optionally apply data assimilation increments or a time-varying tende…

…ncy adjustment to tracers

 - This is a more complete implementation of the online ensemble data assimilation framework
   used in GFDL coupled data assimilation experiments.
 - There are some minor changes to previous DA interfaces.
 - Parameter ASSIM_METHOD ('NONE','OI_ASSIM','EAKF') are the current options.
 - If APPLY_TRACER_TENDENCY_ADJUSTMENT  = True, a time-varying tendency adjustment is provided
   (TENDENCY_ADJUSTMENT_FILE) and applied at each tracer timestep.
 - If USE_BASIN_FILE = True, a basin distribution file (BASIN_FILE) can be read and passed to the
   DA algorithms.

src/core/MOM.F90

@@ -1265,7 +1265,7 @@ subroutine step_MOM_thermo(CS, G, GV, US, u, v, h, tv, fluxes, dtdia, &
   call enable_averages(dtdia, Time_end_thermo, CS%diag)
 
   if (associated(CS%odaCS)) then
-    call apply_oda_tracer_increments(US%T_to_s*dtdia, G, GV, tv, h, CS%odaCS)
+    call apply_oda_tracer_increments(US%T_to_s*dtdia, Time_end_thermo, G, GV, tv, h, CS%odaCS)
   endif
 
   if (associated(fluxes%p_surf) .or. associated(fluxes%p_surf_full)) then
@@ -2796,7 +2796,7 @@ subroutine initialize_MOM(Time, Time_init, param_file, dirs, CS, restart_CSp, &
                       (LEN_TRIM(dirs%input_filename) == 1))
 
   if (CS%ensemble_ocean) then
-    call init_oda(Time, G, GV, CS%odaCS)
+    call init_oda(Time, G, GV, US, CS%diag, CS%odaCS)
   endif
 
   !### This could perhaps go here instead of in finish_MOM_initialization?

src/framework/MOM_interp_infra.F90

@@ -222,7 +222,7 @@ end subroutine time_interp_extern_3d
 
 !> initialize an external field
 integer function init_extern_field(file, fieldname, MOM_domain, domain, verbose, &
-                                   threading, ierr, ignore_axis_atts )
+                                   threading, ierr, ignore_axis_atts, correct_leap_year_inconsistency )
 
   character(len=*),         intent(in)  :: file  !< The name of the file to read
   character(len=*),         intent(in)  :: fieldname !< The name of the field in the file
@@ -237,13 +237,18 @@ integer function init_extern_field(file, fieldname, MOM_domain, domain, verbose,
   logical,        optional, intent(in)  :: ignore_axis_atts !< If present and true, do not issue a
                                                  !! fatal error if the axis Cartesian attribute is
                                                  !! not set to a recognized value.
+  logical,        optional, intent(in)  :: correct_leap_year_inconsistency !< If present and true,
+                                                 !! then allow for leap year inconsistency
+
 
   if (present(MOM_Domain)) then
     init_extern_field = init_external_field(file, fieldname, domain=MOM_domain%mpp_domain, &
-             verbose=verbose, threading=threading, ierr=ierr, ignore_axis_atts=ignore_axis_atts)
+             verbose=verbose, threading=threading, ierr=ierr, ignore_axis_atts=ignore_axis_atts, &
+             correct_leap_year_inconsistency=correct_leap_year_inconsistency)
   else
     init_extern_field = init_external_field(file, fieldname, domain=domain, &
-             verbose=verbose, threading=threading, ierr=ierr, ignore_axis_atts=ignore_axis_atts)
+             verbose=verbose, threading=threading, ierr=ierr, ignore_axis_atts=ignore_axis_atts, &
+             correct_leap_year_inconsistency=correct_leap_year_inconsistency)
   endif
 
 end function init_extern_field