Merge branch 'master' into feature/non-newtonian-viscosity

Author: sbryngelson

.claude/rules/fortran-conventions.md

@@ -23,13 +23,28 @@ Every Fortran module follows this pattern:
 
 ## Forbidden Patterns
 
-Caught by `./mfc.sh precheck` (source lint step 4/5):
+All checks below are enforced by `python3 toolchain/mfc/lint_source.py`
+(runs via `./mfc.sh precheck` and CI). See that file for the full list.
+
+Fortran/Fypp source (`src/`):
 - `dsqrt`, `dexp`, `dlog`, `dble`, `dabs`, `dcos`, `dsin`, `dtan`, etc. → use generic intrinsics
 - `1.0d0`, `2.5d-3` (Fortran `d` exponent literals) → use `1.0_wp`, `2.5e-3_wp`
 - `double precision` → use `real(wp)` or `real(stp)`
 - `real(8)`, `real(4)` → use `wp` or `stp` kind parameters
 - Raw `!$acc` or `!$omp` directives → use Fypp GPU_* macros from `parallel_macros.fpp`
-- Full list of forbidden patterns: `toolchain/bootstrap/precheck.sh`
+- `int(8._wp, ...)` hardcoded byte size → use `storage_size(0._stp)/8`
+- Bare integer kind like `2_wp` → use `2.0_wp`
+- Junk patterns (`...`, `---`, `===`) in code or comments (no separator comments)
+- Duplicate entries in Fypp `#:for ... in [...]` lists
+- Identical adjacent non-trivial lines (copy-paste bugs)
+
+Python (`examples/`, `benchmarks/`, `toolchain/`):
+- `===` separator comments → remove
+- `----` or longer separator comments → remove (3 dashes `---` is allowed for markdown)
+
+Shell (`.github/`, `toolchain/`):
+- `===` or `----` separator comments → remove
+- Echo separators longer than 20 characters → shorten
 
 Enforced by convention/code review (not automated):
 - `goto`, `COMMON` blocks, global `save` variables

.github/scripts/run_case_optimization.sh

@@ -36,9 +36,9 @@ for case in "${benchmarks[@]}"; do
     case_dir="$(dirname "$case")"
     case_name="$(basename "$case_dir")"
     echo ""
-    echo "========================================"
+    echo "===================="
     echo "Case-optimization test: $case_name"
-    echo "========================================"
+    echo "===================="
 
     # Clean any previous output
     rm -rf "$case_dir/D" "$case_dir/p_all" "$case_dir/restart_data"
@@ -65,11 +65,11 @@ for case in "${benchmarks[@]}"; do
 done
 
 echo ""
-echo "========================================"
+echo "===================="
 echo "Case-optimization summary: $passed passed, $failed failed"
 if [ $failed -gt 0 ]; then
     echo "Failed cases:$failed_cases"
 fi
-echo "========================================"
+echo "===================="
 
 [ $failed -eq 0 ] && exit 0 || exit 1

.github/scripts/run_parallel_benchmarks.sh

@@ -20,9 +20,9 @@ cluster="$3"
 # Get the directory where this script lives (pr/.github/scripts/)
 SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 
-echo "=========================================="
+echo "===================="
 echo "Starting benchmark jobs..."
-echo "=========================================="
+echo "===================="
 
 # For Phoenix GPU benchmarks, select a consistent GPU partition so PR and
 # master always land on the same GPU type.
@@ -82,9 +82,9 @@ if [ "${pr_exit}" -ne 0 ] || [ "${master_exit}" -ne 0 ]; then
     echo "WARNING: Benchmark jobs had failures: pr=${pr_exit}, master=${master_exit}"
     echo "Checking for partial results..."
 else
-    echo "=========================================="
+    echo "===================="
     echo "Both benchmark jobs completed successfully!"
-    echo "=========================================="
+    echo "===================="
 fi
 
 pr_yaml="pr/${job_slug}.yaml"

.github/scripts/submit_and_monitor_bench.sh

@@ -36,9 +36,9 @@ if [ ! -f "$yaml_file" ]; then
     echo ""
     output_file="${job_slug}.out"
     echo "[$dir] Last 100 lines of job output ($output_file):"
-    echo "----------------------------------------"
+    echo "--------------------"
     tail -n 100 "$output_file" 2>/dev/null || echo "  Could not read output file"
-    echo "----------------------------------------"
+    echo "--------------------"
     exit 1
 fi
 

.github/workflows/cleanliness.yml

@@ -86,6 +86,12 @@ jobs:
               grep -F 'Wmaybe-uninitialized' master.txt > mMaybe.txt
               diff prMaybe.txt mMaybe.txt
 
+          - name: Conversion Warnings Diff
+            continue-on-error: true
+            run: |
+              grep -F 'Wconversion' pr.txt > prConversion.txt
+              grep -F 'Wconversion' master.txt > mConversion.txt
+              diff prConversion.txt mConversion.txt
 
           - name: Everything Diff
             continue-on-error: true
@@ -106,12 +112,14 @@ jobs:
               pr_argument=$(grep -c -F 'Wunused-dummy-argument' pr.txt)
               pr_value=$(grep -c -F 'Wunused-value' pr.txt)
               pr_uninit=$(grep -c -F 'Wmaybe-uninitialized' pr.txt)
+              pr_conversion=$(grep -c -F 'Wconversion' pr.txt)
               pr_everything=$(grep -c '\-W' pr.txt)
 
               master_variable=$(grep -c -F 'Wunused-variable' master.txt)
               master_argument=$(grep -c -F 'Wunused-dummy-argument' master.txt)
               master_value=$(grep -c -F 'Wunused-value' master.txt)
               master_uninit=$(grep -c -F 'Wmaybe-uninitialized' master.txt)
+              master_conversion=$(grep -c -F 'Wconversion' master.txt)
               master_everything=$(grep -c '\-W' master.txt  )    
 
               echo "pr_everything=$pr_everything" >> $GITHUB_ENV
@@ -124,6 +132,7 @@ jobs:
               echo "Unused Dummy Argument: $pr_argument, Difference: $((pr_argument - master_argument))"
               echo "Unused Value: $pr_value, Difference: $((pr_value - master_value))"
               echo "Maybe Uninitialized: $pr_uninit, Difference: $((pr_uninit - master_uninit))"
+              echo "Conversion: $pr_conversion, Difference: $((pr_conversion - master_conversion))"
               echo "Everything: $pr_everything, Difference: $((pr_everything - master_everything))"
           
 

.github/workflows/lint-source.yml

@@ -17,8 +17,8 @@ jobs:
     - name: Initialize MFC
       run: ./mfc.sh init
 
-    - name: Lint and test the toolchain
-      run: ./mfc.sh lint
+    - name: Precheck (format, spelling, lint, source lint, docs)
+      run: ./mfc.sh precheck -j $(nproc)
 
     - name: Generate toolchain files
       run: ./mfc.sh generate

.github/workflows/lint-toolchain.yml

@@ -39,7 +39,7 @@ All commands run from the repo root via `./mfc.sh`.
 ./mfc.sh test --generate --only <feature>  # Regenerate golden files after intentional output change
 
 # Verification (pre-commit CI checks)
-./mfc.sh precheck -j 8                     # Run all 5 lint checks (same as CI gate)
+./mfc.sh precheck -j 8                     # Run all 6 lint checks (same as CI gate)
 ./mfc.sh format -j 8                       # Auto-format Fortran (.fpp/.f90) + Python
 ./mfc.sh lint                              # Ruff lint + Python unit tests
 ./mfc.sh spelling                          # Spell check

CLAUDE.md

@@ -150,6 +150,7 @@ if (CMAKE_Fortran_COMPILER_ID STREQUAL "GNU")
             -fsignaling-nans
             -finit-real=snan
             -finit-integer=-99999999
+            -Wconversion
             -Wintrinsic-shadow
             -Wunderflow
             -Wrealloc-lhs

CMakeLists.txt

@@ -655,6 +655,7 @@ To restart the simulation from $k$-th time step, see @ref running "Restarting Ca
 | `alpha_wrt(i)`          | Logical | Add the volume fraction of fluid $i$ to the database	|
 | `gamma_wrt`             | Logical | Add the specific heat ratio function to the database	|
 | `heat_ratio_wrt`        | Logical | Add the specific heat ratio to the database	|
+| `ib_state_wrt`          | Logical | Write IB state and loads to a datafile at each time step |
 | `pi_inf_wrt`            | Logical | Add the liquid stiffness function to the database |
 | `pres_inf_wrt`          | Logical | Add the liquid stiffness to the formatted database	 |
 | `c_wrt`                 | Logical | Add the sound speed to the database	 |
@@ -715,6 +716,8 @@ If `file_per_process` is true, then pre_process, simulation, and post_process mu
 
 - `probe_wrt` activates the output of state variables at coordinates specified by `probe(i)%[x;y,z]`.
 
+- `ib_state_wrt` activates the output of data specified by patch_ib(i)%force(:) (and torque, vel, angular_vel, angles, [x,y,z]_centroid) into a single binary datafile for all IBs at all timesteps. During post_processing, this file is converted into separate time histories for each IB.
+
 - `output_partial_domain` activates the output of part of the domain specified by `[x,y,z]_output%%beg` and `[x,y,z]_output%%end`.
 This is useful for large domains where only a portion of the domain is of interest.
 It is not supported when `precision = 1` and `format = 1`.