# Mat Xrd Phase Analysis

> Phase identification from experimental XRD using DARA's tree search (Ray-based).

- Skill: `learningmatter-mit/mat-xrd-phase-analysis` (Agent Skill, multi-file: 7 files)
- Install (CLI): `npx skillmds@latest add learningmatter-mit/mat-xrd-phase-analysis`
- Raw SKILL.md: https://api.skillmd.com/api/skills/learningmatter-mit/mat-xrd-phase-analysis/raw
- Safety review: pending (external: skill-scanner PASS, skillspector PASS)
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: learningmatter-mit (https://skillmd.com/u/learningmatter-mit)
- Updated: 2026-09-22
- Page: https://skillmd.com/skills/learningmatter-mit/mat-xrd-phase-analysis

---


# XRD Phase Analysis (DARA Tree Search)

## Goal

Identify crystalline phases present in an XRD pattern by using DARA's phase search (parallelized tree search with BGMN), following the DARA tutorial
([Tutorial 2: Phase analysis with tree search](https://cedergrouphub.github.io/dara/notebooks/phase_search.html)).

This skill:
- Fetches candidate CIFs for a given chemical system (e.g. `Ge-O-Zn`) using either the COD or ICSD database. Any directory of CIFs works as the candidate set -- including structures pulled from Materials Project -- via `--cif_dir` or the `phases` argument of `search_phases`.
- Runs DARA's `search_phases` to search mixtures of phases.
- Saves plots and a human-readable report alongside the pattern.

## Database Sources

DARA searches for structures in experimental databases. It supports:
1. **CODDatabase** (default, `--database cod`): Open-access. DARA will attempt to download CIFs from `crystallography.net`. If the website is offline or unreachable, DARA will automatically look for a local copy at `~/COD_2024` (or the path defined in `~/.dara.yaml`).
2. **ICSDDatabase** (`--database icsd`): Commercial database. Requires a local copy, default path `~/ICSD_2024` (or configured in `~/.dara.yaml`). Online download is not supported for ICSD.

## Requirements

- Dependencies: `dara-xrd` (and its Ray/BGMN stack). The pip distribution is named
  `dara-xrd` but the **import module is `dara`**:

  ```python
  from dara import search_phases
  ```

  Check for the library itself (`python -c "import dara"`), not for an environment
  name -- `import dara_xrd` will always fail.
- Conda environment: `xrd-agent` (see `conda-envs/xrd-agent`) is the environment this
  repo provisions, but it is one deployment option, not a requirement. Where
  `dara-xrd` is already installed on the default interpreter, call `search_phases`
  directly; the `xrd-agent` env and `scripts/phase_search.py` are conveniences.
- BGMN: DARA will prompt to download or use a local BGMN installation.
- For clusters where only some nodes have internet:
  - You can optionally use a **two-step workflow** (download CIFs on a node with internet, run Ray search elsewhere).

## Script

`scripts/phase_search.py`

- Uses:
  - `CODDatabase.get_cifs_by_chemsys(chemical_system, dest_dir=...)`
  - `search_phases(pattern_path, phases, wavelength, instrument_profile)`
- Output directory (default):
  - `phase_analysis_results/` under the **same directory as the XRD pattern**.

## Usage

Use this script when the node where you run it can reach the database servers (for automatic COD CIF download), or when you have a local directory of CIFs/local database installed.

```bash
# Env: xrd-agent
python .agents/skills/mat-xrd-phase-analysis/scripts/phase_search.py \
  --xrd_data .agents/skills/mat-xrd-phase-analysis/examples/GeO2-ZnO/GeO2-ZnO_700C_60min.xrdml \
  --chemical_system "Ge-O-Zn" \
  --database icsd
```

This will:
1. Create `phase_analysis_results/` next to the XRD file.
2. Search and filter CIFs for `Ge-O-Zn` from the ICSD into `phase_analysis_results/cifs/`.
3. Start a local Ray cluster.
4. Run `search_phases(...)`.
5. Write plots and reports into `phase_analysis_results/`.

You can also provide your own CIFs:

```bash
python .../phase_search.py \
  --xrd_data pattern.xrdml \
  --cif_dir /path/to/my_cifs
```

In this case no database lookup is used; only `--cif_dir` is searched.

Specific example:

```bash
python .../phase_search.py \
  --xrd_data .agents/skills/mat-xrd-phase-analysis/examples/GeO2-ZnO/GeO2-ZnO_700C_60min.xrdml \
  --cif_dir .agents/skills/mat-xrd-phase-analysis/examples/GeO2-ZnO/phase_analysis_results/cifs
```

## Arguments (`phase_search.py`)

- `--xrd_data` (required):
  - Path to XRD pattern (`.xy`, `.xrdml`, or `.raw`).
- `--chemical_system`:
  - String like `"Ge-O-Zn"`. Used with COD or ICSD to fetch CIFs when `--cif_dir` is not given.
- `--cif_dir`:
  - Directory containing `.cif` files to search. When set, skips COD/ICSD lookup.
- `--database` (optional):
  - `cod` (default) or `icsd`. Specifies which database to use when using `--chemical_system`.
- `--output_dir`:
  - Custom output directory. Default: `<xrd_dir>/phase_analysis_results/`.
- `--wavelength` (optional):
  - X-ray source: `Cu`, `Co`, `Cr`, `Fe`, `Mo`, or a numeric wavelength in nm. Default: `Cu`.
- `--instrument_profile` (optional):
  - BGMN instrument profile. Default: `Aeris-fds-Pixcel1d-Medipix3`.
- `--quiet`:
  - Suppress verbose logging/prints.

## Outputs

All outputs go under `<output_dir>` (default: `phase_analysis_results/` under the XRD directory):

- **CIFs**
  - `cifs/`: Candidate phases for the chemical system (when downloaded).

- **Search results**
  - `results_summary.json`:
    - `pattern`, `chemical_system`, `cif_dir`
    - `num_solutions`, `best_rwp`
    - `solutions`: list of `{rank, rwp, phase_files}`.
  - `phase_search_report.txt`:
    - Text report similar to the DARA tutorial:
      - Total number of solutions and best `Rwp`.
      - `Rwp of solution i = ... %` for each solution.
      - `Phases found in solution 0:` with grouped phase file names.
      - Paths to the results directory and summary JSON.

- **Plots**
  - `solution_0_refinement.html`, `solution_0_refinement.png`
  - `solution_1_refinement.html`, `solution_1_refinement.png`, etc. (if multiple solutions)
  - Plots come from `SearchResult.visualize()` (observed / calculated / difference pattern, like the tutorial).

## Notes and Constraints

- **Ray / cluster config**:
  - This script assumes you can start a local Ray cluster with `ray.init(address="local", ...)`.
  - On HPC systems with a preconfigured Ray/GCS, you may need a clean environment or a job script that does not inherit cluster-level Ray environment variables.
- **Internet vs no-internet**:
  - On clusters with **internet on compute nodes**, use Mode A (single-step).
  - On clusters with **internet only on login nodes**, use Mode B (two-step).
- **Performance**:
  - Phase search can be CPU-intensive; adjust `num_cpus` in the script’s `ray.init(...)` if needed.

## Related Skills

- **`mat-xrd-digitizer`**:
  - Use this skill first to convert an image/screenshot of an XRD plot into the `.xy` file required by this phase analysis skill.
- **`mat-xrd-refinement`**:
  - For known-phase Rietveld refinement (given specific CIFs).
- **`mat-xrd-calculator`**:
  - For calculating theoretical XRD patterns from crystal structures.

---

**Author:** Nofit Segal
**Contact:** [GitHub @nofitsegal](https://github.com/nofitsegal)