fix: check for unlimited dimension on variable before adjusting counts

A netcdf file may have an unlimited dimension, but a particular variable may not have the unlimited
dimension.
See #519 for CESM2.3 CLM which has the unlimited cohort dimension.  In the example restart and history files
no state variables (or any variables) have the cohort dimension.
Massive assumption in direct_netcdf_mod.f90 that we want to read the one slice (the latest slice) of the unlimited dimension. This may not be true for all models.

assimilation_code/modules/io/direct_netcdf_mod.f90

@@ -93,7 +93,7 @@ module direct_netcdf_mod
                                  get_index_start, get_index_end , get_num_dims, &
                                  create_diagnostic_structure, &
                                  end_diagnostic_structure, &
-                                 has_unlimited_dim
+                                 has_unlimited_dim, get_io_dim_ids
 
 use io_filenames_mod,     only : get_restart_filename, inherit_copy_units, &
                                  stage_metadata_type, get_file_description, &
@@ -859,15 +859,16 @@ subroutine read_variables(ncfile_in, var_block, start_var, end_var, domain)
 
    slice_start(:) = 1 ! default to read all dimensions start at 1
 
-   if (has_unlimited_dim(domain)) then
+   ret = nf90_inquire(ncfile_in, unlimitedDimID=unlim_dimID)
+   call nc_check(ret, 'read_variables: nf90_inquire', 'unlimitedDimID')
+
+   if (has_unlimited_dim(domain) .and. any(get_io_dim_ids(domain, i) ==  unlim_dimID )) then
 
       counts(num_dims) = 1 ! one slice of unlimited dimesion
-      counts(1:num_dims-1) = get_dim_lengths(domain, i) ! the state
+      counts(1:get_num_dims(domain, i)) = get_dim_lengths(domain, i) ! the state
 
       ! read latest time slice - hack to get started with tiegcm
       ! not sure if it will always be the last time slice
-      ret = nf90_inquire(ncfile_in, unlimitedDimID=unlim_dimID)
-      call nc_check(ret, 'read_variables: nf90_inquire', 'unlimitedDimID')
 
       if (unlim_dimID /= -1) then ! unlimited dimension exists
          ret = nf90_inquire_dimension(ncfile_in, unlim_dimID, len=slice_start(num_dims))
@@ -1588,15 +1589,16 @@ subroutine write_variables(ncid, var_block, start_var, end_var, domain, &
       slice_start(:) = 1 ! default to read all dimensions starting at 1
       counts(:) = 1
 
-      if (has_unlimited_dim(domain)) then
+      ret = nf90_inquire(ncid, unlimitedDimID=unlim_dimID)
+      call nc_check(ret, 'read_variables: nf90_inquire', 'unlimitedDimID')
+
+      if (has_unlimited_dim(domain) .and. any(get_io_dim_ids(domain, i) ==  unlim_dimID )) then
 
          counts(num_dims) = 1 ! one slice of unlimited dimesion
          counts(1:get_num_dims(domain, i)) = get_dim_lengths(domain, i)
 
          ! write the latest time slice - HK hack to get started with tiegcm
          ! not sure if it will always be the last time slice
-         ret = nf90_inquire(ncid, unlimitedDimID=unlim_dimID)
-         call nc_check(ret, 'write_variables: nf90_inquire', 'unlimitedDimID')
          if (unlim_dimID /= -1) then ! unlimited dimension exists
             ret = nf90_inquire_dimension(ncid, unlim_dimID, len=slice_start(num_dims))
             call nc_check(ret, 'write_variables: nf90_inquire dimension', 'unlimitedDim length')