call assim_model_mod rather than model_mod directly for dart programs

Public model_mod routines through assim_mod_mod
model_mod_check use assim_mod_mod::interpolate

FIXMES fixed:
* nc_write_model_atts - was not going though assim_model_mod
* read_model_time in direct_netcdf_mod was not going though assim_model_mod

Left alone model specific programs, i.e. those in models directory and the two obs converters that use model info:
* create_identity_stream_flow_obs (models/wrf_hydro)
* convert_roms_obs (obs_converters/ROMS)

fixes #1056

Author: hkershaw-brown

assimilation_code/modules/assimilation/assim_model_mod.f90

@@ -26,7 +26,8 @@ module assim_model_mod
                           pert_model_copies, get_close_obs, get_close_state,       &
                           convert_vertical_obs, convert_vertical_state,            &
                           interpolate => model_interpolate,                        &
-                          read_model_time, write_model_time
+                          read_model_time, write_model_time, &
+                          nc_write_model_atts
 
 implicit none
 private
@@ -46,7 +47,8 @@ module assim_model_mod
           convert_vertical_obs, &
           convert_vertical_state, &
           read_model_time, &
-          write_model_time
+          write_model_time, &
+          nc_write_model_atts
 
 ! Ensure init code is called exactly once
 logical :: module_initialized = .false.

assimilation_code/modules/io/direct_netcdf_mod.f90

@@ -102,13 +102,10 @@ module direct_netcdf_mod
                                  netcdf_file_type, READ_COPY, WRITE_COPY, &
                                  noutput_state_variables
 
-use assim_model_mod,      only : get_model_size, read_model_time, write_model_time
-
-!>@todo FIXME : should move to assim_model_mod.f90
-use model_mod,            only : nc_write_model_atts
+use assim_model_mod,      only : get_model_size, read_model_time, write_model_time, &
+                                 nc_write_model_atts
 
 use typesizes
-
 use netcdf
 
 implicit none

assimilation_code/modules/io/state_vector_io_mod.f90

@@ -61,8 +61,7 @@ module state_vector_io_mod
                                  assert_restart_names_initialized, &
                                  single_file_initialized
 
-!>@todo FIXME This should go through assim_model_mod
-use model_mod,            only : read_model_time
+use assim_model_mod,            only : read_model_time
 
 use state_structure_mod,  only : get_num_domains
 

assimilation_code/programs/create_fixed_network_seq/create_fixed_network_seq.f90

@@ -16,7 +16,7 @@ program create_fixed_network_seq
                              get_copy_meta_data, get_qc_meta_data, set_qc_meta_data
 use time_manager_mod, only : time_type, set_time, interactive_time, &
                              operator(*), operator(+)
-use        model_mod, only : static_init_model
+use  assim_model_mod, only : static_init_assim_model
 
 implicit none
 
@@ -34,7 +34,7 @@ program create_fixed_network_seq
 call initialize_utilities('Create_fixed_network_seq')
 
 ! Call the underlying model's static initialization for calendar info
-call static_init_model()
+call static_init_assim_model()
 
 ! Initialize the obs_sequence module
 call static_init_obs_sequence

assimilation_code/programs/fill_inflation_restart/fill_inflation_restart.f90

@@ -36,7 +36,7 @@ program fill_inflation_restart
                                   get_restart_filename, set_file_metadata, &
                                   set_io_copy_flag, READ_COPY, WRITE_COPY
 
-use             model_mod, only : get_model_size
+use       assim_model_mod, only : get_model_size
 
 use     mpi_utilities_mod, only : initialize_mpi_utilities, finalize_mpi_utilities
 

assimilation_code/programs/model_mod_check/model_mod_check.f90

@@ -23,7 +23,8 @@ program model_mod_check
 
 use      obs_sequence_mod, only : static_init_obs_sequence
 
-use       assim_model_mod, only : static_init_assim_model
+use       assim_model_mod, only : static_init_assim_model, get_model_size, &
+                                  get_state_meta_data
 
 use      time_manager_mod, only : time_type, print_time, print_date, operator(-), &
                                   get_calendar_type, NO_CALENDAR
@@ -42,8 +43,6 @@ program model_mod_check
 
 use distributed_state_mod, only : create_state_window, free_state_window
 
-use             model_mod, only : get_model_size, get_state_meta_data
-
 use  test_interpolate_mod, only : test_interpolate_single, &
                                   test_interpolate_range, &
                                   find_closest_gridpoint

models/model_mod_tools/model_check_utilities_mod.f90

@@ -24,9 +24,9 @@ module model_check_utilities_mod
 
 use  ensemble_manager_mod, only : ensemble_type
 
-use             model_mod, only : get_model_size, &
+use       assim_model_mod, only : get_model_size, &
                                   get_state_meta_data, &
-                                  model_interpolate
+                                  interpolate
 
 implicit none
 private
@@ -83,7 +83,7 @@ function test_single_interpolation(ens_handle,       &
    write(*,'(A)') ''
 endif
 
-call model_interpolate(ens_handle, ens_size, location, quantity_index, interp_vals, ios_out)
+call interpolate(ens_handle, ens_size, location, quantity_index, interp_vals, ios_out)
 
 num_passed = 0
 do imem = 1, ens_size

models/model_mod_tools/test_interpolate_oned.f90

@@ -32,9 +32,9 @@ module test_interpolate_mod
                                       count_error_codes, &
                                       verify_consistent_istatus
 
-use             model_mod, only : get_model_size, &
+use       assim_model_mod, only : get_model_size, &
                                   get_state_meta_data, &
-                                  model_interpolate
+                                  interpolate
 
 use netcdf
 
@@ -141,7 +141,7 @@ function test_interpolate_range( ens_handle,            &
    X(i) = interp_test_xrange(1) + real(i-1,r8) * interp_test_dx
    loc  = set_location(X(i))
 
-   call model_interpolate(ens_handle, ens_size, loc, quantity_index, field(i,:), ios_out)
+   call interpolate(ens_handle, ens_size, loc, quantity_index, field(i,:), ios_out)
 
    call verify_consistent_istatus(ens_size, field(i,:), ios_out)
 

models/model_mod_tools/test_interpolate_threed_cartesian.f90

@@ -32,9 +32,9 @@ module test_interpolate_mod
                                       count_error_codes, &
                                       verify_consistent_istatus
 
-use             model_mod, only : get_model_size, &
+use       assim_model_mod, only : get_model_size, &
                                   get_state_meta_data, &
-                                  model_interpolate
+                                  interpolate
 
 use netcdf
 
@@ -145,7 +145,7 @@ function test_interpolate_range( ens_handle,            &
          Z(k) = interp_test_zrange(1) + real(k-1,r8) * interp_test_dz
          loc  = set_location(X(i), Y(j), Z(k))
 
-         call model_interpolate(ens_handle, ens_size, loc, quantity_index, &
+         call interpolate(ens_handle, ens_size, loc, quantity_index, &
                                 field(i,j,k,:), ios_out)
 
          call verify_consistent_istatus(ens_size, field(i,j,k,:), ios_out)

models/model_mod_tools/test_interpolate_threed_sphere.f90

@@ -34,9 +34,9 @@ module test_interpolate_mod
                                       count_error_codes, &
                                       verify_consistent_istatus
 
-use             model_mod, only : get_model_size, &
+use       assim_model_mod, only : get_model_size, &
                                   get_state_meta_data, &
-                                  model_interpolate
+                                  interpolate
 
 use netcdf
 
@@ -168,7 +168,7 @@ function test_interpolate_range( ens_handle,            &
          vert(kvert) = interp_test_vertrange(1) + real(kvert-1,r8) * interp_test_dvert
          loc = set_location(lon(ilon), lat(jlat), vert(kvert), vertcoord)
 
-         call model_interpolate(ens_handle, ens_size, loc, quantity_index, &
+         call interpolate(ens_handle, ens_size, loc, quantity_index, &
                                 field(ilon,jlat,kvert,:), ios_out)
 
          call verify_consistent_istatus(ens_size, field(ilon,jlat,kvert,:), ios_out)