init_gs2_diagnostics Subroutine

  subroutine init_gs2_diagnostics (list, nstep, gs2_diagnostics_config_in, header)
    use theta_grid, only: init_theta_grid
    use kt_grids, only: init_kt_grids, ntheta0, naky
    use run_parameters, only: init_run_parameters
    use species, only: init_species, nspec
    use dist_fn, only: init_dist_fn
    use init_g, only: init_init_g
    use gs2_io, only: init_gs2_io
    use gs2_heating, only: init_htype
    use collisions, only: collision_model_switch, init_lorentz_error
    use collisions, only: collision_model_lorentz, collision_model_lorentz_test
    use mp, only: broadcast, proc0, mp_abort
    use le_grids, only: init_weights, wdim
    use gs2_save, only: restart_writable
    use normalisations, only: init_normalisations
    use diagnostics_final_routines, only: init_par_filter
    use standard_header, only: standard_header_type
    implicit none
    !> If true, this is a "list-mode run" and so turn off
    !> [[gs2_diagnostics_knobs:print_flux_line]] and
    !> [[gs2_diagnostics_knobs:print_line]] if set
    logical, intent (in) :: list
    !> Maximum number of steps to take
    integer, intent (in) :: nstep
    !> Input parameters for this module
    type(diagnostics_config_type), intent(in), optional :: gs2_diagnostics_config_in
    !> Header for files with build and run information
    type(standard_header_type), intent(in), optional :: header
    ! Actual value for optional `header` input
    type(standard_header_type) :: local_header
    integer :: nmovie_tot

    if (present(header)) then
      local_header = header
    else
      local_header = standard_header_type()
    end if

    if (initialized) return
    initialized = .true.

    call init_normalisations
    call init_theta_grid
    call init_kt_grids
    call init_run_parameters
    call init_species
    call init_init_g
    call init_dist_fn

    call real_init (list, gs2_diagnostics_config_in, header=local_header)

    nmovie_tot = nstep/nmovie

    ! initialize weights for less accurate integrals used
    ! to provide an error estimate for v-space integrals (energy and untrapped)
    if (write_verr) then
       if (proc0) call init_weights
       call broadcast(wdim)
    end if

    ! allocate heating diagnostic data structures
    if (write_heating) then
       allocate (h_hist(0:navg-1))
       call init_htype (h_hist,  nspec)

       allocate (hk_hist(ntheta0,naky,0:navg-1))
       call init_htype (hk_hist, nspec)

       call init_htype (h,  nspec)

       allocate (hk(ntheta0, naky))
       call init_htype (hk, nspec)
    else
       allocate (h_hist(0))
       allocate (hk(1,1))
       allocate (hk_hist(1,1,0))
    end if

    !GGH Allocate density and velocity perturbation diagnostic structures
    if (write_jext) then
       allocate (j_ext_hist(ntheta0, naky,0:navg-1))
       j_ext_hist = 0
    end if

    call init_gs2_io (append_old, make_movie, &
         write_correlation_extend, &
         write_phi_over_time, write_apar_over_time, write_bpar_over_time, &
         nout, ob_midplane=ob_midplane, header=local_header)

    call broadcast (nout)

    if (write_cerr) then
       if (collision_model_switch == collision_model_lorentz .or. &
            collision_model_switch == collision_model_lorentz_test) then
          call init_lorentz_error
       else
          write_cerr = .false.
       end if
    end if

    if(.not. allocated(pflux_avg)) then
       allocate (pflux_avg(nspec), qflux_avg(nspec), heat_avg(nspec), vflux_avg(nspec))
       pflux_avg = 0.0 ; qflux_avg = 0.0 ; heat_avg = 0.0 ; vflux_avg = 0.0
    endif

    call check_restart_file_writeable(file_safety_check, save_for_restart, save_distfn)

    !Setup the parallel fft if we're writing/using the parallel spectrum
    if (write_kpar .or. write_gs) call init_par_filter
  end subroutine init_gs2_diagnostics