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.github/workflows/docs.yml

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make html
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- name: Deploy
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if: github.event_name == 'push' && github.repository == 'AMReX-Codes/AMReX-Hydro' && github.ref == 'refs/heads/development'
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if: github.event_name == 'push' && github.repository == 'AMReX-Fluids/AMReX-Hydro' && github.ref == 'refs/heads/development'
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uses: JamesIves/[email protected]
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with:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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ACCESS_TOKEN: ${{ secrets.DEPLOY_DOCS_HYDRO }}
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REPOSITORY_NAME: AMReX-Codes/AMReX-Codes.github.io
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REPOSITORY_NAME: AMReX-Fluids/AMReX-Fluids.github.io
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BRANCH: main # The branch the action should deploy to.
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FOLDER: Docs/build/html # The folder the action should deploy.
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TARGET_FOLDER: amrex-hydro/docs_html # The folder the action should deploy to.
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CLEAN: false # Do not remove existing files from the deploy target.
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- name: Deploy Doxygen
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if: github.event_name == 'push' && github.repository == 'AMReX-Codes/AMReX-Hydro' && github.ref == 'refs/heads/development'
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if: github.event_name == 'push' && github.repository == 'AMReX-Fluids/AMReX-Hydro' && github.ref == 'refs/heads/development'
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uses: JamesIves/[email protected]
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with:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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ACCESS_TOKEN: ${{ secrets.DEPLOY_DOCS_HYDRO }}
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REPOSITORY_NAME: AMReX-Codes/AMReX-Codes.github.io
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REPOSITORY_NAME: AMReX-Fluids/AMReX-Fluids.github.io
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BRANCH: main # The branch the action should deploy to.
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FOLDER: Docs/Doxygen/html # The folder the action should deploy.
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TARGET_FOLDER: amrex-hydro/Doxygen/html # The folder the action should deploy to.

CONTRIBUTING.md

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@@ -51,14 +51,14 @@ your fork.
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`development` on the main AMReX-Hydro repository.
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First, let us setup your local git repo. To make your own fork of the main
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repository, press the fork button on the [AMReX-Hydro Github page](https://github.com/AMReX-Codes/AMReX-Hydro).
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repository, press the fork button on the [AMReX-Hydro Github page](https://github.com/AMReX-Fluids/AMReX-Hydro).
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Then, clone AMReX-Hydro on your local computer. If you plan on doing a lot of AMReX-Hydro development,
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we recommend configuring your clone to use ssh access so you won't have to enter your Github
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password every time, which you can do using these commands:
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```
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git clone [email protected]:AMReX-Codes/AMReX-Hydro.git
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git clone [email protected]:AMReX-Fluids/AMReX-Hydro.git
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cd AMReX-Hydro
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# Add your own fork.
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If you instead prefer to use HTTPS authentication, configure your local clone as follows:
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```
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git clone https://github.com/AMReX-Codes/AMReX-Hydro.git
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git clone https://github.com/AMReX-Fluids/AMReX-Hydro.git
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cd AMReX-Hydro
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# Add your own fork.

Docs/Doxygen/main.dox

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*
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* A detailed explanation of the algorithms as implemented can be found in
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* the
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* <a href="https://amrex-codes.github.io/amrex/hydro_html/index.html">AMReX-Hydro
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* <a href="https://amrex-fluids.github.io/amrex-hydro/docs_html/index.html">AMReX-Hydro
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* User Guide</a>.
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*
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* \subsection github GitHub Repository
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*
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* The source code for AMReX-Hydro can be found at the GitHub repository,
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* <a href="https://github.com/AMReX-Codes/AMReX-Hydro">AMReX-Codes/AMReX-Hydro</a>.
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* <a href="https://github.com/AMReX-Fluids/AMReX-Hydro">AMReX-Fluids/AMReX-Hydro</a>.
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*/

Docs/source/BDS.rst

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@@ -19,13 +19,13 @@ boundary conditions are supported. Embedded boundaries are not supported within
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this time.
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If additional functionality is desired, or if questions remain after reading this guide,
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further help is available by submitting an issue through
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`Github <https://github.com/AMReX-Codes/AMReX-Hydro/issues/new>`_
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`Github <https://github.com/AMReX-Fluids/AMReX-Hydro/issues/new>`_
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..
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These lines can be added when API docs are ready.
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These algorithms are applied in the BDS namespace. For API documentation, see
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`Doxygen: BDS Namespace`_.
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.. _`Doxygen: BDS Namespace`: https://amrex-codes.github.io/amrex-hydro/Doxygen/html/namespaceBDS.html
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.. _`Doxygen: BDS Namespace`: https://amrex-fluids.github.io/amrex-hydro/Doxygen/html/namespaceBDS.html
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Pre-MAC
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..
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These lines can be added back when the Doxygen for BDS.rst is ready
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(API ref. `BDS::ComputeEdgeState`_)
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.. _`BDS::ComputeEdgeState`: https://amrex-codes.github.io/amrex-hydro/Doxygen/html/namespaceBDS.html#
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.. _`BDS::ComputeEdgeState`: https://amrex-fluids.github.io/amrex-hydro/Doxygen/html/namespaceBDS.html#
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In the notation below,
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:math:`s` is a scalar field of the form :math:`s=s(x,y,z,t)`
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piecewise trilinear (bilinear in 2D) profiles over the space-time region determined by the characteristic
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domain of dependence of the face.
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We enforce no inflow at an outflow face as described in the post-MAC :ref:`Boundary Conditions Section<no-inflow-at-outflow>`.
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Docs/source/Fluxes.rst

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----------------
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Doxygen links
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`ComputeFluxes <https://amrex-codes.github.io/amrex-hydro/Doxygen/html/namespaceHydroUtils.html#ab70f040557a658e70ba076c9d105bab7>`_
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`ComputeFluxes <https://amrex-fluids.github.io/amrex-hydro/Doxygen/html/namespaceHydroUtils.html#ab70f040557a658e70ba076c9d105bab7>`_
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and
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`EB_ComputeFluxes <https://amrex-codes.github.io/amrex-hydro/Doxygen/html/namespaceHydroUtils.html#ab70f040557a658e70ba076c9d105bab7>`_ .
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`EB_ComputeFluxes <https://amrex-fluids.github.io/amrex-hydro/Doxygen/html/namespaceHydroUtils.html#ab70f040557a658e70ba076c9d105bab7>`_ .
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AMReX-Hydro has the option to compute intesive or extensive, i.e. area-weighted, fluxes.
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Extensive fluxes are always used for problems using R-Z geometry,
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For EB, we simply scale area the by the area fraction in the above equations. For example, we use
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:math:`\alpha_{i-\frac{1}{2},j,k} \area_{i-\frac{1}{2},j,k}` in place of :math:`\area_{i-\frac{1}{2},j,k}`, etc.
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Docs/source/Godunov.rst

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@@ -12,12 +12,12 @@ or piecewise parabolic (PPM) :cite:`ppm, millercolella:2002` reconstructions of
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These alogrithms are applied in the Godunov namespace. For API documentation, see
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`Doxygen: Godunov Namespace`_.
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.. _`Doxygen: Godunov Namespace`: https://amrex-codes.github.io/amrex-hydro/Doxygen/html/namespaceGodunov.html
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.. _`Doxygen: Godunov Namespace`: https://amrex-fluids.github.io/amrex-hydro/Doxygen/html/namespaceGodunov.html
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.. _godunov-pre-mac:
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Pre-MAC (API ref. `Godunov::ExtrapVelToFaces <https://amrex-codes.github.io/amrex-hydro/Doxygen/html/namespaceGodunov.html#a1c1dcedd6781260bd8322588e1290d94>`_)
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Pre-MAC (API ref. `Godunov::ExtrapVelToFaces <https://amrex-fluids.github.io/amrex-hydro/Doxygen/html/namespaceGodunov.html#a1c1dcedd6781260bd8322588e1290d94>`_)
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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We extrapolate the normal velocities to cell faces using a second-order Taylor series expansion
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normal velocity on each face as :math:`\boldsymbol{U}^{MAC,*}`.
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Post-MAC (API ref. `Godnuov::ComputeEdgeState <https://amrex-codes.github.io/amrex-hydro/Doxygen/html/namespaceGodunov.html#addea54945ce554f8b4e28dabc1c74222>`_)
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Post-MAC (API ref. `Godnuov::ComputeEdgeState <https://amrex-fluids.github.io/amrex-hydro/Doxygen/html/namespaceGodunov.html#addea54945ce554f8b4e28dabc1c74222>`_)
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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.. _pre-mac:
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Pre-MAC (API ref. `EBGodunov::ExtrapVelToFaces <https://amrex-codes.github.io/amrex-hydro/Doxygen/html/namespaceEBGodunov.html#abea06da38cd7e2c6a6ed94d761c4e996>`_)
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Pre-MAC (API ref. `EBGodunov::ExtrapVelToFaces <https://amrex-fluids.github.io/amrex-hydro/Doxygen/html/namespaceEBGodunov.html#abea06da38cd7e2c6a6ed94d761c4e996>`_)
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We extrapolate the normal velocities to cell faces using a second-order Taylor series expansion
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Post-MAC (API ref. `EBGondunov::ComputeEdgestate <https://amrex-codes.github.io/amrex-hydro/Doxygen/html/namespaceEBGodunov.html#afb5b3b4bcea09a8aeeb568ddde3a46e4>`_)
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Post-MAC (API ref. `EBGondunov::ComputeEdgestate <https://amrex-fluids.github.io/amrex-hydro/Doxygen/html/namespaceEBGodunov.html#afb5b3b4bcea09a8aeeb568ddde3a46e4>`_)
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Here, the face-centered advective velocity field, which we will call :math:`\U^{MAC}`, is already known.
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\tilde{s}^{R,\nph} & \mbox{if $u^{MAC} < \varepsilon $} \\
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\frac{1}{2} (\tilde{s}^{L,\nph} + \tilde{s}^{R,\nph}) & \mbox{otherwise}
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\end{array} \right.
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Docs/source/Install.rst

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::
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git clone https://github.com/AMReX-Codes/AMReX-Hydro.git
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git clone https://github.com/AMReX-Fluids/AMReX-Hydro.git
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6. In the ``AMReX-Hydro`` folder, create and enter a build directory,
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::
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AMReX-Hydro/build/CMakeFiles/amrex_hydro.dir
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Docs/source/Introduction.rst

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terms for incompressible and low Mach number flow modeling
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in cartesian coordinates with (or without) embedded boundaries and R-Z coordinate systems.
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It is not a stand-alone code, but is used in several application codes, such as
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`incflo <https://amrex-codes.github.io/incflo/docs_html/>`_
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`incflo <https://amrex-fluids.github.io/incflo/docs_html/>`_
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(a variable density incompressible Navier-Stokes solver with adaptive mesh refinement (AMR)),
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`IAMR <https://amrex-codes.github.io/IAMR/docs_html/index.html>`_
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`IAMR <https://amrex-fluids.github.io/IAMR/docs_html/index.html>`_
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(a variable density incompressible Navier-Stokes solver with time subcycling AMR),
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and `MFIX-Exa <https://amrex-codes.github.io/MFIX-Exa/docs_html/>`_
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(a multiphase computational fluid dynamics modeling tool).
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* :ref:`utilities`: to do things like compute slopes, create fluxes from face-centered values, and
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create the convective term from fluxes (used in all but step 2).
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Docs/source/MOL.rst

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These alogrithms are applied in the MOL namespace. For API documentation, see
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`Doxygen: MOL Namespace`_.
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.. _`Doxygen: MOL Namespace`: https://amrex-codes.github.io/amrex-hydro/Doxygen/html/namespaceMOL.html
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.. _`Doxygen: MOL Namespace`: https://amrex-fluids.github.io/amrex-hydro/Doxygen/html/namespaceMOL.html
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Pre-MAC (API ref. `MOL::ExtrapVelToFaces <https://amrex-codes.github.io/amrex-hydro/Doxygen/html/namespaceMOL.html#acdde2acf756048b8ef0bca332e4bf748>`_)
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Pre-MAC (API ref. `MOL::ExtrapVelToFaces <https://amrex-fluids.github.io/amrex-hydro/Doxygen/html/namespaceMOL.html#acdde2acf756048b8ef0bca332e4bf748>`_)
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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For computing the pre-MAC edge states to be MAC-projected, we define on
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Post-MAC (API ref. `MOL::ComputeEdgeState <https://amrex-codes.github.io/amrex-hydro/Doxygen/html/namespaceMOL.html#acdde2acf756048b8ef0bca332e4bf748>`_)
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Post-MAC (API ref. `MOL::ComputeEdgeState <https://amrex-fluids.github.io/amrex-hydro/Doxygen/html/namespaceMOL.html#acdde2acf756048b8ef0bca332e4bf748>`_)
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Once we have the MAC-projected velocities, we extrapolate all quantities to
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All slope computations use second-order limited slopes as described in :ref:`EBslopes`.
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Pre-MAC (API ref. `EBMOL::ExtrapVelToFaces <https://amrex-codes.github.io/amrex-hydro/Doxygen/html/namespaceEBMOL.html#a7add53a153ade9c5cb83e79a61ad1929>`_)
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Pre-MAC (API ref. `EBMOL::ExtrapVelToFaces <https://amrex-fluids.github.io/amrex-hydro/Doxygen/html/namespaceEBMOL.html#a7add53a153ade9c5cb83e79a61ad1929>`_)
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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For computing the pre-MAC edge states to be MAC-projected, we define on every x-face with non-zero area fraction:
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:math:`w_{i,j,k-\frac{1}{2}}` on z-faces.
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Post-MAC (API ref. `EBMOL::ComputeEdgeState <https://amrex-codes.github.io/amrex-hydro/Doxygen/html/namespaceEBMOL.html#a94df1b279b45eac5141dfe0dff0a79bc>`_)
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Post-MAC (API ref. `EBMOL::ComputeEdgeState <https://amrex-fluids.github.io/amrex-hydro/Doxygen/html/namespaceEBMOL.html#a94df1b279b45eac5141dfe0dff0a79bc>`_)
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Once we have the MAC-projected velocities, we predict all quantities to faces with non-zero area fractions as above:
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\frac{1}{2}(s_L + s_R),
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\end{cases}
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Docs/source/Schemes.rst

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:math:`\U^{MAC}` is the MAC-projected velocity at face centers (or centroids for EB).
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We define :math:`\varepsilon = 1.e-8` in `Utils/hydro_constants.H <https://amrex-codes.github.io/amrex-hydro/Doxygen/html/group__Utilities.html#ga57d5ce9bc3bca16e249c611342f3c550>`_. This is an empirically determined constant that works well for flows where velocities are on the order of 1.
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We define :math:`\varepsilon = 1.e-8` in `Utils/hydro_constants.H <https://amrex-fluids.github.io/amrex-hydro/Doxygen/html/group__Utilities.html#ga57d5ce9bc3bca16e249c611342f3c550>`_. This is an empirically determined constant that works well for flows where velocities are on the order of 1.
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.. include:: MOL.rst
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.. include:: Godunov.rst
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.. include:: BDS.rst
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