Merge branch 'master' into 95-code-breaks-if-iswcal=0

.github/workflows/ersem.yml

@@ -41,11 +41,11 @@ jobs:
           with:
               python-version: '3.x'
         - name: Installing GOTM-FABM-ERSEM dependences
-          run: ./github-actions/gotm-fabm-ersem/gotm-fabm-ersem-dep-debian.sh 
+          run: ./github-actions/gotm-fabm-ersem/gotm-fabm-ersem-dep-debian.sh
         - name: Building and installing GOTM-FABM-ERSEM
           run: |
               BRANCH=${{ github.head_ref }}
-              ./github-actions/gotm-fabm-ersem/gotm-fabm-ersem-build.sh -b $BRANCH
+              ./github-actions/gotm-fabm-ersem/gotm-fabm-ersem-build.sh -b $BRANCH -f '-DCMAKE_Fortran_FLAGS="-fcheck=all"'
         - name: Running tutorial
           run: |
               ./github-actions/gotm-fabm-ersem/gotm-tut-config-setup.sh
@@ -70,7 +70,7 @@ jobs:
         - name: Building and installing FABM0d-GOTM-ERSEM
           run: |
               BRANCH=${{ github.head_ref }}
-              ./github-actions/fabm0d-gotm-ersem/fabm0d-gotm-ersem-build.sh -b $BRANCH
+              ./github-actions/fabm0d-gotm-ersem/fabm0d-gotm-ersem-build.sh -b $BRANCH -f '-DCMAKE_Fortran_FLAGS="-fcheck=all"'
         - name: Running tutorial
           run: |
               ./github-actions/fabm0d-gotm-ersem/aquarium-tut-config-setup.sh
@@ -90,11 +90,11 @@ jobs:
           with:
               python-version: '3.x'
         - name: Installing GOTM-FABM-ERSEM dependences
-          run: ./github-actions/gotm-fabm-ersem/gotm-fabm-ersem-dep-debian.sh 
+          run: ./github-actions/gotm-fabm-ersem/gotm-fabm-ersem-dep-debian.sh
         - name: Building and installing GOTM-FABM-ERSEM
           run: |
               BRANCH=${{ github.head_ref }}
-              ./github-actions/gotm-fabm-ersem/gotm-fabm-ersem-build.sh -f "-DCMAKE_Fortran_FLAGS="-pg"" -b $BRANCH
+              ./github-actions/gotm-fabm-ersem/gotm-fabm-ersem-build.sh -f "-DCMAKE_Fortran_FLAGS="-pg -fcheck=all"" -b $BRANCH
         - name: Running config
           run: |
               ./github-actions/gotm-fabm-ersem/gotm-profiling.sh

.readthedocs.yml

@@ -5,6 +5,12 @@
 # Required
 version: 2
 
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.8"
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   builder: html
@@ -15,6 +21,7 @@ formats:
    - pdf
 
 python:
-  version: 3.8
   install:
   - requirements: docs/requirements.txt
+  - method: pip
+    path: .

README.md

@@ -1,4 +1,4 @@
-![Tests](https://github.com/pmlmodelling/ersem/workflows/build-ersem/badge.svg) 
+![Tests](https://img.shields.io/github/actions/workflow/status/pmlmodelling/ersem/ersem.yml?label=tests&style=flat-square) 
 [![Documentation Status](https://readthedocs.org/projects/ersem/badge/?version=latest)](https://ersem.readthedocs.io/en/latest/?badge=latest)
 
 # ERSEM

github-actions/fabm0d-gotm-ersem/fabm0d-gotm-ersem-build.sh

@@ -19,6 +19,7 @@ git clone https://github.com/fabm-model/fabm.git
 
 echo "Cloning GOTM"
 git clone https://github.com/gotm-model/code.git gotm
+# Od driver needs a stable version of GOTM, currently that is v6
 cd gotm && git checkout v6.0 && git submodule update --init --recursive && cd ..
 
 echo "Checking out branch: $BRANCH"

github-actions/gotm-fabm-ersem/gotm-tut-config-setup.sh

@@ -7,4 +7,4 @@ cp ersem/testcases/fabm-ersem-15.06-L4-ben-docdyn-iop.yaml ersem-setups/L4/fabm.
 cd ersem-setups/L4
 
 echo "Running GOTM with repo configuration"
-~/local/gotm/bin/gotm
+~/local/gotm/bin/gotm --ignore_unknown_config

github-actions/gotm-fabm-ersem/gotm_tut.py

@@ -6,6 +6,7 @@
 import sys
 import re
 
+
 try:
     import netCDF4 as nc
 except ImportError:

github-actions/gotm-fabm-ersem/regen_expected_results.py

@@ -0,0 +1,75 @@
+"""
+Script that regenerates expected results. You will need to install GOTM on your machine
+first and use those results to regenerate the expected values
+"""
+
+
+import argparse
+import json
+import netCDF4 as nc
+from numpy import ndarray, interp
+
+class NumpyEncoder(json.JSONEncoder):
+    def default(self, obj):
+        if isinstance(obj, ndarray):
+            temp = [float(v) for v in obj.tolist()]
+            return temp
+        return json.JSONEncoder.default(self, obj)
+
+parser = argparse.ArgumentParser()
+parser.add_argument('-p', '--data-path', type=str, required=True,
+                    help='Path to output file from GOTM run')
+args, _ = parser.parse_known_args()
+data_path = args.data_path
+
+state_vars = \
+    ["N1_p" , "N3_n" , "N4_n" , "N5_s" , "O2_o" , "O3_c" , "O3_bioalk" , "R1_c" , "R1_n" ,
+    "R1_p" , "R2_c" , "R3_c" , "R4_c" , "R4_n" , "R4_p" , "R6_c" , "R6_n" , "R6_p" ,
+    "R6_s" , "R8_c" , "R8_n" , "R8_p" , "R8_s" , "B1_c" , "B1_n" , "B1_p" , "P1_c" ,
+    "P1_n" , "P1_p" , "P1_Chl" , "P1_s" , "P2_c" , "P2_n" , "P2_p" , "P2_Chl" , "P3_c" ,
+    "P3_n" , "P3_p" , "P3_Chl" , "P4_c" , "P4_n" , "P4_p" , "P4_Chl" , "Z4_c" , "Z5_c" ,
+    "Z5_n" , "Z5_p" , "Z6_c" , "Z6_n" , "Z6_p" , "L2_c" , "Q1_c" , "Q1_p" , "Q1_n" ,
+    "Q6_c" , "Q6_p" , "Q6_n" , "Q6_s" , "Q6_pen_depth_c" , "Q6_pen_depth_n" ,
+    "Q6_pen_depth_p" , "Q6_pen_depth_s" , "Q7_c" , "Q7_p" , "Q7_n" , "Q7_pen_depth_c" ,
+    "Q7_pen_depth_n" , "Q7_pen_depth_p" , "Q17_c" , "Q17_p" , "Q17_n" , "bL2_c" ,
+    "ben_col_D1m" , "ben_col_D2m" , "K1_p" , "K3_n" , "K4_n" , "K5_s" , "G2_o" ,
+    "G2_o_deep" , "G3_c" , "ben_nit_G4n" , "H1_c" , "H2_c" , "Y2_c" , "Y3_c" ,
+    "Y4_c"]
+
+gotm_vars_test = ["dates", "N1_p", "N3_n", "N5_s"]
+
+data_dict = {"expected": gotm_vars_test, "expected_state": state_vars}
+
+for key, items in data_dict.items():
+    data = nc.Dataset(data_path, 'r')
+    expected_results = {}
+    for v in items:
+        if key == "expected":
+            if v == "dates":
+                times = data.variables['time']
+                dates = nc.num2date(times[:],
+                                    units=times.units,
+                                    calendar=times.calendar)
+                dates = [str(d).split(" ")[0] for d in dates]
+                expected_results[v] = dates
+            else:
+                depth = 0.0
+                var = data.variables[v]
+                zi = data.variables['zi'][:].squeeze()
+                z = data.variables['z'][:].squeeze()
+                var_time_series = []
+                for i in range(var.shape[0]):
+                    depth_offset = depth + zi[i, -1]
+                    var_time_series.append(interp(depth_offset, z[i, :], var[i, :].squeeze()))
+                expected_results[v] = var_time_series
+
+        elif data.variables[v].ndim == 4:
+            expected_results[v] = data.variables[v][:].squeeze()[-1, :]
+        elif data.variables[v].ndim == 3:
+            expected_results[v] = float(data.variables[v][:].squeeze()[-1])
+        else:
+            raise RuntimeError
+
+    with open(f'{key}.json', 'w') as f:
+        json.dump(expected_results, f, cls=NumpyEncoder)
+

github-actions/pyfabm-ersem/pyfabm_tut.py

@@ -1,4 +1,3 @@
-from matplotlib import cm
 import matplotlib.pylab as plt
 import numpy as np
 import os
@@ -70,7 +69,7 @@ def main():
     axes = plt.gca()
 
     # Set color map
-    cmap = cm.get_cmap('YlOrRd')
+    cmap = plt.colormaps.get_cmap('YlOrRd')
 
     # Plot
     plot = axes.pcolormesh(salinity_array,

pyproject.toml

@@ -0,0 +1,5 @@
+[project]
+name = "ERSEM"
+dynamic = ["version"]
+authors = [{ name = "PML modelling" }]
+readme = "README.md"

src/CMakeLists.txt

@@ -38,7 +38,7 @@ add_library(fabm_models_ersem OBJECT
             zenith_angle.F90
            )
 
-add_dependencies(fabm_models_ersem fabm_base)
+target_link_libraries(fabm_models_ersem PRIVATE fabm_base)
 
 if(FABM_EMBED_VERSION)
   # Dynamically generate "ersem_version" module with git commit/branch information at every build.

src/bacteria_docdyn.F90

@@ -191,8 +191,8 @@ subroutine initialize(self,configunit)
       call self%register_diagnostic_variable(self%id_fR2B1c,'fR2B1c','mg C/m^3/d','uptake of semi-labile DOC ')
       call self%register_diagnostic_variable(self%id_fR3B1c,'fR3B1c','mg C/m^3/d','uptake of semi-refractory DOC ')
       call self%register_diagnostic_variable(self%id_fRPB1c,'fRPB1c','mg C/m^3/d','total uptake of POC')
-      call self%register_diagnostic_variable(self%id_fRPB1n,'fRPB1n','mg N/m^3/d','total uptake of PON')
-      call self%register_diagnostic_variable(self%id_fRPB1p,'fRPB1p','mg P/m^3/d','total uptake of POP')
+      call self%register_diagnostic_variable(self%id_fRPB1n,'fRPB1n','mmol N/m^3/d','total uptake of PON')
+      call self%register_diagnostic_variable(self%id_fRPB1p,'fRPB1p','mmol P/m^3/d','total uptake of POP')
       call self%register_diagnostic_variable(self%id_fR1B1n,'fR1B1n','mmol N/m^3/d','uptake of DON')
       call self%register_diagnostic_variable(self%id_fR1B1p,'fR1B1p','mmol P/m^3/d','uptake of DOP')
 

src/pelagic_base.F90

@@ -331,7 +331,8 @@ subroutine do_bottom(self,_ARGUMENTS_DO_BOTTOM_)
 
          ! Retrieve sinking rate (at centre of cell closest to the bottom)
          ! NB by ERSEM convention, this rate is returned in m/d, positive for sinking, negative for floating!
-         w = self%get_sinking_rate(_ARGUMENTS_LOCAL_)
+        !  Avoid negative sinking rate across the pelagic-benthic boundary to stop mass being moved from benthos to pelagic as conceptually incorrect for vertical movement
+         w = max(0._rk,self%get_sinking_rate(_ARGUMENTS_LOCAL_))
 
          ! Store near-bed vertical velocity. Use FABM convention (m/s, negative for downward) to
          ! allow this custom fuctionality to be ultimately be replaced by a FABM API.