diff --git a/.github/workflows/cuda.yml b/.github/workflows/cuda.yml index 46509162..4608f899 100644 --- a/.github/workflows/cuda.yml +++ b/.github/workflows/cuda.yml @@ -13,7 +13,7 @@ concurrency: jobs: cuda_eb_2d: - if: ${{ github.repository == 'AMReX-Codes/IAMR' || github.event_name != 'schedule' }} + if: ${{ github.repository == 'AMReX-Fluids/IAMR' || github.event_name != 'schedule' }} name: CUDA EB 2D runs-on: ubuntu-20.04 steps: @@ -24,7 +24,7 @@ jobs: - name: Checkout AMReX-Hydro uses: actions/checkout@v3 with: - repository: AMReX-Codes/AMReX-Hydro + repository: AMReX-Fluids/AMReX-Hydro path: AMReX-Hydro - name: Checkout AMReX uses: actions/checkout@v3 @@ -62,7 +62,7 @@ jobs: du -hs ~/.cache/ccache cuda_no_eb_2d: - if: ${{ github.repository == 'AMReX-Codes/IAMR' || github.event_name != 'schedule' }} + if: ${{ github.repository == 'AMReX-Fluids/IAMR' || github.event_name != 'schedule' }} name: CUDA NO EB 2D runs-on: ubuntu-20.04 steps: @@ -73,7 +73,7 @@ jobs: - name: Checkout AMReX-Hydro uses: actions/checkout@v3 with: - repository: AMReX-Codes/AMReX-Hydro + repository: AMReX-Fluids/AMReX-Hydro path: AMReX-Hydro - name: Checkout AMReX uses: actions/checkout@v3 diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index bb1eac7c..2d428555 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -26,7 +26,7 @@ jobs: make html - name: Deploy - if: github.event_name == 'push' && github.repository == 'AMReX-Codes/IAMR' && github.ref == 'refs/heads/development' + if: github.event_name == 'push' && github.repository == 'AMReX-Fluids/IAMR' && github.ref == 'refs/heads/development' uses: JamesIves/github-pages-deploy-action@4.1.5 with: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} diff --git a/.github/workflows/gcc.yml b/.github/workflows/gcc.yml index a5b45e48..6ddba1a9 100644 --- a/.github/workflows/gcc.yml +++ b/.github/workflows/gcc.yml @@ -13,7 +13,7 @@ concurrency: jobs: gcc_eb_3d: - if: ${{ github.repository == 'AMReX-Codes/IAMR' || github.event_name != 'schedule' }} + if: ${{ github.repository == 'AMReX-Fluids/IAMR' || github.event_name != 'schedule' }} name: GCC EB 3D runs-on: ubuntu-latest steps: @@ -24,7 +24,7 @@ jobs: - name: Checkout AMReX-Hydro uses: actions/checkout@v3 with: - repository: AMReX-Codes/AMReX-Hydro + repository: AMReX-Fluids/AMReX-Hydro path: AMReX-Hydro - name: Checkout AMReX uses: actions/checkout@v3 @@ -72,7 +72,7 @@ jobs: mpiexec -n 2 ./amr3d.gnu.MPI.ex regtest.3d.flow_past_cylinder-z max_step=3 ns.v=1 mac_proj.verbose=1 nodal_proj.verbose=1 gcc_no_eb_3d: - if: ${{ github.repository == 'AMReX-Codes/IAMR' || github.event_name != 'schedule' }} + if: ${{ github.repository == 'AMReX-Fluids/IAMR' || github.event_name != 'schedule' }} name: GCC NO EB 3D runs-on: ubuntu-latest steps: @@ -83,7 +83,7 @@ jobs: - name: Checkout AMReX-Hydro uses: actions/checkout@v3 with: - repository: AMReX-Codes/AMReX-Hydro + repository: AMReX-Fluids/AMReX-Hydro path: AMReX-Hydro - name: Checkout AMReX uses: actions/checkout@v3 @@ -131,7 +131,7 @@ jobs: mpiexec -n 2 ./amr3d.gnu.MPI.ex regtest.3d.euler max_step=3 ns.v=1 mac_proj.verbose=1 nodal_proj.verbose=1 gcc_eb_2d: - if: ${{ github.repository == 'AMReX-Codes/IAMR' || github.event_name != 'schedule' }} + if: ${{ github.repository == 'AMReX-Fluids/IAMR' || github.event_name != 'schedule' }} name: GCC EB 2D runs-on: ubuntu-latest steps: @@ -142,7 +142,7 @@ jobs: - name: Checkout AMReX-Hydro uses: actions/checkout@v3 with: - repository: AMReX-Codes/AMReX-Hydro + repository: AMReX-Fluids/AMReX-Hydro path: AMReX-Hydro - name: Checkout AMReX uses: actions/checkout@v3 @@ -191,7 +191,7 @@ jobs: ./amr2d.gnu.OMP.ex regtest.2d.flow_past_cylinder-x max_step=10 ns.v=1 mac_proj.verbose=1 nodal_proj.verbose=1 gcc_no_eb_2d: - if: ${{ github.repository == 'AMReX-Codes/IAMR' || github.event_name != 'schedule' }} + if: ${{ github.repository == 'AMReX-Fluids/IAMR' || github.event_name != 'schedule' }} name: GCC NO EB 2D runs-on: ubuntu-latest steps: @@ -202,7 +202,7 @@ jobs: - name: Checkout AMReX-Hydro uses: actions/checkout@v3 with: - repository: AMReX-Codes/AMReX-Hydro + repository: AMReX-Fluids/AMReX-Hydro path: AMReX-Hydro - name: Checkout AMReX uses: actions/checkout@v3 diff --git a/.github/workflows/hip.yml b/.github/workflows/hip.yml index 2caa55b1..19eb5d03 100644 --- a/.github/workflows/hip.yml +++ b/.github/workflows/hip.yml @@ -13,7 +13,7 @@ concurrency: jobs: hip_eb_3d: - if: ${{ github.repository == 'AMReX-Codes/IAMR' || github.event_name != 'schedule' }} + if: ${{ github.repository == 'AMReX-Fluids/IAMR' || github.event_name != 'schedule' }} name: HIP EB 3D runs-on: ubuntu-20.04 steps: @@ -24,7 +24,7 @@ jobs: - name: Checkout AMReX-Hydro uses: actions/checkout@v3 with: - repository: AMReX-Codes/AMReX-Hydro + repository: AMReX-Fluids/AMReX-Hydro path: AMReX-Hydro - name: Checkout AMReX uses: actions/checkout@v3 diff --git a/.github/workflows/sycl.yml b/.github/workflows/sycl.yml index 29389d8d..4eb16d52 100644 --- a/.github/workflows/sycl.yml +++ b/.github/workflows/sycl.yml @@ -13,7 +13,7 @@ concurrency: jobs: sycl_no_eb_3d: - if: ${{ github.repository == 'AMReX-Codes/IAMR' || github.event_name != 'schedule' }} + if: ${{ github.repository == 'AMReX-Fluids/IAMR' || github.event_name != 'schedule' }} name: SYCL NO EB 3D runs-on: ubuntu-latest steps: @@ -24,7 +24,7 @@ jobs: - name: Checkout AMReX-Hydro uses: actions/checkout@v3 with: - repository: AMReX-Codes/AMReX-Hydro + repository: AMReX-Fluids/AMReX-Hydro path: AMReX-Hydro - name: Checkout AMReX uses: actions/checkout@v3 diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 4ab6da69..8e8a0641 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -51,14 +51,14 @@ your fork. `development` on the main IAMR repository. First, let us setup your local git repo. To make your own fork of the main -repository, press the fork button on the [IAMR Github page](https://github.com/AMReX-Codes/IAMR). +repository, press the fork button on the [IAMR Github page](https://github.com/AMReX-Fluids/IAMR). Then, clone IAMR on your local computer. If you plan on doing a lot of IAMR 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/IAMR.git +git clone git@github.com:AMReX-Fluids/IAMR.git cd IAMR # 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/IAMR.git +git clone https://github.com/AMReX-Fluids/IAMR.git cd IAMR # Add your own fork. diff --git a/Docs/README.md b/Docs/README.md index 4fe27610..03e7ee4b 100644 --- a/Docs/README.md +++ b/Docs/README.md @@ -1 +1 @@ -Online documentation is available at https://amrex-codes.github.io/iamr/docs_html/. +Online documentation is available at https://amrex-fluids.github.io/iamr/docs_html/. diff --git a/Docs/sphinx_documentation/source/Debugging.rst b/Docs/sphinx_documentation/source/Debugging.rst index f375c8b0..15db7be9 100644 --- a/Docs/sphinx_documentation/source/Debugging.rst +++ b/Docs/sphinx_documentation/source/Debugging.rst @@ -56,7 +56,7 @@ for more information and tips. If you believe you've encountered a bug or incorrect behavior in IAMR, please report the issue -on IAMR's github page `here `_ . +on IAMR's github page `here `_ . .. If the issues is ``MLMG failed to converge`` diff --git a/Docs/sphinx_documentation/source/FluidEquations.rst b/Docs/sphinx_documentation/source/FluidEquations.rst index 09b0377c..55e0c03a 100644 --- a/Docs/sphinx_documentation/source/FluidEquations.rst +++ b/Docs/sphinx_documentation/source/FluidEquations.rst @@ -68,4 +68,4 @@ IAMR also has the option to solve for temperature, along with a modified diverge Here, the divergence constraint captures compressibily effects due to thermal diffusion. To enable the temperature solve, use ``ns.do_temp = 1`` and set ``ns.temp_cond_coef`` to represent :math:`\lambda / c_p`, which is taken to be constant. More sophiticated treatments are possible; if interested, please open an issue on github: -https://github.com/AMReX-Codes/IAMR/issues +https://github.com/AMReX-Fluids/IAMR/issues diff --git a/Docs/sphinx_documentation/source/Getting_Started.rst b/Docs/sphinx_documentation/source/Getting_Started.rst index 6e582dbd..24099677 100644 --- a/Docs/sphinx_documentation/source/Getting_Started.rst +++ b/Docs/sphinx_documentation/source/Getting_Started.rst @@ -29,7 +29,7 @@ First, make sure that git is installed on your machine. .. code:: shell - git clone https://github.com/AMReX-Codes/AMReX-Hydro.git + git clone https://github.com/AMReX-Fluids/AMReX-Hydro.git This will create a folder called ``AMReX-Hydro/`` on your machine. @@ -37,7 +37,7 @@ First, make sure that git is installed on your machine. .. code:: shell - git clone https://github.com/AMReX-Codes/IAMR.git + git clone https://github.com/AMReX-Fluids/IAMR.git This will create a folder called ``IAMR/`` on your machine. @@ -229,4 +229,3 @@ for visualization, please see the :ref:`Visualization` Section. looking at and/or select a region and click “Dataset” (under View) in order to look at the actual numbers. You can also export the pictures in several different formats under “File/Export”. - diff --git a/Docs/sphinx_documentation/source/Introduction_Chapter.rst b/Docs/sphinx_documentation/source/Introduction_Chapter.rst index 023fa590..43628616 100644 --- a/Docs/sphinx_documentation/source/Introduction_Chapter.rst +++ b/Docs/sphinx_documentation/source/Introduction_Chapter.rst @@ -9,7 +9,7 @@ It is built on top of AMReX, a publicly available software framework designed fo massively parallel block-structured adaptive mesh refinement (AMR) applications. -Another AMReX-based code, `incflo `_, also solves the variable-density incompressible +Another AMReX-based code, `incflo `_, also solves the variable-density incompressible Navier-Stokes equations in 2-D or 3-D but does not support subcycling in time. Key software and algorithmic features of IAMR include: @@ -34,7 +34,7 @@ Key software and algorithmic features of IAMR include: * Support for particles. -The IAMR source code can be found at https://github.com/AMReX-Codes/IAMR/. +The IAMR source code can be found at https://github.com/AMReX-Fluids/IAMR/. IAMR heavily leverages AMReX (see https://amrex-codes.github.io/) which is supported by ECP as part of the AMReX Co-Design Center. @@ -42,4 +42,4 @@ Active development in IAMR is ongoing in the development branch. Changes are merged into the main branch at the beginning of each month. If you find this documentation doesn't answer your questions or contains errors, -please open an issue on github: https://github.com/AMReX-Codes/IAMR/issues . +please open an issue on github: https://github.com/AMReX-Fluids/IAMR/issues . diff --git a/Docs/sphinx_documentation/source/ProblemSetup.rst b/Docs/sphinx_documentation/source/ProblemSetup.rst index 63b3c3af..c7b4e4f7 100644 --- a/Docs/sphinx_documentation/source/ProblemSetup.rst +++ b/Docs/sphinx_documentation/source/ProblemSetup.rst @@ -354,7 +354,7 @@ Physics Parameters IAMR provides support for gravity, viscosity, and diffusivity. Default treatment is given in the table below. More sophiticated treatments are possible; -if interested, please open an issue on github: https://github.com/AMReX-Codes/IAMR/issues +if interested, please open an issue on github: https://github.com/AMReX-Fluids/IAMR/issues The following inputs must be preceded by "ns." For information on units, see :ref:`sec:units`. @@ -367,4 +367,3 @@ The following inputs must be preceded by "ns." For information on units, see :re +----------------------+-------------------------------------------------------------------------+----------+-----------+ | scal_diff_coefs | Diffusivity of tracer(s). Must specify one value for each tracer. | Real | None | +----------------------+-------------------------------------------------------------------------+----------+-----------+ - diff --git a/Docs/sphinx_documentation/source/TimeStep.rst b/Docs/sphinx_documentation/source/TimeStep.rst index eec0349e..20cd89a8 100644 --- a/Docs/sphinx_documentation/source/TimeStep.rst +++ b/Docs/sphinx_documentation/source/TimeStep.rst @@ -1,6 +1,6 @@ .. include:: CustomCommands.rst -To learn how the convective terms are constructed, see `AMReX-Hydro `_ +To learn how the convective terms are constructed, see `AMReX-Hydro `_ Time Step -- MOL ~~~~~~~~~~~~~~~~ @@ -131,4 +131,3 @@ Addition details are located in the :ref:`BDS section of the AMReX-Hydro docs