_nonlinear_term methods. Used to allow us to pass in these methods, giving us a way to test the integrators on different problems. |
invert_gauss_jordan | mat_inv | Subroutine | Serial Gauss-Jordan elimination |
invert_gauss_jordan_omp | mat_inv | Subroutine | openmp Gauss-Jordan elimination |
invert_lapack | mat_inv | Subroutine | A routine to invert a matrix using lapack routines. |
invert_rhs | dist_fn | Subroutine | FIXME : Add documentation |
invert_rhs_1 | dist_fn | Subroutine | Calculates the "new" distribution function for the passed source calculated using the passed fields and current distribution in g. |
invert_serial | mat_inv | Subroutine | Serial Provides a wrapper around the various serial inversion routines. |
invR | geo_utils | Function | |
invRtgrid | geometry | Subroutine | Calculates invR = 1/R(theta), where R is the distance to the central axis (rmajor not to be confused with rmaj, r_geo etc) rgrid is the submodule radial grid (r_circ for EFIT & deq, rp otherwise) |
is_effectively_zero_shear | theta_grid | Function | Helper function to determine if the shear is small enough that we consider it to be zero for the purposes of periodicity etc. |
is_electron_species | species | Function | Determine if the passed species instance is considered electron like. In other words if spec%type matches any of the recognised electron like types (electron, hybrid_electron) |
is_hybrid_electron_species | species | Function | Determine if the passed species instance corresponds to hybrid electrons |
is_identical | exit_codes | Function | Determines if a passed |
is_idx | gs2_layouts | Interface | |
is_idx_accelx | gs2_layouts | Function | FIXME : Add documentation |
is_idx_e | gs2_layouts | Function | FIXME : Add documentation |
is_idx_g | gs2_layouts | Function | Return the species index, given g-layout and a global index |
is_idx_le | gs2_layouts | Function | FIXME : Add documentation |
is_idx_lz | gs2_layouts | Function | FIXME : Add documentation |
is_idx_parity | gs2_layouts | Function | FIXME : Add documentation |
is_idx_xxf | gs2_layouts | Function | Return the species index, given xxf-layout and a global index |
is_idx_yxf | gs2_layouts | Function | Return the species index, given yxf-layout and a global index |
is_initialised_generic | abstract_config | Function | Is this instance initialised? |
is_input_file_list | file_utils | Function | Returns true if input_filename is a list input: that is, if it ends in |
is_ion_species | species | Function | Determine if the passed species instance corresponds to ions |
is_lower_bounce_point | le_grids | Function | Returns true if the passed theta grid index, ig, is a lower bounce point for the passed pitch angle index, il. |
is_not_zero | warning_helpers | Interface | Is the argument not exactly zero |
is_not_zero_r128 | warning_helpers | Function | |
is_not_zero_r32 | warning_helpers | Function | |
is_not_zero_r64 | warning_helpers | Function | |
is_passing_hybrid_electron | le_grids | Function | Determine if the passed species, ky and lambda indicies correspond to a passing hybrid electron point which should be skipped. |
is_release | runtime_tests | Function | This function is just a call of is_release_runtime_info and is provided for backwards compatibility. |
is_release_runtime_info | runtime_tests | Function | Returns whether current version is a release |
is_responsible_for_any_theta_grid_point | diagnostics_kinetic_energy_transfer | Function | |
is_responsible_for_this_theta_grid_index | diagnostics_kinetic_energy_transfer | Function | |
is_unstable | ballstab | Function | Test stability of current system for passed theta0 and geometry -- return integer |
is_upper_bounce_point | le_grids | Function | Returns true if the passed theta grid index, ig, is a upper bounce point for the passed pitch angle index, il. |
is_zero | warning_helpers | Interface | Is the argument exactly equal to zero |
is_zero_r128 | warning_helpers | Function | |
is_zero_r32 | warning_helpers | Function | |
is_zero_r64 | warning_helpers | Function | |
isign_idx | gs2_layouts | Interface | |
isign_idx_e | gs2_layouts | Function | FIXME : Add documentation |
isign_idx_xxf | gs2_layouts | Function | Return the sign index, given xxf-layout and a global index |
isign_idx_yxf | gs2_layouts | Function | Return the sign index, given yxf-layout and a global index |
it_idx | gs2_layouts | Interface | |
it_idx_accel | gs2_layouts | Function | FIXME : Add documentation |
it_idx_accelx | gs2_layouts | Function | FIXME : Add documentation |
it_idx_e | gs2_layouts | Function | FIXME : Add documentation |
it_idx_f | gs2_layouts | Function | FIXME : Add documentation |
it_idx_g | gs2_layouts | Function | Return the kx index, given g-layout and a global index |
it_idx_gf | gs2_layouts | Function | FIXME : Add documentation |
it_idx_jf | gs2_layouts | Function | FIXME : Add documentation |
it_idx_le | gs2_layouts | Function | FIXME : Add documentation |
it_idx_lz | gs2_layouts | Function | FIXME : Add documentation |
it_idx_yxf | gs2_layouts | Function | Return the kx index, given yxf-layout and a global index |
j0 | spfunc | Interface | |
j1 | spfunc | Interface | |
job_fork | job_manage | Subroutine | FIXME : Add documentation We need to set this for the group proc0, as it is previously only set for the global proc0 |
kahan_sum | summation | Interface | |
kahan_sum_real_1d | summation | Function | Simple Kahan summation designed to limit the error arising from summing a large collection of numbers by taking care to keep track of the required compensation. |
klein_sum | summation | Interface | |
klein_sum_real_1d | summation | Function | Similar approach to Neumaier but introduces two levels of compensation |
kt2ki | fields_implicit | Subroutine | FIXME : Add documentation |
ky_allocate | fields_local | Subroutine | Allocate storage space |
ky_allocate | fields_gf_local | Subroutine | Allocate storage space |
ky_deallocate | fields_local | Subroutine | Deallocate storage space |
ky_deallocate | fields_gf_local | Subroutine | Deallocate storage space |
ky_debug_print | fields_local | Subroutine | Debug printing |
ky_debug_print | fields_gf_local | Subroutine | Debug printing |
ky_get_field_update | fields_local | Subroutine | Get the field update for this ik |
ky_get_field_update | fields_gf_local | Subroutine | Get the field update for this ik |
ky_init | fields_local | Subroutine | Setup properties of ky_type instance |
ky_init | fields_gf_local | Subroutine | Setup properties of ky_type instance |
ky_is_from_it | fields_local | Function | Given it say what the supercell id is |
ky_is_from_it | fields_gf_local | Function | Given it say what the supercell id is |
ky_make_subcom_1 | fields_local | Subroutine | Create the primary subcommunicators |
ky_make_subcom_1 | fields_gf_local | Subroutine | Create the primary subcommunicators |
ky_make_subcom_2 | fields_local | Subroutine | Create the secondary subcommunicators |
ky_make_subcom_2 | fields_gf_local | Subroutine | Create the secondary subcommunicators |
ky_prepare | fields_local | Subroutine | Prepare the field matrix for calculating field updates |
ky_prepare | fields_gf_local | Subroutine | Prepare the field matrix for calculating field updates |
ky_reset | fields_local | Subroutine | A routine to reset the object |
ky_reset | fields_gf_local | Subroutine | A routine to reset the object |
ky_set_locality | fields_local | Subroutine | Set the locality of each object |
ky_set_locality | fields_gf_local | Subroutine | Set the locality of each object |
ky_store_fq | fields_local | Subroutine | Store the field equation at row level |
ky_store_fq | fields_gf_local | Subroutine | Store the field equation at row level |
ky_wait_for_nonblocking_collectives | fields_local | Subroutine | Wait on the nonblocking collective communications if they have been used. |
kz_spectrum | gs2_transforms | Subroutine | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! FIXME : Add documentation |
l2norm | fields_local | Function | Calculate the L2/Frobenius/Euclidiean-norm of a 2D complex array |
l2norm | fields_gf_local | Function | Calculate the L2/Frobenius/Euclidiean-norm of a 2D complex array |
l_fill_2 | redistribute | Subroutine | FIXME : Add documentation |
l_fill_3 | redistribute | Subroutine | FIXME : Add documentation |
l_fill_4 | redistribute | Subroutine | FIXME : Add documentation |
l_redist_12 | redistribute | Subroutine | FIXME : Add documentation |
l_redist_22 | redistribute | Subroutine | FIXME : Add documentation |
l_redist_22_inv | redistribute | Subroutine | FIXME : Add documentation |
l_redist_32 | redistribute | Subroutine | FIXME : Add documentation |
l_redist_32_inv | redistribute | Subroutine | FIXME : Add documentation |
l_redist_42 | redistribute | Subroutine | FIXME : Add documentation |
l_redist_42_inv | redistribute | Subroutine | FIXME : Add documentation |
laguerre_l | gauss_quad | Function | Returns L_n(x) where L_n(x) is an ordinary Laguerre polynomial |
laguerre_lp | gauss_quad | Function | FIXME : Add documentation |
laguerre_norm | gauss_quad | Function | Returns (-1)**n n! L_n(x) where L_n(x) is an ordinary Laguerre polynomial |
land_allreduce | mp | Interface | |
land_allreduce_single_element | mp | Subroutine | FIXME : Add documentation |
lcg | ran | Function | Simple PRNG derived from gfortran documentation Intended to be used to seed a better PRNG. Probably shouldn't be used directly (hence why this is not public). |
legendre_p | gauss_quad | Function | FIXME : Add documentation |
legendre_polynomials | le_grids | Subroutine | FIXME : Add documentation |
legendre_pp | gauss_quad | Function | FIXME : Add documentation |
legendre_transform | le_grids | Subroutine | FIXME : Add documentation |
lgamma_ext | spfunc | Interface | |
lgridset | le_grids | Subroutine | Sets up the pitch angle grid and associated data. Does so by calling other routines. A summary of the actions is below. |
lint_error | le_grids | Subroutine | FIXME : Add documentation |
load_kx_apar | nonlinear_terms | Subroutine | FIXME : Add documentation |
load_kx_bpar | nonlinear_terms | Subroutine | FIXME : Add documentation |
load_kx_phi | nonlinear_terms | Subroutine | FIXME : Add documentation |
load_ky_apar | nonlinear_terms | Subroutine | FIXME : Add documentation |
load_ky_bpar | nonlinear_terms | Subroutine | FIXME : Add documentation |
load_ky_phi | nonlinear_terms | Subroutine | FIXME : Add documentation |
load_wisdom | fft_work | Subroutine | Load FFTW wisdom from file |
local_sum | integration | Interface | |
loftheta | geometry | Subroutine | FIXME : Add documentation |
loop_diagnostics | gs2_diagnostics | Subroutine | Calculate and write the various diagnostic quantities. |
make_standard_header | standard_header | Function | Constructor for |
matmul_wrapper | matrix_multiply | Interface | Provides a wrapper to different matrix multiplication methods |
matmul_wrapper_complex_2d | matrix_multiply | Function | Wrapper to complex matrix multiplication with two 2D matrices |
matrix_inversion_method_get_flag | mat_inv | Function | Helper routine to get access to the matrix_inversion_method's flag in a read-only way. Primarily used for testing. |
matrix_inversion_method_get_name | mat_inv | Function | Helper routine to get access to the matrix_inversion_method's name in a read-only way. Primarily used for testing. |
matrix_multiply_method_get_flag | matrix_multiply | Function | Helper routine to get access to the matrix_multiply_method's flag in a read-only way. Primarily used for testing. |
matrix_multiply_method_get_name | matrix_multiply | Function | Helper routine to get access to the matrix_multiply_method's name in a read-only way. Primarily used for testing. |
max_allreduce | mp | Interface | |
max_allreduce_integer | mp | Subroutine | FIXME : Add documentation |
max_allreduce_integer_array | mp | Subroutine | FIXME : Add documentation |
max_allreduce_real | mp | Subroutine | FIXME : Add documentation |
max_allreduce_real_array | mp | Subroutine | FIXME : Add documentation |
max_reduce | mp | Interface | |
max_reduce_integer | mp | Subroutine | FIXME : Add documentation |
max_reduce_integer_array | mp | Subroutine | FIXME : Add documentation |
max_reduce_real | mp | Subroutine | FIXME : Add documentation |
max_reduce_real_array | mp | Subroutine | FIXME : Add documentation |
maxloc_allreduce | mp | Interface | |
maxloc_allreduce_real | mp | Subroutine | FIXME : Add documentation |
maxloc_allreduce_real_array | mp | Subroutine | FIXME : Add documentation |
measure_gather | redistribute | Interface | |
measure_gather_22 | redistribute | Subroutine | FIXME : Add documentation |
measure_gather_32 | redistribute | Subroutine | FIXME : Add documentation |
measure_gather_33 | redistribute | Subroutine | FIXME : Add documentation |
measure_scatter | redistribute | Interface | |
measure_scatter_22 | redistribute | Subroutine | FIXME : Add documentation |
measure_scatter_23 | redistribute | Subroutine | FIXME : Add documentation |
measure_scatter_33 | redistribute | Subroutine | FIXME : Add documentation |
measure_timestep | gs2_optimisation | Subroutine | FIXME : Add documentation |
mhdballn | ball | Subroutine | |
min_allreduce | mp | Interface | |
min_allreduce_integer | mp | Subroutine | FIXME : Add documentation |
min_allreduce_integer_array | mp | Subroutine | FIXME : Add documentation |
min_allreduce_real | mp | Subroutine | FIXME : Add documentation |
min_allreduce_real_array | mp | Subroutine | FIXME : Add documentation |
min_allreduce_sub | mp | Interface | |
min_allreduce_sub_integer | mp | Subroutine | FIXME : Add documentation |
min_reduce | mp | Interface | |
min_reduce_integer | mp | Subroutine | FIXME : Add documentation |
min_reduce_integer_array | mp | Subroutine | FIXME : Add documentation |
min_reduce_real | mp | Subroutine | FIXME : Add documentation |
min_reduce_real_array | mp | Subroutine | FIXME : Add documentation |
mod2pi | geo_utils | Function | Put |
mp_abort | mp | Subroutine | Abort the simulation, logging an error message |
nb_allgatherv | mp | Interface | |
nb_allgatherv_complex_array_1to1 | mp | Subroutine | A subroutine to do a allgatherv operation, sending recvcnts(iproc) data from the iproc'th processor to all others starting at arr(start). |
nb_allgatherv_complex_array_1to3_sub | mp | Subroutine | A subroutine to do a non-blocking allgatherv operation, sending recvcnts(iproc) data from the iproc'th processor to all others starting at arr(start). |
nb_check_time_step_too_large | nonlinear_terms | Subroutine | Finish nonblocking calculation of the maximum velocity and set the cfl limit. |
nb_max_allreduce | mp | Interface | |
nb_max_allreduce_integer | mp | Subroutine | FIXME : Add documentation |
nb_max_allreduce_integer_array | mp | Subroutine | FIXME : Add documentation |
nb_max_allreduce_real | mp | Subroutine | FIXME : Add documentation |
nb_max_allreduce_real_array | mp | Subroutine | FIXME : Add documentation |
nb_sum_allreduce | mp | Interface | |
nb_sum_allreduce_complex_3array | mp | Subroutine | FIXME : Add documentation |
nb_sum_allreduce_complex_4array | mp | Subroutine | FIXME : Add documentation |
nb_sum_allreduce_complex_5array | mp | Subroutine | FIXME : Add documentation |
nb_sum_allreduce_complex_array | mp | Subroutine | FIXME : Add documentation |
nb_sum_allreduce_integer | mp | Subroutine | FIXME : Add documentation |
nb_sum_allreduce_sub | mp | Interface | |
nb_sum_allreduce_sub_complex_2array | mp | Subroutine | FIXME : Add documentation |
nb_sum_allreduce_sub_complex_4array | mp | Subroutine | FIXME : Add documentation |
nb_sum_reduce | mp | Interface | |
nb_sum_reduce_complex | mp | Subroutine | FIXME : Add documentation |
nb_sum_reduce_complex_2array | mp | Subroutine | FIXME : Add documentation |
nb_sum_reduce_complex_3array | mp | Subroutine | FIXME : Add documentation |
nb_sum_reduce_complex_4array | mp | Subroutine | FIXME : Add documentation |
nb_sum_reduce_complex_4array_sub | mp | Subroutine | FIXME : Add documentation |
nb_sum_reduce_complex_5array | mp | Subroutine | FIXME : Add documentation |
nb_sum_reduce_complex_array | mp | Subroutine | FIXME : Add documentation |
nb_sum_reduce_complex_array_sub | mp | Subroutine | FIXME : Add documentation |
nb_sum_reduce_sub | mp | Interface | |
nbrecv | mp | Interface | |
nbrecv_complex_2d_array | mp | Subroutine | Routine for nonblocking recv of z to dest. Use tag to label message and return handle for later checking. |
nbrecv_complex_2d_array_count | mp | Subroutine | Routine for nonblocking recv of z to dest. Use tag to label message and return handle for later checking. |
nbrecv_complex_3d_array | mp | Subroutine | Routine for nonblocking recv of z to dest. Use tag to label message and return handle for later checking. |
nbrecv_complex_3d_array_count | mp | Subroutine | Routine for nonblocking recv of z to dest. Use tag to label message and return handle for later checking. |
nbrecv_complex_array | mp | Subroutine | Routine for nonblocking recv of z to dest. Use tag to label message and return handle for later checking. |
nbrecv_complex_array_count | mp | Subroutine | Routine for nonblocking recv of z (size=count) to dest. Use tag to label message and return handle for later checking. |
nbrecv_complex_array_sub | mp | Subroutine | Routine for nonblocking recv of z to dest. Use tag to label message and return handle for later checking. |
nbrecv_real_array | mp | Subroutine | Routine for nonblocking recv of z to dest. Use tag to label message and return handle for later checking. |
nbrecv_real_array_count | mp | Subroutine | Routine for nonblocking recv of z (size=count) to dest. Use tag to label message and return handle for later checking. |
nbsend | mp | Interface | |
nbsend_complex_2d_array | mp | Subroutine | Routine for nonblocking send of z to dest. Use tag to label message and return handle for later checking. |
nbsend_complex_2d_array_count | mp | Subroutine | Routine for nonblocking send of z to dest. Use tag to label message and return handle for later checking. |
nbsend_complex_3d_array | mp | Subroutine | Routine for nonblocking send of z to dest. Use tag to label message and return handle for later checking. |
nbsend_complex_3d_array_count | mp | Subroutine | Routine for nonblocking send of z to dest. Use tag to label message and return handle for later checking. |
nbsend_complex_array | mp | Subroutine | Routine for nonblocking send of z to dest. Use tag to label message and return handle for later checking. |
nbsend_complex_array_count | mp | Subroutine | Routine for nonblocking send of z (size=count) to dest. Use tag to label message and return handle for later checking. |
nbsend_complex_array_sub | mp | Subroutine | Routine for nonblocking send of z to dest. Use tag to label message and return handle for later checking. |
nbsend_real_array | mp | Subroutine | Routine for nonblocking send of z to dest. Use to label message and return handle for later checking. |
nbsend_real_array_count | mp | Subroutine | Routine for nonblocking send of z (size=count) to dest. Use tag to label message and return handle for later checking. |
nc_bc | gs2_io | Subroutine | Write various quantities related to BC to output netCDF file |
nc_eigenfunc | gs2_io | Subroutine | Write the normalised fields to netCDF |
nc_exchange | gs2_io | Subroutine | Write the energy exchange to netCDF |
nc_final_an | gs2_io | Subroutine | Write the right-hand sides of the field equations to netCDF, overwriting existing values |
nc_final_epar | gs2_io | Subroutine | Write to netCDF, overwriting existing values |
nc_final_fields | gs2_io | Subroutine | Write the fields to netCDF, overwriting existing values |
nc_final_moments | gs2_io | Subroutine | Write the various low-order moments to the output netCDF file, overwriting existing values |
nc_finish | gs2_io | Subroutine | Close the output netCDF files |
nc_geo | gs2_io | Subroutine | Write various geometric quantities to output netCDF file |
nc_get_grid_scalars | gs2_io_grids | Subroutine | Read scalar geometry data from the input netCDF file |
nc_get_grid_sizes | gs2_io_grids | Subroutine | Read sizes of geometry data from the input netCDF file |
nc_get_grids | gs2_io_grids | Subroutine | Read geometry data from the input netCDF file The no_end_point flag in the input netCDF file tells if the grid data have the duplicate end point data at ntgrid. The default no_end_point behavior: The grid file generated by this module should always store the no_end_point flag. The grid file came from outside (GX) may not have this flag. (GX grid file does not have the end point data.) read_and_pad handles the end point data |
nc_get_lambda_grid | gs2_io_grids | Subroutine | Read lambda grid data from the input netCDF file |
nc_get_lambda_grid_size | gs2_io_grids | Subroutine | Read sizes of lambda grid data from the input netCDF file |
nc_grid_file_close | gs2_io_grids | Subroutine | Close the netCDF file |
nc_grid_file_open | gs2_io_grids | Subroutine | Open the netCDF file If the file already exists, remove it. |
nc_grids_mymovie | gs2_io | Subroutine | Puts the grid data into the movie file |
nc_loop | gs2_io | Subroutine | Write various fields, heating, and frequency diagnostics to netCDF |
nc_loop_corr | gs2_io | Subroutine | Write the correlation function over the physical domain to netCDF |
nc_loop_corr_extend | gs2_io | Subroutine | Write the correlation function over the extended domain to netCDF |
nc_loop_dist | gs2_io | Subroutine | Output the poloidal distributions of the fluxes of particles, perpendicular momentum, parallel momentum, and energy ! JRB |
nc_loop_fullmom | gs2_io | Subroutine | Outputs full not guiding center moments |
nc_loop_moments | gs2_io | Subroutine | Write moments as: volume averaged, field line averaged, and evaulated at theta=0 |
nc_loop_movie | gs2_io | Subroutine | Write as functions of real space |
nc_loop_partsym_tormom | gs2_io | Subroutine | Write the particle flux contribution to toroidal momentum flux to netCDF |
nc_loop_sym | gs2_io | Subroutine | Write the momentum flux as a function of to netCDF |
nc_norms | gs2_io | Subroutine | Write the physical normalisations to the output netCDF file Write the physical normalisations to the output netCDF file |
nc_pflux | gs2_io | Subroutine | FIXME : Add documentation |
nc_pflux_tormom | gs2_io | Subroutine | Write toroidal angular momentum flux to netCDF |
nc_qflux | gs2_io | Subroutine | Write various heat fluxes to netCDF |
nc_species | gs2_io | Subroutine | Write spec to output netCDF file |
nc_sync | gs2_io | Subroutine | Sync the files every nsync writes |
nc_vflux | gs2_io | Subroutine | FIXME : Add documentation |
nc_write_field | gs2_io | Subroutine | Write a field ((/E, A_\Vert, B_\vert/)) to netCDF |
nc_write_grid_scalars | gs2_io_grids | Subroutine | Write scalar geometry data to the output netCDF file |
nc_write_grid_sizes | gs2_io_grids | Subroutine | Writes sizes of geometry data to the output netCDF file |
nc_write_grids | gs2_io_grids | Subroutine | Write geometry data to the output netCDF file Get the no_end_point flag from the input and store it in the output netCDF file. If no_end_point=.true., data at ntgrid are not stored. Data at ntgrid may be generated from the data at -ntgrid with some symmetry assumption. This option is meant to provide compatibility with GX. |
nc_write_heating | gs2_io | Subroutine | Writing heating diagnostics to netCDF |
nc_write_lambda_grid | gs2_io_grids | Subroutine | Write lambda grid data to the output netCDF file |
nc_write_moments | gs2_io | Subroutine | Write various moments to netcdf |
nc_write_omega | gs2_io | Subroutine | Writing the (normalised) complex frequency to netCDF |
nc_write_ql_metric | gs2_io | Subroutine | Writes the QL flux metric by mode number and summed over mode number to netcdf file |
netcdf_error | netcdf_utils | Subroutine | Convert a netCDF error code to a nice error message. Writes to error_unit |
netcdf_write_complex | gs2_io | Interface | Write a |
neumaier_sum | summation | Interface | |
neumaier_sum_real_1d | summation | Function | Very similar to Kahan summation but can perform better when the array contains a large range of inputs (i.e. where there may be elements that are larger the the cummulattive sum at that point) |
new_flux_surface_type | geo_utils | Function | |
new_periodic_spline | splines | Function | Populates a periodic_spline instance |
new_spline | splines | Function | Populates a spline instance |
next_time_step | dump_response | Subroutine | Changes to the next time step in the sequence as determined by the usual rules to reduce the timestep in a nonlinear simulation. |
nl_center | nonlinear_terms | Subroutine | Takes input array evaluated at theta grid points and overwrites it with array evaluated at cell centers note that there is an extra factor of 2 in output array |
noargs_interface | geo_utils | Interface | |
non_linear_term | diagnostics_zonal_transfer | Subroutine | calculate nonlinear term appearing in GKE for now assume electrostatic |
nonblocking_receive_complex_array | mp | Subroutine | FIXME : Add documentation |
nonblocking_send_complex_array | mp | Subroutine | FIXME : Add documentation |
norms_check_if_set | normalisations | Function | Decide if a given normalisation has been set |
norms_finish | normalisations | Subroutine | Reset and free memory |
norms_get_value | normalisations | Function | Get the value of the normalisation associated with |
norms_init | normalisations | Subroutine | Initialise the norms object |
norms_read_parameters | normalisations | Subroutine | FIXME : Add documentation |
norms_reset | normalisations | Subroutine | Reset the properties |
norms_set_logicals | normalisations | Subroutine | Decide if all/some of the normalisations have been set |
norms_set_value | normalisations | Subroutine | Sets the value of a particular normalisation, determined by the
passed |
not_exactly_equal | warning_helpers | Interface | Are two numbers not exactly equal to each other |
not_exactly_equal_r128 | warning_helpers | Function | |
not_exactly_equal_r32 | warning_helpers | Function | |
not_exactly_equal_r64 | warning_helpers | Function | |
nproc_comm | mp | Subroutine | How many procs are in passed communicator |
nprocs | ingen_mod | Subroutine | FIXME : Add documentation |
nprocs_e | ingen_mod | Subroutine | FIXME : Add documentation |
nprocs_le | ingen_mod | Subroutine | FIXME : Add documentation |
nprocs_lz | ingen_mod | Subroutine | FIXME : Add documentation |
nprocs_xxf | ingen_mod | Subroutine | FIXME : Add documentation |
nprocs_yxf | ingen_mod | Subroutine | FIXME : Add documentation |
ntgrid_padding | gs2_io_grids | Subroutine | Generate data at ntgrid point using some symmetry assumption |
num_runs | ingen_mod | Subroutine | FIXME : Add documentation |
number_of_bits_in_use | memory_usage | Function | Try to read the number of kilobytes in use currently from /proc/self/status and return number of bits in use. Will return negative if error encountered. This gets VmHWM. |
open_output_file | file_utils | Subroutine | Open an output file to write (replacing any existing) whose name is
|
optimise_fields | gs2_optimisation | Subroutine | FIXME : Add documentation |
optimise_flags | gs2_optimisation | Subroutine | FIXME : Add documentation |
optimise_gs2 | gs2_optimisation | Subroutine | FIXME : Add documentation |
optimise_layout | gs2_optimisation | Subroutine | FIXME : Add documentation |
optimise_nprocs | gs2_optimisation | Subroutine | FIXME : Add documentation |
optimise_simple | gs2_optimisation | Subroutine | FIXME : Add documentation |
output_flux_line | diagnostics_printout | Subroutine | Write instantaneous heat fluxes to given unit |
output_line | diagnostics_printout | Subroutine | Write growth rates to given unit |
output_results | gs2_optimisation | Subroutine | FIXME : Add documentation |
pairwise_sum | summation | Interface | |
pairwise_sum_real_1d | summation | Function | Unlike Kahan summation and similar methods this approach simply divides the set of numbers in half and sums each half separately. This is applied recursively until the local problem size drops below a certain size, at which point regular summation is applied |
palett | pgplot_utils | Subroutine | FIXME : Add documentation |
papergrid | pgplot_utils | Subroutine | FIXME : Add documentation |
par_spectrum | diagnostics_final_routines | Subroutine | Calculate the parallel spectrum |
parse_command_line | gs2_main | Subroutine | Parse some basic command line arguments. Currently just 'version' and 'help'. |
parse_command_line | multigs2 | Subroutine | Parse the command line to determine user options |
parse_set_file_to_files | multigs2 | Subroutine | |
pbar_interface | geo_utils | Interface | |
pbarfun | geometry | Function | |
pbarofrho | geometry | Function | FIXME : Add documentation |
pc_allocate | fields_local | Subroutine | Allocate storage space |
pc_allocate | fields_gf_local | Subroutine | Allocate storage space |
pc_count_avail | fields_local | Subroutine | Work out how many rows are available in each cell |
pc_count_avail | fields_gf_local | Subroutine | Work out how many rows are available in each cell |
pc_current_nresp | fields_local | Function | Return the current number of rows we're responsible for |
pc_current_nresp | fields_gf_local | Function | Return the current number of rows we're responsible for |
pc_deallocate | fields_local | Subroutine | Deallocate storage space |
pc_deallocate | fields_gf_local | Subroutine | Deallocate storage space |
pc_debug_print | fields_local | Subroutine | Debug printing |
pc_debug_print | fields_gf_local | Subroutine | Debug printing |
pc_decomp | fields_gf_local | Subroutine | The process decomposition works on the gf_lo layout, so if you have a point in gf_lo that is in a supercell you are in that supercell and you own the whole cell associated with that point, otherwise you don't have anything in that supercell, i.e. each cell has a single owner. |
pc_decomp_all_serial_local | fields_local | Subroutine | All serial and local || Decomp_type=0 |
pc_decomp_own_serial_local | fields_local | Subroutine | Serial and local but only for the supercells || Decomp_type=1 for which we have some data |
pc_decomp_owncells_serial_local | fields_local | Subroutine | Serial and local but only for the cells || Decomp_type=2 for which we have some data |
pc_decomp_owncells_simplempi | fields_local | Subroutine | Cells are decomposed based on proc || Decomp_type=3 |
pc_find_locality | fields_local | Subroutine | Work out which cells are local |
pc_find_locality | fields_gf_local | Subroutine | Work out which cells are local |
pc_has_ik | fields_local | Function | Determine if we have any cells with passed ik. |
pc_has_ik | fields_gf_local | Function | Determine if we have any cells with passed ik? |
pc_has_it | fields_local | Function | Determine if we have any cells with passed it. |
pc_has_it | fields_gf_local | Function | Determine if we have any cells with passed it? |
pc_init | fields_local | Subroutine | |
pc_init | fields_gf_local | Subroutine | A routine to initialise the object |
pc_make_decomp | fields_local | Subroutine | A wrapper routine to do the decomposition |
pc_make_decomp | fields_gf_local | Subroutine | A wrapper routine to do the decomposition |
pc_reset | fields_local | Subroutine | A routine to reset the pc object |
pc_reset | fields_gf_local | Subroutine | A routine to reset the pc object |
pe_layout | gs2_layouts | Subroutine | FIXME : Add documentation |
peak_number_of_bits_in_use | memory_usage | Function | Try to read the peak number of kilobytes currently from /proc/self/status and return number of bits in use. Will return negative if error encountered. This gets VmRSS. |
periodic_copy | geometry | Subroutine | Copy the |
periodic_dsplint | splines | Function | FIXME : Add documentation |
periodic_spline | splines | Interface | Constructor for periodic_spline |
periodic_spline_deriv | splines | Function | Bound wrapper to dsplint |
periodic_spline_interp | splines | Function | Bound wrapper to splint |
periodic_splint | splines | Function | FIXME : Add documentation |
periodic_splintint | splines | Function | FIXME : Add documentation |
pfactors | ingen_mod | Subroutine | FIXME : Add documentation |
pfun | leq | Function | FIXME : Add documentation |
pfun_eqfile | geo_utils | Function | |
pglineb | pgplot_utils | Subroutine | FIXME : Add documentation |
phi | geometry | Function | FIXME : Add documentation |
phinorm | gs2_diagnostics | Subroutine | Summed magnitude of all the fields |
plotdata | geometry | Subroutine | FIXME : Add documentation |
point_is_forbidden_and_not_redistributed | gs2_transforms | Function | Small helper function to wrap up logic about if this point corresponds to a forbidden point and if we need to transfer it in the redistribute |
prepare_initial_values_overrides | gs2_main | Subroutine | FIXME : Add documentation |
prepare_kt_grids_overrides | gs2_main | Subroutine | FIXME : Add documentation |
prepare_miller_geometry_overrides | gs2_main | Subroutine | FIXME : Add documentation |
prepare_optimisations_overrides | gs2_main | Subroutine | FIXME : Add documentation |
prepare_profiles_overrides | gs2_main | Subroutine | FIXME : Add documentation |
print_flux_line | diagnostics_printout | Subroutine | Print instantaneous heat fluxes to screen |
print_line | diagnostics_printout | Subroutine | Print out growth rates to screen. Doesn't quite conform to the principle of having all useful results stored in gnostics... takes stuff straight from diagnostics_omega |
print_memory_usage | memory_usage | Subroutine | Writes current estimate of memory use and peak memory use to provided unit. |
print_status | memory_usage | Subroutine | Internal routine which can be used for debugging. Tries to dump the contents of /proc/self/status to output_unit |
print_times | gs2_main | Subroutine | Print timing information to standard output. |
print_with_stars | unit_tests | Subroutine | |
proc_id | gs2_layouts | Interface | |
proc_id_accelx | gs2_layouts | Function | |
proc_id_e | gs2_layouts | Function | FIXME : Add documentation |
proc_id_f | gs2_layouts | Function | FIXME : Add documentation |
proc_id_g | gs2_layouts | Function | Return the processor id that has the point i in the g_lo layout |
proc_id_gf | gs2_layouts | Function | FIXME : Add documentation |
proc_id_jf | gs2_layouts | Function | FIXME : Add documentation |
proc_id_le | gs2_layouts | Function | FIXME : Add documentation |
proc_id_lz | gs2_layouts | Function | FIXME : Add documentation |
proc_id_parity | gs2_layouts | Function | FIXME : Add documentation |
proc_id_xxf | gs2_layouts | Function | Return the processor id that has the point i in the xxf_lo layout |
proc_id_yxf | gs2_layouts | Function | Return the processor id that has the point i in the yxf_lo layout |
proc_message | unit_tests | Function | |
process_check | unit_tests | Subroutine | |
process_test | unit_tests | Subroutine | |
psi | leq | Function | FIXME : Add documentation |
psi_eqfile | geo_utils | Function | |
psi_eqfile_cart | geo_utils | Function | |
psifun | geometry | Function | Calculates the normalised radial coordinate |
qag | quadpack | Subroutine | QAG approximates an integral over a finite interval. |
qage | quadpack | Subroutine | QAGE estimates a definite integral. |
qagi | quadpack | Subroutine | QAGI estimates an integral over a semi-infinite or infinite interval. |
qagp | quadpack | Subroutine | QAGP computes a definite integral. |
qags | quadpack | Subroutine | QAGS estimates the integral of a function. |
qawc | quadpack | Subroutine | QAWC computes a Cauchy principal value. |
qawce | quadpack | Subroutine | QAWCE computes a Cauchy principal value. |
qawf | quadpack | Subroutine | QAWF computes Fourier integrals over the interval [ A, +Infinity ). |
qawfe | quadpack | Subroutine | QAWFE computes Fourier integrals. |
qawo | quadpack | Subroutine | QAWO computes the integrals of oscillatory integrands. |
qaws | quadpack | Subroutine | QAWS estimates integrals with algebraico-logarithmic endpoint singularities. |
qawse | quadpack | Subroutine | QAWSE estimates integrals with algebraico-logarithmic endpoint singularities. |
qc25c | quadpack | Subroutine | QC25C returns integration rules for Cauchy Principal Value integrals. |
qc25o | quadpack | Subroutine | QC25O returns integration rules for integrands with a COS or SIN factor. |
qc25s | quadpack | Subroutine | QC25S returns rules for algebraico-logarithmic end point singularities. |
qcheb | quadpack | Subroutine | QCHEB computes the Chebyshev series expansion. |
qextr | quadpack | Subroutine | QEXTR carries out the Epsilon extrapolation algorithm. |
qfour | quadpack | Subroutine | QFOUR estimates the integrals of oscillatory functions. |
qfun | leq | Function | FIXME : Add documentation |
qfun_eqfile | geo_utils | Function | |
qk15 | quadpack | Subroutine | QK15 carries out a 15 point Gauss-Kronrod quadrature rule. |
qk15i | quadpack | Subroutine | QK15I applies a 15 point Gauss-Kronrod quadrature on an infinite interval. |
qk15w | quadpack | Subroutine | QK15W applies a 15 point Gauss-Kronrod rule for a weighted integrand. |
qk21 | quadpack | Subroutine | QK21 carries out a 21 point Gauss-Kronrod quadrature rule. |
qk31 | quadpack | Subroutine | QK31 carries out a 31 point Gauss-Kronrod quadrature rule. |
qk41 | quadpack | Subroutine | QK41 carries out a 41 point Gauss-Kronrod quadrature rule. |
qk51 | quadpack | Subroutine | QK51 carries out a 51 point Gauss-Kronrod quadrature rule. |
qk61 | quadpack | Subroutine | QK61 carries out a 61 point Gauss-Kronrod quadrature rule. |
qmomo | quadpack | Subroutine | QMOMO computes modified Chebyshev moments. |
qng | quadpack | Subroutine | QNG estimates an integral, using non-adaptive integration. |
qsort | quadpack | Subroutine | QSORT maintains the order of a list of local error estimates. |
quicksort | sorting | Interface | |
qwgtc | quadpack | Function | QWGTC defines the weight function used by QC25C. |
qwgto | quadpack | Function | QWGTO defines the weight functions used by QC25O. |
qwgts | quadpack | Function | QWGTS defines the weight functions used by QC25S. |
r2c | convert | Interface | |
r_1_insertsort | sorting | Subroutine | Sorts real arrays |
r_1_quicksort | sorting | Subroutine | Sort real arrays |
r_fill_2 | redistribute | Subroutine | FIXME : Add documentation |
r_fill_3 | redistribute | Subroutine | FIXME : Add documentation |
r_fill_4 | redistribute | Subroutine | FIXME : Add documentation |
r_insertsort | sorting | Subroutine | Sorts real array |
r_quicksort | sorting | Subroutine | Sort a real array |
r_redist_12 | redistribute | Subroutine | FIXME : Add documentation |
r_redist_22 | redistribute | Subroutine | FIXME : Add documentation |
r_redist_22_inv | redistribute | Subroutine | FIXME : Add documentation |
r_redist_26 | redistribute | Subroutine | FIXME : Add documentation |
r_redist_26_inv | redistribute | Subroutine | FIXME : Add documentation |
r_redist_32 | redistribute | Subroutine | FIXME : Add documentation |
r_redist_32_inv | redistribute | Subroutine | FIXME : Add documentation |
r_redist_33 | redistribute | Subroutine | FIXME : Add documentation DD> |
r_redist_33_inv | redistribute | Subroutine | FIXME : Add documentation |
r_redist_33_inv_mpi_copy | redistribute | Subroutine | FIXME : Add documentation |
r_redist_33_inv_mpi_copy_nonblock | redistribute | Subroutine | This routine does redistributes using entirely non-blocking comms. |
r_redist_33_inv_mpi_copy_persist_end | redistribute | Subroutine | Finish persistent communications associated with redistribute. Unpacks receive buffer. |
r_redist_33_inv_mpi_copy_persist_start | redistribute | Subroutine | Launch persistent communications associated with redistribute. Packs send buffer. |
r_redist_33_mpi_copy | redistribute | Subroutine | FIXME : Add documentation |
r_redist_33_mpi_copy_nonblock | redistribute | Subroutine | This routine does redistributes using entirely non-blocking comms. |
r_redist_33_mpi_copy_persist_end | redistribute | Subroutine | Finish persistent communications associated with redistribute. Unpacks receive buffer. |
r_redist_33_mpi_copy_persist_start | redistribute | Subroutine | Launch persistent communications associated with redistribute. Packs send buffer. |
r_redist_42 | redistribute | Subroutine | FIXME : Add documentation |
r_redist_42_inv | redistribute | Subroutine | FIXME : Add documentation |
r_redist_62 | redistribute | Subroutine | This routine is a copy of R_redist_42, with the dimensionality of from here increased to 6 |
r_redist_62_inv | redistribute | Subroutine | FIXME : Add documentation |
r_swap_elem | sorting | Subroutine | Swaps element at |
radau_p | gauss_quad | Function | Polynomial for Radau-Gauss quadrature |
radau_pp | gauss_quad | Function | Radau-Gauss polynomial derivative |
ranf | ran | Function | Returns a pseudorandom number range in [0., 1.), (i.e. 0<= ranf < 1). The generator is initialized with the given seed if passed, otherwise uses the seed already set (default or otherwise). |
ranf | constant_random | Function | |
range_get_grids | kt_grids_range | Subroutine | FIXME : Add documentation |
range_get_sizes | kt_grids_range | Subroutine | FIXME : Add documentation |
rank_comm | mp | Subroutine | What is rank of current proc in passed communicator |
rb_allocate | fields_local | Subroutine | Allocate storage space |
rb_allocate | fields_gf_local | Subroutine | Allocate storage space |
rb_deallocate | fields_local | Subroutine | Deallocate storage space |
rb_deallocate | fields_gf_local | Subroutine | Deallocate storage space |
rb_debug_print | fields_local | Subroutine | Debug printing |
rb_debug_print | fields_gf_local | Subroutine | Debug printing |
rb_init | fields_local | Subroutine | Initialise the members of the rowblock instance |
rb_init | fields_gf_local | Subroutine | Initialise the members of the rowblock instance |
rb_irex_to_irloc | fields_local | Function | Convert extended row index to local row index |
rb_irex_to_irloc | fields_gf_local | Function | Convert extended row index to local row index |
rb_mv_mult | fields_local | Subroutine | Matrix vector multiplication stored in tmp_sum |
rb_mv_mult | fields_gf_local | Subroutine | Matrix vector multiplication stored in tmp_sum |
rb_mv_mult_fun | fields_local | Function | Matrix vector multiplication |
rb_mv_mult_fun | fields_gf_local | Function | Matrix vector multiplication |
rb_reset | fields_local | Subroutine | A routine to reset the object |
rb_reset | fields_gf_local | Subroutine | A routine to reset the object |
rb_set_nrow | fields_local | Subroutine | Set the nrow variables |
rb_set_nrow | fields_gf_local | Subroutine | Set the nrow variables |
rcenter | eeq | Function | FIXME : Add documentation |
rcenter | deq | Function | FIXME : Add documentation | Not implemented |
rcenter | leq | Function | Return the major radius of the centre of the flux surface |
rcenter_eqfile | geo_utils | Function | Return the major radius of the centre of a given flux surface |
read_and_pad | gs2_io_grids | Subroutine | Helper subroutine to appropriately get geometry data depending on the no_end_point flag. Read geometry data from the input netCDF file with an appropriate size and pad ntgrid data if no_end_point=.true. The array corresponding to the dummy argument array in the upstream subroutine may be non-present optional argument, whose size will be 1 /= 2*ntgrid+1. |
read_and_set | deq | Subroutine | This subroutine reads an DFIT output file containing the axisymmetric magnetic field geometry on a rectangular domain defined by the coordinates (R,Z). |
read_and_set | ideq | Subroutine | FIXME : Add documentation Not really the diameter in this case. Instead, return the normalized minor radius, measured inside the ring, in the plane of the ring, starting at the ring and going inward. |
read_and_set | ceq | Subroutine | |
read_and_set | geq | Subroutine | This subroutine reads a generic NetCDF equilibrium file containing the axisymmetric magnetic field geometry in flux coordinates |
read_and_set | leq | Subroutine | Set module-level parameters and initialise the leq module |
read_and_set_interface | geo_utils | Interface | |
read_and_set_peq | peq | Subroutine | This subroutine reads a generic NetCDF equilibrium file containing the axisymmetric magnetic field geometry in flux coordinates |
read_and_set_teq | peq | Subroutine | This subroutine reads a generic NetCDF equilibrium file containing the axisymmetric magnetic field geometry in flux coordinates |
read_ballstab_config | ballstab | Subroutine | Reads in the ballstab_knobs namelist and populates the member variables |
read_collisions_config | collisions | Subroutine | Reads in the collisions_knobs namelist and populates the member variables |
read_diagnostics_base_config | diagnostics_base_configuration | Subroutine | Reads in the gs2_diagnostics_knobs namelist and populates the member variables |
read_dist_fn_config | dist_fn | Subroutine | Reads in the dist_fn_knobs namelist and populates the member variables |
read_dist_fn_species_config | dist_fn | Subroutine | Reads in the dist_fn_species_knobs namelist and populates the member variables |
read_driver_config | antenna | Subroutine | Reads in the driver namelist and populates the member variables |
read_element | kt_grids_specified | Subroutine | FIXME : Add documentation |
read_fields_config | fields | Subroutine | Reads in the fields_knobs namelist and populates the member variables |
read_gs2d | gs2d | Subroutine | FIXME : Add documentation |
read_hyper_config | hyper | Subroutine | Reads in the hyper_knobs namelist and populates the member variables |
read_ingen_config | ingen_mod | Subroutine | Reads in the ingen_knobs namelist and populates the member variables |
read_init_g_config | init_g | Subroutine | Reads in the init_g_knobs namelist and populates the member variables |
read_interface | abstract_config | Interface | |
read_knobs_config | run_parameters | Subroutine | Reads in the knobs namelist and populates the member variables |
read_kt_grids_box_config | kt_grids_box | Subroutine | Reads in the kt_grids_box_parameters namelist and populates the member variables |
read_kt_grids_config | kt_grids | Subroutine | Reads in the kt_grids_knobs namelist and populates the member variables |
read_kt_grids_range_config | kt_grids_range | Subroutine | Reads in the kt_grids_range_parameters namelist and populates the member variables |
read_kt_grids_single_config | kt_grids_single | Subroutine | Reads in the kt_grids_single_parameters namelist and populates the member variables |
read_kt_grids_specified_config | kt_grids_specified | Subroutine | Reads in the kt_grids_specified_parameters namelist and populates the member variables |
read_kt_grids_specified_element_config | kt_grids_specified | Subroutine | Reads in the kt_grids_specified_element namelist and populates the member variables |
read_layouts_config | gs2_layouts | Subroutine | Reads in the layouts_knobs namelist and populates the member variables |
read_le_grids_config | le_grids | Subroutine | Reads in the le_grids_knobs namelist and populates the member variables |
read_nonlinear_terms_config | nonlinear_terms | Subroutine | Reads in the nonlinear_terms_knobs namelist and populates the member variables |
read_normalisations_config | normalisations | Subroutine | Reads in the normalisations_knobs namelist and populates the member variables |
read_optimisation_config | optimisation_configuration | Subroutine | Reads in the optimisation_config namelist and populates the member variables |
read_parameter_scan_config | parameter_scan | Subroutine | Reads in the parameter_scan_knobs namelist and populates the member variables |
read_parameters | antenna | Subroutine | FIXME : Add documentation |
read_parameters | nonlinear_terms | Subroutine | FIXME : Add documentation |
read_parameters | dist_fn | Subroutine | FIXME : Add documentation |
read_parameters | fields | Subroutine | FIXME : Add documentation |
read_parameters | split_nonlinear_terms | Subroutine | Read the split_nonlinear_terms namelist |
read_parameters | theta_grid | Subroutine | FIXME : Add documentation |
read_parameters | gs2_layouts | Subroutine | FIXME : Add documentation |
read_parameters | gs2_diagnostics | Subroutine | Read the input parameters for the diagnostics module |
read_parameters | theta_grid_params | Subroutine | FIXME : Add documentation |
read_parameters | hyper | Subroutine | FIXME : Add documentation |
read_parameters | theta_grid_gridgen | Subroutine | FIXME : Add documentation |
read_parameters | theta_grid_salpha | Subroutine | FIXME : Add documentation |
read_parameters | le_grids | Subroutine | FIXME : Add documentation |
read_parameters | collisions | Subroutine | FIXME : Add documentation |
read_parameters | run_parameters | Subroutine | FIXME : Add documentation |
read_parameters | optimisation_configuration | Subroutine | |
read_parameters | theta_grid_file | Subroutine | FIXME : Add documentation |
read_parameters | species | Subroutine | FIXME : Add documentation |
read_parameters | parameter_scan | Subroutine | FIXME : Add documentation |
read_parameters | theta_grid_eik | Subroutine | FIXME : Add documentation |
read_parameters | init_g | Subroutine | FIXME : Add documentation |
read_parameters | rungridgen | Subroutine | FIXME : Add documentation |
read_parameters | ballstab | Subroutine | Read parameters |
read_parameters | diagnostics_config | Subroutine | |
read_parameters_box | kt_grids_box | Subroutine | FIXME : Add documentation |
read_parameters_internal | kt_grids | Subroutine | FIXME : Add documentation |
read_parameters_range | kt_grids_range | Subroutine | FIXME : Add documentation |
read_parameters_single | kt_grids_single | Subroutine | FIXME : Add documentation |
read_reinit_config | gs2_reinit | Subroutine | Reads in the reinit_knobs namelist and populates the member variables |
read_response_from_file_gf_local | fields_gf_local | Subroutine | Routine to read the current response matrix data from file dump. One file per connected domain. Each written by the head of the supercell. NOTE: Have to have setup communicators etc. |
read_response_from_file_imp | fields_implicit | Subroutine | A routine to read the response matrix from file and populate the implicit response storage, note we also allocate the response storage objects DD>It may be anticipated that we need to fix the boundary points |
read_response_from_file_local | fields_local | Subroutine | Routine to read the current response matrix data from file dump. One file per connected domain. Each written by the head of the supercell. NOTE: Have to have setup communicators etc. |
read_source_config | dist_fn | Subroutine | Reads in the source_knobs namelist and populates the member variables |
read_species_config | species | Subroutine | Reads in the species_knobs namelist and populates the member variables |
read_species_element_config | species | Subroutine | Reads in the species_parameters namelist and populates the member variables |
read_species_knobs | dist_fn | Subroutine | FIXME : Add documentation |
read_split_nonlinear_terms_config | split_nonlinear_terms | Subroutine | Reads in the split_nonlinear_terms_knobs namelist and populates the member variables |
read_stir_config | antenna | Subroutine | Reads in the stir namelist and populates the member variables |
read_t0_from_restart_file | gs2_save | Subroutine | FIXME : Add documentation |
read_theta_grid_config | theta_grid | Subroutine | Reads in the theta_grid_knobs namelist and populates the member variables |
read_theta_grid_eik_config | theta_grid_eik | Subroutine | Reads in the theta_grid_eik_knobs namelist and populates the member variables |
read_theta_grid_file_config | theta_grid_file | Subroutine | Reads in the theta_grid_file_knobs namelist and populates the member variables |
read_theta_grid_gridgen_config | theta_grid_gridgen | Subroutine | Reads in the theta_grid_gridgen_knobs namelist and populates the member variables |
read_theta_grid_parameters_config | theta_grid_params | Subroutine | Reads in the theta_grid_parameters namelist and populates the member variables |
read_theta_grid_salpha_config | theta_grid_salpha | Subroutine | Reads in the theta_grid_salpha_knobs namelist and populates the member variables |
real_calculate_kinetic_energy_transfer | diagnostics_kinetic_energy_transfer | Subroutine | compute the three-wave couplings |
real_init | gs2_diagnostics | Subroutine | Read the input parameters; open the various text output files according to the relevant input flags; allocate and zero the module-level flux arrays, gs2_diagnostics_knobs and gs2_diagnostics_knobs |
real_init_ballstab | ballstab | Subroutine | Initialise this module |
real_local_sum | integration | Function | A wrapper routine to perform a sum. Used to provide a single point at which we choose a summation method |
real_rectangular_integration | integration | Function | Apply the (left) rectangular rule to integrate y over the domain of x. |
real_trapezoidal_integration | integration | Function | Apply the trapezium rule to integrate y over the domain of x. |
receive | mp | Interface | |
receive_character | mp | Subroutine | FIXME : Add documentation |
receive_complex | mp | Subroutine | FIXME : Add documentation |
receive_complex_2array | mp | Subroutine | FIXME : Add documentation |
receive_complex_3d_array | mp | Subroutine | FIXME : Add documentation |
receive_complex_array | mp | Subroutine | FIXME : Add documentation |
receive_integer | mp | Subroutine | FIXME : Add documentation |
receive_integer_array | mp | Subroutine | FIXME : Add documentation |
receive_logical | mp | Subroutine | FIXME : Add documentation |
receive_logical_array | mp | Subroutine | FIXME : Add documentation |
receive_real | mp | Subroutine | FIXME : Add documentation |
receive_real_4d_array | mp | Subroutine | FIXME : Add documentation |
receive_real_5d_array | mp | Subroutine | FIXME : Add documentation |
receive_real_array | mp | Subroutine | FIXME : Add documentation |
recommend_inversion_method | mat_inv | Function | Times each available method for the given problem size and returns the flag of the fastest one. |
recommend_multiplication_method | matrix_multiply | Function | Times each available method for the given problem size and returns the flag of the fastest one. |
rectangular_integration | integration | Interface | |
recv_init | mp | Interface | |
recv_init_complex_array | mp | Subroutine | Routine to initialise a persistent recv operation |
recv_init_real_array | mp | Subroutine | Routine to initialise a persistent recv operation |
reduce_time_step | gs2_reinit | Subroutine | Reduces the time step by a factor |
regrid | theta_grid_gridgen | Subroutine | FIXME : Add documentation |
release | runtime_tests | Function | This function is just a call of release_runtime_info and is provided for backwards compatibility. |
release_runtime_info | runtime_tests | Function | Returns the release number |
remap_bounds | shm_mpi3 | Interface | |
remap_bounds_1c | shm_mpi3 | Function | FIXME : Add documentation |
remap_bounds_1r | shm_mpi3 | Function | FIXME : Add documentation |
remap_bounds_2c | shm_mpi3 | Function | FIXME : Add documentation |
remap_bounds_2r | shm_mpi3 | Function | FIXME : Add documentation |
remap_bounds_3c | shm_mpi3 | Function | FIXME : Add documentation |
remap_bounds_3r | shm_mpi3 | Function | FIXME : Add documentation |
remove_zonal_flows | fields_implicit | Subroutine | FIXME : Add documentation |
reorder_kx | gs2_diagnostics | Subroutine | FIXME : Add documentation |
replace_all_tabs | file_utils | Subroutine | Replaces each horizontal tab with a single space |
replace_leading_tabs | file_utils | Subroutine | Replaces all leading tabs with space. Note we consider any tabs appearing before the first non-space/tab character. |
report | ingen_mod | Subroutine | FIXME : Add documentation |
report_idle_procs | ingen_mod | Subroutine | This subroutine wraps up the output functionality for the code that creates the list of suggested process counts for the linear computation and checks whether those process counts work well for the non-linear calculations as well. |
report_init_times | gs2_init | Subroutine | Report the time spent in each initialisation level |
report_map_property | redistribute | Subroutine | FIXME : Add documentation |
report_step_statistics | split_nonlinear_terms | Subroutine | |
report_velocity_integration_error_estimate | le_grids | Subroutine | Calculate estimates of the velocity space integration errors and report to screen / specified unit. |
reset_averages_and_counters | gs2_diagnostics_new | Subroutine | Reset cumulative flux and heating averages that are used, e.g. for Trinity. Does not at the moment apply to average growth rates. |
reset_averages_and_counters | diagnostics_fluxes | Subroutine | Set averages in gnostics\%current_results to 0. |
reset_averages_and_counters | diagnostics_nonlinear_convergence | Subroutine | FIXME : Add documentation |
reset_averages_and_counters | diagnostics_heating | Subroutine | FIXME : Add documentation |
reset_ballstab_config | ballstab | Subroutine | Resets the config object to the initial empty state |
reset_collisions_config | collisions | Subroutine | Resets the config object to the initial empty state |
reset_diagnostics_base_config | diagnostics_base_configuration | Subroutine | Resets the config object to the initial empty state |
reset_dist_fn_config | dist_fn | Subroutine | Resets the config object to the initial empty state |
reset_dist_fn_species_config | dist_fn | Subroutine | Resets the config object to the initial empty state |
reset_driver_config | antenna | Subroutine | Resets the config object to the initial empty state |
reset_equations | gs2_main | Subroutine | Effectively resets the state of the diagnostics and time index back to the start of the simulation. Primarily useful to allow one to reuse existing files etc. without having to start a new process. Mostly used in trinity workflows. |
reset_fields_config | fields | Subroutine | Resets the config object to the initial empty state |
reset_fields_gf_local | fields_gf_local | Subroutine | Reset the fields_gf_local module |
reset_fields_local | fields_local | Subroutine | Reset the fields_local module |
reset_hyper_config | hyper | Subroutine | Resets the config object to the initial empty state |
reset_ingen_config | ingen_mod | Subroutine | Resets the config object to the initial empty state |
reset_init | antenna | Subroutine | FIXME : Add documentation |
reset_init | nonlinear_terms | Subroutine | FIXME : Add documentation |
reset_init | fields_implicit | Subroutine | FIXME : Add documentation |
reset_init | fields_test | Subroutine | FIXME : Add documentation |
reset_init | fields | Subroutine | FIXME : Add documentation |
reset_init | gs2_diagnostics | Subroutine | FIXME : Add documentation |
reset_init | collisions | Subroutine | Forces recalculation of coefficients in collision operator when timestep changes. Currently just calls finish_collisions |
reset_init_g_config | init_g | Subroutine | Resets the config object to the initial empty state |
reset_init_times | gs2_init | Subroutine | Reset the time spent in each initialisation level |
reset_interface | abstract_config | Interface | |
reset_knobs_config | run_parameters | Subroutine | Resets the config object to the initial empty state |
reset_kt_grids_box_config | kt_grids_box | Subroutine | Resets the config object to the initial empty state |
reset_kt_grids_config | kt_grids | Subroutine | Resets the config object to the initial empty state |
reset_kt_grids_range_config | kt_grids_range | Subroutine | Resets the config object to the initial empty state |
reset_kt_grids_single_config | kt_grids_single | Subroutine | Resets the config object to the initial empty state |
reset_kt_grids_specified_config | kt_grids_specified | Subroutine | Resets the config object to the initial empty state |
reset_kt_grids_specified_element_config | kt_grids_specified | Subroutine | Resets the config object to the initial empty state |
reset_layouts_config | gs2_layouts | Subroutine | Resets the config object to the initial empty state |
reset_le_grids_config | le_grids | Subroutine | Resets the config object to the initial empty state |
reset_linear_magnitude | gs2_main | Subroutine | FIXME : Add documentation |
reset_mp_times | mp | Subroutine | Resets mp timers to zero |
reset_nonlinear_terms_config | nonlinear_terms | Subroutine | Resets the config object to the initial empty state |
reset_normalisations_config | normalisations | Subroutine | Resets the config object to the initial empty state |
reset_optimisation_config | optimisation_configuration | Subroutine | Resets the config object to the initial empty state |
reset_parameter_scan_config | parameter_scan | Subroutine | Resets the config object to the initial empty state |
reset_redist_times | redistribute | Subroutine | Resets redist timers to zero |
reset_reinit_config | gs2_reinit | Subroutine | Resets the config object to the initial empty state |
reset_source_config | dist_fn | Subroutine | Resets the config object to the initial empty state |
reset_species_config | species | Subroutine | Resets the config object to the initial empty state |
reset_species_element_config | species | Subroutine | Resets the config object to the initial empty state |
reset_split_nonlinear_terms_config | split_nonlinear_terms | Subroutine | Resets the config object to the initial empty state |
reset_step_statistics | split_nonlinear_terms | Subroutine | Reset the step statistics |
reset_stir_config | antenna | Subroutine | Resets the config object to the initial empty state |
reset_theta_grid_config | theta_grid | Subroutine | Resets the config object to the initial empty state |
reset_theta_grid_eik_config | theta_grid_eik | Subroutine | Resets the config object to the initial empty state |
reset_theta_grid_file_config | theta_grid_file | Subroutine | Resets the config object to the initial empty state |
reset_theta_grid_gridgen_config | theta_grid_gridgen | Subroutine | Resets the config object to the initial empty state |
reset_theta_grid_parameters_config | theta_grid_params | Subroutine | Resets the config object to the initial empty state |
reset_theta_grid_salpha_config | theta_grid_salpha | Subroutine | Resets the config object to the initial empty state |
reset_time_step | gs2_reinit | Subroutine | FIXME : Add documentation |
reset_timers | gs2_main | Subroutine | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Private subroutines !!!!!!!!!!!!!!!!!!!!!!!!!!! Reset timers data to 0 |
restart_writable | gs2_save | Function | This function checks to see if we can create a file with name
|
restore_current_scan_parameter_value | gs2_save | Subroutine | FIXME : Add documentation |
rfun | geo_utils | Function | Returns the distance to the magnetic axis as a function of rp (the normalised poloidal flux variable) and theta. |
rfun | leq | Function | FIXME : Add documentation | Should this be equivalent to psi as in others? |
rhofun | deq | Function | FIXME : Add documentation |
rhofun | geometry | Function | FIXME : Add documentation
Only used with ~undocumented |
rhofun_null | geo_utils | Function | |
rk_scheme_validate | rk_schemes | Function | Perform a small check of the consistency. Returns an error code built from bitwise flags to give information about which checks, if any, failed. Success is repesented by zero. |
rmajortgrid | geometry | Subroutine | Calculates rmajor = R(theta), where R is the distance to the central axis (rmajor not to be confused with rmaj, r_geo etc) rgrid is the submodule radial grid (r_circ for EFIT & deq, rp otherwise) |
root | geometry | Subroutine | Find soln where f(soln) ~= fval. Works best if a and b bracket the root. We can then first bisect the bracket to narrow in on the solution. Following this we use the secant method to find the solution. The input xerrbi influences the number of bisection iterations whilst xerrsec is used to set the stopping tolerance on the secant method. |
rp_interface | geo_utils | Interface | |
rpofrho | geometry | Function | FIXME : Add documentation |
Rpos | leq | Function | Return the major radius at |
rpos_eqfile | geo_utils | Function | |
rpos_eqfile_cart | geo_utils | Function | |
rtgrid | geometry | Subroutine | Calculate rgrid for the case of eeq and deq: in this case, rgrid is the distance to the magnetic axis as a function of theta. |
rtheta_interface | geo_utils | Interface | |
rtsec | gk_complex_root | Function | FIXME : Add documentation |
run_diagnostics | gs2_diagnostics_new | Subroutine | Create or write all variables according to the value of istep: istep=-1 --> Create all netcdf variables istep=0 --> Write constant arrays/parameters (e.g. aky) and initial values istep>0 --> Write variables new diagnostic, calulate and write in new variable |
run_diagnostics_to_be_updated | gs2_diagnostics_new | Subroutine | FIXME : Add documentation |
run_eigensolver | gs2_main | Subroutine | Employ the eigenvalue solver to seek eigenmodes using SLEPc |
run_eikcoefs_and_resample | geometry | Subroutine | Run eikcoefs with |
run_gs2 | gs2_main | Subroutine | The main entry point into GS2, runs a single GS2 simulation |
run_ingen | ingen_mod | Subroutine | Entry point: initialise needed modules, run checks, and write namelists |
run_number | ingen_mod | Subroutine | FIXME : Add documentation |
run_old_final_routines | gs2_diagnostics_new | Subroutine | FIXME : Add documentation |
run_optimise_gs2 | gs2_optimisation | Function | Setup, run, and teardown GS2 optimisation preprocessing |
run_stability_check | ballstab | Subroutine | Runs the stability check scan for the module level shat/beta array values |
safe_sqrt | collisions | Function | A wrapper to sqrt which replaces -ve values with 0.0 to avoid NaNs arising from slight floating point discrepancies. We could consider adding a debug check to abort/warn if the passed value is too negative (i.e. if it looks like an error rather than small round off). |
salpha_get_grids | theta_grid_salpha | Subroutine | FIXME : Add documentation DD> The following few lines will cause an issue in the (semi-)valid case where eps=0.0 so adding a guard |
salpha_get_sizes | theta_grid_salpha | Subroutine | FIXME : Add documentation |
save_dt | gs2_time | Subroutine | FIXME : Add documentation |
save_dt_cfl | gs2_time | Subroutine | FIXME : Add documentation |
save_dt_max | gs2_time | Subroutine | Sets the maximum timestep size allowed based on passed value. |
save_dt_min | gs2_time | Subroutine | Sets the minimum timestep size allowed based on passed value. |
save_input | gs2_io | Subroutine | Save the input file in the NetCDF file |
save_restart_dist_fn | gs2_diagnostics | Subroutine | Save some extra information in final restart files |
save_wisdom | fft_work | Subroutine | Save FFTW wisdom to file |
sc_allocate | fields_local | Subroutine | Allocate storage space |
sc_allocate | fields_gf_local | Subroutine | Allocate storage space |
sc_deallocate | fields_local | Subroutine | Deallocate storage space |
sc_deallocate | fields_gf_local | Subroutine | Deallocate storage space |
sc_debug_print | fields_local | Subroutine | Debug printing |
sc_debug_print | fields_gf_local | Subroutine | Debug printing |
sc_dump | fields_local | Subroutine | Debug routine to dump the current supercell |
sc_dump | fields_gf_local | Subroutine | Debug routine to dump the current supercell |
sc_dump_to_file | fields_local | Subroutine | Routine to write the response matrix for this supercell to netcdf file. |
sc_get_field_update | fields_local | Subroutine | Get the field update DD>TAGGED |
sc_get_field_update | fields_gf_local | Subroutine | Get the field update |
sc_get_left_it | fields_local | Function | Given an it value get the it of the left connected cell |
sc_get_left_it | fields_gf_local | Function | Given an it value get the it of the left connected cell |
sc_has_it | fields_local | Function | Is the passed it a member of this supercell |
sc_has_it | fields_gf_local | Function | Is the passed it a member of this supercell |
sc_iex_to_dims | fields_local | Subroutine | Convert the extended domain index to ig, it and ifl |
sc_iex_to_dims | fields_gf_local | Subroutine | Convert the extended domain index to ig, it and ifl |
sc_iex_to_ic | fields_local | Subroutine | Convert the extended domain index to ic |
sc_iex_to_ic | fields_gf_local | Subroutine | Convert the extended domain index to ic |
sc_iex_to_ifl | fields_local | Subroutine | Convert the extended domain index to ifl |
sc_iex_to_ifl | fields_gf_local | Subroutine | Convert the extended domain index to ifl |
sc_iex_to_ig | fields_local | Subroutine | Convert the extended domain index to ig |
sc_iex_to_ig | fields_gf_local | Subroutine | Convert the extended domain index to ig |
sc_iex_to_it | fields_local | Subroutine | Convert the extended domain index to it |
sc_iex_to_it | fields_gf_local | Subroutine | Convert the extended domain index to it |
sc_init | fields_local | Subroutine | Initialise the supercell instance by setting and calculating some basic properties. Does not deal with allocating all storage etc. |
sc_init | fields_gf_local | Subroutine | Initialise the supercell instance by setting and calculating some basic properties. Does not deal with allocating all storage etc. |
sc_invert | fields_local | Subroutine | A routine to invert the field matrix |
sc_invert | fields_gf_local | Subroutine | A routine to invert the field matrix |
sc_invert_local | fields_local | Subroutine | A routine to invert the field matrix locally |
sc_invert_local | fields_gf_local | Subroutine | A routine to invert the field matrix locally |
sc_invert_mpi | fields_local | Subroutine | A routine to invert the field matrix using mpi |
sc_invert_mpi | fields_gf_local | Subroutine | A routine to invert the field matrix using mpi |
sc_make_subcom_1 | fields_local | Subroutine | Create primary (top level) sub communicators |
sc_make_subcom_1 | fields_gf_local | Subroutine | Create primary (top level) sub communicators |
sc_make_subcom_2 | fields_local | Subroutine | Create the secondary (intraobject) subcommunicators |
sc_make_subcom_2 | fields_gf_local | Subroutine | Create the secondary (intraobject) subcommunicators |
sc_prepare | fields_local | Subroutine | Prepare the field matrix for calculating field updates |
sc_prepare | fields_gf_local | Subroutine | Prepare the field matrix for calculating field updates |
sc_pull_rows_to_arr | fields_local | Subroutine | A routine to collect all the row level data and store in passed array Gather the row blocks up for this cell to fill an array DD>FOR NOW USE ALL_REDUCE AS EASIER, BUT SHOULD BE ABLE |
sc_pull_rows_to_arr | fields_gf_local | Subroutine | A routine to collect all the row level data and store in passed array Gather the row blocks up for this cell to fill an array |
sc_push_arr_to_rows | fields_local | Subroutine | A routine to distribute an array to appropriate row blocks |
sc_push_arr_to_rows | fields_gf_local | Subroutine | A routine to distribute an array to appropriate row blocks |
sc_read_from_file | fields_local | Subroutine | Routine to read the response matrix for this supercell from netcdf file. |
sc_reduce_tmpsum | fields_local | Subroutine | Reduce the field update across cells to give the final answer DD>TAGGED: As we currently have to do fm_gather_fields on every time step we only need |
sc_reduce_tmpsum | fields_gf_local | Subroutine | Reduce the field update across cells to give the final answer |
sc_reset | fields_local | Subroutine | A routine to reset the object |
sc_reset | fields_gf_local | Subroutine | A routine to reset the object |
sc_set_locality | fields_local | Subroutine | Set the locality of each object |
sc_set_locality | fields_gf_local | Subroutine | Set the locality of each object |
sc_store_fq | fields_local | Subroutine | Store the field equations at row level |
sc_store_fq | fields_gf_local | Subroutine | Store the field equations at row level |
scalar_func | quadpack | Interface | |
scatter | redistribute | Interface | |
scope | mp | Subroutine | Switch the module communicator (and size/rank variables) between different scopes. |
seikon | geometry | Subroutine | This is not right for cart types, but ok for those compatible with bishop=0. |
self_periodic | dist_fn | Subroutine | Sets sum of homogeneous and inhomogeneous solutions to give a result gnew(ntgrid,2) = gnew(-ntgrid,2) gnew(ntgrid,1) = gnew(-ntgrid,1) ie periodic bcs at the ends of the flux tube. |
send | mp | Interface | |
send_character | mp | Subroutine | FIXME : Add documentation |
send_complex | mp | Subroutine | FIXME : Add documentation |
send_complex_2d_array | mp | Subroutine | FIXME : Add documentation |
send_complex_3d_array | mp | Subroutine | FIXME : Add documentation |
send_complex_array | mp | Subroutine | FIXME : Add documentation |
send_init | mp | Interface | |
send_init_complex_array | mp | Subroutine | Routine to initialise a persistent send operation |
send_init_real_array | mp | Subroutine | Routine to initialise a persistent send operation |
send_integer | mp | Subroutine | FIXME : Add documentation |
send_integer_array | mp | Subroutine | FIXME : Add documentation |
send_logical | mp | Subroutine | FIXME : Add documentation |
send_logical_array | mp | Subroutine | FIXME : Add documentation |
send_real | mp | Subroutine | FIXME : Add documentation |
send_real_4d_array | mp | Subroutine | FIXME : Add documentation |
send_real_5d_array | mp | Subroutine | FIXME : Add documentation |
send_real_array | mp | Subroutine | FIXME : Add documentation |
serf_ext | spfunc | Function | FIXME : Add documentation |
set_antenna_config | antenna | Subroutine | Set the module level config types Will abort if the module has already been initialised to avoid inconsistencies. |
set_ascii_file_switches | gs2_diagnostics_new | Subroutine | This subroutine determines which ascii output files are enabled (i.e., opened, flushed at each write, and then closed). If an ascii file is not enabled here, writing to it will cause some indeterminate unpleasant behaviour |
set_ballstab_config | ballstab | Subroutine | Set the module level config type Will abort if the module has already been initialised to avoid inconsistencies. |
set_beta_prime | ballstab | Subroutine | Sets the current value of beta_prime (or equivalent var) Really just sets the variable that we can use to control the pressure gradient. |
set_ceq_from_chease | ceq | Subroutine | Set the ceq module-level variables from the read_chease module variables. |
set_cfl_time_step_and_check_if_too_large | nonlinear_terms | Subroutine | Calculates the cfl limit from the module level max_vel value saves it using save_dt_cfl and then sets the reset flag based on checking if the current time step is too large. |
set_collisions_config | collisions | Subroutine | Set the module level config type Will abort if the module has already been initialised to avoid inconsistencies. |
set_current_f0_species | species | Subroutine | FIXME : Add documentation |
set_default_error_file_unit | mp | Subroutine | Set the unit for the error file to use in this module, for example for mp_abort |
set_default_netcdf_compression | netcdf_utils | Subroutine | Set the value of use_compression_default |
set_default_netcdf_compression_level | netcdf_utils | Subroutine | Set the value of deflate_level_default |
set_diagnostics_config_config | diagnostics_config | Subroutine | Set the module level config type Will abort if the module has already been initialised to avoid inconsistencies. |
set_dimension_order | gs2_layouts | Interface | |
set_dimension_order_e | gs2_layouts | Subroutine | Sets the order of th sgn x y l s in e_lo |
set_dimension_order_g | gs2_layouts | Subroutine | Sets the order of x y l e s in g_lo |
set_dimension_order_le | gs2_layouts | Subroutine | Sets the order of x y th s in le_lo |
set_dimension_order_lz | gs2_layouts | Subroutine | Sets the order of x y e th s in lz_lo |
set_dimension_order_xxf | gs2_layouts | Subroutine | Sets the order of y th sgn l e s in xxf_lo Note: usually the order is y, theta, sign, then "les" in the order they appear in the g_lo layout |
set_dimension_order_yxf | gs2_layouts | Subroutine | Sets the order of x th sgn l e s in yxf_lo Note: usually the order is x, theta, sign, then "les" in the order they appear in the g_lo layout |
set_dist_fn_config | dist_fn | Subroutine | Set the module level config types Will abort if the module has already been initialised to avoid inconsistencies. |
set_dump_and_read_response | fields | Subroutine | FIXME : Add documentation |
set_fields_config | fields | Subroutine | Set the module level config type Will abort if the module has already been initialised to avoid inconsistencies. |
set_gnew_from_nonadiabatic_dfn | init_g | Subroutine | Take the existing gnew value and, assuming it is the nonadiabatic dfn, calculate the consistent potentials to set the true gnew value. |
set_grids | le_grids | Subroutine | FIXME : Add documentation |
set_gs2_diagnostics_config | gs2_diagnostics | Subroutine | Set the module level config type Will abort if the module has already been initialised to avoid inconsistencies. |
set_gs2_reinit_config | gs2_reinit | Subroutine | Set the module level config type Will abort if the module has already been initialised to avoid inconsistencies. |
set_h_zero | dist_fn_arrays | Subroutine | Assign $g$ a value corresponding to $h$ (g_wesson of CMR's note in g_adjust) of $h = 0$ in order to be consistent with g_adjust. The correct function call to set h = 0 is call set_h_zero(g, phi, bpar, iglo) |
set_heating | collisions | Subroutine | |
set_hyper_config | hyper | Subroutine | Set the module level config type Will abort if the module has already been initialised to avoid inconsistencies. |
set_hzero_lorentz_collisions_matrix | collisions | Subroutine | Special behaviour when h=0 for passing non-zonal electrons |
set_ingen_config | ingen_mod | Subroutine | Set the module level config type Will abort if the module has already been initialised to avoid inconsistencies. |
set_init_fields | fields | Subroutine | FIXME : Add documentation |
set_init_g_config | init_g | Subroutine | Set the module level config type Will abort if the module has already been initialised to avoid inconsistencies. |
set_initial_field_and_dist_fn_values | gs2_init | Subroutine | |
set_initval_overrides_to_current_vals | gs2_main | Subroutine | FIXME : Add documentation |
set_job_id | unit_tests | Subroutine | |
set_kt_grids_box_config | kt_grids_box | Subroutine | Set the module level config type Will abort if the module has already been initialised to avoid inconsistencies. |
set_kt_grids_config | kt_grids | Subroutine | Set the module level config type Will abort if the module has already been initialised to avoid inconsistencies. |
set_kt_grids_range_config | kt_grids_range | Subroutine | Set the module level config type Will abort if the module has already been initialised to avoid inconsistencies. |
set_kt_grids_single_config | kt_grids_single | Subroutine | Set the module level config type Will abort if the module has already been initialised to avoid inconsistencies. |
set_kt_grids_specified_config | kt_grids_specified | Subroutine | Set the module level config types Will abort if the module has already been initialised to avoid inconsistencies. |
set_layouts_config | gs2_layouts | Subroutine | Set the module level config type Will abort if the module has already been initialised to avoid inconsistencies. |
set_le_grids_config | le_grids | Subroutine | Set the module level config type Will abort if the module has already been initialised to avoid inconsistencies. |
set_nonlinear_terms_config | nonlinear_terms | Subroutine | Set the module level config type Will abort if the module has already been initialised to avoid inconsistencies. |
set_normalisations_config | normalisations | Subroutine | Set the module level config type Will abort if the module has already been initialised to avoid inconsistencies. |
set_optimisation_config | optimisation_configuration | Subroutine | Set the module level config type Will abort if the module has already been initialised to avoid inconsistencies. |
set_optimisations_overrides | dist_fn | Subroutine | FIXME : Add documentation |
set_optimised_choice | redistribute | Subroutine | Set choice of redist algorithm based on properties of g_lo |
set_overrides | dist_fn | Interface | |
set_overrides | fields | Subroutine | FIXME : Add documentation |
set_overrides | gs2_layouts | Subroutine | FIXME : Add documentation |
set_overrides | theta_grid_params | Subroutine | FIXME : Add documentation |
set_overrides | kt_grids | Subroutine | FIXME : Add documentation |
set_overrides | run_parameters | Subroutine | FIXME : Add documentation |
set_overrides | species | Subroutine | FIXME : Add documentation |
set_parameter_scan_config | parameter_scan | Subroutine | Set the module level config type Will abort if the module has already been initialised to avoid inconsistencies. |
set_profiles_overrides | dist_fn | Subroutine | FIXME : Add documentation |
set_random_array | constant_random | Subroutine | |
set_redist_character_type | redistribute | Subroutine | FIXME : Add documentation |
set_restart_file | gs2_save | Subroutine | Sets the base of the restart file to be used when writing/reading files. |
set_run_parameters_config | run_parameters | Subroutine | Set the module level config type Will abort if the module has already been initialised to avoid inconsistencies. |
set_save_h | dist_fn | Subroutine | Set the save_h flag based on connections data |
set_scan_parameter | parameter_scan | Subroutine | FIXME : Add documentation |
set_seed | mt19937 | Subroutine | Set initial seed of a mt19937_type instance |
set_seed_from_single_integer | ran | Subroutine | Sets the seed for the random number generator provided by the standard based on a single integer. We use create_seed_from_single_integer to ensure we have enough values in the series rather than just duplicating this number. |
set_shat | ballstab | Subroutine | Sets the value of shat |
set_species_config | species | Subroutine | Set the module level config types Will abort if the module has already been initialised to avoid inconsistencies. |
set_theta_grid_config | theta_grid | Subroutine | Set the module level config type Will abort if the module has already been initialised to avoid inconsistencies. |
set_theta_grid_eik_config | theta_grid_eik | Subroutine | Set the module level config type Will abort if the module has already been initialised to avoid inconsistencies. |
set_theta_grid_file_config | theta_grid_file | Subroutine | Set the module level config type Will abort if the module has already been initialised to avoid inconsistencies. |
set_theta_grid_gridgen_config | theta_grid_gridgen | Subroutine | Set the module level config type Will abort if the module has already been initialised to avoid inconsistencies. |
set_theta_grid_parameters_config | theta_grid_params | Subroutine | Set the module level config type Will abort if the module has already been initialised to avoid inconsistencies. |
set_theta_grid_salpha_config | theta_grid_salpha | Subroutine | Set the module level config type Will abort if the module has already been initialised to avoid inconsistencies. |
set_vgrid | le_grids | Subroutine | FIXME : Add documentation |
set_vnmult | collisions | Subroutine | |
set_xxf_optimised_variables | redistribute | Subroutine | FIXME : Add documentation |
set_yxf_optimised_variables | redistribute | Subroutine | FIXME : Add documentation |
setup_accel_transform_layouts | gs2_layouts | Function | Construct an accel layout instance |
setup_accelx_transform_layouts | gs2_layouts | Function | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Accelerated FFTW3 layouts !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Construct an accelx layout instance |
setup_arrays | ballstab | Subroutine | Allocate+populate arrays |
setup_connected_bc_redistribute | dist_fn | Subroutine | Populates the redistribute types describing the communication pattern required to deal with linked boundary conditions. Only deals with passing particles, including the wfb if passing_wfb is true. DD>Note the communications setup here are often equivalent to an all-to-all type |
setup_connected_bc_redistribute_mixed_wfb | dist_fn | Subroutine | Populates the redistribute types describing the communication pattern required to deal with linked boundary conditions for the mixed wfb. This is used when passing_wfb = trapped_wfb = false. This is the default. |
setup_dist_fn_layouts | gs2_layouts | Function | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Distribution function layouts !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Setup a g_layout (g_lo) type data decomposition object describing the work decomposition for a problem with passed grid sizes running on nproc. Returns the values for the processor with rank iproc. Note this involves collective 1 routines so requires all processors on comm world to take part. This does not require the input nproc to match the nproc of the world communicator. |
setup_energy_layouts | gs2_layouts | Function | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Energy layouts !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Construct an energy layout instance. |
setup_energy_redistribute_local | le_grids | Subroutine | Constructs the redistribute mapping from a g_lo data decomposition to an e_lo decomposition |
setup_fields_implicit_class_arrays | dist_fn | Subroutine | Count the number of unique supercell sizes and setup the fields implicit arrays M_class and N_class. |
setup_fields_layouts | gs2_layouts | Function | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Field layouts
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
M_class(i) = number of i_th supercell
N_class(i) = size of i_th supercell
i_class = number of classes of (different sized) supercells. |
setup_g2gf_redistribute | le_grids | Subroutine | Construct the redistribute for g_lo -> gf_lo |
setup_g2le_redistribute_local | le_grids | Subroutine | Construct a redistribute for g_lo -> le_lo |
setup_generic | abstract_config | Subroutine | Do some standard setup/checking |
setup_get_fields_direct_from_dfn_denominators | dist_fn | Subroutine | Precomputes constants used in the inversion of the field equations: gamtot * phi - gamtot1 * bpar = antot kperp2 * apar = antota beta/2 * gamtot1 * phi + (beta * gamtot2 + 1) * bpar = - beta * antotp |
setup_gf_layouts | gs2_layouts | Function | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Fields Local layout: This is used to calculate velocity space integration and other fields related calculations on a restricted process count for large core count simulations. It takes naky and ntheta and distributed that amongst theta so that a single naky,ntheta point is only owned by a single process. !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Construct a gf_layout_type instance. |
setup_jfields_layouts | gs2_layouts | Function | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Fast field layouts !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Construct a jfields instance |
setup_lambda_layouts | gs2_layouts | Function | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Lambda layouts !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Construct a lambda layout instance |
setup_lambda_redistribute_local | le_grids | Subroutine | Computes the redistribute mapping from the g_lo data decomposition to the lz_lo decomposition |
setup_le_layouts | gs2_layouts | Function | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Lambda-Energy layouts !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Construct a le_layout_type instance. |
setup_parity_layouts | gs2_layouts | Function | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! layouts for parity diagnostic !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Construct a parity layout instance. |
setup_pass_incoming_boundary_to_connections | dist_fn | Subroutine | Setup the redistribute associated with passing the incoming boundary values to the previous connected cell, storing at its connected boundary. This is required in order to allow for non-zero incoming boundary conditions on internal cells. |
setup_passing_lambda_grids | le_grids | Subroutine | Determines the location of lambda (al) grid points in the passing domain and the associated integrations weights. |
setup_persistent | redistribute | Subroutine | FIXME : Add documentation |
setup_special_splines | eeq | Subroutine | |
setup_special_splines | deq | Subroutine | |
setup_special_splines_eqfile_null | geo_utils | Subroutine | |
setup_splines_eqfile | geo_utils | Subroutine | |
setup_trapped_lambda_grids | le_grids | Subroutine | Determines the lambda grid point integration weights in the trapped domain using either new or old (default) methods, determined by [[le_grids_knobs::new_trap_int]] with new=high-order interp, old=finite difference). |
setup_trapped_lambda_grids_new_trap_int | le_grids | Subroutine | Determine trapped pitch angle weights using "new" polynomial interpolation. |
setup_trapped_lambda_grids_old_finite_difference | le_grids | Subroutine | Find the trapped pitch angle weights using an old (finite-difference) integration scheme |
setup_x_redist_local | gs2_transforms | Subroutine | Constructs the redistribute mapping from the g_lo data decomposition to the xxf_lo decomposition. |
setup_x_transform_layouts | gs2_layouts | Function | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! X-space layouts !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Construct an xxf_lo instance. |
setup_y_redist_local | gs2_transforms | Subroutine | Constructs the redistribute mapping from the xxf_lo data decomposition to the yxf_lo decomposition. |
setup_y_transform_layouts | gs2_layouts | Function | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Y-space layouts !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Construct a yxf_lo instance. |
setvgrid | egrid | Subroutine | FIXME : Add documentation GW: F0 now gets multiplied later |
setvgrid_genquad | egrid | Subroutine | FIXME : Add documentation |
sgrnd | mt19937 | Subroutine | Set initial seed of module-level mt19937_type instance |
shared_setup | peq | Subroutine | |
shared_setup_cart | geo_utils | Subroutine | |
shm_alloc | shm_mpi3 | Interface | |
shm_alloc_c | shm_mpi3 | Subroutine | FIXME : Add documentation |
shm_alloc_c1 | shm_mpi3 | Subroutine | FIXME : Add documentation |
shm_alloc_c2 | shm_mpi3 | Subroutine | FIXME : Add documentation |
shm_alloc_c3 | shm_mpi3 | Subroutine | FIXME : Add documentation |
shm_alloc_r | shm_mpi3 | Subroutine | FIXME : Add documentation |
shm_alloc_r1 | shm_mpi3 | Subroutine | FIXME : Add documentation |
shm_alloc_r2 | shm_mpi3 | Subroutine | FIXME : Add documentation |
shm_alloc_r3 | shm_mpi3 | Subroutine | FIXME : Add documentation |
shm_clean | shm_mpi3 | Subroutine | FIXME : Add documentation |
shm_fence | shm_mpi3 | Interface | |
shm_fence_c | shm_mpi3 | Subroutine | FIXME : Add documentation |
shm_fence_r | shm_mpi3 | Subroutine | FIXME : Add documentation |
shm_free | shm_mpi3 | Interface | |
shm_free_c | shm_mpi3 | Subroutine | FIXME : Add documentation |
shm_free_c1 | shm_mpi3 | Subroutine | FIXME : Add documentation |
shm_free_c2 | shm_mpi3 | Subroutine | FIXME : Add documentation |
shm_free_c3 | shm_mpi3 | Subroutine | FIXME : Add documentation |
shm_free_r | shm_mpi3 | Subroutine | FIXME : Add documentation |
shm_free_r1 | shm_mpi3 | Subroutine | FIXME : Add documentation |
shm_free_r2 | shm_mpi3 | Subroutine | FIXME : Add documentation |
shm_free_r3 | shm_mpi3 | Subroutine | FIXME : Add documentation |
shm_get_node_pointer | shm_mpi3 | Interface | |
shm_get_node_pointer_c | shm_mpi3 | Subroutine | FIXME : Add documentation |
shm_get_node_pointer_c1 | shm_mpi3 | Function | FIXME : Add documentation |
shm_get_node_pointer_c2 | shm_mpi3 | Function | FIXME : Add documentation |
shm_get_node_pointer_c3 | shm_mpi3 | Function | FIXME : Add documentation |
shm_get_node_pointer_r | shm_mpi3 | Subroutine | FIXME : Add documentation |
shm_get_node_pointer_r1 | shm_mpi3 | Function | FIXME : Add documentation |
shm_get_node_pointer_r2 | shm_mpi3 | Function | FIXME : Add documentation |
shm_get_node_pointer_r3 | shm_mpi3 | Function | FIXME : Add documentation |
shm_init | shm_mpi3 | Subroutine | FIXME : Add documentation |
shm_node_barrier | shm_mpi3 | Subroutine | FIXME : Add documentation |
shm_node_id | shm_mpi3 | Function | returns node id corresponding to ip -1 in case of error |
shm_onnode | shm_mpi3 | Function | Checks if a node rank belong to the curent node |
shmem_character_get | shmem | Subroutine | FIXME : Add documentation |
shmem_character_put | shmem | Subroutine | FIXME : Add documentation |
shmem_complex_get_array | shmem | Subroutine | FIXME : Add documentation |
shmem_complex_get_scalar | shmem | Subroutine | FIXME : Add documentation |
shmem_complex_put_array | shmem | Subroutine | FIXME : Add documentation |
shmem_complex_put_scalar | shmem | Subroutine | FIXME : Add documentation |
shmem_integer_get | shmem | Interface | |
shmem_integer_get_array | shmem | Subroutine | FIXME : Add documentation |
shmem_integer_get_scalar | shmem | Subroutine | FIXME : Add documentation |
shmem_integer_put | shmem | Interface | |
shmem_integer_put_array | shmem | Subroutine | FIXME : Add documentation |
shmem_integer_put_scalar | shmem | Subroutine | FIXME : Add documentation |
shmem_logical_get | shmem | Interface | |
shmem_logical_get_array | shmem | Subroutine | FIXME : Add documentation |
shmem_logical_get_scalar | shmem | Subroutine | FIXME : Add documentation |
shmem_logical_put | shmem | Interface | |
shmem_logical_put_array | shmem | Subroutine | FIXME : Add documentation |
shmem_logical_put_scalar | shmem | Subroutine | FIXME : Add documentation |
shmem_real_get | shmem | Interface | |
shmem_real_get_array | shmem | Subroutine | FIXME : Add documentation |
shmem_real_get_scalar | shmem | Subroutine | FIXME : Add documentation |
shmem_real_put | shmem | Interface | |
shmem_real_put_array | shmem | Subroutine | FIXME : Add documentation |
shmem_real_put_scalar | shmem | Subroutine | FIXME : Add documentation |
shmem_wait | shmem | Subroutine | FIXME : Add documentation |
should_be | unit_tests | Interface | |
should_be_int | unit_tests | Subroutine | |
should_be_real | unit_tests | Subroutine | |
should_print | unit_tests | Function | |
simulation_run_uuid | standard_header | Function | Return the UUID for this run |
single_get_grids | kt_grids_single | Subroutine | FIXME : Add documentation |
single_get_sizes | kt_grids_single | Subroutine | FIXME : Add documentation |
single_initial_kx | init_g | Subroutine | FIXME : Add documentation |
sinhm_fun | splines | Function | Calculate sinhm(x) = sinh(x) / x - 1 |
size_of | constants | Interface | Returns the number of bytes of storage required by its
argument. Equivalent to |
size_of_cd | constants | Function | |
size_of_cq | constants | Function | |
size_of_cs | constants | Function | |
size_of_i1 | constants | Function | |
size_of_id | constants | Function | |
size_of_ih | constants | Function | |
size_of_is | constants | Function | |
size_of_rd | constants | Function | |
size_of_rq | constants | Function | |
size_of_rs | constants | Function | |
sj0 | spfunc | Function | FIXME : Add documentation |
sj1 | spfunc | Function | FIXME : Add documentation |
slgamma_ext | spfunc | Function | FIXME : Add documentation |
smooth | rungridgen | Subroutine | FIXME : Add documentation |
solfp1 | collisions | Interface | |
solfp1_le_layout | collisions | Subroutine | FIXME : Add documentation |
solfp1_standard_layout | collisions | Subroutine | FIXME : Add documentation |
solfp_ediffuse_le_layout | collisions | Subroutine | FIXME : Add documentation |
solfp_ediffuse_standard_layout | collisions | Subroutine | Energy diffusion subroutine used with energy layout (not le_layout) this is always the case when initializing the conserving terms, otherwise is the case if use_le_layout is no specified in the input file. |
solfp_lorentz | collisions | Interface | |
solfp_lorentz_le_layout | collisions | Subroutine | FIXME : Add documentation |
solfp_lorentz_standard_layout | collisions | Subroutine | FIXME : Add documentation |
sort | geo_utils | Subroutine | FIXME : Add documentation |
source_term_func | split_nonlinear_terms | Interface | Interface to describe the call signatures for routines to calculate the field from gnew (invert_field_func) and to calculate the source term used in the advance_nonlinear_term methods. Used to allow us to pass in these methods, giving us a way to test the integrators on different problems. |
spcof1 | rungridgen | Subroutine | FIXME : Add documentation |
specified_get_grids | kt_grids_specified | Subroutine | FIXME : Add documentation |
specified_get_sizes | kt_grids_specified | Subroutine | FIXME : Add documentation |
sperr1 | rungridgen | Subroutine | FIXME : Add documentation |
spfit1 | rungridgen | Subroutine | FIXME : Add documentation |
spint1 | rungridgen | Subroutine | FIXME : Add documentation |
spline | splines | Interface | Constructor for spline |
spline_deriv | splines | Function | Bound wrapper to dsplint |
spline_interp | splines | Function | Bound wrapper to splint |
splint | splines | Function | FIXME : Add documentation |
splintint | splines | Function | FIXME : Add documentation |
split | mp | Interface | |
split_all | mp | Subroutine | A routine to split the global communicator into sub-groups based on each procs specific colour "col". mp_comm is then overwritten to be the new split communicator This is different to job fork, which has the group and global communicators. The global communicator is replaced. This action can be undone with unsplit_all If the old mp_comm is not mpi_comm_world, you should make sure you have saved its value somewhere before calling this so that its value can be saved. |
split_key | mp | Subroutine | A routine to split the mp_comm communicator into sub-groups based on each procs specific colour "col" and ranked by key. The sub communicator's handle is passed back in new_comm |
split_key_to_commtype | mp | Subroutine | A routine to split the mp_comm communicator into sub-groups based on each procs specific colour "col" and ranked by key. The sub communicator's handle is passed back in new_comm |
split_key_to_commtype_sub | mp | Subroutine | A routine to split a subcommunicator into sub-groups based on each procs specific colour "col" and ranked by key. The sub communicator's handle is passed back in new_comm |
split_nokey | mp | Subroutine | A routine to split the mp_comm communicator into sub-groups based on each procs specific colour "col". The sub communicator's handle is passed back in new_comm |
split_nokey_to_commtype | mp | Subroutine | A routine to split the mp_comm communicator into sub-groups based on each procs specific colour "col". The sub communicator's handle is passed back in new_comm |
split_nokey_to_commtype_sub | mp | Subroutine | A routine to split a subcommunicator into sub-groups based on each procs specific colour "col". The sub communicator's handle is passed back in new_comm |
ssend | mp | Interface | |
ssend_character | mp | Subroutine | FIXME : Add documentation |
ssend_complex | mp | Subroutine | FIXME : Add documentation |
ssend_complex_2array | mp | Subroutine | FIXME : Add documentation |
ssend_complex_array | mp | Subroutine | FIXME : Add documentation |
ssend_integer | mp | Subroutine | FIXME : Add documentation |
ssend_integer_array | mp | Subroutine | FIXME : Add documentation |
ssend_logical | mp | Subroutine | FIXME : Add documentation |
ssend_logical_array | mp | Subroutine | FIXME : Add documentation |
ssend_real | mp | Subroutine | FIXME : Add documentation |
ssend_real_array | mp | Subroutine | FIXME : Add documentation |
ssteqr | lapack_wrapper | Interface | |
standard_header_to_string | standard_header | Function | Return a multiline string with a standard header of the form: |
standard_header_type | standard_header | Interface | |
start_comm | mp | Interface | |
start_persist | mp | Subroutine | Starts a single persistent communication represented by handle |
startall_persist | mp | Subroutine | Starts multiple persistent communications represented by handles |
starts | gs2_io | Function | Return an array of 1-index offsets for writing a time-dependent field to netCDF: |
steqr | lapack_wrapper | Interface | |
strip_comment_and_space | multigs2 | Function | |
strip_comments | file_utils | Subroutine | Remove Fortran comments ( |
sum_allreduce | mp | Interface | |
sum_allreduce_complex | mp | Subroutine | FIXME : Add documentation |
sum_allreduce_complex_2array | mp | Subroutine | FIXME : Add documentation |
sum_allreduce_complex_3array | mp | Subroutine | FIXME : Add documentation |
sum_allreduce_complex_4array | mp | Subroutine | FIXME : Add documentation |
sum_allreduce_complex_5array | mp | Subroutine | FIXME : Add documentation |
sum_allreduce_complex_array | mp | Subroutine | FIXME : Add documentation |
sum_allreduce_integer | mp | Subroutine | FIXME : Add documentation |
sum_allreduce_integer_2array | mp | Subroutine | FIXME : Add documentation |
sum_allreduce_integer_3array | mp | Subroutine | FIXME : Add documentation |
sum_allreduce_integer_array | mp | Subroutine | FIXME : Add documentation |
sum_allreduce_real | mp | Subroutine | FIXME : Add documentation |
sum_allreduce_real_2array | mp | Subroutine | FIXME : Add documentation |
sum_allreduce_real_3array | mp | Subroutine | FIXME : Add documentation |
sum_allreduce_real_4array | mp | Subroutine | FIXME : Add documentation |
sum_allreduce_real_5array | mp | Subroutine | FIXME : Add documentation |
sum_allreduce_real_array | mp | Subroutine | FIXME : Add documentation |
sum_allreduce_sub | mp | Interface | |
sum_allreduce_sub_complex | mp | Subroutine | FIXME : Add documentation |
sum_allreduce_sub_complex_2array | mp | Subroutine | FIXME : Add documentation |
sum_allreduce_sub_complex_3array | mp | Subroutine | FIXME : Add documentation |
sum_allreduce_sub_complex_4array | mp | Subroutine | FIXME : Add documentation |
sum_allreduce_sub_complex_5array | mp | Subroutine | FIXME : Add documentation |
sum_allreduce_sub_complex_array | mp | Subroutine | FIXME : Add documentation |
sum_allreduce_sub_integer | mp | Subroutine | FIXME : Add documentation |
sum_allreduce_sub_integer_array | mp | Subroutine | FIXME : Add documentation |
sum_allreduce_sub_real | mp | Subroutine | FIXME : Add documentation |
sum_allreduce_sub_real_2array | mp | Subroutine | FIXME : Add documentation |
sum_allreduce_sub_real_3array | mp | Subroutine | FIXME : Add documentation |
sum_allreduce_sub_real_4array | mp | Subroutine | FIXME : Add documentation |
sum_allreduce_sub_real_5array | mp | Subroutine | FIXME : Add documentation |
sum_allreduce_sub_real_array | mp | Subroutine | FIXME : Add documentation |
sum_reduce | mp | Interface | |
sum_reduce_complex | mp | Subroutine | FIXME : Add documentation |
sum_reduce_complex_2array | mp | Subroutine | FIXME : Add documentation |
sum_reduce_complex_2array_sub | mp | Subroutine | FIXME : Add documentation |
sum_reduce_complex_3array | mp | Subroutine | FIXME : Add documentation |
sum_reduce_complex_3array_sub | mp | Subroutine | FIXME : Add documentation |
sum_reduce_complex_4array | mp | Subroutine | FIXME : Add documentation |
sum_reduce_complex_4array_sub | mp | Subroutine | FIXME : Add documentation |
sum_reduce_complex_5array | mp | Subroutine | FIXME : Add documentation |
sum_reduce_complex_array | mp | Subroutine | FIXME : Add documentation |
sum_reduce_complex_array_sub | mp | Subroutine | FIXME : Add documentation |
sum_reduce_integer | mp | Subroutine | FIXME : Add documentation |
sum_reduce_integer_2array | mp | Subroutine | FIXME : Add documentation |
sum_reduce_integer_array | mp | Subroutine | FIXME : Add documentation |
sum_reduce_logical | mp | Subroutine | FIXME : Add documentation |
sum_reduce_real | mp | Subroutine | FIXME : Add documentation |
sum_reduce_real_2array | mp | Subroutine | FIXME : Add documentation |
sum_reduce_real_3array | mp | Subroutine | FIXME : Add documentation |
sum_reduce_real_4array | mp | Subroutine | FIXME : Add documentation |
sum_reduce_real_5array | mp | Subroutine | FIXME : Add documentation |
sum_reduce_real_array | mp | Subroutine | FIXME : Add documentation |
sum_reduce_sub | mp | Interface | |
swap_elem | sorting | Interface | |
sym | geometry | Subroutine | Forces symmetry in theta in the passed array. If isign == 0 then
|
tell | ingen_mod | Subroutine | FIXME : Add documentation |
test | mat_inv_benchmark | Function | |
test_function_interface | functional_tests | Interface | |
test_gs2 | functional_tests | Subroutine | Run GS2 and check that |
testall | mp | Interface | |
testall_nostat | mp | Subroutine | A routine to test for all count communications, given by the message handles in requests, to complete. We ignore the status information |
testall_nostat_noflag | mp | Subroutine | A routine to test for all count communications, given by the message handles in requests, to complete. We ignore the status and flag information |
testall_stat | mp | Subroutine | A routine to test for all count communications, given by the message handles in requests, to complete. We return the message statuses and completion flag |
text | ingen_mod | Subroutine | FIXME : Add documentation |
th_bishop | geometry | Subroutine | Finds the angle between the surface tangent vector in the poloidal plane and the direction of increasing major radius. |
theta_grid_gridgen_init | theta_grid_gridgen | Subroutine | FIXME : Add documentation |
time_history_available | gs2_time | Function | Reports how many previous time steps are available by checking if the previous code_dt values have been set to anything. Note we assume that if a time step is set then all more recent values have also been set. |
time_message | mp | Subroutine | This routine counts elapsed time between two calls.
The two elements in |
time_message | job_manage | Subroutine | This routine counts elapsed time between two calls. Currently just a thin wrapper to method of the same name in mp. In the future we probably want to remove the method here and change the relevant use statements. |
timeadv | dist_fn | Subroutine | This function calculates the distribution function at the next timestep. It calculates both the inhomogeneous part, gnew, due to the sources (principly the drive terms and the nonlinear term) and the homogeneous part, g1. The actual evolution of the dist func is done in the subroutine invert_rhs. |
timer_local | mp | Function | Returns CPU time in seconds |
timer_local | job_manage | Function | Returns CPU time in seconds. Currently just a thin wrapper to method of the same name in mp. In the future we probably want to remove the method here and change the relevant use statements. |
timestamp | quadpack | Subroutine | TIMESTAMP prints the current YMDHMS date as a time stamp. |
to_string | print_utils | Interface | |
to_string_complex_real128 | print_utils | Function | |
to_string_complex_real32 | print_utils | Function | |
to_string_complex_real64 | print_utils | Function | |
to_string_integer_int16 | print_utils | Function | |
to_string_integer_int32 | print_utils | Function | |
to_string_integer_int64 | print_utils | Function | |
to_string_integer_int8 | print_utils | Function | Convert |
to_string_logical | print_utils | Function | |
to_string_real_real128 | print_utils | Function | |
to_string_real_real32 | print_utils | Function | |
to_string_real_real64 | print_utils | Function | |
total_term | diagnostics_zonal_transfer | Subroutine | Returns tau, the transfer of free energy as a function of (kx,ky) |
transform2 | gs2_transforms | Interface | |
transform2_2d | gs2_transforms | Subroutine | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! FIXME : Add documentation DD>Reinstating after discussion with RN, if this causes anyone an issue |
transform2_3d | gs2_transforms | Subroutine | FIXME : Add documentation |
transform2_5d | gs2_transforms | Subroutine | FIXME : Add documentation |
transform2_5d_accel | gs2_transforms | Subroutine | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! FIXME : Add documentation |
transform_x | gs2_transforms | Interface | |
transform_x5d | gs2_transforms | Subroutine | FIXME : Add documentation |
transform_y | gs2_transforms | Interface | |
transform_y5d | gs2_transforms | Subroutine | FIXME : Add documentation |
trap_error | le_grids | Subroutine | FIXME : Add documentation |
trapezoidal_integration | integration | Interface | |
tripprod2dtgrid | geometry | Subroutine | Computes something like x cross y dot grad zeta. |
try_again | ingen_mod | Subroutine | FIXME : Add documentation |
try_to_optimise_passing_grid | le_grids | Subroutine | Try to find the optimal way to split the passing lambda grid into two regions in order to minimise the error on the integration weights. The approach taken is trial and error -- we try a number of predetermined splits, spline the error over the trials and then evaluate the spline on a high resolution grid to determine an approximate minmium. |
tuneMinNRow | fields_local | Subroutine | |
unsplit_all | mp | Subroutine | FIXME : Add documentation |
update_scan_parameter_value | parameter_scan | Subroutine | FIXME : Add documentation |
update_time | gs2_time | Subroutine | FIXME : Add documentation |
use_nproc | mp | Subroutine | This function splits mp_comm into two pieces, one with nprocs_new procs, and one with all the remainder. For the remainder, included is set to false. This means that the remainder will lie idle. |
user2code | gs2_time | Subroutine | FIXME : Add documentation |
valid_mediator | diagnostics_kinetic_energy_transfer | Function | return bolean whether a source-mode and target-mode combination yields a valid mediator |
verbosity | runtime_tests | Function | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Functions provided for backwards compatibility ! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! This function is just a call of get_verbosity and is provided for backwards compatibility. |
verify_parameters | ballstab | Subroutine | Check parameters are consistent etc. |
vspace_derivatives | le_derivatives | Subroutine | FIXME : Add documentation |
wait | mp | Interface | |
wait_nostat | mp | Subroutine | This routine waits for the communication, given by the message request, to complete. We ignore the status information |
wait_stat | mp | Subroutine | This routine waits for the communication, given by the message request, to complete. We return the status information |
waitall | mp | Interface | |
waitall_nostat | mp | Subroutine | A routine to wait for all count communications, given by the message handles in requests, to complete. We ignore the status information |
waitall_stat | mp | Subroutine | A routine to wait for all count communications, given by the message handles in requests, to complete. We return the message statuses |
waitany | mp | Interface | |
waitany_nostat | mp | Subroutine | |
waitany_stat | mp | Subroutine | FIXME : Add documentation |
warn_about_deprecated_option | diagnostics_base_configuration | Subroutine | |
warn_about_nonfunctional_selection | diagnostics_base_configuration | Subroutine | Prints a warning about a non-functional diagnostic |
warning | print_utils | Subroutine | Print |
wcoriolis_func | dist_fn | Function | Calculates the value of the Coriolis drift at the location corresponding to the passed indices. |
wdrift_func | dist_fn | Function | Calculates the value of the magnetic drifts (curvature + grad-B)
corresponding to the theta grid location given by |
wnml_antenna | antenna | Subroutine | FIXME : Add documentation |
wnml_ballstab | ballstab | Subroutine | Write a namelist based on current values |
wnml_collisions | collisions | Subroutine | FIXME : Add documentation |
wnml_dist_fn | dist_fn | Subroutine | FIXME : Add documentation |
wnml_dist_fn_species | dist_fn | Subroutine | FIXME : Add documentation |
wnml_fields | fields | Subroutine | FIXME : Add documentation |
wnml_gs2_diagnostics | gs2_diagnostics | Subroutine | Write the diagnostics namelist to file |
wnml_gs2_layouts | gs2_layouts | Subroutine | FIXME : Add documentation |
wnml_gs2_reinit | gs2_reinit | Subroutine | FIXME : Add documentation |
wnml_hyper | hyper | Subroutine | FIXME : Add documentation |
wnml_init_g | init_g | Subroutine | FIXME : Add documentation |
wnml_kt | kt_grids | Subroutine | FIXME : Add documentation |
wnml_kt_grids_box | kt_grids_box | Subroutine | Write namelist for kt_grids_box |
wnml_kt_grids_range | kt_grids_range | Subroutine | FIXME : Add documentation |
wnml_kt_grids_single | kt_grids_single | Subroutine | FIXME : Add documentation |
wnml_kt_grids_specified | kt_grids_specified | Subroutine | FIXME : Add documentation |
wnml_le_grids | le_grids | Subroutine | FIXME : Add documentation |
wnml_nonlinear_terms | nonlinear_terms | Subroutine | FIXME : Add documentation |
wnml_normalisations | normalisations | Subroutine | FIXME : Add documentation |
wnml_run_parameters | run_parameters | Subroutine | FIXME : Add documentation |
wnml_species | species | Subroutine | FIXME : Add documentation |
wnml_theta_grid | theta_grid | Subroutine | FIXME : Add documentation |
wnml_theta_grid_eik | theta_grid_eik | Subroutine | FIXME : Add documentation |
wnml_theta_grid_file | theta_grid_file | Subroutine | FIXME : Add documentation |
wnml_theta_grid_gridgen | theta_grid_gridgen | Subroutine | FIXME : Add documentation |
wnml_theta_grid_params | theta_grid_params | Subroutine | FIXME : Add documentation |
wnml_theta_grid_salpha | theta_grid_salpha | Subroutine | FIXME : Add documentation |
write_ballstab_config | ballstab | Subroutine | Writes out a namelist representing the current state of the config object |
write_collision_error | diagnostics_velocity_space | Subroutine | Calculate and write the collision error |
write_collisional | collisional_heating | Subroutine | FIXME : Add documentation |
write_collisions_config | collisions | Subroutine | Writes out a namelist representing the current state of the config object |
write_complex_rank1 | gs2_io | Subroutine | |
write_complex_rank2 | gs2_io | Subroutine | |
write_complex_rank3 | gs2_io | Subroutine | |
write_complex_rank4 | gs2_io | Subroutine | |
write_complex_scalar | gs2_io | Subroutine | |
write_connection_matrix | redistribute | Subroutine | Write a binary containing an nproc by nproc matrix showing communications in the redistribution lo. Entry (i,j) of connection_matrix shows the number of values sent from proc i to proc j in the forward transform. Entry (i,j) of connection_matrix_inv gives the same information for the inverse transform. Diagonal entries (i,i) show the number of values which are "sent from proc i to itself", i.e. not communicated by MPI, but which still need to be rearranged locally as part of the transform. |
write_cross_phase | diagnostics_turbulence | Subroutine | FIXME : Add documentation |
write_diagnostics_base_config | diagnostics_base_configuration | Subroutine | Writes out a namelist representing the current state of the config object |
write_diffusive_estimates | diagnostics_fluxes | Subroutine | Calculate estimates of the heat and particles fluxes using gamma / k^2 estimate of the diffusivity |
write_dist_fn_config | dist_fn | Subroutine | Writes out a namelist representing the current state of the config object |
write_dist_fn_species_config | dist_fn | Subroutine | Writes out a namelist representing the current state of the config object |
write_driver_config | antenna | Subroutine | Writes out a namelist representing the current state of the config object |
write_dt | gs2_time | Subroutine | FIXME : Add documentation |
write_eigenfunc | diagnostics_fields | Subroutine | Write out the fields, normalized to their value at theta=0 |
write_exit_file | exit_codes | Subroutine | Write exit file containing exit code and message |
write_fields | diagnostics_fields | Subroutine | FIXME : Add documentation |
write_fields_config | fields | Subroutine | Writes out a namelist representing the current state of the config object |
write_flux_line | diagnostics_printout | Subroutine | Print instantaneous heat fluxes to run_name.new.out |
write_fluxes_to_unit | diagnostics_printout | Subroutine | Write instantaneous heat and particle fluxes to screen/file |
write_full_moments_notgc | diagnostics_moments | Subroutine | FIXME : Add documentation |
write_grids_to_file | dump_grids | Subroutine | FIXME : Add documentation |
write_gs2d | gs2d | Subroutine | FIXME : Add documentation |
write_heating | diagnostics_heating | Subroutine | FIXME : Add documentation |
write_hyper_config | hyper | Subroutine | Writes out a namelist representing the current state of the config object |
write_ingen_config | ingen_mod | Subroutine | Writes out a namelist representing the current state of the config object |
write_init_g_config | init_g | Subroutine | Writes out a namelist representing the current state of the config object |
write_init_times | gs2_init | Subroutine | Write the init times to |
write_interface | abstract_config | Interface | |
write_jext | diagnostics_antenna | Subroutine | FIXME : Add documentation |
write_key_val_complex | abstract_config | Subroutine | Writes a {key,val} pair where the value is of type complex |
write_key_val_complex_array | abstract_config | Subroutine | Writes a {key,val} pair where the value is of type complex array |
write_key_val_integer | abstract_config | Subroutine | Writes a {key,val} pair where the value is of type integer |
write_key_val_integer_array | abstract_config | Subroutine | Writes a {key,val} pair where the value is of type integer array |
write_key_val_logical | abstract_config | Subroutine | Writes a {key,val} pair where the value is of type logical |
write_key_val_real | abstract_config | Subroutine | Writes a {key,val} pair where the value is of type real |
write_key_val_real_array | abstract_config | Subroutine | Writes a {key,val} pair where the value is of type real array |
write_key_val_string | abstract_config | Subroutine | Writes a {key,val} pair where the value is of type character |
write_kinetic_energy_transfer | diagnostics_kinetic_energy_transfer | Subroutine | |
write_knobs_config | run_parameters | Subroutine | Writes out a namelist representing the current state of the config object |
write_kt_grids_box_config | kt_grids_box | Subroutine | Writes out a namelist representing the current state of the config object |
write_kt_grids_config | kt_grids | Subroutine | Writes out a namelist representing the current state of the config object |
write_kt_grids_range_config | kt_grids_range | Subroutine | Writes out a namelist representing the current state of the config object |
write_kt_grids_single_config | kt_grids_single | Subroutine | Writes out a namelist representing the current state of the config object |
write_kt_grids_specified_config | kt_grids_specified | Subroutine | Writes out a namelist representing the current state of the config object |
write_kt_grids_specified_element_config | kt_grids_specified | Subroutine | Writes out a namelist representing the current state of the config object |
write_layouts_config | gs2_layouts | Subroutine | Writes out a namelist representing the current state of the config object |
write_le_grids_config | le_grids | Subroutine | Writes out a namelist representing the current state of the config object |
write_line | diagnostics_printout | Subroutine | Print growth rates to run_name.new.out |
write_lorentzian | diagnostics_antenna | Subroutine | FIXME : Add documentation |
write_moments | diagnostics_moments | Subroutine | FIXME : Add documentation |
write_movie | diagnostics_fields | Subroutine | FIXME : Add documentation |
write_namelist_footer | abstract_config | Subroutine | Write the namelist footer |
write_namelist_header | abstract_config | Subroutine | Write the namelist header for this instance |
write_namelists | ingen_mod | Subroutine | FIXME : Add documentation |
write_nonlinear_terms_config | nonlinear_terms | Subroutine | Writes out a namelist representing the current state of the config object |
write_normalisations_config | normalisations | Subroutine | Writes out a namelist representing the current state of the config object |
write_omega | diagnostics_omega | Subroutine | Write omega, omega_average as functions of kx, ky and time to the new netcdf file |
write_optimisation_config | optimisation_configuration | Subroutine | Writes out a namelist representing the current state of the config object |
write_output | rungridgen | Subroutine | FIXME : Add documentation |
write_parameter_scan_config | parameter_scan | Subroutine | Writes out a namelist representing the current state of the config object |
write_phi_fluxes_to_unit | diagnostics_printout | Subroutine | Write instantaneous fluxes from electrostatic potential to screen or file |
write_ql_metric | gs2_diagnostics_new | Subroutine | Calculates and write the QL flux metric to netcdf |
write_reinit_config | gs2_reinit | Subroutine | Writes out a namelist representing the current state of the config object |
write_source_config | dist_fn | Subroutine | Writes out a namelist representing the current state of the config object |
write_species_config | species | Subroutine | Writes out a namelist representing the current state of the config object |
write_species_element_config | species | Subroutine | Writes out a namelist representing the current state of the config object |
write_split_nonlinear_terms_config | split_nonlinear_terms | Subroutine | Writes out a namelist representing the current state of the config object |
write_stability_ascii_1d | ballstab | Subroutine | Routine to write out stability data to 1D ascii file |
write_stability_ascii_2d | ballstab | Subroutine | Routine to write out stability data to 2D ascii file + 1d axis data |
write_standard_moment_properties | diagnostics_moments | Subroutine | FIXME : Add documentation |
write_stir_config | antenna | Subroutine | Writes out a namelist representing the current state of the config object |
write_summary | gs2_optimisation | Subroutine | FIXME : Add documentation |
write_text | print_utils | Subroutine | Print |
write_theta_grid_config | theta_grid | Subroutine | Writes out a namelist representing the current state of the config object |
write_theta_grid_eik_config | theta_grid_eik | Subroutine | Writes out a namelist representing the current state of the config object |
write_theta_grid_file_config | theta_grid_file | Subroutine | Writes out a namelist representing the current state of the config object |
write_theta_grid_gridgen_config | theta_grid_gridgen | Subroutine | Writes out a namelist representing the current state of the config object |
write_theta_grid_parameters_config | theta_grid_params | Subroutine | Writes out a namelist representing the current state of the config object |
write_theta_grid_salpha_config | theta_grid_salpha | Subroutine | Writes out a namelist representing the current state of the config object |
write_time_parallel_statistics | gs2_main | Subroutine | Writes the timing information statistics to optional passed unit |
write_to_unit | config_collection | Subroutine | Writes out the current configuration state to an optionally provided unit.
If no unit is provided then we write to |
write_used_inputs_file | gs2_main | Subroutine | Write an input file containing the current state of all input parameters |
write_velocity_space_checks | diagnostics_velocity_space | Subroutine | FIXME : Add documentation |
write_zonal_transfer | diagnostics_zonal_transfer | Subroutine | FIXME : Add documentation |
wsweetspots | ingen_mod | Subroutine | Writes out sweetspot core counts for a layout sym: character string label for each dimension sdim: size of each dimension nfac: #factors of each sdim facs(i,j): ith factor of jth dimension |
x1c2r | convert | Subroutine | FIXME : Add documentation |
x1r2c | convert | Subroutine | FIXME : Add documentation |
x2c2r | convert | Subroutine | FIXME : Add documentation |
x2r2c | convert | Subroutine | FIXME : Add documentation |
x3c2r | convert | Subroutine | FIXME : Add documentation |
x3r2c | convert | Subroutine | FIXME : Add documentation |
x4c2r | convert | Subroutine | FIXME : Add documentation |
x4r2c | convert | Subroutine | FIXME : Add documentation |
x5c2r | convert | Subroutine | FIXME : Add documentation |
x5r2c | convert | Subroutine | FIXME : Add documentation |
xigridset | le_grids | Subroutine | FIXME : Add documentation |
zbrent | geo_utils | Function | FIXME : Add documentation |
zero_array | array_utils | Interface | Interface to helper functions to zero an array |
zero_array_complex_array_1 | array_utils | Subroutine | Zero out a 1D array |
zero_array_complex_array_2 | array_utils | Subroutine | Zero out a 2D array |
zero_array_complex_array_3 | array_utils | Subroutine | Zero out a 3D array |
zero_array_complex_array_4 | array_utils | Subroutine | Zero out a 4D array |
zero_array_complex_array_5 | array_utils | Subroutine | Zero out a 5D array |
zero_array_real_array_1 | array_utils | Subroutine | Zero out a 1D array |
zero_array_real_array_2 | array_utils | Subroutine | Zero out a 2D array |
zero_array_real_array_3 | array_utils | Subroutine | Zero out a 3D array |
zero_array_real_array_4 | array_utils | Subroutine | Zero out a 4D array |
zero_array_real_array_5 | array_utils | Subroutine | Zero out a 5D array |
zero_dvtype | gs2_heating | Interface | |
zero_dvtype_0 | gs2_heating | Subroutine | FIXME : Add documentation |
zero_dvtype_1 | gs2_heating | Subroutine | FIXME : Add documentation |
zero_dvtype_2 | gs2_heating | Subroutine | FIXME : Add documentation |
zero_dvtype_3 | gs2_heating | Subroutine | FIXME : Add documentation |
zero_htype | gs2_heating | Interface | |
zero_htype_0 | gs2_heating | Subroutine | FIXME : Add documentation |
zero_htype_1 | gs2_heating | Subroutine | FIXME : Add documentation |
zero_htype_2 | gs2_heating | Subroutine | FIXME : Add documentation |
zero_htype_3 | gs2_heating | Subroutine | FIXME : Add documentation |
zero_out_passing_hybrid_electrons | collisions | Subroutine | If we have hybrid electrons then we need to remove the contribution to the conservation terms from the adiabatic passing part. This routine does this for us. |
zgemm | lapack_wrapper | Interface | |
zgemv | lapack_wrapper | Interface | |
zgetrf | lapack_wrapper | Interface | |
zgetri | lapack_wrapper | Interface | |
Zpos | leq | Function | Return the axial coordinate at |
zpos_eqfile | geo_utils | Function | |
zpos_eqfile_cart | geo_utils | Function | |
Ztgrid | geometry | Subroutine | Calculates the vertical height, Z, on the theta grid |