v3fit_input.f

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!*******************************************************************************
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!*******************************************************************************
      MODULE v3fit_input
      USE stel_kinds
      USE data_parameters
      USE combination
      USE pprofile_t
 
      IMPLICIT NONE
 
!*******************************************************************************
!  v3fit input module parameters
!*******************************************************************************
      INTEGER, PARAMETER :: v3fit_max_diagnostics = 1000
      INTEGER, PARAMETER :: v3fit_max_limiters = 1000
      INTEGER, PARAMETER :: v3fit_max_priors = 1000
      INTEGER, PARAMETER :: v3fit_max_combinations = 1000
      INTEGER, PARAMETER :: v3fit_max_signals = v3fit_max_diagnostics          &
     &                                        + v3fit_max_limiters             &
     &                                        + v3fit_max_priors               &
     &                                        + v3fit_max_combinations         &
     &                                        + max_gaussprocess
 
      INTEGER, PARAMETER :: v3fit_max_parameters = 100
 
      INTEGER, PARAMETER :: v3fit_max_spec_size = 150
 
      INTEGER, PARAMETER :: v3fit_max_lif_size = 100
 
      INTEGER, PARAMETER :: v3fit_max_cos_size = 100
 
      INTEGER, PARAMETER :: v3fit_step_name_length = 4
 
!*******************************************************************************
!  DERIVED-TYPE DECLARATIONS
!  1) v3fit_namelist_class
!
!*******************************************************************************
      CHARACTER (len=path_length) :: main_nli_filename = ''
 
!  Equilibrium input files
      CHARACTER (len=path_length) :: vmec_nli_filename = ''
      CHARACTER (len=path_length) :: vmec_wout_input = ''
      CHARACTER (len=path_length) :: vacuum_nli_filename = ''
      CHARACTER (len=path_length) :: siesta_nli_filename = ''
      CHARACTER (len=path_length) :: siesta_restart_filename = ''
 
!  Signal input files
      CHARACTER (len=path_length) :: mdsig_list_filename = ''
      CHARACTER (len=path_length) :: sxrch_dot_filename = ''
      CHARACTER (len=path_length) :: ipch_dot_filename = ''
      CHARACTER (len=path_length) :: thscte_dot_filename = ''
      CHARACTER (len=path_length) :: mse_dot_filename = ''
      CHARACTER (len=path_length) :: ece_dot_filename = ''
      CHARACTER (len=path_length) :: sxrem_ratio_dot_filename = ''
      CHARACTER (len=path_length) :: limiter_grid_file = ''
 
!  Array allocation sizes. These should be set to the maxmium size.
      INTEGER :: na_s_desc = v3fit_max_signals
 
!  Task specification and work variables
      CHARACTER (len=data_name_length)         :: my_task = ''
 
!  Model profile specification
!  Electron Denisty
      CHARACTER (len=p_type_len)           :: pp_ne_ptype = 'none'
      REAL (rprec), DIMENSION(ilb_b:iub_b) :: pp_ne_b = 0.0
      REAL (rprec), DIMENSION(iub_asf)     :: pp_ne_as = 0.0
      REAL (rprec), DIMENSION(iub_asf)     :: pp_ne_af = 0.0
 
!  Soft x-ray emissvity
      CHARACTER (len=p_type_len)           :: pp_sxrem_ptype = 'none'
      REAL (rprec), DIMENSION(ilb_b:iub_b) :: pp_sxrem_b = 0.0
      REAL (rprec), DIMENSION(iub_asf)     :: pp_sxrem_as = 0.0
      REAL (rprec), DIMENSION(iub_asf)     :: pp_sxrem_af = 0.0
 
!  Multi soft x-ray emissvity profile specification.
      INTEGER                              :: num_sxrem_p = 1
      CHARACTER (len=p_type_len), DIMENSION(max_sxrem_profiles)                &
     &   :: pp_sxrem_ptype_a = 'none'
 
      REAL (rprec), DIMENSION(max_sxrem_profiles,ilb_b:iub_b)                  &
     &   :: pp_sxrem_b_a = 0.0
 
      REAL (rprec), DIMENSION(max_sxrem_profiles,iub_asf)                      &
     &   :: pp_sxrem_as_a = 0.0
 
      REAL (rprec), DIMENSION(max_sxrem_profiles,iub_asf)                      &
     &   :: pp_sxrem_af_a = 0.0
 
!  Electron temperature
      CHARACTER (len=p_type_len)           :: pp_te_ptype = 'none'
      REAL (rprec), DIMENSION(ilb_b:iub_b) :: pp_te_b = 0.0
      REAL (rprec), DIMENSION(iub_asf)     :: pp_te_as = 0.0
      REAL (rprec), DIMENSION(iub_asf)     :: pp_te_af = 0.0
 
!  Ion temperature
      CHARACTER (len=p_type_len)           :: pp_ti_ptype = 'none'
      REAL (rprec), DIMENSION(ilb_b:iub_b) :: pp_ti_b = 0.0
      REAL (rprec), DIMENSION(iub_asf)     :: pp_ti_as = 0.0
      REAL (rprec), DIMENSION(iub_asf)     :: pp_ti_af = 0.0
 
!  Effective charge
      CHARACTER (len=p_type_len)           :: pp_ze_ptype = 'none'
      REAL (rprec), DIMENSION(ilb_b:iub_b) :: pp_ze_b = 0.0
      REAL (rprec), DIMENSION(iub_asf)     :: pp_ze_as = 0.0
      REAL (rprec), DIMENSION(iub_asf)     :: pp_ze_af = 0.0
 
!  Soft X-ray emission ratio
      REAL (rprec), DIMENSION(iub_asf) :: sxrem_te_a = 0.0
      REAL (rprec), DIMENSION(iub_asf) :: sxrem_ratio_a = 0.0
 
!  Model Specification Variables
      CHARACTER (len=data_name_length) :: model_eq_type = 'vmec'
      CHARACTER (len=data_name_length) :: model_ne_type = 'pp_ne'
      CHARACTER (len=data_name_length) :: model_sxrem_type = 'none'
      CHARACTER (len=data_name_length),                                        &
     &   DIMENSION(max_sxrem_profiles) ::                                      &
     &      model_sxrem_type_a = 'none'
 
      CHARACTER (len=data_name_length) :: model_te_type = 'none'
      CHARACTER (len=data_name_length) :: model_ti_type = 'none'
      CHARACTER (len=data_name_length) :: model_ze_type = 'none'
      REAL (rprec)                     :: ne_pp_unit = 1.0e18
      REAL (rprec)                     :: ne_min = 0.0
      REAL (rprec)                     :: te_min = 0.0
      REAL (rprec)                     :: ti_min = 0.0
      REAL (rprec)                     :: ze_min = 1.0
      REAL (rprec), DIMENSION(max_sxrem_profiles) :: sxrem_min = 0.0
      REAL (rprec)                     :: e_pressure_fraction = 0.5
      CHARACTER (len=data_name_length) :: emission_file = ''
      REAL (rprec) :: ece_resonance_range = 0.0
      REAL (rprec), DIMENSION(v3fit_max_parameters) :: coosig_wgts = 0.0
 
!  Reconstruction constraints
      INTEGER                            :: n_rc = 0
      CHARACTER (len=data_name_length),                                        &
     &   DIMENSION(v3fit_max_parameters) :: rc_type = ''
 
      INTEGER,                                                                 &
     &   DIMENSION(v3fit_max_parameters) :: rc_index = 0
 
      REAL (rprec),                                                            &
     &   DIMENSION(v3fit_max_parameters) :: rc_value = 0.0
 
!  Derived parameters
      INTEGER                              :: n_dp = 0
      CHARACTER (len=data_name_length),                                        &
     &   DIMENSION(v3fit_max_parameters)   :: dp_type = ''
 
      INTEGER,                                                                 &
     &   DIMENSION(v3fit_max_parameters,2) :: dp_index = 0
 
!  Reconstruction parameters
      INTEGER                              :: n_rp = 0
      CHARACTER (len=data_name_length),                                        &
     &   DIMENSION(v3fit_max_parameters)   :: rp_type = ''
 
      INTEGER,                                                                 &
     &   DIMENSION(v3fit_max_parameters)   :: rp_index = 0
 
      INTEGER,                                                                 &
     &   DIMENSION(v3fit_max_parameters)   :: rp_index2 = 0
 
      REAL (rprec),                                                            &
     &   DIMENSION(v3fit_max_parameters)   :: rp_vrnc = 0.0
 
      CHARACTER (len=data_name_length),                                        &
     &   DIMENSION(v3fit_max_parameters,2) :: rp_range_type = 'infinity'
 
      REAL (rprec),                                                            &
     &   DIMENSION(v3fit_max_parameters,2) :: rp_range_value = 0.0
 
      INTEGER, DIMENSION(v3fit_max_parameters,2,data_max_indices) ::           &
     &   rp_range_index = 0
 
!  Reconstruction parameters
      INTEGER  :: n_lp = 0
      CHARACTER (len=data_name_length),                                        &
     &   DIMENSION(v3fit_max_parameters)   :: lp_type = ''
 
      INTEGER,                                                                 &
     &   DIMENSION(v3fit_max_parameters)   :: lp_index = 0
 
      INTEGER,                                                                 &
     &   DIMENSION(v3fit_max_parameters)   :: lp_index2 = 0
 
      CHARACTER (len=data_name_length),                                        &
     &   DIMENSION(v3fit_max_parameters,v3fit_max_parameters) ::               &
     &      lp_sets = ''
 
      INTEGER,                                                                 &
     &   DIMENSION(v3fit_max_parameters,v3fit_max_parameters) ::               &
     &      lp_sets_index = 0
 
      INTEGER,                                                                 &
     &   DIMENSION(v3fit_max_parameters,v3fit_max_parameters) ::               &
     &      lp_sets_index2 = 0
 
      REAL (rprec),                                                            &
     &   DIMENSION(v3fit_max_parameters,v3fit_max_parameters) ::               &
     &      lp_sets_coeff = 0.0
 
!  Signal data
      INTEGER                         :: n_sdata_o = 0
      INTEGER                         :: iw_sdo_verbose = -1
      REAL (rprec),                                                            &
     &   DIMENSION(v3fit_max_signals) :: sdo_data_a = 0.0
 
      REAL (rprec),                                                            &
     &   DIMENSION(v3fit_max_signals) :: sdo_sigma_a = 0.0
 
      REAL (rprec),                                                            &
     &   DIMENSION(v3fit_max_signals) :: sdo_weight_a = 1.0
 
      LOGICAL                         :: sdo_spec_can_overwrite = .true.
      LOGICAL, DIMENSION(v3fit_max_diagnostics) :: mag_a = .true.
      LOGICAL, DIMENSION(v3fit_max_diagnostics) :: mag_3d_a = .false.
      LOGICAL                         :: mag_force_coil = .false.
 
!  Signal data sigma specification
      INTEGER, DIMENSION(v3fit_max_spec_size)      ::                          &
     &   sdo_s_spec_imin = 0
 
      INTEGER, DIMENSION(v3fit_max_spec_size)      ::                          &
     &   sdo_s_spec_imax = 0
 
      REAL (rprec), DIMENSION(v3fit_max_spec_size) ::                          &
     &   sdo_s_spec_floor = 0.0
 
      REAL (rprec), DIMENSION(v3fit_max_spec_size) ::                          &
     &   sdo_s_spec_fraction = 0.0
 
!  Signal data weight specification
      INTEGER, DIMENSION(v3fit_max_spec_size)      ::                          &
     &   sdo_w_spec_imin = 0
 
      INTEGER, DIMENSION(v3fit_max_spec_size)      ::                          &
     &   sdo_w_spec_imax = 0
 
      REAL (rprec), DIMENSION(v3fit_max_spec_size) ::                          &
     &   sdo_w_spec_weight = 0.0
 
!  Magnetic specification
      INTEGER, DIMENSION(v3fit_max_spec_size)      ::                          &
     &   mag_spec_imin = 0
 
      INTEGER, DIMENSION(v3fit_max_spec_size)      ::                          &
     &   mag_spec_imax = 0
 
      LOGICAL, DIMENSION(v3fit_max_spec_size) ::                               &
     &   mag_spec_use_induced = .true.
 
!  Magnetic integration parameters
      REAL (rprec) :: pol_rad_ratio = 1.0
 
!  Signal factor parameter specification.
      INTEGER, DIMENSION(v3fit_max_spec_size)      ::                          &
     &   sfactor_spec_imin = 0
 
      INTEGER, DIMENSION(v3fit_max_spec_size)      ::                          &
     &   sfactor_spec_imax = 0
 
      REAL (rprec), DIMENSION(v3fit_max_spec_size) ::                          &
     &   sfactor_spec_fac = 0.0
 
!  Signal factor parameter specification.
      INTEGER, DIMENSION(v3fit_max_spec_size)      ::                          &
     &   soffset_spec_imin = 0
 
      INTEGER, DIMENSION(v3fit_max_spec_size)      ::                          &
     &   soffset_spec_imax = 0
 
      REAL (rprec), DIMENSION(v3fit_max_spec_size) ::                          &
     &   soffset_spec_fac = 0.0
 
!  External current signal specification
      REAL (rprec) :: extcurz_s0 = -1.0
      REAL (rprec) :: extcurz_u0 = 0.0
 
!  Geometric information
      REAL (rprec) :: r_major_radius
      REAL (rprec) :: a_minor_radius
 
!  Limiter iso function specification.
      INTEGER                                     :: n_lif = 0
      INTEGER, DIMENSION(v3fit_max_limiters)      :: n_phi_lif = 0
      REAL (rprec), DIMENSION(v3fit_max_limiters,0:4,0:4) ::                   &
     &   lif_arz = 0.0
 
      REAL (rprec), DIMENSION(v3fit_max_limiters) :: lif_rc = 0.0
      REAL (rprec), DIMENSION(v3fit_max_limiters) :: lif_zc = 0.0
      REAL (rprec), DIMENSION(v3fit_max_limiters) ::                           &
     &   lif_sigma = 0.001_dp
 
      REAL (rprec), DIMENSION(v3fit_max_limiters,v3fit_max_lif_size)           &
     &   :: lif_phi_degree = 0.0
 
      LOGICAL, DIMENSION(v3fit_max_limiters)      ::                           &
     &   lif_on_edge = .false.
 
!  Prior signal specification.
      INTEGER                                       :: n_prior = 0
      CHARACTER (len=data_name_length), DIMENSION(v3fit_max_priors)            &
     &   :: prior_name = ''
 
      CHARACTER (len=data_name_length), DIMENSION(v3fit_max_priors)            &
     &   :: prior_param_name = ''
 
      INTEGER, DIMENSION(v3fit_max_priors,2) :: prior_indices = 0
      CHARACTER (len=data_short_name_length),                                  &
     &   DIMENSION(v3fit_max_priors) :: prior_units = ''
 
!  Combinations of other signals specification.
      INTEGER :: n_coosig = 0
      INTEGER, DIMENSION(v3fit_max_combinations) :: n_sig_coosig = 0
      INTEGER, DIMENSION(v3fit_max_combinations,v3fit_max_cos_size) ::         &
     &   coosig_indices = 0
 
      REAL (rprec),                                                            &
     &   DIMENSION(v3fit_max_combinations,v3fit_max_cos_size) ::               &
     &   coosig_coeff = 0.0
 
      CHARACTER(len=combination_type_length),                                  &
     &   DIMENSION(v3fit_max_combinations)       :: coosig_type = 'sum'
 
      CHARACTER (len=data_name_length),                                        &
     &   DIMENSION(v3fit_max_combinations)       :: coosig_name = ''
 
      CHARACTER (len=data_short_name_length),                                  &
     &   DIMENSION(v3fit_max_combinations)       :: coosig_units = ''
 
      INTEGER, DIMENSION(v3fit_max_combinations) :: coosig_wgts_id = -1
 
!  Gaussian Process Signals specification.
      INTEGER :: n_gp = 0
      INTEGER, DIMENSION(max_gaussprocess) :: n_gp_signal = 0
      INTEGER, DIMENSION(max_gaussprocess,v3fit_max_signals) ::                &
     &   gp_signal_indices = 0
 
      CHARACTER(len=data_short_name_length),                                   &
     &   DIMENSION(max_gaussprocess) :: gp_model_type = 'none'
 
      INTEGER, DIMENSION(max_gaussprocess) :: gp_model_index = 0
      REAL(rprec), DIMENSION(max_gaussprocess, v3fit_max_parameters) ::        &
     &   gp_param_vrnc = 0.001
 
      REAL(rprec), DIMENSION(max_gaussprocess) :: gp_tolerance = 1.0e-4
      REAL(rprec), DIMENSION(max_gaussprocess) :: gp_cholesky_fact = 0.0
 
!  Integration parameters.
      CHARACTER (len=data_short_name_length) :: int_method = 'add'
      INTEGER                                :: int_num_points = 40
      REAL (rprec)                           :: int_size = 0.0025
 
!  Initial Plasma Offsets
      REAL (rprec) :: phi_offset = 0
      REAL (rprec) :: z_offset = 0
 
!  Reconstruction step control specification.
      INTEGER                                :: nrstep = 0
      REAL (rprec)                           :: dg2_stop = 0.0
      REAL (rprec)                           :: cut_svd = 0.0
      REAL (rprec)                           :: cut_eff = 0.0
      REAL (rprec)                           :: cut_marg_eff = 0.0
      REAL (rprec)                           :: cut_delta_a = 0.0
      REAL (rprec)                           :: cut_dg2 = 0.0
      REAL (rprec)                           :: astep_max = 0.0
      CHARACTER (len=v3fit_step_name_length) :: step_type = 'sl'
      REAL (rprec)                           :: cut_inv_svd = 1.0e-10
      REAL (rprec)                           :: cut_comp_svd = 0.0
      LOGICAL :: use_central_diff = .false.
 
      LOGICAL :: l_zero_xcdot = .true.
 
!  Declare Namelist
      NAMELIST/v3fit_main_nli/                                                 &
     &   main_nli_filename,                                                    &
!  Equilibrium input files
     &   vmec_nli_filename, vmec_wout_input, vacuum_nli_filename,              &
     &   siesta_nli_filename, siesta_restart_filename,                         &
!  Signal input files
     &   mdsig_list_filename, sxrch_dot_filename, thscte_dot_filename,         &
     &   ipch_dot_filename, mse_dot_filename, ece_dot_filename,                &
     &   sxrem_ratio_dot_filename, limiter_grid_file,                          &
!  Array allocation sizes
     &   na_s_desc,                                                            &
!  Task specification and work variables
     &   my_task,                                                              &
!  Model profile specification
!  Electron Denisty
     &   pp_ne_ptype, pp_ne_b, pp_ne_as, pp_ne_af,                             &
!  Soft x-ray emissvity
     &   pp_sxrem_ptype, pp_sxrem_b, pp_sxrem_as, pp_sxrem_af,                 &
     &   num_sxrem_p, pp_sxrem_ptype_a, pp_sxrem_b_a, pp_sxrem_as_a,           &
     &   pp_sxrem_af_a,                                                        &
!  Electron temperature
     &   pp_te_ptype, pp_te_b, pp_te_as, pp_te_af,                             &
!  Ion temperature
     &   pp_ti_ptype, pp_ti_b, pp_ti_as, pp_ti_af,                             &
!  Effective charge
     &   pp_ze_ptype, pp_ze_b, pp_ze_as, pp_ze_af,                             &
!  Soft x-ray ratio
     &   sxrem_te_a, sxrem_ratio_a,                                            &
!  Model Specification Variables
     &   model_eq_type, model_ne_type, model_sxrem_type, model_ze_type,        &
     &   model_sxrem_type_a, model_te_type, model_ti_type, ne_pp_unit,         &
     &   ne_min, te_min, ti_min, ze_min, sxrem_min, e_pressure_fraction,       &
     &   emission_file, ece_resonance_range, coosig_wgts,                      &
!  Reconstruction constraints
     &   n_rc, rc_type, rc_index, rc_value,                                    &
!  Derived parameters
     &   n_dp, dp_type, dp_index,                                              &
!  Reconstruction parameters
     &   n_rp, rp_type, rp_index, rp_index2, rp_vrnc, rp_range_type,           &
     &   rp_range_value, rp_range_index,                                       &
!  Locking parameters
     &   n_lp, lp_type, lp_index, lp_index2, lp_sets, lp_sets_index,           &
     &   lp_sets_index2, lp_sets_coeff,
!  Signal Data specification
     &   n_sdata_o, iw_sdo_verbose, sdo_data_a, sdo_sigma_a,                   &
     &   sdo_weight_a, mag_a, mag_3d_a, mag_force_coil,                        &
     &   sdo_spec_can_overwrite,                                               &
!  Magnetic integration parameters
     &   pol_rad_ratio,                                                        &
!  Signal factor parameters
     &   sfactor_spec_imin, sfactor_spec_imax, sfactor_spec_fac,               &
!  Signal offset parameters
     &   soffset_spec_imin, soffset_spec_imax, soffset_spec_fac,               &
!  External current signal specification
     &   extcurz_s0, extcurz_u0,                                               &
!  Signal data sigma specification
     &   sdo_s_spec_imin, sdo_s_spec_imax, sdo_s_spec_floor,                   &
     &   sdo_s_spec_fraction,                                                  &
!  Signal data weight specification
     &   sdo_w_spec_imin, sdo_w_spec_imax, sdo_w_spec_weight,                  &
!  Magnetic signal specification
     &   mag_spec_imin, mag_spec_imax, mag_spec_use_induced,                   &
!  Geometric information
     &   r_major_radius, a_minor_radius,                                       &
!  Limiter iso function specification.
     &   n_lif, n_phi_lif, lif_arz, lif_rc, lif_zc, lif_sigma,                 &
     &   lif_phi_degree, lif_on_edge,                                          &
!  Prior signal specification.
     &   n_prior, prior_name, prior_param_name, prior_indices,                 &
     &   prior_units,                                                          &
!  Combinations of other signals specification.
     &   n_coosig, n_sig_coosig, coosig_indices, coosig_coeff,                 &
     &   coosig_type, coosig_name, coosig_units, coosig_wgts_id,               &
!  Gaussian Process Signals specification.
     &   n_gp, n_gp_signal, gp_signal_indices, gp_model_type,                  &
     &   gp_model_index, gp_param_vrnc, gp_tolerance, gp_cholesky_fact,        &
!  Integration parameters.
     &   int_method, int_num_points, int_size,                                 &
!  Initial PLasma Offsets.
     &   phi_offset, z_offset,                                                 &
!  Reconstruction step control specification.
     &   nrstep, dg2_stop, cut_svd, cut_eff, cut_marg_eff, cut_delta_a,        &
     &   cut_dg2, astep_max, step_type, cut_inv_svd, cut_comp_svd,             &
     &   use_central_diff,                                                     &
     &   l_zero_xcdot
 
      CONTAINS
 
!*******************************************************************************
!  UTILITY SUBROUTINES
!*******************************************************************************
!-------------------------------------------------------------------------------
!-------------------------------------------------------------------------------
      SUBROUTINE v3fit_input_read_namelist(namelist_file)
      USE safe_open_mod
      USE v3_utilities, only: err_fatal
 
      IMPLICIT NONE
 
!  Declare Arguments
      CHARACTER (len=*), INTENT(in) :: namelist_file
 
!  local variables
      INTEGER                       :: iou_mnli
      INTEGER                       :: status
      INTEGER                       :: i
      INTEGER                       :: j
      INTEGER                       :: imin
      INTEGER                       :: imax
      REAL (rprec)                  :: start_time
 
!  Start of executable code
      start_time = profiler_get_start_time()
 
!  Initalize a default value of the I\O unit. V3FIT increments from there.
      iou_mnli = 0
      CALL safe_open(iou_mnli, status, trim(namelist_file),                    &
     &               'old', 'formatted')
      CALL assert_eq(0, status, 'v3fit_input_read_namelist' //                 &
     &   ': Safe_open of ' // trim(namelist_file) // ' failed')
 
!  Read the namelist input file.
      READ (iou_mnli, nml=v3fit_main_nli)
      CLOSE (iou_mnli, iostat=status)
      CALL assert_eq(0, status, 'v3fit_input_read_namelist' //                 &
     &   ': Error closing ' // trim(namelist_file) // ' failed')
 
!  Toggle use coil signals for the magnetics from the specification
      DO j = 1, SIZE(mag_spec_imin)
         IF (mag_spec_imin(j) .le. 0) EXIT
         imin = max(min(mag_spec_imin(j), v3fit_max_diagnostics), 1)
         imax = min(max(mag_spec_imax(j), imin), v3fit_max_diagnostics)
         mag_a(imin:imax) = mag_spec_use_induced(j)
      END DO
 
!  Set weights from weight specification.
      DO j = 1, SIZE(sdo_w_spec_imin)
         IF (sdo_w_spec_imin(j) .le. 0) EXIT
         imin = max(min(sdo_w_spec_imin(j), v3fit_max_signals), 1)
         imax = min(max(sdo_w_spec_imax(j), imin), v3fit_max_signals)
         sdo_weight_a(imin:imax) = sdo_w_spec_weight(j)
      END DO
 
!  Set sigmas from the sigma specification.
      DO j = 1,SIZE(sdo_s_spec_imin)
         IF (sdo_s_spec_imin(j) .le. 0) EXIT
         imin = max(min(sdo_s_spec_imin(j), v3fit_max_signals), 1)
         imax = min(max(sdo_s_spec_imax(j), imin), v3fit_max_signals)
         DO i = imin, imax
            IF ((sdo_sigma_a(i) .eq. 0) .or.                                   &
     &          sdo_spec_can_overwrite) THEN
               IF (sdo_s_spec_floor(j) .ge. 0) THEN
                  sdo_sigma_a(i) = max(sdo_s_spec_floor(j),                    &
     &               abs(sdo_s_spec_fraction(j)*sdo_data_a(i)))
               ELSE
                  sdo_sigma_a(i) = sqrt(sdo_s_spec_floor(j)**2.0 +             &
     &               (sdo_s_spec_fraction(j)*sdo_data_a(i))**2.0)
               END IF
            END IF
         END DO
      END DO
 
      IF (main_nli_filename .eq. '') THEN
         main_nli_filename = namelist_file
      END IF
 
      IF ((r_major_radius .gt. 0.0) .and.                                      &
     &    (a_minor_radius .gt. 0.0)) THEN
         IF (n_lif + 1 .le. v3fit_max_limiters) THEN
            n_lif = n_lif + 1 ! Add this as a new limiter.
            lif_arz(n_lif,:,:) = 0.0
            lif_arz(n_lif,0,0) = -a_minor_radius**2.0
            lif_arz(n_lif,2,0) = 1.0
            lif_arz(n_lif,0,2) = 1.0
            lif_rc(n_lif) = r_major_radius
            lif_zc(n_lif) = 0.0
            lif_sigma(n_lif) = 0.001_rprec
            n_phi_lif(n_lif) = v3fit_max_lif_size
            DO i = 1, v3fit_max_lif_size
               lif_phi_degree(n_lif,i) = (i - 1)*360.0                         &
     &                                 / v3fit_max_lif_size
            END DO
            lif_on_edge(n_lif) = .true.
         ELSE
            CALL err_fatal('Adding limiter by specifying ' //                  &
     &                     'major/minor radii causes n_lif to ' //             &
     &                     'exceed v3fit_max_limiters')
         END IF
      END IF
 
!  Search for the last index greater than 0 to determine the number of signals
!  in a combination.
      DO i = 1, n_coosig
         DO j = 1, v3fit_max_cos_size
            IF (coosig_indices(i,j) .eq. 0) THEN
               n_sig_coosig(i) = j - 1
               EXIT ! Exit out of the j loop.
            END IF
         END DO
      END DO
 
 
!-------------------------------------------------------------------------------
!  All the coding between these boxes can be removed once the non _a sxrem
!  values are removed. ***
!-------------------------------------------------------------------------------
!  Check the non _a sxrem profile variables. If pp_sxrem_ptype does not equal
!  'none' then over write the the first elements of the _a versions.
      SELECT CASE (trim(model_sxrem_type))
 
         CASE ('none') ! Do nothing
 
         CASE DEFAULT
            WRITE (*,*) ' *** Overwiting the sxrem profile first ' //          &
     &                  'element.'
            WRITE (*,*) '     Non array soft xray profiles have ' //           &
     &                  'been deprecated'
            model_sxrem_type_a(1) = model_sxrem_type
            pp_sxrem_ptype_a(1) = pp_sxrem_ptype
            pp_sxrem_b_a(1,:) = pp_sxrem_b
            pp_sxrem_as_a(1,:) = pp_sxrem_as
            pp_sxrem_af_a(1,:) = pp_sxrem_af
 
!  We'll assume that any reconstuction parameters that refer to the non _a also
!  are the first element.
            DO i = 1, n_rp
               SELECT CASE(trim(rp_type(i)))
 
                  CASE ('pp_sxrem_b')
                     WRITE (*,1000) 'pp_sxrem_b', 'pp_sxrem_b_a'
                     rp_type(i) = 'pp_sxrem_b_a'
                     rp_index2(i) = rp_index(i)
                     rp_index(i) = 1
 
                  CASE ('pp_sxrem_as')
                     WRITE (*,1000) 'pp_sxrem_as', 'pp_sxrem_as_a'
                     rp_type(i) = 'pp_sxrem_as_a'
                     rp_index2(i) = rp_index(i)
                     rp_index(i) = 1
 
                  CASE ('pp_sxrem_af')
                     WRITE (*,1000) 'pp_sxrem_af', 'pp_sxrem_af_a'
                     rp_type(i) = 'pp_sxrem_af_a'
                     rp_index2(i) = rp_index(i)
                     rp_index(i) = 1
 
               END SELECT
 
!  Need to update ranges as well starting with the lower range.
               SELECT CASE(trim(rp_range_type(i,1)))
 
                  CASE ('pp_sxrem_b')
                     WRITE (*,1001) 'pp_sxrem_b', 'pp_sxrem_b_a'
                     rp_range_type(i,1) = 'pp_sxrem_b_a'
                     rp_range_index(i,1,2) = rp_range_index(i,1,1)
                     rp_range_index(i,1,1) = 1
 
                  CASE ('pp_sxrem_as')
                     WRITE (*,1001) 'pp_sxrem_as', 'pp_sxrem_as_a'
                     rp_range_type(i,1) = 'pp_sxrem_as_a'
                     rp_range_index(i,1,2) = rp_range_index(i,1,1)
                     rp_range_index(i,1,1) = 1
 
                  CASE ('pp_sxrem_af')
                     WRITE (*,1001) 'pp_sxrem_af', 'pp_sxrem_af_a'
                     rp_range_type(i,1) = 'pp_sxrem_af_a'
                     rp_range_index(i,1,2) = rp_range_index(i,1,1)
                     rp_range_index(i,1,1) = 1
 
               END SELECT
 
!  Update the lower ranges.
               SELECT CASE(trim(rp_range_type(i,2)))
 
                  CASE ('pp_sxrem_b')
                     WRITE (*,1002) 'pp_sxrem_b', 'pp_sxrem_b_a'
                     rp_range_type(i,2) = 'pp_sxrem_b_a'
                     rp_range_index(i,2,2) = rp_range_index(i,2,1)
                     rp_range_index(i,2,1) = 1
 
                  CASE ('pp_sxrem_as')
                     WRITE (*,1002) 'pp_sxrem_as', 'pp_sxrem_as_a'
                     rp_range_type(i,2) = 'pp_sxrem_as_a'
                     rp_range_index(i,2,2) = rp_range_index(i,2,1)
                     rp_range_index(i,2,1) = 1
 
                  CASE ('pp_sxrem_af')
                     WRITE (*,1002) 'pp_sxrem_af', 'pp_sxrem_af_a'
                     rp_range_type(i,2) = 'pp_sxrem_af_a'
                     rp_range_index(i,2,2) = rp_range_index(i,2,1)
                     rp_range_index(i,2,1) = 1
 
               END SELECT
            END DO
 
!  Update priors to use _a arrays.
            DO i = 1, n_prior
               SELECT CASE(trim(prior_name(i)))
                  CASE ('pp_sxrem_b')
                     WRITE (*,1003) 'pp_sxrem_b', 'pp_sxrem_b_a'
                     prior_name(i) = 'pp_sxrem_b_a'
                     prior_indices(i,2) = prior_indices(i,1)
 
                  CASE ('pp_sxrem_as')
                     WRITE (*,1003) 'pp_sxrem_as', 'pp_sxrem_as_a'
                     prior_name(i) = 'pp_sxrem_as_a'
                     prior_indices(i,2) = prior_indices(i,1)
 
                  CASE ('pp_sxrem_af')
                     WRITE (*,1003) 'pp_sxrem_af', 'pp_sxrem_af_a'
                     prior_name(i) = 'pp_sxrem_af_a'
                     prior_indices(i,2) = prior_indices(i,1)
               END SELECT
            END DO
      END SELECT
 
1000  FORMAT('Changing reconstruction parameter ',a,' to ', a)
1001  FORMAT('Changing lower parameter constraint ',a,' to ', a)
1002  FORMAT('Changing upper parameter constraint ',a,' to ', a)
1003  FORMAT('Changing prior signal ',a,' to ', a)
!-------------------------------------------------------------------------------
!  All the coding between these boxes can be removed once the non _a sxrem
!  values are removed. ***
!-------------------------------------------------------------------------------
 
      WRITE (*,*) ' *** V3FIT namelist input read from ' //                    &
     &            trim(namelist_file)
 
      CALL profiler_set_stop_time('v3fit_input_read_namelist',                 &
     &                            start_time)
 
      END SUBROUTINE
 
!-------------------------------------------------------------------------------
!-------------------------------------------------------------------------------
      FUNCTION v3fit_input_find_scale_index(index)
 
      IMPLICIT NONE
 
!  Declare Arguments
      INTEGER             :: v3fit_input_find_scale_index
      INTEGER, INTENT(in) :: index
 
!  local variables
      INTEGER             :: i
      REAL (rprec)        :: start_time
 
!  Start of executable code
      start_time = profiler_get_start_time()
 
      v3fit_input_find_scale_index = 0;
      DO i = 1, v3fit_max_spec_size
         IF (sfactor_spec_fac(i) .eq. 0.0) THEN
            EXIT
         END IF
 
         IF (sfactor_spec_imin(i) .le. index .and.                             &
     &       sfactor_spec_imax(i) .ge. index) THEN
            v3fit_input_find_scale_index = i
            EXIT
         END IF
      END DO
 
      CALL profiler_set_stop_time('v3fit_input_find_scale_index',              &
     &                            start_time)
 
      END FUNCTION
 
!-------------------------------------------------------------------------------
!-------------------------------------------------------------------------------
      FUNCTION v3fit_input_find_offset_index(index)
 
      IMPLICIT NONE
 
!  Declare Arguments
      INTEGER             :: v3fit_input_find_offset_index
      INTEGER, INTENT(in) :: index
 
!  local variables
      INTEGER             :: i
      REAL (rprec)        :: start_time
 
!  Start of executable code
      start_time = profiler_get_start_time()
 
      v3fit_input_find_offset_index = 0;
      DO i = 1, v3fit_max_spec_size
         IF (soffset_spec_imin(i) .le. index .and.                             &
     &       soffset_spec_imax(i) .ge. index) THEN
            v3fit_input_find_offset_index = i
            EXIT
         END IF
      END DO
 
      CALL profiler_set_stop_time('v3fit_input_find_offset_index',             &
     &                            start_time)
 
      END FUNCTION
 
!-------------------------------------------------------------------------------
!-------------------------------------------------------------------------------
      SUBROUTINE v3fit_input_write_namelist(namelist_file)
      USE safe_open_mod
 
      IMPLICIT NONE
 
!  Declare Arguments
      CHARACTER (len=*), INTENT(in) :: namelist_file
 
!  local variables
      INTEGER                       :: iou_mnli
      INTEGER                       :: status
      REAL (rprec)                  :: start_time
 
!  Start of executable code
      start_time = profiler_get_start_time()
 
!  FIXME: Update namelist variables from the context.
 
!  Initalize a default value of the I\O unit. SIESTA increments from there.
      iou_mnli = 0
      CALL safe_open(iou_mnli, status, trim(namelist_file),                    &
     &               'replace', 'formatted', delim_in='quote')
      CALL assert_eq(0, status, 'v3fit_input_write_namelist' //                &
     &   ': Safe_open of ' // trim(namelist_file) // ' failed')
 
!  Write the namelist input file.
      WRITE (iou_mnli, nml=siesta_info)
      CLOSE (iou_mnli, iostat=status)
      CALL assert_eq(0, status, 'v3fit_input_write_namelist' //                &
     &   ': Error closing ' // trim(namelist_file) // ' failed')
 
      CALL profiler_set_stop_time('v3fit_input_write_namelist',                &
     &                            start_time)
 
      END SUBROUTINE
 
      END MODULE