Improve diagnostics

.github/workflows/run_test_suite.yml

@@ -26,6 +26,7 @@ jobs:
           sudo apt-get update
           sudo apt install make gfortran netcdf-bin libnetcdf-dev libnetcdff-dev openmpi-bin libopenmpi-dev
       - name: Build docs
+        continue-on-error: true
         run: |
           cd docs/src
           make html

defaults/diagnostics_latest.yaml

@@ -464,7 +464,7 @@ pocToFloor :
    longname : POC Flux Hitting Sea Floor
    units : nmol/cm^2/s
    vertical_grid : none
-   frequency : never
+   frequency : medium
    operator : average
 pocToSed :
    longname : POC Flux to Sediments

defaults/json/diagnostics_latest.json

@@ -2244,7 +2244,7 @@
       "vertical_grid": "layer_avg"
    },
    "pocToFloor": {
-      "frequency": "never",
+      "frequency": "medium",
       "longname": "POC Flux Hitting Sea Floor",
       "operator": "average",
       "units": "nmol/cm^2/s",

docs/py_requirements.txt

@@ -2,4 +2,6 @@ pylint==2.10.2
 Sphinx==1.7.5
 sphinxcontrib-bibtex==0.4.0
 pybtex==0.22
+jinja2<3
+MarkupSafe<2.1
 git+https://github.com/marbl-ecosys/sphinx_rtd_theme.git@version-dropdown

src/marbl_diagnostics_mod.F90

@@ -3473,7 +3473,7 @@ subroutine store_diagnostics_autotrophs(marbl_domain, &
     !-----------------------------------------------------------------------
     integer(int_kind) :: n, m
     real(r8) :: autotrophC_weight(marbl_domain%km)
-    real(r8) :: autotrophC_zint_100m
+    real(r8) :: autotrophC_zint_100m, photoC_NO3_zint_100m
     real(r8) :: limterm(marbl_domain%km)
     !-----------------------------------------------------------------------
 
@@ -3495,6 +3495,7 @@ subroutine store_diagnostics_autotrophs(marbl_domain, &
     diags(ind%photoC_TOT_zint)%field_2d(1) = c0
     diags(ind%photoC_TOT_zint_100m)%field_2d(1) = c0
     diags(ind%photoC_NO3_TOT_zint)%field_2d(1) = c0
+    diags(ind%photoC_NO3_TOT_zint_100m)%field_2d(1) = c0
 
     do n = 1, autotroph_cnt
        ! compute biomass weighted average of limitation terms over 0..100m
@@ -3628,11 +3629,15 @@ subroutine store_diagnostics_autotrophs(marbl_domain, &
             diags(ind%photoC_zint_100m(n))%field_2d(1)
 
        call marbl_diagnostics_share_compute_vertical_integrals(diags(ind%photoC_NO3(n))%field_3d(:, 1), &
-            delta_z, kmt, full_depth_integral=diags(ind%photoC_NO3_zint(n))%field_2d(1))
+            delta_z, kmt, full_depth_integral=diags(ind%photoC_NO3_zint(n))%field_2d(1), &
+            near_surface_integral=photoC_NO3_zint_100m)
 
        diags(ind%photoC_NO3_TOT_zint)%field_2d(1) = diags(ind%photoC_NO3_TOT_zint)%field_2d(1) + &
             diags(ind%photoC_NO3_zint(n))%field_2d(1)
 
+       diags(ind%photoC_NO3_TOT_zint_100m)%field_2d(1) = diags(ind%photoC_NO3_TOT_zint_100m)%field_2d(1) + &
+            photoC_NO3_zint_100m
+
        call marbl_diagnostics_share_compute_vertical_integrals(diags(ind%auto_graze(n))%field_3d(:, 1), &
             delta_z, kmt, full_depth_integral=diags(ind%auto_graze_zint(n))%field_2d(1), &
             near_surface_integral=diags(ind%auto_graze_zint_100m(n))%field_2d(1))