diff --git a/demos/demo_references.bib b/demos/demo_references.bib deleted file mode 100644 index 31fe279..0000000 --- a/demos/demo_references.bib +++ /dev/null @@ -1,18 +0,0 @@ -@Article{LeVeque:1996, - author={LeVeque, Randall J.}, - title={{High-Resolution Conservative Algorithms for Advection in Incompressible Flow}}, - journal={SIAM Journal on Numerical Analysis}, - year={1996}, - volume={33}, - number={2}, - pages={627--665}, - doi={10.1137/0733033} -} - -@Book{Hundsdorfer:2003, - title={Numerical solution of time-dependent advection-diffusion-reaction equations}, - author={Hundsdorfer, Willem H and Verwer, Jan G and Hundsdorfer, WH}, - volume={33}, - year={2003}, - publisher={Springer} -} diff --git a/demos/gray_scott.py b/demos/gray_scott.py index 8ef350d..c059405 100644 --- a/demos/gray_scott.py +++ b/demos/gray_scott.py @@ -160,5 +160,5 @@ def qoi(): # # .. rubric:: References # -# .. bibliography:: demo_references.bib +# .. bibliography:: # :filter: docname in docnames diff --git a/demos/point_discharge2d.py b/demos/point_discharge2d.py index b1eee69..5db8e0d 100644 --- a/demos/point_discharge2d.py +++ b/demos/point_discharge2d.py @@ -9,7 +9,7 @@ # # Consider the same steady-state advection-diffusion test case as in the # motivation for the Goalie manual: the "point discharge with diffusion" -# test case from :cite:`RCJ:14`. In this test case, we solve +# test case from :cite:`Riadh:2014`. In this test case, we solve # # .. math:: # \left\{\begin{array}{rl} @@ -39,11 +39,11 @@ def get_function_spaces(mesh): # Point sources are difficult to represent in numerical models. Here we -# follow :cite:`WBHP:22` in using a Gaussian approximation. Let +# follow :cite:`Wallwork:2022` in using a Gaussian approximation. Let # :math:`(x_0,y_0)=(2,5)` denote the point source location and # :math:`r=0.05606388` be a radius parameter, which has been calibrated # so that the finite element approximation is as close as possible to the -# analytical solution, in some sense (see :cite:`WBHP:22` for details). :: +# analytical solution, in some sense (see :cite:`Wallwork:2022` for details). :: def source(mesh): @@ -210,3 +210,9 @@ def qoi(): # metric-based mesh adaptation to the point discharge test case considered here. # # This tutorial can be dowloaded as a `Python script `__. +# +# +# .. rubric:: References +# +# .. bibliography:: +# :filter: docname in docnames diff --git a/demos/solid_body_rotation.py b/demos/solid_body_rotation.py index af807b5..1c52a74 100644 --- a/demos/solid_body_rotation.py +++ b/demos/solid_body_rotation.py @@ -234,5 +234,5 @@ def qoi(): # # .. rubric:: References # -# .. bibliography:: demo_references.bib +# .. bibliography:: # :filter: docname in docnames diff --git a/goalie/go_mesh_seq.py b/goalie/go_mesh_seq.py index d79706c..9db5ed0 100644 --- a/goalie/go_mesh_seq.py +++ b/goalie/go_mesh_seq.py @@ -72,9 +72,9 @@ def get_enriched_mesh_seq(self, enrichment_method="p", num_enrichments=1): The following global enrichment methods are supported: * h-refinement (``enrichment_method='h'``) - refine each mesh element - uniformly in each direction; + uniformly in each direction; * p-refinement (``enrichment_method='p'``) - increase the function space - polynomial order by one globally. + polynomial order by one globally. :kwarg enrichment_method: the method for enriching the mesh sequence :type enrichment_method: :class:`str` @@ -179,8 +179,8 @@ def indicate_errors( space(s) as arguments to the error indicator :class:`firedrake.function.Function` :returns: solution and indicator data objects - :rtype1: :class:`~.AdjointSolutionData - :rtype2: :class:`~.IndicatorData + :rtype1: :class:`~.AdjointSolutionData` + :rtype2: :class:`~.IndicatorData` """ solver_kwargs = solver_kwargs or {} default_enrichment_kwargs = {"enrichment_method": "p", "num_enrichments": 1} @@ -353,8 +353,8 @@ def fixed_point_iteration( space(s) as arguments to the error indicator :class:`firedrake.function.Function` :returns: solution and indicator data objects - :rtype1: :class:`~.AdjointSolutionData - :rtype2: :class:`~.IndicatorData + :rtype1: :class:`~.AdjointSolutionData` + :rtype2: :class:`~.IndicatorData` """ # TODO #124: adaptor no longer needs solution and indicator data to be passed # explicitly diff --git a/goalie/math.py b/goalie/math.py index bd8971d..a361ff0 100644 --- a/goalie/math.py +++ b/goalie/math.py @@ -9,7 +9,7 @@ def bessi0(x): """ Modified Bessel function of the first kind. - Code taken from :cite:`VVP+:92`. + Code taken from :cite:`Vetterling:1992`. """ if isinstance(x, np.ndarray): if np.isclose(x, 0).any(): diff --git a/goalie/mesh_seq.py b/goalie/mesh_seq.py index ed849fb..1a89eb4 100644 --- a/goalie/mesh_seq.py +++ b/goalie/mesh_seq.py @@ -272,14 +272,14 @@ def get_solver(self): Signature for the function to be returned: ``` - :arg index: the subinterval index - :type index: :class:`int` - :arg ic: map from fields to the corresponding initial condition components - :type ic: :class:`dict` with :class:`str` keys and - :class:`firedrake.function.Function` values - :return: map from fields to the corresponding solutions - :rtype: :class:`dict` with :class:`str` keys and - :class:`firedrake.function.Function` values + :arg index: the subinterval index + :type index: :class:`int` + :arg ic: map from fields to the corresponding initial condition components + :type ic: :class:`dict` with :class:`str` keys and + :class:`firedrake.function.Function` values + :return: map from fields to the corresponding solutions + :rtype: :class:`dict` with :class:`str` keys and + :class:`firedrake.function.Function` values ``` :returns: the function for obtaining the solver