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mat-xrd-refinement

mat-xrd-refinement is a skill for Claude Code, Codex from learningmatter-mit/AtomisticSkills. It costs 24 tokens per session (2,237 once invoked), scanned A, original, MIT.

Perform Rietveld refinement from experimental XRD patterns using DARA (BGMN).

Skill for Claude CodeCodex

not rated 158 today A scan 24 tokens MIT
View the source file learningmatter-mit/AtomisticSkills
Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

agentmods
npx agentmods add skills/learningmatter-mit/atomisticskills/mat-xrd-refinement
Any agent
npx skills add learningmatter-mit/AtomisticSkills --skill mat-xrd-refinement
Clone the repo
git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills

Made for: Claude Code, Codex.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for mat-xrd-refinement

README.md
[![agentmods](https://agentmods.dev/badge/skills/learningmatter-mit/atomisticskills/mat-xrd-refinement.svg)](https://agentmods.dev/skills/learningmatter-mit/atomisticskills/mat-xrd-refinement)
Your own site
<a href="https://agentmods.dev/skills/learningmatter-mit/atomisticskills/mat-xrd-refinement"><img src="https://agentmods.dev/badge/skills/learningmatter-mit/atomisticskills/mat-xrd-refinement.svg" alt="Measured on agentmods" height="20"></a>
Per session 24 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 2,237 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. Scan, not verified.
Origin unknown No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5 $0.00024 $0.02237
Opus 5 $0.00012 $0.01118
Sonnet 5 $0.00005 $0.00447
Haiku 4.5 $0.00002 $0.00224

Measured today against content hash 2fb2dd5c26fe, method: parsed. Prices are Anthropic first-party input rates as of 2026-08-30, from the pricing page.

Security

Grade A, and why

mat-xrd-refinement scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured today.

The scan reads SKILL.md. This mod also ships 4 executable files (scripts/convert_xrd_to_xy.py, scripts/dara_utils.py, scripts/plot.py, …), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

.agents/skills/mat-xrd-refinement/SKILL.md · 148 lines

How it starts

The opening of the file, as written. The whole thing — 148 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Rietveld Refinement

Goal

Perform quantitative Rietveld refinement of powder X-ray diffraction (XRD) patterns using DARA (Data-driven Automated Rietveld Analysis) with BGMN. Use when you have an experimental (or theoretical) pattern in .xy format and candidate phase CIFs.

Requirements

  • Conda environment: xrd-agent (see conda-envs/xrd-agent).
  • Dependencies: dara-xrd, pymatgen. Optional: kaleido for PNG export (use kaleido>=0.2.1,<0.3 to avoid needing Chrome).
  • BGMN: DARA uses BGMN; ensure it is installed. On HPC without network, set --bgmn_dir or DARA_BGMN_DIR to a local BGMN directory.

Scripts

Script Purpose
scripts/refine.py Run Rietveld refinement with known phases; writes plots and summary under refinement_results/.
scripts/convert_xrd_to_xy.py Convert XRD from JSON (xrd-spectrum) or DIF to .xy for DARA.
scripts/dara_utils.py Helpers (e.g. load_xrd_file); used by other scripts.

Instructions

1. Prepare XRD data (.xy format)

Two columns (2θ and intensity), space-separated. Options:

  • From xrd-spectrum JSON: use convert_xrd_to_xy.py with --input_file your_xrd.json. Output is written next to the input as your_xrd.xy.
  • From experimental DIF: use convert_xrd_to_xy.py with --input_file your_data.txt (or .dif). Format is auto-detected if the file contains a header with 2-THETA and INTENSITY.
# From JSON (e.g. xrd-spectrum output)
python .agents/skills/mat-xrd-refinement/scripts/convert_xrd_to_xy.py --input_file path/to/xrd.json

# From DIF
python .agents/skills/mat-xrd-refinement/scripts/convert_xrd_to_xy.py --input_file path/to/scan.txt

Convert arguments:

  • --input_file: Path to JSON or DIF file.
  • --format: auto (default), json, or dif to force format.

2. Run refinement (refine.py)

Refinement uses DARA’s do_refinement_no_saving (no BGMN working files left on disk). Output is written to refinement_results/ under the same directory as the XRD file (no --output_dir argument).

Read the full file on GitHub · 148 lines

Files

What ships with it

23 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. today First seen · 148 lines · 24 tokens per session scan A 2fb2dd5c26fe

Subscribe to this mod's changes

mat-xrd-refinement is a skill published in the GitHub repository learningmatter-mit/AtomisticSkills (158 stars, last pushed today), licensed MIT. It adds 24 tokens to every session and 2,237 once invoked, about $0.0001 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.

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