Merge branch 'master' into convergenceExample

Author: sbryngelson

.github/workflows/bench.yml

@@ -62,6 +62,14 @@ jobs:
             device: gpu
             interface: acc
             build_script: "bash .github/workflows/frontier/build.sh gpu acc bench"
+          - cluster: frontier
+            name: Oak Ridge | Frontier (CCE)
+            group: phoenix
+            labels: frontier
+            flag: f
+            device: gpu
+            interface: omp
+            build_script: "bash .github/workflows/frontier/build.sh gpu omp bench"
     runs-on:
       group: ${{ matrix.group }}
       labels: ${{ matrix.labels }}

.github/workflows/deploy-tap.yml

@@ -1,21 +1,29 @@
 name: Deploy Homebrew Tap
 
 on:
+  # Test formula on PRs (audit only, don't deploy)
+  pull_request:
+    branches: [ master ]
+    paths:
+      - 'packaging/homebrew/mfc.rb'
+      - 'packaging/homebrew/README.md'
+  # Deploy to tap on push to master
   push:
-    branches: [ main, master, homebrew-formula ]
+    branches: [ master, homebrew-new ]
     paths:
       - 'packaging/homebrew/mfc.rb'
       - 'packaging/homebrew/README.md'
     tags:
       - 'v*.*.*'
+  # Allow manual trigger for testing
   workflow_dispatch:
 
 permissions:
   contents: read
 
 jobs:
   deploy-tap:
-    name: Sync/bump formula in tap
+    name: Audit and deploy formula
     runs-on: macos-14
     permissions:
       contents: write
@@ -41,6 +49,13 @@ jobs:
           echo "version=${VERSION}" >> $GITHUB_OUTPUT
           echo "url=${URL}" >> $GITHUB_OUTPUT
           echo "sha256=${SHASUM}" >> $GITHUB_OUTPUT
+          echo "Event: ${{ github.event_name }}" >> $GITHUB_STEP_SUMMARY
+          echo "Version: ${VERSION}" >> $GITHUB_STEP_SUMMARY
+          if [[ "${{ github.event_name }}" == "pull_request" ]]; then
+            echo "Mode: Audit only (PR)" >> $GITHUB_STEP_SUMMARY
+          else
+            echo "Mode: Audit and deploy" >> $GITHUB_STEP_SUMMARY
+          fi
 
       - name: Update formula (for tag events)
         if: github.ref_type == 'tag'
@@ -61,6 +76,7 @@ jobs:
           brew untap mfc/local
 
       - name: Clone or bootstrap tap repository
+        if: github.event_name != 'pull_request'
         env:
           TAP_TOKEN: ${{ secrets.TAP_REPO_TOKEN }}
         run: |
@@ -81,12 +97,14 @@ jobs:
           fi
 
       - name: Copy formula and README into tap
+        if: github.event_name != 'pull_request'
         run: |
           mkdir -p tap-repo/Formula
           cp packaging/homebrew/mfc.rb tap-repo/Formula/mfc.rb
           cp packaging/homebrew/README.md tap-repo/README.md
 
       - name: Commit & push if changed
+        if: github.event_name != 'pull_request'
         env:
           TAP_TOKEN: ${{ secrets.TAP_REPO_TOKEN }}
         run: |

.github/workflows/homebrew.yml

@@ -2,15 +2,10 @@ name: Homebrew Formula Test
 
 on:
   push:
-    branches:
-      - master
-      - homebrew-formula
     paths:
       - 'packaging/homebrew/**'
       - '.github/workflows/homebrew.yml'
   pull_request:
-    branches:
-      - master
     paths:
       - 'packaging/homebrew/**'
       - '.github/workflows/homebrew.yml'
@@ -251,8 +246,8 @@ jobs:
           cp $(brew --prefix mfc)/examples/1D_sodshocktube/case.py "$TESTDIR/"
           
           echo "Running with $(sysctl -n hw.ncpu) processors..."
-          # Use absolute path since mfc wrapper creates its own tmpdir
-          mfc run "$TESTDIR/case.py" -j $(sysctl -n hw.ncpu)
+          # Use absolute path and shorthand syntax (mfc auto-detects and prepends 'run')
+          mfc "$TESTDIR/case.py" -j $(sysctl -n hw.ncpu)
           
           echo "Test case completed successfully!"
       

.github/workflows/phoenix/submit-bench.sh

@@ -42,7 +42,7 @@ sbatch <<EOT
 #SBATCH --account=gts-sbryngelson3 # charge account
 #SBATCH -N1                        # Number of nodes required
 $sbatch_device_opts
-#SBATCH -t 02:00:00                # Duration of the job (Ex: 15 mins)
+#SBATCH -t 03:00:00                # Duration of the job (Ex: 15 mins)
 #SBATCH -q embers                  # QOS Name
 #SBATCH -o$job_slug.out            # Combined output and error messages file
 #SBATCH -W                         # Do not exit until the submitted job terminates.

.github/workflows/test.yml

@@ -48,11 +48,6 @@ jobs:
       - name: Clone
         uses: actions/checkout@v4
 
-      - name: Set up Python 3.13
-        uses: actions/setup-python@v5
-        with:
-          python-version: '3.13'
-
       - name: Setup MacOS
         if:   matrix.os == 'macos'
         run:  |
@@ -81,6 +76,10 @@ jobs:
           source /opt/intel/oneapi/setvars.sh
           printenv >> $GITHUB_ENV
 
+      - name: Set up Python 3.14
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.14'
 
       - name: Build
         run:  |
@@ -111,10 +110,6 @@ jobs:
           - device: 'cpu'
             interface: 'none'
             lbl: 'frontier'
-        exclude:
-          - device: 'gpu'
-            interface: 'omp'
-            lbl: 'frontier'
     runs-on:
       group:  phoenix
       labels: ${{ matrix.lbl }}

CITATION.cff

@@ -9,6 +9,7 @@ url: "https://github.com/MFlowCode/MFC"
 preferred-citation:
   type: article
   title: "MFC 5.0: An exascale many-physics flow solver"
+  journal: "arXiv preprint arXiv.2503.07953"
   doi: "10.48550/arXiv.2503.07953"
   year: 2025
   authors:

CMakeLists.txt

@@ -29,6 +29,7 @@ option(MFC_SYSCHECK      "Build syscheck"                                    OFF
 option(MFC_DOCUMENTATION "Build documentation"                               OFF)
 option(MFC_ALL           "Build everything"                                  OFF)
 option(MFC_SINGLE_PRECISION "Build single precision"                         OFF)
+option(MFC_MIXED_PRECISION "Build mixed precision"                           OFF)
 
 if (MFC_ALL)
     set(MFC_PRE_PROCESS   ON FORCE)
@@ -43,6 +44,10 @@ else()
     add_compile_definitions(MFC_DOUBLE_PRECISION)
 endif()
 
+if (MFC_MIXED_PRECISION)
+    add_compile_definitions(MFC_MIXED_PRECISION)
+endif()
+
 
 # CMake Library Imports
 
@@ -196,7 +201,7 @@ elseif ((CMAKE_Fortran_COMPILER_ID STREQUAL "NVHPC") OR (CMAKE_Fortran_COMPILER_
     add_compile_options(
         $<$<COMPILE_LANGUAGE:Fortran>:-Mfreeform>
         $<$<COMPILE_LANGUAGE:Fortran>:-cpp>
-	      $<$<COMPILE_LANGUAGE:Fortran>:-Minfo=inline>
+        $<$<COMPILE_LANGUAGE:Fortran>:-Minfo=inline>
         $<$<COMPILE_LANGUAGE:Fortran>:-Minfo=accel>
     )
 
@@ -474,10 +479,10 @@ function(MFC_SETUP_TARGET)
             endif()
         endif()
 
-				if (ARGS_LAPACK)
-					find_package(LAPACK REQUIRED)
-					target_link_libraries(${a_target} PRIVATE LAPACK::LAPACK)
-				endif()
+        if (ARGS_LAPACK)
+            find_package(LAPACK REQUIRED)
+            target_link_libraries(${a_target} PRIVATE LAPACK::LAPACK)
+        endif()
 
         if ((MFC_OpenACC AND ARGS_OpenACC) OR (MFC_OpenMP AND ARGS_OpenMP))
             if ((MFC_OpenACC AND ARGS_OpenACC))
@@ -573,7 +578,13 @@ function(MFC_SETUP_TARGET)
                 find_package(hipfort COMPONENTS hip CONFIG REQUIRED)
                 target_link_libraries(${a_target} PRIVATE hipfort::hip hipfort::hipfort-amdgcn)
             elseif(CMAKE_Fortran_COMPILER_ID STREQUAL "LLVMFlang")
-                find_package(hipfort COMPONENTS hip CONFIG REQUIRED)
+
+                if (MFC_Unified)
+                    target_compile_options(${ARGS_TARGET}
+                        PRIVATE -DFRONTIER_UNIFIED)
+                endif()
+
+    		find_package(hipfort COMPONENTS hip CONFIG REQUIRED)
                 target_link_libraries(${a_target} PRIVATE hipfort::hip hipfort::hipfort-amdgcn flang_rt.hostdevice)
             endif()
         elseif (CMAKE_Fortran_COMPILER_ID STREQUAL "Cray")

README.md

@@ -33,16 +33,20 @@
     <img src="https://img.shields.io/badge/discussions-join-brightgreen" />
   </a>
   <a href="https://github.com/codespaces/new?hide_repo_select=true&ref=master&repo=MFlowCode%2FMFC">
-    <img src="https://img.shields.io/badge/Codespaces-Open%20in%201%20click-2ea44f?logo=github" />
-  </a>
-  <a href="https://github.com/MFlowCode/MFC/releases">
-    <img src="https://img.shields.io/github/v/release/MFlowCode/MFC?display_name=release&sort=semver" />
+    <img src="https://img.shields.io/badge/Codespaces-Open-2ea44f?logo=github" />
   </a>
+  <a href="https://hub.docker.com/r/sbryngelson/mfc">
+    <img src="https://img.shields.io/badge/dockerhub-images-important.svg?logo=Docker&style=flat" />
+  </a>	
+	
+  <a href="https://github.com/MFlowCode/homebrew-mfc">
+    <img src="https://img.shields.io/badge/homebrew-mflowcode%2Fmfc%2Fmfc-brown?logo=homebrew&style=flat" />
+  </a>	
 </p>
 
 <p align="center">
   <a href="https://star-history.com/#MFlowCode/MFC&Date">
-    <img src="https://api.star-history.com/svg?repos=MFlowCode/MFC&type=Date" alt="Star History Chart" width="600"/>
+    <img src="https://api.star-history.com/svg?repos=MFlowCode/MFC&type=Date&theme=dark" alt="Star History Chart" width="600"/>
   </a>
 </p>
 
@@ -59,9 +63,10 @@ MFC runs at exascale on the world's fastest supercomputers:
 
 | Path | Command |
 | --- | --- |
-| **Codespaces** (fastest) | Click the "Codespaces" badge above to launch in 1 click |
-| **Homebrew (macOS)** | `brew install mflowcode/mfc/mfc && mfc run $(brew --prefix mfc)/examples/1D_sodshocktube/case.py -n 2` |
-| **Local build** | `./mfc.sh build -j $(nproc) && ./mfc.sh test -j $(nproc)` |
+| **Codespaces** (fastest) 💨 | Click the "Codespaces" badge above to launch in 1 click |
+| **Docker** 🐳 | `docker run -it --rm --entrypoint bash sbryngelson/mfc:latest-cpu` |
+| **Homebrew** (macOS) 🍺 | `brew install mflowcode/mfc/mfc && mfc $(brew --prefix mfc)/examples/1D_sodshocktube/case.py -n 2` |
+| **Local build** 💻 | `./mfc.sh build -j $(nproc) && ./mfc.sh test -j $(nproc)` |
 
 **Welcome!**
 MFC simulates compressible multi-phase flows, [among other things](#what-else-can-this-thing-do). 
@@ -127,26 +132,43 @@ And here is a high-amplitude acoustic wave reflecting and emerging through a cir
 
 ## Getting started
 
+You can navigate [to this webpage](https://mflowcode.github.io/documentation/md_getting-started.html) to get you get started using MFC on your local machine, cluster, or supercomputer!
+It's rather straightforward.
+Some examples are below.
+
+### Codespaces and Containers
+
+  <a href="https://github.com/codespaces/new?hide_repo_select=true&ref=master&repo=MFlowCode%2FMFC">
+    <img src="https://img.shields.io/badge/Codespaces-Open%20in%201%20click-2ea44f?logo=github" />
+  </a>
+  
 For a _very_ quick start, open a GitHub Codespace to load a pre-configured Docker container and familiarize yourself with MFC commands.
 Click <kbd> <> Code</kbd> (green button at top right) → <kbd>Codespaces</kbd> (right tab) → <kbd>+</kbd> (create a codespace).
 
+Alternatively, run MFC directly with Docker on your local machine:
+```bash
+docker run -it --rm --entrypoint bash sbryngelson/mfc:latest-cpu
+```
+Once inside the container, navigate to `/opt/MFC` to access MFC and run examples.
+
 > ****Note:**** Codespaces is a free service with a monthly quota of compute time and storage usage.
 > It is recommended for testing commands, troubleshooting, and running simple case files without installing dependencies or building MFC on your device.
 > Don't conduct any critical work here!
 > To learn more, please see [how Docker & Containers work](https://mflowcode.github.io/documentation/md_docker.html).
 
-You can navigate [to this webpage](https://mflowcode.github.io/documentation/md_getting-started.html) to get you get started using MFC on your local machine, cluster, or supercomputer!
-It's rather straightforward.
-
 ### macOS quick start (Homebrew)
 
+<a href="https://github.com/MFlowCode/homebrew-mfc">
+<img src="https://img.shields.io/badge/homebrew-mflowcode%2Fmfc%2Fmfc-brown?logo=homebrew&style=flat" />
+</a>
+
 Install the prebuilt package and run an example:
 
 ```bash
 brew install mflowcode/mfc/mfc
 mkdir -p ~/mfc_quickstart && cd ~/mfc_quickstart
 cp $(brew --prefix mfc)/examples/1D_sodshocktube/case.py .
-mfc run case.py -n 2
+mfc case.py -n 2
 ```
 
 Use `-n X` to select the number of MPI processes. For developer commands (`build`, `test`, etc.), clone the repo and use `./mfc.sh`.

docs/documentation/case.md

@@ -745,6 +745,7 @@ Details of the transducer acoustic source model can be found in [Maeda and Colon
 | `mu_v` †	        | Real 		|	Viscosity |
 | `k_v` †	          | Real 		|	Thermal conductivity |
 | `cp_v` †	        | Real 		|	Specific heat capacity |
+| `D_v` †           | Real    | Vapor diffusivity in the gas |
 
 These options work only for gas-liquid two-component flows.
 Component indexes are required to be 1 for liquid and 2 for gas.
@@ -836,7 +837,6 @@ When ``polytropic = 'F'``, the gas compression is modeled as non-polytropic due
 | `T0`                  | Real    | Reference temperature                                     |
 | `x0`                  | Real    | Reference length                                          |
 | `Thost`               | Real    | Temperature of the surrounding liquid (host)              |
-| `diffcoefvap`         | Real    | Vapor diffusivity in the gas                              |
 
 - `nBubs_glb` Total number of bubbles. Their initial conditions need to be specified in the ./input/lag_bubbles.dat file. See the example cases for additional information.
 

docs/documentation/getting-started.md

@@ -23,11 +23,12 @@ Run a quick example:
 mkdir -p ~/mfc_quickstart && cd ~/mfc_quickstart
 cp $(brew --prefix mfc)/examples/1D_sodshocktube/case.py .
 # Use -n X to choose the number of MPI processes
-mfc run case.py -n 2
+mfc case.py -n 2
 ```
 
 Notes:
-- The Homebrew wrapper supports only `mfc run ...`. Developer commands like `build`, `test`, `clean` are available when you clone the repo and use `./mfc.sh`.
+- The Homebrew package uses a simplified syntax: just `mfc <case.py>` to run cases.
+- Developer commands like `build`, `test`, `clean` are available when you clone the repo and use `./mfc.sh`.
 - The package bundles a Python venv and prebuilt binaries; no additional setup is required.
 - Examples are installed at `$(brew --prefix mfc)/examples/`.