Merge extended nitrogen cycle, M4AGO scheme and preformed Si tracer into master

.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

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

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

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:

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:

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

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>