Fix memory errors: uninitialized variables, and NetCDF writes to arra…

…ys that are too small (#668)

* move utility routines, data structures, and name generation out of FV3GFS_io.F90

* move RRFS SD state restart io to separate file and rename clm_lake_io.F90

* move rrfs sd emissions input code to FV3GFS_rrfs_sd_io.F90

* register sfc fields in FV3GFS_sfc_io.F90

* move oro reading to FV3GFS_oro_io.F90

* gwd I/O in FV3GFS_oro_io.F90

* store quilt restart data structures in FV3GFS_sfc_io types

* rrfs sd restart in quilt (still under testing)

* bug fixes for RRFS 32-bit physics

ccpp/data/GFS_typedefs.F90

@@ -6821,13 +6821,21 @@ subroutine grid_create (Grid, IM, Model)
       allocate (Grid%ddy_o3    (IM))
       allocate (Grid%jindx1_o3 (IM))
       allocate (Grid%jindx2_o3 (IM))
+
+      Grid%ddy_o3      = clear_val
+      Grid%jindx1_o3   = clear_val
+      Grid%jindx2_o3   = clear_val
     endif
 
 !--- stratosphere h2o active
     if ( Model%h2o_phys ) then
       allocate (Grid%ddy_h    (IM))
       allocate (Grid%jindx1_h (IM))
       allocate (Grid%jindx2_h (IM))
+
+      Grid%ddy_h       = clear_val
+      Grid%jindx1_h    = clear_val
+      Grid%jindx2_h    = clear_val
     endif
 
 !--- iccn active
@@ -6838,6 +6846,13 @@ subroutine grid_create (Grid, IM, Model)
       allocate (Grid%ddx_ci    (IM))
       allocate (Grid%iindx1_ci (IM))
       allocate (Grid%iindx2_ci (IM))
+
+      Grid%ddy_ci      = clear_val
+      Grid%jindx1_ci   = clear_val
+      Grid%jindx2_ci   = clear_val
+      Grid%ddx_ci      = clear_val
+      Grid%iindx1_ci   = clear_val
+      Grid%iindx2_ci   = clear_val
     endif
 
 !--- iaerclm active
@@ -6848,6 +6863,13 @@ subroutine grid_create (Grid, IM, Model)
       allocate (Grid%ddx_aer   (IM))
       allocate (Grid%iindx1_aer(IM))
       allocate (Grid%iindx2_aer(IM))
+
+      Grid%ddy_aer     = clear_val
+      Grid%jindx1_aer  = clear_val
+      Grid%jindx2_aer  = clear_val
+      Grid%ddx_aer     = clear_val
+      Grid%iindx1_aer  = clear_val
+      Grid%iindx2_aer  = clear_val
     endif
 
 !---  Model%do_ugwpv1
@@ -6856,6 +6878,11 @@ subroutine grid_create (Grid, IM, Model)
       allocate (Grid%ddy_j2tau  (IM))
       allocate (Grid%jindx1_tau (IM))
       allocate (Grid%jindx2_tau (IM))
+
+      Grid%ddy_j1tau   = clear_val
+      Grid%ddy_j2tau   = clear_val
+      Grid%jindx1_tau  = clear_val
+      Grid%jindx2_tau  = clear_val
    endif
 
  end subroutine grid_create