add plotting scripts and figures for all working examples

examples/boussinesq/skamarock_klemp_compressible.py

@@ -71,7 +71,7 @@ def skamarock_klemp_compressible_bouss(
 
     # I/O
     output = OutputParameters(
-        dirname=dirname, dumpfreq=dumpfreq, dump_vtus=True, dump_nc=True,
+        dirname=dirname, dumpfreq=dumpfreq, dump_vtus=True, dump_nc=False,
     )
     # list of diagnostic fields, each defined in a class in diagnostics.py
     diagnostic_fields = [CourantNumber(), Divergence(), Perturbation('b')]

examples/compressible_euler/dcmip_3_1_meanflow_quads.py → examples/compressible_euler/dcmip_3_1_gravity_wave.py

@@ -14,29 +14,28 @@
 )
 from gusto import (
     Domain, IO, OutputParameters, SemiImplicitQuasiNewton, SSPRK3, DGUpwind,
-    TrapeziumRule, SUPGOptions, CompressibleKineticEnergy, PotentialEnergy,
-    CompressibleParameters, CompressibleEulerEquations, CompressibleSolver,
+    TrapeziumRule, SUPGOptions, lonlatr_from_xyz, CompressibleParameters,
+    CompressibleEulerEquations, CompressibleSolver, ZonalComponent,
     compressible_hydrostatic_balance, Perturbation, GeneralCubedSphereMesh,
-    lonlatr_from_xyz
 )
 
-dcmip_3_1_meanflow_defaults = {
+dcmip_3_1_gravity_wave_defaults = {
     'ncells_per_edge': 8,
     'nlayers': 10,
-    'dt': 100.0,
+    'dt': 50.0,
     'tmax': 3600.,
     'dumpfreq': 9,
-    'dirname': 'dcmip_3_1_meanflow'
+    'dirname': 'dcmip_3_1_gravity_wave'
 }
 
 
-def dcmip_3_1_meanflow(
-        ncells_per_edge=dcmip_3_1_meanflow_defaults['ncells_per_edge'],
-        nlayers=dcmip_3_1_meanflow_defaults['nlayers'],
-        dt=dcmip_3_1_meanflow_defaults['dt'],
-        tmax=dcmip_3_1_meanflow_defaults['tmax'],
-        dumpfreq=dcmip_3_1_meanflow_defaults['dumpfreq'],
-        dirname=dcmip_3_1_meanflow_defaults['dirname']
+def dcmip_3_1_gravity_wave(
+        ncells_per_edge=dcmip_3_1_gravity_wave_defaults['ncells_per_edge'],
+        nlayers=dcmip_3_1_gravity_wave_defaults['nlayers'],
+        dt=dcmip_3_1_gravity_wave_defaults['dt'],
+        tmax=dcmip_3_1_gravity_wave_defaults['tmax'],
+        dumpfreq=dcmip_3_1_gravity_wave_defaults['dumpfreq'],
+        dirname=dcmip_3_1_gravity_wave_defaults['dirname']
 ):
 
     # ------------------------------------------------------------------------ #
@@ -89,12 +88,10 @@ def dcmip_3_1_meanflow(
 
     # I/O
     output = OutputParameters(
-        dirname=dirname,
-        dumpfreq=dumpfreq,
+        dirname=dirname, dumpfreq=dumpfreq, dump_vtus=False, dump_nc=True
     )
     diagnostic_fields = [
-        Perturbation('theta'), Perturbation('rho'),
-        CompressibleKineticEnergy(), PotentialEnergy(eqns)
+        Perturbation('theta'), Perturbation('rho'), ZonalComponent('u'),
     ]
     io = IO(domain, output, diagnostic_fields=diagnostic_fields)
 
@@ -197,38 +194,38 @@ def dcmip_3_1_meanflow(
         '--ncells_per_edge',
         help="The number of cells per panel edge of the cubed-sphere.",
         type=int,
-        default=dcmip_3_1_meanflow_defaults['ncells_per_edge']
+        default=dcmip_3_1_gravity_wave_defaults['ncells_per_edge']
     )
     parser.add_argument(
         '--nlayers',
         help="The number of layers for the mesh.",
         type=int,
-        default=dcmip_3_1_meanflow_defaults['nlayers']
+        default=dcmip_3_1_gravity_wave_defaults['nlayers']
     )
     parser.add_argument(
         '--dt',
         help="The time step in seconds.",
         type=float,
-        default=dcmip_3_1_meanflow_defaults['dt']
+        default=dcmip_3_1_gravity_wave_defaults['dt']
     )
     parser.add_argument(
         "--tmax",
         help="The end time for the simulation in seconds.",
         type=float,
-        default=dcmip_3_1_meanflow_defaults['tmax']
+        default=dcmip_3_1_gravity_wave_defaults['tmax']
     )
     parser.add_argument(
         '--dumpfreq',
         help="The frequency at which to dump field output.",
         type=int,
-        default=dcmip_3_1_meanflow_defaults['dumpfreq']
+        default=dcmip_3_1_gravity_wave_defaults['dumpfreq']
     )
     parser.add_argument(
         '--dirname',
         help="The name of the directory to write to.",
         type=str,
-        default=dcmip_3_1_meanflow_defaults['dirname']
+        default=dcmip_3_1_gravity_wave_defaults['dirname']
     )
     args, unknown = parser.parse_known_args()
 
-    dcmip_3_1_meanflow(**vars(args))
+    dcmip_3_1_gravity_wave(**vars(args))

examples/compressible_euler/test_compressible_euler_examples.py

@@ -10,10 +10,10 @@ def make_dirname(test_name):
         return f'pytest_{test_name}'
 
 
-def test_dcmip_3_1_meanflow():
-    from dcmip_3_1_meanflow_quads import dcmip_3_1_meanflow
-    test_name = 'dcmip_3_1_meanflow'
-    dcmip_3_1_meanflow(
+def test_dcmip_3_1_gravity_wave():
+    from dcmip_3_1_gravity_wave import dcmip_3_1_gravity_wave
+    test_name = 'dcmip_3_1_gravity_wave'
+    dcmip_3_1_gravity_wave(
         ncells_per_edge=4,
         nlayers=4,
         dt=100,
@@ -24,8 +24,8 @@ def test_dcmip_3_1_meanflow():
 
 
 @pytest.mark.parallel(nprocs=2)
-def test_dcmip_3_1_meanflow_parallel():
-    test_dcmip_3_1_meanflow()
+def test_dcmip_3_1_gravity_wave_parallel():
+    test_dcmip_3_1_gravity_wave()
 
 
 def test_dry_bryan_fritsch():

examples/shallow_water/linear_williamson_2.py

@@ -12,7 +12,8 @@
 from gusto import (
     Domain, IO, OutputParameters, SemiImplicitQuasiNewton, DefaultTransport,
     ForwardEuler, SteadyStateError, ShallowWaterParameters,
-    LinearShallowWaterEquations, GeneralIcosahedralSphereMesh
+    LinearShallowWaterEquations, GeneralIcosahedralSphereMesh,
+    ZonalComponent, MeridionalComponent, RelativeVorticity
 )
 
 linear_williamson_2_defaults = {
@@ -63,9 +64,11 @@ def linear_williamson_2(
 
     # I/O
     output = OutputParameters(
-        dirname=dirname, dumpfreq=dumpfreq,
+        dirname=dirname, dumpfreq=dumpfreq, dump_nc=False, dump_vtus=True
     )
-    diagnostic_fields = [SteadyStateError('u'), SteadyStateError('D')]
+    diagnostic_fields = [SteadyStateError('u'), SteadyStateError('D'),
+                         ZonalComponent('u'), MeridionalComponent('u'),
+                         RelativeVorticity()]
     io = IO(domain, output, diagnostic_fields=diagnostic_fields)
 
     # Transport schemes

examples/shallow_water/moist_convective_williamson_2.py

@@ -17,12 +17,10 @@
 from gusto import (
     Domain, IO, OutputParameters, SemiImplicitQuasiNewton, SSPRK3, DGUpwind,
     TrapeziumRule, ShallowWaterParameters, ShallowWaterEquations,
-    CourantNumber, RelativeVorticity, PotentialVorticity,
-    SteadyStateError, ShallowWaterKineticEnergy, ShallowWaterPotentialEnergy,
-    ShallowWaterPotentialEnstrophy, lonlatr_from_xyz, DG1Limiter, InstantRain,
-    MoistConvectiveSWSolver, ForwardEuler, SWSaturationAdjustment,
-    WaterVapour, CloudWater, Rain, GeneralIcosahedralSphereMesh,
-    xyz_vector_from_lonlatr
+    ZonalComponent, MeridionalComponent, SteadyStateError, lonlatr_from_xyz,
+    DG1Limiter, InstantRain, MoistConvectiveSWSolver, ForwardEuler,
+    RelativeVorticity, SWSaturationAdjustment, WaterVapour, CloudWater, Rain,
+    GeneralIcosahedralSphereMesh, xyz_vector_from_lonlatr
 )
 
 moist_convect_williamson_2_defaults = {
@@ -93,15 +91,13 @@ def moist_convect_williamson_2(
 
     # IO
     output = OutputParameters(
-        dirname=dirname, dumpfreq=dumpfreq, dump_nc=True, dump_vtus=True,
+        dirname=dirname, dumpfreq=dumpfreq, dump_nc=False, dump_vtus=True,
         dumplist_latlon=['D', 'D_error']
     )
     diagnostic_fields = [
-        CourantNumber(), RelativeVorticity(), PotentialVorticity(),
-        ShallowWaterKineticEnergy(), ShallowWaterPotentialEnergy(parameters),
-        ShallowWaterPotentialEnstrophy(), SteadyStateError('u'),
-        SteadyStateError('D'), SteadyStateError('water_vapour'),
-        SteadyStateError('cloud_water')
+        SteadyStateError('u'), SteadyStateError('D'),
+        SteadyStateError('water_vapour'), ZonalComponent('u'),
+        MeridionalComponent('u'), RelativeVorticity()
     ]
     io = IO(domain, output, diagnostic_fields=diagnostic_fields)
 

examples/shallow_water/moist_thermal_williamson_5.py

@@ -23,7 +23,8 @@
     Domain, IO, OutputParameters, Timestepper, RK4, DGUpwind,
     ShallowWaterParameters, ShallowWaterEquations, Sum,
     lonlatr_from_xyz, InstantRain, SWSaturationAdjustment, WaterVapour,
-    CloudWater, Rain, GeneralIcosahedralSphereMesh
+    CloudWater, Rain, GeneralIcosahedralSphereMesh, RelativeVorticity,
+    ZonalComponent, MeridionalComponent
 )
 
 moist_thermal_williamson_5_defaults = {
@@ -106,9 +107,11 @@ def moist_thermal_williamson_5(
     # I/O
     output = OutputParameters(
         dirname=dirname, dumplist_latlon=['D'], dumpfreq=dumpfreq,
-        dump_vtus=False, dump_nc=True
+        dump_vtus=True, dump_nc=False,
+        dumplist=['D', 'b', 'water_vapour', 'cloud_water']
     )
-    diagnostic_fields = [Sum('D', 'topography')]
+    diagnostic_fields = [Sum('D', 'topography'), RelativeVorticity(),
+                         ZonalComponent('u'), MeridionalComponent('u')]
     io = IO(domain, output, diagnostic_fields=diagnostic_fields)
 
     # Physics ------------------------------------------------------------------

examples/shallow_water/thermal_williamson_2.py

@@ -77,6 +77,7 @@ def thermal_williamson_2(
     # IO
     output = OutputParameters(
         dirname=dirname, dumpfreq=dumpfreq, dumplist_latlon=['D', 'D_error'],
+        dump_vtus=False, dump_nc=True
     )
 
     diagnostic_fields = [

examples/shallow_water/williamson_5.py

@@ -13,7 +13,8 @@
 from gusto import (
     Domain, IO, OutputParameters, SemiImplicitQuasiNewton, SSPRK3, DGUpwind,
     TrapeziumRule, ShallowWaterParameters, ShallowWaterEquations, Sum,
-    lonlatr_from_xyz, GeneralIcosahedralSphereMesh
+    lonlatr_from_xyz, GeneralIcosahedralSphereMesh, ZonalComponent,
+    MeridionalComponent, RelativeVorticity
 )
 
 williamson_5_defaults = {
@@ -75,9 +76,10 @@ def williamson_5(
     # I/O
     output = OutputParameters(
         dirname=dirname, dumplist_latlon=['D'], dumpfreq=dumpfreq,
-        dump_vtus=True, dump_nc=False
+        dump_vtus=True, dump_nc=False, dumplist=['D', 'topography']
     )
-    diagnostic_fields = [Sum('D', 'topography')]
+    diagnostic_fields = [Sum('D', 'topography'), RelativeVorticity(),
+                         MeridionalComponent('u'), ZonalComponent('u')]
     io = IO(domain, output, diagnostic_fields=diagnostic_fields)
 
     # Transport schemes