Generalized subroutine to read the state variables from the namelist (get_state_variables)

developer_tests/namelist/test_get_state_variables.f90

@@ -0,0 +1,78 @@
+! DART software - Copyright UCAR. This open source software is provided
+! by UCAR, "as is", without charge, subject to all terms of use at
+! http://www.image.ucar.edu/DAReS/DART/DART_download
+
+program test_get_state_variables
+
+use        utilities_mod, only : find_namelist_in_file, check_namelist_read 
+use    mpi_utilities_mod, only : initialize_mpi_utilities, finalize_mpi_utilities
+use            types_mod, only : vtablenamelength, MISSING_R8
+use    default_model_mod, only : get_state_variables, state_var_type
+
+use test ! fortran-testanything
+
+implicit none
+
+integer :: iunit, io
+logical :: use_clamping
+type(state_var_type) :: state_vars, state_vars_clamp
+
+! DART state vector contents are specified in the input.nml:&model_nml namelist.
+integer, parameter :: MAX_STATE_VARIABLES = 20
+integer, parameter :: NUM_STATE_TABLE_COLUMNS = 3
+character(len=vtablenamelength) :: state_variables(MAX_STATE_VARIABLES * NUM_STATE_TABLE_COLUMNS ) = ' '
+
+namelist /model_nml_noclamp/  &
+   state_variables
+
+namelist /model_nml_clamp/  &
+   state_variables
+
+call initialize_mpi_utilities('test_get_state_variables')
+
+call plan(10)
+
+! Using namelist WITHOUT clamping values
+
+call find_namelist_in_file('input.nml', 'model_nml_noclamp', iunit)
+read(iunit, nml = model_nml_noclamp, iostat = io)
+call check_namelist_read(iunit, io, 'model_nml_noclamp')
+
+call get_state_variables(state_variables, MAX_STATE_VARIABLES, state_vars)
+
+write(*,*) 'state_vars%nvars: ', state_vars%nvars
+write(*,*) 'state_vars%netcdf_var_names: ', state_vars%netcdf_var_names
+write(*,*) 'state_vars%qtys: ', state_vars%qtys
+write(*,*) 'state_vars%updates: ', state_vars%updates
+
+call ok(state_vars%nvars == 5) !OK
+call ok(state_vars%netcdf_var_names(2) == '') !NOT OK
+call ok(state_vars%qtys(3) == 20) !NOT OK
+call ok(state_vars%updates(4) == .true.) !OK
+
+! Using namelist file WITH clamping values
+use_clamping = .true.
+
+call find_namelist_in_file('input.nml', 'model_nml_clamp', iunit)
+read(iunit, nml = model_nml_clamp, iostat = io)
+call check_namelist_read(iunit, io, 'model_nml_clamp')
+
+call get_state_variables(state_variables, MAX_STATE_VARIABLES, use_clamping, state_vars_clamp)
+
+write(*,*) 'state_vars%nvars: ', state_vars_clamp%nvars
+write(*,*) 'state_vars%netcdf_var_names: ', state_vars_clamp%netcdf_var_names
+write(*,*) 'state_vars%qtys: ', state_vars_clamp%qtys
+write(*,*) 'state_vars%clamp_values(:,1): ', state_vars_clamp%clamp_values(:, 1)
+write(*,*) 'state_vars%clamp_values(:,2): ', state_vars_clamp%clamp_values(:, 2)
+write(*,*) 'state_vars%updates: ', state_vars_clamp%updates
+
+call ok(state_vars_clamp%nvars == 7) !NOT OK
+call ok(state_vars_clamp%netcdf_var_names(2) == 'TEMP_CUR') !OK
+call ok(state_vars_clamp%qtys(3) == 356) !OK
+call ok(state_vars_clamp%clamp_values(1,1) == 99) !NOT OK
+call ok(state_vars_clamp%clamp_values(5,2) == 0.0) !OK
+call ok(state_vars_clamp%updates(4) == .false.) !NOT OK
+
+call finalize_mpi_utilities()
+
+end program test_get_state_variables

developer_tests/namelist/work/input.nml

@@ -0,0 +1,71 @@
+&model_nml_clamp
+    state_variables       = 'SALT_CUR ', 'QTY_SALINITY', '0.0', '0.0', 'UPDATE',
+                            'TEMP_CUR ', 'QTY_POTENTIAL_TEMPERATURE', '0.0', '0.0', 'UPDATE',
+                            'UVEL_CUR ', 'QTY_U_CURRENT_COMPONENT  ', '0.0', '0.0', 'UPDATE',
+                            'VVEL_CUR ', 'QTY_V_CURRENT_COMPONENT  ', '0.0', '0.0', 'UPDATE',
+                            'PSURF_CUR', 'QTY_SEA_SURFACE_PRESSURE ', '0.0', '0.0', 'UPDATE'
+  /
+
+&model_nml_noclamp
+    state_variables       = 'SALT_CUR ', 'QTY_SALINITY', 'UPDATE',
+                            'TEMP_CUR ', 'QTY_POTENTIAL_TEMPERATURE', 'UPDATE',
+                            'UVEL_CUR ', 'QTY_U_CURRENT_COMPONENT  ', 'UPDATE',
+                            'VVEL_CUR ', 'QTY_V_CURRENT_COMPONENT  ', 'UPDATE',
+                            'PSURF_CUR', 'QTY_SEA_SURFACE_PRESSURE ', 'UPDATE'
+  /
+
+&utilities_nml
+   module_details = .false.
+   write_nml = 'none'
+  /
+
+&preprocess_nml
+    input_obs_kind_mod_file = '../../../assimilation_code/modules/observations/DEFAULT_obs_kind_mod.F90'
+             quantity_files = '../../../assimilation_code/modules/observations/land_quantities_mod.f90',
+                              '../../../assimilation_code/modules/observations/default_quantities_mod.f90'
+                              '../../../assimilation_code/modules/observations/atmosphere_quantities_mod.f90'
+                              '../../../assimilation_code/modules/observations/ocean_quantities_mod.f90'
+   output_obs_kind_mod_file = '../../../assimilation_code/modules/observations/obs_kind_mod.f90'
+     input_obs_def_mod_file = '../../../observations/forward_operators/DEFAULT_obs_def_mod.F90'
+    output_obs_def_mod_file = '../../../observations/forward_operators/obs_def_mod.f90'
+                input_files = '../../../observations/forward_operators/obs_def_AIRS_mod.f90',
+                              '../../../observations/forward_operators/obs_def_AOD_mod.f90',
+                              '../../../observations/forward_operators/obs_def_AURA_mod.f90',
+                              '../../../observations/forward_operators/obs_def_COSMOS_mod.f90',
+                              '../../../observations/forward_operators/obs_def_CO_Nadir_mod.f90',
+                              '../../../observations/forward_operators/obs_def_GWD_mod.f90',
+                              '../../../observations/forward_operators/obs_def_QuikSCAT_mod.f90',
+                              '../../../observations/forward_operators/obs_def_SABER_mod.f90',
+                              '../../../observations/forward_operators/obs_def_altimeter_mod.f90',
+                              '../../../observations/forward_operators/obs_def_cloud_mod.f90',
+                              '../../../observations/forward_operators/obs_def_dew_point_mod.f90',
+                              '../../../observations/forward_operators/obs_def_dwl_mod.f90',
+                              '../../../observations/forward_operators/obs_def_eval_mod.f90',
+                              '../../../observations/forward_operators/obs_def_gps_mod.f90',
+                              '../../../observations/forward_operators/obs_def_gts_mod.f90',
+                              '../../../observations/forward_operators/obs_def_land_mod.f90',
+                              '../../../observations/forward_operators/obs_def_metar_mod.f90',
+                              '../../../observations/forward_operators/obs_def_ocean_mod.f90',
+                              '../../../observations/forward_operators/obs_def_pe2lyr_mod.f90',
+                              '../../../observations/forward_operators/obs_def_radar_mod.f90',
+                              '../../../observations/forward_operators/obs_def_reanalysis_bufr_mod.f90',
+                              '../../../observations/forward_operators/obs_def_rel_humidity_mod.f90',
+                              '../../../observations/forward_operators/obs_def_sqg_mod.f90',
+                              '../../../observations/forward_operators/obs_def_tower_mod.f90',
+                              '../../../observations/forward_operators/obs_def_tpw_mod.f90',
+                              '../../../observations/forward_operators/obs_def_upper_atm_mod.f90',
+                              '../../../observations/forward_operators/obs_def_vortex_mod.f90',
+                              '../../../observations/forward_operators/obs_def_wind_speed_mod.f90'
+  /
+
+&mpi_utilities_nml
+  /
+
+&obs_kind_nml
+  /
+
+&ensemble_manager_nml
+  /
+
+&state_vector_io_nml
+  /

developer_tests/namelist/work/quickbuild.sh

@@ -0,0 +1,43 @@
+#!/usr/bin/env bash
+
+# DART software - Copyright UCAR. This open source software is provided
+# by UCAR, "as is", without charge, subject to all terms of use at
+# http://www.image.ucar.edu/DAReS/DART/DART_download
+
+main() {
+
+export DART=$(git rev-parse --show-toplevel)
+source "$DART"/build_templates/buildfunctions.sh
+
+MODEL="none"
+EXTRA="$DART"/models/template/threed_model_mod.f90
+dev_test=1
+TEST="namelist"
+LOCATION="threed_sphere"
+
+programs=(
+test_get_state_variables
+)
+
+
+# quickbuild arguments
+arguments "$@"
+
+# clean the directory
+\rm -f -- *.o *.mod Makefile .cppdefs
+
+# build any NetCDF files from .cdl files
+cdl_to_netcdf
+
+# build and run preprocess before making any other DART executables
+buildpreprocess
+
+# build 
+buildit
+
+# clean up
+\rm -f -- *.o *.mod
+
+}
+
+main "$@"

models/MITgcm_ocean/model_mod.f90

@@ -43,7 +43,8 @@ module model_mod
 use random_seq_mod,        only : random_seq_type, init_random_seq, random_gaussian
 
 use default_model_mod,     only : nc_write_model_vars, adv_1step, &
-                                  init_conditions => fail_init_conditions
+                                  init_conditions => fail_init_conditions, &
+                                  get_state_variables, state_var_type
 
 use dart_time_io_mod,      only : write_model_time
 
@@ -127,6 +128,8 @@ module model_mod
 logical          :: calendarDumps       = .false.
 logical          :: pickupStrictlyMatch = .false.
 
+logical, parameter :: use_clamping = .true.
+
 NAMELIST /CAL_NML/ TheCalendar, startDate_1, startDate_2, calendarDumps
 
 ! FIXME: these namelists should probably be in a separate file, and only
@@ -285,7 +288,7 @@ module model_mod
 integer, parameter :: VT_STATEINDX    = 5 ! ... update (state) or not
 integer, parameter :: MAX_STATE_VARIABLES = 20
 integer, parameter :: NUM_STATE_TABLE_COLUMNS = 5
-character(len=vtablenamelength) :: mitgcm_variables(NUM_STATE_TABLE_COLUMNS, MAX_STATE_VARIABLES ) = ' '
+character(len=vtablenamelength) :: mitgcm_variables(NUM_STATE_TABLE_COLUMNS*MAX_STATE_VARIABLES ) = ' '
 
 character(len=256) :: model_shape_file = ' '
 integer  :: assimilation_period_days = 7
@@ -317,7 +320,6 @@ module model_mod
 end type MIT_meta_type
 
 integer :: domain_id
-integer :: nvars
 
 contains
 
@@ -330,10 +332,7 @@ module model_mod
 
 subroutine static_init_model()
 
-character(len=vtablenamelength) :: var_names(MAX_STATE_VARIABLES) = ' '
-integer  :: quantity_list(MAX_STATE_VARIABLES)   = MISSING_I
-real(r8) ::    clamp_vals(MAX_STATE_VARIABLES,2) = MISSING_R8
-logical  ::   update_list(MAX_STATE_VARIABLES)   = .FALSE.
+type(state_var_type) :: state_vars
 
 integer :: i, iunit, io
 integer :: ss, dd
@@ -533,11 +532,11 @@ subroutine static_init_model()
 if (do_output()) write(     *     , *) 'Using grid size : '
 if (do_output()) write(     *     , *) '  Nx, Ny, Nz = ', Nx, Ny, Nz
 
-call parse_variable_input(mitgcm_variables, model_shape_file, nvars, &
-                      var_names, quantity_list, clamp_vals, update_list)
+call get_state_variables(mitgcm_variables, MAX_STATE_VARIABLES, use_clamping, state_vars)
 
-domain_id = add_domain(model_shape_file, nvars, &
-                    var_names, quantity_list, clamp_vals, update_list )
+domain_id = add_domain(model_shape_file, state_vars%nvars, &
+                       state_vars%netcdf_var_names, state_vars%qtys, &
+                       state_vars%clamp_values, state_vars%updates)
 
 if (compress) then ! read in compressed coordinates
 
@@ -2050,91 +2049,6 @@ subroutine write_data_namelistfile
 end subroutine write_data_namelistfile
 
 
-!-----------------------------------------------------------------------
-!>
-!> Fill the array of requested variables, dart kinds, possible min/max
-!> values and whether or not to update the field in the output file.
-!>
-!>@param state_variables the list of variables and kinds from model_mod_nml
-!>@param ngood the number of variable/KIND pairs specified
-
-subroutine parse_variable_input(state_variables, filename, ngood, &
-                     var_names, quantity_list, clamp_vals, update_list)
-
-character(len=*), intent(in)  :: state_variables(:,:)
-character(len=*), intent(in)  :: filename
-integer,          intent(out) :: ngood
-character(len=*), intent(out) :: var_names(:)
-integer,          intent(out) :: quantity_list(:)
-real(r8),         intent(out) :: clamp_vals(:,:)
-logical,          intent(out) :: update_list(:)
-
-integer :: i
-character(len=NF90_MAX_NAME) :: varname
-character(len=NF90_MAX_NAME) :: dartstr
-character(len=NF90_MAX_NAME) :: minvalstring
-character(len=NF90_MAX_NAME) :: maxvalstring
-character(len=NF90_MAX_NAME) :: updateable
-
-ngood = 0
-MyLoop : do i = 1, MAX_STATE_VARIABLES
-
-   varname      = trim(state_variables(VT_VARNAMEINDX,i))
-   dartstr      = trim(state_variables(VT_KINDINDX   ,i))
-   minvalstring = trim(state_variables(VT_MINVALINDX ,i))
-   maxvalstring = trim(state_variables(VT_MAXVALINDX ,i))
-   updateable   = trim(state_variables(VT_STATEINDX  ,i))
-
-   if ( varname == ' ' .and. dartstr == ' ' ) exit MyLoop ! Found end of list.
-
-   if ( varname == ' ' .or. dartstr == ' ' ) then
-      string1 = 'model_nml:model "variables" not fully specified'
-      string2 = 'reading from "'//trim(filename)//'"'
-      call error_handler(E_ERR,'parse_variable_input:',string1,source,text2=string2)
-   endif
-
-   ! Make sure DART quantity is valid
-
-   if( get_index_for_quantity(dartstr) < 0 ) then
-      write(string1,'(''there is no quantity <'',a,''> in obs_kind_mod.f90'')') trim(dartstr)
-      call error_handler(E_ERR,'parse_variable_input:',string1,source)
-   endif
-
-   call to_upper(minvalstring)
-   call to_upper(maxvalstring)
-   call to_upper(updateable)
-
-   var_names(i)     = varname
-   quantity_list(i) = get_index_for_quantity(dartstr)
-   clamp_vals(i, 1) = string_to_real(minvalstring)
-   clamp_vals(i, 2) = string_to_real(maxvalstring)
-   update_list(i)   = string_to_logical(updateable, 'UPDATE')
-
-   ! Adjust clamping in case of log-transform
-   if (quantity_list(i) == QTY_NITRATE_CONCENTRATION     ) call adjust_clamp(clamp_vals(i, 1))
-   if (quantity_list(i) == QTY_PHOSPHATE_CONCENTRATION   ) call adjust_clamp(clamp_vals(i, 1))
-   if (quantity_list(i) == QTY_DISSOLVED_OXYGEN          ) call adjust_clamp(clamp_vals(i, 1))
-   if (quantity_list(i) == QTY_PHYTOPLANKTON_BIOMASS     ) call adjust_clamp(clamp_vals(i, 1))
-   if (quantity_list(i) == QTY_ALKALINITY                ) call adjust_clamp(clamp_vals(i, 1))
-   if (quantity_list(i) == QTY_DISSOLVED_INORGANIC_CARBON) call adjust_clamp(clamp_vals(i, 1))
-   if (quantity_list(i) == QTY_DISSOLVED_ORGANIC_P       ) call adjust_clamp(clamp_vals(i, 1))
-   if (quantity_list(i) == QTY_DISSOLVED_ORGANIC_NITROGEN) call adjust_clamp(clamp_vals(i, 1))
-   if (quantity_list(i) == QTY_DISSOLVED_INORGANIC_IRON  ) call adjust_clamp(clamp_vals(i, 1))
-   if (quantity_list(i) == QTY_SURFACE_CHLOROPHYLL       ) call adjust_clamp(clamp_vals(i, 1))
-
-   ngood = ngood + 1
-
-enddo MyLoop
-
-if (ngood == MAX_STATE_VARIABLES) then
-   string1 = 'WARNING: There is a possibility you need to increase ''MAX_STATE_VARIABLES'''
-   write(string2,'(''WARNING: you have specified at least '',i4,'' perhaps more.'')')ngood
-   call error_handler(E_MSG,'parse_variable_input:',string1,source,text2=string2)
-endif
-
-end subroutine parse_variable_input
-
-
 !-----------------------------------------------------------------------
 !>
 !> We may choose to do a log transformation for the bgc tracers