菜单
Quantify interfacial excess (Gibbsian excess of solute, in at/nm^2) across an interface — either a single value via the Krakauer-Seidman integral method, or a 2D excess map over the surface. Use when the user wants the amount of an element segregated to an interface or grain boundary.
用 Codex 或 Claude 帮你安装 复制这段 Prompt，粘贴到 Codex、Claude 或其他助手里，让它检查 Skill 页面并帮你完成安装。
基于 SOC 职业分类
Voronoi-cell cluster determination (Felfer et al. 2015) — detect and extract clusters via Voronoi-cell volumes, Delaunay triangulation, and a Kolmogorov-Smirnov test against a randomised reference. Use when the user wants the Voronoi/clusterDetermination method specifically (this is NOT DBSCAN — for density-based DBSCAN use /apt-cluster instead).
Create a new ion color scheme or add ions/colors to the existing one. Produces/updates the `colorScheme` workspace variable used by ranging and 3D visualization everywhere else. Use when the user wants custom ion colors, a new color scheme, or to add a missing ion color.
Per-vertex concentration mapping onto a mesh/interface — compute atom-to-mesh distances, clip a slab around the interface, voxelise by nearest vertex, and apply a concentration kernel to colour each vertex. Use when the user wants a concentration map painted onto an isosurface or modelled grain boundary mesh.
Run quality-control checks on an atom probe dataset before analysis — basic stats, voltage curve, detector hit map (FDM), mass spectrum sanity, coordinate ranges, multi-hit fraction, and automated quality metrics. Use when the user wants to assess data quality or sanity-check a reconstruction.
Create a field desorption map (detector hit-density / concentration image) and optionally a movie of detector activity over the course of the experiment. Use when the user wants an FDM, desorption map, detector image, or to watch features evolve during the measurement.
Full pipeline from voxelisation through proxigram — voxelise, build an isoconcentration surface, then compute single- and multi-ion proxigrams across it in one guided sequence. Use when the user wants a proxigram but does not yet have an interface.
| name | apt-interfacial-excess |
| description | Quantify interfacial excess (Gibbsian excess of solute, in at/nm^2) across an interface — either a single value via the Krakauer-Seidman integral method, or a 2D excess map over the surface. Use when the user wants the amount of an element segregated to an interface or grain boundary. |
| argument-hint | [species] |
Quantify the interfacial excess of a species at an interface — the excess number of solute atoms associated with the interface, in at/nm^2. Use the MATLAB MCP server.
The MATLAB workspace must contain:
pos — ranged/allocated atom probe data with atom/ion columns (from /apt-composition)fv — an interface struct with faces and vertices fields (an isosurface or grain boundary, from /apt-isosurface)If there is no interface yet, tell the user to run /apt-isosurface first. For best statistics the parent pos should exclude unranged atoms. The integral method is well suited to quantifying a few hundred atoms segregated at the interface, so reasonable counting statistics matter.
Data-type note: if the pos columns are single precision and a function throws a type error, cast the coordinates with double().
patchCreateExcessValue(posSpecies, parentPos, interface, vertices) builds the Krakauer-Seidman integral curve and reports a single excess value. It has no return value — the result is displayed directly on the figure (below the integral curve). posSpecies is the subset of pos for the segregating species, parentPos is the full parent table (ideally unranged excluded), interface is the fv struct, and vertices optionally restricts the calculation to a sub-region.
posSpecies = pos(pos.atom == 'B', :); % segregating species (atomic symbol)
interface = fv; % interface struct (faces + vertices)
vertices = []; % [] = use the whole interface; else an Nx3 vertex subset
patchCreateExcessValue(posSpecies, pos, interface, vertices);
Use $ARGUMENTS as the species if the user gave one; otherwise ask which element segregates.
Manual GUI step (do not automate): the figure has interactive controls. Tell the user to use the change Limits button to drag/define the two sections used for the linear regression (the bulk slopes on either side of the interface), then the fig/save button to store the result as a figure. The displayed excess updates as they adjust the limits.
To restrict the calculation to a region away from the dataset edges (better statistics), pass a subset of fv.vertices as the vertices argument instead of [].
patchCreateInterfacialExcessMap(pos, interface, lim, deloc) returns IEmap (excess per vertex, in at/nm^2) and renders it as a colored trisurf over the interface; it also prompts to save a .ply. Important: here pos is a raw Nx3 coordinate matrix of the species atoms (the function uses pos(:,1:3)), not a table. lim is the distance window in nm to count atoms near the interface, and deloc is an optional number of delocalisation (smoothing) passes.
posSpecies = pos(pos.atom == 'B', :);
coords = [posSpecies.x posSpecies.y posSpecies.z]; % Nx3 matrix, not a table
lim = 1; % count atoms within this distance (nm) of the interface
deloc = 1; % optional smoothing passes (omit for none)
IEmap = patchCreateInterfacialExcessMap(coords, fv, lim, deloc);
A uiputfile dialog will appear asking where to save the normalized map as .ply; tell the user they can cancel it to skip the export. The rendered map uses the same X/Y-swapped axis convention as the isosurface (it plots vertices(:,2) against vertices(:,1)).
Tell the user:
lim and deloc used, that IEmap (at/nm^2 per vertex) is in the workspace, and the min/max range printed by the function.Suggested follow-ups: /apt-proxigram for the full concentration-vs-distance profile across the same interface, or patchToPly/the built-in .ply export to view the excess map externally.