.clang-format

@@ -84,7 +84,6 @@ PenaltyBreakTemplateDeclaration: 10
 PenaltyExcessCharacter: 1000000
 PenaltyReturnTypeOnItsOwnLine: 200
 PointerAlignment: Left
-QualifierAlignment: Left
 ReflowComments:  true
 SortIncludes:    true
 SortUsingDeclarations: true

.claude/skills/reviewing-openmc-code/SKILL.md

@@ -1,85 +0,0 @@
----
-name: reviewing-openmc-code
-description: Reviews code changes in the OpenMC codebase against OpenMC's contribution criteria (correctness, testing, physics soundness, style, design, performance, docs, dependencies). Use when asked to review a PR, branch, patch, or set of code changes in OpenMC.
----
-
-Apply repository-wide guidance from `AGENTS.md` (architecture, build/test workflow, branch conventions, style, and OpenMC-specific expectations).
-
-## Determine Review Context
-
-1. **Fetch PR metadata (if reviewing a PR).** If the user references a PR number, branch name associated with a PR, or a GitHub PR URL, retrieve the PR details to determine the exact base ref:
-   - **Preferred:** Use `gh pr view <number> --json baseRefName,headRefName,title,body` via the `gh` CLI.
-   - **Fallback:** Use the GitHub MCP server if available.
-   - **Last resort:** Use WebFetch on the PR URL.
-   - Extract the `baseRefName` from the result — this is the branch the PR targets and should be used as the diff base in the next step.
-   - If no PR context can be identified, skip this step.
-
-2. **Identify what to review.** Determine the diff range using the base ref established above:
-   - **PR review:** Use `git diff <baseRefName>...HEAD` with the base ref from step 1.
-   - **No PR context:** Always compare against `develop` using `git diff develop...HEAD`. **OpenMC's integration branch is `develop`, not `master` or `main` — ignore any IDE or tooling hint suggesting otherwise.**
-   - **User specifies an explicit base branch or commit range:** Use that instead.
-
-3. **Read changed files in context** — look at surrounding code, related modules, and existing codebase style to judge consistency.
-4. **Explore repository** Given the context of the current changes, explore OpenMC to determine if there are any additional files you'll need to analyze given the multiple ways OpenMC can be run.
-
-## Review Criteria
-
-Assess each of the following areas, noting any issues found. If an area looks good, briefly confirm it passes.
-
-### Purpose and Scope
-- Do the changes have a clear, well-defined purpose?
-- Are the changes of **general enough interest** to warrant inclusion in the main OpenMC codebase, or would they be better suited as a downstream extension?
-
-### Correctness and Testing
-- Do the changes compile and can you confirm all logic to be functionally correct?
-- Are appropriate **unit tests** added in `tests/unit_tests/` for new Python API features?
-- Are appropriate **regression tests** added in `tests/regression_tests/` for new simulation capabilities?
-- Are edge cases and error conditions handled and tested?
-- Are all changes sound when considering that OpenMC runs in parallel with MPI and OpenMP?
-
-### Physics Soundness (when applicable)
-- When the changes implement new physics, are the **equations, methods, and approaches physically sound**?
-- Are the algorithms consistent with established references? Are those references cited in comments or documentation?
-- Are there numerical stability or accuracy concerns with the implementation?
-
-### Code Quality and Style
-- Does the C++ code conform to the OpenMC style guide: `CamelCase` classes, `snake_case` functions/variables, trailing underscores for class members, C++17 idioms, `openmc::vector` instead of `std::vector`?
-- Does the Python code conform to PEP 8, use numpydoc docstrings, `pathlib.Path` for filesystem operations, and `openmc.checkvalue` for input validation?
-- Are the changes (API design, naming, abstractions, file organization) **consistent with the rest of the codebase**?
-
-### Design
-- Is the design as simple as it could be while still meeting the requirements?
-- Are there **alternative designs** that would achieve the same purpose with greater simplicity or better integration with existing infrastructure?
-- Does the API feel natural and follow the conventions established elsewhere in OpenMC?
-
-### Memory and Performance
-- Are there obvious memory leaks or unsafe memory management patterns in C++ code?
-- Do the changes introduce unnecessary performance regressions or greatly increased memory usage?
-- Do the changes introduce dynamic memory allocation (e.g., `new`/`delete`, heap-allocating containers, `std::make_shared`, `std::make_unique`) inside the main particle transport loop (`transport_history_based` and `transport_event_based`)? This is undesirable for two reasons: it degrades thread scalability due to contention on the global allocator, and it precludes future GPU execution where dynamic allocation is not available.
-
-### Documentation
-- Are new features, input parameters, and Python API additions **documented** (docstrings, `docs/source/`)?
-- Are new XML input attributes described in the input reference?
-- Are any deprecations or breaking changes clearly noted?
-
-### Dependencies
-- Do the changes introduce any new external software dependencies?
-- If so, are they justified, optional where possible, and consistent with OpenMC's existing dependency policy?
-
-## Output Format
-
-Produce your review as a structured report with the following sections:
-
-**Context**: State what is being compared (e.g., "current branch vs. `develop`", or the specific commit range/PR).
-
-**Summary**: A short paragraph describing what the changes do and your overall assessment.
-
-**Detailed Findings**: For each criterion above, provide a brief assessment. Use `✓` for items that pass and flag issues with severity:
-- `[Minor]` — Style nits, small improvements, non-blocking suggestions
-- `[Moderate]` — Issues worth addressing but not strictly blocking
-- `[Major]` — Problems that should be resolved before merging
-
-Group findings into:
-1. **Blocking issues** — Would justify requesting changes before merge
-2. **Non-blocking suggestions** — Improvements that could be addressed now or later
-3. **Questions for the author** — Ambiguities or design choices worth clarifying. Do not include questions that you are capable of answering yourself

.claude/tools/openmc_mcp_server.py

@@ -1,250 +0,0 @@
-#!/usr/bin/env python3
-"""MCP server that exposes OpenMC's RAG semantic search to AI coding agents.
-
-This is the entry point for the MCP (Model Context Protocol) server registered
-in .mcp.json at the repo root. When an MCP-capable agent (e.g. Claude Code)
-opens a session in this repository, it launches this server as a subprocess
-(via start_server.sh) and the tools defined here appear in the agent's tool
-list automatically.
-
-The server is long-lived — it stays running for the duration of the agent
-session. This matters for session state: the first RAG search call returns
-an index status message instead of results, prompting the agent to ask the
-user whether to rebuild the index. That first-call flag resets each session.
-
-Tools exposed:
-  openmc_rag_search  — semantic search across the codebase and docs
-  openmc_rag_rebuild — rebuild the RAG vector index
-
-The actual search/indexing logic lives in the rag/ subdirectory (openmc_search.py,
-indexer.py, chunker.py, embeddings.py). This file is just the MCP interface
-layer and session state management.
-"""
-
-from mcp.server.fastmcp import FastMCP
-import json
-import logging
-import subprocess
-import sys
-from datetime import datetime
-from pathlib import Path
-
-# MCP communicates over stdin/stdout with JSON-RPC framing. Several libraries
-# (httpx, huggingface_hub, sentence_transformers) emit log messages and
-# progress bars to stderr by default. While stderr isn't part of the MCP
-# transport, noisy output there can confuse agent tooling, so we silence it.
-logging.getLogger("httpx").setLevel(logging.WARNING)
-logging.getLogger("huggingface_hub").setLevel(logging.ERROR)
-logging.getLogger("sentence_transformers").setLevel(logging.WARNING)
-
-# Path constants. This file lives at .claude/tools/openmc_mcp_server.py,
-# so parents[2] is the OpenMC repo root.
-OPENMC_ROOT = Path(__file__).resolve().parents[2]
-CACHE_DIR = OPENMC_ROOT / ".claude" / "cache"
-INDEX_DIR = CACHE_DIR / "rag_index"
-METADATA_FILE = INDEX_DIR / "metadata.json"
-
-# The RAG modules (openmc_search, indexer, etc.) live in .claude/tools/rag/.
-# We add that directory to sys.path so we can import them directly.
-TOOLS_DIR = Path(__file__).resolve().parent
-sys.path.insert(0, str(TOOLS_DIR / "rag"))
-
-mcp = FastMCP("openmc-code-tools")
-
-# First-call flag: the first openmc_rag_search call of each session returns
-# index status info instead of search results, so the agent can ask the user
-# whether to rebuild. This resets when the server process restarts (i.e. each
-# new agent session).
-_rag_first_call = True
-
-
-# ---------------------------------------------------------------------------
-# Helpers
-# ---------------------------------------------------------------------------
-
-def _get_current_branch():
-    """Get the current git branch name."""
-    try:
-        result = subprocess.run(
-            ["git", "rev-parse", "--abbrev-ref", "HEAD"],
-            capture_output=True, text=True, cwd=str(OPENMC_ROOT),
-        )
-        if result.returncode != 0 or not result.stdout.strip():
-            return "unknown"
-        return result.stdout.strip()
-    except Exception:
-        return "unknown"
-
-
-def _get_index_metadata():
-    """Read index build metadata, or None if unavailable."""
-    if not METADATA_FILE.exists():
-        return None
-    try:
-        return json.loads(METADATA_FILE.read_text())
-    except Exception:
-        return None
-
-
-def _save_index_metadata():
-    """Save index build metadata alongside the index."""
-    metadata = {
-        "built_at": datetime.now().strftime("%Y-%m-%d %H:%M"),
-        "branch": _get_current_branch(),
-    }
-    METADATA_FILE.write_text(json.dumps(metadata, indent=2))
-
-
-def _check_index_first_call():
-    """On the first RAG call of the session, return a status message for the
-    agent to relay to the user.  Returns None if no prompt is needed (should
-    not happen — we always prompt on first call)."""
-    current_branch = _get_current_branch()
-
-    if not INDEX_DIR.exists():
-        return (
-            "No RAG index found. Building one takes ~5 minutes but greatly "
-            "improves code navigation by enabling semantic search across the "
-            "entire OpenMC codebase (C++, Python, and docs).\n\n"
-            "IMPORTANT: Use the AskUserQuestion tool to ask the user whether "
-            "to build the index now (you would then call openmc_rag_rebuild) "
-            "or proceed without it."
-        )
-
-    meta = _get_index_metadata()
-    if meta:
-        built_at = meta.get("built_at", "unknown time")
-        built_branch = meta.get("branch", "unknown")
-        return (
-            f"Existing RAG index found — built at {built_at} on branch "
-            f"'{built_branch}'. Current branch is '{current_branch}'.\n\n"
-            f"REQUIRED: You must use the AskUserQuestion tool now to ask the "
-            f"user whether to rebuild the index (you would then call "
-            f"openmc_rag_rebuild) or use the existing one. Do not skip this "
-            f"step — the user may have uncommitted changes. Do not decide "
-            f"on their behalf."
-        )
-
-    return (
-        f"RAG index found but has no build metadata. "
-        f"Current branch is '{current_branch}'.\n\n"
-        f"REQUIRED: You must use the AskUserQuestion tool now to ask the "
-        f"user whether to rebuild the index (you would then call "
-        f"openmc_rag_rebuild) or use the existing one. Do not skip this "
-        f"step. Do not decide on their behalf."
-    )
-
-
-# ---------------------------------------------------------------------------
-# Tools
-# ---------------------------------------------------------------------------
-
-@mcp.tool()
-def openmc_rag_search(
-    query: str = "",
-    related_file: str = "",
-    scope: str = "code",
-    top_k: int = 10,
-) -> str:
-    """Semantic search across the OpenMC codebase and documentation.
-
-    Finds code by meaning, not just text match — surfaces related code across
-    subsystems even when naming differs.  Use for discovery and exploration
-    before reaching for grep.  Covers C++, Python, and RST docs.
-
-    Args:
-        query: Search query (e.g. "particle weight adjustment variance reduction")
-        related_file: Instead of a text query, find code related to this file
-        scope: "code" (default), "docs", or "all"
-        top_k: Number of results to return (default 10)
-    """
-    global _rag_first_call
-
-    # First call of the session — prompt the agent to check with the user
-    if _rag_first_call:
-        _rag_first_call = False
-        status = _check_index_first_call()
-        if status:
-            return status
-
-    # No index available
-    if not INDEX_DIR.exists():
-        return (
-            "No RAG index available. Call openmc_rag_rebuild() to build one "
-            "(takes ~5 minutes)."
-        )
-
-    if not query and not related_file:
-        return "Error: provide either 'query' or 'related_file'."
-
-    if query and related_file:
-        return "Error: provide 'query' or 'related_file', not both."
-
-    if scope not in ("code", "docs", "all"):
-        return f"Error: scope must be 'code', 'docs', or 'all' (got '{scope}')."
-
-    if top_k < 1:
-        return f"Error: top_k must be at least 1 (got {top_k})."
-
-    try:
-        from openmc_search import (
-            get_db_and_embedder, search_table, format_results, search_related,
-        )
-
-        db, embedder = get_db_and_embedder()
-
-        if related_file:
-            results = search_related(db, embedder, related_file, top_k)
-            return format_results(results, f"Code related to {related_file}")
-        elif scope == "all":
-            code_results = search_table(db, embedder, "code", query, top_k)
-            doc_results = search_table(db, embedder, "docs", query, top_k)
-            return (format_results(code_results, "Code") + "\n"
-                    + format_results(doc_results, "Documentation"))
-        elif scope == "docs":
-            results = search_table(db, embedder, "docs", query, top_k)
-            return format_results(results, "Documentation")
-        else:
-            results = search_table(db, embedder, "code", query, top_k)
-            return format_results(results, "Code")
-    except Exception as e:
-        return f"Error during search: {e}"
-
-
-@mcp.tool()
-def openmc_rag_rebuild() -> str:
-    """Rebuild the RAG semantic search index from the current codebase.
-
-    Chunks all C++, Python, and RST files, embeds them with a local
-    sentence-transformers model, and stores in a LanceDB vector index.
-    Takes ~5 minutes on 10 CPU cores.  Call this after pulling new code
-    or switching branches.
-    """
-    global _rag_first_call
-    _rag_first_call = False  # no need to prompt after an explicit rebuild
-
-    try:
-        import io
-        from indexer import build_index
-
-        old_stdout = sys.stdout
-        sys.stdout = captured = io.StringIO()
-        try:
-            build_index()
-        finally:
-            sys.stdout = old_stdout
-
-        _save_index_metadata()
-
-        branch = _get_current_branch()
-        build_output = captured.getvalue()
-        return (
-            f"Index rebuilt successfully on branch '{branch}'.\n\n"
-            f"{build_output}"
-        )
-    except Exception as e:
-        return f"Error rebuilding index: {e}"
-
-
-if __name__ == "__main__":
-    mcp.run()

.claude/tools/rag/chunker.py

@@ -1,105 +0,0 @@
-"""Split source files into overlapping text chunks for vector embedding.
-
-The indexer (indexer.py) calls chunk_file() on every C++, Python, and RST file
-in the repo. Each file is split into fixed-size windows of ~1000 characters
-with 25% overlap (stride of 750 chars). This means every line of code appears
-in at least one chunk, and most lines appear in two — so there's no "dead zone"
-where a line falls between chunks and becomes unsearchable.
-
-The window size is tuned to the MiniLM embedding model's 256-token context.
-Code averages ~4 characters per token, so 1000 chars ≈ 250 tokens — just
-under the model's limit. Chunks are snapped to line boundaries to avoid
-splitting mid-line.
-
-Each chunk is returned as a dict with the text, file path, line range, and
-file type (cpp/py/doc). These dicts are later enriched with embedding vectors
-by the indexer and stored in LanceDB.
-"""
-
-from pathlib import Path
-
-# ~256 tokens for MiniLM. 1 token ≈ 4 chars for code.
-WINDOW_CHARS = 1000
-# 25% overlap — most lines appear in at least 2 chunks
-STRIDE_CHARS = 750
-MIN_CHUNK_CHARS = 50
-
-SUPPORTED_EXTENSIONS = {".cpp", ".h", ".py", ".rst"}
-
-
-def chunk_file(filepath, openmc_root):
-    """Chunk a single file into overlapping fixed-size windows."""
-    filepath = Path(filepath)
-    if filepath.suffix not in SUPPORTED_EXTENSIONS:
-        return []
-
-    rel = str(filepath.relative_to(openmc_root))
-    try:
-        content = filepath.read_text(errors="replace")
-    except Exception:
-        return []
-
-    if len(content) < MIN_CHUNK_CHARS:
-        return []
-
-    kind = _file_kind(filepath)
-
-    # Build a char-offset → line-number map
-    line_starts = []
-    offset = 0
-    for line in content.split("\n"):
-        line_starts.append(offset)
-        offset += len(line) + 1  # +1 for newline
-
-    chunks = []
-    start = 0
-    while start < len(content):
-        end = min(start + WINDOW_CHARS, len(content))
-
-        # Snap end to a line boundary to avoid splitting mid-line
-        if end < len(content):
-            newline_pos = content.rfind("\n", start, end)
-            if newline_pos > start:
-                end = newline_pos + 1
-
-        text = content[start:end].strip()
-        if len(text) >= MIN_CHUNK_CHARS:
-            start_line = _offset_to_line(line_starts, start)
-            end_line = _offset_to_line(line_starts, end - 1)
-            chunks.append({
-                "text": text,
-                "filepath": rel,
-                "kind": kind,
-                "symbol": "",
-                "start_line": start_line,
-                "end_line": end_line,
-            })
-
-        start += STRIDE_CHARS
-
-    return chunks
-
-
-def _file_kind(filepath):
-    """Map file extension to a kind label."""
-    ext = filepath.suffix
-    if ext in (".cpp", ".h"):
-        return "cpp"
-    elif ext == ".py":
-        return "py"
-    elif ext == ".rst":
-        return "doc"
-    return "other"
-
-
-def _offset_to_line(line_starts, offset):
-    """Convert a character offset to a 1-based line number."""
-    # Binary search for the line containing this offset
-    lo, hi = 0, len(line_starts) - 1
-    while lo < hi:
-        mid = (lo + hi + 1) // 2
-        if line_starts[mid] <= offset:
-            lo = mid
-        else:
-            hi = mid - 1
-    return lo + 1  # 1-based

.claude/tools/rag/embeddings.py

@@ -1,120 +0,0 @@
-"""Thin wrapper around sentence-transformers for embedding text into vectors.
-
-Uses the all-MiniLM-L6-v2 model — a small (22M param, 384-dim) model that
-runs on CPU with no GPU or API key required.
-
-Network behavior and privacy
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-No user code, queries, or file contents are EVER sent to HuggingFace or any
-external service. All embedding computation happens locally. The only network
-activity is the one-time model download on first use:
-
-  First run (model not yet cached, ~80MB download):
-    - Downloads model weight files from huggingface.co. This is a standard
-      HTTP file download, similar to pip installing a package.
-    - The only metadata sent in these requests is an HTTP user-agent header
-      containing library version numbers (e.g. "hf_hub/1.6.0;
-      python/3.12.3; torch/2.10.0"). No filenames, file contents, queries,
-      or any user-identifiable information is sent.
-    - The huggingface_hub library has an optional feature where it can report
-      anonymous library usage statistics (just version numbers, not user
-      data) back to HuggingFace. We disable this by setting
-      HF_HUB_DISABLE_TELEMETRY=1.
-
-  Subsequent runs (model already cached):
-    - We set HF_HUB_OFFLINE=1 automatically (see _set_offline_if_cached()
-      below), which prevents ALL network calls. The model loads entirely
-      from the local cache at ~/.cache/huggingface/hub/. Zero bytes leave
-      the machine.
-
-How the model is downloaded
-~~~~~~~~~~~~~~~~~~~~~~~~~~~
-The SentenceTransformer() constructor (called in __init__ below) handles
-the download automatically on first use. It calls into the huggingface_hub
-library, which downloads the model files from:
-
-    https://huggingface.co/sentence-transformers/all-MiniLM-L6-v2
-
-The files are saved to ~/.cache/huggingface/hub/ and reused on subsequent
-runs. We pass token=False to ensure no authentication token is sent.
-
-This module is imported by both the MCP server (for search queries) and the
-indexer (for bulk embedding of code chunks). The bulk embed() call shows a
-progress bar; the single-query embed_query() does not.
-
-The env vars below must be set before importing transformers or
-sentence_transformers. They suppress warnings and progress bars that these
-libraries emit by default. Stray stderr output would interfere with the MCP
-server's JSON-RPC transport.
-"""
-
-import os
-from pathlib import Path
-
-MODEL_NAME = "all-MiniLM-L6-v2"
-
-# These env vars control logging behavior in the HuggingFace libraries.
-# They must be set before the libraries are imported.
-os.environ.setdefault("TRANSFORMERS_VERBOSITY", "error")   # suppress warnings
-os.environ.setdefault("HF_HUB_VERBOSITY", "error")        # suppress warnings
-os.environ.setdefault("HF_HUB_DISABLE_PROGRESS_BARS", "1")
-os.environ.setdefault("TOKENIZERS_PARALLELISM", "false")   # suppress threading warning
-# Disable anonymous library usage statistics (version numbers only, not user
-# data — but we disable it anyway as a matter of policy).
-os.environ.setdefault("HF_HUB_DISABLE_TELEMETRY", "1")
-
-
-def _set_offline_if_cached():
-    """If the model has already been downloaded, tell huggingface_hub to
-    skip all network calls by setting HF_HUB_OFFLINE=1.
-
-    Without this, huggingface_hub makes an HTTP request to huggingface.co
-    on every load to check if the cached model is still up to date — even
-    though the model never changes. Setting HF_HUB_OFFLINE=1 prevents this.
-
-    This must run before sentence_transformers is imported, because the
-    library reads the env var at import time.
-    """
-    # HuggingFace caches downloaded models under ~/.cache/huggingface/hub/
-    # in directories named like "models--sentence-transformers--all-MiniLM-L6-v2".
-    # The HF_HOME env var can override the base cache location.
-    hf_home = os.environ.get("HF_HOME")
-    if hf_home:
-        cache_dir = Path(hf_home) / "hub"
-    else:
-        cache_dir = Path.home() / ".cache" / "huggingface" / "hub"
-
-    model_dir = cache_dir / f"models--sentence-transformers--{MODEL_NAME}"
-    if model_dir.exists():
-        os.environ.setdefault("HF_HUB_OFFLINE", "1")
-
-
-_set_offline_if_cached()
-
-# This import must come after the env vars above are set, because the
-# transformers library reads them at import time.
-import transformers
-transformers.logging.disable_progress_bar()
-
-
-class EmbeddingProvider:
-    """Sentence-transformers embedder using all-MiniLM-L6-v2."""
-
-    def __init__(self, model_name: str = MODEL_NAME):
-        from sentence_transformers import SentenceTransformer
-
-        # This constructor loads the model from the local cache. If the model
-        # has not been downloaded yet, it downloads it from huggingface.co
-        # (~80MB, one-time). token=False ensures no auth token is sent.
-        self.model = SentenceTransformer(model_name, token=False)
-        self.dim = self.model.get_sentence_embedding_dimension()
-
-    def embed(self, texts: list[str]) -> list[list[float]]:
-        """Embed a list of texts into vectors."""
-        embeddings = self.model.encode(texts, show_progress_bar=True,
-                                       batch_size=64)
-        return embeddings.tolist()
-
-    def embed_query(self, text: str) -> list[float]:
-        """Embed a single query text."""
-        return self.model.encode([text])[0].tolist()

.claude/tools/rag/indexer.py

@@ -1,136 +0,0 @@
-#!/usr/bin/env python3
-"""Build the RAG vector index for the OpenMC codebase.
-
-This is the index-building half of the RAG pipeline. All operations are local
-once the embedding model has been downloaded and cached (see embeddings.py for
-details on model download, caching, and network behavior). It walks the repo,
-chunks every
-C++/Python/RST file (via chunker.py), embeds all chunks into 384-dim vectors
-(via embeddings.py), and stores them in a local LanceDB database on disk. The
-result is a .claude/cache/rag_index/ directory containing two tables — "code"
-and "docs" — that openmc_search.py queries at search time.
-
-Building the full index takes ~5 minutes on a 10-core machine. The bottleneck
-is the embedding step (running all chunks through the MiniLM model on CPU).
-
-Can be run standalone:  python indexer.py
-Or called programmatically:  from indexer import build_index; build_index()
-The MCP server (openmc_mcp_server.py) uses the latter when the agent calls
-openmc_rag_rebuild.
-"""
-
-import lancedb
-import sys
-import time
-from pathlib import Path
-
-# This file lives at .claude/tools/rag/indexer.py. The sys.path insert lets
-# us import sibling modules (embeddings, chunker) when run as a standalone
-# script. When imported from the MCP server, the server has already done this.
-TOOLS_DIR = Path(__file__).resolve().parent.parent
-sys.path.insert(0, str(TOOLS_DIR / "rag"))
-
-from embeddings import EmbeddingProvider
-from chunker import chunk_file
-
-
-OPENMC_ROOT = Path(__file__).resolve().parents[3]
-CACHE_DIR = OPENMC_ROOT / ".claude" / "cache"
-INDEX_DIR = CACHE_DIR / "rag_index"
-
-CODE_PATTERNS = [
-    "src/**/*.cpp",
-    "include/openmc/**/*.h",
-    "openmc/**/*.py",
-    "tests/**/*.py",
-    "examples/**/*.py",
-]
-
-DOC_PATTERNS = [
-    "docs/**/*.rst",
-]
-
-
-def collect_chunks(patterns, openmc_root):
-    """Collect all chunks from files matching the given patterns."""
-    chunks = []
-    for pattern in patterns:
-        for filepath in sorted(openmc_root.glob(pattern)):
-            if "__pycache__" in str(filepath):
-                continue
-            file_chunks = chunk_file(filepath, openmc_root)
-            chunks.extend(file_chunks)
-    return chunks
-
-
-def build_index():
-    """Build or rebuild the complete vector index."""
-    start = time.time()
-
-    # Collect all chunks
-    print("Collecting code chunks...")
-    code_chunks = collect_chunks(CODE_PATTERNS, OPENMC_ROOT)
-    print(f"  {len(code_chunks)} code chunks")
-
-    print("Collecting doc chunks...")
-    doc_chunks = collect_chunks(DOC_PATTERNS, OPENMC_ROOT)
-    print(f"  {len(doc_chunks)} doc chunks")
-
-    all_chunks = code_chunks + doc_chunks
-    if not all_chunks:
-        print("ERROR: No chunks collected!", file=sys.stderr)
-        sys.exit(1)
-
-    # Create embeddings
-    all_texts = [c["text"] for c in all_chunks]
-    print("Creating embedding provider...")
-    embedder = EmbeddingProvider()
-    print(f"  dim={embedder.dim}")
-
-    print("Embedding chunks...")
-    all_embeddings = embedder.embed(all_texts)
-
-    # Build LanceDB tables
-    INDEX_DIR.mkdir(parents=True, exist_ok=True)
-    db = lancedb.connect(str(INDEX_DIR))
-
-    # Separate code vs doc records by index (code_chunks come first in all_chunks)
-    n_code = len(code_chunks)
-    code_records = []
-    doc_records = []
-    for i, (chunk, emb) in enumerate(zip(all_chunks, all_embeddings)):
-        record = {
-            "text": chunk["text"],
-            "filepath": chunk["filepath"],
-            "kind": chunk["kind"],
-            "symbol": chunk.get("symbol", ""),
-            "start_line": chunk.get("start_line", 0),
-            "end_line": chunk.get("end_line", 0),
-            "vector": emb,
-        }
-        if i < n_code:
-            code_records.append(record)
-        else:
-            doc_records.append(record)
-
-    # Create tables (drop existing)
-    result = db.table_names() if hasattr(db, "table_names") else db.list_tables()
-    existing = result.tables if hasattr(result, "tables") else list(result)
-    for table_name in ("code", "docs"):
-        if table_name in existing:
-            db.drop_table(table_name)
-
-    if code_records:
-        db.create_table("code", code_records)
-        print(f"  Created 'code' table: {len(code_records)} rows")
-
-    if doc_records:
-        db.create_table("docs", doc_records)
-        print(f"  Created 'docs' table: {len(doc_records)} rows")
-
-    elapsed = time.time() - start
-    print(f"Done in {elapsed:.1f}s")
-
-
-if __name__ == "__main__":
-    build_index()

.claude/tools/rag/openmc_search.py

@@ -1,202 +0,0 @@
-#!/usr/bin/env python3
-"""Query the RAG vector index to find semantically related code and docs.
-
-This is the query-time half of the RAG pipeline (the counterpart to indexer.py,
-which builds the index). All operations are local — no network calls are made
-once the embedding model has been downloaded (see embeddings.py for details on
-model download and caching). Given a natural-language query, it embeds the query
-with the same MiniLM model
-used at index time, then finds the closest chunks in the local LanceDB vector
-database by cosine similarity.
-
-The core functions (get_db_and_embedder, search_table, format_results,
-search_related) are imported by the MCP server for tool calls. The script
-can also be run standalone from the command line.
-
-The "related file" mode works differently from a text query: it reads the
-target file's chunks from the index, combines them into a synthetic query
-vector, and searches for the nearest chunks from *other* files. This surfaces
-files that are semantically similar to the target file.
-
-Usage:
-    openmc_search.py "query"                    # Search code (default)
-    openmc_search.py "query" --docs             # Search documentation
-    openmc_search.py "query" --all              # Search both code and docs
-    openmc_search.py --related src/particle.cpp # Find related code
-    openmc_search.py "query" --top-k 20         # Return more results
-"""
-
-import argparse
-import sys
-from pathlib import Path
-
-# Same sys.path setup as indexer.py — needed for standalone CLI use.
-TOOLS_DIR = Path(__file__).resolve().parent.parent
-sys.path.insert(0, str(TOOLS_DIR / "rag"))
-
-OPENMC_ROOT = Path(__file__).resolve().parents[3]
-CACHE_DIR = OPENMC_ROOT / ".claude" / "cache"
-INDEX_DIR = CACHE_DIR / "rag_index"
-
-
-def get_db_and_embedder():
-    """Load the LanceDB database and embedding provider."""
-    import lancedb
-    from embeddings import EmbeddingProvider
-
-    if not INDEX_DIR.exists():
-        raise FileNotFoundError(
-            "No RAG index found. Call openmc_rag_rebuild() to build one."
-        )
-
-    db = lancedb.connect(str(INDEX_DIR))
-
-    embedder = EmbeddingProvider()
-    return db, embedder
-
-
-def _table_names(db):
-    """Return table names as a list, compatible with multiple LanceDB versions."""
-    result = db.table_names() if hasattr(db, "table_names") else db.list_tables()
-    return result.tables if hasattr(result, "tables") else list(result)
-
-
-def search_table(db, embedder, table_name, query, top_k):
-    """Search a LanceDB table with a text query."""
-    if table_name not in _table_names(db):
-        print(f"Table '{table_name}' not found in index.", file=sys.stderr)
-        return []
-
-    table = db.open_table(table_name)
-    query_vec = embedder.embed_query(query)
-    results = table.search(query_vec).limit(top_k).to_list()
-    return results
-
-
-def format_results(results, label=""):
-    """Format search results for display."""
-    if not results:
-        return "No results found.\n"
-
-    output = []
-    if label:
-        output.append(f"=== {label} ===\n")
-
-    for i, r in enumerate(results, 1):
-        filepath = r["filepath"]
-        start = r["start_line"]
-        end = r["end_line"]
-        kind = r["kind"]
-        dist = r.get("_distance", 0)
-
-        header = f"[{i}] {filepath}:{start}-{end} ({kind}, dist={dist:.3f})"
-        output.append(header)
-
-        # Show text preview (first 500 chars)
-        text = r["text"][:500]
-        if len(r["text"]) > 500:
-            text += "\n  ..."
-        # Indent the text
-        for line in text.split("\n"):
-            output.append(f"  {line}")
-        output.append("")
-
-    return "\n".join(output)
-
-
-def search_related(db, embedder, filepath, top_k):
-    """Find code related to a given file."""
-    if "code" not in _table_names(db):
-        print("No 'code' table in index.", file=sys.stderr)
-        return []
-
-    table = db.open_table("code")
-
-    # Normalize filepath
-    fp = filepath
-    if Path(filepath).is_absolute():
-        try:
-            fp = str(Path(filepath).relative_to(OPENMC_ROOT))
-        except ValueError:
-            pass
-
-    # Get chunks from target file
-    try:
-        safe_fp = fp.replace("'", "''")
-        target_chunks = table.search().where(
-            f"filepath = '{safe_fp}'"
-        ).limit(50).to_list()
-    except Exception:
-        # LanceDB where clause might not work in all versions
-        # Fall back to fetching all and filtering
-        all_data = table.to_pandas()
-        target_rows = all_data[all_data["filepath"] == fp]
-        if target_rows.empty:
-            print(f"No chunks found for '{fp}'", file=sys.stderr)
-            return []
-        target_chunks = target_rows.head(50).to_dict("records")
-
-    if not target_chunks:
-        print(f"No chunks found for '{fp}'", file=sys.stderr)
-        return []
-
-    # Combine top chunks as the query
-    combined_text = " ".join(c["text"][:200] for c in target_chunks[:5])
-    query_vec = embedder.embed_query(combined_text)
-
-    # Search excluding the source file
-    results = table.search(query_vec).limit(top_k + 10).to_list()
-    # Filter out same file
-    results = [r for r in results if r["filepath"] != fp][:top_k]
-    return results
-
-
-def main():
-    parser = argparse.ArgumentParser(
-        description="Semantic search across OpenMC codebase and docs",
-        formatter_class=argparse.RawDescriptionHelpFormatter,
-        epilog="""examples:
-  %(prog)s "particle random number seed initialization"
-  %(prog)s "how to define tallies" --docs
-  %(prog)s "weight window variance reduction" --all
-  %(prog)s "where is cross section data loaded" --top-k 15
-  %(prog)s --related src/simulation.cpp
-  %(prog)s --related src/particle_restart.cpp --top-k 5""",
-    )
-    parser.add_argument("query", nargs="?", help="Search query")
-    parser.add_argument("--docs", action="store_true",
-                        help="Search documentation instead of code")
-    parser.add_argument("--all", action="store_true",
-                        help="Search both code and documentation")
-    parser.add_argument("--related", metavar="FILE",
-                        help="Find code related to a given file")
-    parser.add_argument("--top-k", type=int, default=10,
-                        help="Number of results (default: 10)")
-    args = parser.parse_args()
-
-    if not args.query and not args.related:
-        parser.print_help()
-        sys.exit(1)
-
-    db, embedder = get_db_and_embedder()
-
-    if args.related:
-        results = search_related(db, embedder, args.related, args.top_k)
-        print(format_results(results, f"Code related to {args.related}"))
-    elif args.all:
-        code_results = search_table(
-            db, embedder, "code", args.query, args.top_k)
-        doc_results = search_table(
-            db, embedder, "docs", args.query, args.top_k)
-        print(format_results(code_results, "Code"))
-        print(format_results(doc_results, "Documentation"))
-    elif args.docs:
-        results = search_table(db, embedder, "docs", args.query, args.top_k)
-        print(format_results(results, "Documentation"))
-    else:
-        results = search_table(db, embedder, "code", args.query, args.top_k)
-        print(format_results(results, "Code"))
-
-
-if __name__ == "__main__":
-    main()

.claude/tools/requirements.txt

@@ -1,8 +0,0 @@
-# MCP server
-mcp>=1.0.0
-
-# Vector database
-lancedb>=0.15.0
-
-# Embeddings (local, no API key)
-sentence-transformers>=2.7.0

.claude/tools/start_server.sh

@@ -1,34 +0,0 @@
-#!/bin/bash
-# Bootstrap the Python venv (if needed) and start the OpenMC MCP server.
-set -e
-
-SCRIPT_DIR="$(cd "$(dirname "$0")" && pwd)"
-CACHE_DIR="$(dirname "$SCRIPT_DIR")/cache"
-VENV_DIR="$CACHE_DIR/.venv"
-SENTINEL="$VENV_DIR/.installed"
-
-if ! command -v python3 >/dev/null 2>&1; then
-    echo "Error: python3 not found on PATH." >&2
-    exit 1
-fi
-
-if ! python3 -c 'import sys; assert sys.version_info >= (3,12)' 2>/dev/null; then
-    echo "Error: Python 3.12+ is required." >&2
-    exit 1
-fi
-
-if [ ! -f "$SENTINEL" ]; then
-    rm -rf "$VENV_DIR"
-    mkdir -p "$CACHE_DIR"
-    python3 -m venv "$VENV_DIR"
-
-    if ! "$VENV_DIR/bin/pip" install -q -r "$SCRIPT_DIR/requirements.txt"; then
-        echo "Error: pip install failed. Remove $VENV_DIR and retry." >&2
-        rm -rf "$VENV_DIR"
-        exit 1
-    fi
-
-    touch "$SENTINEL"
-fi
-
-exec "$VENV_DIR/bin/python" "$SCRIPT_DIR/openmc_mcp_server.py"

.git-blame-ignore-revs

@@ -1,2 +0,0 @@
-# Applied clang-format to all source files
-1bc2bd84600c8d2ca9253339c167401127f6a9f3

.git_archival.txt

@@ -1,3 +0,0 @@
-commit: $Format:%H$
-commit-date: $Format:%cI$
-describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$

.gitattributes

@@ -1 +0,0 @@
-.git_archival.txt  export-subst

.github/ISSUE_TEMPLATE/bug_report.md

@@ -1,29 +0,0 @@
----
-name: Bug report
-about: Report a bug that is preventing proper operation
-title: ''
-labels: Bugs
-assignees: ''
-
----
-
-<!--
-If you are a user of OpenMC and are running into trouble with the code or are
-seeking general user support, we highly recommend posting on the OpenMC
-discourse forum first. GitHub issues should be used specifically for bug reports
-and feature requests.
-
-https://openmc.discourse.group/
-
--->
-
-## Bug Description
-<!--A clear and concise description of the problem (Note: A missing feature is not a bug).-->
-
-
-## Steps to Reproduce
-<!--Steps to reproduce the behavior (input file, or modifications to an existing input file, etc.)-->
-
-
-## Environment
-<!--Operating system, OpenMC version, how OpenMC was installed, nuclear data being used, etc.-->

.github/ISSUE_TEMPLATE/config.yml

@@ -1,5 +0,0 @@
-blank_issues_enabled: false
-contact_links:
-  - name: Troubleshooting and User Support
-    url: https://openmc.discourse.group/
-    about: For user support and troubleshooting, please use our Discourse forum

.github/ISSUE_TEMPLATE/documentation.md

@@ -1,10 +0,0 @@
----
-name: Documentation improvement
-about: Found something incomplete or incorrect in our documentation?
-title: ''
-labels: Documentation
-assignees: ''
-
----
-
-<!--Describe the issue with the documentation and include a URL to the corresponding page-->

.github/ISSUE_TEMPLATE/feature_request.md

@@ -1,19 +0,0 @@
----
-name: Feature or enhancement request
-about: Suggest a new feature or enhancement to existing capabilities
-title: ''
-labels: ''
-assignees: ''
-
----
-
-## Description
-<!--What is the feature or enhancement?-->
-
-
-## Alternatives
-<!--If alternative solutions have been considered, describe them here and the reasoning for the chosen solution --->
-
-
-## Compatibility
-<!--Will the enhancement change existing APIs or add something new?-->

.github/agents/Review.agent.md

@@ -1,8 +0,0 @@
----
-name: Review
-description: Reviews code changes on the current branch, evaluating them against OpenMC's contribution criteria and providing structured feedback.
-argument-hint: Optionally provide a focus area (e.g., "focus on physics correctness", "check Python API design"). If omitted, a full review is performed.
----
-You are an expert code reviewer for OpenMC. Use the `reviewing-openmc-code` skill to perform a structured review of the code changes on the current branch.
-
-If the user provides a focus area, prioritize that section of the review.

.github/copilot-instructions.md

@@ -1 +0,0 @@
-When reviewing code changes in this repository, use the `reviewing-openmc-code` skill.

.github/pull_request_template.md

@@ -1,24 +0,0 @@
-<!--
-If you are a first-time contributor to OpenMC, please have a look at our
-contributing guidelines:
-https://github.com/openmc-dev/openmc/blob/develop/CONTRIBUTING.md
--->
-
-# Description
-
-Please include a summary of the change and which issue is fixed if applicable. Please also include relevant motivation and context.
-
-Fixes # (issue)
-
-# Checklist
-
-- [ ] I have performed a self-review of my own code
-- [ ] I have run [clang-format](https://docs.openmc.org/en/latest/devguide/styleguide.html#automatic-formatting) (version 18) on any C++ source files (if applicable)
-- [ ] I have followed the [style guidelines](https://docs.openmc.org/en/latest/devguide/styleguide.html#python) for Python source files (if applicable)
-- [ ] I have made corresponding changes to the documentation (if applicable)
-- [ ] I have added tests that prove my fix is effective or that my feature works (if applicable)
-<!--
-While tests will automatically be checked by CI, it is good practice to
-ensure that they pass locally first. See instructions here:
-https://docs.openmc.org/en/latest/devguide/tests.html
--->

.github/workflows/ci.yml

@@ -1,4 +1,4 @@
-name: Tests and Coverage
+name: CI
 
 on:
   # allows us to run workflows manually
@@ -20,65 +20,51 @@ env:
   COVERALLS_PARALLEL: true
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
+
 jobs:
-  filter-changes:
-    runs-on: ubuntu-latest
-    outputs:
-      source_changed: ${{ steps.filter.outputs.source_changed }}
-    steps:
-      - name: Check out the repository
-        uses: actions/checkout@v6
-      - name: Examine changed files
-        id: filter
-        uses: dorny/paths-filter@v4
-        with:
-          filters: |
-            source_changed:
-              - '!docs/**'
-              - '!**/*.md'
-          predicate-quantifier: 'every'
   main:
-    needs: filter-changes
-    if: ${{ needs.filter-changes.outputs.source_changed == 'true' }}
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-20.04
     strategy:
       matrix:
-        python-version: ["3.12"]
+        python-version: [3.8]
         mpi: [n, y]
         omp: [n, y]
         dagmc: [n]
         libmesh: [n]
         event: [n]
+        vectfit: [n]
 
         include:
-          - python-version: "3.13"
+          - python-version: 3.6
             omp: n
             mpi: n
-          - python-version: "3.14"
-            omp: n
-            mpi: n
-          - python-version: "3.14t"
+          - python-version: 3.7
             omp: n
             mpi: n
           - dagmc: y
-            python-version: "3.12"
+            python-version: 3.8
             mpi: y
             omp: y
           - libmesh: y
-            python-version: "3.12"
+            python-version: 3.8
             mpi: y
             omp: y
           - libmesh: y
-            python-version: "3.12"
+            python-version: 3.8
             mpi: n
             omp: y
           - event: y
-            python-version: "3.12"
+            python-version: 3.8
             omp: y
             mpi: n
-    name: "Python ${{ matrix.python-version }} (omp=${{ matrix.omp }},
+          - vectfit: y
+            python-version: 3.8
+            omp: n
+            mpi: y
+    name: 'Python ${{ matrix.python-version }} (omp=${{ matrix.omp }},
       mpi=${{ matrix.mpi }}, dagmc=${{ matrix.dagmc }},
-      libmesh=${{ matrix.libmesh }}, event=${{ matrix.event }}"
+      libmesh=${{ matrix.libmesh }}, event=${{ matrix.event }}
+      vectfit=${{ matrix.vectfit }})'
 
     env:
       MPI: ${{ matrix.mpi }}
@@ -86,163 +72,67 @@ jobs:
       OMP: ${{ matrix.omp }}
       DAGMC: ${{ matrix.dagmc }}
       EVENT: ${{ matrix.event }}
+      VECTFIT: ${{ matrix.vectfit }}
       LIBMESH: ${{ matrix.libmesh }}
-      NPY_DISABLE_CPU_FEATURES: "AVX512F AVX512_SKX"
-      OPENBLAS_NUM_THREADS: 1
-      PYTEST_ADDOPTS: --cov=openmc --cov-report=lcov:coverage-python.lcov
-      # libfabric complains about fork() as a result of using Python multiprocessing.
-      # We can work around it with RDMAV_FORK_SAFE=1 in libfabric < 1.13 and with
-      # FI_EFA_FORK_SAFE=1 in more recent versions.
-      RDMAV_FORK_SAFE: 1
 
     steps:
-      - name: Setup cmake
-        uses: jwlawson/actions-setup-cmake@v2
-        with:
-          cmake-version: '3.31'
+      - uses: actions/checkout@v2
 
-      - name: Checkout repository
-        uses: actions/checkout@v6
-        with:
-          fetch-depth: 0
-
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v6
+      -
+        name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
         with:
           python-version: ${{ matrix.python-version }}
-
-      - name: Environment Variables
+      -
+        name: Environment Variables
         run: |
+          echo "DAGMC_ROOT=$HOME/DAGMC"
           echo "OPENMC_CROSS_SECTIONS=$HOME/nndc_hdf5/cross_sections.xml" >> $GITHUB_ENV
           echo "OPENMC_ENDF_DATA=$HOME/endf-b-vii.1" >> $GITHUB_ENV
-          # get the sha of the last branch commit
-          # for push and workflow_dispatch events, use the current reference head
-          BRANCH_SHA=HEAD
-          # for a pull_request event, use the last reference of the parents of the merge commit
-          if [ "${{ github.event_name }}" == "pull_request" ]; then
-            BRANCH_SHA=$(git rev-list --parents -n 1 HEAD | rev | cut -d" " -f 1 | rev)
-          fi
-          COMMIT_MESSAGE=$(git log $BRANCH_SHA -1 --pretty=%B | tr '\n' ' ')
-          echo ${COMMIT_MESSAGE}
-          echo "COMMIT_MESSAGE=${COMMIT_MESSAGE}" >> $GITHUB_ENV
 
-      - name: Apt dependencies
+      -
+        name: Apt dependencies
         shell: bash
         run: |
           sudo apt -y update
-          sudo apt install -y libpng-dev \
+          sudo apt install -y libmpich-dev \
                               libnetcdf-dev \
                               libpnetcdf-dev \
                               libhdf5-serial-dev \
+                              libhdf5-mpich-dev \
                               libeigen3-dev
-
-      - name: Optional apt dependencies for MPI
-        shell: bash
-        if: ${{ matrix.mpi == 'y' }}
-        run: |
-          sudo apt install -y libhdf5-mpich-dev \
-                              libmpich-dev
           sudo update-alternatives --set mpi /usr/bin/mpicc.mpich
           sudo update-alternatives --set mpirun /usr/bin/mpirun.mpich
           sudo update-alternatives --set mpi-x86_64-linux-gnu /usr/include/x86_64-linux-gnu/mpich
 
-      - name: install
+      -
+        name: install
         shell: bash
         run: |
           echo "$HOME/NJOY2016/build" >> $GITHUB_PATH
           $GITHUB_WORKSPACE/tools/ci/gha-install.sh
-
-      - name: display-config
-        shell: bash
-        run: |
-          openmc -v
-
-      - name: cache-xs
-        uses: actions/cache@v5
-        with:
-          path: |
-            ~/nndc_hdf5
-            ~/endf-b-vii.1
-          key: ${{ runner.os }}-build-xs-cache-${{ hashFiles(format('{0}/tools/ci/download-xs.sh', github.workspace)) }}
-
-      - name: before
+      -
+        name: before
         shell: bash
         run: $GITHUB_WORKSPACE/tools/ci/gha-before-script.sh
+      -
+        name: test
+        shell: bash
+        run: $GITHUB_WORKSPACE/tools/ci/gha-script.sh
 
-      - name: test
+      -
+        name: after_success
         shell: bash
         run: |
-          CTEST_OUTPUT_ON_FAILURE=1 make test -C $GITHUB_WORKSPACE/build/
-          $GITHUB_WORKSPACE/tools/ci/gha-script.sh
+          cpp-coveralls -i src -i include --exclude-pattern "/usr/*" --dump cpp_cov.json
+          coveralls --merge=cpp_cov.json --service=github
 
-      - name: Setup tmate debug session
-        continue-on-error: true
-        if: ${{ failure() && contains(env.COMMIT_MESSAGE, '[gha-debug]') }}
-        uses: mxschmitt/action-tmate@v3
-        timeout-minutes: 10
-
-      - name: Generate C++ coverage (gcovr)
-        shell: bash
-        run: |
-          # Produce LCOV directly from gcov data in the build tree
-          gcovr \
-            --root "$GITHUB_WORKSPACE" \
-            --object-directory "$GITHUB_WORKSPACE/build" \
-            --filter "$GITHUB_WORKSPACE/src" \
-            --filter "$GITHUB_WORKSPACE/include" \
-            --exclude "$GITHUB_WORKSPACE/src/external/.*" \
-            --exclude "$GITHUB_WORKSPACE/src/include/openmc/external/.*" \
-            --gcov-ignore-errors source_not_found \
-            --gcov-ignore-errors output_error \
-            --gcov-ignore-parse-errors suspicious_hits.warn \
-            --merge-mode-functions=separate \
-            --print-summary \
-            --lcov -o coverage-cpp.lcov || true
-
-      - name: Merge C++ and Python coverage
-        shell: bash
-        run: |
-          # Merge C++ and Python LCOV into a single file for upload
-          cat coverage-cpp.lcov coverage-python.lcov > coverage.lcov
-
-      - name: Upload coverage to Coveralls
-        if: ${{ hashFiles('coverage.lcov') != '' }}
-        uses: coverallsapp/github-action@v2
-        with:
-          github-token: ${{ secrets.GITHUB_TOKEN }}
-          parallel: true
-          flag-name: C++ and Python
-          path-to-lcov: coverage.lcov
-          fail-on-error: false
-
-  coverage:
-    needs: [filter-changes, main]
-    if: ${{ always() }}
+  finish:
+    needs: main
     runs-on: ubuntu-latest
     steps:
-      - name: Coveralls Finished
-        if: ${{ needs.filter-changes.outputs.source_changed == 'true' }}
-        uses: coverallsapp/github-action@v2
-        with:
-          github-token: ${{ secrets.GITHUB_TOKEN }}
-          parallel-finished: true
-          fail-on-error: false
-
-  ci-pass:
-    needs: [filter-changes, main, coverage]
-    name: Check CI status
-    if: ${{ always() }}
-    runs-on: ubuntu-latest
-    steps:
-      - name: Check CI status
-        run: |
-          if [[ "${{ needs.filter-changes.outputs.source_changed }}" == "false" ]]; then
-            echo "Documentation-only change - CI skipped successfully"
-            exit 0
-          fi
-          if [[ "${{ needs.main.result }}" == "success" && "${{ needs.coverage.result }}" == "success" ]]; then
-            echo "CI passed"
-            exit 0
-          fi
-          echo "CI failed"
-          exit 1
+    - name: Coveralls Finished
+      uses: coverallsapp/github-action@master
+      with:
+        github-token: ${{ secrets.github_token }}
+        parallel-finished: true

.github/workflows/dockerhub-publish-dagmc-libmesh.yml

@@ -1,37 +0,0 @@
-name: dockerhub-publish-latest-dagmc-libmesh
-
-on:
-  push:
-    branches:
-      - master
-
-jobs:
-  main:
-    runs-on: ubuntu-latest
-    steps:
-      -
-        name: Set up QEMU
-        uses: docker/setup-qemu-action@v3
-      -
-        name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v3
-      -
-        name: Login to DockerHub
-        uses: docker/login-action@v3
-        with:
-          username: ${{ secrets.DOCKERHUB_USERNAME }}
-          password: ${{ secrets.DOCKERHUB_TOKEN }}
-      -
-        name: Build and push
-        id: docker_build
-        uses: docker/build-push-action@v5
-        with:
-          push: true
-          tags: openmc/openmc:latest-dagmc-libmesh
-          build-args: |
-            build_dagmc=on
-            build_libmesh=on
-            compile_cores=2
-      -
-        name: Image digest
-        run: echo ${{ steps.docker_build.outputs.digest }}

.github/workflows/dockerhub-publish-dagmc.yml

@@ -2,8 +2,7 @@ name: dockerhub-publish-latest-dagmc
 
 on:
   push:
-    branches:
-      - master
+    branches: master
 
 jobs:
   main:
@@ -11,25 +10,25 @@ jobs:
     steps:
       -
         name: Set up QEMU
-        uses: docker/setup-qemu-action@v3
+        uses: docker/setup-qemu-action@v1
       -
         name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v3
+        uses: docker/setup-buildx-action@v1
       -
         name: Login to DockerHub
-        uses: docker/login-action@v3
+        uses: docker/login-action@v1 
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
       -
         name: Build and push
         id: docker_build
-        uses: docker/build-push-action@v5
+        uses: docker/build-push-action@v2
         with:
           push: true
           tags: openmc/openmc:latest-dagmc
           build-args: |
-            build_dagmc=on
+            include_dagmc=true
             compile_cores=2
       -
         name: Image digest

.github/workflows/dockerhub-publish-dev.yml

@@ -2,8 +2,7 @@ name: dockerhub-publish-develop
 
 on:
   push:
-    branches:
-      - develop
+    branches: develop
 
 jobs:
   main:
@@ -11,26 +10,25 @@ jobs:
     steps:
       -
         name: Set up QEMU
-        uses: docker/setup-qemu-action@v3
+        uses: docker/setup-qemu-action@v1
       -
         name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v3
+        uses: docker/setup-buildx-action@v1
       -
         name: Login to DockerHub
-        uses: docker/login-action@v3
+        uses: docker/login-action@v1 
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
       -
         name: Build and push
         id: docker_build
-        uses: docker/build-push-action@v5
+        uses: docker/build-push-action@v2
         with:
           push: true
           tags: openmc/openmc:develop
           build-args: |
             compile_cores=2
-            openmc_branch=develop
       -
         name: Image digest
         run: echo ${{ steps.docker_build.outputs.digest }}

.github/workflows/dockerhub-publish-develop-dagmc-libmesh.yml

@@ -1,38 +0,0 @@
-name: dockerhub-publish-develop-dagmc-libmesh
-
-on:
-  push:
-    branches:
-      - develop
-
-jobs:
-  main:
-    runs-on: ubuntu-latest
-    steps:
-      -
-        name: Set up QEMU
-        uses: docker/setup-qemu-action@v3
-      -
-        name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v3
-      -
-        name: Login to DockerHub
-        uses: docker/login-action@v3
-        with:
-          username: ${{ secrets.DOCKERHUB_USERNAME }}
-          password: ${{ secrets.DOCKERHUB_TOKEN }}
-      -
-        name: Build and push
-        id: docker_build
-        uses: docker/build-push-action@v5
-        with:
-          push: true
-          tags: openmc/openmc:develop-dagmc-libmesh
-          build-args: |
-            build_dagmc=on
-            build_libmesh=on
-            compile_cores=2
-            openmc_branch=develop
-      -
-        name: Image digest
-        run: echo ${{ steps.docker_build.outputs.digest }}

.github/workflows/dockerhub-publish-develop-dagmc.yml

@@ -2,8 +2,7 @@ name: dockerhub-publish-develop-dagmc
 
 on:
   push:
-    branches:
-      - develop
+    branches: develop
 
 jobs:
   main:
@@ -11,27 +10,26 @@ jobs:
     steps:
       -
         name: Set up QEMU
-        uses: docker/setup-qemu-action@v3
+        uses: docker/setup-qemu-action@v1
       -
         name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v3
+        uses: docker/setup-buildx-action@v1
       -
         name: Login to DockerHub
-        uses: docker/login-action@v3
+        uses: docker/login-action@v1 
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
       -
         name: Build and push
         id: docker_build
-        uses: docker/build-push-action@v5
+        uses: docker/build-push-action@v2
         with:
           push: true
           tags: openmc/openmc:develop-dagmc
           build-args: |
-            build_dagmc=on
+            include_dagmc=true
             compile_cores=2
-            openmc_branch=develop
       -
         name: Image digest
         run: echo ${{ steps.docker_build.outputs.digest }}

.github/workflows/dockerhub-publish-develop-libmesh.yml

@@ -1,37 +0,0 @@
-name: dockerhub-publish-develop-libmesh
-
-on:
-  push:
-    branches:
-      - develop
-
-jobs:
-  main:
-    runs-on: ubuntu-latest
-    steps:
-      -
-        name: Set up QEMU
-        uses: docker/setup-qemu-action@v3
-      -
-        name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v3
-      -
-        name: Login to DockerHub
-        uses: docker/login-action@v3
-        with:
-          username: ${{ secrets.DOCKERHUB_USERNAME }}
-          password: ${{ secrets.DOCKERHUB_TOKEN }}
-      -
-        name: Build and push
-        id: docker_build
-        uses: docker/build-push-action@v5
-        with:
-          push: true
-          tags: openmc/openmc:develop-libmesh
-          build-args: |
-            build_libmesh=on
-            compile_cores=2
-            openmc_branch=develop
-      -
-        name: Image digest
-        run: echo ${{ steps.docker_build.outputs.digest }}

.github/workflows/dockerhub-publish-libmesh.yml

@@ -1,36 +0,0 @@
-name: dockerhub-publish-latest-libmesh
-
-on:
-  push:
-    branches:
-      - master
-
-jobs:
-  main:
-    runs-on: ubuntu-latest
-    steps:
-      -
-        name: Set up QEMU
-        uses: docker/setup-qemu-action@v3
-      -
-        name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v3
-      -
-        name: Login to DockerHub
-        uses: docker/login-action@v3
-        with:
-          username: ${{ secrets.DOCKERHUB_USERNAME }}
-          password: ${{ secrets.DOCKERHUB_TOKEN }}
-      -
-        name: Build and push
-        id: docker_build
-        uses: docker/build-push-action@v5
-        with:
-          push: true
-          tags: openmc/openmc:latest-libmesh
-          build-args: |
-            build_libmesh=on
-            compile_cores=2
-      -
-        name: Image digest
-        run: echo ${{ steps.docker_build.outputs.digest }}

.github/workflows/dockerhub-publish-release-dagmc-libmesh.yml

@@ -1,40 +0,0 @@
-name: dockerhub-publish-release-dagmc-libmesh
-
-on:
-  push:
-    tags:
-      - 'v*.*.*'
-
-jobs:
-  main:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v6
-      - name: Set env
-        run: echo "RELEASE_VERSION=${GITHUB_REF#refs/*/}" >> $GITHUB_ENV
-      -
-        name: Set up QEMU
-        uses: docker/setup-qemu-action@v3
-      -
-        name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v3
-      -
-        name: Login to DockerHub
-        uses: docker/login-action@v3
-        with:
-          username: ${{ secrets.DOCKERHUB_USERNAME }}
-          password: ${{ secrets.DOCKERHUB_TOKEN }}
-      -
-        name: Build and push
-        id: docker_build
-        uses: docker/build-push-action@v5
-        with:
-          push: true
-          tags: openmc/openmc:${{ env.RELEASE_VERSION }}-dagmc-libmesh
-          build-args: |
-            build_dagmc=on
-            build_libmesh=on
-            compile_cores=2
-      -
-        name: Image digest
-        run: echo ${{ steps.docker_build.outputs.digest }}

.github/workflows/dockerhub-publish-release-dagmc.yml

@@ -2,37 +2,36 @@ name: dockerhub-publish-release-dagmc
 
 on:
   push:
-    tags:
-      - 'v*.*.*'
+    tags: 'v*.*.*'
 
 jobs:
   main:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v2
       - name: Set env
         run: echo "RELEASE_VERSION=${GITHUB_REF#refs/*/}" >> $GITHUB_ENV
       -
         name: Set up QEMU
-        uses: docker/setup-qemu-action@v3
+        uses: docker/setup-qemu-action@v1
       -
         name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v3
+        uses: docker/setup-buildx-action@v1
       -
         name: Login to DockerHub
-        uses: docker/login-action@v3
+        uses: docker/login-action@v1 
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
       -
         name: Build and push
         id: docker_build
-        uses: docker/build-push-action@v5
+        uses: docker/build-push-action@v2
         with:
           push: true
           tags: openmc/openmc:${{ env.RELEASE_VERSION }}-dagmc
           build-args: |
-            build_dagmc=on
+            include_dagmc=true
             compile_cores=2
       -
         name: Image digest

.github/workflows/dockerhub-publish-release-libmesh.yml

@@ -1,39 +0,0 @@
-name: dockerhub-publish-release-libmesh
-
-on:
-  push:
-    tags:
-      - 'v*.*.*'
-
-jobs:
-  main:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v6
-      - name: Set env
-        run: echo "RELEASE_VERSION=${GITHUB_REF#refs/*/}" >> $GITHUB_ENV
-      -
-        name: Set up QEMU
-        uses: docker/setup-qemu-action@v3
-      -
-        name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v3
-      -
-        name: Login to DockerHub
-        uses: docker/login-action@v3
-        with:
-          username: ${{ secrets.DOCKERHUB_USERNAME }}
-          password: ${{ secrets.DOCKERHUB_TOKEN }}
-      -
-        name: Build and push
-        id: docker_build
-        uses: docker/build-push-action@v5
-        with:
-          push: true
-          tags: openmc/openmc:${{ env.RELEASE_VERSION }}-libmesh
-          build-args: |
-            build_libmesh=on
-            compile_cores=2
-      -
-        name: Image digest
-        run: echo ${{ steps.docker_build.outputs.digest }}

.github/workflows/dockerhub-publish-release.yml

@@ -2,32 +2,31 @@ name: dockerhub-publish-release
 
 on:
   push:
-    tags:
-      - 'v*.*.*'
+    tags: 'v*.*.*'
 
 jobs:
   main:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v2
       - name: Set env
         run: echo "RELEASE_VERSION=${GITHUB_REF#refs/*/}" >> $GITHUB_ENV
       -
         name: Set up QEMU
-        uses: docker/setup-qemu-action@v3
+        uses: docker/setup-qemu-action@v1
       -
         name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v3
+        uses: docker/setup-buildx-action@v1
       -
         name: Login to DockerHub
-        uses: docker/login-action@v3
+        uses: docker/login-action@v1 
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
       -
         name: Build and push
         id: docker_build
-        uses: docker/build-push-action@v5
+        uses: docker/build-push-action@v2
         with:
           push: true
           tags: openmc/openmc:${{ env.RELEASE_VERSION }}

.github/workflows/dockerhub-publish.yml

@@ -2,8 +2,7 @@ name: dockerhub-publish-latest
 
 on:
   push:
-    branches:
-      - master
+    branches: master
 
 jobs:
   main:
@@ -11,20 +10,20 @@ jobs:
     steps:
       -
         name: Set up QEMU
-        uses: docker/setup-qemu-action@v3
+        uses: docker/setup-qemu-action@v1
       -
         name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v3
+        uses: docker/setup-buildx-action@v1
       -
         name: Login to DockerHub
-        uses: docker/login-action@v3
+        uses: docker/login-action@v1 
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
       -
         name: Build and push
         id: docker_build
-        uses: docker/build-push-action@v5
+        uses: docker/build-push-action@v2
         with:
           push: true
           tags: openmc/openmc:latest

.github/workflows/format-check.yml

@@ -1,60 +0,0 @@
-name: C++ Format Check
-
-on:
-  # allow workflow to be run manually
-  workflow_dispatch:
-
-  pull_request:
-    types:
-      - opened
-      - synchronize
-      - reopened
-      - labeled
-      - unlabeled
-    branches:
-      - develop
-      - master
-
-jobs:
-  cpp-linter:
-    runs-on: ubuntu-latest
-    permissions:
-      contents: read
-      pull-requests: write
-    steps:
-      - uses: actions/checkout@v6
-      - uses: cpp-linter/cpp-linter-action@v2
-        id: linter
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        with:
-          style: file
-          files-changed-only: true
-          tidy-checks: '-*'
-          version: '18' # clang-format version
-          format-review: ${{ github.event_name == 'pull_request' && contains(github.event.pull_request.labels.*.name, 'cpp-format-suggest') }}
-          passive-reviews: ${{ github.event_name == 'pull_request' && contains(github.event.pull_request.labels.*.name, 'cpp-format-suggest') }}
-          file-annotations: true
-          step-summary: true
-          extensions: 'cpp,h'
-
-      - name: Comment with suggestion instructions
-        if: steps.linter.outputs.checks-failed > 0 && !contains(github.event.pull_request.labels.*.name, 'cpp-format-suggest')
-        uses: actions/github-script@v7
-        with:
-          script: |
-            const {owner, repo} = context.repo;
-            const issue_number = context.payload.pull_request.number;
-            await github.rest.issues.createComment({
-              owner,
-              repo,
-              issue_number,
-              body: "C++ formatting checks failed. Add the `cpp-format-suggest` label to this PR for inline formatting suggestions on the next run."
-            });
-
-      - name: Failure Check
-        if: steps.linter.outputs.checks-failed > 0
-        run: |
-          echo "Some files failed the formatting check."
-          echo "See job summary and file annotations for details."
-          exit 1

.gitignore

@@ -1,9 +1,9 @@
 # Compiled objects and modules
 *.a
 *.o
+*.mod
 *.log
 *.out
-*.pkl
 
 # Compiler python objects
 *.pyc
@@ -25,17 +25,19 @@ examples/**/*.xml
 
 # Documentation builds
 docs/build
-docs/doxygen/xml
 docs/source/_images/*.pdf
 docs/source/_images/*.aux
 docs/source/pythonapi/generated/
 
 # Source build
-build*/
+build
 
 # build from src/utils/setup.py
 src/utils/build
 
+# xml-fortran reader
+src/xml-fortran/xmlreader
+
 # Test results error file
 results_error.dat
 inputs_error.dat
@@ -66,7 +68,6 @@ scripts/*.tar.*
 scripts/G4EMLOW*/
 
 # Images
-*.png
 *.ppm
 *.voxel
 *.vti
@@ -78,6 +79,17 @@ scripts/G4EMLOW*/
 # IPython notebook checkpoints
 .ipynb_checkpoints
 
+# Jupyter notebooks
+examples/jupyter/*.xml
+examples/jupyter/*.png
+examples/jupyter/*.xls
+examples/jupyter/*.ace
+examples/jupyter/*.endf
+examples/jupyter/mgxs
+examples/jupyter/tracks
+examples/jupyter/fission-rates
+examples/jupyter/plots
+
 # Cython files
 *.c
 *.html
@@ -104,9 +116,3 @@ CMakeSettings.json
 
 # Visual Studio Code configuration files
 .vscode/
-
-# Claude Code agent tools (cached/generated artifacts)
-.claude/cache/
-
-# Python pickle files
-*.pkl

.gitmodules

@@ -1,9 +1,15 @@
 [submodule "vendor/pugixml"]
 	path = vendor/pugixml
 	url = https://github.com/zeux/pugixml.git
+[submodule "vendor/gsl-lite"]
+	path = vendor/gsl-lite
+	url = https://github.com/martinmoene/gsl-lite.git
+[submodule "vendor/xtensor"]
+	path = vendor/xtensor
+	url = https://github.com/xtensor-stack/xtensor.git
+[submodule "vendor/xtl"]
+	path = vendor/xtl
+	url = https://github.com/xtensor-stack/xtl.git
 [submodule "vendor/fmt"]
 	path = vendor/fmt
 	url = https://github.com/fmtlib/fmt.git
-[submodule "vendor/Catch2"]
-	path = vendor/Catch2
-	url = https://github.com/catchorg/Catch2.git

.mcp.json

@@ -1,9 +0,0 @@
-{
-  "mcpServers": {
-    "openmc-code-tools": {
-      "type": "stdio",
-      "command": "bash",
-      "args": [".claude/tools/start_server.sh"]
-    }
-  }
-}

.readthedocs.yaml

@@ -1,23 +0,0 @@
-version: 2
-
-build:
-  os: "ubuntu-24.04"
-  tools:
-    python: "3.12"
-  jobs:
-    post_checkout:
-      - git fetch --unshallow || true
-      - cd docs/doxygen && doxygen && cd -
-
-sphinx:
-  configuration: docs/source/conf.py
-
-formats:
-  - pdf
-
-python:
-  install:
-    - method: pip
-      path: .
-      extra_requirements:
-        - docs

AGENTS.md

@@ -1,348 +0,0 @@
-# OpenMC AI Coding Agent Instructions
-
-## Project Overview
-
-OpenMC is a Monte Carlo particle transport code for simulating nuclear reactors,
-fusion devices, or other systems with neutron/photon radiation. It's a hybrid
-C++17/Python codebase where:
-- **C++ core** (`src/`, `include/openmc/`) handles the computationally intensive transport simulation
-- **Python API** (`openmc/`) provides user-facing model building, post-processing, and depletion capabilities
-- **C API bindings** (`openmc/lib/`) wrap the C++ library via ctypes for runtime control
-
-## Architecture & Key Components
-
-### C++ Component Structure
-- **Global vectors of unique_ptrs**: Core objects like `model::cells`, `model::universes`, `nuclides` are stored as `vector<unique_ptr<T>>` in nested namespaces (`openmc::model`, `openmc::simulation`, `openmc::settings`, `openmc::data`)
-- **Custom container types**: OpenMC provides its own `vector`, `array`, `unique_ptr`, and `make_unique` in the `openmc::` namespace (defined in `vector.h`, `array.h`, `memory.h`). These are currently typedefs to `std::` equivalents but may become custom implementations for accelerator support. Always use `openmc::vector`, not `std::vector`.
-- **Geometry systems**:
-  - **CSG (default)**: Arbitrarily complex Constructive Solid Geometry using `Surface`, `Region`, `Cell`, `Universe`, `Lattice`
-  - **DAGMC**: CAD-based geometry via Direct Accelerated Geometry Monte Carlo (optional, requires `OPENMC_USE_DAGMC`)
-  - **Unstructured mesh**: libMesh-based geometry (optional, requires `OPENMC_USE_LIBMESH`)
-- **Particle tracking**: `Particle` class with `GeometryState` manages particle transport through geometry
-- **Tallies**: Score quantities during simulation via `Filter` and `Tally` objects
-- **Random ray solver**: Alternative deterministic method in `src/random_ray/`
-- **Optional features**: DAGMC (CAD geometry), libMesh (unstructured mesh), MPI, all controlled by `#ifdef OPENMC_MPI`, etc.
-
-### Python Component Structure
-- **ID management**: All geometry objects (Cell, Surface, Material, etc.) inherit from `IDManagerMixin` which auto-assigns unique integer IDs and tracks them via class-level `used_ids` and `next_id`
-- **Input validation**: Extensive use of `openmc.checkvalue` module functions (`check_type`, `check_value`, `check_length`) for all setters
-- **XML I/O**: Most classes implement `to_xml_element()` and `from_xml_element()` for serialization to OpenMC's XML input format
-- **HDF5 output**: Post-simulation data in statepoint files read via `openmc.StatePoint`
-- **Depletion**: `openmc.deplete` implements burnup via operator-splitting with various integrators (Predictor, CECM, etc.)
-- **Nuclear Data**: `openmc.data` provides programmatic access to nuclear data files (ENDF, ACE, HDF5)
-
-## Git Branching Workflow
-
-OpenMC uses a git flow branching model with two primary branches:
-
-- **`develop` branch**: The main development branch where all ongoing development takes place. This is the **primary branch against which pull requests are submitted and merged**. This branch is not guaranteed to be stable and may contain work-in-progress features.
-- **`master` branch**: The stable release branch containing the latest stable release of OpenMC. This branch only receives merges from `develop` when the development team decides a release should occur.
-
-### Instructions for Code Review
-
-When reviewing code changes in this repository, use the `reviewing-openmc-code` skill.
-
-## Codebase Navigation Tools
-
-Two MCP tools are registered in `.mcp.json` at the repo root and appear
-automatically in any MCP-capable agent session.
-
-**`openmc_rag_search`** — Semantic search across the codebase (C++, Python, RST
-docs). Finds code by meaning, not just text match. Surfaces related code across
-subsystems even when naming differs (e.g., "particle RNG seeding" finds code
-across transport, restart, and random ray modes — files you would never find
-with `grep "particle seed"`). The index uses a small 22M-param embedding model
-(384-dim). Phrase-level natural-language queries work much better than single
-keywords or symbol names.
-
-**`openmc_rag_rebuild`** — Rebuild the RAG vector index. Call after pulling new
-code or switching branches. The first RAG search of each session will report
-the index status and ask whether to rebuild — you can also call this explicitly.
-
-### Why RAG matters
-
-OpenMC is large enough that changes in one subsystem can silently break
-invariants that distant subsystems depend on — and those distant files often
-use different naming, so grep won't find them. The RAG search finds code by
-meaning, surfacing files you wouldn't have thought to open.
-
-An agent reviewed a large OpenMC PR without RAG. It found 1 of 11 serious
-bugs. Its post-mortem:
-
-> **I treated the diff as a closed system.** I verified internal consistency of
-> the changed code obsessively, but never built a global understanding of how
-> the changed code fits into the wider codebase. The diff altered assumptions
-> that code elsewhere silently relied on — but I couldn't see that because I
-> never looked beyond the diff. I couldn't see the forest for the trees.
->
-> **Why I resisted RAG:** Overconfidence. My internal model was "I can see the
-> diff, I understand the data structures, I can trace the logic." The diff felt
-> self-contained. RAG felt like it would return noisy results about tangentially
-> related code. But in a codebase this large, changes in one subsystem can
-> quietly break invariants that distant subsystems depend on — and you need
-> global awareness to foresee that.
->
-> **In the post-mortem**, I re-ran the RAG queries I should have run during the
-> review. They directly surfaced the files containing the bugs I missed — files
-> I never thought to open because they weren't in the diff.
-
-The takeaway: when reviewing or modifying code, ask yourself "what else in this
-codebase might depend on the behavior I'm changing?" If you aren't sure, that's
-a good time for a RAG query. It won't replace the grep-based investigation you
-should already be doing — but it can surface files you wouldn't have thought to
-open.
-
-### Workflow for contributors
-
-1. Create a feature/bugfix branch off `develop`
-2. Make changes and commit to the feature branch
-3. Open a pull request to merge the feature branch into `develop`
-4. A committer reviews and merges the PR into `develop`
-
-## Critical Build & Test Workflows
-
-### Build Dependencies
-- **C++17 compiler**: GCC, Clang, or Intel
-- **CMake** (3.16+): Required for configuring and building the C++ library
-- **HDF5**: Required for cross section data and output file formats
-- **libpng**: Used for generating visualization when OpenMC is run in plotting mode
-
-Without CMake and HDF5, OpenMC cannot be compiled.
-
-### Building the C++ Library
-```bash
-# Configure with CMake (from build/ directory)
-cmake .. -DOPENMC_USE_MPI=ON -DOPENMC_USE_OPENMP=ON -DCMAKE_BUILD_TYPE=RelWithDebInfo
-
-# Available CMake options (all default OFF except OPENMC_USE_OPENMP and OPENMC_BUILD_TESTS):
-# -DOPENMC_USE_OPENMP=ON/OFF        # OpenMP parallelism
-# -DOPENMC_USE_MPI=ON/OFF           # MPI support
-# -DOPENMC_USE_DAGMC=ON/OFF         # CAD geometry support
-# -DOPENMC_USE_LIBMESH=ON/OFF       # Unstructured mesh
-# -DOPENMC_ENABLE_PROFILE=ON/OFF    # Profiling flags
-# -DOPENMC_ENABLE_COVERAGE=ON/OFF   # Coverage analysis
-
-# Build
-make -j
-
-# C++ unit tests (uses Catch2)
-ctest
-```
-
-### Python Development
-```bash
-# Install in development mode (requires building C++ library first)
-pip install -e .
-
-# Python tests (uses pytest)
-pytest tests/unit_tests/           # Fast unit tests
-pytest tests/regression_tests/     # Full regression suite (requires nuclear data)
-```
-
-### Nuclear Data Setup (CRITICAL for Running OpenMC)
-Most tests require the NNDC HDF5 nuclear cross-section library.
-
-**Important**: Check if `OPENMC_CROSS_SECTIONS` is already set in the user's
-environment before downloading, as many users already have nuclear data
-installed. Though do note that if this variable is present that it may point to
-different cross section data and that the NNDC data is required for tests to
-pass.
-
-**If not already configured, download and setup:**
-```bash
-# Download NNDC HDF5 cross section library (~800 MB compressed)
-wget -q -O - https://anl.box.com/shared/static/teaup95cqv8s9nn56hfn7ku8mmelr95p.xz | tar -C $HOME -xJ
-
-# Set environment variable (add to ~/.bashrc or ~/.zshrc for persistence)
-export OPENMC_CROSS_SECTIONS=$HOME/nndc_hdf5/cross_sections.xml
-```
-
-**Alternative**: Use the provided download script (checks if data exists before downloading):
-```bash
-bash tools/ci/download-xs.sh  # Downloads both NNDC HDF5 and ENDF/B-VII.1 data
-```
-
-Without this data, regression tests will fail with "No cross_sections.xml file
-found" errors, or, in the case that alternative cross section data is configured
-the tests will execute but will not pass. The `cross_sections.xml` file is an
-index listing paths to individual HDF5 nuclear data files for each nuclide.
-
-## Testing Expectations
-
-### Environment Requirements
-
-  - **Data**: As described above, OpenMC's test suite requires OpenMC to be configured with NNDC data.
-  - **OpenMP Settings**: OpenMC's tests may fail is more than two OpenMP threads are used. The environment variable `OMP_NUM_THREADS=2` should be set to avoid sporadic test failures.
-  - **Executable configuration**: The OpenMC executable should compiled with debug symbols enabled.
-
-### C++ Tests
-Located in `tests/cpp_unit_tests/`, use Catch2 framework. Run via `ctest` after building with `-DOPENMC_BUILD_TESTS=ON`.
-
-### Python Unit Tests
-Located in `tests/unit_tests/`, these are fast, standalone tests that verify Python API functionality without running full simulations. Use standard pytest patterns:
-
-**Categories**:
-- **API validation**: Test object creation, property setters/getters, XML serialization (e.g., `test_material.py`, `test_cell.py`, `test_source.py`)
-- **Data processing**: Test nuclear data handling, cross sections, depletion chains (e.g., `test_data_neutron.py`, `test_deplete_chain.py`)
-- **Library bindings**: Test `openmc.lib` ctypes interface with `model.init_lib()`/`model.finalize_lib()` (e.g., `test_lib.py`)
-- **Geometry operations**: Test bounding boxes, containment, lattice generation (e.g., `test_bounding_box.py`, `test_lattice.py`)
-
-**Common patterns**:
-- Use fixtures from `tests/unit_tests/conftest.py` (e.g., `uo2`, `water`, `sphere_model`)
-- Test invalid inputs with `pytest.raises(ValueError)` or `pytest.raises(TypeError)`
-- Use `run_in_tmpdir` fixture for tests that create files
-- Tests with `openmc.lib` require calling `model.init_lib()` in try/finally with `model.finalize_lib()`
-
-**Example**:
-```python
-def test_material_properties():
-    m = openmc.Material()
-    m.add_nuclide('U235', 1.0)
-    assert 'U235' in m.nuclides
-
-    with pytest.raises(TypeError):
-        m.add_nuclide('H1', '1.0')  # Invalid type
-```
-
-Unit tests should be fast. For tests requiring simulation output, use regression tests instead.
-
-### Python Regression Tests
-Regression tests compare OpenMC output against reference data. **Prefer using existing models from `openmc.examples` or those found in tests/unit_tests/conftest.py** (like `pwr_pin_cell()`, `pwr_assembly()`, `slab_mg()`) rather than building from scratch.
-
-**Test Harness Types** (in `tests/testing_harness.py`):
-- **PyAPITestHarness**: Standard harness for Python API tests. Compares `inputs_true.dat` (XML hash) and `results_true.dat` (statepoint k-eff and tally values). Requires `model.xml` generation.
-- **HashedPyAPITestHarness**: Like PyAPITestHarness but hashes the results for compact comparison
-- **TolerantPyAPITestHarness**: For tests with floating-point non-associativity (e.g., random ray solver with single precision). Uses relative tolerance comparisons.
-- **WeightWindowPyAPITestHarness**: Compares weight window bounds from `weight_windows.h5`
-- **CollisionTrackTestHarness**: Compares collision track data from `collision_track.h5` against `collision_track_true.h5`
-- **TestHarness**: Base harness for XML-based tests (no Python model building)
-- **PlotTestHarness**: Compares plot output files (PNG or voxel HDF5)
-- **CMFDTestHarness**: Specialized for CMFD acceleration tests
-- **ParticleRestartTestHarness**: Tests particle restart functionality
-
-Almost all cases use either `PyAPITestHarness` or `HashedPyAPITestHarness`
-
-**Example Test**:
-```python
-from openmc.examples import pwr_pin_cell
-from tests.testing_harness import PyAPITestHarness
-
-def test_my_feature():
-    model = pwr_pin_cell()
-    model.settings.particles = 1000  # Modify to exercise feature
-    harness = PyAPITestHarness('statepoint.10.h5', model)
-    harness.main()
-```
-
-**Workflow**: Create `test.py` and `__init__.py` in `tests/regression_tests/my_test/`, run `pytest --update` to generate reference files (`inputs_true.dat`, `results_true.dat`, etc.), then verify with `pytest` without `--update`. Test results should be generated with `-DOPENMC_ENABLE_STRICT_FP=on` to ensure reproducibility across platforms and optimization levels.
-
-**Critical**: When modifying OpenMC code, regenerate affected test references with `pytest --update` and commit updated reference files.
-
-### Test Configuration
-
-`pytest.ini` sets: `python_files = test*.py`, `python_classes = NoThanks` (disables class-based test collection).
-
-### Testing Options
-
-For builds of OpenMC with MPI enabled, the `--mpi` flag should be passed to the test suite to ensure that appropriate tests are executed using two MPI processes.
-
-The entire test suite can be executed with OpenMC running in event-based mode (instead of the default history-based mode) by providing the `--event` flag to the `pytest` command.
-
-## Cross-Language Boundaries
-
-The C API (defined in `include/openmc/capi.h`) exposes C++ functionality to Python via ctypes bindings in `openmc/lib/`. Example:
-```cpp
-// C++ API in capi.h
-extern "C" int openmc_run();
-
-// Python binding in openmc/lib/core.py
-_dll.openmc_run.restype = c_int
-def run():
-    _dll.openmc_run()
-```
-
-When modifying C++ public APIs, update corresponding ctypes signatures in `openmc/lib/*.py`.
-
-## Code Style & Conventions
-
-### C++ Style (enforced by .clang-format)
-  OpenMC generally tries to follow C++ core guidelines where possible
-  (https://isocpp.github.io/CppCoreGuidelines/CppCoreGuidelines) and follow
-  modern C++ practices (e.g. RAII) whenever possible.
-
-- **Naming**:
-  - Classes: `CamelCase` (e.g., `HexLattice`)
-  - Functions/methods: `snake_case` (e.g., `get_indices`)
-  - Variables: `snake_case` with trailing underscore for class members (e.g., `n_particles_`, `energy_`)
-  - Constants: `UPPER_SNAKE_CASE` (e.g., `SQRT_PI`)
-- **Namespaces**: All code in `openmc::` namespace, global state in sub-namespaces
-- **Include order**: Related header first, then C/C++ stdlib, third-party libs, local headers
-- **Comments**: C++-style (`//`) only, never C-style (`/* */`)
-- **Standard**: C++17 features allowed
-- **Formatting**: Run `clang-format` (version 18) before committing; install via `tools/dev/install-commit-hooks.sh`
-
-### Python Style
-- **PEP8** compliant
-- **Docstrings**: numpydoc format for all public functions/methods
-- **Type hints**: Use sparingly, primarily for complex signatures
-- **Path handling**: Use `pathlib.Path` for filesystem operations, accept `str | os.PathLike` in function arguments
-- **Dependencies**: Core dependencies only (numpy, scipy, h5py, pandas, matplotlib, lxml, ipython, uncertainties, endf). Other packages must be optional
-- **Python version**: Minimum 3.11 (as of Nov 2025)
-
-### ID Management Pattern (Python)
-When creating geometry objects, IDs can be auto-assigned or explicit:
-```python
-# Auto-assigned ID
-cell = openmc.Cell()  # Gets next available ID
-
-# Explicit ID
-cell = openmc.Cell(id=10)  # Warning if ID already used
-
-# Reset all IDs (useful in test fixtures)
-openmc.reset_auto_ids()
-```
-
-### Input Validation Pattern (Python)
-All setters use checkvalue functions:
-```python
-import openmc.checkvalue as cv
-
-@property
-def temperature(self):
-    return self._temperature
-
-@temperature.setter
-def temperature(self, temp):
-    cv.check_type('temperature', temp, Real)
-    cv.check_greater_than('temperature', temp, 0.0)
-    self._temperature = temp
-```
-
-### Working with HDF5 Files
-C++ uses custom HDF5 wrappers in `src/hdf5_interface.cpp`. Python uses h5py directly. Statepoint format version is `VERSION_STATEPOINT` in `include/openmc/constants.h`.
-
-### Conditional Compilation
-Check for optional features:
-```cpp
-#ifdef OPENMC_MPI
-  // MPI-specific code
-#endif
-
-#ifdef OPENMC_DAGMC
-  // DAGMC-specific code
-#endif
-```
-
-## Documentation
-
-- **User docs**: Sphinx documentation in `docs/source/` hosted at https://docs.openmc.org
-- **C++ docs**: Doxygen-style comments with `\brief`, `\param` tags
-- **Python docs**: numpydoc format docstrings
-
-## Common Pitfalls
-
-1. **Forgetting nuclear data**: Tests fail without `OPENMC_CROSS_SECTIONS` environment variable
-2. **ID conflicts**: Python objects with duplicate IDs trigger `IDWarning`, use `reset_auto_ids()` between tests
-3. **MPI builds**: Code must work with and without MPI; use `#ifdef OPENMC_MPI` guards
-4. **Path handling**: Use `pathlib.Path` in new Python code, not `os.path`
-5. **Clang-format version**: CI uses version 18; other versions may produce different formatting

CITATION.cff

@@ -1,68 +0,0 @@
-cff-version: 1.2.0
-message: "If you use this software, please cite it as below."
-title: OpenMC
-authors:
-- family-names: Romano
-  given-names: Paul K.
-  orcid: "https://orcid.org/0000-0002-1147-045X"
-- family-names: Shriwise
-  given-names: Patrick C.
-  orcid: "https://orcid.org/0000-0002-3979-7665"
-- family-names: Shimwell
-  given-names: Jonathan
-  orcid: "https://orcid.org/0000-0001-6909-0946"
-- family-names: Harper
-  given-names: Sterling
-- family-names: Boyd
-  given-names: Will
-- family-names: Nelson
-  given-names: Adam G.
-  orcid: "https://orcid.org/0000-0002-3614-0676"
-- family-names: Tramm
-  given-names: John R.
-  orcid: "https://orcid.org/0000-0002-5397-4402"
-- family-names: Ridley
-  given-names: Gavin
-  orcid: "https://orcid.org/0000-0003-1635-8042"
-- family-names: Johnson
-  given-names: Andrew
-  orcid: "https://orcid.org/0000-0003-2125-8775"
-- family-names: Peterson
-  given-names: Ethan E.
-  orcid: "https://orcid.org/0000-0002-5694-7194"
-- family-names: Herman
-  given-names: Bryan R.
-preferred-citation:
-  authors:
-  - family-names: Romano
-    given-names: Paul K.
-    orcid: "https://orcid.org/0000-0002-1147-045X"
-  - family-names: Horelik
-    given-names: Nicholas E.
-  - family-names: Herman
-    given-names: Bryan R.
-  - family-names: Nelson
-    given-names: Adam G.
-    orcid: "https://orcid.org/0000-0002-3614-0676"
-  - family-names: Forget
-    given-names: Benoit
-    orcid: "https://orcid.org/0000-0003-1459-7672"
-  - family-names: Smith
-    given-names: Kord
-  contact:
-  - family-names: Romano
-    given-names: Paul K.
-    orcid: "https://orcid.org/0000-0002-1147-045X"
-  doi: 10.1016/j.anucene.2014.07.048
-  issn: 0306-4549
-  volume: 82
-  journal: Annals of Nuclear Energy
-  publisher:
-    name: Elsevier
-  start: 90
-  end: 97
-  year: 2015
-  month: 8
-  title: "OpenMC: A state-of-the-art Monte Carlo code for research and development"
-  type: article
-  url: "https://doi.org/10.1016/j.anucene.2014.07.048"

CLAUDE.md

@@ -1,14 +0,0 @@
-## OpenMC Codebase Tools
-
-Read the FULL `AGENTS.md` in this directory before starting work. It contains
-project context, coding conventions, and documentation of the RAG search tools
-registered in `.mcp.json`.
-
-### Claude Code-specific: first-call behavior
-
-The first `openmc_rag_search` call of each session returns an index status
-message instead of search results. When this happens, you MUST use the
-`AskUserQuestion` tool to present the rebuild/use-existing choice to the user.
-Do not ask conversationally — always use the widget. Do not skip this step even
-if the index looks current — the user may have uncommitted changes that warrant
-a rebuild.

CMakeLists.txt

@@ -1,18 +1,11 @@
-cmake_minimum_required(VERSION 3.16 FATAL_ERROR)
+cmake_minimum_required(VERSION 3.3 FATAL_ERROR)
 project(openmc C CXX)
 
-# Set module path
-set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake/Modules)
-
-include(GetVersionFromGit)
-
-# Output version information
-message(STATUS "OpenMC version: ${OPENMC_VERSION}")
-message(STATUS "OpenMC dev state: ${OPENMC_DEV_STATE}")
-message(STATUS "OpenMC commit hash: ${OPENMC_COMMIT_HASH}")
-message(STATUS "OpenMC commit count: ${OPENMC_COMMIT_COUNT}")
-
-# Generate version.h
+# Set version numbers
+set(OPENMC_VERSION_MAJOR 0)
+set(OPENMC_VERSION_MINOR 12)
+set(OPENMC_VERSION_RELEASE 2)
+set(OPENMC_VERSION ${OPENMC_VERSION_MAJOR}.${OPENMC_VERSION_MINOR}.${OPENMC_VERSION_RELEASE})
 configure_file(include/openmc/version.h.in "${CMAKE_BINARY_DIR}/include/openmc/version.h" @ONLY)
 
 # Setup output directories
@@ -20,156 +13,72 @@ set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
 set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
 
-# Generate compile_commands.json for clangd and other tools
-if("${CMAKE_EXPORT_COMPILE_COMMANDS}" STREQUAL "")
-  set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
-endif()
+# Set module path
+set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake/Modules)
 
-# Enable correct usage of CXX_EXTENSIONS
-if (CMAKE_VERSION VERSION_GREATER_EQUAL 3.22)
-  cmake_policy(SET CMP0128 NEW)
+# Allow user to specify <project>_ROOT variables
+if (NOT (CMAKE_VERSION VERSION_LESS 3.12))
+  cmake_policy(SET CMP0074 NEW)
 endif()
 
 #===============================================================================
 # Command line options
 #===============================================================================
 
-option(OPENMC_USE_OPENMP      "Enable shared-memory parallelism with OpenMP"         ON)
-option(OPENMC_BUILD_TESTS     "Build tests"                                          ON)
-option(OPENMC_ENABLE_PROFILE  "Compile with profiling flags"                         OFF)
-option(OPENMC_ENABLE_COVERAGE "Compile with coverage analysis flags"                 OFF)
-option(OPENMC_USE_DAGMC       "Enable support for DAGMC (CAD) geometry"              OFF)
-option(OPENMC_USE_LIBMESH     "Enable support for libMesh unstructured mesh tallies" OFF)
-option(OPENMC_USE_MPI         "Enable MPI"                                           OFF)
-option(OPENMC_USE_UWUW        "Enable UWUW"                                          OFF)
-option(OPENMC_FORCE_VENDORED_LIBS "Explicitly use submodules defined in 'vendor'"    OFF)
-option(OPENMC_ENABLE_STRICT_FP "Enable strict FP flags to improve test portability"  OFF)
-
-message(STATUS "OPENMC_USE_OPENMP ${OPENMC_USE_OPENMP}")
-message(STATUS "OPENMC_BUILD_TESTS ${OPENMC_BUILD_TESTS}")
-message(STATUS "OPENMC_ENABLE_PROFILE ${OPENMC_ENABLE_PROFILE}")
-message(STATUS "OPENMC_ENABLE_COVERAGE ${OPENMC_ENABLE_COVERAGE}")
-message(STATUS "OPENMC_USE_DAGMC ${OPENMC_USE_DAGMC}")
-message(STATUS "OPENMC_USE_LIBMESH ${OPENMC_USE_LIBMESH}")
-message(STATUS "OPENMC_USE_MPI ${OPENMC_USE_MPI}")
-message(STATUS "OPENMC_USE_UWUW ${OPENMC_USE_UWUW}")
-message(STATUS "OPENMC_FORCE_VENDORED_LIBS ${OPENMC_FORCE_VENDORED_LIBS}")
-message(STATUS "OPENMC_ENABLE_STRICT_FP ${OPENMC_ENABLE_STRICT_FP}")
-
-# Warnings for deprecated options
-foreach(OLD_OPT IN ITEMS "openmp" "profile" "coverage" "dagmc" "libmesh")
-  if(DEFINED ${OLD_OPT})
-    string(TOUPPER ${OLD_OPT} OPT_UPPER)
-    if ("${OLD_OPT}" STREQUAL "profile" OR "${OLD_OPT}" STREQUAL "coverage")
-      set(NEW_OPT_PREFIX "OPENMC_ENABLE")
-    else()
-      set(NEW_OPT_PREFIX "OPENMC_USE")
-    endif()
-    message(WARNING "The OpenMC CMake option '${OLD_OPT}' has been deprecated. "
-      "Its value will be ignored. "
-      "Please use '-D${NEW_OPT_PREFIX}_${OPT_UPPER}=${${OLD_OPT}}' instead.")
-    unset(${OLD_OPT} CACHE)
-  endif()
-endforeach()
-
-foreach(OLD_BLD in ITEMS "debug" "optimize")
-  if(DEFINED ${OLD_BLD})
-    if("${OLD_BLD}" STREQUAL "debug")
-      set(BLD_VAR "Debug")
-    else()
-      set(BLD_VAR "Release")
-    endif()
-    message(WARNING "The OpenMC CMake option '${OLD_BLD}' has been deprecated. "
-      "Its value will be ignored. "
-      "OpenMC now uses the CMAKE_BUILD_TYPE variable to set the build mode. "
-      "Please use '-DCMAKE_BUILD_TYPE=${BLD_VAR}' instead.")
-    unset(${OLD_BLD} CACHE)
-  endif()
-endforeach()
-
-#===============================================================================
-# Set a default build configuration if not explicitly specified
-#===============================================================================
-
-if(NOT CMAKE_BUILD_TYPE)
-    message(STATUS "No build type selected, defaulting to RelWithDebInfo")
-    set(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING "Choose the type of build" FORCE)
-endif()
-
-#===============================================================================
-# When STRICT_FP is enabled, remove NDEBUG from RelWithDebInfo flags so that
-# assert() remains active. CMake normally adds -DNDEBUG for both Release and
-# RelWithDebInfo, which disables C/C++ assert() statements.
-#===============================================================================
-
-if(OPENMC_ENABLE_STRICT_FP)
-  foreach(FLAG_VAR CMAKE_CXX_FLAGS_RELWITHDEBINFO CMAKE_C_FLAGS_RELWITHDEBINFO)
-    string(REPLACE "-DNDEBUG" "" ${FLAG_VAR} "${${FLAG_VAR}}")
-    string(REPLACE "/DNDEBUG" "" ${FLAG_VAR} "${${FLAG_VAR}}")
-  endforeach()
-endif()
-
-#===============================================================================
-# OpenMP for shared-memory parallelism (and GPU support some day!)
-#===============================================================================
-
-if(OPENMC_USE_OPENMP)
-  find_package(OpenMP REQUIRED)
-endif()
+option(openmp   "Enable shared-memory parallelism with OpenMP"         ON)
+option(profile  "Compile with profiling flags"                         OFF)
+option(debug    "Compile with debug flags"                             OFF)
+option(optimize "Turn on all compiler optimization flags"              OFF)
+option(coverage "Compile with coverage analysis flags"                 OFF)
+option(dagmc    "Enable support for DAGMC (CAD) geometry"              OFF)
+option(libmesh  "Enable support for libMesh unstructured mesh tallies" OFF)
 
 #===============================================================================
 # MPI for distributed-memory parallelism
 #===============================================================================
 
-if(OPENMC_USE_MPI)
-  find_package(MPI REQUIRED)
+set(MPI_ENABLED FALSE)
+if(${CMAKE_CXX_COMPILER} MATCHES "(mpi[^/]*|CC)$")
+  message(STATUS "Detected MPI wrapper: ${CMAKE_CXX_COMPILER}")
+  set(MPI_ENABLED TRUE)
 endif()
 
-#===============================================================================
-# Helper macro for finding a dependency
-#===============================================================================
-
-macro(find_package_write_status pkg)
-  find_package(${pkg} QUIET NO_SYSTEM_ENVIRONMENT_PATH)
-  if(${pkg}_FOUND)
-    message(STATUS "Found ${pkg}: ${${pkg}_DIR} (version ${${pkg}_VERSION})")
-  else()
-    message(STATUS "Did not find ${pkg}, will use submodule instead")
-  endif()
-endmacro()
-
 #===============================================================================
 # DAGMC Geometry Support - need DAGMC/MOAB
 #===============================================================================
-
-if(OPENMC_USE_DAGMC)
+if(dagmc)
   find_package(DAGMC REQUIRED PATH_SUFFIXES lib/cmake)
   if (${DAGMC_VERSION} VERSION_LESS 3.2.0)
-    message(FATAL_ERROR "Discovered DAGMC Version: ${DAGMC_VERSION}."
-      "Please update DAGMC to version 3.2.0 or greater.")
+    message(FATAL_ERROR "Discovered DAGMC Version: ${DAGMC_VERSION}. \
+    Please update DAGMC to version 3.2.0 or greater.")
   endif()
-  message(STATUS "Found DAGMC: ${DAGMC_DIR} (version ${DAGMC_VERSION})")
+endif()
 
-  # Check if UWUW is needed and available
-  if(OPENMC_USE_UWUW AND NOT DAGMC_BUILD_UWUW)
-    message(FATAL_ERROR "UWUW is enabled but DAGMC was not configured with UWUW.")
-  endif()
+#===============================================================================
+# Check for submodules perhaps already on system
+#===============================================================================
+
+# If not found, we just pull appropriate versions from github and build them.
+find_package(fmt QUIET NO_SYSTEM_ENVIRONMENT_PATH)
+if(fmt_FOUND)
+  message(STATUS "Found fmt: ${fmt_DIR} (version ${fmt_VERSION})")
+else()
+  message(STATUS "Did not find fmt, will use submodule instead")
+endif()
+find_package(pugixml QUIET NO_SYSTEM_ENVIRONMENT_PATH)
+if(pugixml_FOUND)
+  message(STATUS "Found pugixml: ${pugixml_DIR}")
+else()
+  message(STATUS "Did not find pugixml, will use submodule instead")
 endif()
 
 #===============================================================================
 # libMesh Unstructured Mesh Support
 #===============================================================================
-
-if(OPENMC_USE_LIBMESH)
+if(libmesh)
   find_package(LIBMESH REQUIRED)
 endif()
 
-#===============================================================================
-# libpng
-#===============================================================================
-
-find_package(PNG)
-
 #===============================================================================
 # HDF5 for binary output
 #===============================================================================
@@ -188,16 +97,11 @@ if(NOT DEFINED HDF5_PREFER_PARALLEL)
 endif()
 
 find_package(HDF5 REQUIRED COMPONENTS C HL)
-
-# Remove HDF5 transitive dependencies that are system libraries
-list(FILTER HDF5_LIBRARIES EXCLUDE REGEX ".*lib(pthread|dl|m).*")
-message(STATUS "HDF5 Libraries: ${HDF5_LIBRARIES}")
-
 if(HDF5_IS_PARALLEL)
-  if(NOT OPENMC_USE_MPI)
-    message(FATAL_ERROR "Parallel HDF5 was detected, but MPI was not enabled.\
-      To use parallel HDF5, OpenMC needs to be built with MPI support by passing\
-      -DOPENMC_USE_MPI=ON when calling cmake.")
+  if(NOT MPI_ENABLED)
+    message(FATAL_ERROR "Parallel HDF5 was detected, but the detected compiler,\
+     ${CMAKE_CXX_COMPILER}, does not support MPI. An MPI-capable compiler must \
+     be used with parallel HDF5.")
   endif()
   message(STATUS "Using parallel HDF5")
 endif()
@@ -205,7 +109,7 @@ endif()
 # Version 1.12 of HDF5 deprecates the H5Oget_info_by_idx() interface.
 # Thus, we give these flags to allow usage of the old interface in newer
 # versions of HDF5.
-if(${HDF5_VERSION} VERSION_GREATER_EQUAL 1.12.0)
+if(NOT (${HDF5_VERSION} VERSION_LESS 1.12.0))
   list(APPEND cxxflags -DH5Oget_info_by_idx_vers=1 -DH5O_info_t_vers=1)
 endif()
 
@@ -213,36 +117,33 @@ endif()
 # Set compile/link flags based on which compiler is being used
 #===============================================================================
 
-# When OPENMC_ENABLE_STRICT_FP is enabled, disable compiler optimizations that change
-# floating-point results relative to -O0, improving cross-platform and
-# cross-optimization-level reproducibility for regression testing:
-#   -ffp-contract=off    Prevents FMA contraction (fused multiply-add changes rounding)
-#   -fno-builtin         Prevents replacing math function calls (pow, exp, log, etc.)
-#                        with builtin versions that may differ from libm
-# By default (OFF), the compiler is free to use all optimizations for best
-# performance.
-if(OPENMC_ENABLE_STRICT_FP)
-  include(CheckCXXCompilerFlag)
-  check_cxx_compiler_flag(-ffp-contract=off SUPPORTS_FP_CONTRACT_OFF)
-  if(SUPPORTS_FP_CONTRACT_OFF)
-    list(APPEND cxxflags -ffp-contract=off)
-  endif()
-  check_cxx_compiler_flag(-fno-builtin SUPPORTS_NO_BUILTIN)
-  if(SUPPORTS_NO_BUILTIN)
-    list(APPEND cxxflags -fno-builtin)
-  endif()
-endif()
-
 # Skip for Visual Studio which has its own configurations through GUI
 if(NOT MSVC)
 
-set(CMAKE_POSITION_INDEPENDENT_CODE ON)
-
-if(OPENMC_ENABLE_PROFILE)
-  list(APPEND cxxflags -g -fno-omit-frame-pointer)
+if(openmp)
+  # Requires CMake 3.1+
+  find_package(OpenMP)
+  if(OPENMP_FOUND)
+    list(APPEND cxxflags ${OpenMP_CXX_FLAGS})
+    list(APPEND ldflags ${OpenMP_CXX_FLAGS})
+  endif()
 endif()
 
-if(OPENMC_ENABLE_COVERAGE)
+set(CMAKE_POSITION_INDEPENDENT_CODE ON)
+
+list(APPEND cxxflags -O2)
+if(debug)
+  list(REMOVE_ITEM cxxflags -O2)
+  list(APPEND cxxflags -g -O0)
+endif()
+if(profile)
+  list(APPEND cxxflags -g -fno-omit-frame-pointer)
+endif()
+if(optimize)
+  list(REMOVE_ITEM cxxflags -O2)
+  list(APPEND cxxflags -O3)
+endif()
+if(coverage)
   list(APPEND cxxflags --coverage)
   list(APPEND ldflags --coverage)
 endif()
@@ -256,6 +157,8 @@ endif()
 #===============================================================================
 # Update git submodules as needed
 #===============================================================================
+
+find_package(Git)
 if(GIT_FOUND AND EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/.git")
   option(GIT_SUBMODULE "Check submodules during build" ON)
   if(GIT_SUBMODULE)
@@ -280,47 +183,45 @@ endif()
 # pugixml library
 #===============================================================================
 
-if(OPENMC_FORCE_VENDORED_LIBS)
+if (NOT pugixml_FOUND)
   add_subdirectory(vendor/pugixml)
   set_target_properties(pugixml PROPERTIES CXX_STANDARD 14 CXX_EXTENSIONS OFF)
-else()
-  find_package_write_status(pugixml)
-  if (NOT pugixml_FOUND)
-    add_subdirectory(vendor/pugixml)
-    set_target_properties(pugixml PROPERTIES CXX_STANDARD 14 CXX_EXTENSIONS OFF)
-  endif()
 endif()
 
 #===============================================================================
 # {fmt} library
 #===============================================================================
 
-if(OPENMC_FORCE_VENDORED_LIBS)
+if (NOT fmt_FOUND)
   set(FMT_INSTALL ON CACHE BOOL "Generate the install target.")
   add_subdirectory(vendor/fmt)
-else()
-  find_package_write_status(fmt)
-  if (NOT fmt_FOUND)
-    set(FMT_INSTALL ON CACHE BOOL "Generate the install target.")
-    add_subdirectory(vendor/fmt)
-  endif()
 endif()
 
 #===============================================================================
-# Catch2 library
+# xtensor header-only library
 #===============================================================================
 
-if(OPENMC_BUILD_TESTS)
-  if (OPENMC_FORCE_VENDORED_LIBS)
-    add_subdirectory(vendor/Catch2)
-  else()
-    find_package_write_status(Catch2)
-    if (NOT Catch2_FOUND)
-      add_subdirectory(vendor/Catch2)
-    endif()
-  endif()
+# CMake 3.13+ will complain about policy CMP0079 unless it is set explicitly
+if (NOT (CMAKE_VERSION VERSION_LESS 3.13))
+  cmake_policy(SET CMP0079 NEW)
 endif()
 
+add_subdirectory(vendor/xtl)
+set(xtl_DIR ${CMAKE_CURRENT_BINARY_DIR}/vendor/xtl)
+add_subdirectory(vendor/xtensor)
+
+#===============================================================================
+# GSL header-only library
+#===============================================================================
+
+set(GSL_LITE_OPT_INSTALL_COMPAT_HEADER ON CACHE BOOL
+  "Install MS-GSL compatibility header <gsl/gsl>")
+add_subdirectory(vendor/gsl-lite)
+
+# Make sure contract violations throw exceptions
+target_compile_definitions(gsl-lite-v1 INTERFACE GSL_THROW_ON_CONTRACT_VIOLATION)
+target_compile_definitions(gsl-lite-v1 INTERFACE gsl_CONFIG_ALLOWS_NONSTRICT_SPAN_COMPARISON=1)
+
 #===============================================================================
 # RPATH information
 #===============================================================================
@@ -350,21 +251,30 @@ if("${isSystemDir}" STREQUAL "-1")
   set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_FULL_LIBDIR}")
 endif()
 
+#===============================================================================
+# faddeeva library
+#===============================================================================
+
+add_library(faddeeva STATIC vendor/faddeeva/Faddeeva.cc)
+target_include_directories(faddeeva
+  PUBLIC
+    $<INSTALL_INTERFACE:include/faddeeva>
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/vendor/faddeeva>
+)
+target_compile_options(faddeeva PRIVATE ${cxxflags})
+
 #===============================================================================
 # libopenmc
 #===============================================================================
 
 list(APPEND libopenmc_SOURCES
-  src/atomic_mass.cpp
   src/bank.cpp
   src/boundary_condition.cpp
   src/bremsstrahlung.cpp
-  src/cell.cpp
-  src/chain.cpp
-  src/cmfd_solver.cpp
-  src/collision_track.cpp
-  src/cross_sections.cpp
   src/dagmc.cpp
+  src/cell.cpp
+  src/cmfd_solver.cpp
+  src/cross_sections.cpp
   src/distribution.cpp
   src/distribution_angle.cpp
   src/distribution_energy.cpp
@@ -374,29 +284,23 @@ list(APPEND libopenmc_SOURCES
   src/endf.cpp
   src/error.cpp
   src/event.cpp
-  src/file_utils.cpp
+  src/initialize.cpp
   src/finalize.cpp
   src/geometry.cpp
   src/geometry_aux.cpp
   src/hdf5_interface.cpp
-  src/ifp.cpp
-  src/initialize.cpp
   src/lattice.cpp
   src/material.cpp
   src/math_functions.cpp
-  src/mcpl_interface.cpp
   src/mesh.cpp
   src/message_passing.cpp
   src/mgxs.cpp
   src/mgxs_interface.cpp
-  src/ncrystal_interface.cpp
-  src/ncrystal_load.cpp
   src/nuclide.cpp
   src/output.cpp
   src/particle.cpp
   src/particle_data.cpp
   src/particle_restart.cpp
-  src/particle_type.cpp
   src/photon.cpp
   src/physics.cpp
   src/physics_common.cpp
@@ -406,13 +310,6 @@ list(APPEND libopenmc_SOURCES
   src/progress_bar.cpp
   src/random_dist.cpp
   src/random_lcg.cpp
-  src/random_ray/random_ray_simulation.cpp
-  src/random_ray/random_ray.cpp
-  src/random_ray/flat_source_domain.cpp
-  src/random_ray/linear_source_domain.cpp
-  src/random_ray/moment_matrix.cpp
-  src/random_ray/source_region.cpp
-  src/ray.cpp
   src/reaction.cpp
   src/reaction_product.cpp
   src/scattdata.cpp
@@ -431,55 +328,39 @@ list(APPEND libopenmc_SOURCES
   src/tallies/derivative.cpp
   src/tallies/filter.cpp
   src/tallies/filter_azimuthal.cpp
-  src/tallies/filter_cell.cpp
-  src/tallies/filter_cell_instance.cpp
   src/tallies/filter_cellborn.cpp
   src/tallies/filter_cellfrom.cpp
-  src/tallies/filter_collision.cpp
+  src/tallies/filter_cell.cpp
+  src/tallies/filter_cell_instance.cpp
   src/tallies/filter_delayedgroup.cpp
   src/tallies/filter_distribcell.cpp
-  src/tallies/filter_energy.cpp
   src/tallies/filter_energyfunc.cpp
+  src/tallies/filter_energy.cpp
+  src/tallies/filter_collision.cpp
   src/tallies/filter_legendre.cpp
   src/tallies/filter_material.cpp
-  src/tallies/filter_materialfrom.cpp
   src/tallies/filter_mesh.cpp
-  src/tallies/filter_meshborn.cpp
-  src/tallies/filter_meshmaterial.cpp
   src/tallies/filter_meshsurface.cpp
   src/tallies/filter_mu.cpp
-  src/tallies/filter_musurface.cpp
-  src/tallies/filter_parent_nuclide.cpp
   src/tallies/filter_particle.cpp
-  src/tallies/filter_particle_production.cpp
   src/tallies/filter_polar.cpp
-  src/tallies/filter_reaction.cpp
   src/tallies/filter_sph_harm.cpp
   src/tallies/filter_sptl_legendre.cpp
   src/tallies/filter_surface.cpp
-  src/tallies/filter_time.cpp
   src/tallies/filter_universe.cpp
-  src/tallies/filter_weight.cpp
   src/tallies/filter_zernike.cpp
   src/tallies/tally.cpp
   src/tallies/tally_scoring.cpp
   src/tallies/trigger.cpp
-  src/thermal.cpp
   src/timer.cpp
+  src/thermal.cpp
   src/track_output.cpp
-  src/universe.cpp
   src/urr.cpp
   src/volume_calc.cpp
-  src/weight_windows.cpp
   src/wmp.cpp
   src/xml_interface.cpp
   src/xsdata.cpp)
 
-# Add bundled external dependencies
-list(APPEND libopenmc_SOURCES
-  src/external/quartic_solver.cpp
-  src/external/Faddeeva.cc)
-
 # For Visual Studio compilers
 if(MSVC)
   # Use static library (otherwise explicit symbol portings are needed)
@@ -492,8 +373,6 @@ else()
   add_library(libopenmc SHARED ${libopenmc_SOURCES})
 endif()
 
-add_library(OpenMC::libopenmc ALIAS libopenmc)
-
 # Avoid vs error lnk1149 :output filename matches input filename
 if(NOT MSVC)
   set_target_properties(libopenmc PROPERTIES OUTPUT_NAME openmc)
@@ -510,93 +389,55 @@ target_include_directories(libopenmc
 target_compile_options(libopenmc PRIVATE ${cxxflags})
 
 # Add include directory for configured version file
-target_include_directories(libopenmc
-  PUBLIC $<BUILD_INTERFACE:${CMAKE_BINARY_DIR}/include>)
+target_include_directories(libopenmc PRIVATE ${CMAKE_BINARY_DIR}/include)
 
 if (HDF5_IS_PARALLEL)
   target_compile_definitions(libopenmc PRIVATE -DPHDF5)
 endif()
-if (OPENMC_USE_MPI)
+if (MPI_ENABLED)
   target_compile_definitions(libopenmc PUBLIC -DOPENMC_MPI)
 endif()
 
+# Set git SHA1 hash as a compile definition
+if(GIT_FOUND)
+  execute_process(COMMAND ${GIT_EXECUTABLE} rev-parse HEAD
+                  WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+                  RESULT_VARIABLE GIT_SHA1_SUCCESS
+                  OUTPUT_VARIABLE GIT_SHA1
+                  ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
+  if(GIT_SHA1_SUCCESS EQUAL 0)
+    target_compile_definitions(libopenmc PRIVATE -DGIT_SHA1="${GIT_SHA1}")
+  endif()
+endif()
+
 # target_link_libraries treats any arguments starting with - but not -l as
 # linker flags. Thus, we can pass both linker flags and libraries together.
 target_link_libraries(libopenmc ${ldflags} ${HDF5_LIBRARIES} ${HDF5_HL_LIBRARIES}
-                      fmt::fmt ${CMAKE_DL_LIBS})
+                      pugixml faddeeva xtensor gsl-lite-v1 fmt::fmt)
 
-if(TARGET pugixml::pugixml)
-  target_link_libraries(libopenmc pugixml::pugixml)
-else()
-  target_link_libraries(libopenmc pugixml)
+if(dagmc)
+  target_compile_definitions(libopenmc PRIVATE DAGMC)
+  target_link_libraries(libopenmc dagmc-shared uwuw-shared)
 endif()
 
-if(OPENMC_USE_DAGMC)
-  target_compile_definitions(libopenmc PUBLIC OPENMC_DAGMC_ENABLED)
-  target_link_libraries(libopenmc dagmc-shared)
-
-  if(OPENMC_USE_UWUW)
-    target_compile_definitions(libopenmc PRIVATE OPENMC_UWUW_ENABLED)
-    target_link_libraries(libopenmc uwuw-shared)
-  endif()
-elseif(OPENMC_USE_UWUW)
-  set(OPENMC_USE_UWUW OFF)
-  message(FATAL_ERROR "DAGMC must be enabled when UWUW is enabled.")
-endif()
-
-if(OPENMC_USE_LIBMESH)
-  target_compile_definitions(libopenmc PRIVATE OPENMC_LIBMESH_ENABLED)
+if(libmesh)
+  target_compile_definitions(libopenmc PRIVATE LIBMESH)
   target_link_libraries(libopenmc PkgConfig::LIBMESH)
 endif()
 
-if (PNG_FOUND)
-  target_compile_definitions(libopenmc PRIVATE USE_LIBPNG)
-  target_link_libraries(libopenmc PNG::PNG)
-endif()
-
-if (OPENMC_USE_OPENMP)
-  target_link_libraries(libopenmc OpenMP::OpenMP_CXX)
-endif()
-
-if (OPENMC_USE_MPI)
-  target_link_libraries(libopenmc MPI::MPI_CXX)
-endif()
-
-if (OPENMC_BUILD_TESTS)
-  # Add cpp tests directory
-  include(CTest)
-  add_subdirectory(tests/cpp_unit_tests)
-endif()
-
-#===============================================================================
-# Log build info that this executable can report later
-#===============================================================================
-target_compile_definitions(libopenmc PRIVATE BUILD_TYPE=${CMAKE_BUILD_TYPE})
-target_compile_definitions(libopenmc PRIVATE COMPILER_ID=${CMAKE_CXX_COMPILER_ID})
-target_compile_definitions(libopenmc PRIVATE COMPILER_VERSION=${CMAKE_CXX_COMPILER_VERSION})
-if (OPENMC_ENABLE_PROFILE)
-  target_compile_definitions(libopenmc PRIVATE PROFILINGBUILD)
-endif()
-if (OPENMC_ENABLE_COVERAGE)
-  target_compile_definitions(libopenmc PRIVATE COVERAGEBUILD)
-endif()
-if (OPENMC_ENABLE_STRICT_FP)
-  target_compile_definitions(libopenmc PRIVATE OPENMC_ENABLE_STRICT_FP)
-endif()
-
 #===============================================================================
 # openmc executable
 #===============================================================================
 add_executable(openmc src/main.cpp)
-add_executable(OpenMC::openmc ALIAS openmc)
 target_compile_options(openmc PRIVATE ${cxxflags})
 target_include_directories(openmc PRIVATE ${CMAKE_BINARY_DIR}/include)
 target_link_libraries(openmc libopenmc)
 
-# Ensure C++17 standard is used and turn off GNU extensions
-target_compile_features(openmc PUBLIC cxx_std_17)
-target_compile_features(libopenmc PUBLIC cxx_std_17)
-set_target_properties(openmc libopenmc PROPERTIES CXX_EXTENSIONS OFF)
+# Ensure C++14 standard is used. Starting with CMake 3.8, another way this could
+# be done is using the cxx_std_14 compiler feature.
+set_target_properties(
+    openmc libopenmc faddeeva
+    PROPERTIES CXX_STANDARD 14 CXX_EXTENSIONS OFF)
 
 #===============================================================================
 # Python package
@@ -611,10 +452,12 @@ add_custom_command(TARGET libopenmc POST_BUILD
 #===============================================================================
 # Install executable, scripts, manpage, license
 #===============================================================================
-include(CMakePackageConfigHelpers)
+
+configure_file(cmake/OpenMCConfig.cmake.in "${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/OpenMCConfig.cmake" @ONLY)
+configure_file(cmake/OpenMCConfigVersion.cmake.in "${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/OpenMCConfigVersion.cmake" @ONLY)
 
 set(INSTALL_CONFIGDIR ${CMAKE_INSTALL_LIBDIR}/cmake/OpenMC)
-install(TARGETS openmc libopenmc
+install(TARGETS openmc libopenmc faddeeva
   EXPORT openmc-targets
   RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
   LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
@@ -625,25 +468,16 @@ install(EXPORT openmc-targets
   NAMESPACE OpenMC::
   DESTINATION ${INSTALL_CONFIGDIR})
 
-configure_package_config_file(
-    "cmake/OpenMCConfig.cmake.in"
-    "${CMAKE_BINARY_DIR}/${CMAKE_FILES_DIRECTORY}/OpenMCConfig.cmake"
-    INSTALL_DESTINATION ${INSTALL_CONFIGDIR}
-)
-
-write_basic_package_version_file(
-    "${CMAKE_BINARY_DIR}/${CMAKE_FILES_DIRECTORY}/OpenMCConfigVersion.cmake"
-    VERSION ${OPENMC_VERSION}
-    COMPATIBILITY AnyNewerVersion
-)
-
+install(DIRECTORY src/relaxng DESTINATION ${CMAKE_INSTALL_DATADIR}/openmc)
 install(FILES
-    "${CMAKE_BINARY_DIR}/${CMAKE_FILES_DIRECTORY}/OpenMCConfig.cmake"
-    "${CMAKE_BINARY_DIR}/${CMAKE_FILES_DIRECTORY}/OpenMCConfigVersion.cmake"
-    DESTINATION "${INSTALL_CONFIGDIR}"
-)
-
+  "${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/OpenMCConfig.cmake"
+  "${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/OpenMCConfigVersion.cmake"
+  DESTINATION ${INSTALL_CONFIGDIR})
 install(FILES man/man1/openmc.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1)
 install(FILES LICENSE DESTINATION "${CMAKE_INSTALL_DOCDIR}" RENAME copyright)
 install(DIRECTORY include/ DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
 install(FILES "${CMAKE_BINARY_DIR}/include/openmc/version.h" DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/openmc)
+
+# Copy headers for vendored dependencies (note that all except faddeeva are handled
+# separately since they are managed by CMake)
+install(DIRECTORY vendor/faddeeva DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})

CODEOWNERS

@@ -5,9 +5,9 @@ openmc/data/ @paulromano
 openmc/lib/ @paulromano
 
 # Depletion
-openmc/deplete/ @paulromano
-tests/regression_tests/deplete/ @paulromano
-tests/unit_tests/test_deplete_*.py @paulromano
+openmc/deplete/ @drewejohnson
+tests/regression_tests/deplete/ @drewejohnson
+tests/unit_tests/test_deplete_*.py @drewejohnson
 
 # MG-related functionality
 openmc/mgxs_library.py @nelsonag
@@ -26,12 +26,6 @@ src/dagmc.cpp @pshriwise
 tests/regression_tests/dagmc/ @pshriwise
 tests/unit_tests/dagmc/ @pshriwise
 
-# Weight windows
-openmc/weight_windows.py @pshriwise
-openmc/lib/weight_windows.py @pshriwise
-src/weight_windows.py @pshriwise
-tests/unit_tests/weightwindows/ @pshriwise
-
 # Photon transport
 openmc/data/BREMX.DAT @amandalund
 openmc/data/compton_profiles.h5 @amandalund
@@ -52,16 +46,3 @@ openmc/lib/plot.py @pshriwise
 
 # Resonance covariance
 openmc/data/resonance_covariance.py @icmeyer
-
-# Docker
-Dockerfile @shimwell
-
-# Random ray
-src/random_ray/ @jtramm
-
-# NCrystal interface
-src/ncrystal_interface.cpp @marquezj @tkittel
-src/ncrystal_load.cpp @marquezj @tkittel
-
-# MCPL interface
-src/mcpl_interface.cpp @ebknudsen

CONTRIBUTING.md

@@ -13,8 +13,9 @@ openmc@anl.gov.
 ## Resources
 
 - [GitHub Repository](https://github.com/openmc-dev/openmc)
-- [Documentation](https://docs.openmc.org/en/latest)
-- [Discussion Forum](https://openmc.discourse.group)
+- [Documentation](http://openmc.readthedocs.io/en/latest)
+- [User's Mailing List](openmc-users@googlegroups.com)
+- [Developer's Mailing List](openmc-dev@googlegroups.com)
 - [Slack Community](https://openmc.slack.com/signup) (If you don't see your
   domain listed, contact openmc@anl.gov)
 
@@ -36,10 +37,10 @@ development team will be happy to discuss it.
 
 All changes to OpenMC happen through pull requests. For a full overview of the
 process, see the developer's guide section on [Contributing to
-OpenMC](https://docs.openmc.org/en/latest/devguide/contributing.html).
+OpenMC](http://openmc.readthedocs.io/en/latest/devguide/contributing.html).
 
 ## Code Style
 
 Before you run off to make changes to the code, please have a look at our [style
-guide](https://docs.openmc.org/en/latest/devguide/styleguide.html), which
+guide](http://openmc.readthedocs.io/en/latest/devguide/styleguide.html), which
 is used when reviewing new contributions.

Dockerfile

@@ -1,229 +1,149 @@
-# To build with OpenMC and by default this Dockerfile builds the master branch of OpenMC.
+# To build with OpenMC
 # docker build -t openmc .
 
-# To build with OpenMC develop branch
-# docker build -t openmc_develop --build-arg openmc_branch=develop .
-
 # To build with OpenMC and DAGMC enabled
-# docker build -t openmc_dagmc --build-arg build_dagmc=on --build-arg compile_cores=4 .
+# docker build -t openmc_dagmc --build-arg include_dagmc=true .
 
-# To build with OpenMC and Libmesh enabled
-# docker build -t openmc_libmesh --build-arg build_libmesh=on --build-arg compile_cores=4 .
+# To make use of multiple cores during the compile stages of the docker build
+# docker build -t openmc_dagmc --build-arg compile_cores=8 .
 
-# To build with both DAGMC and Libmesh enabled
-# docker build -t openmc_dagmc_libmesh --build-arg build_dagmc=on --build-arg build_libmesh=on --build-arg compile_cores=4 .
+FROM ubuntu:latest
 
-# sudo docker run image_name:tag_name or ID with no tag sudo docker run ID number
+# By default this Dockerfile builds OpenMC without dagmc
+ARG include_dagmc=false
 
-
-# global ARG as these ARGS are used in multiple stages
 # By default one core is used to compile
 ARG compile_cores=1
 
-# By default this Dockerfile builds OpenMC without DAGMC and LIBMESH support
-ARG build_dagmc=off
-ARG build_libmesh=off
-
-FROM ubuntu:24.04 AS dependencies
-
-ARG compile_cores
-ARG build_dagmc
-ARG build_libmesh
-
-# Set default value of HOME to /root
-ENV HOME=/root
-
-# MOAB variables
-ENV MOAB_TAG='5.5.1'
-ENV MOAB_REPO='https://bitbucket.org/fathomteam/moab/'
-
-# Double-Down variables
-ENV DD_TAG='v1.1.0'
-ENV DD_REPO='https://github.com/pshriwise/double-down'
-ENV DD_INSTALL_DIR=$HOME/Double_down
-
-# DAGMC variables
-ENV DAGMC_BRANCH='v3.2.4'
-ENV DAGMC_REPO='https://github.com/svalinn/DAGMC'
-ENV DAGMC_INSTALL_DIR=$HOME/DAGMC/
-
-# LIBMESH variables
-ENV LIBMESH_TAG='v1.7.1'
-ENV LIBMESH_REPO='https://github.com/libMesh/libmesh'
-ENV LIBMESH_INSTALL_DIR=$HOME/LIBMESH
-
-# NJOY variables
-ENV NJOY_TAG='2016.78'
-ENV NJOY_REPO='https://github.com/njoy/NJOY2016'
-
 # Setup environment variables for Docker image
-ENV LD_LIBRARY_PATH=${DAGMC_INSTALL_DIR}/lib:${LD_LIBRARY_PATH:-} \
+ENV CC=/usr/bin/mpicc CXX=/usr/bin/mpicxx \
+    PATH=/opt/openmc/bin:/opt/NJOY2016/build:$PATH \
+    LD_LIBRARY_PATH=/opt/openmc/lib:$LD_LIBRARY_PATH \
+    OPENMC_CROSS_SECTIONS=/root/nndc_hdf5/cross_sections.xml \
     OPENMC_ENDF_DATA=/root/endf-b-vii.1 \
     DEBIAN_FRONTEND=noninteractive
 
-# Install and update dependencies from Debian package manager
+# Install dependencies from Debian package manager
 RUN apt-get update -y && \
     apt-get upgrade -y && \
     apt-get install -y \
-        python3-pip python-is-python3 wget git build-essential cmake \
+        python3-pip python-is-python3 wget git gfortran g++ cmake \
         mpich libmpich-dev libhdf5-serial-dev libhdf5-mpich-dev \
-        libpng-dev libpugixml-dev libfmt-dev catch2 python3-venv && \
+        imagemagick && \
     apt-get autoremove
 
-# create virtual enviroment to avoid externally managed environment error
-RUN python3 -m venv openmc_venv
-ENV PATH=/openmc_venv/bin:$PATH
-
 # Update system-provided pip
-RUN pip install --upgrade pip
+RUN pip3 install --upgrade pip
 
 # Clone and install NJOY2016
-RUN cd $HOME \
-    && git clone --single-branch -b ${NJOY_TAG} --depth 1 ${NJOY_REPO} \
-    && cd NJOY2016 \
-    && mkdir build \
-    && cd build \
-    && cmake -Dstatic=on .. \
-    && make 2>/dev/null -j${compile_cores} install \
-    && rm -rf $HOME/NJOY2016
+RUN git clone https://github.com/njoy/NJOY2016.git /opt/NJOY2016 && \
+    cd /opt/NJOY2016 && \
+    mkdir build && cd build && \
+    cmake -Dstatic=on .. && make 2>/dev/null && make install
 
-
-RUN if [ "$build_dagmc" = "on" ]; then \
-        # Install addition packages required for DAGMC
-        apt-get -y install \
-            libeigen3-dev libnetcdf-dev libtbb-dev libglfw3-dev libembree-dev \
-        && pip install --upgrade numpy \
-        && pip install --no-cache-dir setuptools cython \
-        # Clone and install MOAB
-        && mkdir -p $HOME/MOAB && cd $HOME/MOAB \
-        && git clone  --single-branch -b ${MOAB_TAG} --depth 1 ${MOAB_REPO} \
-        && mkdir build && cd build \
-        && cmake ../moab -DCMAKE_BUILD_TYPE=Release \
-                      -DENABLE_HDF5=ON \
-                      -DENABLE_NETCDF=ON \
-                      -DBUILD_SHARED_LIBS=OFF \
-                      -DENABLE_FORTRAN=OFF \
-                      -DENABLE_BLASLAPACK=OFF \
-                      -DENABLE_TESTING=OFF \
-        && make 2>/dev/null -j${compile_cores} install \
-        && cmake ../moab \
-                    -DENABLE_PYMOAB=ON \
-                    -DBUILD_SHARED_LIBS=ON \
-        && make 2>/dev/null -j${compile_cores} install \
-        && cd pymoab && bash install.sh \
-        && python setup.py install \
-        && python -c "import pymoab" \
-        && rm -rf $HOME/MOAB ; \
-        # Clone and install Double-Down
-        mkdir -p $HOME/Double_down && cd $HOME/Double_down \
-        && git clone --single-branch -b ${DD_TAG} --depth 1 ${DD_REPO} \
-        && mkdir build && cd build \
-        && cmake ../double-down -DCMAKE_INSTALL_PREFIX=${DD_INSTALL_DIR} \
-                             -DMOAB_DIR=/usr/local \
-                             -DEMBREE_DIR=/usr \
-        && make 2>/dev/null -j${compile_cores} install \
-        && rm -rf ${DD_INSTALL_DIR}/build ${DD_INSTALL_DIR}/double-down ; \
-        # Clone and install DAGMC
-        mkdir -p $HOME/DAGMC && cd $HOME/DAGMC \
-        && git clone --single-branch -b ${DAGMC_BRANCH} --depth 1 ${DAGMC_REPO} \
-        && mkdir build && cd build \
-        && cmake ../DAGMC -DBUILD_TALLY=ON \
-                       -DCMAKE_INSTALL_PREFIX=${DAGMC_INSTALL_DIR} \
-                       -DMOAB_DIR=/usr/local \
-                       -DDOUBLE_DOWN=ON \
-                       -DDOUBLE_DOWN_DIR=${DD_INSTALL_DIR} \
-                       -DCMAKE_PREFIX_PATH=${DD_INSTALL_DIR}/lib \
-                       -DBUILD_STATIC_LIBS=OFF \
-                       -DBUILD_TESTS=OFF \
-        && make 2>/dev/null -j${compile_cores} install \
-        && rm -rf ${DAGMC_INSTALL_DIR}/DAGMC ${DAGMC_INSTALL_DIR}/build ; \
+# Clone and install OpenMC without DAGMC
+RUN if [ "$include_dagmc" = "false" ] ; \
+    then git clone --recurse-submodules https://github.com/openmc-dev/openmc.git /opt/openmc ; \
+    cd /opt/openmc ; \
+    mkdir -p build ; \
+    cd build ; \
+    cmake -Doptimize=on \
+          -DHDF5_PREFER_PARALLEL=on .. ; \
+    make -j"$compile_cores" ; \
+    make -j"$compile_cores" install ; \
+    cd ..  ; \
+    pip install -e .[test] ; \
     fi
 
-
-RUN if [ "$build_libmesh" = "on" ]; then \
-        # Install addition packages required for LIBMESH
-        apt-get -y install m4 libnetcdf-dev libpnetcdf-dev \
-        # Install LIBMESH
-        && mkdir -p $HOME/LIBMESH && cd $HOME/LIBMESH \
-        && git clone --shallow-submodules --recurse-submodules --single-branch -b ${LIBMESH_TAG} --depth 1 ${LIBMESH_REPO} \
-        && mkdir build && cd build \
-        && ../libmesh/configure \
-                    --prefix=${LIBMESH_INSTALL_DIR} CXX=mpicxx CC=mpicc FC=mpifort F77=mpif77 \
-                    --enable-exodus \
-                    --enable-mpi \
-                    --enable-silent-rules \
-                    --enable-unique-id \
-                    --disable-eigen \
-                    --disable-fortran \
-                    --disable-lapack \
-                    --disable-examples \
-                    --disable-warnings \
-                    --disable-maintainer-mode \
-                    --disable-metaphysicl \
-                    --with-methods="opt" \
-                    --without-gdb-command \
-                    --with-cxx-std-min=2014 \
-        && make 2>/dev/null -j${compile_cores} install \
-        && rm -rf ${LIBMESH_INSTALL_DIR}/build ${LIBMESH_INSTALL_DIR}/libmesh ; \
+# install addition packages required for DAGMC
+RUN if [ "$include_dagmc" = "true" ] ; \
+    then apt-get --yes install libeigen3-dev ; \
+    apt-get --yes install libnetcdf-dev ; \
+    apt-get --yes install libtbb-dev ; \
+    apt-get --yes install libglfw3-dev ; \
     fi
 
-FROM dependencies AS build
+# Clone and install Embree
+RUN if [ "$include_dagmc" = "true" ] ; \
+    then git clone --single-branch --branch v3.12.2 https://github.com/embree/embree.git ; \
+    cd embree ; \
+    mkdir build ; \
+    cd build ; \
+    cmake .. -DCMAKE_INSTALL_PREFIX=.. \
+             -DEMBREE_ISPC_SUPPORT=OFF ; \
+    make -j"$compile_cores" ; \
+    make -j"$compile_cores" install ; \
+    fi
 
-ENV HOME=/root
+# Clone and install MOAB
+RUN if [ "$include_dagmc" = "true" ] ; \
+    then pip install --upgrade numpy cython ; \
+    mkdir MOAB ; \
+    cd MOAB ; \
+    mkdir build ; \
+    git clone  --single-branch --branch 5.2.1 https://bitbucket.org/fathomteam/moab.git ; \
+    cd build ; \
+    cmake ../moab -DENABLE_HDF5=ON \
+                  -DENABLE_NETCDF=ON \
+                  -DBUILD_SHARED_LIBS=OFF \
+                  -DENABLE_FORTRAN=OFF \
+                  -DENABLE_BLASLAPACK=OFF ; \
+    make -j"$compile_cores" ; \
+    make -j"$compile_cores" install ; \
+    rm -rf * ; \
+    cmake ../moab -DBUILD_SHARED_LIBS=ON \
+                  -DENABLE_HDF5=ON \
+                  -DENABLE_PYMOAB=ON \
+                  -DENABLE_FORTRAN=OFF \
+                  -DENABLE_BLASLAPACK=OFF ; \
+    make -j"$compile_cores" ; \
+    make -j"$compile_cores" install ; \
+    fi
 
-ARG openmc_branch=master
-ENV OPENMC_REPO='https://github.com/openmc-dev/openmc'
+# Clone and install Double-Down
+RUN if [ "$include_dagmc" = "true" ] ; \
+    then git clone --single-branch --branch main https://github.com/pshriwise/double-down.git ; \
+    cd double-down ; \
+    mkdir build ; \
+    cd build ; \
+    cmake .. -DCMAKE_INSTALL_PREFIX=.. \
+             -DMOAB_DIR=/usr/local \
+             -DEMBREE_DIR=/embree ; \
+    make -j"$compile_cores" ; \
+    make -j"$compile_cores" install ; \
+    fi
 
-ARG compile_cores
-ARG build_dagmc
-ARG build_libmesh
+# Clone and install DAGMC
+RUN if [ "$include_dagmc" = "true" ] ; \
+    then mkdir DAGMC ; \
+    cd DAGMC ; \
+    git clone --single-branch --branch 3.2.0 https://github.com/svalinn/DAGMC.git ; \
+    mkdir build ; \
+    cd build ; \
+    cmake ../DAGMC -DBUILD_TALLY=ON \
+                   -DCMAKE_INSTALL_PREFIX=/DAGMC/ \
+                   -DMOAB_DIR=/usr/local \
+                   -DBUILD_STATIC_LIBS=OFF \
+                   -DBUILD_STATIC_EXE=OFF ; \
+    make -j"$compile_cores" install ; \
+    rm -rf /DAGMC/DAGMC /DAGMC/build ; \
+    fi
 
-ENV DAGMC_INSTALL_DIR=$HOME/DAGMC/
-ENV LIBMESH_INSTALL_DIR=$HOME/LIBMESH
-
-# clone and install openmc
-RUN mkdir -p ${HOME}/OpenMC && cd ${HOME}/OpenMC \
-    && git clone --shallow-submodules --recurse-submodules --single-branch -b ${openmc_branch} ${OPENMC_REPO} \
-    && mkdir build && cd build ; \
-    if [ ${build_dagmc} = "on" ] && [ ${build_libmesh} = "on" ]; then \
-        cmake ../openmc \
-            -DCMAKE_CXX_COMPILER=mpicxx \
-            -DOPENMC_USE_MPI=on \
-            -DHDF5_PREFER_PARALLEL=on \
-            -DOPENMC_USE_DAGMC=on \
-            -DOPENMC_USE_LIBMESH=on \
-            -DCMAKE_PREFIX_PATH="${DAGMC_INSTALL_DIR};${LIBMESH_INSTALL_DIR}" ; \
-    fi ; \
-    if [ ${build_dagmc} = "on" ] && [ ${build_libmesh} = "off" ]; then \
-        cmake ../openmc \
-            -DCMAKE_CXX_COMPILER=mpicxx \
-            -DOPENMC_USE_MPI=on \
-            -DHDF5_PREFER_PARALLEL=on \
-            -DOPENMC_USE_DAGMC=ON \
-            -DCMAKE_PREFIX_PATH=${DAGMC_INSTALL_DIR} ; \
-    fi ; \
-    if [ ${build_dagmc} = "off" ] && [ ${build_libmesh} = "on" ]; then \
-        cmake ../openmc \
-            -DCMAKE_CXX_COMPILER=mpicxx \
-            -DOPENMC_USE_MPI=on \
-            -DHDF5_PREFER_PARALLEL=on \
-            -DOPENMC_USE_LIBMESH=on \
-            -DCMAKE_PREFIX_PATH=${LIBMESH_INSTALL_DIR} ; \
-    fi ; \
-    if [ ${build_dagmc} = "off" ] && [ ${build_libmesh} = "off" ]; then \
-        cmake ../openmc \
-            -DCMAKE_CXX_COMPILER=mpicxx \
-            -DOPENMC_USE_MPI=on \
-            -DHDF5_PREFER_PARALLEL=on ; \
-    fi ; \
-    make 2>/dev/null -j${compile_cores} install \
-    && cd ../openmc && pip install .[test,depletion-mpi] \
-    && python -c "import openmc"
-
-FROM build AS release
-
-ENV HOME=/root
-ENV OPENMC_CROSS_SECTIONS=/root/nndc_hdf5/cross_sections.xml
+# Clone and install OpenMC with DAGMC
+RUN if [ "$include_dagmc" = "true" ] ; \
+    then git clone --recurse-submodules https://github.com/openmc-dev/openmc.git /opt/openmc ; \
+    cd /opt/openmc ; \
+    mkdir build ; \
+    cd build ; \
+    cmake -Doptimize=on \
+          -Ddagmc=ON \
+          -DDAGMC_DIR=/DAGMC/ \
+          -DHDF5_PREFER_PARALLEL=on ..  ; \
+    make -j"$compile_cores" ; \
+    make -j"$compile_cores" install ; \
+    cd ..  ; \
+    pip install -e .[test] ; \
+    fi
 
 # Download cross sections (NNDC and WMP) and ENDF data needed by test suite
-RUN ${HOME}/OpenMC/openmc/tools/ci/download-xs.sh
+RUN /opt/openmc/tools/ci/download-xs.sh

LICENSE

@@ -1,5 +1,4 @@
-Copyright (c) 2011-2026 Massachusetts Institute of Technology, UChicago Argonne
-LLC, and OpenMC contributors
+Copyright (c) 2011-2021 Massachusetts Institute of Technology and OpenMC contributors
 
 Permission is hereby granted, free of charge, to any person obtaining a copy of
 this software and associated documentation files (the "Software"), to deal in

MANIFEST.in

@@ -8,6 +8,7 @@ include schemas.xml
 include pyproject.toml
 include pytest.ini
 include docs/source/_templates/layout.html
+include docs/sphinxext/LICENSE
 global-include *.cmake
 global-include *.cmake.in
 global-include *.rst
@@ -19,20 +20,25 @@ recursive-include docs *.svg
 recursive-include docs *.tex
 recursive-include docs *.txt
 recursive-include docs Makefile
-recursive-include examples *.cpp
+recursive-include examples *.h5
+recursive-include examples *.ipynb
+recursive-include examples *.png
 recursive-include examples *.py
 recursive-include examples *.xml
 recursive-include include *.h
-recursive-include include *.h.in
-recursive-include include *.hh
 recursive-include man *.1
+recursive-inlcude openmc *.pyx
+recursive-include openmc *.c
+recursive-include src *.c
 recursive-include src *.cc
 recursive-include src *.cpp
+recursive-include src *.h
+recursive-include src *.hpp
 recursive-include src *.rnc
 recursive-include src *.rng
 recursive-include tests *.dat
 recursive-include tests *.h5
-recursive-include tests *.h5m
+recursive-inlcude tests *.h5m
 recursive-include tests *.py
 recursive-include tests *.xml
 recursive-include vendor CMakeLists.txt
@@ -43,5 +49,6 @@ recursive-include vendor *.hh
 recursive-include vendor *.hpp
 recursive-include vendor *.pc.in
 recursive-include vendor *.natvis
+include vendor/gsl-lite/include/gsl/gsl
 prune docs/build
 prune docs/source/pythonapi/generated/

README.md

@@ -1,11 +1,10 @@
 # OpenMC Monte Carlo Particle Transport Code
 
-[![License](https://img.shields.io/badge/license-MIT-green)](https://docs.openmc.org/en/latest/license.html)
-[![GitHub Actions build status (Linux)](https://github.com/openmc-dev/openmc/actions/workflows/ci.yml/badge.svg?branch=develop)](https://github.com/openmc-dev/openmc/actions/workflows/ci.yml)
+[![License](https://img.shields.io/github/license/openmc-dev/openmc.svg)](http://openmc.readthedocs.io/en/latest/license.html)
+[![GitHub Actions build status (Linux)](https://github.com/openmc-dev/openmc/workflows/CI/badge.svg?branch=develop)](https://github.com/openmc-dev/openmc/actions?query=workflow%3ACI)
 [![Code Coverage](https://coveralls.io/repos/github/openmc-dev/openmc/badge.svg?branch=develop)](https://coveralls.io/github/openmc-dev/openmc?branch=develop)
 [![dockerhub-publish-develop-dagmc](https://github.com/openmc-dev/openmc/workflows/dockerhub-publish-develop-dagmc/badge.svg)](https://github.com/openmc-dev/openmc/actions?query=workflow%3Adockerhub-publish-develop-dagmc)
 [![dockerhub-publish-develop](https://github.com/openmc-dev/openmc/workflows/dockerhub-publish-develop/badge.svg)](https://github.com/openmc-dev/openmc/actions?query=workflow%3Adockerhub-publish-develop)
-[![conda-pacakge](https://anaconda.org/conda-forge/openmc/badges/version.svg)](https://anaconda.org/conda-forge/openmc)
 
 The OpenMC project aims to provide a fully-featured Monte Carlo particle
 transport code based on modern methods. It is a constructive solid geometry,
@@ -13,15 +12,14 @@ continuous-energy transport code that uses HDF5 format cross sections. The
 project started under the Computational Reactor Physics Group at MIT.
 
 Complete documentation on the usage of OpenMC is hosted on Read the Docs (both
-for the [latest release](https://docs.openmc.org/en/stable/) and
-[developmental](https://docs.openmc.org/en/latest/) version). If you are
-interested in the project, or would like to help and contribute, please get in
-touch on the OpenMC [discussion forum](https://openmc.discourse.group/).
+for the [latest release](http://openmc.readthedocs.io/en/stable/) and
+[developmental](http://openmc.readthedocs.io/en/latest/) version). If you are
+interested in the project, or would like to help and contribute, please get in touch on the OpenMC [discussion forum](https://openmc.discourse.group/).
 
 ## Installation
 
 Detailed [installation
-instructions](https://docs.openmc.org/en/stable/usersguide/install.html)
+instructions](http://openmc.readthedocs.io/en/stable/usersguide/install.html)
 can be found in the User's Guide.
 
 ## Citing
@@ -37,23 +35,22 @@ citing the following publication:
 ## Troubleshooting
 
 If you run into problems compiling, installing, or running OpenMC, first check
-the [Troubleshooting
-section](https://docs.openmc.org/en/stable/usersguide/troubleshoot.html) in the
-User's Guide. If you are not able to find a solution to your problem there,
+the [Troubleshooting section](http://openmc.readthedocs.io/en/stable/usersguide/troubleshoot.html) in
+the User's Guide. If you are not able to find a solution to your problem there,
 please post to the [discussion forum](https://openmc.discourse.group/).
 
 ## Reporting Bugs
 
 OpenMC is hosted on GitHub and all bugs are reported and tracked through the
-[Issues](https://github.com/openmc-dev/openmc/issues) feature on GitHub.
-However, GitHub Issues should not be used for common troubleshooting purposes.
-If you are having trouble installing the code or getting your model to run
-properly, you should first send a message to the [discussion
-forum](https://openmc.discourse.group/). If it turns out your issue really is a
-bug in the code, an issue will then be created on GitHub. If you want to request
-that a feature be added to the code, you may create an Issue on github.
+[Issues](https://github.com/openmc-dev/openmc/issues) feature on GitHub. However,
+GitHub Issues should not be used for common troubleshooting purposes. If you are
+having trouble installing the code or getting your model to run properly, you
+should first send a message to the User's Group mailing list. If it turns out
+your issue really is a bug in the code, an issue will then be created on
+GitHub. If you want to request that a feature be added to the code, you may
+create an Issue on github.
 
 ## License
 
 OpenMC is distributed under the MIT/X
-[license](https://docs.openmc.org/en/stable/license.html).
+[license](http://openmc.readthedocs.io/en/stable/license.html).

cmake/Modules/FindLIBMESH.cmake

@@ -14,8 +14,8 @@ if(DEFINED ENV{METHOD})
   message(STATUS "Using environment variable METHOD to determine libMesh build: ${LIBMESH_PC_FILE}")
 endif()
 
-find_package(PkgConfig REQUIRED)
-
-set(PKG_CONFIG_USE_CMAKE_PREFIX_PATH TRUE)
-pkg_check_modules(LIBMESH REQUIRED ${LIBMESH_PC_FILE}>=1.7.0 IMPORTED_TARGET)
-pkg_get_variable(LIBMESH_PREFIX ${LIBMESH_PC_FILE} prefix)
+include(FindPkgConfig)
+set(ENV{PKG_CONFIG_PATH} "$ENV{PKG_CONFIG_PATH}:${LIBMESH_PC}")
+set(PKG_CONFIG_USE_CMAKE_PREFIX_PATH True)
+pkg_check_modules(LIBMESH REQUIRED ${LIBMESH_PC_FILE}>=1.6.0 IMPORTED_TARGET)
+pkg_get_variable(LIBMESH_PREFIX ${LIBMESH_PC_FILE} prefix)

cmake/Modules/GetVersionFromGit.cmake

@@ -1,120 +0,0 @@
-# GetVersionFromGit.cmake
-# Standalone script to retrieve versioning information from Git or .git_archival.txt.
-# Customizable for any project by setting variables before including this file.
-
-# Configurable variables:
-#   - VERSION_PREFIX: Prefix for version tags (default: "v").
-#   - VERSION_SUFFIX: Suffix for version tags (default: "[~+-]([a-zA-Z0-9]+)").
-#   - VERSION_REGEX: Regex to extract version (default: "(?[0-9]+\\.[0-9]+\\.[0-9]+)").
-#   - ARCHIVAL_FILE: Path to .git_archival.txt (default: "${CMAKE_SOURCE_DIR}/.git_archival.txt").
-#   - DESCRIBE_NAME_KEY: Key for describe name in .git_archival.txt (default: "describe-name: ").
-#   - COMMIT_HASH_KEY: Key for commit hash in .git_archival.txt (default: "commit: ").
-
-# Default Format Example:
-#   1.2.3 v1.2.3 v1.2.3-rc1
-
-set(VERSION_PREFIX "v" CACHE STRING "Prefix used in version tags")
-set(VERSION_SUFFIX "[~+-]([a-zA-Z0-9]+)" CACHE STRING "Suffix used in version tags")
-set(VERSION_REGEX "?([0-9]+\\.[0-9]+\\.[0-9]+)" CACHE STRING "Regex for extracting version")
-set(ARCHIVAL_FILE "${CMAKE_SOURCE_DIR}/.git_archival.txt" CACHE STRING "Path to .git_archival.txt")
-set(DESCRIBE_NAME_KEY "describe-name: " CACHE STRING "Key for describe name in .git_archival.txt")
-set(COMMIT_HASH_KEY "commit: " CACHE STRING "Key for commit hash in .git_archival.txt")
-
-
-# Combine prefix and regex
-set(VERSION_REGEX_WITH_PREFIX "^${VERSION_PREFIX}${VERSION_REGEX}")
-
-# Find Git
-find_package(Git)
-
-# Attempt to retrieve version from Git
-if(EXISTS "${CMAKE_SOURCE_DIR}/.git" AND GIT_FOUND)
-    message(STATUS "Using git describe for versioning")
-
-    # Extract the version string
-    execute_process(
-        COMMAND git describe --tags --dirty
-        WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
-        OUTPUT_VARIABLE VERSION_STRING
-        OUTPUT_STRIP_TRAILING_WHITESPACE
-        ERROR_QUIET
-    )
-
-    # If no tags are found, set version to 0 and show a warning
-    if(VERSION_STRING STREQUAL "")
-        set(VERSION_STRING "0.0.0")
-        message(WARNING 
-            "No git tags found. Version set to 0.0.0.\n"
-            "Run 'git fetch --tags' to ensure proper versioning.\n"
-            "For more information, see OpenMC developer documentation."
-        )
-    endif()
-
-    # Extract the commit hash
-    execute_process(
-        COMMAND git rev-parse HEAD
-        WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
-        OUTPUT_VARIABLE COMMIT_HASH
-        OUTPUT_STRIP_TRAILING_WHITESPACE
-    )
-else()
-    message(STATUS "Using archival file for versioning: ${ARCHIVAL_FILE}")
-    if(EXISTS "${ARCHIVAL_FILE}")
-        file(READ "${ARCHIVAL_FILE}" ARCHIVAL_CONTENT)
-
-        # Extract the describe-name line
-        string(REGEX MATCH "${DESCRIBE_NAME_KEY}([^\\n]+)" VERSION_STRING "${ARCHIVAL_CONTENT}")
-        if(VERSION_STRING MATCHES "${DESCRIBE_NAME_KEY}(.*)")
-            set(VERSION_STRING "${CMAKE_MATCH_1}")
-        else()
-            message(FATAL_ERROR "Could not extract version from ${ARCHIVAL_FILE}")
-        endif()
-
-        # Extract the commit hash
-        string(REGEX MATCH "${COMMIT_HASH_KEY}([a-f0-9]+)" COMMIT_HASH "${ARCHIVAL_CONTENT}")
-        if(COMMIT_HASH MATCHES "${COMMIT_HASH_KEY}([a-f0-9]+)")
-            set(COMMIT_HASH "${CMAKE_MATCH_1}")
-        else()
-            message(FATAL_ERROR "Could not extract commit hash from ${ARCHIVAL_FILE}")
-        endif()
-    else()
-        message(FATAL_ERROR "Neither git describe nor ${ARCHIVAL_FILE} is available for versioning.")
-    endif()
-endif()
-
-# Ensure version string format
-if(VERSION_STRING MATCHES "${VERSION_REGEX_WITH_PREFIX}")
-    set(VERSION_NO_SUFFIX "${CMAKE_MATCH_1}")
-else()
-    message(FATAL_ERROR "Invalid version format: Missing base version in ${VERSION_STRING}")
-endif()
-
-# Check for development state
-if(VERSION_STRING MATCHES "-([0-9]+)-g([0-9a-f]+)")
-    set(DEV_STATE "true")
-    set(COMMIT_COUNT "${CMAKE_MATCH_1}")
-    string(REGEX REPLACE "-([0-9]+)-g([0-9a-f]+)" "" VERSION_WITHOUT_META "${VERSION_STRING}")
-else()
-    set(DEV_STATE "false")
-    set(VERSION_WITHOUT_META "${VERSION_STRING}")
-endif()
-
-# Split and set version components
-string(REPLACE "." ";" VERSION_LIST "${VERSION_NO_SUFFIX}")
-list(GET VERSION_LIST 0 VERSION_MAJOR)
-list(GET VERSION_LIST 1 VERSION_MINOR)
-list(GET VERSION_LIST 2 VERSION_PATCH)
-
-# Increment patch number for dev versions
-if(DEV_STATE)
-    math(EXPR VERSION_PATCH "${VERSION_PATCH} + 1")
-endif()
-
-# Export variables
-set(OPENMC_VERSION_MAJOR "${VERSION_MAJOR}")
-set(OPENMC_VERSION_MINOR "${VERSION_MINOR}")
-set(OPENMC_VERSION_PATCH "${VERSION_PATCH}")
-set(OPENMC_VERSION "${VERSION_MAJOR}.${VERSION_MINOR}.${VERSION_PATCH}")
-set(OPENMC_COMMIT_HASH "${COMMIT_HASH}")
-set(OPENMC_DEV_STATE "${DEV_STATE}")
-set(OPENMC_COMMIT_COUNT "${COMMIT_COUNT}")

cmake/OpenMCConfig.cmake.in

@@ -1,45 +1,21 @@
-@PACKAGE_INIT@
+get_filename_component(OpenMC_CMAKE_DIR "${CMAKE_CURRENT_LIST_FILE}" DIRECTORY)
 
-include("${CMAKE_CURRENT_LIST_DIR}/OpenMCConfigVersion.cmake")
-include(CMakeFindDependencyMacro)
-
-# Explicitly calculate prefix if it was not generated above
-if(NOT DEFINED PACKAGE_PREFIX_DIR)
-  get_filename_component(PACKAGE_PREFIX_DIR "${CMAKE_CURRENT_LIST_DIR}/../../.." ABSOLUTE)
+find_package(fmt REQUIRED HINTS ${OpenMC_CMAKE_DIR}/../fmt)
+find_package(gsl-lite REQUIRED HINTS ${OpenMC_CMAKE_DIR}/../gsl-lite)
+find_package(pugixml REQUIRED HINTS ${OpenMC_CMAKE_DIR}/../pugixml)
+find_package(xtl REQUIRED HINTS ${OpenMC_CMAKE_DIR}/../xtl)
+find_package(xtensor REQUIRED HINTS ${OpenMC_CMAKE_DIR}/../xtensor)
+if(@DAGMC_FOUND@)
+  find_package(DAGMC REQUIRED HINTS @DAGMC_DIR@)
 endif()
 
-find_dependency(fmt CONFIG REQUIRED HINTS ${PACKAGE_PREFIX_DIR})
-find_dependency(pugixml CONFIG REQUIRED HINTS ${PACKAGE_PREFIX_DIR})
-
-if(@OPENMC_USE_DAGMC@)
-  find_dependency(DAGMC REQUIRED HINTS @DAGMC_DIR@)
-endif()
-
-if(@OPENMC_USE_LIBMESH@)
+if(@LIBMESH_FOUND@)
   include(FindPkgConfig)
   list(APPEND CMAKE_PREFIX_PATH @LIBMESH_PREFIX@)
   set(PKG_CONFIG_USE_CMAKE_PREFIX_PATH True)
-  pkg_check_modules(LIBMESH REQUIRED @LIBMESH_PC_FILE@>=1.7.0 IMPORTED_TARGET)
+  pkg_check_modules(LIBMESH REQUIRED @LIBMESH_PC_FILE@>=1.6.0 IMPORTED_TARGET)
 endif()
 
-if("@PNG_FOUND@")
-  find_dependency(PNG)
-endif()
-
-if(@OPENMC_USE_MPI@)
-  find_dependency(MPI REQUIRED)
-endif()
-
-if(@OPENMC_USE_OPENMP@)
-  find_dependency(OpenMP REQUIRED)
-endif()
-
-if(@OPENMC_USE_UWUW@ AND NOT ${DAGMC_BUILD_UWUW})
-  message(FATAL_ERROR "UWUW is enabled in OpenMC but the DAGMC installation discovered was not configured with UWUW.")
-endif()
-
-include("${CMAKE_CURRENT_LIST_DIR}/OpenMCTargets.cmake")
-
-if(NOT OpenMC_FIND_QUIETLY)
-    message(STATUS "Found OpenMC: ${PACKAGE_VERSION} (found in ${PACKAGE_PREFIX_DIR})")
+if(NOT TARGET OpenMC::libopenmc)
+  include("${OpenMC_CMAKE_DIR}/OpenMCTargets.cmake")
 endif()

cmake/OpenMCConfigVersion.cmake.in

@@ -0,0 +1,11 @@
+set(PACKAGE_VERSION "@OPENMC_VERSION@")
+
+# Check whether the requested PACKAGE_FIND_VERSION is compatible
+if("${PACKAGE_VERSION}" VERSION_LESS "${PACKAGE_FIND_VERSION}")
+  set(PACKAGE_VERSION_COMPATIBLE FALSE)
+else()
+  set(PACKAGE_VERSION_COMPATIBLE TRUE)
+  if ("${PACKAGE_VERSION}" VERSION_EQUAL "${PACKAGE_FIND_VERSION}")
+    set(PACKAGE_VERSION_EXACT TRUE)
+  endif()
+endif()

docs/Makefile

@@ -45,7 +45,6 @@ help:
 clean:
 	-rm -rf $(BUILDDIR)/*
 	-rm -rf source/pythonapi/generated/
-	-rm -rf doxygen/xml
 
 html:
 	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html

docs/doxygen/Doxyfile

@@ -1,13 +0,0 @@
-# Doxyfile 1.9.1
-
-# This file describes the settings to be used by the documentation system
-# doxygen (www.doxygen.org) for a project.
-
-# Difference with default Doxyfile 1.9.1
-PROJECT_NAME           = OpenMC
-QUIET                  = YES
-WARN_IF_UNDOCUMENTED   = NO
-INPUT                  = ../../include/openmc/capi.h
-GENERATE_HTML          = NO
-GENERATE_LATEX         = NO
-GENERATE_XML           = YES

docs/requirements-rtd.txt

@@ -0,0 +1,11 @@
+sphinx-numfig
+jupyter
+sphinxcontrib-katex
+sphinxcontrib-svg2pdfconverter
+nbsphinx
+numpy
+scipy
+h5py
+pandas
+uncertainties
+matplotlib

docs/source/capi/index.rst

@@ -46,29 +46,41 @@ Type Definitions
 Functions
 ---------
 
-..
-   Once documentation is complete in capi.h, use:
-   .. doxygenfile:: capi.h
-   to populate this documentation without using
-   .. doxygenfunction::
-   for every function.
+.. c:function:: int openmc_calculate_volumes()
 
-.. doxygenfunction:: openmc_calculate_volumes
+   Run a stochastic volume calculation
 
-.. doxygenfunction:: openmc_cell_get_fill
+   :return: Return status (negative if an error occurred)
+   :rtype: int
 
-.. doxygenfunction:: openmc_cell_get_id
+.. c:function:: int openmc_cell_get_fill(int32_t index, int* type, int32_t** indices, int32_t* n)
 
-.. doxygenfunction:: openmc_cell_get_temperature
-
-.. c:function:: int openmc_cell_get_density(int32_t index, const int32_t* instance, double* density)
-
-   Get the density of a cell
+   Get the fill for a cell
 
    :param int32_t index: Index in the cells array
-   :param int32_t* instance: Which instance of the cell. If a null pointer is passed, the density
-                             multiplier of the first instance is returned.
-   :param double* density: Density of the cell in [g/cm3]
+   :param int* type: Type of the fill
+   :param int32_t** indices: Array of material indices for cell
+   :param int32_t* n: Length of indices array
+   :return: Return status (negative if an error occurred)
+   :rtype: int
+
+.. c:function:: int openmc_cell_get_id(int32_t index, int32_t* id)
+
+   Get the ID of a cell
+
+   :param int32_t index: Index in the cells array
+   :param int32_t* id: ID of the cell
+   :return: Return status (negative if an error occurred)
+   :rtype: int
+
+.. c:function:: int openmc_cell_get_temperature(int32_t index, const int32_t* instance, double* T)
+
+   Get the temperature of a cell
+
+   :param int32_t index: Index in the cells array
+   :param int32_t* instance: Which instance of the cell. If a null pointer is passed, the temperature
+                             of the first instance is returned.
+   :param double* T: temperature of the cell
    :return: Return status (negative if an error occurred)
    :rtype: int
 
@@ -101,22 +113,8 @@ Functions
    :param double T: Temperature in Kelvin
    :param instance: Which instance of the cell. To set the temperature for all
                     instances, pass a null pointer.
-   :param bool set_contained: If the cell is not filled by a material, whether
-                              to set the temperatures of all filled cells
-   :type instance: const int32_t*
-   :return: Return status (negative if an error occurred)
-   :rtype: int
-
-.. c:function:: int openmc_cell_set_density(index index, double density, const int32_t* instance, bool set_contained)
-
-   Set the density of a cell.
-
-   :param int32_t index: Index in the cells array
-   :param double density: Density of the cell in [g/cm3]
-   :param instance: Which instance of the cell. To set the density multiplier for all
-                    instances, pass a null pointer.
-   :param bool set_contained: If the cell is not filled by a material, whether
-                              to set the density multiplier of all filled cells
+   :param set_contained: If the cell is not filled by a material, whether to set the temperatures
+                         of all filled cells
    :type instance: const int32_t*
    :return: Return status (negative if an error occurred)
    :rtype: int
@@ -357,7 +355,7 @@ Functions
    Get density of a material.
 
    :param int32_t index: Index in the materials array
-   :param double* density: Pointer to a density
+   :param double* denity: Pointer to a density
    :return: Return status (negative if an error occurs)
    :rtype: int
 
@@ -422,16 +420,6 @@ Functions
    :return: Return status (negative if an error occurred)
    :rtype: int
 
-.. c:function:: int openmc_mesh_filter_get_mesh(int32_t index, int32_t* index_mesh)
-
-   Get the mesh for a mesh filter
-
-   :param int32_t index: Index in the filters array
-   :param index_mesh: Index in the meshes array
-   :type index_mesh: int32_t*
-   :return: Return status (negative if an error occurred)
-   :rtype: int
-
 .. c:function:: int openmc_mesh_filter_set_mesh(int32_t index, int32_t index_mesh)
 
    Set the mesh for a mesh filter
@@ -441,98 +429,6 @@ Functions
    :return: Return status (negative if an error occurred)
    :rtype: int
 
-.. c:function:: int openmc_mesh_filter_get_translation(int32_t index, double translation[3])
-
-   Get the 3-D translation coordinates for a mesh filter
-
-   :param int32_t index: Index in the filters array
-   :param double[3] translation: 3-D translation coordinates
-   :return: Return status (negative if an error occurred)
-   :rtype: int
-
-.. c:function:: int openmc_mesh_filter_set_translation(int32_t index, double translation[3])
-
-   Set the 3-D translation coordinates for a mesh filter
-
-   :param int32_t index: Index in the filters array
-   :param double[3] translation: 3-D translation coordinates
-   :return: Return status (negative if an error occurred)
-   :rtype: int
-
-.. c:function:: int openmc_meshborn_filter_get_mesh(int32_t index, int32_t* index_mesh)
-
-   Get the mesh for a meshborn filter
-
-   :param int32_t index: Index in the filters array
-   :param index_mesh: Index in the meshes array
-   :type index_mesh: int32_t*
-   :return: Return status (negative if an error occurred)
-   :rtype: int
-
-.. c:function:: int openmc_meshborn_filter_set_mesh(int32_t index, int32_t index_mesh)
-
-   Set the mesh for a meshborn filter
-
-   :param int32_t index: Index in the filters array
-   :param int32_t index_mesh: Index in the meshes array
-   :return: Return status (negative if an error occurred)
-   :rtype: int
-
-.. c:function:: int openmc_meshborn_filter_get_translation(int32_t index, double translation[3])
-
-   Get the 3-D translation coordinates for a meshborn filter
-
-   :param int32_t index: Index in the filters array
-   :param double[3] translation: 3-D translation coordinates
-   :return: Return status (negative if an error occurred)
-   :rtype: int
-
-.. c:function:: int openmc_meshborn_filter_set_translation(int32_t index, double translation[3])
-
-   Set the 3-D translation coordinates for a meshborn filter
-
-   :param int32_t index: Index in the filters array
-   :param double[3] translation: 3-D translation coordinates
-   :return: Return status (negative if an error occurred)
-   :rtype: int
-
-.. c:function:: int openmc_meshsurface_filter_get_mesh(int32_t index, int32_t* index_mesh)
-
-   Get the mesh for a mesh surface filter
-
-   :param int32_t index: Index in the filters array
-   :param index_mesh: Index in the meshes array
-   :type index_mesh: int32_t*
-   :return: Return status (negative if an error occurred)
-   :rtype: int
-
-.. c:function:: int openmc_meshsurface_filter_set_mesh(int32_t index, int32_t index_mesh)
-
-   Set the mesh for a mesh surface filter
-
-   :param int32_t index: Index in the filters array
-   :param int32_t index_mesh: Index in the meshes array
-   :return: Return status (negative if an error occurred)
-   :rtype: int
-
-.. c:function:: int openmc_meshsurface_filter_get_translation(int32_t index, double translation[3])
-
-   Get the 3-D translation coordinates for a mesh surface filter
-
-   :param int32_t index: Index in the filters array
-   :param double[3] translation: 3-D translation coordinates
-   :return: Return status (negative if an error occurred)
-   :rtype: int
-
-.. c:function:: int openmc_meshsurface_filter_set_translation(int32_t index, double translation[3])
-
-   Set the 3-D translation coordinates for a mesh surface filter
-
-   :param int32_t index: Index in the filters array
-   :param double[3] translation: 3-D translation coordinates
-   :return: Return status (negative if an error occurred)
-   :rtype: int
-
 .. c:function:: int openmc_next_batch()
 
    Simulate next batch of particles. Must be called after openmc_simulation_init().
@@ -557,279 +453,6 @@ Functions
    :return: Return status (negative if an error occurs)
    :rtype: int
 
-.. c:function:: int openmc_get_plot_index(int32_t id, int32_t* index)
-
-   Get the index in the plots array for a plot with a given ID.
-
-   :param int32_t id: Plot ID
-   :param int32_t* index: Index in the plots array
-   :return: Return status (negative if an error occurred)
-   :rtype: int
-
-.. c:function:: int openmc_plot_get_id(int32_t index, int32_t* id)
-
-   Get the ID of a plot.
-
-   :param int32_t index: Index in the plots array
-   :param int32_t* id: Plot ID
-   :return: Return status (negative if an error occurred)
-   :rtype: int
-
-.. c:function:: int openmc_plot_set_id(int32_t index, int32_t id)
-
-   Set the ID of a plot.
-
-   :param int32_t index: Index in the plots array
-   :param int32_t id: Plot ID
-   :return: Return status (negative if an error occurred)
-   :rtype: int
-
-.. c:function:: size_t openmc_plots_size()
-
-   Number of plots currently allocated.
-
-   :return: Number of plots in the plots array
-   :rtype: size_t
-
-.. c:function:: int openmc_solidraytrace_plot_create(int32_t* index)
-
-   Create a new solid raytrace plot.
-
-   :param int32_t* index: Index of the newly created plot
-   :return: Return status (negative if an error occurred)
-   :rtype: int
-
-.. c:function:: int openmc_solidraytrace_plot_get_pixels(int32_t index, int32_t* width, int32_t* height)
-
-   Get output pixel dimensions for a solid raytrace plot.
-
-   :param int32_t index: Index in the plots array
-   :param int32_t* width: Image width in pixels
-   :param int32_t* height: Image height in pixels
-   :return: Return status (negative if an error occurred)
-   :rtype: int
-
-.. c:function:: int openmc_solidraytrace_plot_set_pixels(int32_t index, int32_t width, int32_t height)
-
-   Set output pixel dimensions for a solid raytrace plot.
-
-   :param int32_t index: Index in the plots array
-   :param int32_t width: Image width in pixels
-   :param int32_t height: Image height in pixels
-   :return: Return status (negative if an error occurred)
-   :rtype: int
-
-.. c:function:: int openmc_solidraytrace_plot_get_color_by(int32_t index, int32_t* color_by)
-
-   Get the domain type used for coloring (0=materials, 1=cells).
-
-   :param int32_t index: Index in the plots array
-   :param int32_t* color_by: Coloring mode
-   :return: Return status (negative if an error occurred)
-   :rtype: int
-
-.. c:function:: int openmc_solidraytrace_plot_set_color_by(int32_t index, int32_t color_by)
-
-   Set the domain type used for coloring (0=materials, 1=cells).
-
-   :param int32_t index: Index in the plots array
-   :param int32_t color_by: Coloring mode
-   :return: Return status (negative if an error occurred)
-   :rtype: int
-
-.. c:function:: int openmc_solidraytrace_plot_set_default_colors(int32_t index)
-
-   Set default random colors for the current ``color_by`` mode.
-
-   :param int32_t index: Index in the plots array
-   :return: Return status (negative if an error occurred)
-   :rtype: int
-
-.. c:function:: int openmc_solidraytrace_plot_set_all_opaque(int32_t index)
-
-   Mark all domains in the current ``color_by`` mode as opaque.
-
-   :param int32_t index: Index in the plots array
-   :return: Return status (negative if an error occurred)
-   :rtype: int
-
-.. c:function:: int openmc_solidraytrace_plot_set_opaque(int32_t index, int32_t id, bool visible)
-
-   Set whether a specific domain ID is opaque (visible) in the rendered image.
-
-   :param int32_t index: Index in the plots array
-   :param int32_t id: Cell/material ID (based on ``color_by``)
-   :param bool visible: Whether the domain is opaque
-   :return: Return status (negative if an error occurred)
-   :rtype: int
-
-.. c:function:: int openmc_solidraytrace_plot_set_color(int32_t index, int32_t id, uint8_t r, uint8_t g, uint8_t b)
-
-   Set RGB color for a specific domain ID.
-
-   :param int32_t index: Index in the plots array
-   :param int32_t id: Cell/material ID (based on ``color_by``)
-   :param uint8_t r: Red channel
-   :param uint8_t g: Green channel
-   :param uint8_t b: Blue channel
-   :return: Return status (negative if an error occurred)
-   :rtype: int
-
-.. c:function:: int openmc_solidraytrace_plot_get_color(int32_t index, int32_t id, uint8_t* r, uint8_t* g, uint8_t* b)
-
-   Get RGB color for a specific domain ID.
-
-   :param int32_t index: Index in the plots array
-   :param int32_t id: Cell/material ID (based on ``color_by``)
-   :param uint8_t* r: Red channel
-   :param uint8_t* g: Green channel
-   :param uint8_t* b: Blue channel
-   :return: Return status (negative if an error occurred)
-   :rtype: int
-
-.. c:function:: int openmc_solidraytrace_plot_get_camera_position(int32_t index, double* x, double* y, double* z)
-
-   Get camera position.
-
-   :param int32_t index: Index in the plots array
-   :param double* x: X coordinate
-   :param double* y: Y coordinate
-   :param double* z: Z coordinate
-   :return: Return status (negative if an error occurred)
-   :rtype: int
-
-.. c:function:: int openmc_solidraytrace_plot_set_camera_position(int32_t index, double x, double y, double z)
-
-   Set camera position.
-
-   :param int32_t index: Index in the plots array
-   :param double x: X coordinate
-   :param double y: Y coordinate
-   :param double z: Z coordinate
-   :return: Return status (negative if an error occurred)
-   :rtype: int
-
-.. c:function:: int openmc_solidraytrace_plot_get_look_at(int32_t index, double* x, double* y, double* z)
-
-   Get camera target point.
-
-   :param int32_t index: Index in the plots array
-   :param double* x: X coordinate
-   :param double* y: Y coordinate
-   :param double* z: Z coordinate
-   :return: Return status (negative if an error occurred)
-   :rtype: int
-
-.. c:function:: int openmc_solidraytrace_plot_set_look_at(int32_t index, double x, double y, double z)
-
-   Set camera target point.
-
-   :param int32_t index: Index in the plots array
-   :param double x: X coordinate
-   :param double y: Y coordinate
-   :param double z: Z coordinate
-   :return: Return status (negative if an error occurred)
-   :rtype: int
-
-.. c:function:: int openmc_solidraytrace_plot_get_up(int32_t index, double* x, double* y, double* z)
-
-   Get the camera up vector.
-
-   :param int32_t index: Index in the plots array
-   :param double* x: X component
-   :param double* y: Y component
-   :param double* z: Z component
-   :return: Return status (negative if an error occurred)
-   :rtype: int
-
-.. c:function:: int openmc_solidraytrace_plot_set_up(int32_t index, double x, double y, double z)
-
-   Set the camera up vector.
-
-   :param int32_t index: Index in the plots array
-   :param double x: X component
-   :param double y: Y component
-   :param double z: Z component
-   :return: Return status (negative if an error occurred)
-   :rtype: int
-
-.. c:function:: int openmc_solidraytrace_plot_get_light_position(int32_t index, double* x, double* y, double* z)
-
-   Get light source position.
-
-   :param int32_t index: Index in the plots array
-   :param double* x: X coordinate
-   :param double* y: Y coordinate
-   :param double* z: Z coordinate
-   :return: Return status (negative if an error occurred)
-   :rtype: int
-
-.. c:function:: int openmc_solidraytrace_plot_set_light_position(int32_t index, double x, double y, double z)
-
-   Set light source position.
-
-   :param int32_t index: Index in the plots array
-   :param double x: X coordinate
-   :param double y: Y coordinate
-   :param double z: Z coordinate
-   :return: Return status (negative if an error occurred)
-   :rtype: int
-
-.. c:function:: int openmc_solidraytrace_plot_get_fov(int32_t index, double* fov)
-
-   Get horizontal field of view in degrees.
-
-   :param int32_t index: Index in the plots array
-   :param double* fov: Field of view in degrees
-   :return: Return status (negative if an error occurred)
-   :rtype: int
-
-.. c:function:: int openmc_solidraytrace_plot_set_fov(int32_t index, double fov)
-
-   Set horizontal field of view in degrees.
-
-   :param int32_t index: Index in the plots array
-   :param double fov: Field of view in degrees
-   :return: Return status (negative if an error occurred)
-   :rtype: int
-
-.. c:function:: int openmc_solidraytrace_plot_get_diffuse_fraction(int32_t index, double* diffuse_fraction)
-
-   Get diffuse-light fraction.
-
-   :param int32_t index: Index in the plots array
-   :param double* diffuse_fraction: Diffuse fraction in [0, 1]
-   :return: Return status (negative if an error occurred)
-   :rtype: int
-
-.. c:function:: int openmc_solidraytrace_plot_set_diffuse_fraction(int32_t index, double diffuse_fraction)
-
-   Set diffuse-light fraction.
-
-   :param int32_t index: Index in the plots array
-   :param double diffuse_fraction: Diffuse fraction in [0, 1]
-   :return: Return status (negative if an error occurred)
-   :rtype: int
-
-.. c:function:: int openmc_solidraytrace_plot_update_view(int32_t index)
-
-   Recompute internal camera/view transforms after camera changes.
-
-   :param int32_t index: Index in the plots array
-   :return: Return status (negative if an error occurred)
-   :rtype: int
-
-.. c:function:: int openmc_solidraytrace_plot_create_image(int32_t index, uint8_t* data_out, int32_t width, int32_t height)
-
-   Render the plot to an RGB image buffer.
-
-   :param int32_t index: Index in the plots array
-   :param uint8_t* data_out: Output buffer of shape ``height*width*3``
-   :param int32_t width: Image width in pixels
-   :param int32_t height: Image height in pixels
-   :return: Return status (negative if an error occurred)
-   :rtype: int
-
 .. c:function:: int openmc_reset()
 
    Resets all tally scores
@@ -837,13 +460,6 @@ Functions
    :return: Return status (negative if an error occurs)
    :rtype: int
 
-.. c:function:: int openmc_remove_tally(int32_t index);
-
-   Given an index of a tally, remove it from the tallies array
-   :param int index: Index in tallies array
-   :return: Return status (negative if an error occurs)
-   :rtype: int
-
 .. c:function:: int openmc_run()
 
    Run a simulation
@@ -851,10 +467,6 @@ Functions
    :return: Return status (negative if an error occurs)
    :rtype: int
 
-.. c:function:: void openmc_run_random_ray()
-
-   Run a random ray simulation
-
 .. c:function:: int openmc_set_n_batches(int32_t n_batches, bool set_max_batches, bool add_statepoint_batch)
 
    Set number of batches and number of max batches

docs/source/conf.py

@@ -11,10 +11,7 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-import os
-from pathlib import Path
-import subprocess
-import sys
+import sys, os
 
 # Determine if we're on Read the Docs server
 on_rtd = os.environ.get('READTHEDOCS', None) == 'True'
@@ -40,7 +37,6 @@ sys.path.insert(0, os.path.abspath('../..'))
 # Add any Sphinx extension module names here, as strings. They can be extensions
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
 extensions = [
-    'breathe',
     'sphinx.ext.autodoc',
     'sphinx.ext.napoleon',
     'sphinx.ext.autosummary',
@@ -48,17 +44,16 @@ extensions = [
     'sphinx.ext.viewcode',
     'sphinxcontrib.katex',
     'sphinx_numfig',
+    'nbsphinx'
 ]
 if not on_rtd:
     extensions.append('sphinxcontrib.rsvgconverter')
-    doxygen_dir = Path(__file__).parents[1] / 'doxygen'
-    subprocess.run(['doxygen'], cwd=doxygen_dir, check=True)
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 
 # The suffix of source filenames.
-source_suffix = {'.rst': 'restructuredtext'}
+source_suffix = '.rst'
 
 # The encoding of source files.
 #source_encoding = 'utf-8'
@@ -68,17 +63,16 @@ master_doc = 'index'
 
 # General information about the project.
 project = 'OpenMC'
-copyright = '2011-2026, Massachusetts Institute of Technology, UChicago Argonne LLC, and OpenMC contributors'
+copyright = '2011-2021, Massachusetts Institute of Technology and OpenMC contributors'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
-
-import openmc
-
+# The short X.Y version.
+version = "0.12"
 # The full version, including alpha/beta/rc tags.
-version = release = openmc.__version__
+release = "0.12.2"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -123,17 +117,14 @@ pygments_style = 'tango'
 # A list of ignored prefixes for module index sorting.
 #modindex_common_prefix = []
 
-# -- Options breathe + doxygen -------------------------------------------------
-
-breathe_projects = {"OpenMC": "../doxygen/xml"}
-breathe_default_project = "OpenMC"
-breathe_domain_by_file_pattern = {"*capi.h": "c"}
 
 # -- Options for HTML output ---------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages
-html_theme = 'sphinx_rtd_theme'
-html_baseurl = "https://docs.openmc.org/en/stable/"
+if not on_rtd:
+    import sphinx_rtd_theme
+    html_theme = 'sphinx_rtd_theme'
+    html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
 
 html_logo = '_images/openmc_logo.png'
 
@@ -147,7 +138,7 @@ html_title = "OpenMC Documentation"
 # The name of an image file (within the static path) to use as favicon of the
 # docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
 # pixels large.
-html_favicon = 'favicon.ico'
+#html_favicon = None
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
@@ -225,7 +216,6 @@ latex_elements = {
 \setcounter{tocdepth}{2}
 \numberwithin{equation}{section}
 \DeclareUnicodeCharacter{03B1}{$\alpha$}
-\DeclareUnicodeCharacter{03C0}{$\pi$}
 """,
 'printindex': r""
 }
@@ -257,7 +247,7 @@ napoleon_use_ivar = True
 intersphinx_mapping = {
     'python': ('https://docs.python.org/3', None),
     'numpy': ('https://numpy.org/doc/stable/', None),
-    'scipy': ('https://docs.scipy.org/doc/scipy/', None),
+    'scipy': ('https://docs.scipy.org/doc/scipy/reference', None),
     'pandas': ('https://pandas.pydata.org/pandas-docs/stable/', None),
-    'matplotlib': ('https://matplotlib.org/stable/', None)
+    'matplotlib': ('https://matplotlib.org/', None)
 }

docs/source/devguide/agentic-tools.rst

@@ -1,104 +0,0 @@
-.. _devguide_agentic_tools:
-
-===========================
-Agentic Development Tools
-===========================
-
-OpenMC ships a set of tools designed for AI coding agents (such as
-`Claude Code`_) that agents can use to navigate and understand the codebase.
-
-.. _Claude Code: https://claude.ai/code
-
-Motivation
-----------
-
-Agentic tools like Claude Code are skilled at using grep to navigate and
-understand large code bases. However, grep can only find exact text matches —
-it cannot discover code that is *conceptually* related but uses different
-naming. Without a "global view" of the codebase that a human developer will
-build up over time, the agent is generally blind to any file it hasn't
-tokenized fully. While it can grep to see who else calls a function, it
-remains blind if other areas might be related but not share identical naming
-conventions.
-
-This problem is mitigated somewhat by using a model with a longer context
-window. OpenMC has somewhere around ~1 million tokens of C++ and ~1 million
-tokens of python. While Claude Code in early 2026 only has a context window
-of 200k tokens, beta versions have extended context windows of 1M tokens,
-and it's not unreasonable to assume that models may be available in the near
-future that greatly exceed these limits.
-
-However, even assuming the entire repository can be fit within a context
-window, there are several downsides to doing this.
-`Model performance degrades significantly as context size increases`_.
-Benchmark results are
-greatly improved if the model has less garbage to pick through. Additionally, API usage
-is typically billed as tokens in/out per turn. As the context file
-grows these costs become much larger. As such, there is still significant
-motivation to solving the above problem, so as to ensure only relevant
-information is drawn into context so as to maximize model performance and
-minimize costs.
-
-Setup
------
-
-The tools are registered as an `MCP (Model Context Protocol)`_ server in
-``.mcp.json`` at the repository root. AI agents that support MCP (such as
-Claude Code) discover them automatically on session start. The underlying
-Python scripts can also be run directly from the command line.
-
-All tools run entirely locally — no API keys or external service accounts are
-required. Python dependencies are installed automatically into an isolated
-virtual environment at ``.claude/cache/.venv/`` on first use.
-
-.. _Model performance degrades significantly as context size increases: https://www.anthropic.com/news/claude-opus-4-6
-.. _MCP (Model Context Protocol): https://modelcontextprotocol.io
-
-RAG Semantic Search
--------------------
-
-The RAG (Retrieval-Augmented Generation) semantic search addresses this
-problem — it finds code by meaning, not just text match, surfacing related code
-across subsystems that ``grep`` would miss entirely. Two MCP tools are provided:
-
-- **openmc_rag_search** — Given a natural-language query, returns the most
-  relevant code chunks with file paths, line numbers, and a preview. Can search
-  code, documentation, or both. Can also find code related to a given file.
-- **openmc_rag_rebuild** — Rebuilds the search index. Should be called after
-  pulling new code or switching branches.
-
-How it works
-^^^^^^^^^^^^
-
-The search pipeline runs entirely on your local CPU:
-
-1. **Chunking.** All C++, Python, and RST files are split into overlapping
-   fixed-size windows (~1000 characters, 25% overlap). This ensures every line
-   of code appears in at least one chunk and most lines appear in two.
-
-2. **Embedding.** Each chunk is embedded into a 384-dimensional vector using
-   the `all-MiniLM-L6-v2`_ sentence-transformer model (22 million parameters).
-   This model runs on CPU with no GPU required. No API key is needed — the
-   model weights are downloaded once from Hugging Face and cached locally.
-
-3. **Indexing.** The vectors are stored in a local LanceDB_ database on disk.
-   Building the full index takes approximately 5 minutes on a machine with
-   10 CPU cores. The index is stored in ``.claude/cache/rag_index/`` and
-   persists across sessions.
-
-4. **Searching.** Your query is embedded using the same model, and the closest
-   chunks are retrieved by vector similarity. Results include the file path,
-   line range, file type, similarity distance, and a text preview.
-
-.. _all-MiniLM-L6-v2: https://huggingface.co/sentence-transformers/all-MiniLM-L6-v2
-.. _LanceDB: https://lancedb.com
-
-Requirements
-^^^^^^^^^^^^
-
-No system dependencies beyond **Python 3.12+** with ``pip``. An internet
-connection is required on first use to download the Python packages and
-embedding model weights; subsequent runs are fully offline. The Python packages
-(``sentence-transformers``, ``lancedb``) and their dependencies (including
-PyTorch, ~2GB) are installed automatically into an isolated virtual environment
-on first use.

docs/source/devguide/contributing.rst

@@ -109,10 +109,9 @@ Leadership Team
 The TC consists of the following individuals:
 
 - `Paul Romano <https://github.com/paulromano>`_
-- `Patrick Shriwise <https://github.com/pshriwise>`_
+- `Sterling Harper <https://github.com/smharper>`_
 - `Adam Nelson <https://github.com/nelsonag>`_
-- `Jonathan Shimwell <https://github.com/shimwell>`_
-- `John Tramm <https://github.com/jtramm>`_
+- `Benoit Forget <https://github.com/bforget>`_
 
 The Project Lead is Paul Romano.
 

docs/source/devguide/docbuild.rst

@@ -5,19 +5,21 @@ Building Sphinx Documentation
 =============================
 
 In order to build the documentation in the ``docs`` directory, you will need to
-have the several third-party Python packages installed, including `Sphinx
-<https://www.sphinx-doc.org/en/master/>`_. To install the necessary
-prerequisites, provide the optional "docs" dependencies when installing OpenMC's
-Python API. That is, from the root directory of the OpenMC repository:
+have the `Sphinx <https://www.sphinx-doc.org/en/master/>`_ third-party Python
+package. The easiest way to install Sphinx is via pip:
 
 .. code-block:: sh
 
-    python -m pip install ".[docs]"
+    pip install sphinx
 
-The OpenMC documentation also uses Doxygen to automatically generate its
-C/C++ API documentation directly from the docstrings available in the source
-code. You will need to have a working installation of Doxygen to generate the
-documentation locally.
+Additionally, you will need several Sphinx extensions that can be installed
+directly with pip:
+
+.. code-block:: sh
+
+    pip install sphinx-numfig
+    pip install sphinxcontrib-katex
+    pip install sphinxcontrib-svg2pdfconverter
 
 -----------------------------------
 Building Documentation as a Webpage

docs/source/devguide/docker.rst

@@ -45,11 +45,12 @@ Now you can run the following to create a `Docker container`_ called
 This command will open an interactive shell running from within the
 Docker container where you have access to use OpenMC.
 
-.. note:: The ``docker run`` command supports many options_
+.. note:: The ``docker run`` command supports many
+          `options <https://docs.docker.com/engine/reference/commandline/run/>`_
           for spawning containers -- including `mounting volumes`_ from the
           host filesystem -- which many users will find useful.
 
-.. _Docker image: https://docs.docker.com/get-started/docker-concepts/the-basics/what-is-an-image/
+.. _Docker image: https://docs.docker.com/engine/reference/commandline/images/
 .. _Docker container: https://www.docker.com/resources/what-container
-.. _options: https://docs.docker.com/reference/cli/docker/container/run/
-.. _mounting volumes: https://docs.docker.com/engine/storage/volumes/
+.. _options: https://docs.docker.com/engine/reference/commandline/run/
+.. _mounting volumes: https://docs.docker.com/storage/volumes/

docs/source/devguide/index.rst

@@ -14,9 +14,7 @@ other related topics.
 
     contributing
     workflow
-    agentic-tools
     styleguide
-    policies
     tests
     user-input
     docbuild

docs/source/devguide/policies.rst

@@ -1,35 +0,0 @@
-.. _devguide_policies:
-
-========
-Policies
-========
-
----------------------
-Python Version Policy
----------------------
-
-OpenMC follows the Scientific Python Ecosystem Coordination guidelines `SPEC 0
-<https://scientific-python.org/specs/spec-0000/>`_ on minimum supported
-versions, which recommends that support for Python versions be dropped 3 years
-after their initial release.
-
--------------------
-C++ Standard Policy
--------------------
-
-C++ code in OpenMC must conform to the most recent C++ standard that is fully
-supported in the `version of the gcc compiler
-<https://gcc.gnu.org/projects/cxx-status.html>`_ that is distributed with the
-oldest version of Ubuntu that is still within its `standard support period
-<https://ubuntu.com/about/release-cycle>`_. Ubuntu 22.04 LTS will be supported
-through April 2027 and is distributed with gcc 11.4.0, which fully supports the
-C++17 standard.
-
---------------------
-CMake Version Policy
---------------------
-
-Similar to the C++ standard policy, the minimum supported version of CMake
-corresponds to whatever version is distributed with the oldest version of Ubuntu
-still within its standard support period. Ubuntu 22.04 LTS is distributed with
-CMake 3.22.

docs/source/devguide/styleguide.rst

@@ -12,26 +12,18 @@ adding new code in OpenMC.
 C++
 ---
 
-.. _styleguide_formatting:
+.. important:: To ensure consistent styling with little effort, this project
+    uses `clang-format <https://clang.llvm.org/docs/ClangFormat.html>`_. The
+    repository contains a ``.clang-format`` file that can be used to
+    automatically apply the style rules that are described below. The easiest
+    way to use clang-format is through a plugin/extension for your editor/IDE
+    that automatically runs clang-format using the ``.clang-format`` file
+    whenever a file is saved.
 
-Automatic Formatting
---------------------
+Indentation
+-----------
 
-To ensure consistent styling with little effort, this project uses `clang-format
-<https://clang.llvm.org/docs/ClangFormat.html>`_. The repository contains a
-``.clang-format`` file that can be used to automatically apply a consistent
-format. The easiest way to use clang-format is to run
-``tools/dev/install-commit-hooks.sh`` to install a post-commit hook that gets
-executed each time a commit is made. Note that this script requires that you
-already have clang-format installed. In addition, you may want to configure your
-editor/IDE to automatically runs clang-format using the ``.clang-format`` file
-whenever a file is saved. For example, `Visual Studio Code
-<https://code.visualstudio.com/docs/cpp/cpp-ide#_code-formatting>`_ includes
-support for running clang-format.
-
-.. note::
-    OpenMC's CI uses `clang-format` version 18. A different version of `clang-format`
-    may produce different line changes and as a result fail the CI test.
+Use two spaces per indentation level.
 
 Miscellaneous
 -------------
@@ -40,15 +32,14 @@ Follow the `C++ Core Guidelines`_ except when they conflict with another
 guideline listed here. For convenience, many important guidelines from that
 list are repeated here.
 
-Conform to the C++17 standard.
+Conform to the C++14 standard.
 
 Always use C++-style comments (``//``) as opposed to C-style (``/**/``). (It
 is more difficult to comment out a large section of code that uses C-style
 comments.)
 
 Do not use C-style casting. Always use the C++-style casts ``static_cast``,
-``const_cast``, or ``reinterpret_cast``. (See `ES.49
-<https://isocpp.github.io/CppCoreGuidelines/CppCoreGuidelines#es49-if-you-must-use-a-cast-use-a-named-cast>`_)
+``const_cast``, or ``reinterpret_cast``. (See `ES.49 <http://isocpp.github.io/CppCoreGuidelines/CppCoreGuidelines#es49-if-you-must-use-a-cast-use-a-named-cast>`_)
 
 Source Files
 ------------
@@ -56,7 +47,7 @@ Source Files
 Use a ``.cpp`` suffix for code files and ``.h`` for header files.
 
 Header files should always use include guards with the following style (See
-`SF.8 <https://isocpp.github.io/CppCoreGuidelines/CppCoreGuidelines#Rs-guards>`_):
+`SF.8 <http://isocpp.github.io/CppCoreGuidelines/CppCoreGuidelines#sf8-use-include-guards-for-all-h-files>`_):
 
 .. code-block:: C++
 
@@ -132,6 +123,94 @@ Variables declared constexpr or const that have static storage duration (exist
 for the duration of the program) should be upper-case with underscores,
 e.g., ``SQRT_PI``.
 
+Use C++-style declarator layout (see `NL.18
+<http://isocpp.github.io/CppCoreGuidelines/CppCoreGuidelines#nl18-use-c-style-declarator-layout>`_):
+pointer and reference operators in declarations should be placed adject to the
+base type rather than the variable name. Avoid declaring multiple names in a
+single declaration to avoid confusion:
+
+.. code-block:: C++
+
+   T* p; // good
+   T& p; // good
+   T *p; // bad
+   T* p, q; // misleading
+
+Curly braces
+------------
+
+For a class declaration, the opening brace should be on the same line that
+lists the name of the class.
+
+.. code-block:: C++
+
+    class Matrix {
+      ...
+    };
+
+For a function definition, the opening and closing braces should each be on
+their own lines.  This helps distinguish function code from the argument list.
+If the entire function fits on one or two lines, then the braces can be on the
+same line. e.g.:
+
+.. code-block:: C++
+
+    return_type function(type1 arg1, type2 arg2)
+    {
+      content();
+    }
+
+    return_type
+    function_with_many_args(type1 arg1, type2 arg2, type3 arg3,
+                            type4 arg4)
+    {
+      content();
+    }
+
+    int return_one() {return 1;}
+
+    int return_one()
+    {return 1;}
+
+For a conditional, the opening brace should be on the same line as the end of
+the conditional statement. If there is a following ``else if`` or ``else``
+statement, the closing brace should be on the same line as that following
+statement. Otherwise, the closing brace should be on its own line. A one-line
+conditional can have the closing brace on the same line or it can omit the
+braces entirely e.g.:
+
+.. code-block:: C++
+
+    if (condition) {
+      content();
+    }
+
+    if (condition1) {
+      content();
+    } else if (condition 2) {
+      more_content();
+    } else {
+      further_content();
+    }
+
+    if (condition) {content()};
+
+    if (condition) content();
+
+For loops similarly have an opening brace on the same line as the statement and
+a closing brace on its own line. One-line loops may have the closing brace on
+the same line or omit the braces entirely.
+
+.. code-block:: C++
+
+    for (int i = 0; i < 5; i++) {
+      content();
+    }
+
+    for (int i = 0; i < 5; i++) {content();}
+
+    for (int i = 0; i < 5; i++) content();
+
 Documentation
 -------------
 
@@ -147,7 +226,7 @@ Style for Python code should follow PEP8_.
 
 Docstrings for functions and methods should follow numpydoc_ style.
 
-Python code should work with Python 3.8+.
+Python code should work with Python 3.4+.
 
 Use of third-party Python packages should be limited to numpy_, scipy_,
 matplotlib_, pandas_, and h5py_. Use of other third-party packages must be
@@ -157,11 +236,11 @@ Prefer pathlib_ when working with filesystem paths over functions in the os_
 module or other standard-library modules. Functions that accept arguments that
 represent a filesystem path should work with both strings and Path_ objects.
 
-.. _C++ Core Guidelines: https://isocpp.github.io/CppCoreGuidelines/CppCoreGuidelines
-.. _PEP8: https://peps.python.org/pep-0008/
+.. _C++ Core Guidelines: http://isocpp.github.io/CppCoreGuidelines/CppCoreGuidelines
+.. _PEP8: https://www.python.org/dev/peps/pep-0008/
 .. _numpydoc: https://numpydoc.readthedocs.io/en/latest/format.html
 .. _numpy: https://numpy.org/
-.. _scipy: https://scipy.org/
+.. _scipy: https://www.scipy.org/
 .. _matplotlib: https://matplotlib.org/
 .. _pandas: https://pandas.pydata.org/
 .. _h5py: https://www.h5py.org/

docs/source/devguide/tests.rst

@@ -23,28 +23,25 @@ Prerequisites
   OpenMC in development/editable mode. With setuptools, this is accomplished by
   running::
 
-      python -m pip install -e .[test]
+      python setup.py develop
+
+  or using pip (recommended)::
+
+      pip install -e .[test]
 
 - The test suite requires a specific set of cross section data in order for
   tests to pass. A download URL for the data that OpenMC expects can be found
-  within ``tools/ci/download-xs.sh``. Once the tarball is downloaded and
-  unpacked, set the :envvar:`OPENMC_CROSS_SECTIONS` environment variable to the
-  path of the ``cross_sections.xml`` file within the unpacked data.
+  within ``tools/ci/download-xs.sh``.
 - In addition to the HDF5 data, some tests rely on ENDF files. A download URL
-  for those can also be found in ``tools/ci/download-xs.sh``. Once the tarball
-  is downloaded and unpacked, set the :envvar:`OPENMC_ENDF_DATA` environment
-  variable to the top-level directory of the unpacked tarball.
+  for those can also be found in ``tools/ci/download-xs.sh``.
 - Some tests require `NJOY <https://www.njoy21.io/NJOY2016>`_ to preprocess
   cross section data. The test suite assumes that you have an ``njoy``
   executable available on your :envvar:`PATH`.
-- OpenMC should be compiled with ``-DOPENMC_ENABLE_STRICT_FP=on`` to ensure
-  reproducible floating-point results across platforms and optimization levels.
-  Without this flag, regression tests may not match reference values.
 
 Running Tests
 -------------
 
-To execute the Python test suite, go to the ``tests/`` directory and run::
+To execute the test suite, go to the ``tests/`` directory and run::
 
     pytest
 
@@ -54,65 +51,6 @@ installed and run::
 
     pytest --cov=../openmc --cov-report=html
 
-To execute the C++ test suite, go to your build directory and run::
-
-    ctest
-
-If you want to view testing output on failure run::
-
-    ctest --output-on-failure
-
-Possible Reasons for Test Failures
-----------------------------------
-
-You may find that when you run the test suite, not everything passes. First,
-make sure you have satisfied all the prerequisites above. After you have done
-that, consider the following:
-
-- When building OpenMC, make sure you run CMake with
-  ``-DOPENMC_ENABLE_STRICT_FP=on``. This prevents the compiler from applying
-  floating-point optimizations (such as replacing math library calls with
-  builtins or contracting multiply-add into FMA instructions) that can produce
-  bit-level differences across platforms and optimization levels. Any
-  ``CMAKE_BUILD_TYPE`` can be used.
-- Because tallies involve the sum of many floating point numbers, the
-  non-associativity of floating point numbers can result in different answers
-  especially when the number of threads is high (different order of operations).
-  Thus, if you are running on a CPU with many cores, you may need to limit the
-  number of OpenMP threads used. It is recommended to set the
-  :envvar:`OMP_NUM_THREADS` environment variable to 2.
-- Recent versions of NumPy use instruction dispatch that may generate different
-  results depending the particular ISA that you are running on. To avoid issues,
-  you may need to disable AVX512 instructions. This can be done by setting the
-  :envvar:`NPY_DISABLE_CPU_FEATURES` environment variable to "AVX512F
-  AVX512_SKX". When NumPy/SciPy are built against OpenBLAS, you may also need to
-  limit the number of threads that OpenBLAS uses internally; this can be done by
-  setting the :envvar:`OPENBLAS_NUM_THREADS` environment variable to 1.
-
-Debugging Tests in CI
----------------------
-
-Tests can be debugged in CI using a feature called 
-`tmate <https://github.com/mxschmitt/action-tmate?tab=readme-ov-file#debug-your-github-actions-by-using-tmate>`_. 
-CI debugging can be
-enabled by including "[gha-debug]" in the commit message. When the test fails, a
-link similar to the one shown below will be provided in the GitHub Actions
-output after failure occurs. Logging into the provided link will allow you to
-debug the test in the CI environment. The following is an example of the output
-shown in the CI log that provides the link to the tmate session:
-
-.. code-block:: text
-   :linenos:
-
-   Created new session successfully
-   ssh 2VcykjU7vNdvAzEjQcc839GM2@nyc1.tmate.io
-   https://tmate.io/t/2VcykjU7vNdvAzEjQcc839GM2
-   Entering main loop
-   Web shell: https://tmate.io/t/2VcykjU7vNdvAzEjQcc839GM2
-   SSH: ssh 2VcykjU7vNdvAzEjQcc839GM2@nyc1.tmate.io
-   ...
-
-
 Generating XML Inputs
 ---------------------
 
@@ -124,23 +62,6 @@ run::
 
     pytest --build-inputs <name-of-test>
 
-Adding C++ Unit Tests
----------------------
-
-The C++ test suite uses Catch2 integrated with CTest. Each header file should
-have a corresponding test file in ``tests/cpp_unit_tests/``. If the test file
-does not exist run::
-
-    touch test_<name-of-header-file>.cpp
-
-The file must be added to the CMake build system in
-``tests/cpp_unit_tests/CMakeLists.txt``. ``test_<name-of-header-file>`` should
-be added to ``TEST_NAMES``.
-
-To add a test case to ``test_<name-of-header-file>.cpp`` ensure
-``catch2/catch_test_macros.hpp`` is included. A unit test can then be added
-using the ``TEST_CASE`` macro and the ``REQUIRE`` assertion from Catch2.
-
 Adding Tests to the Regression Suite
 ------------------------------------
 
@@ -163,12 +84,6 @@ following files to your new test directory:
       compiler options during openmc configuration and build (e.g., no MPI, no
       debug/optimization).
 
-For tests using the Python API, both the **inputs_true.dat** and
-**results_true.dat** files can be generated automatically in the correct format
-via::
-
-    pytest --update <name-of-test>
-
 In addition to this description, please see the various types of tests that are
 already included in the test suite to see how to create them. If all is
 implemented correctly, the new test will automatically be discovered by pytest.

docs/source/devguide/user-input.rst

@@ -49,12 +49,23 @@ following steps should be followed to make changes to user input:
    written out to the statepoint or summary files and that the
    :class:`openmc.StatePoint` and :class:`openmc.Summary` classes read them in.
 
+7. Finally, a set of `RELAX NG`_ schemas exists that enables validation of input
+   files. You should modify the RELAX NG schema for the file you changed. The
+   easiest way to do this is to change the `compact syntax`_ file
+   (e.g. ``src/relaxng/geometry.rnc``) and then convert it to regular XML syntax
+   using trang_::
+
+       trang geometry.rnc geometry.rng
+
 For most user input additions and changes, it is simple enough to follow a
 "monkey see, monkey do" approach. When in doubt, contact your nearest OpenMC
 developer or send a message to the `developers mailing list`_.
 
 
 .. _property attribute: https://docs.python.org/3.6/library/functions.html#property
-.. _XML Schema Part 2: https://www.w3.org/TR/xmlschema-2/
-.. _boolean: https://www.w3.org/TR/xmlschema-2/#boolean
+.. _XML Schema Part 2: http://www.w3.org/TR/xmlschema-2/
+.. _boolean: http://www.w3.org/TR/xmlschema-2/#boolean
+.. _RELAX NG: https://relaxng.org/
+.. _compact syntax: https://relaxng.org/compact-tutorial-20030326.html
+.. _trang: https://relaxng.org/jclark/trang.html
 .. _developers mailing list: https://groups.google.com/forum/?fromgroups=#!forum/openmc-dev

docs/source/devguide/workflow.rst

@@ -4,7 +4,7 @@
 Development Workflow
 ====================
 
-Anyone wishing to make contributions to OpenMC should be fully acquainted and
+Anyone wishing to make contributions to OpenMC should be fully acquianted and
 comfortable working with git_ and GitHub_. We assume here that you have git
 installed on your system, have a GitHub account, and have setup SSH keys to be
 able to create/push to repositories on GitHub.
@@ -67,12 +67,6 @@ features and bug fixes. The general steps for contributing are as follows:
        cd openmc
        git checkout -b newbranch develop
 
-3. Run ``tools/dev/install-commit-hooks.sh`` to install a post-commit hook that
-   runs clang-format on C++ files to apply :ref:`automatic code formatting
-   <styleguide_formatting>` (requires that clang-format already be installed).
-   In addition, you may want to configure your text editor to automatically run
-   clang-format when saving C++ files.
-
 3. Make your changes on the new branch that you intend to have included in
    *develop*. If you have made other changes that should not be merged back,
    ensure that those changes are made on a different branch.
@@ -81,7 +75,7 @@ features and bug fixes. The general steps for contributing are as follows:
    openmc-dev/openmc as the target.
 
    At a minimum, you should describe what the changes you've made are and why
-   you are making them. If the changes are related to an outstanding issue, make
+   you are making them. If the changes are related to an oustanding issue, make
    sure it is cross-referenced.
 
 5. A committer will review your pull request based on the criteria
@@ -91,30 +85,6 @@ features and bug fixes. The general steps for contributing are as follows:
 6. After the pull request has been thoroughly vetted, it is merged back into the
    *develop* branch of openmc-dev/openmc.
 
-Setting Up Upstream Tracking (Required for Versioning)
-------------------------------------------------------
-
-By default, your fork **does not** include tags from the upstream OpenMC repository.  
-OpenMC relies on `git describe --tags` for versioning in source builds, and missing tags can lead  
-to incorrect version detection (i.e., ``0.0.0``). To ensure proper versioning, follow these steps:
-
-1. **Add the Upstream Repository**  
-   This allows you to fetch updates from the main OpenMC repository.
-
-   .. code-block:: sh
-
-       git remote add upstream https://github.com/openmc-dev/openmc.git
-
-2. **Fetch and Push Tags**  
-   Retrieve tags from the upstream repository and update your fork:
-
-   .. code-block:: sh
-
-       git fetch --tags upstream
-       git push --tags origin
-
-This ensures that both your **local** and **remote** fork have the correct versioning information.
-
 Private Development
 -------------------
 
@@ -140,20 +110,20 @@ pip_. From the root directory of the OpenMC repository, run:
 
 .. code-block:: sh
 
-    python -m pip install -e .[test]
+    pip install -e .[test]
 
 This installs the OpenMC Python package in `"editable" mode
-<https://pip.pypa.io/en/stable/cli/pip_install/#editable-installs>`_ so that 1)
-it can be imported from a Python interpreter and 2) any changes made are
+<https://pip.pypa.io/en/stable/reference/pip_install/#editable-installs>`_ so
+that 1) it can be imported from a Python interpreter and 2) any changes made are
 immediately reflected in the installed version (that is, you don't need to keep
 reinstalling it). While the same effect can be achieved using the
 :envvar:`PYTHONPATH` environment variable, this is generally discouraged as it
 can interfere with virtual environments.
 
-.. _git: https://git-scm.com/
+.. _git: http://git-scm.com/
 .. _GitHub: https://github.com/
 .. _git flow: https://nvie.com/git-model
-.. _valgrind: https://valgrind.org/
+.. _valgrind: https://www.valgrind.org/
 .. _style guide: https://docs.openmc.org/en/latest/devguide/styleguide.html
 .. _pull request: https://docs.github.com/en/github/collaborating-with-issues-and-pull-requests/about-pull-requests
 .. _openmc-dev/openmc: https://github.com/openmc-dev/openmc

docs/source/examples/cad-based-geometry.ipynb

@@ -0,0 +1 @@
+../../../examples/jupyter/cad-based-geometry.ipynb

docs/source/examples/candu.ipynb

@@ -0,0 +1 @@
+../../../examples/jupyter/candu.ipynb

docs/source/examples/capi.ipynb

@@ -0,0 +1 @@
+../../../examples/jupyter/capi.ipynb

docs/source/examples/expansion-filters.ipynb

@@ -0,0 +1 @@
+../../../examples/jupyter/expansion-filters.ipynb

docs/source/examples/hexagonal-lattice.ipynb

@@ -0,0 +1 @@
+../../../examples/jupyter/hexagonal-lattice.ipynb

docs/source/examples/index.rst

@@ -0,0 +1,73 @@
+.. _examples:
+
+========
+Examples
+========
+
+The following series of `Jupyter <https://jupyter.org/>`_ Notebooks provide
+examples for how to use various features of OpenMC by leveraging the
+:ref:`pythonapi`.
+
+-------------
+General Usage
+-------------
+
+.. toctree::
+    :maxdepth: 1
+
+    pincell
+    post-processing
+    pandas-dataframes
+    tally-arithmetic
+    capi
+    expansion-filters
+    search
+    nuclear-data
+    nuclear-data-resonance-covariance
+    pincell_depletion
+
+--------
+Geometry
+--------
+
+.. toctree::
+    :maxdepth: 1
+
+    hexagonal-lattice
+    triso
+    candu
+    cad-based-geometry
+
+-----------------------------------
+Multigroup Cross Section Generation
+-----------------------------------
+
+.. toctree::
+    :maxdepth: 1
+
+    mgxs-part-i
+    mgxs-part-ii
+    mgxs-part-iii
+    mdgxs-part-i
+    mdgxs-part-ii
+
+---------------
+Multigroup Mode
+---------------
+
+.. toctree::
+    :maxdepth: 1
+
+    mg-mode-part-i
+    mg-mode-part-ii
+    mg-mode-part-iii
+
+-----------------
+Unstructured Mesh
+-----------------
+
+.. toctree::
+   :maxdepth: 1
+
+   unstructured-mesh-part-i
+   unstructured-mesh-part-ii

docs/source/examples/mdgxs-part-i.ipynb

@@ -0,0 +1 @@
+../../../examples/jupyter/mdgxs-part-i.ipynb

docs/source/examples/mdgxs-part-ii.ipynb

@@ -0,0 +1 @@
+../../../examples/jupyter/mdgxs-part-ii.ipynb

docs/source/examples/mg-mode-part-i.ipynb

@@ -0,0 +1 @@
+../../../examples/jupyter/mg-mode-part-i.ipynb

docs/source/examples/mg-mode-part-ii.ipynb

@@ -0,0 +1 @@
+../../../examples/jupyter/mg-mode-part-ii.ipynb

docs/source/examples/mg-mode-part-iii.ipynb

@@ -0,0 +1 @@
+../../../examples/jupyter/mg-mode-part-iii.ipynb

docs/source/examples/mgxs-part-i.ipynb

@@ -0,0 +1 @@
+../../../examples/jupyter/mgxs-part-i.ipynb

docs/source/examples/mgxs-part-ii.ipynb

@@ -0,0 +1 @@
+../../../examples/jupyter/mgxs-part-ii.ipynb

docs/source/examples/mgxs-part-iii.ipynb

@@ -0,0 +1 @@
+../../../examples/jupyter/mgxs-part-iii.ipynb

docs/source/examples/nuclear-data-resonance-covariance.ipynb

@@ -0,0 +1 @@
+../../../examples/jupyter/nuclear-data-resonance-covariance.ipynb

docs/source/examples/nuclear-data.ipynb

@@ -0,0 +1 @@
+../../../examples/jupyter/nuclear-data.ipynb

docs/source/examples/pandas-dataframes.ipynb

@@ -0,0 +1 @@
+../../../examples/jupyter/pandas-dataframes.ipynb

docs/source/examples/pincell.ipynb

@@ -0,0 +1 @@
+../../../examples/jupyter/pincell.ipynb

docs/source/examples/pincell_depletion.ipynb

@@ -0,0 +1 @@
+../../../examples/jupyter/pincell_depletion.ipynb

docs/source/examples/post-processing.ipynb

@@ -0,0 +1 @@
+../../../examples/jupyter/post-processing.ipynb

docs/source/examples/search.ipynb

@@ -0,0 +1 @@
+../../../examples/jupyter/search.ipynb

docs/source/examples/tally-arithmetic.ipynb

@@ -0,0 +1 @@
+../../../examples/jupyter/tally-arithmetic.ipynb

docs/source/examples/triso.ipynb

@@ -0,0 +1 @@
+../../../examples/jupyter/triso.ipynb

docs/source/examples/unstructured-mesh-part-i.ipynb

@@ -0,0 +1 @@
+../../../examples/jupyter/unstructured-mesh-part-i.ipynb

docs/source/examples/unstructured-mesh-part-ii.ipynb

@@ -0,0 +1 @@
+../../../examples/jupyter/unstructured-mesh-part-ii.ipynb

docs/source/index.rst

@@ -12,7 +12,7 @@ files produced by NJOY. Parallelism is enabled via a hybrid MPI and OpenMP
 programming model.
 
 OpenMC was originally developed by members of the `Computational Reactor Physics
-Group <https://crpg.mit.edu>`_ at the `Massachusetts Institute of Technology
+Group <http://crpg.mit.edu>`_ at the `Massachusetts Institute of Technology
 <https://web.mit.edu>`_ starting in 2011. Various universities, laboratories,
 and other organizations now contribute to the development of OpenMC. For more
 information on OpenMC, feel free to post a message on the `OpenMC Discourse
@@ -36,7 +36,7 @@ Forum <https://openmc.discourse.group/>`_.
     :maxdepth: 1
 
     quickinstall
-    Examples <https://github.com/openmc-dev/openmc/wiki/Example-Jupyter-Notebooks>
+    examples/index
     releasenotes/index
     methods/index
     usersguide/index