diff --git a/animate/interpolation.py b/animate/interpolation.py index 54d2ddb..fb15eef 100644 --- a/animate/interpolation.py +++ b/animate/interpolation.py @@ -105,7 +105,7 @@ def project(source, target_space, **kwargs): projection operator when applied to :class:`firedrake.cofunction.Cofunction`\s. For details on the approach for achieving boundedness through mass lumping and - post-processing, see :cite:`FPP+:2009`. + post-processing, see :cite:`Farrell:2009`. :arg source: the function to be transferred :type source: :class:`firedrake.function.Function` or @@ -296,7 +296,7 @@ def _validate_matching_spaces(Vs, Vt): def clement_interpolant(source, target_space=None, boundary=False): r""" Compute the Clement interpolant of a :math:`\mathbb P0` source field, i.e. take the - volume average over neighbouring cells at each vertex. See :cite:`Cle:75`. + volume average over neighbouring cells at each vertex. See :cite:`Clement:1975`. :arg source: the :math:`\mathbb P0` source field :kwarg target_space: the :math:`\mathbb P1` space to interpolate into diff --git a/animate/metric.py b/animate/metric.py index 9a7ac25..8069433 100644 --- a/animate/metric.py +++ b/animate/metric.py @@ -799,9 +799,9 @@ def compute_isotropic_dwr_metric( Compute an isotropic metric from some error indicator using an element-based formulation. - The formulation is based on that presented in :cite:`CPB:13`. Note that + The formulation is based on that presented in :cite:`Carpio:2013`. Note that normalisation is implicit in the metric construction and involves the - `convergence_rate` parameter, named :math:`alpha` in :cite:`CPB:13`. + `convergence_rate` parameter, named :math:`alpha` in :cite:`Carpio:2013`. Whilst an element-based formulation is used to derive the metric, the result is projected into :math:`\mathbb P1` space, by default. @@ -834,9 +834,9 @@ def compute_anisotropic_dwr_metric( r""" Compute an anisotropic metric from some error indicator, given a Hessian field. - The formulation used is based on that presented in :cite:`CPB:13`. Note that + The formulation used is based on that presented in :cite:`Carpio:2013`. Note that normalisation is implicit in the metric construction and involves the - `convergence_rate` parameter, named :math:`alpha` in :cite:`CPB:13`. + `convergence_rate` parameter, named :math:`alpha` in :cite:`Carpio:2013`. If a Hessian is not provided then an isotropic formulation is used. @@ -936,7 +936,7 @@ def compute_weighted_hessian_metric( Compute a vertex-wise anisotropic metric from a list of error indicators, given a list of corresponding Hessian fields. - The formulation used is based on that presented in :cite:`PPP+:06`. It is + The formulation used is based on that presented in :cite:`Power:2006`. It is assumed that the error indicators have been constructed in the appropriate way. :arg error_indicators: list of error indicators @@ -987,7 +987,7 @@ def determine_metric_complexity(H_interior, H_boundary, target, p, **kwargs): Solve an algebraic problem to obtain coefficients for the interior and boundary metrics to obtain a given metric complexity. - See :cite:`LDA:10` for details. Note that we use a slightly different formulation + See :cite:Loseille:2010` for details. Note that we use a slightly different formulation here. :arg H_interior: Hessian component from domain interior diff --git a/demos/bubble_shear.py b/demos/bubble_shear.py index bf54c10..66c27db 100644 --- a/demos/bubble_shear.py +++ b/demos/bubble_shear.py @@ -511,3 +511,9 @@ def adapt_metric_advection(mesh, t_start, t_end, c): # to maintain numerical stability (look at CFL condition). # # This demo can also be accessed as a `Python script `__. +# +# +# .. rubric:: References +# +# .. bibliography:: +# :filter: docname in docnames diff --git a/demos/combining_metrics.py b/demos/combining_metrics.py index adcd7d8..384ee4a 100644 --- a/demos/combining_metrics.py +++ b/demos/combining_metrics.py @@ -23,9 +23,8 @@ # intersection of two metrics produces a metric whose associated ellipsoid is # the largest ellipsoid that can fit within the ellipsoids of the two metrics: # -# .. figure:: combining_ellipse_intersection.jpg -# :figwidth: 70% -# :align: center +# .. raw:: html +# :file: combining_ellipse_intersection.svg # # Below we first set up two metrics: Metric 1 asks for a medium resolution of # :math:`hm=0.025` in the left, and a coarse resolution of :math:`hc=0.1` in diff --git a/demos/demo_references.bib b/demos/demo_references.bib deleted file mode 100644 index be1e854..0000000 --- a/demos/demo_references.bib +++ /dev/null @@ -1,24 +0,0 @@ -@article{FPP+:2009, - title={Conservative interpolation between unstructured meshes via supermesh construction}, - author={Farrell, Patrick E and Piggott, Matthew D and Pain, Christopher C and Gorman, Gerard J and Wilson, Cian R}, - journal={Computer methods in applied mechanics and engineering}, - volume={198}, - number={33-36}, - pages={2632--2642}, - year={2009}, - publisher={Elsevier} -} - -@article{Barral:2016, - title={Anisotropic mesh adaptation in Firedrake with PETSc DMPlex}, - author={Barral, Nicolas and Knepley, Matthew G and Lange, Michael and Piggott, Matthew D and Gorman, Gerard J}, - journal={arXiv preprint arXiv:1610.09874}, - year={2016} -} - -@phdthesis{Wilson:2010, - title={Modelling multiple-material flows on adaptive unstructured meshes}, - author={Wilson, Cian}, - year={2010}, - school={Imperial College London} -} \ No newline at end of file diff --git a/demos/ping_pong.py b/demos/ping_pong.py index 08e4757..5391bf1 100644 --- a/demos/ping_pong.py +++ b/demos/ping_pong.py @@ -175,7 +175,7 @@ # :math:`\mathbb P1` fields specifically, it is possible to achieve this using 'mass # lumping'. Recall the linear system above. Lumping amounts to replacing the mass matrix # :math:`\underline{\mathbf{M}_B}` with a diagonal matrix, whose entries correspond to -# the sums over the corresponding mass matrix rows. (See :cite:`FPP+:2009` for details.) +# the sums over the corresponding mass matrix rows. (See :cite:`Farrell:2009` for details.) # # The resulting bounded projection operator can be used in Animate by passing # ``bounded=True`` to the ``project`` function. :: @@ -247,7 +247,8 @@ # # This demo can also be accessed as a `Python script `__. # +# # .. rubric:: References # -# .. bibliography:: demo_references.bib +# .. bibliography:: # :filter: docname in docnames