update url (#121)

.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/[email protected]
         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/[email protected]
         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.

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 [email protected]:AMReX-Codes/AMReX-Hydro.git
+git clone [email protected]: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.

Docs/Doxygen/main.dox

@@ -21,11 +21,11 @@
  *
  *  A detailed explanation of the algorithms as implemented can be found in
  *  the
- *  <a href="https://amrex-codes.github.io/amrex/hydro_html/index.html">AMReX-Hydro
+ *  <a href="https://amrex-fluids.github.io/amrex-hydro/docs_html/index.html">AMReX-Hydro
  *  User Guide</a>.
  *   
  *  \subsection github GitHub Repository 
  *
  *  The source code for AMReX-Hydro can be found at the GitHub repository,
- *  <a href="https://github.com/AMReX-Codes/AMReX-Hydro">AMReX-Codes/AMReX-Hydro</a>. 
+ *  <a href="https://github.com/AMReX-Fluids/AMReX-Hydro">AMReX-Fluids/AMReX-Hydro</a>. 
  */

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 <https://github.com/AMReX-Codes/AMReX-Hydro/issues/new>`_
+`Github <https://github.com/AMReX-Fluids/AMReX-Hydro/issues/new>`_
 
 ..
   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<no-inflow-at-outflow>`.
-
-
-

Docs/source/Fluxes.rst

@@ -7,9 +7,9 @@ Computing Fluxes
 ----------------
 
 Doxygen links
-`ComputeFluxes <https://amrex-codes.github.io/amrex-hydro/Doxygen/html/namespaceHydroUtils.html#ab70f040557a658e70ba076c9d105bab7>`_
+`ComputeFluxes <https://amrex-fluids.github.io/amrex-hydro/Doxygen/html/namespaceHydroUtils.html#ab70f040557a658e70ba076c9d105bab7>`_
 and
-`EB_ComputeFluxes <https://amrex-codes.github.io/amrex-hydro/Doxygen/html/namespaceHydroUtils.html#ab70f040557a658e70ba076c9d105bab7>`_ .
+`EB_ComputeFluxes <https://amrex-fluids.github.io/amrex-hydro/Doxygen/html/namespaceHydroUtils.html#ab70f040557a658e70ba076c9d105bab7>`_ .
 
 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.
-

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 <https://amrex-codes.github.io/amrex-hydro/Doxygen/html/namespaceGodunov.html#a1c1dcedd6781260bd8322588e1290d94>`_)
+Pre-MAC (API ref. `Godunov::ExtrapVelToFaces <https://amrex-fluids.github.io/amrex-hydro/Doxygen/html/namespaceGodunov.html#a1c1dcedd6781260bd8322588e1290d94>`_)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 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 <https://amrex-codes.github.io/amrex-hydro/Doxygen/html/namespaceGodunov.html#addea54945ce554f8b4e28dabc1c74222>`_)
+Post-MAC (API ref. `Godnuov::ComputeEdgeState <https://amrex-fluids.github.io/amrex-hydro/Doxygen/html/namespaceGodunov.html#addea54945ce554f8b4e28dabc1c74222>`_)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 
@@ -238,7 +238,7 @@ EBGodunov attempts to use fourth-order limited slopes wherever possible, as desc
 
 .. _pre-mac:
 
-Pre-MAC (API ref. `EBGodunov::ExtrapVelToFaces <https://amrex-codes.github.io/amrex-hydro/Doxygen/html/namespaceEBGodunov.html#abea06da38cd7e2c6a6ed94d761c4e996>`_)
+Pre-MAC (API ref. `EBGodunov::ExtrapVelToFaces <https://amrex-fluids.github.io/amrex-hydro/Doxygen/html/namespaceEBGodunov.html#abea06da38cd7e2c6a6ed94d761c4e996>`_)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 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 <https://amrex-codes.github.io/amrex-hydro/Doxygen/html/namespaceEBGodunov.html#afb5b3b4bcea09a8aeeb568ddde3a46e4>`_)
+Post-MAC (API ref. `EBGondunov::ComputeEdgestate <https://amrex-fluids.github.io/amrex-hydro/Doxygen/html/namespaceEBGodunov.html#afb5b3b4bcea09a8aeeb568ddde3a46e4>`_)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 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.
-
-

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
-

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 <https://amrex-codes.github.io/incflo/docs_html/>`_
+`incflo <https://amrex-fluids.github.io/incflo/docs_html/>`_
 (a variable density incompressible Navier-Stokes solver with adaptive mesh refinement (AMR)),
-`IAMR <https://amrex-codes.github.io/IAMR/docs_html/index.html>`_
+`IAMR <https://amrex-fluids.github.io/IAMR/docs_html/index.html>`_
 (a variable density incompressible Navier-Stokes solver with time subcycling AMR),
 and `MFIX-Exa <https://amrex-codes.github.io/MFIX-Exa/docs_html/>`_
 (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).
-
-

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 <https://amrex-codes.github.io/amrex-hydro/Doxygen/html/namespaceMOL.html#acdde2acf756048b8ef0bca332e4bf748>`_)
+Pre-MAC (API ref. `MOL::ExtrapVelToFaces <https://amrex-fluids.github.io/amrex-hydro/Doxygen/html/namespaceMOL.html#acdde2acf756048b8ef0bca332e4bf748>`_)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 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 <https://amrex-codes.github.io/amrex-hydro/Doxygen/html/namespaceMOL.html#acdde2acf756048b8ef0bca332e4bf748>`_)
+Post-MAC (API ref. `MOL::ComputeEdgeState <https://amrex-fluids.github.io/amrex-hydro/Doxygen/html/namespaceMOL.html#acdde2acf756048b8ef0bca332e4bf748>`_)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 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 <https://amrex-codes.github.io/amrex-hydro/Doxygen/html/namespaceEBMOL.html#a7add53a153ade9c5cb83e79a61ad1929>`_)
+Pre-MAC (API ref. `EBMOL::ExtrapVelToFaces <https://amrex-fluids.github.io/amrex-hydro/Doxygen/html/namespaceEBMOL.html#a7add53a153ade9c5cb83e79a61ad1929>`_)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 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 <https://amrex-codes.github.io/amrex-hydro/Doxygen/html/namespaceEBMOL.html#a94df1b279b45eac5141dfe0dff0a79bc>`_)
+Post-MAC (API ref. `EBMOL::ComputeEdgeState <https://amrex-fluids.github.io/amrex-hydro/Doxygen/html/namespaceEBMOL.html#a94df1b279b45eac5141dfe0dff0a79bc>`_)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 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}
-

Docs/source/Schemes.rst

@@ -60,12 +60,11 @@ 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 <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.
+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.
 
 
 .. include:: MOL.rst
 
 .. include:: Godunov.rst
 
 .. include:: BDS.rst
-

Docs/source/bcs.rst

@@ -66,7 +66,6 @@ For the post-MAC edge state,
 API documentation can be found in the Doxygen Technical Reference,
 functions `SetXEdgeBCs`_, `SetYEdgeBCs`_, `SetZEdgeBCs`_ .
 
-.. _`SetXEdgeBCs`: https://amrex-codes.github.io/amrex-hydro/Doxygen/html/namespaceHydroBC.html#ab90f8ce229a7ebbc521dc27d65f2db9a
-.. _`SetYEdgeBCs`: https://amrex-codes.github.io/amrex-hydro/Doxygen/html/namespaceHydroBC.html#a6865c2cfd50cc95f9b69ded1e8ac78ab
-.. _`SetZEdgeBCs`: https://amrex-codes.github.io/amrex-hydro/Doxygen/html/namespaceHydroBC.html#a19ddc5ac50e9a6b9a98bc17f3815a62e
-
+.. _`SetXEdgeBCs`: https://amrex-fluids.github.io/amrex-hydro/Doxygen/html/namespaceHydroBC.html#ab90f8ce229a7ebbc521dc27d65f2db9a
+.. _`SetYEdgeBCs`: https://amrex-fluids.github.io/amrex-hydro/Doxygen/html/namespaceHydroBC.html#a6865c2cfd50cc95f9b69ded1e8ac78ab
+.. _`SetZEdgeBCs`: https://amrex-fluids.github.io/amrex-hydro/Doxygen/html/namespaceHydroBC.html#a19ddc5ac50e9a6b9a98bc17f3815a62e

Docs/source/index.rst

@@ -8,7 +8,7 @@ AMReX-Hydro is set of routines that support the construction of convective
 terms for incompressible and low Mach number flow modeling.
 It supports Cartesian coordinates with (or without) embedded boundaries and R-Z coordinate systems.
 It's freely available
-on GitHub: https://github.com/AMReX-Codes/AMReX-Hydro .
+on GitHub: https://github.com/AMReX-Fluids/AMReX-Hydro .
 
 AMReX-Hydro is built on top of AMReX: https://github.com/AMReX-Codes/amrex ,
 a publicly available software framework designed for
@@ -32,4 +32,4 @@ applications.
 
 API documentation can be found in the `Doxygen Technical Reference`_.
 
-.. _`Doxygen Technical Reference`: https://amrex-codes.github.io/amrex-hydro/Doxygen/html/
+.. _`Doxygen Technical Reference`: https://amrex-fluids.github.io/amrex-hydro/Doxygen/html/