Merge branch 'master' into fix/low-risk-bugfixes-batch

Author: sbryngelson

.github/workflows/coverage.yml

@@ -4,6 +4,7 @@ on:
   push:
     branches: [master]
   pull_request:
+    types: [opened, synchronize, reopened, ready_for_review]
   workflow_dispatch:
 
 concurrency:
@@ -28,7 +29,7 @@ jobs:
 
   run:
     name: Coverage Test on CodeCov
-    if: needs.file-changes.outputs.checkall == 'true'
+    if: needs.file-changes.outputs.checkall == 'true' && github.event.pull_request.draft != true
     needs: file-changes
     runs-on: "ubuntu-latest"
     steps:

.github/workflows/frontier/build.sh

@@ -25,7 +25,7 @@ if [ "$job_device" = "gpu" ]; then
   fi
 fi
 
-. ./mfc.sh load -c $compiler_flag -m g
+. ./mfc.sh load -c $compiler_flag -m $([ "$job_device" = "gpu" ] && echo "g" || echo "c")
 
 # Only set up build cache for test suite, not benchmarks
 if [ "$run_bench" != "bench" ]; then

.github/workflows/frontier_amd/build.sh

@@ -25,7 +25,7 @@ if [ "$job_device" = "gpu" ]; then
   fi
 fi
 
-. ./mfc.sh load -c $compiler_flag -m g
+. ./mfc.sh load -c $compiler_flag -m $([ "$job_device" = "gpu" ] && echo "g" || echo "c")
 
 # Only set up build cache for test suite, not benchmarks
 if [ "$run_bench" != "bench" ]; then

.lychee.toml

@@ -28,4 +28,5 @@ exclude = [
     "https://cpe\\.ext\\.hpe\\.com",                   # HPE Cray docs have broken SSL cert
     "https://sc22\\.supercomputing\\.org",              # Returns 415 to automated requests
     "https://strawberryperl\\.com",                    # Frequently times out
+    "https://www\\.olcf\\.ornl\\.gov/summit",            # Returns 503 to automated requests
 ]

.typos.toml

@@ -28,6 +28,7 @@ choises = "choises"   # appears in comment explaining validation purpose
 ordr = "ordr"         # typo for "order" in "weno_ordr" - tests param suggestions
 unknwn = "unknwn"     # typo for "unknown" - tests unknown param detection
 tru = "tru"           # typo for "true" in "when_tru" - tests dependency keys
+PNGs = "PNGs"
 
 [files]
-extend-exclude = ["docs/documentation/references*", "docs/references.bib", "tests/", "toolchain/cce_simulation_workgroup_256.sh", "build-docs/"]
+extend-exclude = ["docs/documentation/references*", "docs/references.bib", "tests/", "toolchain/cce_simulation_workgroup_256.sh", "build-docs/", "build/", "build_test/"]

CLAUDE.md

@@ -108,6 +108,7 @@ IMPORTANT: Follow this loop for ALL code changes. Do not skip steps.
 YOU MUST run `./mfc.sh precheck` before any commit. This is enforced by pre-commit hooks.
 YOU MUST run tests relevant to your changes before claiming work is done.
 NEVER commit code that does not compile or fails tests.
+NEVER use heredocs for git commit messages. Use simple `git commit -m "message"` instead.
 
 ## Architecture
 

docs/documentation/case.md

@@ -347,11 +347,11 @@ Additional details on this specification can be found in [The Naca Airfoil Serie
 
 - Please see [Patch Parameters](#sec-patches) for the descriptions of `model_filepath`, `model_scale`, `model_rotate`, `model_translate`, `model_spc`, and `model_threshold`.
 
-- `moving_ibm` sets the method by which movement will be applied to the immersed boundary. Using 0 will result in no movement. Using 1 will result 1-way coupling where the boundary moves at a constant rate and applied forces to the fluid based upon it's own motion. In 1-way coupling, the fluid does not apply forces back onto the IB.
+- `moving_ibm` sets the method by which movement will be applied to the immersed boundary. Using 0 will result in no movement. Using 1 will result 1-way coupling where the boundary moves at a constant rate and applied forces to the fluid based upon it's own motion. In 1-way coupling, the fluid does not apply forces back onto the IB. Using 2 will result in 2-way coupling, where the boundary pushes on the fluid and the fluid pushes back on the boundary via pressure and viscous forces. If external forces are applied, the boundary will also experience those forces.
 
-- `vel(i)` is the initial linear velocity of the IB in the x, y, z direction for i=1, 2, 3. When `moving_ibm` equals 1, this velocity is constant.
+- `vel(i)` is the initial linear velocity of the IB in the x, y, z direction for i=1, 2, 3. When `moving_ibm` equals 2, this velocity is just the starting speed of the object, which will then accelerate due to external forces. If `moving_ibm` equals 1, then this is constant if it is a number, or can be described analytically with an expression. 
 
-- `angular_vel(i)` is the initial angular velocity of the IB about the x, y, z axes for i=1, 2, 3 in radians per second. When `moving_ibm` equals 1, this angular velocity is constant.
+- `angular_vel(i)` is the initial angular velocity of the IB about the x, y, z axes for i=1, 2, 3 in radians per second. When `moving_ibm` equals 2, this rotation rate is just the starting rate of the object, which will then change due to external torques. If `moving_ibm` equals 1, then this is constant if it is a number, or can be described analytically with an expression. 
 
 ### 5. Fluid Material's {#sec-fluid-materials}
 
@@ -651,7 +651,7 @@ To restart the simulation from $k$-th time step, see @ref running "Restarting Ca
 
 The table lists formatted database output parameters. The parameters define variables that are outputted from simulation and file types and formats of data as well as options for post-processing.
 
-- `format` specifies the choice of the file format of data file outputted by MFC by an integer of 1 and 2. `format = 1` and `2` correspond to Silo-HDF5 format and binary format, respectively.
+- `format` specifies the choice of the file format of data file outputted by MFC by an integer of 1 and 2. `format = 1` and `2` correspond to Silo-HDF5 format and binary format, respectively. Both formats are supported by `./mfc.sh viz` (see @ref visualization "Flow Visualization"). Silo-HDF5 requires the h5py Python package; binary has no extra dependencies.
 
 - `precision` specifies the choice of the floating-point format of the data file outputted by MFC by an integer of 1 and 2. `precision = 1` and `2` correspond to single-precision and double-precision formats, respectively.
 

docs/documentation/getting-started.md

@@ -204,6 +204,24 @@ MFC is **unit-agnostic**: the solver performs no internal unit conversions. What
 
 The only requirement is **consistency** — all inputs must use the same unit system. Note that some parameters use **transformed stored forms** rather than standard physical values (e.g., `gamma` expects \f$1/(\gamma-1)\f$, not \f$\gamma\f$ itself). See @ref sec-stored-forms for details.
 
+## Visualizing Results
+
+After running post_process, visualize the output directly from the command line:
+
+```shell
+# List available variables
+./mfc.sh viz examples/2D_shockbubble/ --list-vars --step 0
+
+# Render a pressure snapshot
+./mfc.sh viz examples/2D_shockbubble/ --var pres --step 1000
+
+# Generate a video
+./mfc.sh viz examples/2D_shockbubble/ --var pres --step all --mp4
+```
+
+Output images and videos are saved to the `viz/` subdirectory of the case.
+For more options, see @ref visualization "Flow Visualization" or run `./mfc.sh viz -h`.
+
 ## Helpful Tools
 
 ### Parameter Lookup

docs/documentation/running.md

@@ -73,6 +73,14 @@ using 4 cores:
 ./mfc.sh run examples/2D_shockbubble/case.py -t simulation post_process -n 4
 ```
 
+- Visualizing post-processed output:
+
+```shell
+./mfc.sh viz examples/2D_shockbubble/ --var pres --step 1000
+```
+
+See @ref visualization "Flow Visualization" for the full set of visualization options.
+
 ---
 
 ## Running on GPUs

docs/documentation/troubleshooting.md

@@ -37,6 +37,7 @@ This guide covers debugging tools, common issues, and troubleshooting workflows
 ./mfc.sh run case.py -v        # Run with verbose output
 ./mfc.sh test --only <UUID>    # Run a specific test
 ./mfc.sh clean                 # Clean and start fresh
+./mfc.sh viz case_dir/ --list-vars --step 0  # Inspect post-processed data
 ```
 
 ---
@@ -457,6 +458,47 @@ Common issues:
 
 ---
 
+## Visualization Issues
+
+### "No 'binary/' or 'silo_hdf5/' directory found"
+
+**Cause:** Post-processing has not been run, or the case directory path is wrong.
+
+**Fix:**
+1. Run post_process first:
+   ```bash
+   ./mfc.sh run case.py -t post_process
+   ```
+2. Verify the path points to the case directory (containing `binary/` or `silo_hdf5/`)
+
+### "Variable 'X' not found"
+
+**Cause:** The requested variable was not written during post-processing.
+
+**Fix:**
+1. List available variables:
+   ```bash
+   ./mfc.sh viz case_dir/ --list-vars --step 0
+   ```
+2. Ensure your case file enables the desired output (e.g., ``prim_vars_wrt = 'T'``, ``cons_vars_wrt = 'T'``)
+
+### "h5py is required to read Silo-HDF5 files"
+
+**Cause:** The case was post-processed with `format=1` (Silo-HDF5) but `h5py` is not installed.
+
+**Fix:**
+- Install h5py: `pip install h5py`
+- Or re-run post_process with `format=2` in your case file to produce binary output
+
+### Visualization looks wrong or has artifacts
+
+**Possible causes and fixes:**
+1. **Color range:** Try setting explicit `--vmin` and `--vmax` values
+2. **Wrong variable:** Use `--list-vars` to check available variables
+3. **3D slice position:** Adjust `--slice-axis` and `--slice-value` to view the correct plane
+
+---
+
 ## Getting Help
 
 If you can't resolve an issue: