Update tracer init/query routines and Update documentation (#289)

* update new tracer number setting and update documentation

* refactor tracer init/query methods merging sizes and numbers to sizes, update documentation

columnphysics/icepack_intfc.F90

@@ -39,17 +39,15 @@ module icepack_intfc
       use icepack_parameters, only: p15, p25, p75, p333, p666
 
       use icepack_tracers, only: icepack_compute_tracers
-      use icepack_tracers, only: icepack_query_tracer_sizes
-      use icepack_tracers, only: icepack_write_tracer_sizes
       use icepack_tracers, only: icepack_init_tracer_flags
       use icepack_tracers, only: icepack_query_tracer_flags
       use icepack_tracers, only: icepack_write_tracer_flags
       use icepack_tracers, only: icepack_init_tracer_indices
       use icepack_tracers, only: icepack_query_tracer_indices
       use icepack_tracers, only: icepack_write_tracer_indices
-      use icepack_tracers, only: icepack_init_tracer_numbers
-      use icepack_tracers, only: icepack_query_tracer_numbers
-      use icepack_tracers, only: icepack_write_tracer_numbers
+      use icepack_tracers, only: icepack_init_tracer_sizes
+      use icepack_tracers, only: icepack_query_tracer_sizes
+      use icepack_tracers, only: icepack_write_tracer_sizes
 
       use icepack_itd, only: icepack_init_itd
       use icepack_itd, only: icepack_init_itd_hist

configuration/driver/icedrv_InitMod.F90

@@ -12,7 +12,7 @@ module icedrv_InitMod
       use icepack_intfc, only: icepack_warnings_flush, icepack_warnings_aborted
       use icepack_intfc, only: icepack_query_parameters, icepack_query_tracer_flags
       use icepack_intfc, only: icepack_write_tracer_flags, icepack_write_tracer_indices
-      use icepack_intfc, only: icepack_write_tracer_numbers
+      use icepack_intfc, only: icepack_write_tracer_sizes
       use icedrv_system, only: icedrv_system_abort
 
       implicit none
@@ -68,7 +68,7 @@ subroutine icedrv_initialize
 
       ! generate some output
       call icepack_write_tracer_flags(nu_diag)
-      call icepack_write_tracer_numbers(nu_diag)
+      call icepack_write_tracer_sizes(nu_diag)
       call icepack_write_tracer_indices(nu_diag)
       call icepack_warnings_flush(nu_diag)
       if (icepack_warnings_aborted()) call icedrv_system_abort(string=subname, &

configuration/driver/icedrv_RunMod.F90

@@ -12,7 +12,7 @@ module icedrv_RunMod
       use icepack_intfc, only: icepack_warnings_aborted
       use icepack_intfc, only: icepack_query_parameters
       use icepack_intfc, only: icepack_query_tracer_flags
-      use icepack_intfc, only: icepack_query_tracer_numbers
+      use icepack_intfc, only: icepack_query_tracer_sizes
       use icedrv_system, only: icedrv_system_abort
 
       implicit none
@@ -262,7 +262,7 @@ subroutine coupling_prep
       !-----------------------------------------------------------------
 
          call icepack_query_parameters(puny_out=puny, rhofresh_out=rhofresh)
-         call icepack_query_tracer_numbers(nbtrcr_out=nbtrcr)
+         call icepack_query_tracer_sizes(nbtrcr_out=nbtrcr)
          call icepack_warnings_flush(nu_diag)
          if (icepack_warnings_aborted()) call icedrv_system_abort(string=subname, &
              file=__FILE__,line= __LINE__)

configuration/driver/icedrv_init.F90

@@ -13,12 +13,12 @@ module icedrv_init
       use icepack_intfc, only: icepack_init_parameters
       use icepack_intfc, only: icepack_init_fsd
       use icepack_intfc, only: icepack_init_tracer_flags
-      use icepack_intfc, only: icepack_init_tracer_numbers
+      use icepack_intfc, only: icepack_init_tracer_sizes
       use icepack_intfc, only: icepack_init_tracer_indices
       use icepack_intfc, only: icepack_init_trcr
       use icepack_intfc, only: icepack_query_parameters
       use icepack_intfc, only: icepack_query_tracer_flags
-      use icepack_intfc, only: icepack_query_tracer_numbers
+      use icepack_intfc, only: icepack_query_tracer_sizes
       use icepack_intfc, only: icepack_query_tracer_indices
       use icepack_intfc, only: icepack_warnings_flush, icepack_warnings_aborted
       use icedrv_system, only: icedrv_system_abort
@@ -734,7 +734,9 @@ subroutine input_data
            tfrz_option_in=tfrz_option, kalg_in=kalg, &
            fbot_xfer_type_in=fbot_xfer_type, &
            wave_spec_type_in=wave_spec_type, wave_spec_in=wave_spec)
-      call icepack_init_tracer_numbers(ntrcr_in=ntrcr)
+      call icepack_init_tracer_sizes(ntrcr_in=ntrcr, &
+           ncat_in=ncat, nilyr_in=nilyr, nslyr_in=nslyr, nblyr_in=nblyr, &
+           nfsd_in=nfsd)
       call icepack_init_tracer_flags(tr_iage_in=tr_iage, &
            tr_FY_in=tr_FY, tr_lvl_in=tr_lvl, tr_aero_in=tr_aero, &
            tr_pond_in=tr_pond, tr_pond_cesm_in=tr_pond_cesm, &
@@ -745,9 +747,7 @@ subroutine input_data
            nt_qsno_in=nt_qsno, nt_iage_in=nt_iage, &
            nt_fy_in=nt_fy, nt_alvl_in=nt_alvl, nt_vlvl_in=nt_vlvl, &
            nt_apnd_in=nt_apnd, nt_hpnd_in=nt_hpnd, nt_ipnd_in=nt_ipnd, &
-           nt_aero_in=nt_aero, nt_fsd_in=nt_fsd, &
-           ncat_in=ncat, nilyr_in=nilyr, nslyr_in=nslyr, nblyr_in=nblyr, &
-           nfsd_in=nfsd)
+           nt_aero_in=nt_aero, nt_fsd_in=nt_fsd)
 
       call icepack_warnings_flush(nu_diag)
       if (icepack_warnings_aborted()) call icedrv_system_abort(string=subname, &
@@ -842,7 +842,7 @@ subroutine init_state
       !-----------------------------------------------------------------
 
          call icepack_query_parameters(heat_capacity_out=heat_capacity)
-         call icepack_query_tracer_numbers(ntrcr_out=ntrcr)
+         call icepack_query_tracer_sizes(ntrcr_out=ntrcr)
          call icepack_query_tracer_flags(tr_iage_out=tr_iage, &
               tr_FY_out=tr_FY, tr_lvl_out=tr_lvl, tr_aero_out=tr_aero, &
               tr_pond_cesm_out=tr_pond_cesm, tr_pond_lvl_out=tr_pond_lvl, &

configuration/driver/icedrv_init_column.F90

@@ -17,11 +17,11 @@ module icedrv_init_column
       use icepack_intfc, only: icepack_max_algae, icepack_max_aero, icepack_max_fe
       use icepack_intfc, only: icepack_max_nbtrcr
       use icepack_intfc, only: icepack_warnings_flush, icepack_warnings_aborted
-      use icepack_intfc, only: icepack_init_tracer_numbers, icepack_init_tracer_flags
+      use icepack_intfc, only: icepack_init_tracer_sizes, icepack_init_tracer_flags
       use icepack_intfc, only: icepack_init_tracer_indices
       use icepack_intfc, only: icepack_init_parameters
-      use icepack_intfc, only: icepack_query_tracer_numbers, icepack_query_tracer_flags
-      use icepack_intfc, only: icepack_query_tracer_indices, icepack_query_tracer_sizes
+      use icepack_intfc, only: icepack_query_tracer_sizes, icepack_query_tracer_flags
+      use icepack_intfc, only: icepack_query_tracer_indices
       use icepack_intfc, only: icepack_query_parameters
       use icepack_intfc, only: icepack_init_zbgc
       use icepack_intfc, only: icepack_init_thermo
@@ -151,7 +151,7 @@ subroutine init_shortwave
          call icepack_query_parameters(shortwave_out=shortwave)
          call icepack_query_parameters(dEdd_algae_out=dEdd_algae)
          call icepack_query_parameters(modal_aero_out=modal_aero)
-         call icepack_query_tracer_numbers(ntrcr_out=ntrcr, &
+         call icepack_query_tracer_sizes(ntrcr_out=ntrcr, &
               nbtrcr_sw_out=nbtrcr_sw)
          call icepack_query_tracer_flags(tr_brine_out=tr_brine, &
               tr_zaero_out=tr_zaero, tr_bgc_N_out=tr_bgc_N)
@@ -405,12 +405,12 @@ subroutine init_bgc()
       !-----------------------------------------------------------------
 
       call icepack_query_parameters(solve_zsal_out=solve_zsal)
-      call icepack_query_tracer_numbers(nbtrcr_out=nbtrcr, ntrcr_out=ntrcr, &
-           ntrcr_o_out=ntrcr_o)
-      call icepack_query_tracer_indices(nt_sice_out=nt_sice, nt_bgc_S_out=nt_bgc_S)
       call icepack_query_tracer_sizes(max_nbtrcr_out=max_nbtrcr, &
            max_algae_out=max_algae, max_don_out=max_don, max_doc_out=max_doc, &
            max_dic_out=max_dic, max_aero_out=max_aero, max_fe_out=max_fe)
+      call icepack_query_tracer_sizes(nbtrcr_out=nbtrcr, ntrcr_out=ntrcr, &
+           ntrcr_o_out=ntrcr_o)
+      call icepack_query_tracer_indices(nt_sice_out=nt_sice, nt_bgc_S_out=nt_bgc_S)
       call icepack_warnings_flush(nu_diag)
       if (icepack_warnings_aborted()) call icedrv_system_abort(string=subname, &
           file=__FILE__,line= __LINE__)
@@ -842,7 +842,7 @@ subroutine init_zbgc
       ! query Icepack values
       !-----------------------------------------------------------------
 
-      call icepack_query_tracer_numbers(ntrcr_out=ntrcr)
+      call icepack_query_tracer_sizes(ntrcr_out=ntrcr)
       call icepack_query_tracer_flags(tr_aero_out=tr_aero)
       call icepack_query_parameters(ktherm_out=ktherm, shortwave_out=shortwave, &
            scale_bgc_out=scale_bgc, skl_bgc_out=skl_bgc, z_tracers_out=z_tracers, &
@@ -1753,7 +1753,10 @@ subroutine init_zbgc
       if (icepack_warnings_aborted()) call icedrv_system_abort(string=subname, &
           file=__FILE__, line=__LINE__)
 
-      call icepack_init_tracer_numbers( &
+      call icepack_init_tracer_sizes( &
+           n_algae_in=n_algae,                                                                   &
+           n_DOC_in=n_DOC,             n_DON_in=n_DON,               n_DIC_in=n_DIC,             &
+           n_fed_in=n_fed,             n_fep_in=n_fep,               n_zaero_in=n_zaero,         &
            ntrcr_in=ntrcr, ntrcr_o_in=ntrcr_o, nbtrcr_in=nbtrcr, nbtrcr_sw_in=nbtrcr_sw)
       call icepack_warnings_flush(nu_diag)
       if (icepack_warnings_aborted()) call icedrv_system_abort(string=subname, &
@@ -1785,9 +1788,6 @@ subroutine init_zbgc
            nlt_bgc_DIC_in=nlt_bgc_DIC, nlt_bgc_DOC_in=nlt_bgc_DOC,   nlt_bgc_PON_in=nlt_bgc_PON, &
            nlt_bgc_DON_in=nlt_bgc_DON, nlt_bgc_Fed_in=nlt_bgc_Fed,   nlt_bgc_Fep_in=nlt_bgc_Fep, &
            nlt_bgc_chl_in=nlt_bgc_chl, nlt_bgc_hum_in=nlt_bgc_hum,   nlt_zaero_in=nlt_zaero,     &
-           n_algae_in=n_algae,                                                                   &
-           n_DOC_in=n_DOC,             n_DON_in=n_DON,               n_DIC_in=n_DIC,             &
-           n_fed_in=n_fed,             n_fep_in=n_fep,               n_zaero_in=n_zaero,         &
            bio_index_o_in=bio_index_o, bio_index_in=bio_index)
       call icepack_warnings_flush(nu_diag)
       if (icepack_warnings_aborted()) call icedrv_system_abort(string=subname, &

configuration/driver/icedrv_restart_bgc.F90

@@ -12,7 +12,7 @@ module icedrv_restart_bgc
       use icepack_intfc, only: icepack_max_algae, icepack_max_doc, icepack_max_don
       use icepack_intfc, only: icepack_max_dic, icepack_max_aero, icepack_max_fe
       use icepack_intfc, only: icepack_warnings_flush, icepack_warnings_aborted
-      use icepack_intfc, only: icepack_query_parameters, icepack_query_tracer_numbers
+      use icepack_intfc, only: icepack_query_parameters, icepack_query_tracer_sizes
       use icepack_intfc, only: icepack_query_tracer_flags, icepack_query_tracer_indices
       use icedrv_system, only: icedrv_system_abort
 
@@ -77,7 +77,7 @@ subroutine write_restart_bgc()
       call icepack_query_parameters(skl_bgc_out=skl_bgc)
       call icepack_query_parameters(solve_zsal_out=solve_zsal)
       call icepack_query_parameters(z_tracers_out=z_tracers)
-      call icepack_query_tracer_numbers(nbtrcr_out=nbtrcr)
+      call icepack_query_tracer_sizes(nbtrcr_out=nbtrcr)
       call icepack_query_tracer_flags(tr_bgc_Nit_out=tr_bgc_Nit, & 
          tr_bgc_Am_out=tr_bgc_Am, &
          tr_bgc_Sil_out=tr_bgc_Sil, tr_bgc_hum_out=tr_bgc_hum, &
@@ -377,7 +377,7 @@ subroutine read_restart_bgc()
       call icepack_query_parameters(skl_bgc_out=skl_bgc)
       call icepack_query_parameters(solve_zsal_out=solve_zsal)
       call icepack_query_parameters(z_tracers_out=z_tracers)
-      call icepack_query_tracer_numbers(nbtrcr_out=nbtrcr)
+      call icepack_query_tracer_sizes(nbtrcr_out=nbtrcr)
 
 
       call icepack_query_tracer_flags(tr_bgc_Nit_out=tr_bgc_Nit, & 

configuration/driver/icedrv_step.F90

@@ -13,10 +13,9 @@ module icedrv_step
       use icedrv_system, only: icedrv_system_abort
       use icepack_intfc, only: icepack_warnings_flush
       use icepack_intfc, only: icepack_warnings_aborted
-      use icepack_intfc, only: icepack_query_tracer_sizes
       use icepack_intfc, only: icepack_query_tracer_flags
       use icepack_intfc, only: icepack_query_tracer_indices
-      use icepack_intfc, only: icepack_query_tracer_numbers
+      use icepack_intfc, only: icepack_query_tracer_sizes
       use icepack_intfc, only: icepack_query_parameters
 
       implicit none
@@ -162,7 +161,7 @@ subroutine step_therm1 (dt)
       if (icepack_warnings_aborted()) call icedrv_system_abort(string=subname, &
           file=__FILE__,line= __LINE__)
 
-      call icepack_query_tracer_numbers( &
+      call icepack_query_tracer_sizes( &
            ntrcr_out=ntrcr)
       call icepack_warnings_flush(nu_diag)
       if (icepack_warnings_aborted()) call icedrv_system_abort(string=subname, &
@@ -374,7 +373,7 @@ subroutine step_therm2 (dt)
       ! query icepack values
       !-----------------------------------------------------------------
 
-      call icepack_query_tracer_numbers(ntrcr_out=ntrcr, nbtrcr_out=nbtrcr)
+      call icepack_query_tracer_sizes(ntrcr_out=ntrcr, nbtrcr_out=nbtrcr)
       call icepack_query_tracer_flags(tr_fsd_out=tr_fsd)
       call icepack_warnings_flush(nu_diag)
       if (icepack_warnings_aborted()) call icedrv_system_abort(string=subname, &
@@ -480,7 +479,7 @@ subroutine update_state (dt, daidt, dvidt, dagedt, offset)
       ! query icepack values
       !-----------------------------------------------------------------
 
-      call icepack_query_tracer_numbers(ntrcr_out=ntrcr)
+      call icepack_query_tracer_sizes(ntrcr_out=ntrcr)
       call icepack_warnings_flush(nu_diag)
       if (icepack_warnings_aborted()) call icedrv_system_abort(string=subname, &
           file=__FILE__,line= __LINE__)
@@ -639,7 +638,7 @@ subroutine step_dyn_ridge (dt, ndtd)
       ! query icepack values
       !-----------------------------------------------------------------
 
-         call icepack_query_tracer_numbers(ntrcr_out=ntrcr, nbtrcr_out=nbtrcr)
+         call icepack_query_tracer_sizes(ntrcr_out=ntrcr, nbtrcr_out=nbtrcr)
          call icepack_warnings_flush(nu_diag)
          if (icepack_warnings_aborted()) call icedrv_system_abort(string=subname, &
              file=__FILE__,line= __LINE__)
@@ -808,7 +807,7 @@ subroutine step_radiation (dt)
       allocate(nt_zaero(max_aero))
       allocate(nt_bgc_N(max_algae))
 
-      call icepack_query_tracer_numbers(ntrcr_out=ntrcr, nbtrcr_sw_out=nbtrcr_sw)
+      call icepack_query_tracer_sizes(ntrcr_out=ntrcr, nbtrcr_sw_out=nbtrcr_sw)
       call icepack_warnings_flush(nu_diag)
       if (icepack_warnings_aborted()) call icedrv_system_abort(string=subname, &
           file=__FILE__,line= __LINE__)
@@ -1123,7 +1122,7 @@ subroutine biogeochemistry (dt)
 
       !-----------------------------------------------------------------
 
-      call icepack_query_tracer_numbers(ntrcr_out=ntrcr, nbtrcr_out=nbtrcr)
+      call icepack_query_tracer_sizes(ntrcr_out=ntrcr, nbtrcr_out=nbtrcr)
       call icepack_query_tracer_flags(tr_zaero_out=tr_zaero)
       call icepack_query_tracer_indices(nlt_zaero_out=nlt_zaero)
       call icepack_query_tracer_indices(bio_index_o_out=bio_index_o)