Add NUOPC cap and rearrange driver directory (CICE-Consortium#376)

* NUOPC branch

* initial CICE6 port to CESM+NUOPC

* clean up nu_diag initialization due to complexity added by nuopc cap

* add nu_diag_set flag to work around the nu_diag setting in the nuopc cap

* update cice driver directories

* update documentation

* update documentation

* update documentation

* update documentation

* fix minor bug in cice.setup that affects settings parsing without final carriage return

* update documentation

* rename drivers/subroutine to drivers/direct and update documentation

cice.setup

@@ -849,7 +849,7 @@ EOF2
 
         cat ${ICE_SCRIPTS}/options/set_env.${name} >> ${fsmods}
 
-cat >> ${fimods} << EOF2
+cat >> ${fsmods} << EOF2
 
 EOF2
 

cicecore/cicedynB/general/ice_init.F90

@@ -16,7 +16,7 @@ module ice_init
       use ice_communicate, only: my_task, master_task, ice_barrier
       use ice_constants, only: c0, c1, c2, c3, p2, p5
       use ice_exit, only: abort_ice
-      use ice_fileunits, only: nu_nml, nu_diag, nml_filename, diag_type, &
+      use ice_fileunits, only: nu_nml, nu_diag, nu_diag_set, nml_filename, diag_type, &
           ice_stdout, get_fileunit, release_fileunit, bfbflag, flush_fileunit, &
           ice_IOUnitsMinUnit, ice_IOUnitsMaxUnit
 #ifdef CESMCOUPLED
@@ -466,11 +466,17 @@ subroutine input_data
          history_file  = trim(runid) // ".cice" // trim(inst_suffix) //".h"
          restart_file  = trim(runid) // ".cice" // trim(inst_suffix) //".r"
          incond_file   = trim(runid) // ".cice" // trim(inst_suffix) //".i"
-         inquire(file='ice_modelio.nml'//trim(inst_suffix),exist=exists)
-         if (exists) then
-            call get_fileUnit(nu_diag)
-            call shr_file_setIO('ice_modelio.nml'//trim(inst_suffix),nu_diag)
-         end if
+         ! Note by tcraig - this if test is needed because the nuopc cap sets
+         ! nu_diag before this routine is called.  This creates a conflict.
+         ! In addition, in the nuopc cap, shr_file_setIO will fail if the
+         ! needed namelist is missing (which it is in the CIME nuopc implementation)
+         if (.not. nu_diag_set) then
+            inquire(file='ice_modelio.nml'//trim(inst_suffix),exist=exists)
+            if (exists) then
+               call get_fileUnit(nu_diag)
+               call shr_file_setIO('ice_modelio.nml'//trim(inst_suffix),nu_diag)
+            end if
+         endif
       else
          ! each task gets unique ice log filename when if test is true, for debugging
          if (1 == 0) then