From c3bbd9cde90ec3704bae094dafe7a8f35c5c5c1a Mon Sep 17 00:00:00 2001 From: acse-ej321 <89605848+acse-ej321@users.noreply.github.com> Date: Tue, 19 Nov 2024 09:22:28 +0000 Subject: [PATCH] update citations for html (#132) Linked to https://github.com/mesh-adaptation/mesh-adaptation-docs/issues/50 should be evaluated in combination with: https://github.com/mesh-adaptation/mesh-adaptation-docs/issues/50 https://github.com/mesh-adaptation/animate/pull/160 https://github.com/mesh-adaptation/goalie/pull/232 Locally the main warning remaining after all the PRs should be about 'duplicate_citations', though all citations should still render. --- demos/demo_references.bib | 30 ------------------------------ demos/lineal_spring.py | 2 +- demos/monge_ampere1.py | 2 +- demos/monge_ampere_3d.py | 4 ++-- movement/monge_ampere.py | 10 +++++----- movement/spring.py | 6 +++--- 6 files changed, 12 insertions(+), 42 deletions(-) delete mode 100644 demos/demo_references.bib diff --git a/demos/demo_references.bib b/demos/demo_references.bib deleted file mode 100644 index 95d5ab3..0000000 --- a/demos/demo_references.bib +++ /dev/null @@ -1,30 +0,0 @@ -@Article{Farhat:1998, - title={Torsional springs for two-dimensional dynamic unstructured fluid meshes}, - author={Farhat, Charbel and Degand, Christoph and Koobus, Bruno and Lesoinne, Michel}, - journal={Computer methods in applied mechanics and engineering}, - volume={163}, - number={1-4}, - pages={231--245}, - year={1998}, - publisher={Elsevier} -} - -@Article{McRae:2018, - author={McRae, A. T. T. and Cotter, C. J. and Budd, C., J.}, - title={Optimal-transport-based mesh adaptivity on the plane and sphere using finite elements}, - journal={SIAM Journal on Scientific Computing}, - year={2018}, - volume={40}, - number={2}, - pages={1121--1148}, - doi={10.1137/16M1109515} -} -@inproceedings{park2019, - title={Verification of unstructured grid adaptation components}, - author={Park, Michael A and Balan, Aravind and Anderson, William K and Galbraith, Marshall C and Caplan, Philip and Carson, Hugh A and Michal, Todd R and Krakos, Joshua A and Kamenetskiy, Dmitry S and Loseille, Adrien and others}, - booktitle={AIAA Scitech 2019 Forum}, - pages={1723}, - year={2019}, - doi={10.2514/6.2019-1723} -} - diff --git a/demos/lineal_spring.py b/demos/lineal_spring.py index 2f65ac3..5fb0118 100644 --- a/demos/lineal_spring.py +++ b/demos/lineal_spring.py @@ -230,5 +230,5 @@ def update_boundary_displacement(t): # # .. rubric:: References # -# .. bibliography:: demo_references.bib +# .. bibliography:: # :filter: docname in docnames diff --git a/demos/monge_ampere1.py b/demos/monge_ampere1.py index aed6d01..e6b2ec1 100644 --- a/demos/monge_ampere1.py +++ b/demos/monge_ampere1.py @@ -195,5 +195,5 @@ def ring_monitor(mesh): # # .. rubric:: References # -# .. bibliography:: demo_references.bib +# .. bibliography:: # :filter: docname in docnames diff --git a/demos/monge_ampere_3d.py b/demos/monge_ampere_3d.py index 28302c9..e6cdfaf 100644 --- a/demos/monge_ampere_3d.py +++ b/demos/monge_ampere_3d.py @@ -3,7 +3,7 @@ # In this demo we demonstrate that the Monge-Ampère mesh movement # can also be applied to 3D meshes. We employ the `sinatan3` function -# from :cite:`park2019` to introduce an interesting pattern. +# from :cite:`Park:2019` to introduce an interesting pattern. from firedrake import * @@ -98,5 +98,5 @@ def monitor(mesh): # # .. rubric:: References # -# .. bibliography:: demo_references.bib +# .. bibliography:: # :filter: docname in docnames diff --git a/movement/monge_ampere.py b/movement/monge_ampere.py index 9ea3ada..aa69058 100644 --- a/movement/monge_ampere.py +++ b/movement/monge_ampere.py @@ -46,7 +46,7 @@ def MongeAmpereMover(mesh, monitor_function, method="relaxation", **kwargs): :class:`~.MongeAmpereMover_Relaxation`. If the argument is set to `"quasi_newton"` then it is solved in its elliptic form using a quasi-Newton method in :class:`~.MongeAmpereMover_QuasiNewton`. Descriptions of both methods may be found in - :cite:`MCB:18`. + :cite:`McRae:2018`. The physical mesh coordinates :math:`\mathbf{x}` are updated according to @@ -109,7 +109,7 @@ class MongeAmpereMover_Base(PrimeMover, metaclass=abc.ABCMeta): Currently implemented subclasses: :class:`~.MongeAmpereMover_Relaxation` and :class:`~.MongeAmpereMover_QuasiNewton`. Descriptions of both methods may be found in - :cite:`MCB:18`. + :cite:`McRae:2018`. """ def __init__(self, mesh, monitor_function, **kwargs): @@ -366,7 +366,7 @@ class MongeAmpereMover_Relaxation(MongeAmpereMover_Base): = m(\mathbf{x})\det(\mathbf{I} + \mathbf{H}(\phi)) - \theta, where :math:`\tau` is the pseudo-time variable. Forward Euler is used for the - pseudo-time integration (see :cite:`MCB:18` for details). + pseudo-time integration (see :cite:`McRae:2018` for details). This approach typically takes tens or hundreds of iterations to converge, but each iteration is relatively cheap. @@ -424,7 +424,7 @@ def pseudotimestepper(self): """ Setup the pseudo-timestepper for the relaxation method. - Forward Euler is used for the pseudo-time integration (see :cite:`MCB:18` for + Forward Euler is used for the pseudo-time integration (see :cite:`McRae:2018` for details). The pseudo-timestep may be set through the `pseudo_timestep` keyword argument to the constructor. @@ -555,7 +555,7 @@ class MongeAmpereMover_QuasiNewton(MongeAmpereMover_Base): :math:`\phi` with respect to :math:`\boldsymbol{\xi}`. In this mesh mover, the elliptic Monge-Ampère equation is solved using a quasi-Newton - method (see :cite:`MCB:18` for details). + method (see :cite:`McRae:2018` for details). This approach typically takes fewer than ten iterations to converge, but each iteration is relatively expensive. diff --git a/movement/spring.py b/movement/spring.py index 92a597a..0432835 100644 --- a/movement/spring.py +++ b/movement/spring.py @@ -16,7 +16,7 @@ def SpringMover(*args, method="lineal", **kwargs): """ Movement of a ``mesh`` is determined by reinterpreting it as a structure of stiff beams and solving an associated discrete linear elasticity problem. (See - :cite:`FDK+:98` for details.) + :cite:`Farhat:1998` for details.) :arg mesh: the physical mesh to be moved :type mesh: :class:`firedrake.mesh.MeshGeometry` @@ -237,7 +237,7 @@ class SpringMover_Lineal(SpringMover_Base): Movement of a ``mesh`` is determined by reinterpreting it as a structure of stiff beams and solving an associated discrete linear elasticity problem. - We consider the 'lineal' case, as described in :cite:`FDK+:98`. + We consider the 'lineal' case, as described in :cite:`Farhat:1998`. """ @PETSc.Log.EventDecorator() @@ -285,7 +285,7 @@ class SpringMover_Torsional(SpringMover_Lineal): Movement of a ``mesh`` is determined by reinterpreting it as a structure of stiff beams and solving an associated discrete linear elasticity problem. - We consider the 'torsional' case, as described in :cite:`FDK+:98`. + We consider the 'torsional' case, as described in :cite:`Farhat:1998`. """ def __init__(self, *args, **kwargs):