Adds linoz src sink function and namelist variables plus code cleanup

E3SM-Project · Oct 12, 2024 · dac5eb8 · dac5eb8
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diff --git a/components/eamxx/cime_config/namelist_defaults_scream.xml b/components/eamxx/cime_config/namelist_defaults_scream.xml
@@ -252,18 +252,28 @@ be lost if SCREAM_HACK_XML is not enabled.
 
     <!-- MAM4xx-Aerosol-Microphysics -->
     <mam4_aero_microphys inherit="atm_proc_base">
+      <!--Aerosol Microphysics processes on/off switches -->
+      <mam4_do_cond   type="logical" doc="">true</mam4_do_cond>
+      <mam4_do_newnuc type="logical" doc="">true</mam4_do_newnuc>
+      <mam4_do_coag   type="logical" doc="">true</mam4_do_coag>
+      <mam4_do_rename type="logical" doc="">true</mam4_do_rename>
+      <!-- LINOZ parameters -->
+      <mam4_o3_tau    type="real"    doc="">172800.0</mam4_o3_tau>
+      <mam4_o3_sfc    type="real"    doc="">3.0E-008</mam4_o3_sfc>
+      <mam4_o3_lbl    type="integer" doc="">4</mam4_o3_lbl>
       <mam4_linoz_ymd type="integer" > 20100101</mam4_linoz_ymd>
-      <mam4_linoz_file_name type="file" doc=""> ${DIN_LOC_ROOT}/atm/scream/mam4xx/linoz/ne30pg2/linoz1850-2015_2010JPL_CMIP6_10deg_58km_ne30pg2_c20240724.nc</mam4_linoz_file_name>
       <mam4_linoz_file_name hgrid="ne4np4.pg2" type="file" doc=""> ${DIN_LOC_ROOT}/atm/scream/mam4xx/linoz/ne4pg2/linoz1850-2015_2010JPL_CMIP6_10deg_58km_ne4pg2_c20240724.nc</mam4_linoz_file_name>
+      <mam4_linoz_file_name type="file" doc=""> ${DIN_LOC_ROOT}/atm/scream/mam4xx/linoz/ne30pg2/linoz1850-2015_2010JPL_CMIP6_10deg_58km_ne30pg2_c20240724.nc</mam4_linoz_file_name>
+      <!--Invariants-->
       <mam4_oxid_ymd type="integer" > 20150101 </mam4_oxid_ymd>
-      <mam4_oxid_file_name  type="file" doc="">${DIN_LOC_ROOT}/atm/scream/mam4xx/invariants/ne30pg2/oxid_1.9x2.5_L26_1850-2015_ne30pg2_c20241009.nc</mam4_oxid_file_name>
       <mam4_oxid_file_name  hgrid="ne4np4.pg2" type="file" doc="">${DIN_LOC_ROOT}/atm/scream/mam4xx/invariants/ne4pg2/oxid_1.9x2.5_L26_1850-2015_ne4pg2_c20241009.nc</mam4_oxid_file_name>
-
+      <mam4_oxid_file_name  type="file" doc="">${DIN_LOC_ROOT}/atm/scream/mam4xx/invariants/ne30pg2/oxid_1.9x2.5_L26_1850-2015_ne30pg2_c20241009.nc</mam4_oxid_file_name>
       <mam4_chlorine_loading_ymd type="integer" doc=""> 20100101 </mam4_chlorine_loading_ymd>
       <mam4_linoz_chlorine_file type="file" doc=""> ${DIN_LOC_ROOT}/atm/scream/mam4xx/linoz/Linoz_Chlorine_Loading_CMIP6_0003-2017_c20171114.nc</mam4_linoz_chlorine_file>
+      <!--Photolysis-->
       <mam4_rsf_file type="file" doc=""> ${DIN_LOC_ROOT}/atm/scream/mam4xx/photolysis/RSF_GT200nm_v3.0_c080811.nc</mam4_rsf_file>
       <mam4_xs_long_file type="file" doc=""> ${DIN_LOC_ROOT}/atm/scream/mam4xx/photolysis/temp_prs_GT200nm_JPL10_c130206.nc</mam4_xs_long_file>
-
+      <!--Vertical emissions-->
       <verti_emiss_ymd type="integer"> 20100101 </verti_emiss_ymd>
       <!-- For all other grids -->
       <mam4_so2_verti_emiss_file_name type="file" doc="">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne30pg2/elevated/cmip6_mam4_so2_elev_1x1_2010_clim_ne30pg2_c20241008.nc </mam4_so2_verti_emiss_file_name>

diff --git a/components/eamxx/src/physics/mam/eamxx_mam_microphysics_process_interface.cpp b/components/eamxx/src/physics/mam/eamxx_mam_microphysics_process_interface.cpp
diff --git a/components/eamxx/src/physics/mam/eamxx_mam_microphysics_process_interface.hpp b/components/eamxx/src/physics/mam/eamxx_mam_microphysics_process_interface.hpp
@@ -48,9 +48,6 @@ class MAMMicrophysics final : public scream::AtmosphereProcess {
   // The name of the subcomponent
   std::string name() const { return "mam_aero_microphysics"; }
 
-  // set aerosol microphysics configuration parameters (called by constructor)
-  void configure(const ekat::ParameterList &params);
-
   // grid
   void set_grids(
       const std::shared_ptr<const GridsManager> grids_manager) override;
@@ -68,13 +65,14 @@ class MAMMicrophysics final : public scream::AtmosphereProcess {
   // Finalize
   void finalize_impl(){/*Do nothing*/};
 
-  // performs some checks on the tracers group
-  void set_computed_group_impl(const FieldGroup &group) override;
-
  private:
   // number of horizontal columns and vertical levels
   int ncol_, nlev_;
 
+  // Namelist for LINOZ
+  int o3_lbl_;
+  Real o3_tau_, o3_sfc_;
+
   // The orbital year, used for zenith angle calculations:
   // If > 0, use constant orbital year for duration of simulation
   // If < 0, use year from timestamp for orbital parameters
@@ -228,7 +226,7 @@ class MAMMicrophysics final : public scream::AtmosphereProcess {
   std::shared_ptr<const AbstractGrid> grid_;
 
   // sets defaults for "namelist parameters"
-  void set_defaults_();
+  void set_namelist_params_();
 
   mam_coupling::TracerTimeState linoz_time_state_;
   view_2d work_photo_table_;

diff --git a/components/eamxx/src/physics/mam/impl/compute_o3_column_density.cpp b/components/eamxx/src/physics/mam/impl/compute_o3_column_density.cpp
@@ -18,7 +18,7 @@ void compute_o3_column_density(
   // NOTE: if we need o2 column densities, set_ub_col and setcol must be changed
   Kokkos::parallel_for(
       Kokkos::TeamThreadRange(team, mam4::nlev), [&](const int k) {
-        Real pdel = atm.hydrostatic_dp(k);
+        const Real pdel = atm.hydrostatic_dp(k);
         // extract aerosol state variables into "working arrays" (mass
         // mixing ratios) (in EAM, this is done in the gas_phase_chemdr
         // subroutine defined within
@@ -41,11 +41,12 @@ void compute_o3_column_density(
           invariants_k[i] = invariants(k, i);
         }
         // compute the change in o3 density for this column above its neighbor
-        mam4::mo_photo::set_ub_col(o3_col_deltas[k + 1], vmr, invariants_k,
-                                   pdel);
+        mam4::mo_photo::set_ub_col(o3_col_deltas[k + 1],      // out
+                                   vmr, invariants_k, pdel);  // out
       });
   // sum the o3 column deltas to densities
-  mam4::mo_photo::setcol(o3_col_deltas, o3_col_dens);
+  mam4::mo_photo::setcol(o3_col_deltas,  // in
+                         o3_col_dens);   // out
 }
 
 }  // namespace scream::impl
diff --git a/components/eamxx/src/physics/mam/impl/gas_phase_chemistry.cpp b/components/eamxx/src/physics/mam/impl/gas_phase_chemistry.cpp
@@ -253,9 +253,10 @@ void gas_phase_chemistry(
 
   // solve chemical system implicitly
   Real prod_out[clscnt4], loss_out[clscnt4];
-  mam4::gas_chemistry::imp_sol(qq, reaction_rates, het_rates, extfrc_rates, dt,
-                               permute_4, clsmap_4, factor, epsilon, prod_out,
-                               loss_out);
+  mam4::gas_chemistry::imp_sol(qq,                                       // out
+                               reaction_rates, het_rates, extfrc_rates,  // in
+                               dt, permute_4, clsmap_4, factor,          // in
+                               epsilon, prod_out, loss_out);             // out
 
   // save h2so4 change by gas phase chem (for later new particle nucleation)
   if(ndx_h2so4 > 0) {

diff --git a/components/eamxx/src/physics/mam/impl/helper_micro.hpp b/components/eamxx/src/physics/mam/impl/helper_micro.hpp
@@ -395,15 +395,19 @@ inline std::shared_ptr<AbstractRemapper> create_horiz_remapper(
         horiz_interp_tgt_grid, IdentityRemapper::SrcAliasTgt);
   } else {
     EKAT_REQUIRE_MSG(tracer_data.ncols_data <= ncols_model,
-                     "Error! We do not allow to coarsen spa data to fit the "
+                     "Error! We do not allow to coarsen tracer external "
+                     "forcing data to fit the "
                      "model. We only allow\n"
-                     "       spa data to be at the same or coarser resolution "
+                     "       tracer external forcing data to be at the same or "
+                     "coarser resolution "
                      "as the model.\n");
     // We must have a valid map file
     EKAT_REQUIRE_MSG(
         map_file != "",
-        "ERROR: Spa data is on a different grid than the model one,\n"
-        "       but spa_remap_file is missing from SPA parameter list.");
+        "ERROR: tracer external forcing data is on a different grid than the "
+        "model one,\n"
+        "       but tracer external forcing data remap file is missing from "
+        "tracer external forcing data parameter list.");
 
     remapper =
         std::make_shared<RefiningRemapperP2P>(horiz_interp_tgt_grid, map_file);
@@ -447,13 +451,13 @@ inline std::shared_ptr<AtmosphereInput> create_tracer_data_reader(
 }  // create_tracer_data_reader
 
 inline void update_tracer_data_from_file(
-    std::shared_ptr<AtmosphereInput> &scorpio_reader,
+    const std::shared_ptr<AtmosphereInput> &scorpio_reader,
     const int time_index,  // zero-based
     AbstractRemapper &tracer_horiz_interp, TracerData &tracer_data) {
   // 1. read from field
   scorpio_reader->read_variables(time_index);
-  // 2. Run the horiz remapper (it is a do-nothing op if spa data is on same
-  // grid as model)
+  // 2. Run the horiz remapper (it is a do-nothing op if tracer external forcing
+  // data is on same grid as model)
   tracer_horiz_interp.remap(/*forward = */ true);
   //
   const int nvars = tracer_data.nvars_;
@@ -472,19 +476,20 @@ inline void update_tracer_data_from_file(
 
 }  // update_tracer_data_from_file
 inline void update_tracer_timestate(
-    std::shared_ptr<AtmosphereInput> &scorpio_reader, const util::TimeStamp &ts,
-    AbstractRemapper &tracer_horiz_interp, TracerTimeState &time_state,
-    TracerData &data_tracer) {
+    const std::shared_ptr<AtmosphereInput> &scorpio_reader,
+    const util::TimeStamp &ts, AbstractRemapper &tracer_horiz_interp,
+    TracerTimeState &time_state, TracerData &data_tracer) {
   // Now we check if we have to update the data that changes monthly
-  // NOTE:  This means that SPA assumes monthly data to update.  Not
+  // NOTE:  This means that tracer external forcing assumes monthly data to
+  // update.  Not
   //        any other frequency.
   const auto month = ts.get_month() - 1;  // Make it 0-based
   if(month != time_state.current_month) {
     const auto tracer_data = data_tracer.data;
     const int nvars        = data_tracer.nvars_;
     const auto ps          = data_tracer.ps;
 
-    // Update the SPA time state information
+    // Update the tracer external forcing time state information
     time_state.current_month = month;
     time_state.t_beg_month =
         util::TimeStamp({ts.get_year(), month + 1, 1}, {0, 0, 0})
@@ -505,7 +510,7 @@ inline void update_tracer_timestate(
     // Assume the data is saved monthly and cycles in one year
     // Add offset_time_index to support cases where data is saved
     // from other periods of time.
-    // Update the SPA forcing data for this month and next month
+    // Update the tracer external forcing data for this month and next month
     // Start by copying next months data to this months data structure.
     // NOTE: If the timestep is bigger than monthly this could cause the wrong
     // values
@@ -685,11 +690,12 @@ inline void perform_vertical_interpolation(const const_view_1d &altitude_int,
 }
 
 inline void advance_tracer_data(
-    std::shared_ptr<AtmosphereInput> &scorpio_reader,
-    AbstractRemapper &tracer_horiz_interp, const util::TimeStamp &ts,
-    TracerTimeState &time_state, TracerData &data_tracer,
-    const const_view_2d &p_tgt, const const_view_2d &zi_tgt,
-    const view_2d output[]) {
+    const std::shared_ptr<AtmosphereInput> &scorpio_reader,   // in
+    AbstractRemapper &tracer_horiz_interp,                    // out
+    const util::TimeStamp &ts,                                // in
+    TracerTimeState &time_state, TracerData &data_tracer,     // out
+    const const_view_2d &p_tgt, const const_view_2d &zi_tgt,  // in
+    const view_2d output[]) {                                 // out
   /* Update the TracerTimeState to reflect the current time, note the addition
    * of dt */
   time_state.t_now = ts.frac_of_year_in_days();

diff --git a/components/eamxx/tests/single-process/mam/aero_microphys/input.yaml b/components/eamxx/tests/single-process/mam/aero_microphys/input.yaml
@@ -10,6 +10,15 @@ time_stepping:
 
 atmosphere_processes:
   atm_procs_list: [mam4_aero_microphys]
+  mam4_aero_microphys:
+    mam4_do_cond: true
+    mam4_do_newnuc: true
+    mam4_do_coag: true
+    mam4_do_rename: true
+    mam4_o3_tau: 172800.0
+    mam4_o3_sfc: 3.0E-008
+    mam4_o3_lbl: 4
+
   mam4_aero_microphys:
    mam4_linoz_ymd : 20100101   
    mam4_linoz_file_name : ${SCREAM_DATA_DIR}/mam4xx/linoz/ne2np4/linoz1850-2015_2010JPL_CMIP6_10deg_58km_ne2np4_c20240724.nc
@@ -46,10 +55,10 @@ initial_conditions:
   topography_filename: ${TOPO_DATA_DIR}/${EAMxx_tests_TOPO_FILE}
   phis : 1.0
   pbl_height: 1.0
-  dgnum : [1.37146e-07 ,3.45899e-08 ,1.00000e-06 ,9.99601e-08] 
-  dgnumwet : [1.37452e-07 ,3.46684e-08 ,1.00900e-06 ,9.99601e-08]
-  wetdens : [5.08262e-12 ,1.54035e-13 ,3.09018e-13 ,9.14710e-22]  
   #These should come from the input file
+  dgnum: [1.246662106183775E-007, 4.081134799487888E-008, 1.103139143795796E-006, 1.000000011686097E-007]
+  dgnumwet: [2.367209731605067E-007, 6.780643470563889E-008, 3.028011448344027E-006, 1.000000096285154E-007]
+  wetdens: [1038.67760516297, 1046.20002003441, 1031.74623165457, 1086.79731859184]
 
 # The parameters for I/O control
 Scorpio:

diff --git a/externals/mam4xx b/externals/mam4xx