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Electron density contour map in a plane (molecular plane or three atoms)

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Avaliação

Dificuldade
5/5
Tempo estimado
3-5 dias
Facilidade para iniciantes
35/100
Tipo de issue
Funcionalidade
Clareza
Claramente especificada
Status de atividade
Ativa
Stack de tecnologia
c
Domínio
data-visualization

Direção de pesquisa

Start by reading ComputeMoCmd in src/viz and the MoDiagramCanvas pattern; the issue calls for a wx-free evaluator library, CLI, tests, a headless render tool and an MO-panel integration. Run the evaluator and rendering tests, then compare point values and plane plots against Multiwfn. Done means the specified density, plane, contour, canvas and export workflows pass the listed numerical and headless-render checks.

Escrita pelo modelo de indexação a partir do texto da issue.

Descrição

enhancement

Summary

A 2D contour map of the electron density (and spin density) in a chosen plane, the classic textbook figure. ECCE already computes the density from each calculation's MO coefficients, occupations and basis (ComputeMoCmd, MO panel "Density" / "Spin Density"), but only on an axis-aligned 3D grid for isosurfaces. The MO panel's "Contour" style draws a single isovalue on the 3D surface, not a map in a plane.

The new application icon (benzene in-plane density, log-spaced contours, viridis) shows this kind of figure. It is currently drawn from a model density; once this feature exists, the icon should be regenerated from ECCE's own output.

Design

Per the project rule, analysis goes in a wx-free library with a CLI and tests; the panel only gathers options and draws.

  1. Point evaluator. Move the density evaluation out of ComputeMoCmd (src/viz) into a wx-free library: ρ(r) = Σ_μν P_μν φ_μ(r) φ_ν(r) from the stored MOs and occupations, at arbitrary points. The 3D grid command then calls the same code, so there is one implementation.
  2. Plane. Default: the least-squares plane through all atoms, used when it fits (RMS deviation below a threshold, e.g. benzene, water). Otherwise the plane through three atoms the user selects. In-plane axes from the principal axes; a margin around the projected atoms.
  3. Contours. Marching squares on a plane grid (resolution about 0.05 Å, adjustable). Log-spaced levels by default (the density spans orders of magnitude), with a linear option, a level count, and limits. Contours of the core density are capped, so the nuclei do not turn into solid blots.
  4. Canvas. A header-only canvas in the MoDiagramCanvas pattern: contour lines in viridis, atom positions and labels, a scale bar in Å, and a colour key giving the level values (e/bohr³). It must be paintable to a bitmap headlessly, with a render tool and a test.
  5. Panel. In the MO panel, beside the isosurface controls: field (density, spin density, a selected MO with signed contours, dashed for negative), plane choice, levels. Export to PNG/SVG.

Verification

  • Evaluator: the density integrated over a large 3D grid gives N electrons (e.g. 10 for water, 42 for benzene) to within grid error. Cusps sit at the nuclei.
  • Against an independent oracle: Multiwfn's plane contour plots of the same Gaussian and ORCA outputs, and point values of ρ at chosen points compared numerically, not by eye.
  • Headless renders for water, benzene and an open-shell case (spin density), reviewed as PNGs.
  • A plane through three atoms of a non-planar molecule (e.g. through H–C–H of CH₄).

Estimate

2–3 days, most of it the evaluator extraction and the oracle comparison.

Linguagem predominante
C
Estrelas
10
Forks
8
Merge médio
57min
PRs com merge (30d)
2

Preparar o ambiente

Este projeto não oferece contêiner de desenvolvimento, Dockerfile nem guia de contribuição, então a configuração fica por sua conta: comece pelo README e veja nosso guia da primeira contribuição para os passos gerais.

Primeiros passos

  1. Leia a issue inteira e depois o guia de contribuição do projeto.
  2. Comente na issue dizendo que vai assumir — evita que duas pessoas façam o mesmo trabalho.
  3. Faça um fork do repositório e trabalhe em uma branch.
  4. Abra um pull request que referencie o número da issue.

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