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Use GitHub notebook preview instead of nbviewer (#4513)
* Use GitHub notebook preview instead of nbviewer nbviewer is slow and occasionally fails the linkcheck.
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docs/source/notebooks.rst

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@@ -28,16 +28,15 @@ Colab <https://fem-on-colab.github.io/index.html>`__ by `Francesco
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Ballarin <https://www.francescoballarin.it>`__, you can run the notebooks on
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Google Colab through your web browser, without installing Firedrake.
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We also provide links to non-interactive renderings of the notebooks using
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`Jupyter nbviewer <https://nbviewer.jupyter.org>`__.
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Non-interactive renderings of the notebooks can also be seen on `GitHub
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<https://github.com/firedrakeproject/firedrake/tree/release/docs/notebooks>`__.
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A first example
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===============
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In this notebook, we solve the symmetric positive definite "Helmholtz"
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equation, and learn about meshes and function spaces. A rendered
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version of this notebook is available `here
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<https://nbviewer.jupyter.org/github/firedrakeproject/firedrake/blob/release/docs/notebooks/01-spd-helmholtz.ipynb>`__
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version of this notebook is available `here <https://github.com/firedrakeproject/firedrake/blob/release/docs/notebooks/01-spd-helmholtz.ipynb>`__
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and there is a version `on Colab <https://colab.research.google.com/github/firedrakeproject/notebooks/blob/main/01-spd-helmholtz.ipynb>`__
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@@ -47,7 +46,7 @@ Incorporating strong boundary conditions
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Next, we modify the problem slightly and solve the Poisson equation.
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We introduce strong (Dirichlet) boundary conditions and `how to use
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them
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<https://nbviewer.jupyter.org/github/firedrakeproject/firedrake/blob/release/docs/notebooks/02-poisson.ipynb>`__.
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<https://github.com/firedrakeproject/firedrake/blob/release/docs/notebooks/02-poisson.ipynb>`__.
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You can run this notebook yourself `on Colab <https://colab.research.google.com/github/firedrakeproject/notebooks/blob/main/02-poisson.ipynb>`__
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@@ -58,7 +57,7 @@ Moving on from scalar problems, we look at our first vector-valued problem,
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namely the equations of linear elasticity. In this notebook, we learn about
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some of UFL's support for tensor algebra, and start looking at `configuring
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linear solvers
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<https://nbviewer.jupyter.org/github/firedrakeproject/firedrake/blob/release/docs/notebooks/03-elasticity.ipynb>`__.
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<https://github.com/firedrakeproject/firedrake/blob/release/docs/notebooks/03-elasticity.ipynb>`__.
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You can run this notebook yourself `on Colab
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<https://colab.research.google.com/github/firedrakeproject/notebooks/blob/main/03-elasticity.ipynb>`__
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Burgers' equation, and also treats simple timestepping schemes. We
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learn about formulating nonlinear, as opposed to linear problems, and
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also a little bit about how to write `efficient Firedrake code
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<https://nbviewer.jupyter.org/github/firedrakeproject/firedrake/blob/release/docs/notebooks/04-burgers.ipynb>`__.
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<https://github.com/firedrakeproject/firedrake/blob/release/docs/notebooks/04-burgers.ipynb>`__.
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You can run this notebook yourself `on Colab
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<https://colab.research.google.com/github/firedrakeproject/notebooks/blob/main/04-burgers.ipynb>`__
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@@ -79,7 +78,7 @@ A mixed formulation of the Poisson equation
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===========================================
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`In this notebook
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<https://nbviewer.jupyter.org/github/firedrakeproject/firedrake/blob/release/docs/notebooks/05-mixed-poisson.ipynb>`__.,
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<https://github.com/firedrakeproject/firedrake/blob/release/docs/notebooks/05-mixed-poisson.ipynb>`__.,
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we look at our first mixed finite element problem. A dual formulation of the
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Poisson equation. This equation also appears in the context of flow in porous
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media, as Darcy flow. We introduce mixed function spaces and how to work with
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Now that we've learnt how to solve some PDEs, we might want to consider
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optimisation subject to PDE constraints. `This notebook
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<https://nbviewer.jupyter.org/github/firedrakeproject/firedrake/blob/release/docs/notebooks/06-pde-constrained-optimisation.ipynb>`__
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<https://github.com/firedrakeproject/firedrake/blob/release/docs/notebooks/06-pde-constrained-optimisation.ipynb>`__
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introduces the use of `dolfin-adjoint <http://www.dolfin-adjoint.org/>`__ to
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solve PDE constrained optimisation problems. We solve the Stokes equations and
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minimise energy loss due to heat, controlling inflow/outflow in a pipe. You can
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The next notebook looks a little bit at the support Firedrake has for
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geometric multigrid, and how you can configure complex multilevel
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solvers purely using `PETSc options
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<https://nbviewer.jupyter.org/github/firedrakeproject/firedrake/blob/release/docs/notebooks/07-geometric-multigrid.ipynb>`__.
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<https://github.com/firedrakeproject/firedrake/blob/release/docs/notebooks/07-geometric-multigrid.ipynb>`__.
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You can run this notebook yourself `on Colab
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<https://colab.research.google.com/github/firedrakeproject/notebooks/blob/main/07-geometric-multigrid.ipynb>`__
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and PETSc enable solvers and preconditioners to be composed in
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arbitrarily complex ways to `create an optimal solution strategy for a
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particular problem
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<https://nbviewer.jupyter.org/github/firedrakeproject/firedrake/blob/release/docs/notebooks/08-composable-solvers.ipynb>`__.
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<https://github.com/firedrakeproject/firedrake/blob/release/docs/notebooks/08-composable-solvers.ipynb>`__.
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You can run this notebook yourself `on Colab
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<https://colab.research.google.com/github/firedrakeproject/notebooks/blob/main/08-composable-solvers.ipynb>`__
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Building on the theme of composable solvers, we now explore
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`Firedrake's capabilities in the area of static condensation and
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hybridisation
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<https://nbviewer.jupyter.org/github/firedrakeproject/firedrake/blob/release/docs/notebooks/09-hybridisation.ipynb>`__.
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<https://github.com/firedrakeproject/firedrake/blob/release/docs/notebooks/09-hybridisation.ipynb>`__.
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You can run this notebook yourself `on Colab
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<https://colab.research.google.com/github/firedrakeproject/notebooks/blob/main/09-hybridisation.ipynb>`__
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In this notebook, we take a look under the hood at the sorts of performance
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optimisation that Firedrake's compilers can generate. In this case, we focus on
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`sum factorisation for tensor product elements
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<https://nbviewer.jupyter.org/github/firedrakeproject/firedrake/blob/release/docs/notebooks/10-sum-factorisation.ipynb>`__.
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<https://github.com/firedrakeproject/firedrake/blob/release/docs/notebooks/10-sum-factorisation.ipynb>`__.
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You can run this notebook yourself `on Colab
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<https://colab.research.google.com/github/firedrakeproject/notebooks/blob/main/10-sum-factorisation.ipynb>`__
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In some cases, it can be useful to extract adjoint solution data which is
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written to tape by `dolfin-adjoint`. This notebook shows how to do that:
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`solving adjoint equations using firedrake-adjoint
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<https://nbviewer.jupyter.org/github/firedrakeproject/firedrake/blob/release/docs/notebooks/11-extract-adjoint-solutions.ipynb>`__.
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<https://github.com/firedrakeproject/firedrake/blob/release/docs/notebooks/11-extract-adjoint-solutions.ipynb>`__.
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You can run this notebook yourself `on Colab
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<https://colab.research.google.com/github/firedrakeproject/notebooks/blob/main/11-extract-adjoint-solutions.ipynb>`__
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When it comes to running Firedrake on a high performance computer
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there are a range of different techniques to get the best performance
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from your code. The `HPC demonstration
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<https://nbviewer.jupyter.org/github/firedrakeproject/firedrake/blob/release/docs/notebooks/12-HPC_demo.ipynb>`__
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<https://github.com/firedrakeproject/firedrake/blob/release/docs/notebooks/12-HPC_demo.ipynb>`__
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notebook builds up a multigrid solver for an elliptic problem
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specifically designed for solving very large problems using Firedrake on
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HPC. You can run this notebook yourself `on Colab

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