Merge upstream/master into ruff, resolve case.py conflict

Kept upstream patch type 13 reclassification (3D->2D) with ruff formatting.
Auto-formatted new upstream example files for ruff import sorting.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: sbryngelson

.github/scripts/clean-build.sh

@@ -0,0 +1,15 @@
+#!/bin/bash
+# Provides clean_build(): renames build/ aside and deletes it in the background.
+# mv is a metadata-only operation that succeeds even with stale NFS file handles,
+# unlike rm -rf which fails on ESTALE. The background delete is best-effort and
+# scoped to this job's PID to avoid races with concurrent matrix jobs.
+#
+# Usage: source .github/scripts/clean-build.sh
+#        clean_build
+
+clean_build() {
+    # Clean up leftover stale directories from previous runs before adding a new one.
+    rm -rf build.stale.* 2>/dev/null || true
+    mv build "build.stale.$$" 2>/dev/null || true
+    rm -rf "build.stale.$$" 2>/dev/null & disown
+}

.github/scripts/prebuild-case-optimization.sh

@@ -22,7 +22,8 @@ case "$cluster" in
     *) echo "ERROR: Unknown cluster '$cluster'"; exit 1 ;;
 esac
 
-rm -rf build
+source .github/scripts/clean-build.sh
+clean_build
 
 . ./mfc.sh load -c "$flag" -m g
 

.github/scripts/retry-sbatch.sh

@@ -0,0 +1,40 @@
+#!/bin/bash
+# Provides retry_sbatch(): submits a job script string via sbatch with retries.
+# Only retries on known transient SLURM/infrastructure errors (socket timeouts,
+# connection failures). Hard failures (bad account, invalid partition, QOS
+# violations) are not retried.
+#
+# Usage: source .github/scripts/retry-sbatch.sh
+#        job_id=$(retry_sbatch "$script_contents")
+
+retry_sbatch() {
+    local script_contents="$1"
+    local max_attempts=3
+    local attempt=1
+    local submit_output job_id last_output=""
+
+    while [ $attempt -le $max_attempts ]; do
+        echo "sbatch attempt $attempt of $max_attempts..." >&2
+        submit_output=$(printf '%s\n' "$script_contents" | sbatch 2>&1) || true
+        job_id=$(echo "$submit_output" | grep -oE 'Submitted batch job ([0-9]+)' | grep -oE '[0-9]+$')
+        if [ -n "$job_id" ]; then
+            echo "$job_id"
+            return 0
+        fi
+        last_output="$submit_output"
+        echo "sbatch failed: $submit_output" >&2
+        if ! echo "$submit_output" | grep -qiE "timed out|connection refused|connection reset|temporarily unavailable"; then
+            echo "Non-transient sbatch failure — not retrying." >&2
+            return 1
+        fi
+        if [ $attempt -lt $max_attempts ]; then
+            echo "Transient error — retrying in 30s..." >&2
+            sleep 30
+        fi
+        attempt=$((attempt + 1))
+    done
+
+    echo "sbatch failed after $max_attempts attempts. Last error: $last_output" >&2
+    return 1
+}
+

.github/scripts/submit-slurm-job.sh

@@ -85,9 +85,9 @@ if [ "$device" = "cpu" ]; then
     case "$cluster" in
         phoenix)
             sbatch_device_opts="\
-#SBATCH -p cpu-small
-#SBATCH --ntasks-per-node=24
-#SBATCH --mem-per-cpu=2G"
+#SBATCH -p cpu-small,cpu-medium,cpu-large
+#SBATCH --ntasks-per-node=12
+#SBATCH --mem-per-cpu=8G"
             ;;
         frontier|frontier_amd)
             sbatch_device_opts="\
@@ -161,8 +161,9 @@ rm -f "$output_file"
 # --- Module load mode (short form) ---
 module_mode=$([ "$device" = "gpu" ] && echo "g" || echo "c")
 
-# --- Submit ---
-submit_output=$(sbatch <<EOT
+# --- Submit (with retries for transient SLURM errors) ---
+source "${SCRIPT_DIR}/retry-sbatch.sh"
+_sbatch_script=$(cat <<EOT
 #!/bin/bash
 #SBATCH -J ${job_prefix}-${job_slug}
 #SBATCH --account=${account}
@@ -192,12 +193,8 @@ $sbatch_script_contents
 EOT
 )
 
-job_id=$(echo "$submit_output" | grep -oE '[0-9]+')
-if [ -z "$job_id" ]; then
-    echo "ERROR: Failed to submit job. sbatch output:"
-    echo "$submit_output"
-    exit 1
-fi
+job_id=$(retry_sbatch "$_sbatch_script")
+unset _sbatch_script
 
 echo "Submitted batch job $job_id"
 echo "$job_id" > "$id_file"

.github/workflows/common/bench.sh

@@ -25,7 +25,8 @@ fi
 # Phoenix builds inside SLURM; Frontier pre-builds via build.sh on the login node.
 # Phoenix: always nuke stale builds (heterogeneous compute nodes → ISA mismatch risk).
 if [ "$job_cluster" = "phoenix" ]; then
-    rm -rf build
+    source .github/scripts/clean-build.sh
+    clean_build
 fi
 
 if [ ! -d "build" ]; then

.github/workflows/common/test.sh

@@ -8,12 +8,26 @@ set -euo pipefail
 source .github/scripts/gpu-opts.sh
 build_opts="$gpu_opts"
 
+# --- Phoenix TMPDIR setup ---
+# Phoenix compute nodes have a small /tmp. With 8 parallel test threads each
+# spawning MPI processes, it fills up and ORTE session dir creation fails.
+# Redirect TMPDIR to project storage, same as bench.sh.
+if [ "$job_cluster" = "phoenix" ]; then
+    tmpbuild=/storage/project/r-sbryngelson3-0/sbryngelson3/mytmp_build
+    currentdir=$tmpbuild/run-$(( RANDOM % 9000 ))
+    mkdir -p $tmpbuild
+    mkdir -p $currentdir
+    export TMPDIR=$currentdir
+    trap 'rm -rf "$currentdir" || true' EXIT
+fi
+
 # --- Build (if not pre-built on login node) ---
 # Phoenix builds inside SLURM; Frontier pre-builds via build.sh on the login node.
 # Phoenix builds inside SLURM on heterogeneous compute nodes — always start fresh
 # to avoid SIGILL from stale binaries compiled on a different microarchitecture.
 if [ "$job_cluster" = "phoenix" ]; then
-    rm -rf build
+    source .github/scripts/clean-build.sh
+    clean_build
 fi
 
 if [ ! -d "build" ]; then

.github/workflows/frontier/build.sh

@@ -20,7 +20,8 @@ build_opts="$gpu_opts"
 
 . ./mfc.sh load -c $compiler_flag -m $([ "$job_device" = "gpu" ] && echo "g" || echo "c")
 
-rm -rf build
+source .github/scripts/clean-build.sh
+clean_build
 
 source .github/scripts/retry-build.sh
 if [ "$run_bench" == "bench" ]; then

docs/documentation/case.md

@@ -267,11 +267,11 @@ The number has to be a positive integer.
 - `num_fluids` defines the total number of fluids defined in each of the patches.
 The number has to be a positive integer.
 
-- `patch_icpp(j)%%geometry` defines the type of geometry of $j$-th patch by using an integer from 1 to 13.
+- `patch_icpp(j)%%geometry` defines the type of geometry of $j$-th patch by using an integer from 1 to 21.
 Definition of the patch type for each integer is listed in table [Patch Types](#patch-types).
 
 - `[x,y,z]_centroid`, `length_[x,y,z]`, and/or `radius` are used to uniquely define the geometry of the patch with given type.
-Requisite combinations of the parameters for each type can be found in is listed in table [Patch types](#patch-types).
+Requisite combinations of the parameters for each type are listed in table [Patch types](#patch-types).
 
 - `patch_icpp(j)%%alter_patch(i)` activates alternation of `patch(i)` with `patch(j)`.
 For instance, in a 2D simulation, when a cylindrical `patch(2)` is immersed in a rectangular `patch(1)`:
@@ -1087,8 +1087,8 @@ This boundary condition can be used for subsonic inflow (`bc_[x,y,z]%[beg,end]`
 | 10   | Cylinder 		           | 3     | Y      | Requires `[x,y,z]_centroid`, `radius`, and `length_[x,y,z]`. |
 | 11   | Sweep plane 	           | 3     | Y      | Not coordinate-aligned. Requires `x[y,z]_centroid` and `normal(i)`. |
 | 12   | Ellipsoid 		           | 3     | Y      | Requires `[x,y,z]_centroid` and `radii(i)`. |
-| 13   | N/A        	           | N/A   | N/A    | No longer exists. Empty. |
-| 14   | Spherical Harmonic      | 3     | N      | Requires `[x,y,z]_centroid`, `radius`, `epsilon`, `beta` |
+| 13   | 2D modal (Fourier)      | 2     | Y      | Requires `x_centroid`, `y_centroid`, `radius`. Optional: `fourier_cos(n)`, `fourier_sin(n)` (n=1..10), `modal_clip_r_to_min`, `modal_r_min`, `modal_use_exp_form`. |
+| 14   | 3D spherical harmonic   | 3     | Y      | Requires `x_centroid`, `y_centroid`, `z_centroid`, `radius`. Optional: `sph_har_coeff(l,m)` (l=0..5, m=-l..l). |
 | 15   | N/A                     | N/A   | N/A    | No longer exists. Empty.  |
 | 16   | 1D bubble pulse         | 1     | N      | Requires `x_centroid`, `length_x` |
 | 17   | Spiral                  | 2     | N      | Requires `[x,y]_centroid` |
@@ -1102,6 +1102,19 @@ This includes types exclusive to one-, two-, and three-dimensional problems.
 The patch type number (`#`) corresponds to the input value in `input.py` labeled  `patch_icpp(j)%%geometry` where $j$ is the patch index.
 Each patch requires a different set of parameters, which are also listed in this table.
 
+**Geometry 13: 2D modal (Fourier):**  
+Boundary is at polar angle \f$\theta = \mathrm{atan2}(y - y_{\mathrm{centroid}}, x - x_{\mathrm{centroid}})\f$.
+
+- **Additive form** (default, `modal_use_exp_form` false):  
+  \f$R_{\mathrm{boundary}} = \mathrm{radius} + \sum_n \bigl[ \mathtt{fourier\_cos}(n)\cos(n\theta) + \mathtt{fourier\_sin}(n)\sin(n\theta) \bigr]\f$.  
+  Coefficients are absolute: same units as `radius` (length).  
+  If this formula gives \f$R_{\mathrm{boundary}} < 0\f$ at some \f$\theta\f$, it is clipped to zero.  
+  With `modal_clip_r_to_min` true, if \f$R_{\mathrm{boundary}} <\f$ `modal_r_min` at some \f$\theta\f$, it is clipped to `modal_r_min`.  
+  
+- **Exponential form** (`modal_use_exp_form` true):  
+  \f$R_{\mathrm{boundary}} = \mathrm{radius} \times \exp\bigl( \sum_n [\ldots] \bigr)\f$.  
+  Coefficients are relative (dimensionless); the sum scales the radius.
+
 ### Immersed Boundary Patch Types {#immersed-boundary-patch-types}
 
 | #    | Name               | Dim.   |

examples/2D_patch_modal_shape/case.py

@@ -0,0 +1,125 @@
+#!/usr/bin/env python3
+"""Minimal 2D acoustic case with geometry 13 (2D modal Fourier shape). Additive form."""
+
+import json
+import math
+
+Nx, Ny = 64, 64
+Lx, Ly = 8.0, 8.0
+dx = Lx / (Nx + 1)
+p_inf = 101325.0
+rho_inf = 1.0
+gam = 1.4
+# Patch 2: same pressure, higher sound speed (different gas) -> lower density
+c_ratio = 1.5
+rho2 = rho_inf / (c_ratio * c_ratio)
+c = math.sqrt(gam * p_inf / rho_inf)
+cfl = 0.3
+mydt = cfl * dx / c
+Tfinal = 10.0 / c
+Nt = int(Tfinal / mydt)
+
+# Acoustic source (similar to 2D_acoustic_support5)
+t_cross = Lx / c  # domain crossing time
+gauss_sigma_time = 0.03 * t_cross
+acoustic_delay = 0.15 * t_cross
+acoustic_loc_x = -3.5
+acoustic_loc_y = 0.0
+acoustic_aperture = 6.0
+acoustic_foc_length = 3.5
+
+config = {
+    "run_time_info": "T",
+    "x_domain%beg": -4.0,
+    "x_domain%end": 4.0,
+    "y_domain%beg": -4.0,
+    "y_domain%end": 4.0,
+    "m": Nx,
+    "n": Ny,
+    "p": 0,
+    "dt": mydt,
+    "t_step_start": 0,
+    "t_step_stop": Nt,
+    "t_step_save": max(1, int(Nt / 10)),
+    "num_patches": 2,
+    "model_eqns": 2,
+    "alt_soundspeed": "F",
+    "num_fluids": 2,
+    "mpp_lim": "F",
+    "mixture_err": "F",
+    "time_stepper": 3,
+    "weno_order": 5,
+    "weno_eps": 1.0e-16,
+    "mapped_weno": "T",
+    "null_weights": "F",
+    "mp_weno": "F",
+    "riemann_solver": 2,
+    "wave_speeds": 1,
+    "avg_state": 2,
+    "bc_x%beg": -8,
+    "bc_x%end": -8,
+    "bc_y%beg": -8,
+    "bc_y%end": -8,
+    "format": 1,
+    "precision": 2,
+    "prim_vars_wrt": "T",
+    "parallel_io": "T",
+    "omega_wrt(3)": "T",
+    "fd_order": 2,
+    "patch_icpp(1)%geometry": 3,
+    "patch_icpp(1)%x_centroid": 0.0,
+    "patch_icpp(1)%y_centroid": 0.0,
+    "patch_icpp(1)%length_x": 8.0,
+    "patch_icpp(1)%length_y": 8.0,
+    "patch_icpp(1)%vel(1)": 0.0,
+    "patch_icpp(1)%vel(2)": 0.0,
+    "patch_icpp(1)%pres": p_inf,
+    "patch_icpp(1)%alpha_rho(1)": rho_inf,
+    "patch_icpp(1)%alpha_rho(2)": 0.0,
+    "patch_icpp(1)%alpha(1)": 1.0,
+    "patch_icpp(1)%alpha(2)": 0.0,
+    "patch_icpp(2)%geometry": 13,
+    "patch_icpp(2)%x_centroid": 0.0,
+    "patch_icpp(2)%y_centroid": 0.0,
+    "patch_icpp(2)%radius": 1.0,
+    "patch_icpp(2)%fourier_cos(1)": 0.2,
+    "patch_icpp(2)%fourier_sin(1)": 0.1,
+    "patch_icpp(2)%fourier_sin(3)": -0.3,
+    "patch_icpp(2)%fourier_cos(5)": 0.5,
+    "patch_icpp(2)%modal_clip_r_to_min": "T",
+    "patch_icpp(2)%modal_r_min": 0.5,
+    "patch_icpp(2)%vel(1)": 0.0,
+    "patch_icpp(2)%vel(2)": 0.0,
+    "patch_icpp(2)%pres": p_inf,
+    "patch_icpp(2)%alpha_rho(1)": 0.0,
+    "patch_icpp(2)%alpha_rho(2)": rho2,
+    "patch_icpp(2)%alpha(1)": 0.0,
+    "patch_icpp(2)%alpha(2)": 1.0,
+    "patch_icpp(2)%alter_patch(1)": "T",
+    "bc_x%grcbc_in": "F",
+    "bc_x%grcbc_out": "T",
+    "bc_x%grcbc_vel_out": "F",
+    "bc_x%pres_out": p_inf,
+    "bc_y%grcbc_in": "F",
+    "bc_y%grcbc_out": "T",
+    "bc_y%grcbc_vel_out": "F",
+    "bc_y%pres_out": p_inf,
+    "fluid_pp(1)%gamma": 1.0 / (gam - 1.0),
+    "fluid_pp(1)%pi_inf": 0.0,
+    "fluid_pp(2)%gamma": 1.0 / (gam - 1.0),
+    "fluid_pp(2)%pi_inf": 0.0,
+    # Acoustic source (similar to 2D_acoustic_support5)
+    "acoustic_source": "T",
+    "num_source": 1,
+    "acoustic(1)%support": 5,
+    "acoustic(1)%loc(1)": acoustic_loc_x,
+    "acoustic(1)%loc(2)": acoustic_loc_y,
+    "acoustic(1)%pulse": 2,
+    "acoustic(1)%npulse": 1,
+    "acoustic(1)%mag": 1.0,
+    "acoustic(1)%gauss_sigma_time": gauss_sigma_time,
+    "acoustic(1)%foc_length": acoustic_foc_length,
+    "acoustic(1)%aperture": acoustic_aperture,
+    "acoustic(1)%delay": acoustic_delay,
+}
+print(json.dumps(config))