EAMxx:Adds loop to update file read for marine organics, cleanup

components/eamxx/cime_config/namelist_defaults_scream.xml

@@ -548,7 +548,6 @@ be lost if SCREAM_HACK_XML is not enabled.
     <!-- CA RRM grid -->
     <topography_filename hgrid="ne0np4_CAx32v1">${DIN_LOC_ROOT}/atm/cam/topo/USGS-gtopo30_CA_ne32_x32_v1_pg2_16xdel2.nc</topography_filename>
 
-    <restart_casename>${CASE}.scream</restart_casename>
     <!-- Fields that we need to initialize, but are not in an initial condition file need to be inited here -->
     <surf_evap>0.0</surf_evap> <!-- TODO, Delete this when the IC fixes come in -->
     <precip_liq_surf_mass>0.0</precip_liq_surf_mass>
@@ -634,7 +633,6 @@ be lost if SCREAM_HACK_XML is not enabled.
   <Scorpio>
     <output_yaml_files type="array(string)"/>
     <model_restart>
-      <filename_prefix>./${CASE}.scream</filename_prefix>
       <iotype>default</iotype>
       <output_control locked="true">
         <Frequency>${REST_N}</Frequency>

components/eamxx/src/physics/mam/eamxx_mam_srf_and_online_emissions_process_interface.cpp

@@ -247,7 +247,7 @@ void MAMSrfOnlineEmiss::set_grids(
   // Field to be read from file
   const std::string soil_erod_fld_name = "mbl_bsn_fct_geo";
 
-  // Dimensions of the filed
+  // Dimensions of the field
   const std::string soil_erod_dname = "ncol";
 
   // initialize the file read
@@ -267,7 +267,7 @@ void MAMSrfOnlineEmiss::set_grids(
   const std::vector<std::string> marine_org_fld_name = {
       "TRUEPOLYC", "TRUEPROTC", "TRUELIPC"};
 
-  // Dimensions of the filed
+  // Dimensions of the field
   const std::string marine_org_dname = "ncol";
 
   // initialize the file read
@@ -526,6 +526,7 @@ void MAMSrfOnlineEmiss::run_impl(const double dt) {
           constituent_fluxes(icol, species_index) = fluxes_in_mks_units(icol);
         });
   }  // for loop for species
+  Kokkos::fence();
 }  // run_impl ends
 // =============================================================================
 }  // namespace scream

components/eamxx/src/physics/mam/eamxx_mam_srf_and_online_emissions_process_interface.hpp

@@ -6,7 +6,6 @@
 
 // For MAM4 aerosol configuration
 #include <physics/mam/mam_coupling.hpp>
-#include <physics/mam/online_emission.hpp>
 #include <physics/mam/srf_emission.hpp>
 
 // For reading marine organics file
@@ -62,9 +61,8 @@ class MAMSrfOnlineEmiss final : public scream::AtmosphereProcess {
   const_view_1d soil_erodibility_;
 
  public:
+  // For reading surface emissions and marine organics file
   using srfEmissFunc = mam_coupling::srfEmissFunctions<Real, DefaultDevice>;
-  using onlineEmiss  = mam_coupling::onlineEmissions<Real, DefaultDevice>;
-  // For reading marine organics file
   using marineOrganicsFunc =
       marine_organics::marineOrganicsFunctions<Real, DefaultDevice>;
 

components/eamxx/src/physics/mam/readfiles/marine_organics_impl.hpp

@@ -85,8 +85,8 @@ marineOrganicsFunctions<S, D>::create_data_reader(
     const std::shared_ptr<AbstractRemapper> &horiz_remapper,
     const std::string &data_file) {
   std::vector<Field> io_fields;
-  for(int i = 0; i < horiz_remapper->get_num_fields(); ++i) {
-    io_fields.push_back(horiz_remapper->get_src_field(i));
+  for(int ifld = 0; ifld < horiz_remapper->get_num_fields(); ++ifld) {
+    io_fields.push_back(horiz_remapper->get_src_field(ifld));
   }
   const auto io_grid = horiz_remapper->get_src_grid();
   return std::make_shared<AtmosphereInput>(data_file, io_grid, io_fields, true);
@@ -126,9 +126,16 @@ void marineOrganicsFunctions<S, D>::update_marine_organics_data_from_file(
       "field");
   // Recall, the fields are registered in the order:
   // Read the field from the file
-#if 0
-  input = horiz_interp.get_tgt_field(0).get_view<const Real *>();
-#endif
+
+  for(int ifld = 0; ifld < horiz_interp.get_num_fields(); ++ifld) {
+    auto sector = horiz_interp.get_tgt_field(ifld).get_view<const Real *>();
+    const auto emiss = Kokkos::subview(marineOrganics_input.data.emiss_sectors,
+                                       ifld, Kokkos::ALL());
+    Kokkos::deep_copy(emiss, sector);
+  }
+
+  Kokkos::fence();
+
   stop_timer(
       "EAMxx::marineOrganics::update_marine_organics_data_from_file::get_"
       "field");

components/eamxx/src/physics/mam/srf_emission_impl.hpp

@@ -102,9 +102,6 @@ void srfEmissFunctions<S, D>::perform_time_interpolation(
   // NOTE: we *assume* data_beg and data_end have the *same* hybrid v coords.
   //       IF this ever ceases to be the case, you can interp those too.
 
-  using ExeSpace = typename KT::ExeSpace;
-  using ESU      = ekat::ExeSpaceUtils<ExeSpace>;
-
   // Gather time stamp info
   auto &t_now   = time_state.t_now;
   auto &t_beg   = time_state.t_beg_month;