Merge pull request #403 from NCAR/bug-fix_read_state

bug-fix: add a check for unlimited dimension in read_variables

CHANGELOG.rst

@@ -22,6 +22,13 @@ individual files.
 
 The changes are now listed with the most recent at the top.
 
+**October 13 2022 :: Bug-fix for read variables. Tag v10.5.3**
+
+- Per-file check for unlimited dimension before variable read. Netcdf 
+  dimension counts adjusted accordingly. Fixes problems when reading from 
+  DART created netcdf files, for example, from fill_inflation_restart
+- Bug-fix for verbose printing of state_structure info
+
 **October 10 2022 :: Bug-fix for obs_converter builds. Tag v10.5.2**
 
 - Bug fix for converter builds using the template model_mod.f90

assimilation_code/modules/io/direct_netcdf_mod.f90

@@ -855,24 +855,31 @@ subroutine read_variables(ncfile_in, var_block, start_var, end_var, domain)
    num_dims = get_io_num_dims(domain, i)
    allocate(counts(num_dims))
    allocate(slice_start(num_dims))
+   counts(:) = 1
+
+   slice_start(:) = 1 ! default to read all dimensions start at 1
 
    if (has_unlimited_dim(domain)) then
 
-      slice_start(:) = 1 ! default to read all dimensions start at 1
       counts(num_dims) = 1 ! one slice of unlimited dimesion
       counts(1:num_dims-1) = 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')
-      ret = nf90_inquire_dimension(ncfile_in, unlim_dimID, len=slice_start(num_dims))
-      call nc_check(ret, 'read_variables: nf90_inquiredimension', 'unlimitedDim length')
+
+      if (unlim_dimID /= -1) then ! unlimited dimension exists
+         ret = nf90_inquire_dimension(ncfile_in, unlim_dimID, len=slice_start(num_dims))
+         call nc_check(ret, 'read_variables: nf90_inquire_dimension', 'unlimitedDim length')
+         if (slice_start(num_dims) == 0) slice_start(num_dims) = 1 ! newly created file
+      else  ! file does not have an unlimited dimension because it was created by DART
+          slice_start(num_dims) = 1
+      endif
 
    else
 
-      slice_start(:) = 1 ! default to read all dimensions start at 1
-      counts(:) = get_dim_lengths(domain, i) ! the state
+      counts(1:get_num_dims(domain,i)) = get_dim_lengths(domain, i) ! the state
    endif
 
    ret = nf90_inq_varid(ncfile_in, get_variable_name(domain, i), var_id)
@@ -1579,6 +1586,7 @@ subroutine write_variables(ncid, var_block, start_var, end_var, domain, &
       allocate(counts(num_dims))
       allocate(slice_start(num_dims))
       slice_start(:) = 1 ! default to read all dimensions starting at 1
+      counts(:) = 1
 
       if (has_unlimited_dim(domain)) then
 
@@ -1599,9 +1607,10 @@ subroutine write_variables(ncid, var_block, start_var, end_var, domain, &
 
       else
 
-         counts(:) = get_dim_lengths(domain, i)
+         counts(1:get_num_dims(domain, i)) = get_dim_lengths(domain, i)
       endif
 
+
 !>@todo FIXME, the first variable in the second domain is not found when using coamps_nest.
       ret = nf90_inq_varid(ncid, trim(get_variable_name(domain, i)), var_id)
       call nc_check(ret, 'write_variables:', 'nf90_inq_varid "'//trim(get_variable_name(domain,i))//'"')

assimilation_code/modules/io/state_structure_mod.f90

@@ -1812,6 +1812,7 @@ subroutine state_structure_info(dom_id)
 
 200 format(4x,i2,', length = ',I8,', name = "',A,'"')
 201 format(4x,i2,':         ',2x,'  length = ',I8,', name = "',A,'"')
+202 format(4x,i2,':         ',2x,'  ID = ',I8,', length = ',I8,', name = "',A,'"')
 
 ! report on each variable in this domain
 
@@ -1848,7 +1849,7 @@ subroutine state_structure_info(dom_id)
    array_lengths(1:num_dims) = get_io_dim_lengths(dom_id,ivar)
    do jdim = 1, num_dims
        dim_name = get_dim_name(dom_id, ivar, jdim)
-       write(*,200) jdim, array_ids(jdim), array_lengths(jdim), trim(dim_name)
+       write(*,202) jdim, array_ids(jdim), array_lengths(jdim), trim(dim_name)
    enddo
 
    if ( state%domain(dom_id)%info_file /= 'NULL' ) then

conf.py

@@ -21,7 +21,7 @@
 author = 'Data Assimilation Research Section'
 
 # The full version, including alpha/beta/rc tags
-release = '10.5.2'
+release = '10.5.3'
 master_doc = 'README'
 
 # -- General configuration ---------------------------------------------------