Agent examples: an LLM driving the MCP tools (real runs, replayed in CI)

[drthyang]

The first worked examples from the LLM-usage plan. Both were run for real by Claude (Opus 5.5) in Claude Code against the materia MCP server, then written up in docs/AGENT_EXAMPLES.md.

Examples

1. Look at a structure before any data (Mn₃Ga). The prompt asks for the space group, the Wyckoff sites, the first Cu Kα reflections, and any unphysical distance. The model answered in 4 calls, passing refs between them:

• P6₃/mmc, with Mn on 6h (one free coordinate) and Ga on 2d (no free coordinates);
• 100 at 18.9°, 101 at 27.8°, 2-10 at 33.0°, 200 at 38.3°;
• the shortest contact is Mn–Mn at 2.665 Å, which is normal.

2. A PDF fit block by block, then local vs average (GaTa₄Se₈, X-ray, 1.5–28 Å).

Block	Rw
scale + cell	35.3 %
+ anisotropic ADPs	19.3 %
+ Qdamp/Qbroad	12.2 %
+ δ1	8.61 %
+ positions	8.33 % (the demo's published fit is 8.12 %)

The run states three judgement calls:

• Qdamp freed even though no calibration standard ships with the data.
• Qbroad dropped because it sat at its bound.
• δ1 rather than δ2 (one correlated-motion law).

It then ran a boxcar scan. The 1.5–7.5 Å box fits worst (11.0% against 3–6%), and U(Se2) nearly doubles with r while the cell stays flat. A reverse scan agrees within the esds, so the drift is in the data. Conclusion: the local structure differs from the cubic average, and naming the distortion needs a lower-symmetry model.

Keeping the page honest

• examples/mcp/ holds the app's bundled demo data as plain files, so a model can load them by path. It also includes the MnO CIF and a POWGEN .irf for the Rietveld example that comes next.
• src/mcp/examples.test.ts does two jobs:
  • Every file must equal its TypeScript source; UPDATE_MCP_EXAMPLES=1 rewrites them.
  • Each example's tool sequence is replayed through an MCP client, and the page's claims are asserted. It takes about 33 s. MCP_EXAMPLES_FULL=1 adds each block's Rw and the reverse scan (about 80 s), which I ran and which passes.
• Speed: refining all the blocks at once reaches the same minimum (Rw 8.33%, Qdamp 0.0439, δ1 1.778), which keeps the CI replay short.

Next

• Example 2 (Rietveld with the skill): needs check_cell_symmetry and export_bundle. This session's materia server was started before those merged, so it has to be reconnected before that run can be recorded.
• Example 3 (magnetic structure from leftover peaks): needs a synthetic dataset designed first.

Both are listed under "Other planned work" in AGENT_TOOLS.

Tests: 196 files, 1,490 tests pass. tsc -b and eslint . are clean.

🤖 Generated with Claude Code