diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 35a0ffec9..014f83280 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -37,24 +37,24 @@ jobs: make html - name: Deploy - if: github.event_name == 'push' && github.repository == 'AMReX-Codes/AMReX-Hydro' && github.ref == 'refs/heads/development' + if: github.event_name == 'push' && github.repository == 'AMReX-Fluids/AMReX-Hydro' && github.ref == 'refs/heads/development' uses: JamesIves/github-pages-deploy-action@3.7.1 with: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} ACCESS_TOKEN: ${{ secrets.DEPLOY_DOCS_HYDRO }} - REPOSITORY_NAME: AMReX-Codes/AMReX-Codes.github.io + REPOSITORY_NAME: AMReX-Fluids/AMReX-Fluids.github.io BRANCH: main # The branch the action should deploy to. FOLDER: Docs/build/html # The folder the action should deploy. TARGET_FOLDER: amrex-hydro/docs_html # The folder the action should deploy to. CLEAN: false # Do not remove existing files from the deploy target. - name: Deploy Doxygen - if: github.event_name == 'push' && github.repository == 'AMReX-Codes/AMReX-Hydro' && github.ref == 'refs/heads/development' + if: github.event_name == 'push' && github.repository == 'AMReX-Fluids/AMReX-Hydro' && github.ref == 'refs/heads/development' uses: JamesIves/github-pages-deploy-action@3.7.1 with: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} ACCESS_TOKEN: ${{ secrets.DEPLOY_DOCS_HYDRO }} - REPOSITORY_NAME: AMReX-Codes/AMReX-Codes.github.io + REPOSITORY_NAME: AMReX-Fluids/AMReX-Fluids.github.io BRANCH: main # The branch the action should deploy to. FOLDER: Docs/Doxygen/html # The folder the action should deploy. TARGET_FOLDER: amrex-hydro/Doxygen/html # The folder the action should deploy to. diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 8a90982f7..4c143fc32 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -51,14 +51,14 @@ your fork. `development` on the main AMReX-Hydro repository. First, let us setup your local git repo. To make your own fork of the main -repository, press the fork button on the [AMReX-Hydro Github page](https://github.com/AMReX-Codes/AMReX-Hydro). +repository, press the fork button on the [AMReX-Hydro Github page](https://github.com/AMReX-Fluids/AMReX-Hydro). Then, clone AMReX-Hydro on your local computer. If you plan on doing a lot of AMReX-Hydro development, we recommend configuring your clone to use ssh access so you won't have to enter your Github password every time, which you can do using these commands: ``` -git clone git@github.com:AMReX-Codes/AMReX-Hydro.git +git clone git@github.com:AMReX-Fluids/AMReX-Hydro.git cd AMReX-Hydro # Add your own fork. @@ -78,7 +78,7 @@ machine, see If you instead prefer to use HTTPS authentication, configure your local clone as follows: ``` -git clone https://github.com/AMReX-Codes/AMReX-Hydro.git +git clone https://github.com/AMReX-Fluids/AMReX-Hydro.git cd AMReX-Hydro # Add your own fork. diff --git a/Docs/Doxygen/main.dox b/Docs/Doxygen/main.dox index 261f770d0..8d9dbd278 100644 --- a/Docs/Doxygen/main.dox +++ b/Docs/Doxygen/main.dox @@ -21,11 +21,11 @@ * * A detailed explanation of the algorithms as implemented can be found in * the - * AMReX-Hydro + * AMReX-Hydro * User Guide. * * \subsection github GitHub Repository * * The source code for AMReX-Hydro can be found at the GitHub repository, - * AMReX-Codes/AMReX-Hydro. + * AMReX-Fluids/AMReX-Hydro. */ diff --git a/Docs/source/BDS.rst b/Docs/source/BDS.rst index 1e42161b7..42804dfdf 100644 --- a/Docs/source/BDS.rst +++ b/Docs/source/BDS.rst @@ -19,13 +19,13 @@ boundary conditions are supported. Embedded boundaries are not supported within this time. If additional functionality is desired, or if questions remain after reading this guide, further help is available by submitting an issue through -`Github `_ +`Github `_ .. These lines can be added when API docs are ready. These algorithms are applied in the BDS namespace. For API documentation, see `Doxygen: BDS Namespace`_. - .. _`Doxygen: BDS Namespace`: https://amrex-codes.github.io/amrex-hydro/Doxygen/html/namespaceBDS.html + .. _`Doxygen: BDS Namespace`: https://amrex-fluids.github.io/amrex-hydro/Doxygen/html/namespaceBDS.html Pre-MAC @@ -41,7 +41,7 @@ Post-MAC .. These lines can be added back when the Doxygen for BDS.rst is ready (API ref. `BDS::ComputeEdgeState`_) - .. _`BDS::ComputeEdgeState`: https://amrex-codes.github.io/amrex-hydro/Doxygen/html/namespaceBDS.html# + .. _`BDS::ComputeEdgeState`: https://amrex-fluids.github.io/amrex-hydro/Doxygen/html/namespaceBDS.html# In the notation below, :math:`s` is a scalar field of the form :math:`s=s(x,y,z,t)` @@ -66,6 +66,3 @@ Obtaining the edge states is a two step process: piecewise trilinear (bilinear in 2D) profiles over the space-time region determined by the characteristic domain of dependence of the face. We enforce no inflow at an outflow face as described in the post-MAC :ref:`Boundary Conditions Section`. - - - diff --git a/Docs/source/Fluxes.rst b/Docs/source/Fluxes.rst index e720c1726..31cac7773 100644 --- a/Docs/source/Fluxes.rst +++ b/Docs/source/Fluxes.rst @@ -7,9 +7,9 @@ Computing Fluxes ---------------- Doxygen links -`ComputeFluxes `_ +`ComputeFluxes `_ and -`EB_ComputeFluxes `_ . +`EB_ComputeFluxes `_ . AMReX-Hydro has the option to compute intesive or extensive, i.e. area-weighted, fluxes. Extensive fluxes are always used for problems using R-Z geometry, @@ -100,4 +100,3 @@ where :math:`\area_{i-\frac{1}{2},j,k}` is the area of the lower x-face of cell- For EB, we simply scale area the by the area fraction in the above equations. For example, we use :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. - diff --git a/Docs/source/Godunov.rst b/Docs/source/Godunov.rst index 2eb4511fe..c34ac8612 100644 --- a/Docs/source/Godunov.rst +++ b/Docs/source/Godunov.rst @@ -12,12 +12,12 @@ or piecewise parabolic (PPM) :cite:`ppm, millercolella:2002` reconstructions of These alogrithms are applied in the Godunov namespace. For API documentation, see `Doxygen: Godunov Namespace`_. -.. _`Doxygen: Godunov Namespace`: https://amrex-codes.github.io/amrex-hydro/Doxygen/html/namespaceGodunov.html +.. _`Doxygen: Godunov Namespace`: https://amrex-fluids.github.io/amrex-hydro/Doxygen/html/namespaceGodunov.html .. _godunov-pre-mac: -Pre-MAC (API ref. `Godunov::ExtrapVelToFaces `_) +Pre-MAC (API ref. `Godunov::ExtrapVelToFaces `_) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ We extrapolate the normal velocities to cell faces using a second-order Taylor series expansion @@ -184,7 +184,7 @@ and :math:`\tilde{w}^{n+\frac{1}{2}}_{i,j,k+\frac{1}{2}}`. We refer to this uniq normal velocity on each face as :math:`\boldsymbol{U}^{MAC,*}`. -Post-MAC (API ref. `Godnuov::ComputeEdgeState `_) +Post-MAC (API ref. `Godnuov::ComputeEdgeState `_) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -238,7 +238,7 @@ EBGodunov attempts to use fourth-order limited slopes wherever possible, as desc .. _pre-mac: -Pre-MAC (API ref. `EBGodunov::ExtrapVelToFaces `_) +Pre-MAC (API ref. `EBGodunov::ExtrapVelToFaces `_) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ We extrapolate the normal velocities to cell faces using a second-order Taylor series expansion @@ -385,7 +385,7 @@ and :math:`\tilde{w}^{n+\frac{1}{2}}_{i,j,k+\frac{1}{2}}`. We refer to these uni normal velocity on each face as :math:`\boldsymbol{U}^{MAC,*}`. -Post-MAC (API ref. `EBGondunov::ComputeEdgestate `_) +Post-MAC (API ref. `EBGondunov::ComputeEdgestate `_) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Here, the face-centered advective velocity field, which we will call :math:`\U^{MAC}`, is already known. @@ -446,5 +446,3 @@ the subscripts, we define \tilde{s}^{R,\nph} & \mbox{if $u^{MAC} < \varepsilon $} \\ \frac{1}{2} (\tilde{s}^{L,\nph} + \tilde{s}^{R,\nph}) & \mbox{otherwise} \end{array} \right. - - diff --git a/Docs/source/Install.rst b/Docs/source/Install.rst index f58c2f0a8..856012509 100644 --- a/Docs/source/Install.rst +++ b/Docs/source/Install.rst @@ -56,7 +56,7 @@ Clone and Configure AMReX-Hydro :: - git clone https://github.com/AMReX-Codes/AMReX-Hydro.git + git clone https://github.com/AMReX-Fluids/AMReX-Hydro.git 6. In the ``AMReX-Hydro`` folder, create and enter a build directory, @@ -102,4 +102,3 @@ Make The Object Files :: AMReX-Hydro/build/CMakeFiles/amrex_hydro.dir - diff --git a/Docs/source/Introduction.rst b/Docs/source/Introduction.rst index 22d6b19b1..4b0bdd2d0 100644 --- a/Docs/source/Introduction.rst +++ b/Docs/source/Introduction.rst @@ -8,9 +8,9 @@ AMReX-Hydro is set of routines that support the construction of convective terms for incompressible and low Mach number flow modeling in cartesian coordinates with (or without) embedded boundaries and R-Z coordinate systems. It is not a stand-alone code, but is used in several application codes, such as -`incflo `_ +`incflo `_ (a variable density incompressible Navier-Stokes solver with adaptive mesh refinement (AMR)), -`IAMR `_ +`IAMR `_ (a variable density incompressible Navier-Stokes solver with time subcycling AMR), and `MFIX-Exa `_ (a multiphase computational fluid dynamics modeling tool). @@ -48,5 +48,3 @@ Here we group the AMReX-Hydro routines into a few general categories and map the * :ref:`utilities`: to do things like compute slopes, create fluxes from face-centered values, and create the convective term from fluxes (used in all but step 2). - - diff --git a/Docs/source/MOL.rst b/Docs/source/MOL.rst index 4792e4b2f..a5af38635 100644 --- a/Docs/source/MOL.rst +++ b/Docs/source/MOL.rst @@ -10,10 +10,10 @@ second-order limited slopes as described in :ref:`slopes`. These alogrithms are applied in the MOL namespace. For API documentation, see `Doxygen: MOL Namespace`_. -.. _`Doxygen: MOL Namespace`: https://amrex-codes.github.io/amrex-hydro/Doxygen/html/namespaceMOL.html +.. _`Doxygen: MOL Namespace`: https://amrex-fluids.github.io/amrex-hydro/Doxygen/html/namespaceMOL.html -Pre-MAC (API ref. `MOL::ExtrapVelToFaces `_) +Pre-MAC (API ref. `MOL::ExtrapVelToFaces `_) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ For computing the pre-MAC edge states to be MAC-projected, we define on @@ -44,7 +44,7 @@ We similarly compute :math:`v_{i,j-\frac{1}{2},k}` on y-faces and :math:`w_{i,j,k-\frac{1}{2}}` on z-faces. -Post-MAC (API ref. `MOL::ComputeEdgeState `_) +Post-MAC (API ref. `MOL::ComputeEdgeState `_) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Once we have the MAC-projected velocities, we extrapolate all quantities to @@ -82,7 +82,7 @@ discussed above. All slope computations use second-order limited slopes as described in :ref:`EBslopes`. -Pre-MAC (API ref. `EBMOL::ExtrapVelToFaces `_) +Pre-MAC (API ref. `EBMOL::ExtrapVelToFaces `_) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ For computing the pre-MAC edge states to be MAC-projected, we define on every x-face with non-zero area fraction: @@ -114,7 +114,7 @@ We similarly compute :math:`v_{i,j-\frac{1}{2},k}` on y-faces and :math:`w_{i,j,k-\frac{1}{2}}` on z-faces. -Post-MAC (API ref. `EBMOL::ComputeEdgeState `_) +Post-MAC (API ref. `EBMOL::ComputeEdgeState `_) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Once we have the MAC-projected velocities, we predict all quantities to faces with non-zero area fractions as above: @@ -140,4 +140,3 @@ Then, at each face we then upwind based on :math:`u^{MAC}_{i-\frac{1}{2},j,k}` s_R, & \mathrm{if} \; u^{MAC}_{i-\frac{1}{2},j,k}\; \le \; -\varepsilon \; \mathrm{else} \\ \frac{1}{2}(s_L + s_R), \end{cases} - diff --git a/Docs/source/Schemes.rst b/Docs/source/Schemes.rst index 1f203395c..f799347c3 100644 --- a/Docs/source/Schemes.rst +++ b/Docs/source/Schemes.rst @@ -60,7 +60,7 @@ And for the third dimension, :math:`\U^{MAC}` is the MAC-projected velocity at face centers (or centroids for EB). -We define :math:`\varepsilon = 1.e-8` in `Utils/hydro_constants.H `_. This is an empirically determined constant that works well for flows where velocities are on the order of 1. +We define :math:`\varepsilon = 1.e-8` in `Utils/hydro_constants.H `_. This is an empirically determined constant that works well for flows where velocities are on the order of 1. .. include:: MOL.rst @@ -68,4 +68,3 @@ We define :math:`\varepsilon = 1.e-8` in `Utils/hydro_constants.H