bgcNICE tests and bug fix

columnphysics/icepack_zbgc.F90

@@ -953,9 +953,11 @@ subroutine icepack_biogeochemistry(dt, &
          else
             first_ice(n) = .true.
             if (tr_brine) trcrn(nt_fbri,n) = c1
-            do mm = 1,nbtrcr
-               trcrn(nt_zbgc_frac-1+mm,n) = zbgc_frac_init(mm)
-            enddo
+            if (z_tracers) then
+               do mm = 1,nbtrcr
+                  trcrn(nt_zbgc_frac-1+mm,n) = zbgc_frac_init(mm)
+               enddo
+            endif
             if (n == 1) Rayleigh_criteria = .false.
             if (solve_zsal) trcrn(nt_bgc_S:nt_bgc_S+nblyr-1,n) = c0
          endif

configuration/driver/icedrv_forcing.F90

@@ -73,8 +73,12 @@ module icedrv_forcing
          ocn_data_format, & ! 'bin'=binary or 'nc'=netcdf
          bgc_data_format, & ! 'bin'=binary or 'nc'=netcdf
          atm_data_type,   & ! 'default', 'clim', 'CFS'
-         ocn_data_type,   & ! 'default'
-         bgc_data_type,   & ! 'default'
+         ocn_data_type,   & ! 'default', 'SHEBA'
+         bgc_data_type,   & ! 'default', 'ISPOL', 'NICE'
+         atm_data_file,   & ! atmospheric forcing data file
+         ocn_data_file,   & ! ocean forcing data file
+         ice_data_file,   & ! ice forcing data file
+         bgc_data_file,   & ! biogeochemistry forcing data file
          precip_units       ! 'mm_per_month', 'mm_per_sec', 'mks'
 
       character(char_len_long), public :: & 
@@ -547,7 +551,8 @@ subroutine atm_CFS
       character (char_len_long) filename
       character(len=*), parameter :: subname='(atm_CFS)'
 
-      filename = trim(data_dir)//'/CFS/cfsv2_2015_220_70_01hr.txt'
+!      atm_data_file = 'cfsv2_2015_220_70_01hr.txt'
+      filename = trim(data_dir)//'/CFS/'//trim(atm_data_file)
 
       write (nu_diag,*) 'Reading ',filename
 
@@ -869,8 +874,9 @@ subroutine atm_ISPOL
       character (char_len_long) filename
 
       character(len=*), parameter :: subname='(atm_ISPOL)'
-
-      filename = trim(data_dir)//'/ISPOL_2004/ISPOL_atm_forcing.txt'
+
+!      atm_data_file = 'ISPOL_atm_forcing.txt'
+      filename = trim(data_dir)//'/ISPOL_2004/'//trim(atm_data_file)
 
       write (nu_diag,*) 'Reading ',filename
 
@@ -927,7 +933,8 @@ subroutine atm_NICE
 
       character(len=*), parameter :: subname='(atm_NICE)'
 
-      filename = trim(data_dir)//'/NICE_2015/NICE_atm_forcing.txt'
+!      atm_data_file = 'NICE_atm_forcing.txt'
+      filename = trim(data_dir)//'/NICE_2015/'//trim(atm_data_file)
 
       write (nu_diag,*) 'Reading ',filename
 
@@ -980,8 +987,8 @@ subroutine ocn_NICE
 
       character(len=*), parameter :: subname='(ocn_NICE)'
 
-      filename = &
-         trim(data_dir)//'/NICE_2015/oceanmixed_daily_3.txt'
+!      ocn_data_file = 'oceanmixed_daily_3.txt'
+      filename = trim(data_dir)//'/NICE_2015/'//trim(ocn_data_file)
 
       write (nu_diag,*) 'Reading ',filename
 
@@ -1030,8 +1037,8 @@ subroutine ocn_ISPOL
 
       character(len=*), parameter :: subname='(ocn_ISPOL)'
 
-      filename = &
-        trim(data_dir)//'/ISPOL_2004/pop_frc.gx1v3.051202_but_hblt_from_010815_ispol.txt'
+!      ocn_data_file = 'pop_frc.gx1v3.051202_but_hblt_from_010815_ispol.txt'
+      filename = trim(data_dir)//'/ISPOL_2004/'//trim(ocn_data_file)
 
       write (nu_diag,*) 'Reading ',filename
 
@@ -1101,8 +1108,8 @@ subroutine ice_open_clos
 
       character (char_len_long) filename
 
-      filename = &
-          trim(data_dir)//'/SHEBA/open_clos_lindsay.dat'
+!      ice_data_file = 'open_clos_lindsay.dat'
+      filename = trim(data_dir)//'/SHEBA/'//trim(ice_data_file)
 
       write (nu_diag,*) 'Reading ',filename
 

configuration/driver/icedrv_forcing_bgc.F90

@@ -32,7 +32,7 @@ module icedrv_forcing_bgc
 
       subroutine init_forcing_bgc
 
-        use icedrv_forcing, only: data_dir, bgc_data_type
+        use icedrv_forcing, only: data_dir, bgc_data_type, bgc_data_file
 
         integer (kind=int_kind) :: &
            ntime, &
@@ -50,9 +50,9 @@ subroutine init_forcing_bgc
             trim(bgc_data_type) == 'NICE') then
 
            if (trim(bgc_data_type) == 'ISPOL') &
-           filename = trim(data_dir)//'/ISPOL_2004/nutrients_daily_ISPOL_WOA_field3.txt'
+           filename = trim(data_dir)//'/ISPOL_2004/'//trim(bgc_data_file)
            if (trim(bgc_data_type) == 'NICE') &
-           filename = trim(data_dir)//'/NICE_2015/nutrients_daily_ISPOL_WOA_field3.txt'
+           filename = trim(data_dir)//'/NICE_2015/'//trim(bgc_data_file)
 
           write (nu_diag,*) 'Reading ',filename
 

configuration/driver/icedrv_init.F90

@@ -65,6 +65,8 @@ subroutine input_data
       use icedrv_flux, only: default_season
       use icedrv_forcing, only: precip_units,    fyear_init,      ycycle
       use icedrv_forcing, only: atm_data_type,   ocn_data_type,   bgc_data_type
+      use icedrv_forcing, only: atm_data_file,   ocn_data_file,   bgc_data_file
+      use icedrv_forcing, only: ice_data_file
       use icedrv_forcing, only: atm_data_format, ocn_data_format, bgc_data_format
       use icedrv_forcing, only: data_dir
       use icedrv_forcing, only: oceanmixed_ice, restore_ocn, trestore
@@ -145,6 +147,8 @@ subroutine input_data
         tfrz_option,     default_season,                   &
         precip_units,    fyear_init,      ycycle,          &
         atm_data_type,   ocn_data_type,   bgc_data_type,   &
+        atm_data_file,   ocn_data_file,   bgc_data_file,   &
+        ice_data_file,                                     &
         atm_data_format, ocn_data_format, bgc_data_format, &
         data_dir,        trestore,        restore_ocn
 
@@ -217,13 +221,17 @@ subroutine input_data
       ycycle          = 1         ! number of years in forcing cycle
       atm_data_format = 'bin'     ! file format ('bin'=binary or 'nc'=netcdf)
       atm_data_type   = 'default' ! source of atmospheric forcing data
+      atm_data_file   = ' '       ! atmospheric forcing data file
       precip_units    = 'mks'     ! 'mm_per_month' or
                                   ! 'mm_per_sec' = 'mks' = kg/m^2 s
       oceanmixed_ice  = .false.   ! if true, use internal ocean mixed layer
       ocn_data_format = 'bin'     ! file format ('bin'=binary or 'nc'=netcdf)
       ocn_data_type   = 'default' ! source of ocean forcing data
+      ocn_data_file   = ' '       ! ocean forcing data file
+      ice_data_file   = ' '       ! ice forcing data file (opening, closing)
       bgc_data_format = 'bin'     ! file format ('bin'=binary or 'nc'=netcdf)
       bgc_data_type   = 'default' ! source of BGC forcing data
+      bgc_data_file   = ' '       ! biogeochemistry forcing data file
       data_dir    = ' '           ! root location of data files
       restore_ocn     = .false.   ! restore sst if true
       trestore        = 90        ! restoring timescale, days (0 instantaneous)
@@ -534,6 +542,15 @@ subroutine input_data
          write(nu_diag,*)    ' bgc_data_type             = ', &
                                trim(bgc_data_type)
 
+         write(nu_diag,*)    ' atm_data_file             = ', &
+                               trim(atm_data_file)
+         write(nu_diag,*)    ' ocn_data_file             = ', &
+                               trim(ocn_data_file)
+         write(nu_diag,*)    ' bgc_data_file             = ', &
+                               trim(bgc_data_file)
+         write(nu_diag,*)    ' ice_data_file             = ', &
+                               trim(ice_data_file)
+
          if (trim(atm_data_type)=='default') &
          write(nu_diag,*)    ' default_season            = ', trim(default_season)
 

configuration/scripts/icepack_in

@@ -244,6 +244,10 @@
     fyear_init      = 2015
     ycycle          = 1
     data_dir        = '/Users/ftuser/Desktop/CICE-Consortium/ICEPACK_DATA/'
+    atm_data_file   = 'unknown_atm_data_file'
+    ocn_data_file   = 'unknown_ocn_data_file'
+    bgc_data_file   = 'unknown_bgc_data_file'
+    ice_data_file   = 'open_clos_lindsay.dat'
     atm_data_format = 'bin'
     ocn_data_format = 'bin'
     bgc_data_format = 'bin'

configuration/scripts/options/set_nml.alt04

@@ -17,3 +17,6 @@
     restore_ocn     = .true.
     trestore        = 0
     atm_data_type   = 'CFS'
+    atm_data_file   = 'cfsv2_2015_220_70_01hr.txt'
+    ocn_data_type   = 'SHEBA'
+    ice_data_file   = 'open_clos_lindsay.dat'

configuration/scripts/options/set_nml.bgcISPOL

@@ -7,6 +7,9 @@
  atm_data_type   = 'ISPOL'
  ocn_data_type   = 'ISPOL'
  bgc_data_type   = 'ISPOL'
+ atm_data_file   = 'ISPOL_atm_forcing_05092018.txt'
+ ocn_data_file   = 'pop_frc.gx1v3.051202_but_hblt_from_010815_ispol.txt'
+ bgc_data_file   = 'nutrients_daily_ISPOL_WOA_field3.txt'
  tr_brine        = .true.
  tr_zaero        = .true.
  z_tracers       = .true.

configuration/scripts/options/set_nml.bgcNICE

@@ -7,6 +7,9 @@
  atm_data_type   = 'NICE'
  ocn_data_type   = 'NICE'
  bgc_data_type   = 'NICE'
+ atm_data_file   = 'NICE_atm_forcing_05092018.txt'
+ ocn_data_file   = 'oceanmixed_daily_3.txt'
+ bgc_data_file   = 'nutrients_daily_ISPOL_WOA_field3.txt'
  tr_brine        = .true.
  tr_zaero        = .false.
  z_tracers       = .true.

configuration/scripts/options/set_nml.bgcsklNICE

@@ -4,15 +4,15 @@ year_init	 = 2015
  fyear_init      = 2015
  restore_ocn     = .true.
  trestore        = 1
- bgc_data_type   = 'unknown'
  tr_brine        = .true.
  skl_bgc         = .true.
  atm_data_type   = 'NICE'
  ocn_data_type   = 'NICE'
  bgc_data_type   = 'NICE'
+ atm_data_file   = 'NICE_atm_forcing_05092018.txt'
+ ocn_data_file   = 'oceanmixed_daily_3.txt'
+ bgc_data_file   = 'nutrients_daily_ISPOL_WOA_field3.txt'
  bgc_flux_type   = 'Jin2006'
- sil_data_type   = 'default'
- nit_data_type   = 'default'
  tr_bgc_Nit      = .true.
  tr_bgc_C        = .true.
  tr_bgc_Am       = .true.

configuration/scripts/tests/base_suite.ts

@@ -3,6 +3,7 @@ smoke          col     1x1        diag1,run1year
 smoke          col     1x1        debug,run1year
 smoke          col     1x1        debug,bgcISPOL
 smoke          col     1x1        debug,bgcNICE
+smoke          col     1x1        debug,bgcsklNICE
 smoke          col     1x1        debug,run1year,thermo1
 smoke          col     1x1        debug,run1year,swccsm3
 smoke          col     1x1        debug,run1year,alt01
@@ -17,7 +18,6 @@ restart        col     1x1        pondcesm
 restart        col     1x1        pondlvl
 restart        col     1x1        pondtopo
 restart        col     1x1        bgcISPOL
-restart        col     1x1        bgcNICE
 restart        col     1x1        thermo1
 restart        col     1x1        swccsm3
 restart        col     1x1        alt01

configuration/scripts/tests/travis_suite.ts

@@ -3,6 +3,7 @@ smoke          col     1x1        diag1,run1year
 smoke          col     1x1        debug,run1year
 smoke          col     1x1        debug,bgcISPOL
 smoke          col     1x1        debug,bgcNICE
+smoke          col     1x1        debug,bgcsklNICE
 smoke          col     1x1        debug,run1year,thermo1
 smoke          col     1x1        debug,run1year,swccsm3
 smoke          col     1x1        debug,run1year,alt01
@@ -14,7 +15,6 @@ restart        col     1x1        pondcesm
 restart        col     1x1        pondlvl
 restart        col     1x1        pondtopo
 restart        col     1x1        bgcISPOL
-restart        col     1x1        bgcNICE
 restart        col     1x1        thermo1
 restart        col     1x1        swccsm3
 restart        col     1x1        alt01

doc/source/icepack_index.rst

@@ -56,7 +56,6 @@ either Celsius or Kelvin units).
    "awtvdf", "weighting factor for visible, diffuse albedo", "0.63282"
    "awtvdr", "weighting factor for visible, direct albedo", "0.00318"
    "**B**", "", ""
-   "bgc_data_dir", ":math:`\bullet` data directory for bgc", ""
    "bgc_data_type", ":math:`\bullet` forcing type for biogeochemistry", ""
    "bgc_flux_type", ":math:`\bullet` ice-ocean flux velocity type", ""
    "bgc_tracer_type", "tracer_type for bgc tracers", ""

doc/source/science_guide/sg_bgc.rst

@@ -299,8 +299,8 @@ subroutine **icepack\_init\_ocean\_conc** in **icepack\_zbgc.F90** unless
 coupled to the ocean biogeochemistry. Silicate and nitrate may be read
 from a file. This option is specified in the namelist by setting the
 variables ``bgc_data_type`` to ``ISPOL``  or ``NICE``. The location of 
-forcing files is specified in ``bgc_data_dir`` and the filename is hardcoded 
-in **icedrv\_forcing** (NJ - needs to be updated).
+forcing files is specified in ``data_dir`` and the filename is also in
+namelist, ``bgc_data_file``.
 
 
 Skeletal Layer BGC

doc/source/user_guide/ug_case_settings.rst

@@ -205,6 +205,10 @@ column physics.
    "", "``ISPOL``", "ISPOL experiment data  (see :ref:`force`)", ""
    "", "``NICE``", "N-ICE experiment data  (see :ref:`force`)", ""
    "``data_dir``", "path/", "path to forcing data directory", ""
+   "``atm_data_file``", "filename", "file containing atmospheric data", ""
+   "``ocn_data_file``", "filename", "file containing ocean data", ""
+   "``ice_data_file``", "filename", "file containing ice opening, closing data", ""
+   "``bgc_data_file``", "filename", "file containing biogeochemistry data", ""
    "``calc_strair``", "true", "calculate wind stress and speed", ""
    "", "false", "read wind stress and speed from files", ""
    "``highfreq``", "true/false", "high-frequency atmo coupling", ""
@@ -251,10 +255,9 @@ column physics.
    "``scale_bgc``", "true/false", "Initialize biogeochemical profiles to scale with prognosed salinity profile", "``.false.``"
    "``solve_zsal``", "true/false", "prognostic salinity tracer used with ktherm = 1", "``.false.``"
    "``restart_zsal``", "true/false", "restarts zsalinity", "``.false.``"
-   "``bgc_data_dir``", "``/nitrate_and_silicate/forcing_directory/``", "", "'``/nitrate_and_silicate/forcing_directory/``'"
    "``bgc_data_type``", "``default``", "fixed, spatially homogeneous constant values defined in the code", ""
    "", "``clim``", "monthly climatology data file (see icedrv_forcing_bgc.F90) :cite:`GLBA06`", ""
-   "", "``NICE``", "NICE experiment data", ""
+   "", "``NICE``", "N-ICE experiment data", ""
    "", "``ISPOL``", "ISPOL experiment data", ""
    "``tr_bgc_Nit``", "true/false", "nitrate tracer", "``.true.``"
    "``tr_bgc_C``", "true/false", "dissolved organic carbon tracers and dissolved inorganic carbon tracers (not yet implemented)", "``.true.``"

doc/source/user_guide/ug_running.rst

@@ -256,7 +256,11 @@ Icepack requires near surface atmospheric data at a single point which are set
 in ``forcing_nml`` with the ``atm_data_type`` in the namelist (see :ref:`tabsettings`).
 The required fields to force icepack include: downwelling long wave and shortwave 
 radiative fluxes, latent and sensible heat fluxes, precipitation rate, and near 
-surface potential temperature and specific humidity.
+surface potential temperature and specific humidity.  The filenames ``atm_data_file``,
+``ocn_data_file``, ``ice_data_file``, and ``bgc_data_file``
+must also be provided for options other than the default and climatological forcing
+cases.  Current filenames can be found in the options scripts in
+**configuration/scripts/options** and in the forcing data directories.
 
 
 1) **Climate Forecast System (CFS)**