Moving EL Bubbles with MPI Decomposition

.gitignore

@@ -114,3 +114,4 @@ cce_*/
 cce_*.log
 run_cce_*.sh
 .ffmt_cache/
+**/.ffmt_cache/

claude-code-review.yml

@@ -0,0 +1,330 @@
+name: Claude Code Review
+
+on:
+  pull_request_target:
+    types: [opened, ready_for_review, reopened, labeled]
+  issue_comment:
+    types: [created]
+
+jobs:
+  claude-review:
+    if: >
+      (
+        github.event_name == 'pull_request_target' &&
+        (
+          github.event.action == 'opened' ||
+          github.event.action == 'ready_for_review' ||
+          github.event.action == 'reopened' ||
+          (
+            github.event.action == 'labeled' &&
+            github.event.label.name == 'claude-full-review'
+          )
+        )
+      ) ||
+      (
+        github.event_name == 'issue_comment' &&
+        github.event.issue.pull_request != null &&
+        contains(github.event.comment.body, '@claude full review')
+      )
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      pull-requests: write
+      issues: write
+      actions: read
+
+    steps:
+      - name: Install dependencies
+        shell: bash
+        run: |
+          set -euo pipefail
+          sudo apt-get update
+          sudo apt-get install -y unzip jq
+
+      - name: Determine PR number
+        id: mode
+        shell: bash
+        env:
+          GH_TOKEN: ${{ github.token }}
+        run: |
+          set -euo pipefail
+
+          if [[ "${{ github.event_name }}" == "pull_request_target" ]]; then
+            PR_NUMBER="${{ github.event.pull_request.number }}"
+          elif [[ "${{ github.event_name }}" == "issue_comment" ]]; then
+            PR_NUMBER="${{ github.event.issue.number }}"
+          else
+            echo "Unsupported event"
+            exit 1
+          fi
+
+          PR_HEAD_REF="$(gh pr view "$PR_NUMBER" --repo "${{ github.repository }}" --json headRefName --jq .headRefName)"
+
+          echo "pr_number=$PR_NUMBER" >> "$GITHUB_OUTPUT"
+          echo "pr_head_ref=$PR_HEAD_REF" >> "$GITHUB_OUTPUT"
+
+      - name: Checkout base repo
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Fetch PR head
+        shell: bash
+        env:
+          PR_NUMBER: ${{ steps.mode.outputs.pr_number }}
+        run: |
+          set -euo pipefail
+          # Fetch the PR merge ref — works for both same-repo and fork PRs
+          # (fork branches don't exist on origin, but pull/<n>/head always does)
+          git fetch origin "pull/${PR_NUMBER}/head"
+
+      - name: Resolve review state
+        id: state
+        shell: bash
+        env:
+          GH_TOKEN: ${{ github.token }}
+        run: |
+          set -euo pipefail
+
+          PR_NUMBER="${{ steps.mode.outputs.pr_number }}"
+          REPO="${{ github.repository }}"
+
+          mkdir -p .claude-review/context
+
+          CURRENT_HEAD_SHA="$(gh pr view "$PR_NUMBER" --repo "$REPO" --json headRefOid --jq .headRefOid)"
+          echo "current_head_sha=$CURRENT_HEAD_SHA" >> "$GITHUB_OUTPUT"
+
+          LAST_COMMENT_B64="$(
+            gh api --paginate "repos/$REPO/issues/$PR_NUMBER/comments?per_page=100" \
+              --jq '.[] | select(.body | contains("<!-- claude-review: thread=primary;")) | @base64' \
+              | tail -n1 || true
+          )"
+
+          EXISTING_COMMENT_ID=""
+
+          if [[ -n "${LAST_COMMENT_B64:-}" ]]; then
+            LAST_COMMENT_JSON="$(printf '%s' "$LAST_COMMENT_B64" | base64 -d)"
+            EXISTING_COMMENT_ID="$(printf '%s' "$LAST_COMMENT_JSON" | jq -r '.id // empty')"
+          fi
+
+          echo "existing_comment_id=${EXISTING_COMMENT_ID:-}" >> "$GITHUB_OUTPUT"
+
+      - name: Build review diff and changed-file list
+        id: review_input
+        shell: bash
+        env:
+          GH_TOKEN: ${{ github.token }}
+        run: |
+          set -euo pipefail
+
+          PR_NUMBER="${{ steps.mode.outputs.pr_number }}"
+          REPO="${{ github.repository }}"
+
+          mkdir -p .claude-review
+
+          gh pr diff "$PR_NUMBER" --repo "$REPO" > .claude-review/review.diff.raw
+          gh pr view "$PR_NUMBER" --repo "$REPO" --json files --jq '.files[].path' > .claude-review/changed_files.txt.raw
+
+          # Filter out tests/ directory — golden files don't need code review
+          grep -v '^tests/' .claude-review/changed_files.txt.raw > .claude-review/changed_files.txt || true
+          # Strip diff hunks for tests/ files
+          awk '
+            /^diff --git a\/tests\// { skip=1; next }
+            /^diff --git /           { skip=0 }
+            !skip                    { print }
+          ' .claude-review/review.diff.raw > .claude-review/review.diff
+
+          sed -i '/^[[:space:]]*$/d' .claude-review/changed_files.txt || true
+
+          echo "review_diff_path=.claude-review/review.diff" >> "$GITHUB_OUTPUT"
+          echo "changed_files_path=.claude-review/changed_files.txt" >> "$GITHUB_OUTPUT"
+
+      - name: Prefetch bounded context for changed files only
+        id: context
+        shell: bash
+        env:
+          GH_TOKEN: ${{ github.token }}
+        run: |
+          set -euo pipefail
+
+          REPO="${{ github.repository }}"
+          HEAD_SHA="${{ steps.state.outputs.current_head_sha }}"
+          COUNT=0
+
+          mkdir -p .claude-review/context
+
+          # Prioritize src/ files for context (most likely to need review)
+          sort -t/ -k1,1 -s < "${{ steps.review_input.outputs.changed_files_path }}" | \
+            awk '/^src\//{print; next} {rest[NR]=$0} END{for(i in rest) print rest[i]}' > .claude-review/sorted_files.txt
+
+          while IFS= read -r path; do
+            [[ -z "$path" ]] && continue
+            COUNT=$((COUNT + 1))
+            [[ "$COUNT" -gt 10 ]] && break
+
+            SAFE_NAME="$(printf '%s' "$path" | tr '/ ' '__')"
+            RAW="$(gh api "repos/$REPO/contents/$path?ref=$HEAD_SHA" 2>/dev/null || true)"
+            [[ -z "$RAW" ]] && continue
+
+            ENCODING="$(printf '%s' "$RAW" | jq -r '.encoding // empty')"
+            [[ "$ENCODING" != "base64" ]] && continue
+
+            CONTENT="$(printf '%s' "$RAW" | jq -r '.content // empty' | tr -d '\n' | base64 -d 2>/dev/null || true)"
+            [[ -z "$CONTENT" ]] && continue
+
+            LINE_COUNT="$(printf '%s' "$CONTENT" | wc -l | tr -d ' ')"
+            if [[ "$LINE_COUNT" -le 1500 ]]; then
+              printf '%s' "$CONTENT" > ".claude-review/context/$SAFE_NAME"
+            fi
+          done < .claude-review/sorted_files.txt
+
+          echo "context_dir=.claude-review/context" >> "$GITHUB_OUTPUT"
+
+      - name: Initialize review output
+        shell: bash
+        run: |
+          set -euo pipefail
+          mkdir -p .claude-review
+          : > .claude-review/output.md
+
+      - name: Run Claude Code Review
+        continue-on-error: true
+        uses: anthropics/claude-code-action@v1
+        with:
+          claude_code_oauth_token: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }}
+          github_token: ${{ github.token }}
+          plugin_marketplaces: "https://github.com/anthropics/claude-code.git"
+          plugins: "code-review@claude-code-plugins"
+          claude_args: >
+            --dangerously-skip-permissions
+            --max-turns 40
+            --allowedTools
+            "Bash"
+          prompt: |
+            You are running in GitHub Actions review automation.
+
+            PR NUMBER: ${{ steps.mode.outputs.pr_number }}
+            CURRENT HEAD SHA: ${{ steps.state.outputs.current_head_sha }}
+
+            Review ONLY the prepared inputs for this run.
+
+            Prepared inputs:
+            - Diff to review: ${{ steps.review_input.outputs.review_diff_path }}
+            - Changed files list: ${{ steps.review_input.outputs.changed_files_path }}
+            - Optional full-file context for small changed files: ${{ steps.context.outputs.context_dir }}
+
+            Hard scope rules:
+            - Do NOT inspect checked-out repository code except:
+              - ./CLAUDE.md
+              - ./.claude/rules/*.md (max 10 files)
+              - ${{ steps.review_input.outputs.review_diff_path }}
+              - ${{ steps.review_input.outputs.changed_files_path }}
+              - files inside ${{ steps.context.outputs.context_dir }}
+            - Do NOT fetch or inspect any other repository files.
+            - Do NOT inspect unchanged files outside the reviewed diff.
+            - Do NOT follow imports, includes, callers, callees, or related modules outside changed files.
+            - Do NOT mention any file path not present in the changed files list.
+            - Every finding must be grounded in at least one changed hunk from the reviewed diff.
+            - Other changed files may be used as supporting context only.
+            - Nearby unchanged lines in changed files may be used as supporting context only.
+            - Do NOT raise findings about code outside changed files.
+            - Do NOT provide general repo suggestions or unrelated improvement ideas.
+            - Do NOT include positive confirmations like "No issues with X"
+            - If confidence is low, omit the finding.
+
+            Allowed workflow:
+            1) ls -1 .claude/rules 2>/dev/null || true
+            2) cat CLAUDE.md 2>/dev/null || true
+            3) find .claude/rules -maxdepth 1 -name "*.md" -print | head -n 10 | xargs -I{} cat "{}" 2>/dev/null || true
+            4) cat "${{ steps.review_input.outputs.changed_files_path }}"
+            5) cat "${{ steps.review_input.outputs.review_diff_path }}"
+            6) Optionally inspect files inside "${{ steps.context.outputs.context_dir }}" only
+            7) Write the final review markdown to .claude-review/output.md, then STOP
+            8) Do NOT post, update, or create GitHub comments yourself
+
+            Review policy:
+            - Review the full PR diff.
+            - Do NOT restate the full PR summary.
+            - If there are no high-confidence findings, leave .claude-review/output.md empty and STOP.
+
+            Review standard (in priority order per CLAUDE.md "Code Review Priorities"):
+            1. Correctness (logic bugs, numerical issues, array bounds)
+            2. Precision discipline (stp vs wp mixing)
+            3. Memory management (@:ALLOCATE/@:DEALLOCATE pairing, GPU pointer setup)
+            4. MPI correctness (halo exchange, buffer sizing, GPU_UPDATE calls)
+            5. GPU code (GPU_* Fypp macros only, no raw pragmas)
+            6. Physics consistency (pressure formula matches model_eqns)
+            7. Compiler portability (4 CI-gated compilers + AMD flang for GPU)
+            - Avoid style nitpicks.
+            - A finding is valid only if it is supported by changed lines, with changed-file context used only to confirm it.
+
+            Output rules:
+            - Write markdown only to .claude-review/output.md
+            - If there are findings, use exactly this format:
+
+            Claude Code Review
+
+            Head SHA: <sha>
+
+            Files changed:
+            - <count>
+            - <up to 10 paths from changed_files.txt>
+
+            Findings:
+            - <only high-confidence issues grounded in changed hunks>
+
+            <!-- claude-review: thread=primary; reviewed_sha=<current_head_sha>; mode=full -->
+
+            - Always include the hidden marker exactly once at the end of the file.
+            - If there are no findings, write nothing.
+
+      - name: Publish review comment
+        shell: bash
+        env:
+          GH_TOKEN: ${{ github.token }}
+        run: |
+          set -euo pipefail
+
+          PR_NUMBER="${{ steps.mode.outputs.pr_number }}"
+          REPO="${{ github.repository }}"
+          COMMENT_ID="${{ steps.state.outputs.existing_comment_id }}"
+          OUTPUT_FILE=".claude-review/output.md"
+
+          if [[ ! -f "$OUTPUT_FILE" ]]; then
+            echo "No output file; nothing to publish."
+            exit 0
+          fi
+
+          if [[ ! -s "$OUTPUT_FILE" ]] || [[ -z "$(tr -d '[:space:]' < "$OUTPUT_FILE")" ]]; then
+            echo "Review output is empty; not posting a comment."
+            exit 0
+          fi
+
+          BODY_JSON="$(jq -Rs '{body: .}' < "$OUTPUT_FILE")"
+
+          if [[ -n "${COMMENT_ID:-}" ]]; then
+            gh api \
+              --method PATCH \
+              "repos/$REPO/issues/comments/$COMMENT_ID" \
+              --input - <<< "$BODY_JSON" >/dev/null
+            echo "Updated existing primary review comment: $COMMENT_ID"
+          else
+            gh api \
+              --method POST \
+              "repos/$REPO/issues/$PR_NUMBER/comments" \
+              --input - <<< "$BODY_JSON" >/dev/null
+            echo "Created new primary review comment."
+          fi
+
+      - name: Fallback job summary on failure
+        if: failure()
+        shell: bash
+        run: |
+          set -euo pipefail
+          if [[ -f .claude-review/output.md ]] && [[ -s .claude-review/output.md ]]; then
+            {
+              echo "## Claude Code Review"
+              echo
+              cat .claude-review/output.md
+            } >> "$GITHUB_STEP_SUMMARY"
+          fi

docs/documentation/case.md

@@ -266,6 +266,16 @@ Setup: Only requires specifying `init_dir` and filename pattern via `zeros_defau
 Implementation: All variables and file handling are managed in `src/common/include/ExtrusionHardcodedIC.fpp` with no manual grid configuration needed.
 Usage: Ideal for initializing simulations from lower-dimensional solutions, enabling users to add perturbations or modifications to the base extruded fields for flow instability studies.
 
+The following parameters support hardcoded initial conditions that read interface data from files:
+
+| Parameter        | Type    | Description                                               |
+| ---:             | :---:   | :---                                                      |
+| `interface_file` | String  | Path to interface geometry data file                      |
+| `normFac`        | Real    | Interface normalization factor                            |
+| `normMag`        | Real    | Interface normal magnitude                                |
+| `g0_ic`          | Real    | Initial gas volume fraction for interfacial IC            |
+| `p0_ic`          | Real    | Initial pressure for interfacial IC                       |
+
 #### Parameter Descriptions
 
 - `num_patches` defines the total number of patches defined in the domain.
@@ -349,7 +359,7 @@ Definitions for currently implemented immersed boundary patch types are listed i
 
 - `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 [NACA airfoil](https://en.wikipedia.org/wiki/NACA_airfoil).
+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)
 
 - `slip` applies a slip boundary to the surface of the patch if true and a no-slip boundary condition to the surface if false.