Add 3DVar and error covariance toolbox (dirac test) main programs.

CMakeLists.txt

@@ -36,6 +36,9 @@ ecbuild_debug( "   atlas_orca_FEATURES: [${atlas_orca_FEATURES}]" )
 find_package( oops REQUIRED )
 ecbuild_debug( "   oops_FEATURES : [${oops_FEATURES}]" )
 
+find_package( saber REQUIRED)
+ecbuild_debug( "   saber_FEATURES : [${saber_FEATURES}]" )
+
 find_package( ufo REQUIRED)
 ecbuild_debug( "   ufo_FEATURES : [${ufo_FEATURES}]" )
 

src/mains/CMakeLists.txt

@@ -11,6 +11,12 @@ if( ${nemo-feedback_FOUND} )
                           LIBS    orcamodel nemo_feedback
                           DEFINITIONS NEMO_FEEDBACK_EXISTS
                         )
+
+  ecbuild_add_executable( TARGET  orcamodel_3DVar.x
+                          SOURCES orcamodel3DVar.cc
+                          LIBS    orcamodel nemo_feedback
+                          DEFINITIONS NEMO_FEEDBACK_EXISTS
+                        )
 else()
   message("      compiling without feedback file support")
   ecbuild_add_executable( TARGET  orcamodel_hofx.x
@@ -22,6 +28,19 @@ else()
                           SOURCES orcamodelHofX3D.cc
                           LIBS    orcamodel
                         )
+
+  ecbuild_add_executable( TARGET  orcamodel_3DVar.x
+                          SOURCES orcamodel3DVar.cc
+                          LIBS    orcamodel
+                        )
 endif()
+
+ecbuild_add_executable( TARGET  orcamodel_ErrorCovarianceToolbox.x
+                        SOURCES orcamodelErrorCovarianceToolbox.cc
+                        LIBS    orcamodel
+                      )
+
 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" )

src/mains/orcamodel3DVar.cc

@@ -0,0 +1,36 @@
+/*
+ * (C) British Crown Copyright 2024 MetOffice
+ *
+ * This software is licensed under the terms of the Apache Licence Version 2.0
+ * which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
+ */
+
+#include "atlas/library/Library.h"
+#include "oops/generic/instantiateModelFactory.h"
+
+#include "oops/runs/Run.h"
+#include "oops/runs/Variational.h"
+#include "saber/oops/instantiateCovarFactory.h"
+
+#include "ufo/ObsTraits.h"
+#include "ufo/instantiateObsFilterFactory.h"
+#if defined(NEMO_FEEDBACK_EXISTS)
+  #include "nemo-feedback/instantiateObsFilterFactory.h"
+#endif
+
+#include "orca-jedi/utilities/OrcaModelTraits.h"
+
+int main(int argc,  char ** argv) {
+  oops::Run run(argc, argv);
+  oops::instantiateModelFactory<orcamodel::OrcaModelTraits>();
+  atlas::Library::instance().initialise();
+  saber::instantiateCovarFactory<orcamodel::OrcaModelTraits>();
+  ufo::instantiateObsFilterFactory();
+#if defined(NEMO_FEEDBACK_EXISTS)
+  nemo_feedback::instantiateObsFilterFactory<ufo::ObsTraits>();
+#endif
+  oops::Variational<orcamodel::OrcaModelTraits , ufo::ObsTraits> var;
+  int i = run.execute(var);
+  atlas::Library::instance().finalise();
+  return i;
+}

src/mains/orcamodelErrorCovarianceToolbox.cc

@@ -0,0 +1,25 @@
+/*
+ * (C) British Crown Copyright 2024 MetOffice
+ *
+ * This software is licensed under the terms of the Apache Licence Version 2.0
+ * which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
+ */
+
+#include "atlas/library/Library.h"
+
+#include "saber/oops/ErrorCovarianceToolbox.h"
+#include "saber/oops/instantiateCovarFactory.h"
+
+#include "oops/runs/Run.h"
+#include "orca-jedi/utilities/OrcaModelTraits.h"
+
+int main(int argc,  char ** argv) {
+  oops::Run run(argc, argv);
+  atlas::Library::instance().initialise();
+  saber::instantiateCovarFactory<orcamodel::OrcaModelTraits>();
+
+  saber::ErrorCovarianceToolbox<orcamodel::OrcaModelTraits> var;
+  int i = run.execute(var);
+  atlas::Library::instance().finalise();
+  return i;
+}

src/orca-jedi/CMakeLists.txt

@@ -35,15 +35,20 @@ utilities/Types.h
 utilities/Types.cc
 utilities/IOUtils.h
 utilities/IOUtils.cc
+utilities/ModelData.h
+utilities/ModelData.cc
 variablechanges/VariableChangeParameters.h
 variablechanges/VariableChange.h
+variablechanges/LinearVariableChange.h
+variablechanges/LinearVariableChange.cc
+variablechanges/LinearVariableChangeParameters.h
 )
 
 
 
 ecbuild_add_library( TARGET   orcamodel
                      SOURCES  ${oops_orcamodel_src_files}
-                     PUBLIC_LIBS  oops ufo atlas atlas-orca eckit netcdf
+                     PUBLIC_LIBS  oops saber ufo atlas atlas-orca eckit netcdf
                      INSTALL_HEADERS LISTED
                      LINKER_LANGUAGE ${OOPS_LINKER_LANGUAGE}
                     )

src/orca-jedi/state/State.cc

@@ -359,4 +359,31 @@ atlas::Field State::getField(int i) const {
   return stateFields_[i];
 }
 
+/// \brief Output state fieldset as an atlas fieldset.
+/// \param fset Atlas fieldset to output to.
+void State::toFieldSet(atlas::FieldSet & fset) const {
+  oops::Log::debug() << "State toFieldSet starting" << std::endl;
+
+  fset = atlas::FieldSet();
+
+  for (size_t i=0; i < vars_.size(); ++i) {
+    // copy variable from increments to new field set
+    atlas::Field field = stateFields_[i];
+    std::string fieldName = field.name();
+    oops::Log::debug() << "Copy state toFieldSet " << fieldName << std::endl;
+
+    fset->add(field);
+  }
+  oops::Log::debug() << "State toFieldSet done" << std::endl;
+}
+
+void State::accumul(const double & zz, const State & xx) {
+
+  std::string err_message =
+      "orcamodel::State::accumul not implemented";
+  throw eckit::NotImplemented(err_message, Here());
+
+}
+
+
 }  // namespace orcamodel

src/orca-jedi/state/State.h

@@ -106,6 +106,9 @@ class State : public util::Printable,
   oops::Variables & variables() {return vars_;}
 
   atlas::Field getField(int) const;
+  void toFieldSet(atlas::FieldSet &) const;
+
+  void accumul(const double &, const State &);
 
  private:
   void setupStateFields();

src/orca-jedi/utilities/ModelData.cc

@@ -0,0 +1,35 @@
+/*
+ * (C) Crown Copyright 2023 Met Office.
+ *
+ * This software is licensed under the terms of the Apache Licence Version 2.0
+ * which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
+ */
+
+
+#include <ostream>
+
+#include "orca-jedi/utilities/ModelData.h"
+
+
+namespace orcamodel {
+
+
+const eckit::LocalConfiguration ModelData::modelData() const {
+  eckit::LocalConfiguration model_data;
+
+  //
+  // retrieve data that need to be shared with other system components
+  // and stored them into the data structure 'model_data'
+  //
+
+  return model_data;
+}
+
+
+void ModelData::print(std::ostream & os) const {
+  os << "orcamodel::ModelData::ModelData(): " << modelData();
+}
+
+
+}  // namespace orcamodel
+

src/orca-jedi/utilities/ModelData.h

@@ -0,0 +1,40 @@
+/*
+ * (C) Crown Copyright 2023 Met Office.
+ *
+ * This software is licensed under the terms of the Apache Licence Version 2.0
+ * which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
+ */
+
+
+#pragma once
+
+#include <ostream>
+#include <string>
+
+#include "eckit/config/LocalConfiguration.h"
+
+#include "oops/util/Printable.h"
+
+#include "orca-jedi/geometry/Geometry.h"
+
+
+namespace orcamodel {
+
+class Geometry;
+
+
+class ModelData : public util::Printable {
+ public:
+  explicit ModelData(const Geometry &) {}
+  ~ModelData() {}
+
+  static const std::string classname() {return "orcamodel::ModelData";}
+
+  const eckit::LocalConfiguration modelData() const;
+
+ private:
+  void print(std::ostream &) const override;
+};
+
+
+}  // namespace orcamodel

src/orca-jedi/utilities/OrcaModelTraits.h

@@ -15,7 +15,9 @@
 #include "orca-jedi/model/ModelBiasIncrement.h"
 #include "orca-jedi/model/ModelBiasCovariance.h"
 #include "orca-jedi/state/State.h"
+#include "orca-jedi/utilities/ModelData.h"
 #include "orca-jedi/variablechanges/VariableChange.h"
+#include "orca-jedi/variablechanges/LinearVariableChange.h"
 
 namespace orcamodel {
 
@@ -35,6 +37,8 @@ struct OrcaModelTraits {
   typedef orcamodel::ModelBiasCovariance       ModelAuxCovariance;
   typedef orcamodel::State                     State;
   typedef orcamodel::VariableChange            VariableChange;
+  typedef orcamodel::LinearVariableChange      LinearVariableChange;
+  typedef orcamodel::ModelData                 ModelData;
 };
 
 }  // namespace orcamodel

src/orca-jedi/variablechanges/LinearVariableChange.cc

@@ -0,0 +1,43 @@
+/*
+ * (C) British Crown Copyright 2021 Met Office
+ *
+ * This software is licensed under the terms of the Apache Licence Version 2.0
+ * which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
+*/
+
+#include <string>
+
+#include "eckit/exception/Exceptions.h"
+
+#include "orca-jedi/variablechanges/LinearVariableChange.h"
+
+#include "oops/util/Printable.h"
+#include "orca-jedi/geometry/Geometry.h"
+#include "orca-jedi/state/State.h"
+#include "orca-jedi/variablechanges/LinearVariableChangeParameters.h"
+
+namespace orcamodel {
+
+// -----------------------------------------------------------------------------
+//LinearVariableChange::LinearVariableChange(const Parameters_ &, const Geometry &) {}      
+LinearVariableChange::LinearVariableChange(const Geometry &, const Parameters_ &) {}
+LinearVariableChange::LinearVariableChange(const Geometry &, const eckit::Configuration &) {}
+// -----------------------------------------------------------------------------
+//LinearVariableChange::~LinearVariableChange() {}
+
+void LinearVariableChange::changeVarTL(Increment & dx, const oops::Variables & vars) 
+const { }
+
+void LinearVariableChange::changeVarInverseTL(Increment & dx, const oops::Variables & vars)
+const { }
+
+void LinearVariableChange::changeVarAD(Increment & dx, const oops::Variables & vars) 
+const { }
+
+void LinearVariableChange::changeVarInverseAD(Increment & dx, const oops::Variables & vars)
+const { }
+
+void LinearVariableChange::changeVarTraj(const State & xbg, const oops::Variables & xfg)
+{ }
+
+}

src/orca-jedi/variablechanges/LinearVariableChange.h

@@ -0,0 +1,56 @@
+/*
+ * (C) British Crown Copyright 2021 Met Office
+ *
+ * This software is licensed under the terms of the Apache Licence Version 2.0
+ * which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
+*/
+
+#pragma once
+
+#include <memory>
+#include <ostream>
+#include <string>
+
+#include "eckit/config/Configuration.h"
+
+#include "oops/util/Printable.h"
+#include "orca-jedi/geometry/Geometry.h"
+#include "orca-jedi/state/State.h"
+#include "orca-jedi/variablechanges/LinearVariableChangeParameters.h"
+
+// Forward declarations
+namespace oops {
+  class Variables;
+}
+
+namespace orcamodel {
+
+// -----------------------------------------------------------------------------
+
+class LinearVariableChange: public util::Printable {
+// private util::ObjectCounter<LinearVariableChange>
+ public:
+  typedef LinearVariableChangeParameters Parameters_;
+  static const std::string classname() {
+    return "orcamodel::LinearVariableChange";
+  }
+
+  LinearVariableChange(const Geometry &, const Parameters_ &);
+  LinearVariableChange(const Geometry &, const eckit::Configuration &);
+
+  void changeVarTL(Increment &, const oops::Variables &) const;
+  void changeVarInverseTL(Increment &, const oops::Variables &) const;
+  void changeVarAD(Increment &, const oops::Variables &) const;
+  void changeVarInverseAD(Increment &, const oops::Variables &) const;
+
+  void changeVarTraj(const State &, const oops::Variables &);
+
+
+ private:
+  void print(std::ostream & out) const override {
+    out << "orcamodel::LinearVariableChange::print Not Implemented"; };
+};
+
+}  // namespace orcamodel
+
+

src/orca-jedi/variablechanges/LinearVariableChangeParameters.h

@@ -0,0 +1,28 @@
+/*
+ * (C) Crown Copyright 2021, the Met Office. All rights reserved.
+ *
+ * Refer to COPYRIGHT.txt of this distribution for details.
+ */
+
+#pragma once
+
+#include <string>
+#include <vector>
+
+#include "eckit/exception/Exceptions.h"
+#include "oops/util/DateTime.h"
+#include "oops/base/Variables.h"
+#include "oops/base/LinearVariableChangeParametersBase.h"
+#include "oops/util/parameters/Parameter.h"
+#include "oops/util/parameters/RequiredParameter.h"
+#include "oops/util/parameters/OptionalParameter.h"
+
+
+class LinearVariableChangeParameters :
+    public oops::LinearVariableChangeParametersBase {
+  OOPS_CONCRETE_PARAMETERS(LinearVariableChangeParameters,
+                           oops::LinearVariableChangeParametersBase)
+ public:
+  // No linear variable change. No additional parameters
+};
+