Add reference data for 3dvar and dirac application tests. Turn off

creation of json schema again for 3dvar and errorcovariancetoolbox
applications.

Author: frld

src/mains/CMakeLists.txt

@@ -42,5 +42,7 @@ ecbuild_add_executable( TARGET  orcamodel_ErrorCovarianceToolbox.x
 
 oops_output_json_schema( "orcamodel_hofx.x" )
 oops_output_json_schema( "orcamodel_hofx3D.x" )
-oops_output_json_schema( "orcamodel_3DVar.x" )
-oops_output_json_schema( "orcamodel_ErrorCovarianceToolbox.x" )
+# The applications below throw an error generating json schema.
+# This appears to be a generic issue see also oops/qg/mains/CMakeLists.txt
+#oops_output_json_schema( "orcamodel_3DVar.x" )
+#oops_output_json_schema( "orcamodel_ErrorCovarianceToolbox.x" )

src/orca-jedi/interpolator/Interpolator.cc

@@ -208,9 +208,26 @@ void Interpolator::apply(const oops::Variables& vars, const Increment& inc,
   for (size_t jvar=0; jvar < nvars; ++jvar) nvals += nlocs_ * varSizes[jvar];
   result.resize(nvals);
 
-  auto res_iter = result.begin();
+  std::size_t out_idx = 0;
   for (size_t jvar=0; jvar < nvars; ++jvar) {
-      executeInterpolation<double>(vars[jvar].name(), varSizes[jvar], state, mask, res_iter);
+    auto gv_varname = vars[jvar].name();
+    atlas::Field tgt_field = atlasObsFuncSpace_.createField<double>(
+        atlas::option::name(gv_varname) |
+        atlas::option::levels(varSizes[jvar]));
+    interpolator_.execute(inc.incrementFields()[gv_varname], tgt_field);
+    auto field_view = atlas::array::make_view<double, 2>(tgt_field);
+    atlas::field::MissingValue mv(inc.incrementFields()[gv_varname]);
+    bool has_mv = static_cast<bool>(mv);
+    for (std::size_t klev=0; klev < varSizes[jvar]; ++klev) {
+      for (std::size_t iloc=0; iloc < nlocs_; iloc++) {
+        if (has_mv && mv(field_view(iloc, klev))) {
+          result[out_idx] = util::missingValue<double>();
+        } else {
+          result[out_idx] = field_view(iloc, klev);
+        }
+        ++out_idx;
+      }
+    }
   }
 }
 

src/tests/testinput/3dvar_ice_obs.yaml

@@ -101,3 +101,6 @@ output:
   state variables: [ ice_area_fraction ]
   nemo field file: testoutput/3dvar_ice2.nc
   output nemo field file: testoutput/analysis_3dvar_ice.nc
+test:
+  reference filename: testoutput/test_3dvar_ice_obs.ref
+  test output filename: testoutput/test_3dvar_ice_obs.out

src/tests/testinput/dirac.yaml

@@ -36,3 +36,6 @@ background:
 output dirac:
   date: 2021-06-30T12:00:00Z
   output path: testoutput/dirac_cov_%id%.nc
+test:
+  reference filename: testoutput/test_dirac.ref
+  test output filename: testoutput/test_dirac.out

src/tests/testoutput/CMakeLists.txt

@@ -12,6 +12,8 @@ list( APPEND orcajedi_test_output
   test_hofx3d_nc_prof_2vars.ref
   test_hofx3d_nc_ssh_amm1.ref
   test_hofx3d_nc_ssh_amm1r.ref
+  test_3dvar_ice_obs.ref
+  test_dirac.ref
 )
 
 foreach(FILENAME ${orcajedi_test_output})

src/tests/testoutput/test_3dvar_ice_obs.ref

@@ -0,0 +1,16 @@
+CostJb   : Nonlinear Jb = 0.0000000000000000e+00
+CostJo   : Nonlinear Jo(Sea Ice) = 1.5000000000000000e+00, nobs = 48, Jo/n = 3.1250000000000000e-02, err = 2.0000000000000000e+00
+CostFunction: Nonlinear J = 1.5000000000000000e+00
+DRIPCGMinimizer: reduction in residual norm = 7.2455060481720379e-01
+CostFunction::addIncrement: Analysis: 
+ Model state valid at time: 2021-06-29T12:00:00Z
+    1 variables: ice_area_fraction
+    atlas field norms:
+        ice_area_fraction: 3.20155e-03
+
+
+
+
+CostJb   : Nonlinear Jb = 0.00000e+00
+CostJo   : Nonlinear Jo(Sea Ice) = 1.13468e+00, nobs = 48, Jo/n = 2.36392e-02, err = 2.00000e+00
+CostFunction: Nonlinear J = 1.13468e+00

src/tests/testoutput/test_dirac.ref

@@ -0,0 +1,10 @@
+Input Dirac increment:Increment valid at time: 2021-06-30T12:00:00Z
+    1 variables: ice_area_fraction
+    atlas field:
+        ice_area_fraction num: 26553 mean: 3.76605e-05 rms: 6.13682e-03 min: 0.00000e+00 max: 1.00000e+00
+
+Covariance(SABER) * Increment:Increment valid at time: 2021-06-30T12:00:00Z
+    1 variables: ice_area_fraction
+    atlas field:
+        ice_area_fraction num: 26553 mean: 3.76605e-05 rms: 6.13682e-03 min: 0.00000e+00 max: 1.00000e+00
+