A polynya test case

.github/workflows/test_suite.yml

@@ -73,6 +73,7 @@ jobs:
         mv ../test .
         cd test
         python3 ThermoIntegration_test.py
+        python3 PolynyaIntegration_test.py
         ./run_test_jan2010_integration.sh python3
         ./run_test_advection.sh python3
 
@@ -182,5 +183,6 @@ jobs:
         mv ../test .
         cd test
         python ThermoIntegration_test.py
+        python PolynyaIntegration_test.py
         ./run_test_jan2010_integration.sh python
         ./run_test_advection.sh python

run/CMakeLists.txt

@@ -19,3 +19,6 @@ execute_process(
     COMMAND "${Python_EXECUTABLE}" "${CMAKE_CURRENT_SOURCE_DIR}/make_init_benchmark.py"
     WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}"
 )
+execute_process(
+    COMMAND "${Python_EXECUTABLE}" "${CMAKE_CURRENT_SOURCE_DIR}/make_init_polynya.py"
+    WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}")

run/config_polynya.cfg

@@ -0,0 +1,33 @@
+[model]
+init_file = init_polynya.nc
+start = 2023-01-01T00:00:00Z
+stop = 2023-01-05T00:00:00Z
+time_step = P0-0T00:01:00
+missing_value = 1e20
+
+[Modules]
+DiagnosticOutputModule = Nextsim::ConfigOutput
+DynamicsModule = Nextsim::MEVPDynamics
+AtmosphereBoundaryModule = Nextsim::FluxConfiguredAtmosphere
+OceanBoundaryModule = Nextsim::FluxConfiguredOcean
+IceThermodynamicsModule = Nextsim::ThermoWinton
+
+[ConfigOutput]
+period = P0-0T04:00:00
+field_names = hice,cice,u,v
+filename = polynya.diagnostic.nc
+
+[FluxConfiguredOcean]
+qio = 2.30
+sss = 28
+sst = -1.54
+mld = 10.
+current_u = 0.
+current_v = 0.
+
+[FluxConfiguredAtmosphere]
+Q_ia = 30
+Q_ow = 300
+dQia_dT = 0
+wind_u = 16
+wind_v = 12

run/make_init_polynya.py

@@ -0,0 +1,49 @@
+from make_init_base import initMaker
+
+# Creates initial conditions for the Bjornsson et al. (2001) polynya case
+
+# Domain size [km]
+x = 100
+y = 50
+res = 2
+
+nfirst = y // res
+nsecond = x // res
+nLayers = 3
+
+fname = "init_polynya.nc"
+
+# The model expects everything in metres
+initializer = initMaker(fname, nfirst, nsecond, res*1e3, isWinton=True, checkZeros=False)
+
+# Ice everywhere and all boundaries closed, except the x = 100 km end
+initializer.mask[:, :] = 1.
+initializer.mask[0, :] = 0.
+initializer.mask[-1, :] = 0.
+initializer.mask[:, 0] = 0.
+#initializer.mask[:, -1] = 0. ## right
+
+# Uniform concentration of 90%
+initializer.cice[:, :] = 0.9
+
+# Uniform thickness of 20 cm
+initializer.hice[:, :] = 0.2
+
+# Undamaged ice
+initializer.damage[:, :] = 1.
+
+# Ice and ocean temperature and salinity at the freezing point
+ice_salinity = 5  # should match Ice::s in constants.hpp
+mu: float = -0.055  # should match Water::mu in constants.hpp
+ocean_temperature = -1.54
+ocean_salinity = ocean_temperature / mu
+
+initializer.sss[:, :] = ocean_salinity
+initializer.sst[:, :] = ocean_temperature
+initializer.tsurf[:, :] = ice_salinity * mu
+initializer.tbott = initializer.tsurf
+initializer.tintr = initializer.tsurf
+
+# All other variables are zero or not needed
+
+# The file is written when initializer goes out of scope

test/PolynyaIntegration_test.py

@@ -0,0 +1,193 @@
+import os
+import subprocess
+import sys
+import unittest
+
+import netCDF4
+import numpy as np
+
+
+class Polynya(unittest.TestCase):
+    """
+    A test class based on the Bjornsson et al. (2001) polynya case. We run the model for 5 days and check the output
+    against known values. The main purpose of this test is to check that the model is running and that the output is
+    reasonable.
+
+    NB! This test is very sensitive to small perturbations in the model. If the test fails, run the full-resolution
+    version, cited below, and compare the results. You may need to adjust the "known good values" of the test
+    accordingly.
+
+    See Bjornsson et al. (2001) doi:10.3402/tellusa.v53i2.12184 for details.
+    """
+
+    # A few useful global variables for the class
+    executable = "../nextsim"
+
+    init_file = "init_polynya.nc"
+    config_file = "PolynyaIntegration.cfg"
+    diagnostics_file = "polynya.diagnostic.nc"
+
+    # Load the data once and re-use for all tests
+    hice = np.array([])
+    cice = np.array([])
+    uice = np.array([])
+    vice = np.array([])
+
+    @classmethod
+    def setUpClass(cls):
+        """
+        A set-up class which,
+          - Creates the initialisation file, using make_init_column.py
+          - Runs the model
+          - Loads the neccesary variables from the output file
+        """
+
+        # Make the init column
+        cls.__make_init_column()
+
+        # Create the config file
+        cls.__make_cfg_file()
+
+        # Run the model
+        subprocess.run(cls.executable + " --config-file " + cls.config_file, shell=True, check=True)
+
+        # Load the basic variables
+        root = netCDF4.Dataset(cls.diagnostics_file, "r", format="NETCDF4")
+        cls.cice = np.squeeze(np.array(root.variables["cice"][:].data))
+        cls.hice = np.squeeze(np.array(root.variables["hice"][:].data))
+        cls.uice = np.array(root.variables["u"][:].data)
+        cls.vice = np.array(root.variables["v"][:].data)
+
+    @classmethod
+    def __make_cfg_file(cls):
+        cfg = open(cls.config_file, "w")
+        cfg.write("""
+[model]
+init_file = init_polynya.nc
+start = 2023-01-01T00:00:00Z
+stop = 2023-01-05T00:00:00Z
+time_step = P0-0T00:30:00
+missing_value = 1e20
+
+[Modules]
+DiagnosticOutputModule = Nextsim::ConfigOutput
+DynamicsModule = Nextsim::BBMDynamics
+AtmosphereBoundaryModule = Nextsim::FluxConfiguredAtmosphere
+OceanBoundaryModule = Nextsim::FluxConfiguredOcean
+IceThermodynamicsModule = Nextsim::ThermoWinton
+
+[ConfigOutput]
+period = P0-0T00:01:00
+field_names = hice,cice,u,v
+filename = polynya.diagnostic.nc
+
+[FluxConfiguredOcean]
+qio = 2.30
+sss = 28
+sst = -1.54
+mld = 10.
+current_u = 0.
+current_v = 0.
+
+[FluxConfiguredAtmosphere]
+Q_ia = 30
+Q_ow = 300
+dQia_dT = 0
+wind_u = 16
+wind_v = 12
+        """)
+        cfg.close()
+
+    @classmethod
+    def __make_init_column(cls):
+        sys.path.append('../run')
+        sys.path.append('../../run')
+        from make_init_base import initMaker
+
+        # Creates initial conditions for the Bjornsson et al. (2001) polynya case
+
+        # Domain size [km]
+        x = 100
+        y = 50
+        res = 4
+
+        nfirst = y // res
+        nsecond = x // res
+
+        fname = cls.init_file
+
+        # The model expects everything in metres
+        initializer = initMaker(fname, nfirst, nsecond, res*1e3, checkZeros=False)
+
+        # Ice everywhere and all boundaries closed, except the x = 100 km end
+        initializer.mask[:, :] = 1.
+        initializer.mask[0, :] = 0.
+        initializer.mask[-1, :] = 0.
+        initializer.mask[:, 0] = 0.
+        #initializer.mask[:, -1] = 0. ## right
+
+        # Uniform concentration of 90%
+        initializer.cice[:, :] = 0.9
+
+        # Uniform thickness of 20 cm
+        initializer.hice[:, :] = 0.2
+
+        # Undamaged ice
+        initializer.damage[:, :] = 1.
+
+        # Ice and ocean temperature and salinity at the freezing point
+        ice_salinity = 5  # should match Ice::s in constants.hpp
+        mu: float = -0.055  # should match Water::mu in constants.hpp
+        ocean_temperature = -1.54
+        ocean_salinity = ocean_temperature / mu
+
+        initializer.sss[:, :] = ocean_salinity
+        initializer.sst[:, :] = ocean_temperature
+
+        # All other variables are zero or not needed
+
+        # The file is written when initializer goes out of scope
+
+    @classmethod
+    def tearDownClass(cls):
+        """
+        A tear-down class that deletes the netCDF output and temporary files
+        """
+
+        if os.path.isfile(cls.diagnostics_file):
+            os.remove(cls.diagnostics_file)
+
+        if os.path.isfile(cls.init_file):
+            os.remove(cls.init_file)
+
+        if os.path.isfile(cls.config_file):
+            os.remove(cls.config_file)
+
+    def test_iceThickness(self):
+        """
+        Test the ice thickness against standard max, min, and mean values
+        The maximum varies by (at least) 3 cm between platforms, making a test of it useless
+        """
+
+        mean = 0.1323
+        min = 0.0000
+        hice = self.hice[:,:,:,0]
+        self.assertAlmostEqual(min, hice.min(), 4, "Min ice thickness not ~= " + str(min) + " m")
+        self.assertAlmostEqual(mean, hice.mean(), 4, "Mean ice thickness not ~= " + str(mean) + " m")
+
+    def test_concentration(self):
+        """
+        Test the ice concentration against standard max, min, and mean values
+        The min and max are easy, but the mean is sensitive
+        """
+
+        mean = 0.4402
+        max = 1.0000
+        min = 0.0000
+        cice = self.cice[:,:,:,0]
+        self.assertAlmostEqual(max, cice.max(), 4, "Max conentration not ~= " + str(max))
+        self.assertAlmostEqual(min, cice.min(), 4, "Min concentration not ~= " + str(min))
+        self.assertAlmostEqual(mean, cice.mean(), 2, "Mean concentration not ~= " + str(mean))
+
+if __name__ == '__main__':
+    unittest.main()