Merge branch 'main' into TBendall/update_ref_profile

gusto/recovery/recovery_options.py

@@ -16,15 +16,15 @@ def __init__(self, domain, boundary_method=None, use_vector_spaces=False):
         Args:
             domain (:class:`Domain`): the model's domain object, containing the
                 mesh and the compatible function spaces.
-
-            boundary_method (:variable:'dict', optional): A dictionary containing the space
-                the boundary method is to be applied to along with specified method. Acceptable keys are "DG",
-                "HDiv" and "theta". acceptable values are (BoundaryMethod.taylor/hcurl/extruded),
-                passed as ('space', 'boundary method'). Defaults to None
-
-            use_vector_spaces (bool, optional):. Determines if we need to use DG / CG
-                space for the embedded and recovery space for the HDiv field instead of the usual
-                HDiv, HCurl spaces. Defaults to False
+            boundary_method (:variable:'dict', optional): A dictionary
+                containing the space the boundary method is to be applied to
+                along with specified method. Acceptable keys are "DG", "HDiv"
+                and "theta". Acceptable values are
+                (BoundaryMethod.taylor/hcurl/extruded). Defaults to None.
+            use_vector_spaces (bool, optional):. Determines if we need to use
+                the vector DG1 / CG1 space for the embedded and recovery space
+                for the HDiv field instead of the usual HDiv, HCurl spaces.
+                Defaults to False.
         """
         family = domain.family
         mesh = domain.mesh
@@ -36,7 +36,7 @@ def __init__(self, domain, boundary_method=None, use_vector_spaces=False):
 
         valid_keys = ['DG', 'HDiv', 'theta']
         if boundary_method is not None:
-            for key in boundary_method:
+            for key in boundary_method.keys():
                 if key not in valid_keys:
                     raise KeyError(f'Recovery spaces: boundary method key {key} not valid. Valid keys are DG, HDiv, theta')
 
@@ -47,7 +47,7 @@ def __init__(self, domain, boundary_method=None, use_vector_spaces=False):
         # Check if extruded and if so builds theta spaces
         if hasattr(mesh, "_base_mesh"):
             # check if boundary method is present
-            if hasattr(boundary_method, 'theta'):
+            if boundary_method is not None and 'theta' in boundary_method.keys():
                 theta_boundary_method = boundary_method['theta']
             else:
                 theta_boundary_method = None
@@ -71,7 +71,7 @@ def __init__(self, domain, boundary_method=None, use_vector_spaces=False):
         # ----------------------------------------------------------------------
         # Building the DG options
         # ----------------------------------------------------------------------
-        if hasattr(boundary_method, 'DG'):
+        if boundary_method is not None and 'DG' in boundary_method.keys():
             DG_boundary_method = boundary_method['DG']
         else:
             DG_boundary_method = None
@@ -91,7 +91,7 @@ def __init__(self, domain, boundary_method=None, use_vector_spaces=False):
         # Building HDiv options
         # ----------------------------------------------------------------------
 
-        if hasattr(boundary_method, 'HDiv'):
+        if boundary_method is not None and 'HDiv' in boundary_method.keys():
             HDiv_boundary_method = boundary_method['HDiv']
         else:
             HDiv_boundary_method = None
@@ -102,16 +102,17 @@ def __init__(self, domain, boundary_method=None, use_vector_spaces=False):
 
             HDiv_embedding_Space = Vu_DG1
             HDiv_recovered_Space = Vu_CG1
+            project_high_method = 'interpolate'
 
         else:
-
             HDiv_embedding_Space = self.de_Rham.HDiv
             HDiv_recovered_Space = self.de_Rham.HCurl
+            project_high_method = 'project'
 
         self.HDiv_options = RecoveryOptions(embedding_space=HDiv_embedding_Space,
                                             recovered_space=HDiv_recovered_Space,
                                             injection_method='recover',
-                                            project_high_method='project',
+                                            project_high_method=project_high_method,
                                             project_low_method='project',
                                             broken_method='project',
                                             boundary_method=HDiv_boundary_method)

gusto/time_discretisation/imex_runge_kutta.py

@@ -5,7 +5,9 @@
 from firedrake.fml import replace_subject, all_terms, drop
 from firedrake.utils import cached_property
 from gusto.core.labels import time_derivative, implicit, explicit
-from gusto.time_discretisation.time_discretisation import TimeDiscretisation
+from gusto.time_discretisation.time_discretisation import (
+    TimeDiscretisation, wrapper_apply
+)
 import numpy as np
 
 
@@ -209,6 +211,7 @@ def final_solver(self):
         solver_name = self.field_name+self.__class__.__name__
         return NonlinearVariationalSolver(problem, solver_parameters=self.solver_parameters, options_prefix=solver_name)
 
+    @wrapper_apply
     def apply(self, x_out, x_in):
         self.x1.assign(x_in)
         solver_list = self.solvers

gusto/time_discretisation/implicit_runge_kutta.py

@@ -8,7 +8,9 @@
 from firedrake.utils import cached_property
 
 from gusto.core.labels import time_derivative
-from gusto.time_discretisation.time_discretisation import TimeDiscretisation
+from gusto.time_discretisation.time_discretisation import (
+    TimeDiscretisation, wrapper_apply
+)
 
 
 __all__ = ["ImplicitRungeKutta", "ImplicitMidpoint", "QinZhang"]
@@ -142,6 +144,7 @@ def solve_stage(self, x0, stage):
 
         self.k[stage].assign(self.x_out)
 
+    @wrapper_apply
     def apply(self, x_out, x_in):
 
         for i in range(self.nStages):

gusto/time_discretisation/time_discretisation.py

@@ -188,6 +188,9 @@ def setup(self, equation, apply_bcs=True, *active_labels):
         # -------------------------------------------------------------------- #
 
         if self.wrapper is not None:
+
+            wrapper_bcs = bcs if apply_bcs else None
+
             if self.wrapper_name == "mixed_options":
 
                 self.wrapper.wrapper_spaces = equation.spaces
@@ -199,7 +202,7 @@ def setup(self, equation, apply_bcs=True, *active_labels):
                         raise ValueError(f"The option defined for {field} is for a field that does not exist in the equation set")
 
                     field_idx = equation.field_names.index(field)
-                    subwrapper.setup(equation.spaces[field_idx])
+                    subwrapper.setup(equation.spaces[field_idx], wrapper_bcs)
 
                     # Update the function space to that needed by the wrapper
                     self.wrapper.wrapper_spaces[field_idx] = subwrapper.function_space
@@ -218,7 +221,7 @@ def setup(self, equation, apply_bcs=True, *active_labels):
                 if self.wrapper_name == "supg":
                     self.wrapper.setup()
                 else:
-                    self.wrapper.setup(self.fs)
+                    self.wrapper.setup(self.fs, wrapper_bcs)
                 self.fs = self.wrapper.function_space
                 if self.solver_parameters is None:
                     self.solver_parameters = self.wrapper.solver_parameters
@@ -480,6 +483,7 @@ def rhs(self):
 
         return r.form
 
+    @wrapper_apply
     def apply(self, x_out, x_in):
         """
         Apply the time discretisation to advance one whole time step.
@@ -570,6 +574,7 @@ def rhs(self):
 
         return r.form
 
+    @wrapper_apply
     def apply(self, x_out, x_in):
         """
         Apply the time discretisation to advance one whole time step.
@@ -731,6 +736,7 @@ def solver_bdf2(self):
         return NonlinearVariationalSolver(problem, solver_parameters=self.solver_parameters,
                                           options_prefix=solver_name)
 
+    @wrapper_apply
     def apply(self, x_out, x_in):
         """
         Apply the time discretisation to advance one whole time step.

gusto/time_discretisation/wrappers.py

@@ -46,8 +46,8 @@ def setup(self, original_space):
 
         Args:
             original_space (:class:`FunctionSpace`): the space that the
-        prognostic variable is defined on. This is a subset space of
-        a mixed function space when using a MixedFSWrapper.
+                prognostic variable is defined on. This is a subset space of
+                a mixed function space when using a MixedFSWrapper.
         """
         self.original_space = original_space
 
@@ -85,8 +85,17 @@ class EmbeddedDGWrapper(Wrapper):
     the original space.
     """
 
-    def setup(self, original_space):
-        """Sets up function spaces and fields needed for this wrapper."""
+    def setup(self, original_space, post_apply_bcs):
+        """
+        Sets up function spaces and fields needed for this wrapper.
+
+        Args:
+            original_space (:class:`FunctionSpace`): the space that the
+                prognostic variable is defined on.
+            post_apply_bcs (list of :class:`DirichletBC`): list of Dirichlet
+                boundary condition objects to be passed to the projector used
+                in the post-apply step.
+        """
 
         assert isinstance(self.options, EmbeddedDGOptions), \
             'Embedded DG wrapper can only be used with Embedded DG Options'
@@ -121,7 +130,8 @@ def setup(self, original_space):
             self.x_projected = Function(equation.spaces[self.time_discretisation.idx])
 
         if self.options.project_back_method == 'project':
-            self.x_out_projector = Projector(self.x_out, self.x_projected)
+            self.x_out_projector = Projector(self.x_out, self.x_projected,
+                                             bcs=post_apply_bcs)
         elif self.options.project_back_method == 'recover':
             self.x_out_projector = Recoverer(self.x_out, self.x_projected)
         else:
@@ -169,8 +179,17 @@ class RecoveryWrapper(Wrapper):
     field is then returned to the original space.
     """
 
-    def setup(self, original_space):
-        """Sets up function spaces and fields needed for this wrapper."""
+    def setup(self, original_space, post_apply_bcs):
+        """
+        Sets up function spaces and fields needed for this wrapper.
+
+        Args:
+            original_space (:class:`FunctionSpace`): the space that the
+                prognostic variable is defined on.
+            post_apply_bcs (list of :class:`DirichletBC`): list of Dirichlet
+                boundary condition objects to be passed to the projector used
+                in the post-apply step.
+        """
 
         assert isinstance(self.options, RecoveryOptions), \
             'Recovery wrapper can only be used with Recovery Options'
@@ -213,7 +232,8 @@ def setup(self, original_space):
         if self.options.project_low_method == 'interpolate':
             self.x_out_projector = Interpolator(self.x_out, self.x_projected)
         elif self.options.project_low_method == 'project':
-            self.x_out_projector = Projector(self.x_out, self.x_projected)
+            self.x_out_projector = Projector(self.x_out, self.x_projected,
+                                             bcs=post_apply_bcs)
         elif self.options.project_low_method == 'recover':
             self.x_out_projector = Recoverer(self.x_out, self.x_projected,
                                              method=self.options.broken_method)