Merge pull request #98 from mvertens/feature/oslo_aero_integrate

noresm_v7_cam6_3_123: Add oslo-aero as an new aerosol scheme

Addition of oslo-aero as new aerosol scheme

Summary: Addition of oslo-aero as a new aerosol scheme via primarily the addition of new cpp-ifdefs. 

Contributors: @mvertens @ingvisau @gold2718 

Reviewers: @gold2718 

Purpose of changes: #97: Add oslo-aero as new aerosol scheme

Github PR URL: #98

Changes made to build system: Changes for turning on oslo-aero 

Changes made to the namelist: new oslo-aero namelists

Changes to the defaults for the boundary datasets: oslo-aero boundary datasets

Substantial timing or memory changes: to be determined

The main aim of this PR is to being carrying out simulations with oslo-aero as the aerosol scheme used in CAM.  New OSLO_AERO CPP-ifdefs have been introduced that enable oslo-aero to be activated. This will be the first step for future object-oriented refactorization that is planned. 

Testing: NOTE: Regression testing of aux_cam_noresm completed.  
- Tests added for Oslo Aero
- Substantial changes were needed to ensure restart and BfB behavior when channging task count. This makes it impossible to compare with the release version of Oslo Aero.

AEROCOM is not enabled in this PR 

closes #89: Implement Oslo-aero in noresm_develop
closes #97: Add oslo-aero as new aerosol scheme

.gitignore

@@ -4,6 +4,7 @@ chem_proc
 cime
 components
 manage_externals.log
+src/chemistry/oslo_aero
 src/physics/ali_arms/
 src/physics/camnor_phys
 src/physics/carma/base

Externals.cfg

@@ -29,7 +29,7 @@ required = True
 
 [cime]
 protocol = git
-tag = cime6.0.105_noresm_v4
+tag = cime6.0.173_noresm_v0
 repo_url = https://github.com/NorESMhub/cime.git
 local_path = cime
 required = True

Externals_CAM.cfg

@@ -63,11 +63,18 @@ required = True
 
 [camnor_phys]
 protocol = git
-tag = camnor_noresm_v0.0.4
+tag = camnor_noresm_v0.0.5
 repo_url = https://github.com/NorESMhub/CAM-Nor-physics
 local_path = src/physics/camnor_phys
 required = True
 
+[oslo_aero]
+protocol = git
+tag = noresm_oslo_aero_v0
+repo_url = https://github.com/NorESMhub/OSLO_AERO
+local_path = src/chemistry/oslo_aero
+required = True
+
 [hemco]
 protocol = git
 tag = hemco-cesm1_2_0_hemco3_6_2_cesm

bld/build-namelist

@@ -569,6 +569,11 @@ if ($cfg->get('debug')) {
 my $prescribe_aerosols = $TRUE;
 if ($simple_phys) {$prescribe_aerosols = $FALSE;}
 
+if( $chem =~ /_oslo/){
+$prescribe_aerosols = $FALSE;
+print " ==> Using Oslo aerosols: PRESCRIBED AERO = FALSE (not yet implemented) \n"
+}
+
 # Chemistry deposition lists
 if ( ($chem ne 'none') or ( $prog_species ) ){
     my $chem_proc_src = $cfg->get('chem_proc_src');
@@ -928,7 +933,15 @@ else {
 my $aer_model = 'bam';
 if ($prescribed_aero_model eq 'modal' or $chem =~ /_mam/) {$aer_model = 'mam';}
 
-if ($aer_model eq 'mam' ) {
+if ($chem =~ /_mam_oslo/) {$aer_model = 'oslo';}
+
+   #do nothing here
+
+if ($aer_model eq 'oslo') {
+
+   #do nothing here
+
+} elsif ($aer_model eq 'mam' ) {
 
   my $aero_modes = '3mode';
   if ($chem =~ /_mam7/) {$aero_modes = '7mode';}
@@ -1542,7 +1555,7 @@ elsif ($carma eq 'tholin') {
 
 # turn on stratospheric aerosol forcings in CAM6 configurations
 my $chem_has_ocs = chem_has_species($cfg, 'OCS');
-if (($phys =~ /cam6/ or $phys =~ /cam_dev/) and $chem =~ /_mam/) {
+if (($phys =~ /cam6/ or $phys =~ /cam_dev/) and $chem =~ /_mam/ and $chem ne 'trop_mam_oslo') {
   # turn on volc forcings in cam6 -- prognostic or prescribed
   if ( $chem_has_ocs ) {
       # turn on prognostic stratospheric aerosols
@@ -1684,6 +1697,7 @@ if ($chem =~ /ghg_mam4/) {
     }
     add_default($nl, 'flbc_file');
 }
+
 if ( $prog_species ) {
     my $ddval;
     my $emisval;
@@ -2594,10 +2608,96 @@ if (($chem eq 'trop_mam4') or ($chem eq 'waccm_sc_mam4') or ($chem eq 'ghg_mam4'
         add_default($nl, $file);
     }
 }
-if ($chem eq 'trop_mam7') {
+
+if ($chem eq 'trop_mam_oslo' ) {
 
     my %species;
 
+    # Surface emission datasets:
+    %species = ();
+    %species = (%species,
+                 'DMS    -> ' => 'dms_oslo_emis_file',
+                 'SO2    -> ' => 'so2_oslo_emis_file',
+                 'BC_AX    -> ' => 'bc_ax_oslo_emis_file',
+                 'BC_N     -> ' =>'bc_n_oslo_emis_file',
+                 'BC_NI    -> ' =>'bc_ni_oslo_emis_file',
+                 'SO4_PR   -> ' =>'so4_pr_oslo_emis_file',
+                 'OM_NI    -> ' =>'om_ni_oslo_emis_file',
+	 	           'monoterp -> ' => 'monoterp_oslo_emis_file',
+		           'isoprene -> ' => 'isoprene_oslo_emis_file',
+                 );
+
+    my $first = 1;
+    my $pre = "";
+    my $val = "";
+    foreach my $id (sort keys %species) {
+        my $rel_filepath = get_default_value($species{$id} );
+        my $abs_filepath = set_abs_filepath($rel_filepath, $inputdata_rootdir);
+        $val .= $pre . quote_string($id . $abs_filepath);
+        if ($first) {
+            $pre = ",";
+            $first = 0;
+        }
+    }
+    add_default($nl, 'srf_emis_specifier', 'val'=>$val);
+    unless (defined $nl->get_value('srf_emis_type')) {
+        add_default($nl, 'srf_emis_type',      'val'=>'CYCLICAL');
+        add_default($nl, 'srf_emis_cycle_yr',  'val'=>'2000');
+    }
+
+    # Vertical emission datasets:
+    %species = ();
+    %species = ('SO2     -> ' => 'so2_oslo_ext_file',
+                'BC_AX   -> ' => 'bc_ax_oslo_ext_file',
+                'BC_N    -> ' => 'bc_n_oslo_ext_file',
+                'BC_NI   -> ' => 'bc_ni_oslo_ext_file',
+                'OM_NI   -> ' => 'om_ni_oslo_ext_file',
+                'SO4_PR  -> ' => 'so4_pr_oslo_ext_file');
+
+    $first = 1;
+    $pre = "";
+    $val = "";
+    foreach my $id (sort keys %species) {
+        my $rel_filepath = get_default_value($species{$id} );
+        my $abs_filepath = set_abs_filepath($rel_filepath, $inputdata_rootdir);
+        $val .= $pre . quote_string($id . $abs_filepath);
+        if ($first) {
+            $pre = ",";
+            $first = 0;
+        }
+    }
+    add_default($nl, 'ext_frc_specifier', 'val'=>$val);
+    unless (defined $nl->get_value('ext_frc_type')) {
+        add_default($nl, 'ext_frc_type',      'val'=>"'CYCLICAL'");
+	add_default($nl, 'ext_frc_cycle_yr',  'val'=>'2000');
+    }
+
+    # Prescribed species
+    add_default($nl, 'tracer_cnst_specifier', 'val'=>"'O3','OH','NO3','HO2'");
+    unless (defined $nl->get_value('tracer_cnst_type')) {
+	 add_default($nl, 'tracer_cnst_type',    'ver'=>'fixed_ox');
+	 add_default($nl, 'tracer_cnst_cycle_yr','ver'=>'fixed_ox');
+    }
+
+    my @files = ('tracer_cnst_datapath', 'tracer_cnst_file', 'tracer_cnst_filelist');
+    foreach my $file (@files) {
+        add_default($nl, $file, 'ver'=>'fixed_ox');
+    }
+
+    add_default($nl, 'fstrat_list', 'val'=>"' '");
+    add_default($nl, 'flbc_list', 'val'=>"' '");
+
+    # Datasets
+    my @files = ('soil_erod_file',
+                 'xs_long_file', 'rsf_file', 'exo_coldens_file' );
+    foreach my $file (@files) {
+        add_default($nl, $file);
+    }
+}
+
+if ($chem eq 'trop_mam7') {
+    my %species;
+
     # Surface emission datasets:
     %species = ();
     %species = ('DMS       -> ' => 'dms_emis_file',
@@ -2625,6 +2725,7 @@ if ($chem eq 'trop_mam7') {
             $first = 0;
         }
     }
+
     add_default($nl, 'srf_emis_specifier', 'val'=>$val);
     unless (defined $nl->get_value('srf_emis_type')) {
         add_default($nl, 'srf_emis_type',    'val'=>'CYCLICAL');
@@ -2807,6 +2908,7 @@ if ($chem =~ /waccm_ma/ or $chem =~ /waccm_tsmlt/) {
     add_default($nl, 'efield_potential_max', 'val'=>'120.D0');
 }
 
+
 # Determine the source of the prescribed GHG values.
 
 my $lbc_file = $nl->get_value('flbc_file');
@@ -2917,6 +3019,31 @@ $use_simple_phys = '.false.';
 if ($simple_phys) {$use_simple_phys = '.true.';}
 $nl->set_variable_value('phys_ctl_nl', 'use_simple_phys', $use_simple_phys);
 
+#Cam-Oslo options
+ add_default($nl, 'volc_fraction_coarse');
+ add_default($nl, 'aerotab_table_dir');
+ add_default($nl, 'ocean_filepath');
+ add_default($nl, 'dms_source');
+ add_default($nl, 'opom_source');
+#add_default($nl, 'dms_source_type');
+#add_default($nl, 'dms_cycle_year');
+#add_default($nl, 'ocean_filename');
+#add_default($nl, 'ocean_filepath');
+#add_default($nl, 'opom_source');
+unless (defined $nl->get_value('ocean_filename')) {
+    add_default($nl, 'ocean_filename');
+}
+unless (defined $nl->get_value('opom_source_type')) {
+    add_default($nl, 'opom_source_type');
+    add_default($nl, 'opom_cycle_year');
+}
+unless (defined $nl->get_value('dms_source_type')) {
+    add_default($nl, 'dms_source_type');
+    add_default($nl, 'dms_cycle_year');
+}
+#add_default($nl, 'opom_source_type');
+#add_default($nl, 'opom_cycle_year');
+
 # WACCM-X runtime options
 add_default($nl, 'waccmx_opt');
 

bld/config_files/definition.xml

@@ -106,8 +106,8 @@ meteor_smoke (Meteor Smoke), mixed_sulfate (Meteor Smoke and Sulfate), pmc (Pola
 sulfate (Sulfate Aerosols), tholin (early earth haze), test_detrain (Detrainment), test_growth (Particle Growth), test_passive (Passive Dust),
 test_radiative (Radiatively Active Dust), test_swelling (Sea Salt), test_tracers (Asian Monsoon), test_tracers2 (Guam).
 </entry>
-<entry id="chem" valid_values="none,ghg_mam4,terminator,trop_mam3,trop_mam4,trop_mam7,trop_mozart,trop_strat_mam4_ts2,trop_strat_mam4_vbs,trop_strat_mam4_vbsext,trop_strat_mam5_ts2,trop_strat_mam5_vbs,trop_strat_mam5_vbsext,waccm_ma,waccm_mad,waccm_ma_sulfur,waccm_sc,waccm_sc_mam4,waccm_mad_mam4,waccm_ma_mam4,waccm_tsmlt_mam4,waccm_tsmlt_mam4_vbsext,waccm_mad_mam5,waccm_ma_mam5,waccm_tsmlt_mam5,waccm_tsmlt_mam5_vbsext" value="">
-  Chemistry package: none,ghg_mam4,terminator,trop_mam3,trop_mam4,trop_mam7,trop_mozart,trop_strat_mam4_ts2,trop_strat_mam4_vbs,trop_strat_mam4_vbsext,trop_strat_mam5_ts2,trop_strat_mam5_vbs,trop_strat_mam5_vbsext,waccm_ma,waccm_mad,waccm_ma_sulfur,waccm_sc,waccm_sc_mam4,waccm_mad_mam4,waccm_ma_mam4,waccm_tsmlt_mam4,waccm_tsmlt_mam4_vbsext,waccm_mad_mam5,waccm_ma_mam5,waccm_tsmlt_mam5,waccm_tsmlt_mam5_vbsext
+<entry id="chem" valid_values="none,ghg_mam4,terminator,trop_mam3,trop_mam4,trop_mam7,trop_mam_oslo,trop_mozart,trop_strat_mam4_ts2,trop_strat_mam4_vbs,trop_strat_mam4_vbsext,trop_strat_mam5_ts2,trop_strat_mam5_vbs,trop_strat_mam5_vbsext,waccm_ma,waccm_mad,waccm_ma_sulfur,waccm_sc,waccm_sc_mam4,waccm_mad_mam4,waccm_ma_mam4,waccm_tsmlt_mam4,waccm_tsmlt_mam4_vbsext,waccm_mad_mam5,waccm_ma_mam5,waccm_tsmlt_mam5,waccm_tsmlt_mam5_vbsext" value="">
+  Chemistry package: none,ghg_mam4,terminator,trop_mam3,trop_mam4,trop_mam7,trop_mam_oslo,trop_mozart,trop_strat_mam4_ts2,trop_strat_mam4_vbs,trop_strat_mam4_vbsext,trop_strat_mam5_ts2,trop_strat_mam5_vbs,trop_strat_mam5_vbsext,waccm_ma,waccm_mad,waccm_ma_sulfur,waccm_sc,waccm_sc_mam4,waccm_mad_mam4,waccm_ma_mam4,waccm_tsmlt_mam4,waccm_tsmlt_mam4_vbsext,waccm_mad_mam5,waccm_ma_mam5,waccm_tsmlt_mam5,waccm_tsmlt_mam5_vbsext
 </entry>
 <entry id="prog_species" valid_values="DST,SSLT,SO4,GHG,OC,BC,CARBON16" value="" list="1">
 Prognostic mozart species packages: list of any subset of the following: DST,SSLT,SO4,GHG,OC,BC,CARBON16
@@ -224,7 +224,7 @@ User specified C compiler options to append to Makefile defaults.
 <entry id="fc" value="">
 User specified Fortran compiler overrides Makefile default.
 </entry>
-<entry id="fc_type" valid_values="cray,pgi,intel,gnu,pathscale,ibm,nag,nvhpc,pgi-gpu,nvhpc-gpu" value="">
+<entry id="fc_type" valid_values="intel,gnu" value="">
 Type of Fortran compiler.  Used when -fc specifies a generic wrapper script
 such as mpif90 or ftn.
 </entry>

bld/configure

@@ -64,12 +64,15 @@ OPTIONS
                           test_tracers, test_tracers2].
                         Default: none.
     -chem <name>       Build CAM with specified prognostic chemistry package
-                       [ none | ghg_mam4 | terminator | trop_mam3 | trop_mam4 | trop_mam7 | trop_mozart | trop_strat_mam4_ts2 |
+                       [ none | ghg_mam4 | terminator | trop_mam3 | trop_mam4 | trop_mam7 | trop_mam_oslo | trop_mozart | trop_strat_mam4_ts2 |
                          trop_strat_mam4_vbs | trop_strat_mam4_vbsext | trop_strat_mam5_ts2 | trop_strat_mam5_vbs |
                          trop_strat_mam5_vbsext | waccm_ma | waccm_mad | waccm_ma_sulfur | waccm_sc | waccm_sc_mam4 |
                          waccm_mad_mam4 | waccm_ma_mam4 | waccm_tsmlt_mam4 | waccm_tsmlt_mam4_vbsext | waccm_mad_mam5 |
                          waccm_ma_mam5 | waccm_tsmlt_mam5 | waccm_tsmlt_mam5_vbsext ].
-                        Default: trop_mam4 for cam6 and trop_mam3 for cam5.
+                        Default: trop_mam_oslo when -camnor is specified
+                        Default: trop_mam5 for cam7
+                        Default: trop_mam4 for cam6
+                        Default: trop_mam3 for cam5.
      -[no]clubb_sgs     Switch on [off] CLUBB_SGS.  Default: on for cam6, otherwise off.
      -clubb_opts <list> Comma separated list of CLUBB options to turn on/off.  By default they are all off.
                         Current option is: clubb_do_adv (Advect CLUBB moments)
@@ -154,13 +157,13 @@ OPTIONS
      -cosp_libdir <dir> Directory containing COSP library.
      -esmf_libdir <dir> Directory containing ESMF library and esmf.mk file.
      -fc <name>         User specified Fortran compiler.  Overrides Makefile default.
-     -fc_type <name>    Type of Fortran compiler [pgi | intel | gnu | pathscale
-                        | ibm | nag].  This argument is used in conjunction
+     -fc_type <name>    Type of Fortran compiler [intel | gnu].
+                        This argument is used in conjunction
                         with the -fc argument when the name of the fortran
-                        compiler refers to a wrapper script (e.g., mpif90
-                        or ftn).  In this case the user needs to specify
+                        compiler refers to a wrapper script (e.g., mpif90).
+                        In this case the user needs to specify
                         the type of Fortran compiler that is being invoked
-                        by the wrapper script.  Default: pgi
+                        by the wrapper script.  Default: gnu
      -fflags <string>   A string of user specified Fortran compiler flags.  Appended to
                         Makefile defaults.  See -fopt to override optimization flags.
      -fopt <string>     A string of user specified Fortran compiler optimization flags.
@@ -589,6 +592,9 @@ my $chem_pkg = 'trop_mam4';
 if ($simple_phys or $phys_pkg =~ m/^cam[34]$/ or $phys_pkg eq 'spcam_sam1mom') {
     $chem_pkg = 'none';
 }
+elsif ($camnor) {
+    $chem_pkg = 'trop_mam_oslo';
+}
 elsif ($phys_pkg eq 'cam5' or $phys_pkg eq 'spcam_m2005') {
     $chem_pkg = 'trop_mam3';
 }
@@ -1409,6 +1415,8 @@ if ($chem_pkg =~ '_mam3') {
     $chem_cppdefs = ' -DMODAL_AERO -DMODAL_AERO_5MODE ';
 } elsif ($chem_pkg =~ '_mam7') {
     $chem_cppdefs = ' -DMODAL_AERO -DMODAL_AERO_7MODE ';
+} elsif ($chem_pkg =~ '_oslo') {
+    $chem_cppdefs = ' -DOSLO_AERO';
 }
 
 # CARMA sectional microphysics
@@ -2094,6 +2102,10 @@ sub write_filepath
       }
     }
 
+    if ($chem =~/_oslo/) {
+	print $fh "$camsrcdir/src/chemistry/oslo_aero/src_cam\n";
+    }
+
     # offline unit driver (defaults to stub)
     print $fh "$camsrcdir/src/unit_drivers\n";
     print $fh "$camsrcdir/src/unit_drivers/${offline_drv}\n";
@@ -2130,7 +2142,11 @@ sub write_filepath
     if ($chem_src_dir) {
         print $fh "$chem_src_dir\n";
     }
-    if ($chem =~ /_mam/) {
+    if ($chem =~/_oslo/) {
+        # print $fh "$camsrcdir/src/chemistry/oslo_aero/object\n"; BUG: this does not compile
+        print $fh "$camsrcdir/src/chemistry/oslo_aero/src\n";
+        print $fh "$camsrcdir/src/chemistry/oslo_aero/cam_intr\n";
+    } elsif ($chem =~ /_mam/) {
         print $fh "$camsrcdir/src/chemistry/modal_aero\n";
     } else {
         print $fh "$camsrcdir/src/chemistry/bulk_aero\n";

bld/namelist_files/namelist_defaults_cam.xml

@@ -2278,9 +2278,10 @@
 <nucleate_ice_subgrid_strat microphys="mg2"            >1.2D0</nucleate_ice_subgrid_strat>
 <nucleate_ice_subgrid_strat microphys="mg3"            >1.2D0</nucleate_ice_subgrid_strat>
 
-<use_hetfrz_classnuc               >.false.</use_hetfrz_classnuc>
-<use_hetfrz_classnuc phys="cam6"   >.true.</use_hetfrz_classnuc>
-<use_hetfrz_classnuc phys="cam_dev">.true.</use_hetfrz_classnuc>
+<use_hetfrz_classnuc                     >.false.</use_hetfrz_classnuc>
+<use_hetfrz_classnuc phys="cam6"         >.true.</use_hetfrz_classnuc>
+<use_hetfrz_classnuc phys="cam_dev"      >.true.</use_hetfrz_classnuc>
+<use_hetfrz_classnuc chem="trop_mam_oslo">.true.</use_hetfrz_classnuc>
 <hetfrz_bc_scalfac>0.01D0</hetfrz_bc_scalfac>
 <hetfrz_dust_scalfac>0.05D0</hetfrz_dust_scalfac>
 
@@ -3338,6 +3339,7 @@
            ' C3H6_O3 + ISOP_O3 + MVK_O3 + MACR_O3 + MTERP_O3 + BCARY_O3 + S_O3 + SO_O3'
 </rxn_rate_sums>
 
+
 <!-- HEMCO: Harmonized Emissions Component -->
 <use_hemco>.false.</use_hemco>
 <hemco_data_root>atm/cam/geoschem/emis/ExtData/HEMCO</hemco_data_root>
@@ -3365,4 +3367,17 @@
 <hemco_grid_xdim hgrid="1.9x2.5">144</hemco_grid_xdim>
 <hemco_grid_ydim hgrid="1.9x2.5">91</hemco_grid_ydim>
 
+<!-- CAM-Oslo variables -->
+<dme_energy_adjust>.true.</dme_energy_adjust>
+<volc_fraction_coarse   >0.0</volc_fraction_coarse>
+<aerotab_table_dir>noresm-only/atm/cam/camoslo/AeroTab_8jun17/</aerotab_table_dir>
+<dms_source>lana</dms_source>
+<dms_source_type>CYCLICAL</dms_source_type>
+<dms_cycle_year>2000</dms_cycle_year>
+<opom_source>odowd</opom_source>
+<opom_source_type>CYCLICAL</opom_source_type>
+<opom_cycle_year>2000</opom_cycle_year>
+<ocean_filename>Lana_ocean_1849_2006.nc</ocean_filename>
+<ocean_filepath>noresm-only/atm/cam/camoslo</ocean_filepath>
+
 </namelist_defaults>