Add support for a COBALT_param_doc file (#59)

* Add cobalt_param_doc.F90

Using the file parser from MOM6, add the option to read parameters
from COBALT_input and COBALT_override files and write pramerters to
COBALT_param_doc files. The COBALT_input files must be specific in
the input.nml

* Replace most calls to g_tracer_add_param

Add a call to read the name and loaction of the COBALT param files
from the namelist to generic_COBALT

Replace calls to g_tracer_add_param with get_param but do not change deaults.
The descriptions are just the parameter name, and the units are included where
they were documenemted in the code.

* Add support for a COBALT_param_doc file

Using the file parser from MOM6, add the option to read parameters
from COBALT_input and COBALT_override files and write pramerters to
COBALT_param_doc files. The COBALT_input files must be specific in
the input.nml

* Replace most calls to g_tracer_add_param

Replace calls to g_tracer_add_param with get_param but do not change deaults.
The descriptions are just the parameter name, and the units are included where
they were documenemted in the code.

* Fix typo

Fix error in line continue statement.

* Add missing description

Add description for RHO_0 and NKML

* Cange parameters with sperd or spery

Remove unit changes from per-day or per-year to per-second from
the default values to do that calculation outside the get param
call. This should not change the solution.

* Use scale argument in get_param

Where default values were rescaled by time (sperd or spery), nutrients
(carbon to nitrogen), concentration (micromoles to moles) or light, the
optional argument scale is now set in get_param so that the values in
the parameter doc files are consistent with the literature.

---------

Co-authored-by: Theresa Morrison <[email protected]>
Co-authored-by: Theresa Morrison <[email protected]>
Co-authored-by: Theresa Morrison <[email protected]>

generic_tracers/cobalt_param_doc.F90

@@ -0,0 +1,86 @@
+! this module will contain a few main routines: one to get the
+module cobalt_param_doc 
+
+use MOM_cpu_clock,     only : cpu_clock_id, cpu_clock_begin, cpu_clock_end, CLOCK_COMPONENT
+use MOM_data_override, only : data_override
+use MOM_domains,       only : domain2D, same_domain
+use MOM_error_handler, only : MOM_error, FATAL, WARNING, callTree_enter, callTree_leave
+use MOM_file_parser,   only : param_file_type, open_param_file, close_param_file
+use MOM_file_parser,   only : read_param, get_param, log_param, log_version
+use MOM_io,            only : file_exists, close_file, slasher, ensembler
+use MOM_io,            only : open_namelist_file, check_nml_error
+use MOM_time_manager,  only : time_type, time_type_to_real, real_to_time_type
+use MOM_time_manager,  only : operator(+), operator(-), operator(>)
+use posix, only : mkdir, stat, stat_buf
+
+implicit none ; private
+
+public get_COBALT_param_file
+
+!> Container for paths and parameter file names.
+!type, public :: directories
+!  character(len=240) :: &
+!    restart_input_dir = ' ',& !< The directory to read restart and input files.
+!    restart_output_dir = ' ',&!< The directory into which to write restart files.
+!    output_directory = ' '    !< The directory to use to write the model output.
+!  character(len=2048) :: &
+!    input_filename  = ' '     !< A string that indicates the input files or how
+!                              !! the run segment should be started.
+!end type directories
+
+contains
+!! This subroutine is analagous to the get_mom_input routine within the MOM_get_input module. There are additional
+!> arguments used in the MOM version which are commented out and not used here. These features may be needed as we 
+!> add more complexity to the parameter files in COBALT so I have commented them out rather than deleting them.
+subroutine get_COBALT_param_file(param_file)
+  type(param_file_type), optional, intent(out) :: param_file   !< A structure to parse for run-time parameters.
+  !type(directories),     optional, intent(out) :: dirs         !< Container for paths and parameter filenames.
+  !logical,               optional, intent(in)  :: check_params !< If present and False will stop error checking for
+  !                                                             !! run-time parameters.
+  !character(len=*),      optional, intent(in)  :: default_input_filename !< If present, is the value assumed for
+  !                                                             !! input_filename if input_filename is no listed
+  !                                                             !! in the namelist MOM_input_nml.
+  ! Local variables
+  integer, parameter :: npf = 5 ! Maximum number of parameter files
+
+  character(len=240) :: &
+    output_directory = ' ', &      ! Directory to use to write the model output.
+    parameter_filename(npf) = ' '  ! List of files containing parameters.
+
+  character(len=2048) :: &
+    input_filename             ! A string that indicates the input files or how
+                               ! the run segment should be started.
+  character(len=240) :: output_dir
+  integer :: unit, io, ierr, valid_param_files
+
+  type(stat_buf) :: buf
+
+  namelist /cobalt_input_nml/ parameter_filename
+
+  ! Open namelist
+  if (file_exists('input.nml')) then
+    unit = open_namelist_file(file='input.nml')
+  else
+    call MOM_error(FATAL,'Required namelist file input.nml does not exist.')
+  endif
+
+  ! Read namelist parameters
+  ierr=1 ; do while (ierr /= 0)
+    read(unit, nml=cobalt_input_nml, iostat=io, end=10)
+    ierr = check_nml_error(io, 'cobalt_input_nml')
+  enddo
+10 call close_file(unit)
+
+  output_dir = trim(slasher(ensembler(output_directory)))
+  valid_param_files = 0
+  do io=1,npf
+     if (len_trim(trim(parameter_filename(io))) > 0) then
+       call open_param_file(trim(parameter_filename(io)), param_file, &
+                            component="COBALT", doc_file_dir=output_dir)
+        valid_param_files = valid_param_files + 1
+     endif
+   enddo
+
+end subroutine get_COBALT_param_file
+
+end module cobalt_param_doc 

generic_tracers/cobalt_types.F90

@@ -55,10 +55,16 @@ module cobalt_types
   integer, parameter, public :: SMALL      = 4 !< ID for small phytoplankton 
 
   real, parameter, public :: sperd = 24.0 * 3600.0    !< number of seconds in a day (sec)
+  real, parameter, public :: I_sperd = 1.0/sperd      !< inverse of number of seconds in a day (sec)
   real, parameter, public :: spery = 365.25 * sperd   !< number of seconds in a year (sec)
+  real, parameter, public :: I_spery = 1.0/spery      !< inverse of number of seconds in a year (sec)
   real, parameter, public :: epsln=1.0e-30            !< small, but non-zero value for numerical stability
   real, parameter, public :: missing_value1=-1.0e+10  !< large negative value to represent missing value in diags
   real, parameter, public :: vb_nh3 = 25.             !< Liquid molar volume at boiling point for NH3 (cm3 mol−1)
+  real, parameter, public :: micromol2mol = 1.0e6     !< convert micromoles to moles (used in concentration parameters)
+  real, parameter, public :: c2n = 106.0/16.0         !< convert nutrient ratios relative to carbon to ratios relative to nitrogen
+  real, parameter, public :: micromolQpersec2W = 2.77e18/6.022e17 !< convert photosynthetically available radiation (micromole quanta
+                                                      !! per-second) to watts. 
 
   !> An auxiliary type for storing varible names
   type vardesc