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name: spectra-diffraction-and-visualization description: "Use pymatgen diffraction calculators, spectrum objects, plotting helpers, FEFF plotting expectations, and optional visualization APIs safely." disable-model-invocation: true metadata: disco-role: operating license: NOASSERTION

Spectra, Diffraction, and Visualization

Use this sub-skill when a task mentions XRDCalculator, NDCalculator, TEMCalculator, DiffractionPattern, XAS, XPS, SpectrumPlotter, headless spectrum or diffraction plotting, optional VTK/chemview structure visualization, or FEFF DOS/cross-section plotting file expectations.

Read This First

• For imports, signatures, return objects, calculator options, plotting helpers, optional visualization APIs, and FEFF helper inputs, read references/api-reference.md.
• For headless-safe recipes covering XRD/ND/TEM, toy XAS/XPS-style spectrum plotting, XAS site weighting, optional visualization, and FEFF caveats, read references/workflows.md.
• For predictable failures involving wavelength labels, scattering data, malformed structures, matplotlib backends, XAS stitching/site weighting, VTK/chemview imports, FEFF inputs, and units, read references/troubleshooting.md.
• To prove the baseline install can compute diffraction peaks and save spectra plots without a GUI, run scripts/diffraction_spectrum_smoke.py with python scripts/diffraction_spectrum_smoke.py --help, then run it with --output-dir.

Routing Boundaries

• Stay here for Python API workflows involving diffraction calculators, DiffractionPattern data, XAS/XPS spectrum objects, generic SpectrumPlotter plots, FEFF plotting input expectations, and visualization dependency decisions.
• Route structure creation, parsing, symmetry cleanup, oxidation-state setup, local environments, and transformations to ../structures-local-environments-and-transformations/SKILL.md before diffraction or visualization work.
• Route command syntax for pmg plot, pmg view, feff_plot_dos, feff_plot_cross_section, console-script discovery, and persistent configuration to ../cli-and-configuration/SKILL.md.
• Route Wulff, slab, surface-energy, Pourbaix, interfacial-reactivity, and electrochemical plotting to ../surfaces-interfaces-and-electrochemistry/SKILL.md.
• Do not treat VTK, chemview, Plotly static export, or FEFF output files as baseline requirements; they are optional or user-data-dependent.

Default Approach

1. Start from an in-memory Structure supplied by the user or produced by another sub-skill; keep reusable examples fixture-free.
2. In automation, select a noninteractive matplotlib backend before importing plotting helpers, then save figures explicitly instead of calling show().
3. Use calculator get_pattern() methods when the user needs peak data, and get_plot() / SpectrumPlotter.save_plot() only when they need plot files.
4. Validate XAS compatibility before combining spectra: matching structures, absorbing element, edge, spectrum type/mode, distinct site-wise absorbing indices, and overlapping energy grids.
5. Explain FEFF helpers as file-based plotters for existing FEFF outputs, not as FEFF calculation generators.