Tidying up.

src/orca-jedi/increment/Increment.cc

@@ -37,11 +37,6 @@
 #include "atlas/mesh.h"
 #include "atlas-orca/grid/OrcaGrid.h"
 
-#include <boost/uuid/uuid.hpp>             // uuid class DJL
-#include <boost/uuid/uuid_generators.hpp>  // generators DJL
-#include <boost/uuid/uuid_io.hpp>          // streaming operators etc. DJL
-
-
 namespace orcamodel {
 
 // -----------------------------------------------------------------------------
@@ -232,8 +227,6 @@ void Increment::diff(const State & x1, const State & x2) {
     atlas::field::MissingValue mv2(field2);
     bool has_mv2 = static_cast<bool>(mv2);
     bool has_mv = has_mv1 || has_mv2;
-    oops::Log::debug() << "DJL Increment::diff mv1 " << mv1 << " mv2 " << mv2 << " has_mv "
-        << has_mv << std::endl;
 
     std::string fieldName1 = field1.name();
     std::string fieldName2 = field2.name();
@@ -284,18 +277,11 @@ void Increment::setval(const double & val) {
           if (!has_mv || (has_mv && !mv(field_view(j, k)))) {
             field_view(j, k) = val;
           }
-        } else {
-          field_view(j, k) = -99;            /// DJL
         }
       }
     }
   }
 
-  // DJL write debug fields to file
-    boost::uuids::uuid uuid = boost::uuids::random_generator()();
-    writeFieldsToFile("incsetval"+ boost::uuids::to_string(uuid) +".nc", *geom_,
-        validTime(), incrementFields_);
-
   oops::Log::trace() << "Increment(ORCA)::setval done" << std::endl;
 }
 
@@ -559,7 +545,7 @@ void Increment::read(const eckit::Configuration & conf) {
   throw eckit::NotImplemented(err_message, Here());
 }
 
-/// \brief write out increments fields to a file using params specified filename.
+/// \brief Write out increments fields to a file using params specified filename.
 void Increment::write(const OrcaIncrementParameters & params) const {
   oops::Log::debug() << "orcamodel::increment::write" << std::endl;
 
@@ -572,10 +558,16 @@ void Increment::write(const OrcaIncrementParameters & params) const {
   oops::Log::debug() << "Increment::write to filename "
                      << nemo_field_path << std::endl;
 
+  for (size_t i=0; i < vars_.size(); ++i) {
+    auto gv_varname = vars_[i].name();
+// halo exchange update ghost points
+    geom_->functionSpace().haloExchange(incrementFields_[gv_varname]);
+  }
+
   writeFieldsToFile(nemo_field_path, *geom_, time_, incrementFields_);
 }
 
-/// \brief write out increments fields to a file using config specified filename.
+/// \brief Write out increments fields to a file using config specified filename.
 void Increment::write(const eckit::Configuration & config) const {
   write(oops::validateAndDeserialize<OrcaIncrementParameters>(config));
 }

src/orca-jedi/interpolator/Interpolator.cc

@@ -31,13 +31,6 @@
 
 #include "orca-jedi/interpolator/Interpolator.h"
 
-#include <boost/uuid/uuid.hpp>             // uuid class DJL
-#include <boost/uuid/uuid_generators.hpp>  // generators DJL
-#include <boost/uuid/uuid_io.hpp>          // streaming operators etc. DJL
-
-#include "orca-jedi/utilities/IOUtils.h"  // DJL
-
-
 namespace eckit {
 class Configuration;
 }
@@ -193,7 +186,6 @@ template void Interpolator::executeInterpolation<float>(
 void Interpolator::apply(const oops::Variables& vars, const Increment& inc,
            const std::vector<bool> & mask,
            std::vector<double>& result) const {
-  // DJL question can the atlas templates help?
   // input is inc output is result
   const size_t nvars = vars.size();
 
@@ -226,7 +218,6 @@ void Interpolator::apply(const oops::Variables& vars, const Increment& inc,
     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);
-    oops::Log::debug() << "DJL Interpolator::apply mv " << mv << " has_mv " << has_mv << std::endl;
     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))) {
@@ -254,10 +245,6 @@ void Interpolator::applyAD(const oops::Variables& vars, Increment& inc,
   oops::Log::trace() << "orcamodel::Interpolator::applyAD start "
                      << std::endl;
 
-  oops::Log::debug() << "DJL ** Interpolator::applyAD this needs checking **" << std::endl;
-
-// ** Trying to do the opposite of apply DJL
-
   const size_t nvars = vars.size();
 
   for (size_t j=0; j < nvars; ++j) {
@@ -277,65 +264,38 @@ void Interpolator::applyAD(const oops::Variables& vars, Increment& inc,
     inc.geometry()->variableSizes(vars);
   size_t nvals = 0;
 
-// DJL write debug fields to file
-    boost::uuids::uuid uuid = boost::uuids::random_generator()();
-    std::shared_ptr<const Geometry> geom = inc.geometry();
-    writeFieldsToFile("applyADpre"+ boost::uuids::to_string(uuid) +".nc", *geom,
-        inc.validTime(), inc.incrementFields());
-
   for (size_t jvar=0; jvar < nvars; ++jvar) nvals += nlocs_ * varSizes[jvar];
-//    result.resize(nvals);
-
 
   std::size_t out_idx = 0;
   for (size_t jvar=0; jvar < nvars; ++jvar) {
-    oops::Log::debug() << "DJL ** jvar " << jvar << " " << nvars
-                       << "varSizes " << varSizes[jvar]
-                       << std::endl;
     auto gv_varname = vars[jvar].name();
-//      atlas::Field tgt_field = atlasObsFuncSpace_.createField<double>(
-//          atlas::option::name(gv_varname) |
-//          atlas::option::levels(varSizes[jvar]));
-//      atlas::Field incField = inc.incrementFields()[jvar];
-
     auto tgt_field = atlasObsFuncSpace_.createField<double>(
       atlas::option::name(gv_varname) |
       atlas::option::levels(varSizes[jvar]));
 
 // Copying observation array vector to an atlas observation field (tgt_field)
-// DJL not sure if the missing value aspect does anything here
     auto field_view = atlas::array::make_view<double, 2>(tgt_field);
-//    field_view.assign(0.0);
     atlas::field::MissingValue mv(inc.incrementFields()[gv_varname]);
     bool has_mv = static_cast<bool>(mv);
-    oops::Log::debug() << "DJL Interpolator::applyAD mv "
-        << mv << " has_mv " << has_mv << std::endl;
 
     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))) {
              field_view(iloc, klev) = util::missingValue<double>();
           } else {
-        oops::Log::debug() << "DJL iloc " << iloc << " klev " << klev << " out_idx "
-                          << out_idx << " resultin[out_idx] " << resultin[out_idx] << std::endl;
              field_view(iloc, klev) = resultin[out_idx];
           }
         ++out_idx;
       }
     }
 
-// halo exchange update ghost points DJL
+// halo exchange update ghost points
+    std::shared_ptr<const Geometry> geom = inc.geometry();
     geom->functionSpace().haloExchange(inc.incrementFields()[gv_varname]);
 
     interpolator_.execute_adjoint(inc.incrementFields()[gv_varname], tgt_field);
   }    // jvar
 
-// DJL write debug fields to file
-//    boost::uuids::uuid uuid = boost::uuids::random_generator()();
-//    std::shared_ptr<const Geometry> geom = inc.geometry();
-    writeFieldsToFile("applyAD"+ boost::uuids::to_string(uuid) +".nc", *geom, inc.validTime(),
-        inc.incrementFields());
-
   oops::Log::trace() << "orcamodel::Interpolator::applyAD done "
                      << std::endl;
 }

src/orca-jedi/state/State.cc

@@ -164,14 +164,14 @@ State & State::operator=(const State & rhs) {
 
 // Interactions with Increments
 
+/// \brief Add increment to state.
+/// \brief Requires increment and state to have the same field names (currently).
+/// \param Increment.
 State & State::operator+=(const Increment & dx) {
   oops::Log::trace() << "State(ORCA)::add increment starting" << std::endl;
 
   ASSERT(this->validTime() == dx.validTime());
 
-// DJL assumes state and increments have the same fields in the field set
-// DJL add something to enforce/check this
-
   auto ghost = atlas::array::make_view<int32_t, 1>(
       geom_->mesh().nodes().ghost());
   for (int i = 0; i< stateFields_.size(); i++)
@@ -187,6 +187,8 @@ State & State::operator+=(const Increment & dx) {
     oops::Log::debug() << "orcamodel::Increment::add:: state field name = " << fieldName
                        << " increment field name = " << fieldNamei
                        << std::endl;
+    ASSERT(fieldName == fieldNamei);
+
     auto field_view = atlas::array::make_view<double, 2>(field);
     auto field_viewi = atlas::array::make_view<double, 2>(fieldi);
     for (atlas::idx_t j = 0; j < field_view.shape(0); ++j) {

src/tests/testinput/3dvar_ice_obs.yaml

@@ -44,7 +44,7 @@ cost function:
         obsdataout:
           engine:
             type: H5File
-            obsfile: testoutput/test_3dvar_obsdataout.nc
+            obsfile: testoutput/obsdataout_3dvar_ice.nc
         simulated variables: [ice_area_fraction]
       get values:
         time interpolation: linear
@@ -91,17 +91,13 @@ variational:
       write increment: true
       increment:
         state component:
-          output path: testoutput/increments_ice.nc
+          output path: testoutput/increments_3dvar_ice.nc
           date: 2021-06-30T00:00:00Z
-#          type: in
 final:
   diagnostics:
     departures: oman
 output:
   date: 2021-06-30T00:00:00Z
   state variables: [ ice_area_fraction ]
   nemo field file: testoutput/3dvar_ice2.nc
-  output nemo field file: testoutput/3dvar_ice_analysis.nc
-#  steps: ["2021-06-29T12:00:00Z"]
-#test:
-#  reference filename: testoutput/test_3dvar_ice_obs.ref
+  output nemo field file: testoutput/analysis_3dvar_ice.nc

src/tests/testinput/dirac.yaml

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