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Agent skill

Mat Xrd Phase Analysis

by learningmatter-mit in learningmatter-mit/AtomisticSkills

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

MITAuto-check passed

Install Mat Xrd Phase Analysis

skills CLI
$ npx skills add learningmatter-mit/AtomisticSkills --skill mat-xrd-phase-analysis -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install learningmatter-mit/AtomisticSkills mat-xrd-phase-analysis --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/mat-xrd-phase-analysis .claude/skills/mat-xrd-phase-analysis && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
mat-xrd-phase-analysis
GitHub stars
176
Token cost
~1.6k tokens
SKILL.md length
697 words
Files
7 (incl. scripts)
Skills in repo
129
Repo updated
First seen
Licence
MIT

At a glance

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

  • Works in 2 steps: CODDatabase (default, --database cod):… → ICSDDatabase (--database icsd):…
  • SKILL.md covers Goal, Database Sources, Requirements and Script, plus 5 more sections
  • Runs Python scripts from its folder; calls python

What it does

Mat Xrd Phase Analysis is an agent skill from learningmatter-mit/AtomisticSkills. Phase identification from experimental XRD using DARA's tree search (Ray-based).

Its SKILL.md is about 1.6k tokens, which your agent loads only when the skill is triggered. The skill folder holds 10 other files, including scripts (for example `examples/GeO2-ZnO/README.md`, `examples/GeO2-ZnO/phase_analysis_results/results_summary.json` and `scripts/dara_utils.py`).

The repository describes itself as: Integrating AtomisticSkills into Agentic IDEs (Cursor, Claude Code, Codex, Google Antigravity, Hermes Agent, etc). The licence is MIT.

Example prompts

  • “/mat-xrd-phase-analysis”

Requirements

  • Python 3

Workflow steps

2 steps, taken from the first numbered list in SKILL.md.

  1. CODDatabase (default, --database cod): Open-access. DARA will attempt to download CIFs from crystallography.net. If the website is offline…
  2. ICSDDatabase (--database icsd): Commercial database. Requires a local copy, default path ~/ICSD_2024 (or configured in ~/.dara.yaml)…

What it can do on your machine

Read from SKILL.md and the folder at commit 6257444. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    Ships 2 files in scripts/ (Python), which the agent can run.

    Shell commands in SKILL.md call:

    • python

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    Links to these hosts (documentation or services it may open):

    • cedergrouphub.github.io
    • github.com

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Mat Xrd Phase Analysis loads about 1.6k tokens when it runs. Until then it costs about 26 tokens; SKILL.md has 697 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~26
When it runs · the whole SKILL.md, loaded when a task matches
~1.6k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.

SKILL.md

The full file from learningmatter-mit/AtomisticSkills at commit 6257444, republished under its MIT licence (© learningmatter-mit). 697 words, ~1,641 tokens.

Download SKILL.mdSave it as .claude/skills/mat-xrd-phase-analysis/SKILL.md (or your agent's skills folder). This skill also uses 6 other files; get the full folder from GitHub.
name
mat-xrd-phase-analysis
description
Phase identification from experimental XRD using DARA's tree search (Ray-based).
metadata.category
materials
metadata.venv
cpu

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).

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.

  • Environment: cpu (it includes dara-xrd; venv/run creates it on first use). Where dara-xrd is already installed on another interpreter, call search_phases directly; scripts/phase_search.py is a convenience.

  • 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
${CLAUDE_SKILL_DIR}/../../venv/run cpu python ${CLAUDE_SKILL_DIR}/scripts/phase_search.py \
  --xrd_data ${CLAUDE_SKILL_DIR}/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 ${CLAUDE_SKILL_DIR}/examples/GeO2-ZnO/GeO2-ZnO_700C_60min.xrdml \
  --cif_dir ${CLAUDE_SKILL_DIR}/examples/GeO2-ZnO/phase_analysis_results/cifs
Show full SKILL.md (316 more words)Show less

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.
  • 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

© learningmatter-mit, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 6 other files (scripts) in skills/mat-xrd-phase-analysis of learningmatter-mit/AtomisticSkills.

  • SKILL.md
  • examples/GeO2-ZnO/GeO2-ZnO_700C_60min.xrdml
  • examples/GeO2-ZnO/README.md
  • examples/GeO2-ZnO/phase_analysis_results/results_summary.json
  • examples/GeO2-ZnO/phase_analysis_results/solution_0_refinement.png
  • scripts/dara_utils.py
  • scripts/phase_search.py

Open the folder on GitHubat commit 6257444

Compare with similar skills

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Gsd Phaseopen-gsd/gsd-core10k1 repos~603Automated safety check: NotesMIT
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Questions about Mat Xrd Phase Analysis

What does Mat Xrd Phase Analysis do?

Phase identification from experimental XRD using DARA's tree search (Ray-based). Mat Xrd Phase Analysis is an agent skill from learningmatter-mit/AtomisticSkills. Phase identification from experimental XRD using DARA's tree search (Ray-based).

How do I install Mat Xrd Phase Analysis in Claude Code?

Run `npx skills add learningmatter-mit/AtomisticSkills --skill mat-xrd-phase-analysis -a claude-code`. Or copy the skill folder (skills/mat-xrd-phase-analysis in learningmatter-mit/AtomisticSkills) into .claude/skills/mat-xrd-phase-analysis in your project. Claude Code loads it when a task matches its description.

How do I install Mat Xrd Phase Analysis in Codex?

Run `npx skills add learningmatter-mit/AtomisticSkills --skill mat-xrd-phase-analysis -a codex`. Or copy the skill folder (skills/mat-xrd-phase-analysis in learningmatter-mit/AtomisticSkills) into .agents/skills/mat-xrd-phase-analysis in your project. Codex loads it when a task matches its description.

Can I use Mat Xrd Phase Analysis in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add learningmatter-mit/AtomisticSkills --skill mat-xrd-phase-analysis -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/mat-xrd-phase-analysis, .gemini/skills/mat-xrd-phase-analysis, .github/skills/mat-xrd-phase-analysis and .opencode/skills/mat-xrd-phase-analysis in your project.

What does Mat Xrd Phase Analysis need to run?

Going by SKILL.md and its folder, Mat Xrd Phase Analysis needs Python for the scripts in its folder and the command-line tools its instructions call (python). Our summary lists: Python 3.

Does Mat Xrd Phase Analysis access the network?

SKILL.md names 2 domains. As links in the text: cedergrouphub.github.io and github.com. This is read from the text; nothing was executed.

Is Mat Xrd Phase Analysis safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.

What licence does Mat Xrd Phase Analysis use?

Mat Xrd Phase Analysis is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Mat Xrd Phase Analysis use?

About 1.6k tokens (SKILL.md is roughly 6.6k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Mat Xrd Phase Analysis?

Skills that share tags, products or a category with Mat Xrd Phase Analysis: More Trees Automation (ComposioHQ/awesome-claude-skills, 77k stars), Pierre Trees File Tree (pierrecomputer/pierre, 6.2k stars), Gsd Phase (open-gsd/gsd-core, 10k stars) and Experimental Design (aiming-lab/AutoResearchClaw, 15k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Mat Xrd Phase Analysis?

learningmatter-mit (a GitHub organization) maintains it in learningmatter-mit/AtomisticSkills, which has 176 GitHub stars. The repository holds 129 skills in this directory. The repository was last updated on October 7, 2026.

Source: learningmatter-mit/AtomisticSkills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.