JEDI increment write to cubed sphere history (#983)

This PR, a companion to Global Workflow PR [#2420](NOAA-EMC/global-workflow#2420) changes the variational YAML for JEDI to write to cubed sphere history rather than the Gaussian grid. With the new changes to Global Workflow, the new gdas_fv3jedi_jediinc2fv3.x OOPS app will read the JEDI increment from the cubed sphere history, compute the FV3 increment, and interpolate/write it the the Gaussian grid. The only meaningful difference is that the internal calculations, namely computation of the hydrostatic layer thickness increment, will be computed on the native grid rather than on the Gaussian grid, before interpolation rather than after. This makes more sense physically. Eventually the FV3 increment will be written and read to/from cubed sphere history anyway.
NOAA-EMC · Mar 28, 2024 · 18ba5da · 18ba5da
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diff --git a/parm/atm/utils/gdas_jediinc2fv3.yaml.j2 → parm/atm/utils/fv3jedi_fv3inc.yaml.j2 b/parm/atm/utils/gdas_jediinc2fv3.yaml.j2 → parm/atm/utils/fv3jedi_fv3inc.yaml.j2
@@ -9,11 +9,11 @@ background:
       field table filename: ./fv3jedi/field_table
     akbk: ./fv3jedi/akbk.nc4
     layout:
-    - ${{ layout_x }}
-    - ${{ layout_y }}
-    npx: ${{ npx_ges }}
-    npy: ${{ npy_ges }}
-    npz: ${{ npz_ges }}
+    - {{ layout_x }}
+    - {{ layout_y }}
+    npx: {{ npx_ges }}
+    npy: {{ npy_ges }}
+    npz: {{ npz_ges }}
     field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_restart.yaml
   input:
     datapath: ./bkg
@@ -33,11 +33,11 @@ jedi increment:
       field table filename: ./fv3jedi/field_table
     akbk: ./fv3jedi/akbk.nc4
     layout:
-    - ${{ layout_x }}
-    - ${{ layout_y }}
-    npx: ${{ npx_ges }}
-    npy: ${{ npy_ges }}
-    npz: ${{ npz_ges }}
+    - {{ layout_x }}
+    - {{ layout_y }}
+    npx: {{ npx_ges }}
+    npy: {{ npy_ges }}
+    npz: {{ npz_ges }}
     field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_history.yaml
   input:
     filetype: cube sphere history
@@ -50,11 +50,11 @@ fv3 increment:
       field table filename: ./fv3jedi/field_table
     akbk: ./fv3jedi/akbk.nc4
     layout:
-    - ${{ layout_x }}
-    - ${{ layout_y }}
-    npx: ${{ npx_ges }}
-    npy: ${{ npy_ges }}
-    npz: ${{ npz_ges }}
+    - {{ layout_x }}
+    - {{ layout_y }}
+    npx: {{ npx_ges }}
+    npy: {{ npy_ges }}
+    npz: {{ npz_ges }}
     field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_fv3inc.yaml
   output:
     filetype: auxgrid

diff --git a/parm/atm/variational/3dvar_drpcg.yaml.j2 b/parm/atm/variational/3dvar_drpcg.yaml.j2
@@ -84,9 +84,10 @@ final:
   increment:
     output:
       state component:
-        filetype: auxgrid
-        gridtype: gaussian
-        filename: ./anl/atminc.
+        filetype: cube sphere history
+        filename: ./anl/atminc.{{ current_cycle | to_fv3time }}.nc4
+        provider: ufs
+        fields to write: [ugrd,vgrd,tmp,pressfc,spfh,icmr,clwmr,o3mr]
     geometry:
       fms initialization:
         namelist filename: ./fv3jedi/fmsmpp.nml
@@ -98,4 +99,4 @@ final:
       npx: {{ npx_anl }}
       npy: {{ npy_anl }}
       npz: {{ npz_anl }}
-      field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_restart.yaml
+      field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_history.yaml
diff --git a/test/fv3jedi/CMakeLists.txt b/test/fv3jedi/CMakeLists.txt
@@ -4,10 +4,10 @@ file(MAKE_DIRECTORY ${PROJECT_BINARY_DIR}/test/fv3jedi/testoutput)
 file(MAKE_DIRECTORY ${PROJECT_BINARY_DIR}/test/fv3jedi/fv3jedi)
 
 # Test YAMLs
-file(CREATE_LINK ${PROJECT_SOURCE_DIR}/test/fv3jedi/testinput/gdasapp_fv3jedi_jediinc2fv3.yaml ${PROJECT_BINARY_DIR}/test/fv3jedi/testinput/gdasapp_fv3jedi_jediinc2fv3.yaml SYMBOLIC)
+file(CREATE_LINK ${PROJECT_SOURCE_DIR}/test/fv3jedi/testinput/gdasapp_fv3jedi_fv3inc.yaml ${PROJECT_BINARY_DIR}/test/fv3jedi/testinput/gdasapp_fv3jedi_fv3inc.yaml SYMBOLIC)
 
 # Test reference files
-file(CREATE_LINK ${PROJECT_SOURCE_DIR}/test/fv3jedi/testoutput/gdasapp_fv3jedi_jediinc2fv3.ref ${PROJECT_BINARY_DIR}/test/fv3jedi/testoutput/gdasapp_fv3jedi_jediinc2fv3.ref SYMBOLIC)
+file(CREATE_LINK ${PROJECT_SOURCE_DIR}/test/fv3jedi/testoutput/gdasapp_fv3jedi_fv3inc.ref ${PROJECT_BINARY_DIR}/test/fv3jedi/testoutput/gdasapp_fv3jedi_fv3inc.ref SYMBOLIC)
 
 # FV3 files
 file(CREATE_LINK ${PROJECT_SOURCE_DIR}/parm/io/fv3jedi_fieldmetadata_fv3inc.yaml ${PROJECT_BINARY_DIR}/test/fv3jedi/fv3jedi/fv3jedi_fieldmetadata_fv3inc.yaml SYMBOLIC)
@@ -17,7 +17,7 @@ file(CREATE_LINK ${PROJECT_SOURCE_DIR}/sorc/fv3-jedi/test/Data/fv3files/fmsmpp.n
 file(CREATE_LINK ${PROJECT_SOURCE_DIR}/sorc/fv3-jedi/test/Data/fv3files/field_table_gfdl ${PROJECT_BINARY_DIR}/test/fv3jedi/fv3jedi/field_table_gfdl SYMBOLIC)
 
 # Tests
-add_test(NAME test_gdasapp_fv3jedi_jediinc2fv3
-         COMMAND srun -n6 ${CMAKE_BINARY_DIR}/bin/gdas_fv3jedi_jediinc2fv3.x ${PROJECT_BINARY_DIR}/test/fv3jedi/testinput/gdasapp_fv3jedi_jediinc2fv3.yaml
+add_test(NAME test_gdasapp_fv3jedi_fv3inc
+         COMMAND srun -n6 ${CMAKE_BINARY_DIR}/bin/gdas_fv3jedi_fv3inc.x ${PROJECT_BINARY_DIR}/test/fv3jedi/testinput/gdasapp_fv3jedi_fv3inc.yaml
          WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/test/fv3jedi)
 
diff --git a/...estinput/gdasapp_fv3jedi_jediinc2fv3.yaml → ...edi/testinput/gdasapp_fv3jedi_fv3inc.yaml b/...estinput/gdasapp_fv3jedi_jediinc2fv3.yaml → ...edi/testinput/gdasapp_fv3jedi_fv3inc.yaml
@@ -60,7 +60,7 @@ fv3 increment:
     provider: ufs
 
 test:
-  reference filename: testoutput/gdasapp_fv3jedi_jediinc2fv3.ref
-  test output filename: testoutput/gdasapp_fv3jedi_jediinc2fv3.test.out
+  reference filename: testoutput/gdasapp_fv3jedi_fv3inc.ref
+  test output filename: testoutput/gdasapp_fv3jedi_fv3inc.test.out
   float relative tolerance: 1.0e-3
 
diff --git a/...estoutput/gdasapp_fv3jedi_jediinc2fv3.ref → ...edi/testoutput/gdasapp_fv3jedi_fv3inc.ref b/...estoutput/gdasapp_fv3jedi_jediinc2fv3.ref → ...edi/testoutput/gdasapp_fv3jedi_fv3inc.ref
diff --git a/utils/fv3jedi/CMakeLists.txt b/utils/fv3jedi/CMakeLists.txt
@@ -1,5 +1,5 @@
 # Increment post processing
-ecbuild_add_executable( TARGET gdas_fv3jedi_jediinc2fv3.x
-                        SOURCES gdas_fv3jedi_jediinc2fv3.cc gdas_fv3jedi_jediinc2fv3.h)
-target_compile_features( gdas_fv3jedi_jediinc2fv3.x PUBLIC cxx_std_17)
-target_link_libraries( gdas_fv3jedi_jediinc2fv3.x PUBLIC NetCDF::NetCDF_CXX oops fv3jedi)
+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)
diff --git a/utils/fv3jedi/fv3jedi_fv3inc.cc b/utils/fv3jedi/fv3jedi_fv3inc.cc
@@ -0,0 +1,8 @@
+#include "fv3jedi_fv3inc.h"
+#include "oops/runs/Run.h"
+
+int main(int argc,  char ** argv) {
+  oops::Run run(argc, argv);
+  gdasapp::fv3inc fv3inc;
+  return run.execute(fv3inc);
+}
diff --git a/utils/fv3jedi/gdas_fv3jedi_jediinc2fv3.h → utils/fv3jedi/fv3jedi_fv3inc.h b/utils/fv3jedi/gdas_fv3jedi_jediinc2fv3.h → utils/fv3jedi/fv3jedi_fv3inc.h
@@ -20,11 +20,11 @@
 namespace gdasapp {
 
   // Main application class
-  class jediinc2fv3 : public oops::Application {
+  class fv3inc : public oops::Application {
    public:
-    explicit jediinc2fv3(const eckit::mpi::Comm & comm = oops::mpi::world())
+    explicit fv3inc(const eckit::mpi::Comm & comm = oops::mpi::world())
       : Application(comm) {}
-    static const std::string classname() {return "gdasapp::jediinc2fv3";}
+    static const std::string classname() {return "gdasapp::fv3inc";}
 
     int execute(const eckit::Configuration & fullConfig, bool validate) const {
       // Setup variable change
@@ -83,7 +83,7 @@ namespace gdasapp {
 
    private:
     std::string appname() const {
-      return "gdasapp::jediinc2fv3";
+      return "gdasapp::fv3inc";
     }
   };
 }  // namespace gdasapp
diff --git a/utils/fv3jedi/gdas_fv3jedi_jediinc2fv3.cc b/utils/fv3jedi/gdas_fv3jedi_jediinc2fv3.cc