diff --git a/README.md b/README.md index 6bdb62b..c6489ac 100644 --- a/README.md +++ b/README.md @@ -57,7 +57,7 @@ state : date: # ISO8601 datetime state variables: # list of the model state variables matching the `name` field above nemo field file: # input background data - variance field file: # input error data + nemo error field file: # input error data ``` ## Help diff --git a/examples/hofx3d_nc_orca1_checker_ice_mpi.yaml b/examples/hofx3d_nc_orca1_checker_ice_mpi.yaml index 5dd403b..2ee7513 100644 --- a/examples/hofx3d_nc_orca1_checker_ice_mpi.yaml +++ b/examples/hofx3d_nc_orca1_checker_ice_mpi.yaml @@ -15,7 +15,7 @@ state : date: 2021-06-29T12:00:00Z state variables: [ ice_area_fraction ] nemo field file: your_example_data/orca1_sic.nc - variance field file: your_example_data/orca1_sic_err.nc + nemo error field file: your_example_data/orca1_sic_err.nc observations: observers: - obs space: diff --git a/examples/hofx3d_odb_prof_example.yaml b/examples/hofx3d_odb_prof_example.yaml index efed5d3..0f1435f 100644 --- a/examples/hofx3d_odb_prof_example.yaml +++ b/examples/hofx3d_odb_prof_example.yaml @@ -11,14 +11,14 @@ geometry : - name: sea_water_temperature_background_error nemo field name: t_tot_var model space: volume - variable type: background variance + variable type: background error variance grid name: eORCA12_T number levels: 75 state : date: 2021-08-21T00:00:00Z state variables: [ sea_water_temperature, sea_water_temperature_background_error, depth ] nemo field file: your_example_data/eorca12_20210630.nc - variance field file: your_example_data/eorca12_err_20210630.nc + nemo error field file: your_example_data/eorca12_err_20210630.nc time window: begin: 2021-08-20T00:00:00Z length: P2D diff --git a/examples/hofx_nc_ice_mpi.yaml b/examples/hofx_nc_ice_mpi.yaml index dee39bc..99173ec 100644 --- a/examples/hofx_nc_ice_mpi.yaml +++ b/examples/hofx_nc_ice_mpi.yaml @@ -15,7 +15,7 @@ geometry: - name: ice_area_fraction_background_error nemo field name: seaice_tot_var model space: surface - variable type: background variance + variable type: background error variance grid name: eORCA12_T source mesh halo: 0 number levels: 2 @@ -24,7 +24,7 @@ initial condition : date: 2021-06-28T23:00:00Z state variables: [ ice_area_fraction, ice_area_fraction_background_error ] nemo field file: your_example_data/eorca12_20210630.nc - variance field file: your_example_data/eorca12_err_20210630.nc + nemo error field file: your_example_data/eorca12_err_20210630.nc model : name: PseudoModel tstep: P1D @@ -32,15 +32,15 @@ model : states: - date: 2021-06-28T23:00:00Z nemo field file: your_example_data/eorca12_20210630.nc - variance field file: your_example_data/eorca12_err_20210630.nc + nemo error field file: your_example_data/eorca12_err_20210630.nc state variables: [ ice_area_fraction ] - date: 2021-06-29T23:00:00Z nemo field file: your_example_data/eorca12_20210630.nc - variance field file: your_example_data/eorca12_err_20210630.nc + nemo error field file: your_example_data/eorca12_err_20210630.nc state variables: [ ice_area_fraction ] - date: 2021-07-01T23:00:00Z nemo field file: your_example_data/eorca12_20210630.nc - variance field file: your_example_data/eorca12_err_20210630.nc + nemo error field file: your_example_data/eorca12_err_20210630.nc state variables: [ ice_area_fraction ] observations: observers: diff --git a/src/orca-jedi/geometry/Geometry.cc b/src/orca-jedi/geometry/Geometry.cc index c939e5c..bcc027a 100644 --- a/src/orca-jedi/geometry/Geometry.cc +++ b/src/orca-jedi/geometry/Geometry.cc @@ -226,7 +226,7 @@ const oops::Variables & Geometry::variables() const { } /// \brief Check if a variable's data is a member of a type (e.g if it can be -/// sourced from the background file, variance file, or MDT file). +/// sourced from the background file, error file, or MDT file). /// \param[in] variable_name Name of variable. /// \param[in] variable_type Type of variable. /// \return Boolean for membership. diff --git a/src/orca-jedi/geometry/GeometryParameters.h b/src/orca-jedi/geometry/GeometryParameters.h index b845c33..10d4508 100644 --- a/src/orca-jedi/geometry/GeometryParameters.h +++ b/src/orca-jedi/geometry/GeometryParameters.h @@ -26,7 +26,9 @@ class NemoFieldParameters : public oops::Parameters { oops::RequiredParameter nemoName {"nemo field name", this}; oops::RequiredParameter modelSpace {"model space", this}; oops::Parameter variableType {"variable type", - "type of variable (default is 'background' other option is 'background variance')", + "type of variable (default is 'background' other options are 'background error variance' and" + "'background error standard deviation' both are included for clarity, but both variables are" + " read from the error file", "background", this}; oops::Parameter fieldPrecision{"field precision", diff --git a/src/orca-jedi/state/State.cc b/src/orca-jedi/state/State.cc index 9334079..bd359a8 100644 --- a/src/orca-jedi/state/State.cc +++ b/src/orca-jedi/state/State.cc @@ -82,8 +82,10 @@ State::State(const Geometry & geom, nemo_file_name = params.nemoFieldFile.value(); readFieldsFromFile(nemo_file_name, *geom_, validTime(), "background", stateFields_); - nemo_file_name = params.varianceFieldFile.value().value_or(""); - readFieldsFromFile(nemo_file_name, *geom_, validTime(), "background variance", + nemo_file_name = params.errorFieldFile.value().value_or(""); + readFieldsFromFile(nemo_file_name, *geom_, validTime(), "background error standard deviation", + stateFields_); + readFieldsFromFile(nemo_file_name, *geom_, validTime(), "background error variance", stateFields_); } geom_->log_status(); diff --git a/src/orca-jedi/state/StateParameters.h b/src/orca-jedi/state/StateParameters.h index fe99117..f7b9057 100644 --- a/src/orca-jedi/state/StateParameters.h +++ b/src/orca-jedi/state/StateParameters.h @@ -22,8 +22,8 @@ class OrcaStateParameters : public oops::Parameters { public: oops::RequiredParameter nemoFieldFile{"nemo field file", this}; - oops::OptionalParameter varianceFieldFile{ - "variance field file", "", this}; + oops::OptionalParameter errorFieldFile{ + "nemo error field file", "", this}; oops::OptionalParameter analyticInit{"analytic initialisation", this}; oops::OptionalParameter outputNemoFieldFile{ "output nemo field file", "", this}; diff --git a/src/tests/orca-jedi/test_geometry.cc b/src/tests/orca-jedi/test_geometry.cc index 96c6da7..4a766e4 100644 --- a/src/tests/orca-jedi/test_geometry.cc +++ b/src/tests/orca-jedi/test_geometry.cc @@ -32,7 +32,7 @@ CASE("test basic geometry") { nemo_var_mappings[1].set("name", "sea_ice_area_fraction_error") .set("nemo field name", "sic_tot_var") .set("model space", "surface") - .set("variable type", "background variance"); + .set("variable type", "background error variance"); nemo_var_mappings[2].set("name", "sea_surface_foundation_temperature") .set("nemo field name", "votemper") .set("model space", "surface"); @@ -52,11 +52,11 @@ CASE("test basic geometry") { EXPECT(geometry.variable_in_variable_type("sea_ice_area_fraction", "background")); EXPECT(geometry.variable_in_variable_type("sea_ice_area_fraction_error", - "background variance")); + "background error variance")); EXPECT(!geometry.variable_in_variable_type("sea_ice_area_fraction_error", "background")); EXPECT(!geometry.variable_in_variable_type("sea_ice_area_fraction", - "background variance")); + "background error variance")); } SECTION("test geometry variable sizes") { diff --git a/src/tests/orca-jedi/test_interpolator.cc b/src/tests/orca-jedi/test_interpolator.cc index da32462..d99c593 100644 --- a/src/tests/orca-jedi/test_interpolator.cc +++ b/src/tests/orca-jedi/test_interpolator.cc @@ -65,7 +65,7 @@ CASE("test interpolator") { nemo_var_mappings[1].set("name", "sea_ice_area_fraction_error") .set("nemo field name", "sic_tot_var") .set("model space", "surface") - .set("variable type", "background variance"); + .set("variable type", "background error variance"); nemo_var_mappings[2].set("name", "sea_surface_foundation_temperature") .set("nemo field name", "votemper") .set("model space", "surface"); @@ -85,7 +85,7 @@ CASE("test interpolator") { settings_map["ORCA2_T"].state_config.set("state variables", state_variables); settings_map["ORCA2_T"].state_config.set("date", "2021-06-30T00:00:00Z"); settings_map["ORCA2_T"].state_config.set("nemo field file", "../Data/orca2_t_nemo.nc"); - settings_map["ORCA2_T"].state_config.set("variance field file", "../Data/orca2_t_bkg_var.nc"); + settings_map["ORCA2_T"].state_config.set("nemo error field file", "../Data/orca2_t_bkg_var.nc"); settings_map["ORCA2_T"].lons = std::vector{0, 120, 270}; settings_map["ORCA2_T"].lats = std::vector{88, 0, 30}; @@ -135,7 +135,7 @@ CASE("test interpolator") { settings_map["AMM1"].state_config.set("state variables", state_variables); settings_map["AMM1"].state_config.set("date", "2021-06-30T00:00:00Z"); settings_map["AMM1"].state_config.set("nemo field file", "../Data/amm1_nemo.nc"); - settings_map["AMM1"].state_config.set("variance field file", "../Data/amm1_nemo.nc"); + settings_map["AMM1"].state_config.set("nemo error field file", "../Data/amm1_nemo.nc"); settings_map["AMM1"].lons = std::vector{-17.5, -6.78, -16.1}; settings_map["AMM1"].lats = std::vector{58.16, 58.91, 63.55}; diff --git a/src/tests/orca-jedi/test_interpolator_parallel.cc b/src/tests/orca-jedi/test_interpolator_parallel.cc index 8a336f4..069323f 100644 --- a/src/tests/orca-jedi/test_interpolator_parallel.cc +++ b/src/tests/orca-jedi/test_interpolator_parallel.cc @@ -47,7 +47,7 @@ CASE("test serial interpolator") { nemo_var_mappings[1].set("name", "sea_surface_height_anomaly_error") .set("nemo field name", "ssh_tot_std") .set("model space", "surface") - .set("variable type", "background variance"); + .set("variable type", "background error standard deviation"); nemo_var_mappings[2].set("name", "sea_surface_foundation_temperature") .set("nemo field name", "votemper") .set("model space", "surface"); @@ -103,7 +103,7 @@ CASE("test serial interpolator") { state_config.set("date", "2021-06-30T00:00:00Z"); state_config.set("analytic initialisation", true); state_config.set("nemo field file", "../Data/orca2_t_nemo.nc"); - state_config.set("variance field file", "../Data/orca2_t_bkg_var.nc"); + state_config.set("nemo error field file", "../Data/orca2_t_bkg_var.nc"); OrcaStateParameters stateParams; stateParams.validateAndDeserialize(state_config); State state(geometry, stateParams); @@ -194,7 +194,7 @@ CASE("test checkerboard interpolator") { nemo_var_mappings[1].set("name", "sea_surface_height_anomaly_error") .set("nemo field name", "ssh_tot_std") .set("model space", "surface") - .set("variable type", "background variance"); + .set("variable type", "background error standard deviation"); nemo_var_mappings[2].set("name", "sea_surface_foundation_temperature") .set("nemo field name", "votemper") .set("model space", "surface"); @@ -249,7 +249,7 @@ CASE("test checkerboard interpolator") { state_config.set("date", "2021-06-30T00:00:00Z"); state_config.set("analytic initialisation", true); state_config.set("nemo field file", "../Data/orca2_t_nemo.nc"); - state_config.set("variance field file", "../Data/orca2_t_bkg_var.nc"); + state_config.set("nemo error field file", "../Data/orca2_t_bkg_var.nc"); OrcaStateParameters stateParams; stateParams.validateAndDeserialize(state_config); State state(geometry, stateParams); diff --git a/src/tests/orca-jedi/test_state.cc b/src/tests/orca-jedi/test_state.cc index afd3217..da65300 100644 --- a/src/tests/orca-jedi/test_state.cc +++ b/src/tests/orca-jedi/test_state.cc @@ -39,7 +39,7 @@ CASE("test basic state") { .set("field precision", "double") .set("nemo field name", "sic_tot_var") .set("model space", "surface") - .set("variable type", "background variance"); + .set("variable type", "background error variance"); nemo_var_mappings[2].set("name", "sea_surface_foundation_temperature") .set("field precision", "double") .set("nemo field name", "votemper") @@ -61,12 +61,12 @@ CASE("test basic state") { SECTION("test state parameters") { state_config.set("nemo field file", "../Data/orca2_t_nemo.nc"); - state_config.set("variance field file", "../Data/orca2_t_bkg_var.nc"); + state_config.set("nemo error field file", "../Data/orca2_t_bkg_var.nc"); params.validateAndDeserialize(state_config); EXPECT(params.nemoFieldFile.value() == state_config.getString("nemo field file")); - EXPECT(params.varianceFieldFile.value() == - state_config.getString("variance field file")); + EXPECT(params.errorFieldFile.value() == + state_config.getString("nemo error field file")); EXPECT(params.analyticInit.value().value_or(true)); auto datetime = static_cast(state_config.getString("date")); EXPECT(params.date.value() == datetime); @@ -105,7 +105,7 @@ CASE("test basic state") { } state_config.set("nemo field file", "../Data/orca2_t_nemo.nc"); - state_config.set("variance field file", "../Data/orca2_t_bkg_var.nc"); + state_config.set("nemo error field file", "../Data/orca2_t_bkg_var.nc"); state_config.set("output nemo field file", "../testoutput/orca2_t_output.nc"); params.validateAndDeserialize(state_config); State state(geometry, params); diff --git a/src/tests/testinput/hofx3d_nc_potm.yaml b/src/tests/testinput/hofx3d_nc_potm.yaml index 62bff77..53c6848 100644 --- a/src/tests/testinput/hofx3d_nc_potm.yaml +++ b/src/tests/testinput/hofx3d_nc_potm.yaml @@ -11,14 +11,14 @@ geometry : - name: sea_water_potential_temperature_background_error nemo field name: t_tot_var model space: volume - variable type: background variance + variable type: background error variance grid name: ORCA2_T number levels: 3 state : date: 2021-06-30T00:00:00Z state variables: [ sea_water_potential_temperature, sea_water_potential_temperature_background_error, depth ] nemo field file: Data/orca2_t_nemo.nc - variance field file: Data/orca2_t_bkg_var.nc + nemo error field file: Data/orca2_t_bkg_var.nc time window: begin: 2021-06-29T12:00:00Z length: P1D diff --git a/src/tests/testinput/hofx3d_nc_prof_2vars.yaml b/src/tests/testinput/hofx3d_nc_prof_2vars.yaml index 48b8ced..1086655 100644 --- a/src/tests/testinput/hofx3d_nc_prof_2vars.yaml +++ b/src/tests/testinput/hofx3d_nc_prof_2vars.yaml @@ -11,14 +11,14 @@ geometry : - name: sea_water_potential_temperature_background_error nemo field name: t_tot_var model space: volume - variable type: background variance + variable type: background error variance - name: salinity nemo field name: vosaline model space: volume - name: salinity_background_error nemo field name: t_tot_var model space: volume - variable type: background variance + variable type: background error variance grid name: ORCA2_T number levels: 3 state : @@ -30,7 +30,7 @@ state : - salinity - salinity_background_error nemo field file: Data/orca2_t_nemo.nc - variance field file: Data/orca2_t_bkg_var.nc + nemo error field file: Data/orca2_t_bkg_var.nc time window: begin: 2021-06-29T12:00:00Z length: P1D diff --git a/src/tests/testinput/hofx3d_nc_sic.yaml b/src/tests/testinput/hofx3d_nc_sic.yaml index 70bfd8f..2d99c0b 100644 --- a/src/tests/testinput/hofx3d_nc_sic.yaml +++ b/src/tests/testinput/hofx3d_nc_sic.yaml @@ -14,14 +14,14 @@ geometry : - name: ice_area_fraction_background_error nemo field name: sic_tot_var model space: surface - variable type: background variance + variable type: background error variance grid name: ORCA2_T number levels: 10 state : date: 2021-06-30T00:00:00Z state variables: [ ice_area_fraction, ice_area_fraction_background_error ] nemo field file: Data/orca2_t_nemo.nc - variance field file: Data/orca2_t_bkg_var.nc + nemo error field file: Data/orca2_t_bkg_var.nc time window: begin: 2021-06-29T12:00:00Z length: P1D diff --git a/src/tests/testinput/hofx3d_nc_ssh_amm1.yaml b/src/tests/testinput/hofx3d_nc_ssh_amm1.yaml index 783278f..633e1f6 100644 --- a/src/tests/testinput/hofx3d_nc_ssh_amm1.yaml +++ b/src/tests/testinput/hofx3d_nc_ssh_amm1.yaml @@ -11,7 +11,7 @@ geometry : - name: sea_surface_height_anomaly_background_error nemo field name: sossheig model space: surface - variable type: background variance + variable type: background error standard deviation grid name: Data/amm1_atlas_grid_spec.yaml number levels: 1 partitioner: serial @@ -22,7 +22,7 @@ state : - sea_surface_height_anomaly - sea_surface_height_anomaly_background_error nemo field file: &field_file Data/amm1_nemo.nc - variance field file: *field_file + nemo error field file: *field_file observations: observers: - obs space: diff --git a/src/tests/testinput/hofx3d_nc_ssh_amm1r.yaml b/src/tests/testinput/hofx3d_nc_ssh_amm1r.yaml index fd60b3c..301eaa7 100644 --- a/src/tests/testinput/hofx3d_nc_ssh_amm1r.yaml +++ b/src/tests/testinput/hofx3d_nc_ssh_amm1r.yaml @@ -11,7 +11,7 @@ geometry : - name: sea_surface_height_anomaly_background_error nemo field name: sossheig model space: surface - variable type: background variance + variable type: background error variance grid name: Data/amm1r_atlas_grid_spec.yaml number levels: 1 partitioner: serial @@ -22,7 +22,7 @@ state : - sea_surface_height_anomaly - sea_surface_height_anomaly_background_error nemo field file: &field_file Data/amm1r_nemo.nc - variance field file: *field_file + nemo error field file: *field_file observations: observers: - obs space: diff --git a/src/tests/testinput/hofx3d_nc_sst.yaml b/src/tests/testinput/hofx3d_nc_sst.yaml index fa05dfe..85b32f0 100644 --- a/src/tests/testinput/hofx3d_nc_sst.yaml +++ b/src/tests/testinput/hofx3d_nc_sst.yaml @@ -11,18 +11,18 @@ geometry : - name: ice_area_fraction_background_error nemo field name: sic_tot_var model space: surface - variable type: background variance + variable type: background error variance - name: sea_surface_temperature_background_error nemo field name: t_tot_var model space: surface - variable type: background variance + variable type: background error variance grid name: ORCA2_T number levels: 1 state : date: 2021-06-30T00:00:00Z state variables: [ sea_surface_temperature, sea_surface_temperature_background_error ] nemo field file: Data/orca2_t_nemo.nc - variance field file: Data/orca2_t_bkg_var.nc + nemo error field file: Data/orca2_t_bkg_var.nc time window: begin: 2021-06-29T12:00:00Z length: P1D diff --git a/src/tests/testinput/hofx_nc_potm_amm1r.yaml b/src/tests/testinput/hofx_nc_potm_amm1r.yaml index 87a9204..391f690 100644 --- a/src/tests/testinput/hofx_nc_potm_amm1r.yaml +++ b/src/tests/testinput/hofx_nc_potm_amm1r.yaml @@ -15,7 +15,7 @@ geometry : - name: sea_water_potential_temperature_background_error nemo field name: vosaline model space: volume - variable type: background variance + variable type: background error variance grid name: Data/amm1r_atlas_grid_spec.yaml number levels: 1 partitioner: serial @@ -26,18 +26,18 @@ initial condition : - sea_water_potential_temperature - sea_water_potential_temperature_background_error nemo field file: &field_file Data/amm1r_nemo.nc - variance field file: *field_file + nemo error field file: *field_file model : name: PseudoModel tstep: P1D states: - date: 2021-06-29T23:00:00Z nemo field file: *field_file - variance field file: *field_file + nemo error field file: *field_file state variables: *state_variables - date: 2021-06-30T23:00:00Z nemo field file: *field_file - variance field file: *field_file + nemo error field file: *field_file state variables: *state_variables observations: observers: diff --git a/src/tests/testinput/hofx_nc_sic.yaml b/src/tests/testinput/hofx_nc_sic.yaml index f4cbbe7..c12b5bd 100644 --- a/src/tests/testinput/hofx_nc_sic.yaml +++ b/src/tests/testinput/hofx_nc_sic.yaml @@ -18,7 +18,7 @@ geometry: - name: ice_area_fraction_background_error nemo field name: sic_tot_var model space: surface - variable type: background variance + variable type: background error variance grid name: ORCA2_T number levels: 2 initial condition : @@ -26,18 +26,18 @@ initial condition : state variables: [ ice_area_fraction, ice_area_fraction_background_error ] #analytic_init: zeroed state nemo field file: Data/orca2_t_nemo.nc - variance field file: Data/orca2_t_bkg_var.nc + nemo error field file: Data/orca2_t_bkg_var.nc model : name: PseudoModel tstep: P1D states: - date: 2021-06-29T23:00:00Z nemo field file: Data/orca2_t_nemo.nc - variance field file: Data/orca2_t_bkg_var.nc + nemo error field file: Data/orca2_t_bkg_var.nc state variables: [ ice_area_fraction ] - date: 2021-06-30T23:00:00Z nemo field file: Data/orca2_t_nemo.nc - variance field file: Data/orca2_t_bkg_var.nc + nemo error field file: Data/orca2_t_bkg_var.nc state variables: [ ice_area_fraction ] observations: observers: diff --git a/src/tests/testinput/hofx_nc_ssh.yaml b/src/tests/testinput/hofx_nc_ssh.yaml index 8c3c480..9714489 100644 --- a/src/tests/testinput/hofx_nc_ssh.yaml +++ b/src/tests/testinput/hofx_nc_ssh.yaml @@ -12,7 +12,7 @@ geometry : - name: sea_surface_height_anomaly_background_error nemo field name: ssh_tot_std model space: surface - variable type: background variance + variable type: background error standard deviation grid name: ORCA2_T number levels: 1 partitioner: serial @@ -22,18 +22,18 @@ initial condition : - sea_surface_height_anomaly - sea_surface_height_anomaly_background_error nemo field file: Data/orca2_t_nemo.nc - variance field file: Data/orca2_t_bkg_var.nc + nemo error field file: Data/orca2_t_bkg_var.nc model : name: PseudoModel tstep: P1D states: - date: 2021-06-29T23:00:00Z nemo field file: Data/orca2_t_nemo.nc - variance field file: Data/orca2_t_bkg_var.nc + nemo error field file: Data/orca2_t_bkg_var.nc state variables: &state_variables [ sea_surface_height_anomaly ] - date: 2021-06-30T23:00:00Z nemo field file: Data/orca2_t_nemo.nc - variance field file: Data/orca2_t_bkg_var.nc + nemo error field file: Data/orca2_t_bkg_var.nc state variables: *state_variables observations: observers: diff --git a/src/tests/testinput/hofx_nc_ssh_amm1.yaml b/src/tests/testinput/hofx_nc_ssh_amm1.yaml index 10f3d01..1008ad4 100644 --- a/src/tests/testinput/hofx_nc_ssh_amm1.yaml +++ b/src/tests/testinput/hofx_nc_ssh_amm1.yaml @@ -12,7 +12,7 @@ geometry : - name: sea_surface_height_anomaly_background_error nemo field name: sossheig model space: surface - variable type: background variance + variable type: background error standard deviation grid name: Data/amm1_atlas_grid_spec.yaml number levels: 1 partitioner: serial @@ -23,18 +23,18 @@ initial condition : - sea_surface_height_anomaly - sea_surface_height_anomaly_background_error nemo field file: &field_file Data/amm1_nemo.nc - variance field file: *field_file + nemo error field file: *field_file model : name: PseudoModel tstep: P1D states: - date: 2021-06-29T23:00:00Z nemo field file: *field_file - variance field file: *field_file + nemo error field file: *field_file state variables: &state_variables [ sea_surface_height_anomaly ] - date: 2021-06-30T23:00:00Z nemo field file: *field_file - variance field file: *field_file + nemo error field file: *field_file state variables: *state_variables observations: observers: diff --git a/src/tests/testinput/hofx_nc_ssh_checkerboard.yaml b/src/tests/testinput/hofx_nc_ssh_checkerboard.yaml index 7be8e02..7afbd7b 100644 --- a/src/tests/testinput/hofx_nc_ssh_checkerboard.yaml +++ b/src/tests/testinput/hofx_nc_ssh_checkerboard.yaml @@ -10,7 +10,7 @@ geometry : - name: sea_surface_height_anomaly_background_error nemo field name: ssh_tot_std model space: surface - variable type: background variance + variable type: background error standard deviation grid name: ORCA2_T number levels: 1 partitioner: checkerboard @@ -20,18 +20,18 @@ initial condition : - sea_surface_height_anomaly - sea_surface_height_anomaly_background_error nemo field file: Data/orca2_t_nemo.nc - variance field file: Data/orca2_t_bkg_var.nc + nemo error field file: Data/orca2_t_bkg_var.nc model : name: PseudoModel tstep: P1D states: - date: 2021-06-29T23:00:00Z nemo field file: Data/orca2_t_nemo.nc - variance field file: Data/orca2_t_bkg_var.nc + nemo error field file: Data/orca2_t_bkg_var.nc state variables: &state_variables [ sea_surface_height_anomaly ] - date: 2021-06-30T23:00:00Z nemo field file: Data/orca2_t_nemo.nc - variance field file: Data/orca2_t_bkg_var.nc + nemo error field file: Data/orca2_t_bkg_var.nc state variables: *state_variables observations: observers: diff --git a/src/tests/testinput/hofx_nc_ssh_eorca025.yaml b/src/tests/testinput/hofx_nc_ssh_eorca025.yaml index 45fb4d9..fb63f53 100644 --- a/src/tests/testinput/hofx_nc_ssh_eorca025.yaml +++ b/src/tests/testinput/hofx_nc_ssh_eorca025.yaml @@ -12,7 +12,7 @@ geometry : - name: sea_surface_height_anomaly_background_error nemo field name: sossheig model space: surface - variable type: background variance + variable type: background error standard deviation grid name: eORCA025_T number levels: 1 partitioner: checkerboard @@ -23,18 +23,18 @@ initial condition : - sea_surface_height_anomaly - sea_surface_height_anomaly_background_error nemo field file: Data/eorca025_t_nemo.nc - variance field file: Data/eorca025_t_nemo.nc + nemo error field file: Data/eorca025_t_nemo.nc model : name: PseudoModel tstep: P1D states: - date: 2021-06-29T23:00:00Z nemo field file: Data/eorca025_t_nemo.nc - variance field file: Data/eorca025_t_bkg_var.nc + nemo error field file: Data/eorca025_t_bkg_var.nc state variables: &state_variables [ sea_surface_height_anomaly ] - date: 2021-06-30T23:00:00Z nemo field file: Data/eorca025_t_nemo.nc - variance field file: Data/eorca025_t_nemo.nc + nemo error field file: Data/eorca025_t_nemo.nc state variables: *state_variables observations: observers: diff --git a/src/tests/testinput/hofx_nc_sst.yaml b/src/tests/testinput/hofx_nc_sst.yaml index 7cbf5b4..e78e3b2 100644 --- a/src/tests/testinput/hofx_nc_sst.yaml +++ b/src/tests/testinput/hofx_nc_sst.yaml @@ -15,29 +15,29 @@ geometry : - name: ice_area_fraction_background_error nemo field name: sic_tot_var model space: surface - variable type: background variance + variable type: background error variance - name: sea_surface_temperature_background_error nemo field name: t_tot_var model space: surface - variable type: background variance + variable type: background error variance grid name: ORCA2_T number levels: 1 initial condition : date: 2021-06-28T23:00:00Z state variables: [ sea_surface_temperature, sea_surface_temperature_background_error ] nemo field file: Data/orca2_t_nemo.nc - variance field file: Data/orca2_t_bkg_var.nc + nemo error field file: Data/orca2_t_bkg_var.nc model : name: PseudoModel tstep: P1D states: - date: 2021-06-29T23:00:00Z nemo field file: Data/orca2_t_nemo.nc - variance field file: Data/orca2_t_bkg_var.nc + nemo error field file: Data/orca2_t_bkg_var.nc state variables: &state_variables [ sea_surface_temperature ] - date: 2021-06-30T23:00:00Z nemo field file: Data/orca2_t_nemo.nc - variance field file: Data/orca2_t_bkg_var.nc + nemo error field file: Data/orca2_t_bkg_var.nc state variables: *state_variables observations: observers: diff --git a/src/tests/testinput/hofx_odb_sic.yaml b/src/tests/testinput/hofx_odb_sic.yaml index b45a286..186a783 100644 --- a/src/tests/testinput/hofx_odb_sic.yaml +++ b/src/tests/testinput/hofx_odb_sic.yaml @@ -18,7 +18,7 @@ geometry: - name: ice_area_fraction_background_error nemo field name: sic_tot_var model space: surface - variable type: background variance + variable type: background error variance grid name: ORCA2_T number levels: 2 initial condition : @@ -26,22 +26,22 @@ initial condition : state variables: [ ice_area_fraction, ice_area_fraction_background_error ] #analytic_init: zeroed state nemo field file: orca-jedi/src/tests/Data/orca2_t_nemo.nc - variance field file: orca-jedi/src/tests/Data/orca2_t_bkg_var.nc + nemo error field file: orca-jedi/src/tests/Data/orca2_t_bkg_var.nc model : name: PseudoModel tstep: P1D states: - date: 2021-06-28T23:00:00Z nemo field file: orca-jedi/src/tests/Data/orca2_t_nemo.nc - variance field file: orca-jedi/src/tests/Data/orca2_t_bkg_var.nc + nemo error field file: orca-jedi/src/tests/Data/orca2_t_bkg_var.nc state variables: &state_variables [ ice_area_fraction ] - date: 2021-06-29T23:00:00Z nemo field file: orca-jedi/src/tests/Data/orca2_t_nemo.nc - variance field file: orca-jedi/src/tests/Data/orca2_t_bkg_var.nc + nemo error field file: orca-jedi/src/tests/Data/orca2_t_bkg_var.nc state variables: *state_variables - date: 2021-07-01T23:00:00Z nemo field file: orca-jedi/src/tests/Data/orca2_t_nemo.nc - variance field file: orca-jedi/src/tests/Data/orca2_t_bkg_var.nc + nemo error field file: orca-jedi/src/tests/Data/orca2_t_bkg_var.nc state variables: *state_variables observations: observers: