[Dart-dev] DART/branches Revision: 11928

[dart at ucar.edu]

thoar at ucar.edu
2017-09-05 15:04:46 -0600 (Tue, 05 Sep 2017)
142
Merging changes from rma_trunk onto rma_coamps.
This is the development branch for the NOPP proposal.
Merging r11888 through r11927 into '.'




Index: DART/branches/coamps
===================================================================
--- DART/branches/coamps	2017-09-05 20:47:21 UTC (rev 11927)
+++ DART/branches/coamps	2017-09-05 21:04:46 UTC (rev 11928)

Property changes on: DART/branches/coamps
___________________________________________________________________
Modified: svn:mergeinfo
## -12,6 +12,7 ##
 /DART/branches/rma_cice:10649-10852
 /DART/branches/rma_clm:8905-9126
 /DART/branches/rma_diag:9623-9737
+/DART/branches/rma_fix_clm_restarts:9634-11919
 /DART/branches/rma_fixed_filenames:10702-10895
 /DART/branches/rma_kinds_to_state_structure:8952-9431
 /DART/branches/rma_kinds_to_state_strucutre:8903-8951
## -33,7 +34,7 ##
 /DART/branches/rma_sprint:8095-8166
 /DART/branches/rma_state_structure_test_dir:9472-9676
 /DART/branches/rma_state_structure_unit_test:9691-10268
-/DART/branches/rma_trunk:11712-11887
+/DART/branches/rma_trunk:11712-11927
 /DART/branches/rma_trunk_clamping:8786-8801
 /DART/branches/rma_trunk_filename:8011-8157
 /DART/branches/rma_trunk_get_state_fun:8568-8596
Modified: DART/branches/coamps/assimilation_code/modules/assimilation/assim_tools_mod.f90
===================================================================
--- DART/branches/coamps/assimilation_code/modules/assimilation/assim_tools_mod.f90	2017-09-05 20:47:21 UTC (rev 11927)
+++ DART/branches/coamps/assimilation_code/modules/assimilation/assim_tools_mod.f90	2017-09-05 21:04:46 UTC (rev 11928)
@@ -11,11 +11,16 @@
 !> 
 !> @{
 use      types_mod,       only : r8, i8, i4, digits12, PI, missing_r8
+
+use    options_mod,       only : get_missing_ok_status
+
 use  utilities_mod,       only : file_exist, get_unit, check_namelist_read, do_output,    &
                                  find_namelist_in_file, register_module, error_handler,   &
                                  E_ERR, E_MSG, nmlfileunit, do_nml_file, do_nml_term,     &
                                  open_file, close_file, timestamp
+
 use       sort_mod,       only : index_sort 
+
 use random_seq_mod,       only : random_seq_type, random_gaussian, init_random_seq,       &
                                  random_uniform
 
@@ -74,7 +79,6 @@
 
 public :: filter_assim, &
           set_assim_tools_trace, &
-          get_missing_ok_status, &
           test_state_copies, &
           update_ens_from_weights  ! Jeff thinks this routine is in the wild.
 
@@ -151,15 +155,6 @@
 logical  :: rectangular_quadrature          = .true.
 logical  :: gaussian_likelihood_tails       = .false.
 
-! Some models are allowed to have MISSING_R8 values in the DART state vector.
-! If they are encountered, it is not necessarily a FATAL error.
-! Most of the time, if a MISSING_R8 is encountered, DART should die.
-! CLM should have allow_missing_in_clm = .true.
-! maybe POP - but in POP the missing values are land and all ensemble members
-! have the same missing values.  CLM is different in that only some ensemble members may
-! have missing values and so we have a deficient ensemble size at those state locations.
-logical  :: allow_missing_in_clm = .false.
-
 ! False by default; if true, expect to read in an ascii table
 ! to adjust the impact of obs on other state vector and obs values.
 logical            :: adjust_obs_impact  = .false.
@@ -208,7 +203,7 @@
    print_every_nth_obs, rectangular_quadrature, gaussian_likelihood_tails, &
    output_localization_diagnostics, localization_diagnostics_file,         &
    special_localization_obs_types, special_localization_cutoffs,           &
-   allow_missing_in_clm, distribute_mean, close_obs_caching,               &
+   distribute_mean, close_obs_caching,                                     &
    adjust_obs_impact, obs_impact_filename, allow_any_impact_values,        &
    convert_all_state_verticals_first, convert_all_obs_verticals_first,     &
    lanai_bitwise ! don't document this one -- only used for regression tests
@@ -389,7 +384,7 @@
 type(time_type)      :: obs_time, this_obs_time
 
 logical :: do_adapt_inf_update
-logical :: missing_in_state
+logical :: missing_in_state, allow_missing_in_state
 ! for performance, local copies 
 logical :: local_single_ss_inflate
 logical :: local_varying_ss_inflate
@@ -412,7 +407,6 @@
 integer :: istatus 
 integer :: vstatus(obs_ens_handle%my_num_vars) !< for vertical conversion status.
 
-
 ! we are going to read/write the copies array
 call prepare_to_update_copies(ens_handle)
 call prepare_to_update_copies(obs_ens_handle)
@@ -597,6 +591,8 @@
    num_close_states_calls_made = 0
 endif
 
+allow_missing_in_state = get_missing_ok_status()