lint terminator physics test

integration-tests/physics/test_terminator_toy.py

@@ -4,108 +4,109 @@
 """
 
 from gusto import *
-from firedrake import IcosahedralSphereMesh, Constant, ge, le, exp, cos, \
-    sin, conditional, interpolate, SpatialCoordinate, VectorFunctionSpace, \
-    Function, assemble, dx, FunctionSpace, pi, max_value, acos, as_vector, \
+from firedrake import IcosahedralSphereMesh, Constant, cos, \
+    sin, SpatialCoordinate, Function, max_value, as_vector, \
     errornorm, norm
 import numpy as np
 
+
 def run_terminator_toy(dirname):
 
     # ------------------------------------------------------------------------ #
     # Set up model objects
     # ------------------------------------------------------------------------ #
 
-    # A much larger timestep than in proper simulations, as this 
+    # A much larger timestep than in proper simulations, as this
     # tests moving towards a steady state with no flow.
     dt = 100000.
 
     # Make the mesh and domain
     R = 6371220.
     mesh = IcosahedralSphereMesh(radius=R,
                                  refinement_level=3, degree=2)
-    
+
     domain = Domain(mesh, dt, 'BDM', 1)
-    
+
     # get lat lon coordinates
     x = SpatialCoordinate(mesh)
     lamda, theta, _ = lonlatr_from_xyz(x[0], x[1], x[2])
 
     domain = Domain(mesh, dt, 'BDM', 1)
-    
+
     # Define the interacting species
     X = ActiveTracer(name='X', space='DG',
-                 variable_type=TracerVariableType.mixing_ratio,
-                 transport_eqn=TransportEquationType.advective)
+                     variable_type=TracerVariableType.mixing_ratio,
+                     transport_eqn=TransportEquationType.advective)
 
     X2 = ActiveTracer(name='X2', space='DG',
-                 variable_type=TracerVariableType.mixing_ratio,
-                 transport_eqn=TransportEquationType.advective)
-                 
+                      variable_type=TracerVariableType.mixing_ratio,
+                      transport_eqn=TransportEquationType.advective)
+
     tracers = [X, X2]
-    
+
     # Equation
     V = domain.spaces("HDiv")
-    eqn = CoupledTransportEquation(domain, active_tracers=tracers, Vu = V)
-    
+    eqn = CoupledTransportEquation(domain, active_tracers=tracers, Vu=V)
+
     output = OutputParameters(dirname=dirname+"/terminator_toy",
                               dumpfreq=10)
     io = IO(domain, output)
-    
+
     # Define the reaction rates:
     theta_c = np.pi/9.
     lamda_c = -np.pi/3.
-    
+
     k1 = max_value(0, sin(theta)*sin(theta_c) + cos(theta)*cos(theta_c)*cos(lamda-lamda_c))
     k2 = 1
-    
+
     physics_schemes = [(TerminatorToy(eqn, k1=k1, k2=k2, species1_name='X',
                         species2_name='X2'), BackwardEuler(domain))]
-                        
+
     # Set up a non-divergent, time-varying, velocity field
     def u_t(t):
         return as_vector((Constant(0)*lamda, Constant(0)*lamda, Constant(0)*lamda))
-      
+
     transport_scheme = SSPRK3(domain)
     transport_method = [DGUpwind(eqn, 'X'), DGUpwind(eqn, 'X2')]
-    
+
     X_0 = 4e-6 + 0*lamda
     X2_0 = 0*lamda
-    
-    transport_scheme = SSPRK3(domain)#, limiter=MixedLimiter)
+
+    transport_scheme = SSPRK3(domain)
     transport_method = [DGUpwind(eqn, 'X'), DGUpwind(eqn, 'X2')]
 
-    stepper = SplitPrescribedTransport(eqn, transport_scheme, io, 
+    stepper = SplitPrescribedTransport(eqn, transport_scheme, io,
                                        spatial_methods=transport_method,
                                        physics_schemes=physics_schemes,
                                        prescribed_transporting_velocity=u_t)
-                                       
+
     stepper.fields("X").interpolate(X_0)
     stepper.fields("X2").interpolate(X2_0)
-
-    #True fields to compare to
-
+
     stepper.run(t=0, tmax=10*dt)
-
+
+    # Compute the steady state solution to compare to
     steady_space = domain.spaces('DG')
     X_steady = Function(steady_space)
     X2_steady = Function(steady_space)
-    
+
     X_T_0 = 4e-6
     r = k1/(4*k2)
     D_val = sqrt(r**2 + 2*X_T_0*r)
-    
+
     X_steady.interpolate(D_val - r)
     X2_steady.interpolate(0.5*(X_T_0 - D_val + r))
-    
+
     return stepper, X_steady, X2_steady
-
+
+
 def test_terminator_toy_setup(tmpdir):
     dirname=str(tmpdir)
     stepper, X_steady, X2_steady = run_terminator_toy(dirname)
     X_field = stepper.fields("X")
     X2_field = stepper.fields("X2")
-
-    #Compute 
+
+    # Assert that the physics scheme has sufficiently moved 
+    # the species fields near their steady state solutions 
     assert errornorm(X_field, X_steady)/norm(X_steady) < 0.25, "The X field is not sufficiently close to the steady state profile"
     assert errornorm(X2_field, X2_steady)/norm(X2_steady) < 0.25, "The X2 field is not sufficiently close to the steady state profile"