merge upstream

Author: wilfonba

.github/pull_request_template.md

@@ -2,22 +2,24 @@
 
 Summarize your changes and the motivation behind them.
 
-Fixes #(issue)
+Closes #(issue number).
 
-### Type of change
+### Type of change (delete unused ones)
 
-- [ ] Bug fix
-- [ ] New feature
-- [ ] Refactor
-- [ ] Documentation
-- [ ] Other: _describe_
+- Bug fix
+- New feature
+- Refactor
+- Documentation
+- Other (describe)
 
 ## Testing
 
 How did you test your changes?
 
 ## Checklist
 
+__Check these like this `[x]` to indicate which of the below applies.__
+
 - [ ] I added or updated tests for new behavior
 - [ ] I updated documentation if user-facing behavior changed
 
@@ -33,10 +35,6 @@ See the [developer guide](https://mflowcode.github.io/documentation/contributing
 
 ## AI code reviews
 
-Reviews are not triggered automatically. To request a review, comment on the PR:
-- `@coderabbitai review` — incremental review (new changes only)
-- `@coderabbitai full review` — full review from scratch
-- `/review` — Qodo review
-- `/improve` — Qodo code suggestions
+Reviews are not retriggered automatically. To request a review, comment on the PR:
 - `@claude full review` — Claude full review (also triggers on PR open/reopen/ready)
-- Add label `claude-full-review` — Claude full review via label
+- Or add label `claude-full-review` — Claude full review via label

.github/workflows/fp-stability.yml

@@ -24,8 +24,9 @@ name: FP Stability
 # On FAIL: verrou_dd_sym runs to identify the responsible function symbols.
 # Logs are uploaded as CI artifacts.
 #
-# Verrou (Valgrind 3.26.0 + edf-hpc/verrou@a58d434) is built once and cached.
-# Build takes ~20 min uncached; cached runs restore in ~30 s.
+# Verrou (the pinned Valgrind+Verrou pair; versions live in toolchain/bootstrap/verrou.sh)
+# is installed by fp-stability on first use and cached. The prebuilt download is seconds;
+# a cache miss with no prebuilt falls back to a ~20-min source build.
 
 on:
   push:
@@ -68,37 +69,21 @@ jobs:
         uses: actions/cache@v4
         with:
           path: ~/.local/verrou
-          key: verrou-a58d434-valgrind-3.26.0-${{ runner.os }}
+          # Key off the installer's content so any version bump (or other edit) in
+          # verrou.sh auto-busts the cache and forces a fresh install — no hand-synced
+          # version string to drift out of date.
+          key: verrou-${{ hashFiles('toolchain/bootstrap/verrou.sh') }}-${{ runner.os }}
 
       - name: Install system dependencies
         run: |
           sudo apt-get update -y
           sudo apt-get install -y \
             build-essential automake python3 python3-numpy libc6-dbg \
-            cmake gfortran
+            cmake gfortran zstd
 
-      - name: Build Verrou
-        if: steps.cache-verrou.outputs.cache-hit != 'true'
-        run: |
-          cd /tmp
-          wget -q https://sourceware.org/pub/valgrind/valgrind-3.26.0.tar.bz2
-          tar xf valgrind-3.26.0.tar.bz2
-
-          git clone https://github.com/edf-hpc/verrou.git
-          git -C verrou checkout a58d434
-
-          # Merge Verrou into Valgrind source tree and patch
-          cp -r verrou valgrind-3.26.0/verrou
-          cd valgrind-3.26.0
-          cat verrou/valgrind.*diff | patch -p1
-
-          ./autogen.sh
-          ./configure --enable-only64bit --prefix="$HOME/.local/verrou"
-          make -j"$(nproc)"
-          make install
-
-      - name: Verify Verrou
-        run: ~/.local/verrou/bin/valgrind --version
+      # Verrou is installed by `fp-stability` itself on first use (downloads the
+      # prebuilt artifact; aborts if that fails). The cache above restores it across
+      # runs so the download only happens on a cache miss.
 
       - name: Build MFC (debug, serial)
         # FFLAGS=-fno-inline prevents gfortran from inlining small functions into

docs/documentation/case.md

@@ -322,24 +322,16 @@ This is enabled by adding ``'elliptic_smoothing': "T",`` and ``'elliptic_smoothi
 | Parameter            | Type    | Description |
 | ---:                 | :----:  | :---                |
 | `num_ibs`            | Integer | Number of immersed boundary patches |
+| `num_stl_models`     | Integer | Number of STL/OBJ model entries in the `stl_models` array |
 | `num_particle_beds`  | Integer | Number of particle bed specifications to generate immersed boundary patches from |
 | `ib_neighborhood_radius` | Integer | Parameter that controls the neighborhood size for IB detection. |
 | `geometry`           | Integer | Geometry configuration of the patch.|
 | `x[y,z]_centroid`    | Real    | Centroid of the applied geometry in the [x,y,z]-direction. |
 | `length_x[y,z]`      | Real    | Length, if applicable, in the [x,y,z]-direction. |
 | `radius`             | Real    | Radius, if applicable, of the applied geometry. |
-| `theta`              | Real    | Angle of attach applied to airfoil IB patches |
-| `c`                  | Real    | NACA airfoil parameters (see below) |
-| `t`                  | Real    | NACA airfoil parameters (see below) |
-| `m`                  | Real    | NACA airfoil parameters (see below) |
-| `p`                  | Real    | NACA airfoil parameters (see below) |
+| `airfoil_id`         | Integer | Index into `ib_airfoil` array for NACA airfoil geometry patches. |
+| `model_id`           | Integer | Index into `stl_models` array for STL/OBJ geometry patches. |
 | `slip`               | Logical | Apply a slip boundary |
-| `model_filepath`     | String  | Path to an STL or OBJ file (not all OBJs are supported).     |
-| `model_scale(i)`     | Real    | Model's (applied) scaling factor for component $i$.          |
-| `model_rotate(i)`    | Real    | Model's (applied) angle of rotation about axis $i$.          |
-| `model_translate(i)` | Real    | Model's $i$-th component of (applied) translation.           |
-| `model_spc`          | Integer | Number of samples per cell when discretizing the model into the grid. |
-| `model_threshold`    | Real    | Ray fraction inside the model patch above which the fraction is set to one.|
 | `moving_ibm`         | Integer | Sets the method used for IB movement. |
 | `vel(i)`             | Real    | Initial velocity of the moving IB in the i-th direction. |
 | `angular_vel(i)`     | Real    | Initial angular velocity of the moving IB in the i-th direction. |
@@ -350,6 +342,17 @@ This is enabled by adding ``'elliptic_smoothing': "T",`` and ``'elliptic_smoothi
 
 These parameters should be prepended with `patch_ib(j)%` where $j$ is the patch index.
 
+STL/OBJ model geometry parameters are set on the `stl_models` array (indexed by `model_id`):
+
+| Parameter            | Type    | Description |
+|:---------------------|:--------|:------------|
+| `model_filepath`     | String  | Path to an STL or OBJ file (not all OBJs are supported). |
+| `model_scale(i)`     | Real    | Model's scaling factor for component $i$. |
+| `model_translate(i)` | Real    | Model's $i$-th component of translation. |
+| `model_threshold`    | Real    | Winding number threshold above which a cell is marked as inside the model. |
+
+These parameters should be prepended with `stl_models(k)%` where $k$ is the model index.
+
 #### Parameter Descriptions
 
 - `geometry` defines the type of geometry of an immersed boundary patch with an integer number.
@@ -361,15 +364,13 @@ Definitions for currently implemented immersed boundary patch types are listed i
 
 - `radius` is the radius to be used for circular patches.
 
-- `theta` allows for the angle of attach of airfoil patches to be changed.
-
-- `c`, `t`, `p`, and `m` specify the parameters for a NACA airfoil.
-`m` is the maximum camber, `p` is the location of maximum camber, `c` is the coord length, and `t` is the thickness.
-Additional details on this specification can be found in [The Naca Airfoil Series](https://web.stanford.edu/~cantwell/AA200_Course_Material/The%20NACA%20airfoil%20series.pdf)
+- `c`, `t`, `p`, and `m` specify the parameters for a NACA airfoil (set on the referenced `ib_airfoil` entry).
+`m` is the maximum camber, `p` is the location of maximum camber, `c` is the chord length, and `t` is the thickness.
+Additional details on this specification can be found in [NACA airfoil](https://en.wikipedia.org/wiki/NACA_airfoil).
 
 - `slip` applies a slip boundary to the surface of the patch if true and a no-slip boundary condition to the surface if false.
 
-- Please see [Patch Parameters](#sec-patches) for the descriptions of `model_filepath`, `model_scale`, `model_rotate`, `model_translate`, `model_spc`, and `model_threshold`.
+- For STL/OBJ geometry (geometry 5 or 12), set `model_id` to index into the `stl_models` array and specify `model_filepath`, `model_scale`, `model_translate`, and `model_threshold` on that entry.
 
 - `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.
 

examples/2D_bubbly_steady_shock/case.py

@@ -144,12 +144,12 @@
             "patch_ib(1)%geometry": 4,
             "patch_ib(1)%x_centroid": 1.5e-03 / x0,
             "patch_ib(1)%y_centroid": 1.5e-03 / x0,
-            "patch_ib(1)%c": 1.0e-03 / x0,
-            "patch_ib(1)%t": 0.15,
-            "patch_ib(1)%p": 0.4,
-            "patch_ib(1)%m": 0.02,
+            "patch_ib(1)%airfoil_id": 1,
             "patch_ib(1)%slip": "F",
-            "patch_ib(1)%theta": 15,
+            "ib_airfoil(1)%c": 1.0e-03 / x0,
+            "ib_airfoil(1)%t": 0.15,
+            "ib_airfoil(1)%p": 0.4,
+            "ib_airfoil(1)%m": 0.02,
             # Fluids Physical Parameters
             "fluid_pp(1)%gamma": 1.0e00 / (gam_l - 1.0e00),
             "fluid_pp(1)%pi_inf": gam_l * (pi_inf_l) / (gam_l - 1.0),

examples/2D_ibm_airfoil/case.py

@@ -90,10 +90,11 @@
             "patch_ib(1)%geometry": 4,
             "patch_ib(1)%x_centroid": 1.0e-03,
             "patch_ib(1)%y_centroid": 3.0e-03,
-            "patch_ib(1)%c": 1.0e-03,
-            "patch_ib(1)%t": 0.15,
-            "patch_ib(1)%p": 0.4,
-            "patch_ib(1)%m": 0.02,
+            "patch_ib(1)%airfoil_id": 1,
+            "ib_airfoil(1)%c": 1.0e-03,
+            "ib_airfoil(1)%t": 0.15,
+            "ib_airfoil(1)%p": 0.4,
+            "ib_airfoil(1)%m": 0.02,
             "patch_ib(1)%angles(3)": -0.5235987756,  # 30 degrees clockwise rotation, in radians
             # Fluids Physical Parameters
             # Use the same stiffness as the air bubble

examples/2D_ibm_steady_shock/case.py

@@ -145,12 +145,12 @@
             "patch_ib(1)%geometry": 4,
             "patch_ib(1)%x_centroid": 1.5e-03 / x0,
             "patch_ib(1)%y_centroid": 1.5e-03 / x0,
-            "patch_ib(1)%c": 1.0e-03 / x0,
-            "patch_ib(1)%t": 0.15,
-            "patch_ib(1)%p": 0.4,
-            "patch_ib(1)%m": 0.02,
+            "patch_ib(1)%airfoil_id": 1,
             "patch_ib(1)%slip": "F",
-            "patch_ib(1)%theta": 15,
+            "ib_airfoil(1)%c": 1.0e-03 / x0,
+            "ib_airfoil(1)%t": 0.15,
+            "ib_airfoil(1)%p": 0.4,
+            "ib_airfoil(1)%m": 0.02,
             # Fluids Physical Parameters
             # Surrounding liquid
             "fluid_pp(1)%gamma": 1.0e00 / (n_tait - 1.0e00),

examples/2D_ibm_stl_MFCCharacter/case.py

@@ -68,12 +68,13 @@
             "patch_icpp(1)%pres": 100000,
             "patch_icpp(1)%alpha_rho(1)": (1.0) * rho1,
             "patch_icpp(1)%alpha(1)": 1.0,
+            "num_stl_models": 1,
             "patch_ib(1)%geometry": 5,
-            "patch_ib(1)%model_filepath": "Character_IBM.stl",
-            "patch_ib(1)%model_translate(1)": -0.0469828735,
-            "patch_ib(1)%model_translate(2)": -0.0094892600,
-            "patch_ib(1)%model_spc": 200,
-            "patch_ib(1)%model_threshold": 0.99,
+            "patch_ib(1)%model_id": 1,
+            "stl_models(1)%model_filepath": "Character_IBM.stl",
+            "stl_models(1)%model_translate(1)": -0.0469828735,
+            "stl_models(1)%model_translate(2)": -0.0094892600,
+            "stl_models(1)%model_threshold": 0.99,
             "patch_ib(1)%slip": "F",
             # Fluids Physical Parameters
             "fluid_pp(1)%gamma": 1.0e00 / (gam_a - 1.0e00),

examples/2D_ibm_stl_test/case.py

@@ -69,12 +69,13 @@
             "patch_icpp(1)%pres": 100000,
             "patch_icpp(1)%alpha_rho(1)": (1.0) * rho1,
             "patch_icpp(1)%alpha(1)": 1.0,
+            "num_stl_models": 1,
             "patch_ib(1)%geometry": 5,
-            "patch_ib(1)%model_filepath": "Circle_IBM.stl",
-            "patch_ib(1)%model_translate(1)": -0.05,
-            "patch_ib(1)%model_translate(2)": -0.05,
-            "patch_ib(1)%model_spc": 100,
-            "patch_ib(1)%model_threshold": 0.95,
+            "patch_ib(1)%model_id": 1,
+            "stl_models(1)%model_filepath": "Circle_IBM.stl",
+            "stl_models(1)%model_translate(1)": -0.05,
+            "stl_models(1)%model_translate(2)": -0.05,
+            "stl_models(1)%model_threshold": 0.95,
             "patch_ib(1)%slip": "F",
             # Fluids Physical Parameters
             "fluid_pp(1)%gamma": 1.0e00 / (gam_a - 1.0e00),

examples/2D_ibm_stl_wedge/case.py

@@ -69,12 +69,13 @@
             "patch_icpp(1)%pres": 10918.2549,
             "patch_icpp(1)%alpha_rho(1)": (1.0) * rho1,
             "patch_icpp(1)%alpha(1)": 1.0,
+            "num_stl_models": 1,
             "patch_ib(1)%geometry": 5,
-            "patch_ib(1)%model_filepath": "Wedge2D_IBM.stl",
-            "patch_ib(1)%model_translate(1)": -0.0500000000,
-            "patch_ib(1)%model_translate(2)": -0.0373970250,
-            "patch_ib(1)%model_spc": 200,
-            "patch_ib(1)%model_threshold": 0.95,
+            "patch_ib(1)%model_id": 1,
+            "stl_models(1)%model_filepath": "Wedge2D_IBM.stl",
+            "stl_models(1)%model_translate(1)": -0.0500000000,
+            "stl_models(1)%model_translate(2)": -0.0373970250,
+            "stl_models(1)%model_threshold": 0.95,
             "patch_ib(1)%slip": "F",
             # Fluids Physical Parameters
             "fluid_pp(1)%gamma": 1.0e00 / (gam_a - 1.0e00),

examples/3D_ibm_stl_ellipsoid/case.py

@@ -81,13 +81,14 @@
             "patch_icpp(1)%alpha_rho(1)": (1.0) * rho1,
             "patch_icpp(1)%alpha(1)": 1.0e00,
             # Patch: Model Immersed Boundary
+            "num_stl_models": 1,
             "patch_ib(1)%geometry": 12,
-            "patch_ib(1)%model_filepath": "Ellipsoid_IBM.stl",
-            "patch_ib(1)%model_translate(1)": -0.02056,
-            "patch_ib(1)%model_translate(2)": -0.01,
-            "patch_ib(1)%model_translate(3)": -0.01,
-            "patch_ib(1)%model_spc": 20,
-            "patch_ib(1)%model_threshold": 0.01,
+            "patch_ib(1)%model_id": 1,
+            "stl_models(1)%model_filepath": "Ellipsoid_IBM.stl",
+            "stl_models(1)%model_translate(1)": -0.02056,
+            "stl_models(1)%model_translate(2)": -0.01,
+            "stl_models(1)%model_translate(3)": -0.01,
+            "stl_models(1)%model_threshold": 0.01,
             "patch_ib(1)%slip": "F",
             # Fluids Physical Parameters
             "fluid_pp(1)%gamma": 1.0e00 / (gam_a - 1.0e00),