Add JEDI-based diagnostic analysis calculation utillity

parm/atm/jcb-base.yaml.j2

@@ -9,8 +9,7 @@ app_path_observation_chronicle: "{{PARMgfs}}/gdas/jcb-gdas/observation_chronicle
 
 # Places where we deviate from the generic file name of a yaml
 # ------------------------------------------------------------
-#final_increment_file: final_increment_gaussian
-final_increment_file: atmosphere_final_increment_cubed_sphere
+final_increment_file: atmosphere_final_increment_fms_nonrestart
 output_ensemble_increments_file: atmosphere_output_ensemble_increments_cubed_sphere
 model_file: atmosphere_model_pseudo
 initial_condition_file: atmosphere_background  # Initial conditions for 4D apps is background

parm/io/fv3jedi_fieldmetadata_fv3inc.yaml

@@ -26,4 +26,3 @@ field metadata:
 
 - long name: layer_thickness
   io name: delz_inc
-

utils/fv3jedi/CMakeLists.txt

@@ -3,3 +3,9 @@ ecbuild_add_executable( TARGET fv3jedi_fv3inc.x
                         SOURCES fv3jedi_fv3inc.cc fv3jedi_fv3inc.h)
 target_compile_features( fv3jedi_fv3inc.x PUBLIC cxx_std_17)
 target_link_libraries( fv3jedi_fv3inc.x PUBLIC NetCDF::NetCDF_CXX oops fv3jedi)
+
+# Analysis calculation
+ecbuild_add_executable( TARGET fv3jedi_analcalc.x
+                        SOURCES fv3jedi_analcalc.cc fv3jedi_analcalc.h)
+target_compile_features( fv3jedi_analcalc.x PUBLIC cxx_std_17)
+target_link_libraries( fv3jedi_analcalc.x PUBLIC NetCDF::NetCDF_CXX oops fv3jedi)

utils/fv3jedi/fv3jedi_analcalc.cc

@@ -0,0 +1,8 @@
+#include "fv3jedi_analcalc.h"
+#include "oops/runs/Run.h"
+
+int main(int argc,  char ** argv) {
+  oops::Run run(argc, argv);
+  gdasapp::analcalc analcalc;
+  return run.execute(analcalc);
+}

utils/fv3jedi/fv3jedi_analcalc.h

@@ -0,0 +1,105 @@
+#pragma once
+
+#include <iostream>
+#include <memory>
+#include <string>
+#include <vector>
+
+#include "eckit/config/LocalConfiguration.h"
+
+#include "fv3jedi/Geometry/Geometry.h"
+#include "fv3jedi/Increment/Increment.h"
+#include "fv3jedi/State/State.h"
+
+#include "oops/mpi/mpi.h"
+#include "oops/runs/Application.h"
+#include "oops/util/ConfigFunctions.h"
+#include "oops/util/DateTime.h"
+#include "oops/util/Logger.h"
+
+namespace gdasapp {
+
+  // Main application class
+  class analcalc : public oops::Application {
+   public:
+    explicit analcalc(const eckit::mpi::Comm & comm = oops::mpi::world())
+      : Application(comm) {}
+    static const std::string classname() {return "gdasapp::analcalc";}
+
+    int execute(const eckit::Configuration & fullConfig, bool validate) const {
+      // Get geometry configurations
+      const eckit::LocalConfiguration bkgGeomConfig(fullConfig, "background geometry");
+      const eckit::LocalConfiguration incrGeomConfig(fullConfig, "increment geometry");
+      const eckit::LocalConfiguration anlFullResGeomConfig(fullConfig, \
+                                                           "full resolution analysis geometry");
+      const eckit::LocalConfiguration anlEnsResGeomConfig(fullConfig, \
+                                                          "ensemble resolution analysis geometry");
+
+      // Setup geometries
+      const fv3jedi::Geometry incrGeom(incrGeomConfig, this->getComm());
+      const fv3jedi::Geometry bkgGeom(bkgGeomConfig, this->getComm());
+      const fv3jedi::Geometry anlFullResGeom(anlFullResGeomConfig, this->getComm());
+      const fv3jedi::Geometry anlEnsResGeom(anlEnsResGeomConfig, this->getComm());
+
+      // Get additions configuration
+      int nhrs;
+      std::vector<eckit::LocalConfiguration> additionsConfig;
+      if ( fullConfig.has("additions") ) {
+        fullConfig.get("additions", additionsConfig);
+        nhrs = additionsConfig.size();
+      } else {
+        eckit::LocalConfiguration additionsFromTemplateConfig(fullConfig, \
+                                                              "additions from template");
+        eckit::LocalConfiguration templateConfig(additionsFromTemplateConfig, "template");
+        std::string pattern;
+        std::vector<std::string> fcstHours;
+        additionsFromTemplateConfig.get("pattern", pattern);
+        additionsFromTemplateConfig.get("forecast hours", fcstHours);
+
+        nhrs = fcstHours.size();
+        for ( int ihrs = 0; ihrs < nhrs; ihrs++ ) {
+          eckit::LocalConfiguration thisAdditionsConfig(templateConfig);
+          util::seekAndReplace(thisAdditionsConfig, pattern, fcstHours[ihrs]);
+          additionsConfig.push_back(thisAdditionsConfig);
+        }
+      }
+
+      // Loops through forecast hours
+      for ( int ihrs = 0; ihrs < nhrs; ihrs++ ) {
+        // Get elements of individual additions configurations
+        const eckit::LocalConfiguration bkgConfig(additionsConfig[ihrs], "background");
+        const eckit::LocalConfiguration incrConfig(additionsConfig[ihrs], "increment");
+        const eckit::LocalConfiguration anlFullResConfig(additionsConfig[ihrs], \
+                                                         "full resolution analysis");
+        const eckit::LocalConfiguration anlEnsResConfig(additionsConfig[ihrs], \
+                                                        "ensemble resolution analysis");
+
+        // Initialize background
+        fv3jedi::State xxBkg(bkgGeom, bkgConfig);
+
+        // Initialize increment
+        oops::Variables incrVars(incrConfig, "added variables");
+        fv3jedi::Increment dx(incrGeom, incrVars, xxBkg.validTime());
+        dx.read(incrConfig);
+
+        // Add increment to background state
+        fv3jedi::State xxAnlFullRes(anlFullResGeom, xxBkg);
+        xxAnlFullRes += dx;
+
+        // Interpolate full resolution analysis to ensemble resolution
+        fv3jedi::State xxAnlEnsRes(anlEnsResGeom, xxAnlFullRes);
+
+        // Write analysis state
+        xxAnlFullRes.write(anlFullResConfig);
+        xxAnlEnsRes.write(anlEnsResConfig);
+      }
+
+      return 0;
+    }
+
+   private:
+    std::string appname() const {
+      return "gdasapp::analcalc";
+    }
+  };
+}  // namespace gdasapp

utils/fv3jedi/fv3jedi_fv3inc.h

@@ -103,7 +103,7 @@ namespace gdasapp {
         // Inputs setup
         // ---------------------------------------------------------------------------------
 
-        // Get input configurations
+        // Get I/O configurations
         eckit::LocalConfiguration stateInputConfig(membersConfig[imem], "background input");
         eckit::LocalConfiguration jediIncrInputConfig(membersConfig[imem], "jedi increment input");
         eckit::LocalConfiguration fv3IncrOuputConfig(membersConfig[imem], "fv3 increment output");