FHI-vibes output support and Output Analyzer improvements

Andrei Sobolevrequested to merge
fhi-vibes-output into master

Output Analyzer — structure viewer

  • Animation controls for relaxation and MD trajectories: play/pause, previous/next frame, frame counter
  • Expand/collapse modal for the structure viewer; atom hover and drag work correctly after toggling
  • Initial structure shown even when the run terminated prematurely
  • Disclaimer text displayed when the output file did not terminate regularly, with the parsed error block

Output Analyzer — parsing

  • Retrofit to the new pyfhiaims-based RootParser; old normal-parser path removed
  • Fix crash on output files with no species defined (aims.no_species.out)
  • Fix errorRe regex that caused incorrect error detection
  • Parse FHI-aims warnings and surface them in a dedicated section
  • Fix non-converged MD_light output parsing (#107 (closed))
  • Chemical formula atom counts rendered as subscript

Spectroscopy dashboard (new)

  • Detects raman_spectrum.dat and ir_spectrum.dat in the uploaded folder and shows a Spectroscopy section
  • Spectra are Gaussian-broadened (σ = 5 cm⁻¹, discrete convolution) and max-normalised before display
  • Y-axis labelled Raman intensity (norm.) or IR intensity (norm.) depending on data
  • Per-spectrum line colour picker and line thickness slider in the controls panel
  • InteractiveGraph extended with a lineShape style option (used by other plotters via addLineGroup)

Control Generator — bug fix

  • FormElement.isExplicitlyIncluded() now respects field visibility; previously, fields in hidden sections (e.g. the Raman section when IR spectroscopy was selected) were still included in the generated control.in / vibes.in, producing spurious DFPT dielectric keywords

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