Adds MAM4xx Surface emissions process interface for EAMxx

components/eamxx/cime_config/namelist_defaults_scream.xml

@@ -242,8 +242,7 @@ be lost if SCREAM_HACK_XML is not enabled.
     </mam4_aci>
 
     <!-- MAM4xx-Dry Deposition -->
-    <mam4_drydep inherit="atm_proc_base">
-    </mam4_drydep>
+    <mam4_drydep inherit="atm_proc_base" />
 
     <!-- CLD fraction -->
     <cldFraction inherit="atm_proc_base"/>
@@ -266,8 +265,41 @@ be lost if SCREAM_HACK_XML is not enabled.
     </mam4_optics>
 
     <!-- MAM4xx-Wetscav -->
-    <mam4_wetscav inherit="atm_proc_base">
-    </mam4_wetscav>
+    <mam4_wetscav inherit="atm_proc_base" />
+
+    <!-- MAM4xx-Surface-Emissions -->
+    <mam4_srf_online_emiss inherit="atm_proc_base">
+
+      <srf_emis_specifier_for_DMS    hgrid="ne4np4.pg2" type="file" doc="File containing surface emissions data for DMS">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne4pg2/surface/DMSflux.2010.ne4pg2_conserv.POPmonthlyClimFromACES4BGC_c20240814.nc</srf_emis_specifier_for_DMS>
+      <srf_emis_specifier_for_SO2    hgrid="ne4np4.pg2" type="file" doc="File containing surface emissions data for SO2">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne4pg2/surface/cmip6_mam4_so2_surf_ne4pg2_2010_clim_c20240815.nc</srf_emis_specifier_for_SO2>
+      <srf_emis_specifier_for_bc_a4  hgrid="ne4np4.pg2" type="file" doc="File containing surface emissions data for bc_a4">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne4pg2/surface/cmip6_mam4_bc_a4_surf_ne4pg2_2010_clim_c20240815.nc</srf_emis_specifier_for_bc_a4>
+      <srf_emis_specifier_for_num_a1 hgrid="ne4np4.pg2" type="file" doc="File containing surface emissions data for num_a1">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne4pg2/surface/cmip6_mam4_num_a1_surf_ne4pg2_2010_clim_c20240815.nc</srf_emis_specifier_for_num_a1>
+      <srf_emis_specifier_for_num_a2 hgrid="ne4np4.pg2" type="file" doc="File containing surface emissions data for num_a2">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne4pg2/surface/cmip6_mam4_num_a2_surf_ne4pg2_2010_clim_c20240815.nc</srf_emis_specifier_for_num_a2>
+      <srf_emis_specifier_for_num_a4 hgrid="ne4np4.pg2" type="file" doc="File containing surface emissions data for num_a4">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne4pg2/surface/cmip6_mam4_num_a4_surf_ne4pg2_2010_clim_c20240815.nc</srf_emis_specifier_for_num_a4>
+      <srf_emis_specifier_for_pom_a4 hgrid="ne4np4.pg2" type="file" doc="File containing surface emissions data for pom_a4">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne4pg2/surface/cmip6_mam4_pom_a4_surf_ne4pg2_2010_clim_c20240815.nc</srf_emis_specifier_for_pom_a4>
+      <srf_emis_specifier_for_so4_a1 hgrid="ne4np4.pg2" type="file" doc="File containing surface emissions data for so4_a1">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne4pg2/surface/cmip6_mam4_so4_a1_surf_ne4pg2_2010_clim_c20240815.nc</srf_emis_specifier_for_so4_a1>
+      <srf_emis_specifier_for_so4_a2 hgrid="ne4np4.pg2" type="file" doc="File containing surface emissions data for so4_a2">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne4pg2/surface/cmip6_mam4_so4_a2_surf_ne4pg2_2010_clim_c20240815.nc</srf_emis_specifier_for_so4_a2>
+      <!-- For all other grids -->      
+      <srf_emis_specifier_for_DMS     type="file" doc="File containing surface emissions data for DMS">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne30pg2/surface/DMSflux.2010.ne30pg2_conserv.POPmonthlyClimFromACES4BGC_c20240816.nc</srf_emis_specifier_for_DMS>
+      <srf_emis_specifier_for_SO2     type="file" doc="File containing surface emissions data for SO2">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne30pg2/surface/cmip6_mam4_so2_surf_ne30pg2_2010_clim_c20240816.nc</srf_emis_specifier_for_SO2>
+      <srf_emis_specifier_for_bc_a4   type="file" doc="File containing surface emissions data for bc_a4">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne30pg2/surface/cmip6_mam4_bc_a4_surf_ne30pg2_2010_clim_c20240816.nc</srf_emis_specifier_for_bc_a4>
+      <srf_emis_specifier_for_num_a1  type="file" doc="File containing surface emissions data for num_a1">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne30pg2/surface/cmip6_mam4_num_a1_surf_ne30pg2_2010_clim_c20240816.nc</srf_emis_specifier_for_num_a1>
+      <srf_emis_specifier_for_num_a2  type="file" doc="File containing surface emissions data for num_a2">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne30pg2/surface/cmip6_mam4_num_a2_surf_ne30pg2_2010_clim_c20240816.nc</srf_emis_specifier_for_num_a2>
+      <srf_emis_specifier_for_num_a4  type="file" doc="File containing surface emissions data for num_a4">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne30pg2/surface/cmip6_mam4_num_a4_surf_ne30pg2_2010_clim_c20240816.nc</srf_emis_specifier_for_num_a4>
+      <srf_emis_specifier_for_pom_a4  type="file" doc="File containing surface emissions data for pom_a4">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne30pg2/surface/cmip6_mam4_pom_a4_surf_ne30pg2_2010_clim_c20240816.nc</srf_emis_specifier_for_pom_a4>
+      <srf_emis_specifier_for_so4_a1  type="file" doc="File containing surface emissions data for so4_a1">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne30pg2/surface/cmip6_mam4_so4_a1_surf_ne30pg2_2010_clim_c20240816.nc</srf_emis_specifier_for_so4_a1>
+      <srf_emis_specifier_for_so4_a2  type="file" doc="File containing surface emissions data for so4_a2">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne30pg2/surface/cmip6_mam4_so4_a2_surf_ne30pg2_2010_clim_c20240816.nc</srf_emis_specifier_for_so4_a2>
+
+      <!-- Mapping Files for finer resolutions -->
+      <srf_remap_file type="file" doc="File containing mapping data from the grid of emission files to the model grid. Unused if the grid is the same."/>
+      <srf_remap_file hgrid="ne120np4.pg2">${DIN_LOC_ROOT}/atm/scream/maps/map_ne30pg2_to_ne120pg2_20231201.nc</srf_remap_file>
+      <srf_remap_file hgrid="ne256np4.pg2">${DIN_LOC_ROOT}/atm/scream/maps/map_ne30pg2_to_ne256pg2_20231201.nc</srf_remap_file>
+      <srf_remap_file hgrid="ne512np4.pg2">${DIN_LOC_ROOT}/atm/scream/maps/map_ne30pg2_to_ne512pg2_20231201.nc</srf_remap_file>
+      <srf_remap_file hgrid="ne1024np4.pg2">${DIN_LOC_ROOT}/atm/scream/maps/map_ne30pg2_to_ne1024pg2_20231201.nc</srf_remap_file>
+    </mam4_srf_online_emiss>
+
+    <!-- MAM4xx-constituent fluxes -->
+    <mam4_constituent_fluxes inherit="atm_proc_base" />
 
     <!-- nudging -->
     <nudging inherit="atm_proc_base">

components/eamxx/cime_config/testdefs/testmods_dirs/scream/mam4xx/srf_online_emiss_constituent_fluxes/shell_commands

@@ -0,0 +1,17 @@
+
+#!/bin/sh
+#------------------------------------------------------
+# MAM4xx adds additionaltracers to the simulation
+# Increase number of tracers for MAM4xx simulations
+#------------------------------------------------------
+
+$CIMEROOT/../components/eamxx/cime_config/testdefs/testmods_dirs/scream/mam4xx/update_eamxx_num_tracers.sh -b
+
+#------------------------------------------------------
+#Update IC file and add the processes
+#------------------------------------------------------
+$CIMEROOT/../components/eamxx/scripts/atmchange initial_conditions::Filename='$DIN_LOC_ROOT/atm/scream/init/screami_mam4xx_ne4np4L72_c20240208.nc' -b
+$CIMEROOT/../components/eamxx/scripts/atmchange physics::atm_procs_list="mam4_constituent_fluxes,mac_aero_mic,rrtmgp,mam4_srf_online_emiss" -b
+
+
+

components/eamxx/src/physics/mam/CMakeLists.txt

@@ -45,7 +45,9 @@ add_library(mam
   eamxx_mam_optics_process_interface.cpp
   eamxx_mam_dry_deposition_process_interface.cpp
   eamxx_mam_aci_process_interface.cpp
-  eamxx_mam_wetscav_process_interface.cpp)
+  eamxx_mam_wetscav_process_interface.cpp
+  eamxx_mam_srf_and_online_emissions_process_interface.cpp
+  eamxx_mam_constituent_fluxes_interface.cpp)
 target_compile_definitions(mam PUBLIC EAMXX_HAS_MAM)
 add_dependencies(mam mam4xx)
 target_include_directories(mam PUBLIC

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

@@ -198,23 +198,6 @@ void store_liquid_cloud_fraction(
       });
 }
 
-void compute_recipical_pseudo_density(haero::ThreadTeamPolicy team_policy,
-                                      MAMAci::const_view_2d pdel,
-                                      const int nlev,
-                                      // output
-                                      MAMAci::view_2d rpdel) {
-  Kokkos::parallel_for(
-      team_policy, KOKKOS_LAMBDA(const haero::ThreadTeam &team) {
-        const int icol = team.league_rank();
-        Kokkos::parallel_for(
-            Kokkos::TeamVectorRange(team, 0, nlev), [&](int kk) {
-              EKAT_KERNEL_ASSERT_MSG(0 < pdel(icol, kk),
-                                     "Error: pdel should be > 0.\n");
-              rpdel(icol, kk) = 1 / pdel(icol, kk);
-            });
-      });
-}
-
 void call_function_dropmixnuc(
     haero::ThreadTeamPolicy team_policy, const Real dt,
     mam_coupling::DryAtmosphere &dry_atmosphere, const MAMAci::view_2d rpdel,
@@ -397,7 +380,7 @@ void call_function_dropmixnuc(
                   progs_at_col, haero_atm, state_q_at_lev_col, klev);
 
               // get the start index for aerosols species in the state_q array
-              int istart = mam4::aero_model::pcnst - mam4::ndrop::ncnst_tot;
+              int istart = mam4::utils::aero_start_ind();
 
               // create colum views of state_q
               for(int icnst = istart; icnst < mam4::aero_model::pcnst;

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

@@ -253,7 +253,7 @@ void MAMAci::set_grids(
                       frz_unit, grid_name);
 
   // heterogeneous freezing by deposition nucleation [cm^-3 s^-1]
-  add_field<Computed>("hetfrz_depostion_nucleation_tend", scalar3d_layout_mid,
+  add_field<Computed>("hetfrz_deposition_nucleation_tend", scalar3d_layout_mid,
                       frz_unit, grid_name);
 }  // function set_grids ends
 
@@ -390,8 +390,8 @@ void MAMAci::initialize_impl(const RunType run_type) {
       get_field_out("hetfrz_immersion_nucleation_tend").get_view<Real **>();
   hetfrz_contact_nucleation_tend_ =
       get_field_out("hetfrz_contact_nucleation_tend").get_view<Real **>();
-  hetfrz_depostion_nucleation_tend_ =
-      get_field_out("hetfrz_depostion_nucleation_tend").get_view<Real **>();
+  hetfrz_deposition_nucleation_tend_ =
+      get_field_out("hetfrz_deposition_nucleation_tend").get_view<Real **>();
 
   //---------------------------------------------------------------------------------
   // Allocate memory for the class members
@@ -597,7 +597,7 @@ void MAMAci::run_impl(const double dt) {
                               // output
                               cloud_frac_, cloud_frac_prev_);
 
-  compute_recipical_pseudo_density(team_policy, dry_atm_.p_del, nlev_,
+  mam_coupling::compute_recipical_pseudo_density(team_policy, dry_atm_.p_del, nlev_,
                                    // output
                                    rpdel_);
 
@@ -642,7 +642,7 @@ void MAMAci::run_impl(const double dt) {
       team_policy, hetfrz_, dry_atm_, dry_aero_, factnum_, dt, nlev_,
       // ## output to be used by the other processes ##
       hetfrz_immersion_nucleation_tend_, hetfrz_contact_nucleation_tend_,
-      hetfrz_depostion_nucleation_tend_,
+      hetfrz_deposition_nucleation_tend_,
       // work arrays
       diagnostic_scratch_);
 

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

@@ -123,7 +123,7 @@ class MAMAci final : public scream::AtmosphereProcess {
   // added correctly to the cloud-micorphysics scheme.
   view_2d hetfrz_immersion_nucleation_tend_;
   view_2d hetfrz_contact_nucleation_tend_;
-  view_2d hetfrz_depostion_nucleation_tend_;
+  view_2d hetfrz_deposition_nucleation_tend_;
 
   view_2d diagnostic_scratch_[hetro_scratch_];
 

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

@@ -0,0 +1,84 @@
+#ifndef EAMXX_MAM_CONSTITUTE_FLUXES_FUNCTIONS_HPP
+#define EAMXX_MAM_CONSTITUTE_FLUXES_FUNCTIONS_HPP
+
+#include <mam4xx/mam4.hpp>
+#include <physics/mam/eamxx_mam_constituent_fluxes_interface.hpp>
+
+namespace scream {
+
+namespace {
+
+void update_gas_aerosols_using_constituents(
+    const int ncol, const int nlev, const double dt,
+    const mam_coupling::DryAtmosphere &dry_atm,
+    const MAMConstituentFluxes::const_view_2d &constituent_fluxes,
+    // output
+    const mam_coupling::AerosolState &wet_aero) {
+  using C                      = physics::Constants<Real>;
+  static constexpr auto gravit = C::gravit;  // Gravity [m/s2]
+  static constexpr int pcnst   = mam4::aero_model::pcnst;
+
+  // Declare local variables
+  const int surface_lev = nlev - 1;
+
+  // get the start index for gas species in the state_q array
+  int istart = mam4::utils::gasses_start_ind();
+
+  // number of constituents to update (currently updating only MAM4xx
+  // constituents)
+  const int nconstituents = pcnst - istart;
+
+  // Create a policy to loop over columns annd number of constituents
+  // to update
+  // FIXME: TODO:We don't need a team for "nconstituents", so we can make the
+  // kookos_for simple by using just ncols
+  const auto policy = ekat::ExeSpaceUtils<MAMConstituentFluxes::KT::ExeSpace>::
+      get_default_team_policy(ncol, nconstituents);
+
+  // Loop through all columns to update tracer mixing rations
+  Kokkos::parallel_for(
+      policy, KOKKOS_LAMBDA(const haero::ThreadTeam &team) {
+        const int icol = team.league_rank();
+
+        //----------------------------------------------------------------------
+        // To form EAM like state%q array, we need prognostics (gas and aerosol
+        // mmrs) atmosphere (qv, qc, nc, ni, etc.)
+        //----------------------------------------------------------------------
+
+        // Get prognostics
+        mam4::Prognostics progs_at_col =
+            mam_coupling::aerosols_for_column(wet_aero,  // output
+                                              icol);     // input
+        // Get atmospheric quantities
+        const haero::Atmosphere haero_atm =
+            atmosphere_for_column(dry_atm,  // output
+                                  icol);    // input
+
+        // Form state%q like array at surface level
+        Real state_q_at_surf_lev[pcnst] = {};
+        mam4::utils::extract_stateq_from_prognostics(
+            progs_at_col, haero_atm,  // input
+            state_q_at_surf_lev,      // output
+            surface_lev);             // input
+
+        // Compute the units conversion factor (kg/m2/s to kg/kg)
+        EKAT_KERNEL_ASSERT_MSG(dry_atm.p_del(icol, surface_lev) != 0,
+                               "Error! dry_atm.pdel must be non-zero!\n");
+        const Real rpdel       = 1.0 / dry_atm.p_del(icol, surface_lev);
+        const Real unit_factor = dt * gravit * rpdel;
+
+        // Update state vector with constituent fluxes
+        for(int icnst = istart; icnst < pcnst; ++icnst) {
+          state_q_at_surf_lev[icnst] +=
+              constituent_fluxes(icol, icnst) * unit_factor;
+        }
+        mam4::utils::inject_stateq_to_prognostics(state_q_at_surf_lev,  // input
+                                                  progs_at_col,  // output
+                                                  surface_lev);  // input
+      });                                                        // icol loop
+}
+
+}  // namespace
+}  // namespace scream
+
+#endif  // ifdef EAMXX_MAM_CONSTITUTE_FLUXES_FUNCTIONS_HPP