Merge extended nitrogen cycle, M4AGO scheme and preformed Si tracer i…

…nto master (#269) This merge brings in i) the extended nitrogen cycle developments carried out in the ESM2025 project (optionally), ii) the preformed silicate tracer, iii) bluefix (cyanobacteria) only in the euphotic zone (switch available to revert back to MLD, if needed for testing: leuphotic_cya), and iv) the M4AGO sinking scheme (Maerz et al. 2020) as submodule (optionally) into iHAMOCC/BLOM master. About the extended nitrogen cycle: The extended nitrogen cycle incorporates two new tracers: ammonium and nitrite. The extended nitrogen cycle features an explicit representation of the following processes: - ammonification (detritus -> NH4) - updated bluefix approach (N2-fixation) with NH4 release, also adjusted for the new BLOM coordinates (euphotic zone only as option or as before) - 2-step nitrification (NH4 -> NO2 and NO2 -> NO3), with N2O release during the first step, both steps resulting in dark-ocean carbon fixation - phytoplankton uptake of NH4 and NO3 - canonical denitrification steps (NO3 -> NO2 -> N2O -> N2) - dissimilatory nitrite/nitrate reduction (NO2 -> NH4) - anammox, including dark-ocean carbon fixation And capabilities for - online coupled air-sea gas exchange of N2O and NH3 in addition to the previously coupled gas fluxes - online coupled deposition of NOy and NHx are represented (if applicable, in both the water column and the sediment).
NorESMhub · May 31, 2024 · 916352e · 916352e
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diff --git a/.gitmodules b/.gitmodules
@@ -1,3 +1,6 @@
 [submodule "CVMix-src"]
 	path = pkgs/CVMix-src
 	url = [email protected]:CVMix/CVMix-src.git
+[submodule "pkgs/M4AGO-sinking-scheme"]
+	path = pkgs/M4AGO-sinking-scheme
+	url = [email protected]:jmaerz/M4AGO-sinking-scheme
diff --git a/Externals_BLOM.cfg b/Externals_BLOM.cfg
@@ -5,5 +5,12 @@ repo_url = https://github.com/CVMix/CVMix-src
 local_path = pkgs/CVMix-src
 required = True
 
+[M4AGO]
+tag = dev-1.0.0
+protocol = git
+repo_url = https://github.com/jmaerz/M4AGO-sinking-scheme
+local_path = pkgs/M4AGO-sinking-scheme
+required = True
+
 [externals_description]
 schema_version = 1.0.0
diff --git a/cesm/mod_cesm.F90 b/cesm/mod_cesm.F90
@@ -30,7 +30,9 @@ module mod_cesm
    use mod_forcing, only: trxday, srxday, swa, nsf, lip, sop, eva, rnf, rfi, &
                           fmltfz, sfl, ztx, mty, ustarw, slp, abswnd, &
                           lamult, lasl, ustokes, vstokes, atmco2, atmbrf, &
-                          flxdms, flxbrf, use_stream_relaxation
+                          flxdms, flxbrf,                                 &
+                          atmn2o,atmnh3,atmnhxdep,atmnoydep,              &
+                          use_stream_relaxation
    use mod_ben02, only: initai, rdcsic, rdctsf, fnlzai
    use mod_seaice, only: ficem
    use mod_checksum, only: csdiag, chksummsk
@@ -81,7 +83,11 @@ module mod_cesm
       atmco2_da, &       ! Atmospheric CO2 concentration [ppm].
       atmbrf_da, &       ! Atmospheric bromoform concentration [ppt].
       flxdms_da, &       ! dms surface flux computed by mediator [kg m-2 s-1]
-      flxbrf_da          ! brf surface flux computed by mediator [kg m-2 s-1]
+      flxbrf_da, &       ! brf surface flux computed by mediator [kg m-2 s-1]
+      atmn2o_da, &       ! Atmospheric nitrous oxide concentration [ppt].
+      atmnh3_da, &       ! Atmopsheric ammonia concentration [ppt].
+      atmnhxdep_da, &    ! Atmospheric nhx deposition field [kgN m-2 s-1]. 
+      atmnoydep_da       ! Atmospheric noy deposition field [kgN m-2 s-1].
 
    logical :: &
       smtfrc             ! If true, time smooth CESM forcing fields.
@@ -93,8 +99,10 @@ module mod_cesm
              frzpot, mltpot, swa_da, nsf_da, hmlt_da, lip_da, sop_da, eva_da, &
              rnf_da, rfi_da, fmltfz_da, sfl_da, ztx_da, mty_da, ustarw_da, &
              slp_da, abswnd_da, ficem_da, lamult_da, lasl_da, flxdms_da, flxbrf_da, &
-             ustokes_da, vstokes_da, atmco2_da, atmbrf_da, smtfrc, l1ci, l2ci, &
-             inicon_cesm, inifrc_cesm, getfrc_cesm
+             ustokes_da, vstokes_da, atmco2_da, atmbrf_da,atmn2o_da,atmnh3_da,&
+             atmnhxdep_da,atmnoydep_da, &
+             smtfrc, l1ci, l2ci,inicon_cesm, inifrc_cesm, getfrc_cesm
+
 contains
 
    subroutine inicon_cesm
@@ -122,9 +130,9 @@ subroutine inifrc_cesm
          ! If SST restoring is requested prepare interpolation and
          ! read climatological sea-ice concentration and surface temperature.
          if (trxday > 0._r8) then
-            call initai
-            call rdcsic
-            call rdctsf
+           call initai
+           call rdcsic
+           call rdctsf
          endif
 
          ! If SSS restoring is requested, read climatological sea surface salinity.
@@ -189,6 +197,10 @@ subroutine getfrc_cesm
            vstokes(i, j) = w1*vstokes_da(i, j, l1ci) + w2*vstokes_da(i, j, l2ci)
            atmco2(i, j)  = w1*atmco2_da(i, j, l1ci)  + w2*atmco2_da(i, j, l2ci)
            atmbrf(i, j)  = w1*atmbrf_da(i, j, l1ci)  + w2*atmbrf_da(i, j, l2ci)
+           atmn2o(i, j)  = w1*atmn2o_da(i, j, l1ci)  + w2*atmn2o_da(i, j, l2ci)
+           atmnh3(i, j)  = w1*atmnh3_da(i, j, l1ci)  + w2*atmnh3_da(i, j, l2ci)
+           atmnhxdep(i, j)  = w1*atmnhxdep_da(i, j, l1ci)  + w2*atmnhxdep_da(i, j, l2ci)
+           atmnoydep(i, j)  = w1*atmnoydep_da(i, j, l1ci)  + w2*atmnoydep_da(i, j, l2ci)
         enddo
         enddo
         do l = 1, isu(j)
@@ -228,6 +240,10 @@ subroutine getfrc_cesm
       call ncdefvar('vstokes_da', 'x y', ndouble, 8)
       call ncdefvar('atmco2_da', 'x y', ndouble, 8)
       call ncdefvar('atmbrf_da', 'x y', ndouble, 8)
+      call ncdefvar('atmn2o_da', 'x y', ndouble, 8)
+      call ncdefvar('atmnh3_da', 'x y', ndouble, 8)
+      call ncdefvar('atmnoydep_da', 'x y', ndouble, 8)
+      call ncdefvar('atmnoydep_da', 'x y', ndouble, 8)
       call ncdefvar('ztx_da', 'x y', ndouble, 8)
       call ncdefvar('mty_da', 'x y', ndouble, 8)
       call ncedef
@@ -272,6 +288,14 @@ subroutine getfrc_cesm
                   ip, 1, 1._r8, 0._r8, 8)
       call ncwrtr('atmbrf_da', 'x y', atmbrf_da(1 - nbdy, 1 - nbdy, l2ci), &
                   ip, 1, 1._r8, 0._r8, 8)
+      call ncwrtr('atmn2o_da', 'x y', atmn2o_da(1 - nbdy, 1 - nbdy, l2ci), &
+                  ip, 1, 1._r8, 0._r8, 8)
+      call ncwrtr('atmnh3_da', 'x y', atmnh3_da(1 - nbdy, 1 - nbdy, l2ci), &
+                  ip, 1, 1._r8, 0._r8, 8)
+      call ncwrtr('atmnhxdep_da', 'x y', atmnhxdep_da(1 - nbdy, 1 - nbdy, l2ci), &
+                  ip, 1, 1._r8, 0._r8, 8)
+      call ncwrtr('atmnoydep_da', 'x y', atmnoydep_da(1 - nbdy, 1 - nbdy, l2ci), &
+                  ip, 1, 1._r8, 0._r8, 8)
       call ncwrtr('ztx_da', 'x y', ztx_da(1 - nbdy, 1 - nbdy, l2ci), &
                   iu, 1, 1._r8, 0._r8, 8)
       call ncwrtr('mty_da', 'x y', mty_da(1 - nbdy, 1 - nbdy, l2ci), &
@@ -307,6 +331,10 @@ subroutine getfrc_cesm
          call chksummsk(vstokes, ip, 1, 'vstokes')
          call chksummsk(atmco2, ip, 1, 'atmco2')
          call chksummsk(atmbrf, ip, 1, 'atmbrf')
+         call chksummsk(atmn2o, ip, 1, 'atmn2o')
+         call chksummsk(atmnh3, ip, 1, 'atmnh3')
+         call chksummsk(atmnhxdep, ip, 1, 'atmnhxdep')
+         call chksummsk(atmnoydep, ip, 1, 'atmnoydep')
       endif
 
    end subroutine getfrc_cesm

diff --git a/cime_config/buildlib_2.1 b/cime_config/buildlib_2.1
@@ -65,6 +65,7 @@ def _main_func():
                      os.path.join(comp_root_dir_ocn, "channel"),
                      os.path.join(comp_root_dir_ocn, "single_column"),
                      os.path.join(comp_root_dir_ocn, "pkgs", "CVMix-src", "src", "shared"),
+                     os.path.join(comp_root_dir_ocn, "pkgs", "M4AGO-sinking-scheme", "src"),
                      os.path.join(comp_root_dir_ocn, "phy")]
 
             if turbclo != 0 and tracers != 0:

diff --git a/cime_config/buildlib_2.2 b/cime_config/buildlib_2.2
@@ -66,6 +66,7 @@ def _main_func():
                      os.path.join(comp_root_dir_ocn, "channel"),
                      os.path.join(comp_root_dir_ocn, "single_column"),
                      os.path.join(comp_root_dir_ocn, "pkgs", "CVMix-src", "src", "shared"),
+                     os.path.join(comp_root_dir_ocn, "pkgs", "M4AGO-sinking-scheme", "src"),
                      os.path.join(comp_root_dir_ocn, "phy")]
 
             if turbclo != 0 and tracers != 0:

diff --git a/cime_config/buildnml b/cime_config/buildnml
@@ -80,6 +80,10 @@ def buildnml(case, caseroot, compname):
     blom_tracer_modules       = case.get_value("BLOM_TRACER_MODULES")
     blom_atrc                 = case.get_value("BLOM_ATRC")
     hamocc_ciso               = case.get_value("HAMOCC_CISO")
+    hamocc_extncycle          = case.get_value("HAMOCC_EXTNCYCLE")
+    hamocc_n2oc               = case.get_value("HAMOCC_N2OC")
+    hamocc_atmndepc           = case.get_value("HAMOCC_ATMNDEPC")
+    hamocc_m4ago              = case.get_value("HAMOCC_M4AGO")
     hamocc_sedbypass          = case.get_value("HAMOCC_SEDBYPASS")
     hamocc_sedspinup          = case.get_value("HAMOCC_SEDSPINUP")
     hamocc_sedspinup_yr_start = case.get_value("HAMOCC_SEDSPINUP_YR_START")
@@ -185,6 +189,10 @@ def buildnml(case, caseroot, compname):
         config["blom_tracer_modules"] = blom_tracer_modules
         config["blom_atrc"] = blom_atrc
         config["hamocc_ciso"] = "yes" if hamocc_ciso else "no"
+        config["hamocc_extncycle"] = "yes" if hamocc_extncycle else "no"
+        config["hamocc_n2oc"] = "yes" if hamocc_n2oc else "no"
+        config["hamocc_atmndepc"] = "yes" if hamocc_atmndepc else "no"
+        config["hamocc_m4ago"] = "yes" if hamocc_m4ago else "no"
         config["hamocc_sedbypass"] = "yes" if hamocc_sedbypass else "no"
         config["hamocc_sedspinup"] = "yes" if hamocc_sedspinup else "no"
         config["hamocc_sedspinup_yr_start"] = hamocc_sedspinup_yr_start

diff --git a/cime_config/config_component.xml b/cime_config/config_component.xml
@@ -140,6 +140,53 @@
     <desc>Scenario for nitrogen deposition data. Requires module ecosys</desc>
   </entry>
 
+  <entry id="HAMOCC_EXTNCYCLE">
+    <type>logical</type>
+    <valid_values>TRUE,FALSE</valid_values>
+    <default_value>FALSE</default_value>
+    <values>
+       <value compset="_BGC.*%N2OC">TRUE</value>
+       <value compset="_BGC.*%NH3C">TRUE</value>
+       <value compset="_BGC.*%ATMNDEPC">TRUE</value>
+    </values>	    
+    <group>run_component_blom</group>
+    <file>env_run.xml</file>
+    <desc>Set preprocessor option to activate the extended nitrogen cycle code. Requires module ecosys</desc>
+  </entry>
+
+  <entry id="HAMOCC_ATMNDEPC">
+    <type>logical</type>
+    <valid_values>TRUE,FALSE</valid_values>
+    <default_value>FALSE</default_value>
+    <values>
+       <value compset="_BGC.*%ATMNDEPC">TRUE</value>
+    </values>
+    <group>run_component_blom</group>
+    <file>env_run.xml</file>
+    <desc>Nitrogen deposition coupled from atmosphere. Requires module ecosys and extncycle</desc>
+  </entry>
+
+  <entry id="HAMOCC_N2OC">
+    <type>logical</type>
+    <valid_values>TRUE,FALSE</valid_values>
+    <default_value>FALSE</default_value>
+    <values>
+       <value compset="_BGC.*%N2OC%NH3C">TRUE</value>
+    </values>
+    <group>run_component_blom</group>
+    <file>env_run.xml</file>
+    <desc>N2O and NH3 fluxes coupled from atmosphere. Requires module ecosys and extncycle</desc>
+  </entry>
+
+  <entry id="HAMOCC_M4AGO">
+    <type>logical</type>
+    <valid_values>TRUE,FALSE</valid_values>
+    <default_value>FALSE</default_value>
+    <group>run_component_blom</group>
+    <file>env_run.xml</file>
+    <desc>Set preprocessor option to activate the M4AGO sinking scheme. Requires module ecosys</desc>
+  </entry>
+
   <entry id="HAMOCC_CISO">
     <type>logical</type>
     <valid_values>TRUE,FALSE</valid_values>