Align merge branch toward dev/ufs-weather-model: fix 3 latent bugs

While minimizing the diff against dev/ufs-weather-model (without changing
answers, breaking exact-restart, or removing CESM-specific code), three
latent bugs were found where the CESM-side code had diverged from the
correct UFS version. Each fix both realigns with UFS and corrects a real
defect; all three are answer-neutral for CESM configs (dormant or no-op on
the active code paths).

1. w3iogrmd.F90: restore the IF(IERR.NE.0) CALL EXTIOF check after the
   main mod_def CAPCHNK read. The Functional Charnock cherry-pick (of the
   older 14e6bed) had reverted this region to a state lacking the I/O
   error check that dev/ufs-weather-model has. No-op on a successful read.

2. wav_shr_mod.F90 (timeInit): read the dummy argument ymd instead of an
   uninitialized local 'date'. A dev/unified refactor had added an unset
   local integer 'date' and changed tdate=abs(ymd) -> tdate=abs(date) and
   if(ymd<0) -> if(date<0), so the routine read an undefined variable.
   Only reachable via the optDate alarm path (interval alarms never call
   it), so the validated interval-alarm config is unaffected.

3. wav_comp_nuopc.F90 (InitializeRealize): guard the diagnose_mesh size
   argument by mesh type. In the unstructured-mesh branch gindex is never
   allocated (gindex_sea is used and deallocated), so size(gindex) read an
   unallocated array. Use nseal_cpl for the unstructured path, matching
   UFS. Only fires for unstructured mesh with dbug_flag>5; structured
   grids (e.g. wgx3v7) never reach it.

Verified: full coupled build succeeds; ERS_Ld3.TL319_t232_wg37.GW_JRA
passes exact-restart (COMPARE_base_rest) and reproduces merge_develop
bit-for-bit across WW3, coupler, MOM6, and CICE.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

Author: alperaltuntas

model/src/w3iogrmd.F90

@@ -1611,6 +1611,7 @@ SUBROUTINE W3IOGR ( INXOUT, NDSM, IMOD, FEXT &
            SSDSHCK,                                          &
            IKTAB, DCKI, QBI, SATINDICES, SATWEIGHTS,         &
            DIKCUMUL, CUMULW, SINTAILPAR, CAPCHNK
+      IF (IERR.NE.0) CALL EXTIOF(NDSE,IERR,'W3IOGR','mod_def.'//FILEXT(:IEXT),51)
       IF (SINTAILPAR(1).GT.0.5) THEN
         CALL INSIN4(.FALSE.)
         READ (NDSM,IOSTAT=IERR)                       &

model/src/wav_comp_nuopc.F90

@@ -823,7 +823,11 @@ subroutine InitializeRealize(gcomp, importState, exportState, clock, rc)
          elementDistgrid=Distgrid,rc=rc)
     if (ChkErr(rc,__LINE__,u_FILE_u)) return
     if (dbug_flag > 5) then
-      call diagnose_mesh(EMesh, size(gindex), 'EMesh', rc=rc)
+      if (unstr_mesh) then
+        call diagnose_mesh(EMesh, nseal_cpl, 'EMesh', rc=rc)
+      else
+        call diagnose_mesh(EMesh, size(gindex), 'EMesh', rc=rc)
+      end if
       if (ChkErr(rc,__LINE__,u_FILE_u)) return
     end if
 

model/src/wav_shr_mod.F90

@@ -1298,8 +1298,7 @@ subroutine timeInit( Time, ymd, cal, tod, rc)
 
     ! local variables
     integer :: year, mon, day ! year, month, day as integers
-    integer :: tdate          ! temporary date
-    integer :: date           ! coded-date (yyyymmdd)
+    integer :: tdate          ! temporary date (yyyymmdd)
     integer, parameter          :: SecPerDay = 86400 ! Seconds per day
     character(len=*), parameter :: subname = ' (wav_shr_mod:timeInit) '
     !-------------------------------------------------------------------------------
@@ -1312,9 +1311,9 @@ subroutine timeInit( Time, ymd, cal, tod, rc)
       rc = ESMF_FAILURE
     end if
 
-    tdate = abs(date)
+    tdate = abs(ymd)
     year = int(tdate/10000)
-    if (date < 0) year = -year
+    if (ymd < 0) year = -year
     mon = int( mod(tdate,10000)/  100)
     day = mod(tdate,  100)