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

.gitignore

@@ -207,6 +207,7 @@ test_normal_dist
 test_beta_dist
 test_kde_dist
 test_window
+test_parse_variables
 
 # Directories to NOT IGNORE ... same as executable names
 # as far as I know, these must be listed after the executables

assimilation_code/modules/io/state_structure_mod.f90

@@ -68,6 +68,8 @@ module state_structure_mod
 
 use      sort_mod, only : index_sort
 
+use default_model_mod, only : state_var_type
+
 use netcdf
 
 implicit none
@@ -281,6 +283,7 @@ module state_structure_mod
    module procedure add_domain_blank
    module procedure add_domain_from_file
    module procedure add_domain_from_spec
+   module procedure add_domain_from_state_type
 end interface
 
 interface get_index_start
@@ -313,8 +316,6 @@ module state_structure_mod
 !> into the state_strucutre. 
 !>
 !> Returns a dom_id that can be used to harvest information of a particular domain
-!>
-!> Does this need to be a function or a subroutine?
 
 
 function add_domain_from_file(info_file, num_vars, var_names, kind_list, clamp_vals, update_list) result(dom_id)
@@ -365,6 +366,58 @@ function add_domain_from_file(info_file, num_vars, var_names, kind_list, clamp_v
 end function add_domain_from_file
 
 
+!-------------------------------------------------------------------------------
+!> Given an info_file, reads in a state_var_type including nvars, netcdf
+!> variable names, qtys (kinds), clamp values (optional), and updates into the
+!> state_structure
+!>
+!> Returns a dom_id that can be used to harvest information of a particular domain
+
+
+function add_domain_from_state_type(info_file, vars) result(dom_id)
+
+character(len=*), intent(in) :: info_file
+type(state_var_type), intent(in) :: vars
+integer :: dom_id
+
+integer :: ivar
+
+! add to domains
+call assert_below_max_num_domains('add_domain_from_state_type')
+state%num_domains = state%num_domains + 1
+!>@todo dom_id should be a handle.
+dom_id = state%num_domains
+
+! save information about the information file
+state%domain(dom_id)%info_file = info_file
+state%domain(dom_id)%method = 'file'
+
+! set number of variables in this domain
+state%domain(dom_id)%num_variables = vars%nvars
+
+! load up the variable names
+allocate(state%domain(dom_id)%variable(vars%nvars))
+
+do ivar = 1, vars%nvars
+   state%domain(dom_id)%variable(ivar)%varname = vars%netcdf_var_names(ivar)
+enddo
+
+! load up variable id's and sizes
+call load_state_variable_info(state%domain(dom_id),dom_id)
+
+! load up the domain unique dimension info
+call load_unique_dim_info(dom_id)
+
+! load up any cf-conventions if they exist
+call load_common_cf_conventions(state%domain(dom_id))
+
+call set_dart_kinds(dom_id, vars%nvars, vars%qtys)
+if (allocated(vars%clamp_values)) call set_clamping(dom_id, vars%nvars, vars%clamp_values)
+call set_update_list(dom_id, vars%nvars, vars%updates)
+
+end function add_domain_from_state_type
+
+
 !-------------------------------------------------------------------------------
 !> Defines a skeleton structure for the state structure.  Dimension can be
 !> added to variables with add_dimension_to_variable.

developer_tests/namelist/test_parse_variables.f90

@@ -0,0 +1,85 @@
+! 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_parse_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, r8
+use    default_model_mod, only : parse_variables_clamp, parse_variables, &
+                                 state_var_type, &
+                                 MAX_STATE_VARIABLE_FIELDS_CLAMP, &
+                                 MAX_STATE_VARIABLE_FIELDS
+use         obs_kind_mod, only : QTY_SALINITY, QTY_POTENTIAL_TEMPERATURE, &
+                                 QTY_U_CURRENT_COMPONENT
+
+use test ! fortran-testanything
+
+implicit none
+
+integer :: iunit, io
+type(state_var_type) :: state_vars, state_vars_clamp
+
+character(len=vtablenamelength) :: state_variables(MAX_STATE_VARIABLE_FIELDS) = ' '
+character(len=vtablenamelength) :: state_variables_clamp(MAX_STATE_VARIABLE_FIELDS_CLAMP) = ' '
+
+namelist /model_nml/  &
+   state_variables
+
+namelist /model_nml_clamp/  &
+   state_variables_clamp
+
+call initialize_mpi_utilities('test_parse_variables')
+
+call plan(28)
+
+! Using namelist entry WITHOUT clamping values
+
+call find_namelist_in_file('input.nml', 'model_nml', iunit)
+read(iunit, nml = model_nml, iostat = io)
+call check_namelist_read(iunit, io, 'model_nml')
+
+state_vars = parse_variables(state_variables)
+
+call ok(state_vars%nvars == 3)
+call ok(state_vars%netcdf_var_names(1) == 'SALT_CUR')
+call ok(state_vars%netcdf_var_names(2) == 'TEMP_CUR')
+call ok(state_vars%netcdf_var_names(3) == 'UVEL_CUR')
+call ok(state_vars%qtys(1) == QTY_SALINITY)
+call ok(state_vars%qtys(2) == QTY_POTENTIAL_TEMPERATURE)
+call ok(state_vars%qtys(3) == QTY_U_CURRENT_COMPONENT)
+call ok(allocated(state_vars_clamp%clamp_values) .eqv. .false.)
+call ok(state_vars%updates(1) .eqv. .true.)
+call ok(state_vars%updates(2) .eqv. .false.)
+call ok(state_vars%updates(3) .eqv. .true.)
+
+! Using namelist entry WITH clamping values
+
+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')
+
+state_vars_clamp = parse_variables_clamp(state_variables_clamp)
+
+call ok(state_vars_clamp%nvars == 3)
+call ok(state_vars_clamp%netcdf_var_names(1) == 'SALT_CUR')
+call ok(state_vars_clamp%netcdf_var_names(2) == 'TEMP_CUR')
+call ok(state_vars_clamp%netcdf_var_names(3) == 'UVEL_CUR')
+call ok(state_vars_clamp%qtys(1) == QTY_SALINITY)
+call ok(state_vars_clamp%qtys(2) == QTY_POTENTIAL_TEMPERATURE)
+call ok(state_vars_clamp%qtys(3) == QTY_U_CURRENT_COMPONENT)
+call ok(allocated(state_vars_clamp%clamp_values) .eqv. .true.)
+call ok(state_vars_clamp%clamp_values(1,1) == 0.0_r8)
+call ok(state_vars_clamp%clamp_values(1,2) == 0.0_r8)
+call ok(state_vars_clamp%clamp_values(2,1) == 0.0_r8)
+call ok(state_vars_clamp%clamp_values(2,2) == 0.0_r8)
+call ok(state_vars_clamp%clamp_values(3,1) == 0.0_r8)
+call ok(state_vars_clamp%clamp_values(3,2) == 0.0_r8)
+call ok(state_vars_clamp%updates(1) .eqv. .true.)
+call ok(state_vars_clamp%updates(2) .eqv. .false.)
+call ok(state_vars_clamp%updates(3) .eqv. .true.)
+
+call finalize_mpi_utilities()
+
+end program test_parse_variables

developer_tests/namelist/work/input.nml

@@ -0,0 +1,67 @@
+&model_nml_clamp
+    state_variables_clamp = 'SALT_CUR ', 'QTY_SALINITY', '0.0', '0.0', 'UPDATE',
+                            'TEMP_CUR ', 'QTY_POTENTIAL_TEMPERATURE', '0.0', '0.0', 'NO_COPY_BACK',
+                            'UVEL_CUR ', 'QTY_U_CURRENT_COMPONENT  ', '0', '0.0', 'UPDATE',
+  /
+
+&model_nml
+    state_variables = 'SALT_CUR ', 'QTY_SALINITY', 'UPDATE',
+                      'TEMP_CUR ', 'QTY_POTENTIAL_TEMPERATURE', 'NO_COPY_BACK',
+                      'UVEL_CUR ', 'QTY_U_CURRENT_COMPONENT  ', '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="$DART"/models/template/threed_model_mod.f90
+dev_test=1
+TEST="namelist"
+LOCATION="threed_sphere"
+
+programs=(
+test_parse_variables
+)
+
+
+# quickbuild arguments
+arguments "$@"
+
+# 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 "$@"