Merge branch 'develop' into feature/gdas-cycle-ci

parm/io/fv3jedi_fieldmetadata_fv3inc.yaml

@@ -19,11 +19,28 @@ field metadata:
   io name: o3mr_inc
 
 - long name: cloud_liquid_ice
-  io name: icmr_inc
+  io name: ice_wat_inc
 
 - long name: air_pressure_thickness
   io name: delp_inc
 
 - long name: hydrostatic_layer_thickness
   io name: delz_inc
 
+- long name: rain_water
+  io name: rainwat_inc
+
+- long name: snow_water
+  io name: snowwat_inc
+
+- long name: graupel
+  io name: graupel_inc
+
+- long name: cloud_ice_number_concentration
+  io name: ice_nc_inc
+
+- long name: rain_number_concentration
+  io name: rain_nc_inc
+
+- long name: sgs_tke
+  io name: sgs_tke_inc

utils/CMakeLists.txt

@@ -22,3 +22,4 @@ add_subdirectory(test)
 add_subdirectory(obsproc)
 add_subdirectory(fv3jedi)
 add_subdirectory(chem)
+add_subdirectory(land)

utils/land/CMakeLists.txt

@@ -0,0 +1,5 @@
+# Ensemble recenter of land
+ecbuild_add_executable( TARGET gdasapp_land_ensrecenter.x
+                        SOURCES land_ensrecenter.cc )
+target_compile_features( gdasapp_land_ensrecenter.x PUBLIC cxx_std_17)
+target_link_libraries( gdasapp_land_ensrecenter.x PUBLIC NetCDF::NetCDF_CXX oops atlas fv3jedi)

utils/land/land_ensrecenter.cc

@@ -0,0 +1,8 @@
+#include "land_ensrecenter.h"
+#include "oops/runs/Run.h"
+
+int main(int argc,  char ** argv) {
+  oops::Run run(argc, argv);
+  gdasapp::FV3LandEnsRecenter fv3landensrecenter;
+  return run.execute(fv3landensrecenter);
+}

utils/land/land_ensrecenter.h

@@ -0,0 +1,174 @@
+#pragma once
+
+#include <algorithm>
+#include <iostream>
+#include <numeric>
+#include <string>
+#include <vector>
+
+#include "eckit/config/LocalConfiguration.h"
+
+#include "oops/base/FieldSet3D.h"
+#include "oops/base/GeometryData.h"
+#include "oops/mpi/mpi.h"
+#include "oops/runs/Application.h"
+#include "oops/util/ConfigFunctions.h"
+#include "oops/util/DateTime.h"
+#include "oops/util/Duration.h"
+#include "oops/util/FieldSetHelpers.h"
+#include "oops/util/FieldSetOperations.h"
+#include "oops/util/Logger.h"
+
+#include "fv3jedi/Geometry/Geometry.h"
+#include "fv3jedi/Increment/Increment.h"
+#include "fv3jedi/State/State.h"
+
+
+namespace gdasapp {
+  /**
+   * FV3LandEnsRecenter Class Implementation
+   *
+   * Generates an analysis increment for the ensemble forecast of land surface vars
+   * based off of the difference between the forecast ensemble mean and the
+   * deterministic land surface forecast plus the analysis increment.
+   */
+
+  class FV3LandEnsRecenter : public oops::Application {
+   public:
+    explicit FV3LandEnsRecenter(const eckit::mpi::Comm & comm = oops::mpi::world())
+      : Application(comm) {}
+    static const std::string classname() {return "gdasapp::FV3LandEnsRecenter";}
+
+    int execute(const eckit::Configuration & fullConfig, bool /*validate*/) const {
+        /// Setup the FV3 geometry, we are going to assume that things are on the same grid
+        /// as we do not fully trust OOPS interpolation for land compared to other tools
+        const eckit::LocalConfiguration geomConfig(fullConfig, "geometry");
+        const fv3jedi::Geometry geom(geomConfig, this->getComm());
+
+        /// Get the valid time
+        std::string strdt;
+        fullConfig.get("date", strdt);
+        util::DateTime cycleDate = util::DateTime(strdt);
+
+        /// Get the list of variables to process
+        oops::Variables varList(fullConfig, "variables");
+
+        /// Read the determinstic background
+        const eckit::LocalConfiguration bkgConfig(fullConfig, "deterministic background");
+        fv3jedi::State detbkg(geom, varList, cycleDate);
+        detbkg.read(bkgConfig);
+        oops::Log::info() << "Determinstic background: " << std::endl << detbkg << std::endl;
+        oops::Log::info() << "=========================" << std::endl;
+
+        /// Read the ensemble and get the mean
+        const eckit::LocalConfiguration ensBkgConfig(fullConfig, "ensemble backgrounds");
+        std::vector<fv3jedi::State> ensMembers;
+        int nens = 0;
+        ensBkgConfig.get("number of members", nens);
+        std::string pattern;
+        ensBkgConfig.get("pattern", pattern);
+        size_t zpad = 0;
+        ensBkgConfig.get("zero padding", zpad);
+        eckit::LocalConfiguration ensMemConfig(ensBkgConfig, "template");
+        fv3jedi::State ensmean(geom, varList, cycleDate);
+        ensmean.zero();
+        const double rr = 1.0/static_cast<double>(nens);
+        for (size_t i = 1; i < nens+1; ++i) {
+          /// replace template as appropriate
+          if (!pattern.empty()) {
+            util::seekAndReplace(ensMemConfig, pattern, i, zpad);
+          }
+          fv3jedi::State ensmem(geom, varList, cycleDate);
+          ensmem.read(ensMemConfig);
+          ensmean.accumul(rr, ensmem);
+        }
+        oops::Log::info() << "Ensemble mean background: " << std::endl << ensmean << std::endl;
+        oops::Log::info() << "=========================" << std::endl;
+
+        /// Read the deterministic increment (if specified)
+        fv3jedi::Increment detinc(geom, varList, cycleDate);
+        if (fullConfig.has("deterministic increment")) {
+          const eckit::LocalConfiguration detIncConfig(fullConfig, "deterministic increment");
+          detinc.read(detIncConfig);
+        } else {
+          detinc.zero();  // assume no increment
+        }
+        oops::Log::info() << "Determinstic increment: " << std::endl << detinc << std::endl;
+        oops::Log::info() << "=========================" << std::endl;
+
+        /// Difference the deterministic and ensemble mean forecasts
+        std::string anchor;
+        anchor = "deterministic";
+        if (fullConfig.has("recenter to")) {
+          fullConfig.get("recenter to", anchor);
+        }
+        if (anchor != "deterministic" && anchor != "ensemble mean") {
+          throw eckit::BadValue("'recenter to' must be 'deterministic' or 'ensemble mean'");
+        }
+        fv3jedi::Increment recenter(geom, varList, cycleDate);
+        std::string incrstr;
+        std::string recenterstr;
+        if (anchor == "deterministic") {
+          incrstr = "New ensemble mean increment: ";
+          recenter.diff(detbkg, ensmean);
+          recenterstr = "Difference between deterministic and ensemble mean forecasts: ";
+        } else if (anchor == "ensemble mean") {
+          incrstr = "New deterministic increment: ";
+          recenter.diff(ensmean, detbkg);
+          recenterstr = "Difference between ensemble mean and deterministic forecasts: ";
+        }
+        oops::Log::info() << recenterstr << std::endl << recenter << std::endl;
+        oops::Log::info() << "=========================" << std::endl;
+        /// Add the difference to the deterministic increment
+        fv3jedi::Increment ensinc(geom, varList, cycleDate);
+        ensinc.zero();
+        ensinc += recenter;
+        ensinc += detinc;
+
+        /// Mask out the increment (if applicable)
+        if (fullConfig.has("increment mask")) {
+          /// Get the configuration
+          const eckit::LocalConfiguration incrMaskConfig(fullConfig, "increment mask");
+          std::string maskvarname;
+          incrMaskConfig.get("variable", maskvarname);
+          double minvalue = incrMaskConfig.getDouble("minvalue", -9e36);
+          double maxvalue = incrMaskConfig.getDouble("maxvalue", 9e36);
+          oops::Variables maskVars(incrMaskConfig, "variable");
+          fv3jedi::State maskbkg(geom, maskVars, cycleDate);
+          maskbkg.read(bkgConfig);
+          atlas::FieldSet xbFs;
+          maskbkg.toFieldSet(xbFs);
+          /// Create the atlas fieldset for the output increment
+          atlas::FieldSet ensincFs;
+          ensinc.toFieldSet(ensincFs);
+          /// Loop over all points, if the mask is in range, zero out the increments
+          auto bkgMask = atlas::array::make_view<double, 2>(xbFs[maskvarname]);
+          for (atlas::idx_t jnode = 0; jnode < bkgMask.shape(0); ++jnode) {
+            if (bkgMask(jnode, 0) > minvalue && bkgMask(jnode, 0) < maxvalue) {
+              for (auto & var : varList.variables()) {
+                auto inc = atlas::array::make_view<double, 2>(ensincFs[var]);
+                for (atlas::idx_t level = 0; level < ensincFs[var].shape(1); ++level) {
+                  inc(jnode, level) = 0;
+                }
+              }
+            }
+          }
+          ensinc.fromFieldSet(ensincFs);
+        }
+
+        /// Write out the new increment
+        oops::Log::info() << incrstr << std::endl << ensinc << std::endl;
+        oops::Log::info() << "=========================" << std::endl;
+        const eckit::LocalConfiguration outIncConfig(fullConfig, "output increment");
+        ensinc.write(outIncConfig);
+
+        return 0;
+    }
+
+   private:
+      // -----------------------------------------------------------------------------
+      std::string appname() const {
+        return "gdasapp::FV3LandEnsRecenter";
+    }
+  };
+}  // namespace gdasapp