tmm: added PISCES test case

examples/tmm/PISCES.py

@@ -0,0 +1,48 @@
+import cftime
+import os
+
+import numpy as np
+import fabmos.transport.tmm
+import fabmos
+
+tm_config_dir = "."  # directory with a TM configuration from http://kelvin.earth.ox.ac.uk/spk/Research/TMM/TransportMatrixConfigs/
+calendar = "360_day"  # any valid calendar recognized by cftime, see https://cfconventions.org/cf-conventions/cf-conventions.html#calendar
+
+script_dir = os.path.dirname(__file__)
+fabm_yaml = os.path.join(
+    script_dir, "../../extern/fabm/extern/pisces/testcases/fabm.yaml"
+)
+
+domain = fabmos.transport.tmm.create_domain(tm_config_dir)
+
+sim = fabmos.transport.tmm.Simulator(domain, calendar=calendar, fabm_config=fabm_yaml)
+
+# Crude estimate of turbulent diffusivity from temperature-only MLD
+# PISCES uses this to determine turbocline depth
+temp = fabmos.transport.tmm.get_mat_array(
+    "GCM/Theta_gcm.mat",
+    "Tgcm",
+    domain._grid_file,
+    times=fabmos.transport.tmm.climatology_times(calendar),
+)
+Kzval = np.where(temp.values < temp.values[:, :1, :, :] - 0.5, 1e-5, 1e-3)
+Kz = fabmos.transport.tmm._wrap_ongrid_array(
+    Kzval, domain._grid_file, times=fabmos.transport.tmm.climatology_times(calendar)
+)
+sim.fabm.get_dependency("vertical_tracer_diffusivity").set(
+    Kz, on_grid=fabmos.input.OnGrid.ALL, climatology=True
+)
+
+sim.fabm.get_dependency("surface_air_pressure").set(101325.0)
+
+out = sim.output_manager.add_netcdf_file(
+    "output.nc", interval=7, interval_units=fabmos.TimeUnit.DAYS, save_initial=False
+)
+out.request(*sim.fabm.state_variables, time_average=True)
+
+start = cftime.datetime(2000, 1, 1, calendar=calendar)
+stop = cftime.datetime(2001, 1, 1, calendar=calendar)
+sim.start(start, timestep=7200, transport_timestep=12 * 3600)
+while sim.time < stop:
+    sim.advance()
+sim.finish()