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

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#215 0 comentarios 0 reacciones 0 asignados Ver en GitHub

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Evaluación

Dificultad
5/5
Tiempo estimado
3-5 días
Aptitud para principiantes
35/100
Tipo de issue
Nueva funcionalidad
Claridad
Bien especificado
Estado de actividad
Activo
Stack tecnológico
c
Área
data-visualization

Línea de trabajo

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.

Escrito por el modelo de indexación a partir del texto del issue.

Descripción

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.

Lenguaje dominante
C
Estrellas
10
Forks
8
Merge medio
21 min
PR fusionados (30 d)
1

Preparar el entorno

Este proyecto no incluye contenedor de desarrollo, Dockerfile ni guía de contribución, así que la configuración corre por tu cuenta: empieza por su README y consulta nuestra guía para la primera contribución para los pasos generales.

Primeros pasos

  1. Lee el issue completo y luego la guía de contribución del proyecto.
  2. Comenta en el issue que vas a ocuparte — evita que dos personas hagan lo mismo.
  3. Haz un fork del repositorio y trabaja en una rama.
  4. Abre un pull request que haga referencia al número del issue.

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