matterviz 0.4.1 → 0.4.3

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (499) hide show
  1. package/dist/EmptyState.svelte +10 -4
  2. package/dist/FilePicker.svelte +48 -60
  3. package/dist/Icon.svelte +7 -4
  4. package/dist/MillerIndexInput.svelte +2 -2
  5. package/dist/api/optimade.js +10 -7
  6. package/dist/app.css +68 -0
  7. package/dist/brillouin/BrillouinZone.svelte +90 -91
  8. package/dist/brillouin/BrillouinZone.svelte.d.ts +5 -7
  9. package/dist/brillouin/BrillouinZoneControls.svelte +3 -6
  10. package/dist/brillouin/BrillouinZoneExportPane.svelte +18 -14
  11. package/dist/brillouin/BrillouinZoneInfoPane.svelte +6 -10
  12. package/dist/brillouin/BrillouinZoneScene.svelte +46 -68
  13. package/dist/brillouin/BrillouinZoneScene.svelte.d.ts +1 -1
  14. package/dist/brillouin/compute.js +10 -16
  15. package/dist/brillouin/geometry.js +2 -2
  16. package/dist/chempot-diagram/ChemPotDiagram.svelte +48 -50
  17. package/dist/chempot-diagram/ChemPotDiagram2D.svelte +61 -169
  18. package/dist/chempot-diagram/ChemPotDiagram2D.svelte.d.ts +1 -1
  19. package/dist/chempot-diagram/ChemPotDiagram3D.svelte +559 -755
  20. package/dist/chempot-diagram/ChemPotDiagram3D.svelte.d.ts +1 -1
  21. package/dist/chempot-diagram/async-compute.svelte.js +13 -14
  22. package/dist/chempot-diagram/color.d.ts +21 -1
  23. package/dist/chempot-diagram/color.js +70 -1
  24. package/dist/chempot-diagram/compute.d.ts +7 -0
  25. package/dist/chempot-diagram/compute.js +85 -26
  26. package/dist/chempot-diagram/controls-state.svelte.js +1 -1
  27. package/dist/chempot-diagram/export.js +1 -6
  28. package/dist/chempot-diagram/temperature.js +9 -10
  29. package/dist/colors/index.d.ts +0 -4
  30. package/dist/colors/index.js +19 -20
  31. package/dist/composition/BarChart.svelte +30 -26
  32. package/dist/composition/BubbleChart.svelte +17 -17
  33. package/dist/composition/Composition.svelte +10 -19
  34. package/dist/composition/Formula.svelte +20 -27
  35. package/dist/composition/FormulaFilter.svelte +115 -184
  36. package/dist/composition/PieChart.svelte +55 -41
  37. package/dist/composition/format.js +7 -9
  38. package/dist/composition/index.d.ts +2 -0
  39. package/dist/composition/index.js +14 -0
  40. package/dist/composition/parse.d.ts +2 -2
  41. package/dist/composition/parse.js +61 -115
  42. package/dist/constants.d.ts +0 -1
  43. package/dist/constants.js +17 -26
  44. package/dist/convex-hull/ConvexHull.svelte +12 -15
  45. package/dist/convex-hull/ConvexHull.svelte.d.ts +1 -1
  46. package/dist/convex-hull/ConvexHull2D.svelte +93 -94
  47. package/dist/convex-hull/ConvexHull2D.svelte.d.ts +1 -1
  48. package/dist/convex-hull/ConvexHull3D.svelte +127 -186
  49. package/dist/convex-hull/ConvexHull3D.svelte.d.ts +1 -1
  50. package/dist/convex-hull/ConvexHull4D.svelte +131 -180
  51. package/dist/convex-hull/ConvexHull4D.svelte.d.ts +1 -1
  52. package/dist/convex-hull/ConvexHullChrome.svelte +36 -40
  53. package/dist/convex-hull/ConvexHullControls.svelte +46 -48
  54. package/dist/convex-hull/ConvexHullStats.svelte +193 -195
  55. package/dist/convex-hull/ConvexHullTooltip.svelte +5 -12
  56. package/dist/convex-hull/GasPressureControls.svelte +5 -12
  57. package/dist/convex-hull/StructurePopup.svelte +18 -22
  58. package/dist/convex-hull/StructurePopup.svelte.d.ts +2 -0
  59. package/dist/convex-hull/TemperatureSlider.svelte +4 -10
  60. package/dist/convex-hull/canvas-interactions.svelte.js +2 -1
  61. package/dist/convex-hull/gas-thermodynamics.js +21 -53
  62. package/dist/convex-hull/helpers.d.ts +8 -10
  63. package/dist/convex-hull/helpers.js +37 -43
  64. package/dist/convex-hull/hull-state.svelte.d.ts +1 -1
  65. package/dist/convex-hull/thermodynamics.js +37 -44
  66. package/dist/coordination/CoordinationBarPlot.svelte +49 -53
  67. package/dist/coordination/CoordinationBarPlot.svelte.d.ts +1 -1
  68. package/dist/coordination/calc-coordination.d.ts +1 -1
  69. package/dist/coordination/calc-coordination.js +28 -25
  70. package/dist/element/BohrAtom.svelte +5 -9
  71. package/dist/element/ElementHeading.svelte +4 -1
  72. package/dist/element/ElementPhoto.svelte +11 -9
  73. package/dist/element/ElementStats.svelte +12 -10
  74. package/dist/element/ElementTile.svelte +44 -67
  75. package/dist/element/Nucleus.svelte +4 -2
  76. package/dist/element/data.d.ts +3 -2
  77. package/dist/element/data.js +5 -1
  78. package/dist/element/helpers.d.ts +4 -0
  79. package/dist/element/helpers.js +18 -0
  80. package/dist/element/index.d.ts +2 -5
  81. package/dist/element/index.js +4 -19
  82. package/dist/feedback/DragOverlay.svelte +5 -5
  83. package/dist/feedback/DragOverlay.svelte.d.ts +2 -2
  84. package/dist/feedback/StatusMessage.svelte +7 -4
  85. package/dist/fermi-surface/FermiSlice.svelte +21 -18
  86. package/dist/fermi-surface/FermiSurface.svelte +35 -44
  87. package/dist/fermi-surface/FermiSurface.svelte.d.ts +7 -13
  88. package/dist/fermi-surface/FermiSurfaceControls.svelte +6 -20
  89. package/dist/fermi-surface/FermiSurfaceControls.svelte.d.ts +1 -1
  90. package/dist/fermi-surface/FermiSurfaceScene.svelte +64 -136
  91. package/dist/fermi-surface/FermiSurfaceScene.svelte.d.ts +1 -1
  92. package/dist/fermi-surface/FermiSurfaceTooltip.svelte +9 -6
  93. package/dist/fermi-surface/compute.js +25 -58
  94. package/dist/fermi-surface/parse.js +54 -88
  95. package/dist/file-viewer/JsonBrowser.svelte +1043 -0
  96. package/dist/file-viewer/JsonBrowser.svelte.d.ts +9 -0
  97. package/dist/file-viewer/PlotPanel.svelte +350 -0
  98. package/dist/file-viewer/PlotPanel.svelte.d.ts +9 -0
  99. package/dist/file-viewer/TrajectoryWithDos.svelte +30 -0
  100. package/dist/file-viewer/TrajectoryWithDos.svelte.d.ts +10 -0
  101. package/dist/file-viewer/detect.d.ts +11 -0
  102. package/dist/file-viewer/detect.js +381 -0
  103. package/dist/file-viewer/eligibility.d.ts +4 -0
  104. package/dist/file-viewer/eligibility.js +53 -0
  105. package/dist/file-viewer/host-protocol.d.ts +50 -0
  106. package/dist/file-viewer/host-transfer.d.ts +25 -0
  107. package/dist/file-viewer/host-transfer.js +42 -0
  108. package/dist/file-viewer/index.d.ts +5 -0
  109. package/dist/file-viewer/index.js +5 -0
  110. package/dist/file-viewer/main.d.ts +44 -0
  111. package/dist/file-viewer/main.js +535 -0
  112. package/dist/file-viewer/parse.d.ts +9 -0
  113. package/dist/file-viewer/parse.js +170 -0
  114. package/dist/file-viewer/plot-utils.d.ts +24 -0
  115. package/dist/file-viewer/plot-utils.js +191 -0
  116. package/dist/file-viewer/types.d.ts +4 -0
  117. package/dist/file-viewer/types.js +5 -0
  118. package/dist/heatmap-matrix/HeatmapMatrix.svelte +153 -219
  119. package/dist/heatmap-matrix/HeatmapMatrix.svelte.d.ts +2 -2
  120. package/dist/heatmap-matrix/HeatmapMatrixControls.svelte +9 -7
  121. package/dist/heatmap-matrix/HeatmapMatrixControls.svelte.d.ts +1 -1
  122. package/dist/heatmap-matrix/index.d.ts +5 -0
  123. package/dist/icons.d.ts +4 -0
  124. package/dist/icons.js +4 -0
  125. package/dist/index.d.ts +2 -2
  126. package/dist/index.js +1 -1
  127. package/dist/io/ExportPane.svelte +11 -7
  128. package/dist/io/decompress.d.ts +4 -1
  129. package/dist/io/decompress.js +24 -36
  130. package/dist/io/export.d.ts +11 -4
  131. package/dist/io/export.js +75 -19
  132. package/dist/io/fetch.d.ts +0 -3
  133. package/dist/io/fetch.js +0 -11
  134. package/dist/io/file-drop.js +60 -35
  135. package/dist/io/index.d.ts +0 -1
  136. package/dist/io/index.js +2 -9
  137. package/dist/io/is-binary.d.ts +9 -0
  138. package/dist/io/is-binary.js +45 -1
  139. package/dist/io/url-drop.d.ts +2 -0
  140. package/dist/io/url-drop.js +40 -40
  141. package/dist/isosurface/Isosurface.svelte +700 -215
  142. package/dist/isosurface/Isosurface.svelte.d.ts +7 -1
  143. package/dist/isosurface/IsosurfaceControls.svelte +590 -116
  144. package/dist/isosurface/IsosurfaceControls.svelte.d.ts +1 -1
  145. package/dist/isosurface/VolumeSlice.svelte +224 -0
  146. package/dist/isosurface/VolumeSlice.svelte.d.ts +28 -0
  147. package/dist/isosurface/coloring.d.ts +20 -0
  148. package/dist/isosurface/coloring.js +118 -0
  149. package/dist/isosurface/geometry-worker-types.d.ts +38 -0
  150. package/dist/isosurface/geometry.worker.d.ts +1 -0
  151. package/dist/isosurface/geometry.worker.js +59 -0
  152. package/dist/isosurface/grid.d.ts +10 -0
  153. package/dist/isosurface/grid.js +31 -0
  154. package/dist/isosurface/index.d.ts +4 -0
  155. package/dist/isosurface/index.js +4 -0
  156. package/dist/isosurface/parse-vaspwave.d.ts +3 -0
  157. package/dist/isosurface/parse-vaspwave.js +138 -0
  158. package/dist/isosurface/parse.js +6 -6
  159. package/dist/isosurface/profile.d.ts +12 -0
  160. package/dist/isosurface/profile.js +19 -0
  161. package/dist/isosurface/sampling.d.ts +34 -0
  162. package/dist/isosurface/sampling.js +408 -0
  163. package/dist/isosurface/slice-rendering.d.ts +13 -0
  164. package/dist/isosurface/slice-rendering.js +79 -0
  165. package/dist/isosurface/slice.d.ts +22 -2
  166. package/dist/isosurface/slice.js +200 -116
  167. package/dist/isosurface/types.d.ts +24 -1
  168. package/dist/isosurface/types.js +120 -8
  169. package/dist/json-path.d.ts +4 -0
  170. package/dist/json-path.js +89 -0
  171. package/dist/labels.d.ts +6 -2
  172. package/dist/labels.js +44 -14
  173. package/dist/layout/FullscreenButton.svelte +2 -1
  174. package/dist/layout/FullscreenToggle.svelte +10 -4
  175. package/dist/layout/InfoCard.svelte +8 -21
  176. package/dist/layout/InfoTag.svelte +1 -3
  177. package/dist/layout/NumberRangeInput.svelte +46 -0
  178. package/dist/layout/NumberRangeInput.svelte.d.ts +12 -0
  179. package/dist/layout/PropertyFilter.svelte +2 -6
  180. package/dist/layout/SettingsSection.svelte +57 -62
  181. package/dist/layout/SettingsSection.svelte.d.ts +6 -7
  182. package/dist/layout/SubpageGrid.svelte +3 -1
  183. package/dist/layout/ViewerChrome.svelte +16 -11
  184. package/dist/layout/ViewerChrome.svelte.d.ts +2 -1
  185. package/dist/layout/fullscreen.js +3 -5
  186. package/dist/layout/fullscreen.svelte.js +1 -2
  187. package/dist/layout/index.d.ts +1 -0
  188. package/dist/layout/index.js +1 -0
  189. package/dist/layout/json-tree/JsonNode.svelte +22 -59
  190. package/dist/layout/json-tree/JsonTree.svelte +101 -172
  191. package/dist/layout/json-tree/JsonValue.svelte +9 -32
  192. package/dist/layout/json-tree/utils.d.ts +0 -3
  193. package/dist/layout/json-tree/utils.js +50 -188
  194. package/dist/marching-cubes.d.ts +8 -1
  195. package/dist/marching-cubes.js +115 -48
  196. package/dist/math.d.ts +5 -2
  197. package/dist/math.js +48 -38
  198. package/dist/overlays/ContextMenu.svelte +19 -34
  199. package/dist/overlays/CopyButton.svelte +11 -5
  200. package/dist/overlays/DragControlTab.svelte +6 -1
  201. package/dist/overlays/DraggablePane.svelte +110 -74
  202. package/dist/overlays/DraggablePane.svelte.d.ts +2 -1
  203. package/dist/overlays/GlassChip.svelte +32 -0
  204. package/dist/overlays/GlassChip.svelte.d.ts +8 -0
  205. package/dist/overlays/InfoPaneCards.svelte +11 -23
  206. package/dist/overlays/index.d.ts +7 -0
  207. package/dist/overlays/index.js +26 -0
  208. package/dist/overlays/portal.d.ts +2 -0
  209. package/dist/overlays/portal.js +14 -0
  210. package/dist/periodic-table/PeriodicTable.svelte +113 -145
  211. package/dist/periodic-table/PeriodicTable.svelte.d.ts +5 -3
  212. package/dist/periodic-table/PeriodicTableControls.svelte +37 -115
  213. package/dist/periodic-table/TableInset.svelte +9 -4
  214. package/dist/phase-diagram/IsobaricBinaryPhaseDiagram.svelte +68 -105
  215. package/dist/phase-diagram/IsobaricBinaryPhaseDiagram.svelte.d.ts +6 -8
  216. package/dist/phase-diagram/PhaseDiagramControls.svelte +70 -94
  217. package/dist/phase-diagram/PhaseDiagramControls.svelte.d.ts +1 -1
  218. package/dist/phase-diagram/PhaseDiagramEditorPane.svelte +2 -1
  219. package/dist/phase-diagram/PhaseDiagramExportPane.svelte +12 -12
  220. package/dist/phase-diagram/PhaseDiagramTooltip.svelte +54 -58
  221. package/dist/phase-diagram/TdbInfoPanel.svelte +21 -15
  222. package/dist/phase-diagram/build-diagram.js +4 -9
  223. package/dist/phase-diagram/diagram-input.d.ts +1 -2
  224. package/dist/phase-diagram/parse.js +15 -15
  225. package/dist/phase-diagram/svg-to-diagram.js +28 -27
  226. package/dist/phase-diagram/utils.js +2 -3
  227. package/dist/plot/bar/BarPlot.svelte +461 -426
  228. package/dist/plot/bar/BarPlot.svelte.d.ts +2 -0
  229. package/dist/plot/bar/BarPlotControls.svelte +1 -3
  230. package/dist/plot/bar/BarPlotControls.svelte.d.ts +4 -6
  231. package/dist/plot/bar/SpacegroupBarPlot.svelte +46 -77
  232. package/dist/plot/bar/data.d.ts +5 -4
  233. package/dist/plot/bar/data.js +2 -1
  234. package/dist/plot/box/BoxPlot.svelte +322 -226
  235. package/dist/plot/box/BoxPlot.svelte.d.ts +2 -0
  236. package/dist/plot/box/Violin.svelte.d.ts +1 -0
  237. package/dist/plot/box/box-plot.js +1 -1
  238. package/dist/plot/core/auto-place.d.ts +1 -1
  239. package/dist/plot/core/auto-place.js +2 -2
  240. package/dist/plot/core/axis-utils.d.ts +12 -7
  241. package/dist/plot/core/axis-utils.js +48 -48
  242. package/dist/plot/core/components/AxisLabel.svelte +82 -20
  243. package/dist/plot/core/components/AxisLabel.svelte.d.ts +1 -0
  244. package/dist/plot/core/components/ColorBar.svelte +101 -106
  245. package/dist/plot/core/components/ColorScaleSelect.svelte +1 -1
  246. package/dist/plot/core/components/FillArea.svelte +10 -17
  247. package/dist/plot/core/components/HierarchyControls.svelte +249 -0
  248. package/dist/plot/{sunburst/SunburstControls.svelte.d.ts → core/components/HierarchyControls.svelte.d.ts} +12 -8
  249. package/dist/plot/core/components/InteractiveAxisLabel.svelte +1 -1
  250. package/dist/plot/core/components/InteractiveAxisLabel.svelte.d.ts +1 -1
  251. package/dist/plot/core/components/Line.svelte +18 -9
  252. package/dist/plot/core/components/Line.svelte.d.ts +2 -0
  253. package/dist/plot/core/components/PlotAxis.svelte +40 -17
  254. package/dist/plot/core/components/PlotControls.svelte +65 -41
  255. package/dist/plot/core/components/PlotLegend.svelte +31 -35
  256. package/dist/plot/core/components/PlotMarginals.svelte +616 -0
  257. package/dist/plot/core/components/PlotMarginals.svelte.d.ts +15 -0
  258. package/dist/plot/core/components/PlotTooltip.svelte +1 -1
  259. package/dist/plot/core/components/PortalSelect.svelte +4 -8
  260. package/dist/plot/core/components/ReferenceLine.svelte +27 -24
  261. package/dist/plot/core/components/ReferenceLine3D.svelte +54 -57
  262. package/dist/plot/core/components/ReferencePlane.svelte +7 -8
  263. package/dist/plot/core/components/ZeroLines.svelte +4 -8
  264. package/dist/plot/core/components/ZoomRect.svelte +1 -2
  265. package/dist/plot/core/components/index.d.ts +1 -0
  266. package/dist/plot/core/components/index.js +1 -0
  267. package/dist/plot/core/data-cleaning-signal.d.ts +46 -0
  268. package/dist/plot/core/data-cleaning-signal.js +467 -0
  269. package/dist/plot/core/data-cleaning.d.ts +2 -42
  270. package/dist/plot/core/data-cleaning.js +27 -474
  271. package/dist/plot/core/data-transform.d.ts +1 -2
  272. package/dist/plot/core/data-transform.js +9 -15
  273. package/dist/plot/core/fill-utils.d.ts +3 -1
  274. package/dist/plot/core/fill-utils.js +28 -6
  275. package/dist/plot/core/index.d.ts +1 -0
  276. package/dist/plot/core/index.js +1 -0
  277. package/dist/plot/core/interactions.js +0 -2
  278. package/dist/plot/core/layout.d.ts +15 -6
  279. package/dist/plot/core/layout.js +57 -38
  280. package/dist/plot/core/marginals.d.ts +170 -0
  281. package/dist/plot/core/marginals.js +436 -0
  282. package/dist/plot/core/pan-zoom.svelte.d.ts +2 -4
  283. package/dist/plot/core/pan-zoom.svelte.js +34 -17
  284. package/dist/plot/core/placed-tween.svelte.d.ts +3 -0
  285. package/dist/plot/core/placed-tween.svelte.js +68 -21
  286. package/dist/plot/core/reference-line.js +1 -1
  287. package/dist/plot/core/scales.d.ts +23 -0
  288. package/dist/plot/core/scales.js +39 -13
  289. package/dist/plot/core/svg.js +0 -1
  290. package/dist/plot/core/types/fills.d.ts +101 -0
  291. package/dist/plot/core/types/fills.js +15 -0
  292. package/dist/plot/core/types/plot-3d.d.ts +87 -0
  293. package/dist/plot/core/types/plot-3d.js +4 -0
  294. package/dist/plot/core/types/reference-lines.d.ts +140 -0
  295. package/dist/plot/core/types/reference-lines.js +9 -0
  296. package/dist/plot/core/types.d.ts +29 -324
  297. package/dist/plot/core/types.js +23 -20
  298. package/dist/plot/core/utils/hierarchy-chart.d.ts +52 -0
  299. package/dist/plot/core/utils/hierarchy-chart.js +191 -0
  300. package/dist/plot/core/utils/hierarchy-labels.d.ts +20 -0
  301. package/dist/plot/core/utils/hierarchy-labels.js +100 -0
  302. package/dist/plot/core/utils/label-placement.js +2 -2
  303. package/dist/plot/histogram/Histogram.svelte +314 -340
  304. package/dist/plot/histogram/Histogram.svelte.d.ts +7 -7
  305. package/dist/plot/histogram/HistogramControls.svelte +30 -28
  306. package/dist/plot/histogram/histogram.d.ts +31 -0
  307. package/dist/plot/histogram/histogram.js +70 -0
  308. package/dist/plot/histogram/index.d.ts +1 -0
  309. package/dist/plot/histogram/index.js +1 -0
  310. package/dist/plot/index.d.ts +1 -0
  311. package/dist/plot/index.js +1 -0
  312. package/dist/plot/sankey/Sankey.svelte +78 -69
  313. package/dist/plot/sankey/Sankey.svelte.d.ts +2 -2
  314. package/dist/plot/sankey/SankeyControls.svelte +22 -16
  315. package/dist/plot/sankey/sankey.js +13 -9
  316. package/dist/plot/scatter/BinnedScatterPlot.svelte +311 -141
  317. package/dist/plot/scatter/BinnedScatterPlot.svelte.d.ts +7 -0
  318. package/dist/plot/scatter/ElementScatter.svelte +4 -1
  319. package/dist/plot/scatter/ScatterPlot.svelte +517 -410
  320. package/dist/plot/scatter/ScatterPlot.svelte.d.ts +2 -0
  321. package/dist/plot/scatter/ScatterPlotControls.svelte +18 -19
  322. package/dist/plot/scatter/ScatterPlotControls.svelte.d.ts +1 -1
  323. package/dist/plot/scatter/ScatterPoint.svelte +16 -9
  324. package/dist/plot/scatter/adaptive-density.d.ts +1 -1
  325. package/dist/plot/scatter/adaptive-density.js +36 -20
  326. package/dist/plot/scatter/binned-scatter-types.d.ts +3 -2
  327. package/dist/plot/scatter/binned-scatter-types.js +6 -1
  328. package/dist/plot/scatter/scatter-data.d.ts +1 -1
  329. package/dist/plot/scatter/scatter-data.js +8 -7
  330. package/dist/plot/scatter-3d/ScatterPlot3D.svelte +25 -34
  331. package/dist/plot/scatter-3d/ScatterPlot3D.svelte.d.ts +2 -2
  332. package/dist/plot/scatter-3d/ScatterPlot3DControls.svelte +8 -5
  333. package/dist/plot/scatter-3d/ScatterPlot3DScene.svelte +113 -116
  334. package/dist/plot/scatter-3d/ScatterPlot3DScene.svelte.d.ts +2 -2
  335. package/dist/plot/scatter-3d/Surface3D.svelte +4 -13
  336. package/dist/plot/sunburst/Sunburst.svelte +269 -347
  337. package/dist/plot/sunburst/Sunburst.svelte.d.ts +2 -2
  338. package/dist/plot/sunburst/index.d.ts +1 -1
  339. package/dist/plot/sunburst/index.js +2 -1
  340. package/dist/plot/sunburst/render.d.ts +2 -2
  341. package/dist/plot/sunburst/render.js +47 -22
  342. package/dist/plot/sunburst/sunburst.d.ts +5 -1
  343. package/dist/plot/sunburst/sunburst.js +10 -3
  344. package/dist/plot/treemap/Treemap.svelte +1022 -0
  345. package/dist/plot/treemap/Treemap.svelte.d.ts +90 -0
  346. package/dist/plot/treemap/index.d.ts +4 -0
  347. package/dist/plot/treemap/index.js +4 -0
  348. package/dist/plot/treemap/labels.d.ts +38 -0
  349. package/dist/plot/treemap/labels.js +80 -0
  350. package/dist/plot/treemap/treemap.d.ts +28 -0
  351. package/dist/plot/treemap/treemap.js +102 -0
  352. package/dist/rdf/RdfPlot.svelte +37 -59
  353. package/dist/rdf/RdfPlot.svelte.d.ts +1 -1
  354. package/dist/rdf/calc-rdf.js +63 -52
  355. package/dist/rdf/index.d.ts +0 -1
  356. package/dist/sanitize.js +85 -27
  357. package/dist/scene/SceneCamera.svelte +1 -1
  358. package/dist/scene/SceneCamera.svelte.d.ts +1 -1
  359. package/dist/scene/bind-renderer.svelte.js +14 -6
  360. package/dist/scene/index.d.ts +1 -2
  361. package/dist/scene/index.js +1 -1
  362. package/dist/scene/{props.js → props.svelte.js} +15 -1
  363. package/dist/settings.d.ts +19 -9
  364. package/dist/settings.js +229 -525
  365. package/dist/spectral/Bands.svelte +207 -221
  366. package/dist/spectral/BandsAndDos.svelte +11 -9
  367. package/dist/spectral/BrillouinBandsDos.svelte +19 -42
  368. package/dist/spectral/Dos.svelte +92 -93
  369. package/dist/spectral/helpers.d.ts +3 -3
  370. package/dist/spectral/helpers.js +65 -140
  371. package/dist/state.svelte.js +5 -18
  372. package/dist/structure/Arrow.svelte +5 -18
  373. package/dist/structure/ArrowInstances.svelte +160 -0
  374. package/dist/structure/ArrowInstances.svelte.d.ts +16 -0
  375. package/dist/structure/AtomLegend.svelte +120 -85
  376. package/dist/structure/AtomLegend.svelte.d.ts +2 -3
  377. package/dist/structure/Bond.svelte +31 -23
  378. package/dist/structure/CanvasTooltip.svelte +15 -3
  379. package/dist/structure/CellSelect.svelte +45 -35
  380. package/dist/structure/Cylinder.svelte +24 -40
  381. package/dist/structure/InstancedAtoms.svelte +114 -0
  382. package/dist/structure/InstancedAtoms.svelte.d.ts +15 -0
  383. package/dist/structure/Lattice.svelte +85 -149
  384. package/dist/structure/SiteLabels.svelte +122 -0
  385. package/dist/structure/SiteLabels.svelte.d.ts +18 -0
  386. package/dist/structure/Structure.svelte +636 -504
  387. package/dist/structure/Structure.svelte.d.ts +4 -2
  388. package/dist/structure/StructureCarousel.svelte +637 -0
  389. package/dist/structure/StructureCarousel.svelte.d.ts +19 -0
  390. package/dist/structure/StructureControls.svelte +165 -425
  391. package/dist/structure/StructureControls.svelte.d.ts +1 -1
  392. package/dist/structure/StructureExportPane.svelte +17 -21
  393. package/dist/structure/StructureInfoPane.svelte +128 -133
  394. package/dist/structure/StructureInfoPane.svelte.d.ts +1 -1
  395. package/dist/structure/StructureScene.svelte +535 -578
  396. package/dist/structure/StructureScene.svelte.d.ts +6 -2
  397. package/dist/structure/StructureViewport.svelte +451 -0
  398. package/dist/structure/StructureViewport.svelte.d.ts +65 -0
  399. package/dist/structure/atom-label-placement.d.ts +16 -12
  400. package/dist/structure/atom-label-placement.js +70 -37
  401. package/dist/structure/atom-properties.d.ts +2 -0
  402. package/dist/structure/atom-properties.js +105 -38
  403. package/dist/structure/bond-order-perception.js +3 -8
  404. package/dist/structure/bonding.d.ts +9 -3
  405. package/dist/structure/bonding.js +95 -46
  406. package/dist/structure/edit-history.d.ts +6 -0
  407. package/dist/structure/edit-history.js +27 -0
  408. package/dist/structure/export.d.ts +1 -0
  409. package/dist/structure/export.js +89 -105
  410. package/dist/structure/format-detect.d.ts +1 -0
  411. package/dist/structure/format-detect.js +20 -0
  412. package/dist/structure/geometry.d.ts +9 -0
  413. package/dist/structure/geometry.js +27 -0
  414. package/dist/structure/index.d.ts +16 -1
  415. package/dist/structure/index.js +15 -10
  416. package/dist/structure/measure.d.ts +1 -1
  417. package/dist/structure/measure.js +6 -12
  418. package/dist/structure/parse.d.ts +2 -1
  419. package/dist/structure/parse.js +272 -313
  420. package/dist/structure/partial-occupancy.js +10 -5
  421. package/dist/structure/pbc.js +85 -107
  422. package/dist/structure/polyhedra.d.ts +0 -1
  423. package/dist/structure/polyhedra.js +7 -21
  424. package/dist/structure/prop-groups.d.ts +85 -0
  425. package/dist/structure/prop-groups.js +18 -0
  426. package/dist/structure/supercell.d.ts +1 -2
  427. package/dist/structure/supercell.js +7 -13
  428. package/dist/symmetry/SymmetryElements.svelte +11 -15
  429. package/dist/symmetry/SymmetryStats.svelte +55 -71
  430. package/dist/symmetry/WyckoffTable.svelte +10 -28
  431. package/dist/symmetry/cell-transform.js +6 -14
  432. package/dist/symmetry/index.d.ts +1 -0
  433. package/dist/symmetry/index.js +13 -10
  434. package/dist/symmetry/spacegroups.js +3 -2
  435. package/dist/table/HeatmapTable.svelte +1142 -447
  436. package/dist/table/HeatmapTable.svelte.d.ts +12 -2
  437. package/dist/table/ToggleMenu.svelte +168 -53
  438. package/dist/table/ToggleMenu.svelte.d.ts +1 -1
  439. package/dist/table/index.d.ts +21 -6
  440. package/dist/table/index.js +34 -21
  441. package/dist/theme/ThemeControl.svelte +16 -8
  442. package/dist/theme/embedded.d.ts +18 -0
  443. package/dist/theme/embedded.js +206 -0
  444. package/dist/theme/index.d.ts +5 -5
  445. package/dist/theme/index.js +5 -12
  446. package/dist/theme/themes.mjs +44 -66
  447. package/dist/tooltip/KCoords.svelte +4 -1
  448. package/dist/tooltip/TooltipContent.svelte +3 -6
  449. package/dist/tooltip/TooltipContent.svelte.d.ts +1 -1
  450. package/dist/tooltip/index.d.ts +8 -1
  451. package/dist/trajectory/Trajectory.svelte +613 -386
  452. package/dist/trajectory/Trajectory.svelte.d.ts +1 -1
  453. package/dist/trajectory/TrajectoryError.svelte +12 -74
  454. package/dist/trajectory/TrajectoryExportPane.svelte +14 -32
  455. package/dist/trajectory/TrajectoryInfoPane.svelte +127 -164
  456. package/dist/trajectory/TrajectoryInfoPane.svelte.d.ts +2 -1
  457. package/dist/trajectory/extract.js +61 -49
  458. package/dist/trajectory/format-detect.d.ts +2 -0
  459. package/dist/trajectory/format-detect.js +17 -13
  460. package/dist/trajectory/frame-reader.d.ts +2 -0
  461. package/dist/trajectory/frame-reader.js +35 -32
  462. package/dist/trajectory/helpers.d.ts +2 -0
  463. package/dist/trajectory/helpers.js +34 -56
  464. package/dist/trajectory/index.d.ts +1 -0
  465. package/dist/trajectory/index.js +5 -8
  466. package/dist/trajectory/parse/ase.js +1 -1
  467. package/dist/trajectory/parse/h5-utils.d.ts +13 -0
  468. package/dist/trajectory/parse/h5-utils.js +109 -0
  469. package/dist/trajectory/parse/hdf5.d.ts +1 -1
  470. package/dist/trajectory/parse/hdf5.js +116 -106
  471. package/dist/trajectory/parse/index.d.ts +6 -6
  472. package/dist/trajectory/parse/index.js +25 -33
  473. package/dist/trajectory/parse/lammps.js +8 -12
  474. package/dist/trajectory/parse/vasp.js +10 -7
  475. package/dist/trajectory/parse/vaspout-electronic.d.ts +13 -0
  476. package/dist/trajectory/parse/vaspout-electronic.js +207 -0
  477. package/dist/trajectory/parse/vaspout-h5.d.ts +4 -0
  478. package/dist/trajectory/parse/vaspout-h5.js +281 -0
  479. package/dist/trajectory/parse/xyz.js +59 -9
  480. package/dist/trajectory/plotting.d.ts +8 -9
  481. package/dist/trajectory/plotting.js +113 -64
  482. package/dist/utils.d.ts +3 -0
  483. package/dist/utils.js +7 -0
  484. package/dist/xrd/XrdPlot.svelte +79 -118
  485. package/dist/xrd/broadening.js +2 -1
  486. package/dist/xrd/calc-xrd.js +24 -62
  487. package/dist/xrd/parse.d.ts +0 -1
  488. package/dist/xrd/parse.js +69 -95
  489. package/package.json +94 -34
  490. package/readme.md +6 -5
  491. package/dist/api/mp.d.ts +0 -6
  492. package/dist/api/mp.js +0 -22
  493. package/dist/plot/sunburst/SunburstControls.svelte +0 -200
  494. package/dist/scene/types.d.ts +0 -26
  495. package/dist/tooltip/types.d.ts +0 -8
  496. package/dist/trajectory/constants.d.ts +0 -6
  497. package/dist/trajectory/constants.js +0 -11
  498. /package/dist/{scene/types.js → file-viewer/host-protocol.js} +0 -0
  499. /package/dist/{tooltip/types.js → isosurface/geometry-worker-types.js} +0 -0
@@ -17,6 +17,6 @@ type $$ComponentProps = {
17
17
  controls_open?: boolean;
18
18
  export_pane_open?: boolean;
19
19
  };
20
- declare const ChemPotDiagram3D: import("svelte").Component<$$ComponentProps, {}, "height" | "width" | "temperature" | "fullscreen" | "wrapper" | "controls_open" | "export_pane_open" | "hover_info">;
20
+ declare const ChemPotDiagram3D: import("svelte").Component<$$ComponentProps, {}, "height" | "width" | "fullscreen" | "wrapper" | "controls_open" | "export_pane_open" | "temperature" | "hover_info">;
21
21
  type ChemPotDiagram3D = ReturnType<typeof ChemPotDiagram3D>;
22
22
  export default ChemPotDiagram3D;
@@ -1,24 +1,13 @@
1
1
  // Async wrapper for compute_chempot_diagram via Web Worker.
2
2
  // Falls back to synchronous main-thread computation during SSR.
3
- import { compute_chempot_diagram, formula_key_from_composition } from './compute';
3
+ import { compute_chempot_diagram, entry_fingerprint } from './compute';
4
4
  import { to_error } from '../utils';
5
5
  let worker = null;
6
6
  let next_id = 0;
7
7
  const pending = new Map();
8
8
  const pending_by_key = new Map();
9
9
  function make_compute_request_key(entries, config) {
10
- const keyed_entries = entries
11
- .map((entry) => [
12
- formula_key_from_composition(entry.composition),
13
- entry.energy,
14
- entry.energy_per_atom ?? ``,
15
- entry.e_form_per_atom ?? ``,
16
- entry.is_stable ?? ``,
17
- entry.e_above_hull ?? ``,
18
- entry.exclude_from_hull ?? ``,
19
- ].join(`:`))
20
- .sort();
21
- return `${keyed_entries.join(`,`)}|${JSON.stringify(config)}`;
10
+ return `${entries.map(entry_fingerprint).sort().join(`,`)}|${JSON.stringify(config)}`;
22
11
  }
23
12
  function track_pending(request_key, promise) {
24
13
  pending_by_key.set(request_key, promise);
@@ -53,6 +42,16 @@ function get_worker() {
53
42
  return worker;
54
43
  }
55
44
  export function compute_chempot_async(entries, config = {}) {
45
+ // Never throw synchronously: callers handle errors via .catch() only, so key
46
+ // construction or Worker instantiation failures (e.g. CSP) must reject instead
47
+ try {
48
+ return compute_chempot_async_unsafe(entries, config);
49
+ }
50
+ catch (err) {
51
+ return Promise.reject(to_error(err));
52
+ }
53
+ }
54
+ function compute_chempot_async_unsafe(entries, config) {
56
55
  const request_key = make_compute_request_key(entries, config);
57
56
  const existing = pending_by_key.get(request_key);
58
57
  if (existing)
@@ -68,7 +67,7 @@ export function compute_chempot_async(entries, config = {}) {
68
67
  pending.set(id, { resolve, reject });
69
68
  try {
70
69
  // $state.snapshot strips Svelte $state proxies (not structured-cloneable)
71
- // eslint-disable-next-line unicorn/require-post-message-target-origin
70
+ // oxlint-disable-next-line unicorn/require-post-message-target-origin
72
71
  wkr.postMessage($state.snapshot({ id, entries, config }));
73
72
  }
74
73
  catch (err) {
@@ -1,7 +1,27 @@
1
1
  import { type D3InterpolateName } from '../colors';
2
+ import type { PhaseData } from '../convex-hull/types';
2
3
  import type { Vec2 } from '../math';
3
- export declare function make_chempot_color_scale(values: number[], interpolator_name: D3InterpolateName, reverse: boolean): ((val: number) => string) | null;
4
+ import { type FormulaEnergyStats } from './compute';
5
+ import type { ChemPotColorMode } from './types';
6
+ export declare const ARITY_COLORS: readonly ["#3498db", "#2ecc71", "#e67e22", "#9b59b6"];
4
7
  export declare function get_chempot_color_bar_config(color_scale: D3InterpolateName, reverse: boolean): {
5
8
  color_scale_fn: (frac: number) => string;
6
9
  color_scale_domain: Vec2;
7
10
  };
11
+ export interface ChemPotDomainColorData {
12
+ colors: Map<string, string>;
13
+ color_range: {
14
+ min: number;
15
+ max: number;
16
+ label: string;
17
+ } | null;
18
+ }
19
+ export declare function get_domain_color_data(opts: {
20
+ formulas: string[];
21
+ color_mode: ChemPotColorMode;
22
+ color_scale: D3InterpolateName;
23
+ reverse_color_scale: boolean;
24
+ entries: PhaseData[];
25
+ el_refs: Record<string, PhaseData>;
26
+ energy_stats: Map<string, FormulaEnergyStats>;
27
+ }): ChemPotDomainColorData;
@@ -1,12 +1,24 @@
1
1
  import { get_d3_interpolator } from '../colors';
2
+ import { extract_formula_elements } from '../composition/parse';
3
+ import { group } from 'd3-array';
2
4
  import { scaleSequential } from 'd3-scale';
5
+ import { best_form_energy_for_formula as best_form_energy, formula_key_from_composition, } from './compute';
6
+ // Categorical palette for arity mode (element count)
7
+ export const ARITY_COLORS = [`#3498db`, `#2ecc71`, `#e67e22`, `#9b59b6`];
8
+ // Exhaustively typed over the numeric color modes so adding a new mode
9
+ // fails compilation here instead of rendering an undefined colorbar title
10
+ const COLOR_MODE_LABELS = {
11
+ energy: `Energy per atom (eV)`,
12
+ formation_energy: `Formation energy (eV/atom)`,
13
+ entries: `Entry count`,
14
+ };
3
15
  // Resolve D3 interpolator with optional reverse for chempot color scales.
4
16
  function get_chempot_interpolator(name, reverse) {
5
17
  const raw = get_d3_interpolator(name);
6
18
  return reverse ? (frac) => raw(1 - frac) : raw;
7
19
  }
8
20
  // Build sequential color scale from values and D3 interpolator name.
9
- export function make_chempot_color_scale(values, interpolator_name, reverse) {
21
+ function make_chempot_color_scale(values, interpolator_name, reverse) {
10
22
  const finite_values = values.filter(Number.isFinite);
11
23
  if (finite_values.length === 0)
12
24
  return null;
@@ -30,3 +42,60 @@ export function get_chempot_color_bar_config(color_scale, reverse) {
30
42
  color_scale_domain: [0, 1],
31
43
  };
32
44
  }
45
+ // Per-formula domain colors plus color-bar range for the active color mode.
46
+ // Shared by ChemPotDiagram2D and ChemPotDiagram3D.
47
+ export function get_domain_color_data(opts) {
48
+ const { formulas, color_mode, entries, el_refs, energy_stats } = opts;
49
+ const colors = new Map();
50
+ if (color_mode === `none`)
51
+ return { colors, color_range: null };
52
+ if (color_mode === `arity`) {
53
+ for (const formula of formulas) {
54
+ const n_elements = extract_formula_elements(formula).length;
55
+ const color_idx = Math.min(n_elements, ARITY_COLORS.length) - 1;
56
+ colors.set(formula, ARITY_COLORS[Math.max(0, color_idx)]);
57
+ }
58
+ return { colors, color_range: null };
59
+ }
60
+ const entries_by_formula = color_mode === `formation_energy`
61
+ ? group(entries, (entry) => formula_key_from_composition(entry.composition))
62
+ : new Map();
63
+ const get_value = (formula) => {
64
+ if (color_mode === `energy`)
65
+ return energy_stats.get(formula)?.min_energy_per_atom ?? null;
66
+ if (color_mode === `formation_energy`) {
67
+ return best_form_energy(entries_by_formula.get(formula) ?? [], formula, el_refs) ?? null;
68
+ }
69
+ return energy_stats.get(formula)?.matching_entry_count ?? 0;
70
+ };
71
+ const value_by_formula = new Map();
72
+ for (const formula of formulas) {
73
+ const value = get_value(formula);
74
+ if (value == null || !Number.isFinite(value))
75
+ continue;
76
+ value_by_formula.set(formula, value);
77
+ }
78
+ const values = [...value_by_formula.values()];
79
+ const scale = make_chempot_color_scale(values, opts.color_scale, opts.reverse_color_scale);
80
+ for (const formula of formulas) {
81
+ const value = value_by_formula.get(formula);
82
+ colors.set(formula, value != null && scale ? scale(value) : `#999`);
83
+ }
84
+ if (values.length === 0)
85
+ return { colors, color_range: null };
86
+ let [min_val, max_val] = [values[0], values[0]];
87
+ for (const value of values) {
88
+ if (value < min_val)
89
+ min_val = value;
90
+ if (value > max_val)
91
+ max_val = value;
92
+ }
93
+ return {
94
+ colors,
95
+ color_range: {
96
+ min: min_val,
97
+ max: Math.max(max_val, min_val + 1e-6),
98
+ label: COLOR_MODE_LABELS[color_mode],
99
+ },
100
+ };
101
+ }
@@ -8,6 +8,12 @@ export declare function get_min_entries_and_el_refs(entries: PhaseData[]): {
8
8
  el_refs: Record<string, PhaseData>;
9
9
  };
10
10
  export declare function best_form_energy_for_formula(entries: PhaseData[], formula: string, el_refs: Record<string, PhaseData>): number | undefined;
11
+ export interface FormulaEnergyStats {
12
+ matching_entry_count: number;
13
+ min_energy_per_atom: number | null;
14
+ max_energy_per_atom: number | null;
15
+ }
16
+ export declare function get_energy_stats_by_formula(entries: PhaseData[]): Map<string, FormulaEnergyStats>;
11
17
  export declare const renormalize_entries: (entries: PhaseData[], el_refs: Record<string, PhaseData>, elements: string[]) => PhaseData[];
12
18
  export declare function build_hyperplanes(min_entries: PhaseData[], el_refs: Record<string, PhaseData>, elements: string[]): {
13
19
  hyperplanes: number[][];
@@ -44,5 +50,6 @@ export interface VisibleDomainLabel {
44
50
  }
45
51
  export declare function get_visible_domain_labels(face_positions: ArrayLike<number>, face_domain_map: string[], label_font_size_by_formula: ReadonlyMap<string, number>, pinned_labels?: VisibleDomainLabel[]): VisibleDomainLabel[];
46
52
  export declare function get_ternary_combinations(elements: string[]): string[][];
53
+ export declare function entry_fingerprint(entry: PhaseData): string;
47
54
  export declare function make_nd_cache_key(entries: PhaseData[], formal_chempots: boolean, default_min_limit: number, limits: ChemPotDiagramConfig[`limits`]): string;
48
55
  export declare function compute_chempot_diagram(entries: PhaseData[], config?: ChemPotDiagramConfig): ChemPotDiagramData;
@@ -34,16 +34,28 @@ const get_reduced_formula = (composition) => {
34
34
  .map(([elem, amt]) => [elem, Math.round(amt * factor)]));
35
35
  };
36
36
  // === Entry Helpers ===
37
- // Get energy per atom for a PhaseData entry
37
+ // Energy per atom; NaN for invalid/non-finite so UI can skip without throwing.
38
38
  export function get_energy_per_atom(entry) {
39
- if (typeof entry.energy_per_atom === `number`)
40
- return entry.energy_per_atom;
41
- const atoms = count_atoms_in_composition(entry.composition);
42
- if (atoms <= 0) {
43
- throw new Error(`Invalid composition with non-positive atom count: ${JSON.stringify(entry.composition)}`);
39
+ if (typeof entry.energy_per_atom === `number`) {
40
+ return Number.isFinite(entry.energy_per_atom) ? entry.energy_per_atom : Number.NaN;
44
41
  }
42
+ const atoms = count_atoms_in_composition(entry.composition);
43
+ if (atoms <= 0 || !Number.isFinite(entry.energy))
44
+ return Number.NaN;
45
45
  return entry.energy / atoms;
46
46
  }
47
+ // Same-formula EPA total order (keep aligned with make_nd_cache_key / entry_fingerprint).
48
+ function prefer_min_entry(candidate, candidate_epa, existing, existing_epa) {
49
+ if (candidate_epa !== existing_epa)
50
+ return candidate_epa < existing_epa;
51
+ if (Boolean(candidate.exclude_from_hull) !== Boolean(existing.exclude_from_hull)) {
52
+ return !candidate.exclude_from_hull;
53
+ }
54
+ if ((candidate.is_stable === true) !== (existing.is_stable === true)) {
55
+ return candidate.is_stable === true;
56
+ }
57
+ return (candidate.e_above_hull ?? Infinity) < (existing.e_above_hull ?? Infinity);
58
+ }
47
59
  // Cache for reduced formula strings -- avoids recomputing get_reduced_formula
48
60
  // in hot loops. Key is object identity (WeakMap), value is the formula string.
49
61
  const formula_cache = new WeakMap();
@@ -69,8 +81,10 @@ export function get_min_entries_and_el_refs(entries) {
69
81
  for (const entry of entries) {
70
82
  const key = formula_key_from_composition(entry.composition);
71
83
  const epa = get_energy_per_atom(entry);
84
+ if (!Number.isFinite(epa))
85
+ continue;
72
86
  const existing = by_formula.get(key);
73
- if (!existing || epa < existing.epa) {
87
+ if (!existing || prefer_min_entry(entry, epa, existing.entry, existing.epa)) {
74
88
  by_formula.set(key, { entry, epa });
75
89
  }
76
90
  }
@@ -89,14 +103,20 @@ export function get_min_entries_and_el_refs(entries) {
89
103
  function compute_form_energy_per_atom(entry, el_refs) {
90
104
  const atom_count = count_atoms_in_composition(entry.composition);
91
105
  const energy_per_atom = get_energy_per_atom(entry);
106
+ if (!(atom_count > 0) || !Number.isFinite(energy_per_atom))
107
+ return Number.NaN;
92
108
  let ref_energy = 0;
93
109
  for (const [element, amount] of Object.entries(entry.composition)) {
94
110
  if (amount <= 0)
95
111
  continue;
96
112
  const fraction = amount / atom_count;
97
113
  const ref_entry = el_refs[element];
98
- if (ref_entry)
99
- ref_energy += fraction * get_energy_per_atom(ref_entry);
114
+ if (ref_entry) {
115
+ const ref_epa = get_energy_per_atom(ref_entry);
116
+ if (!Number.isFinite(ref_epa))
117
+ return Number.NaN;
118
+ ref_energy += fraction * ref_epa;
119
+ }
100
120
  }
101
121
  return energy_per_atom - ref_energy;
102
122
  }
@@ -107,23 +127,57 @@ export function best_form_energy_for_formula(entries, formula, el_refs) {
107
127
  if (formula_key_from_composition(entry.composition) !== formula)
108
128
  continue;
109
129
  const e_form = entry.e_form_per_atom ?? compute_form_energy_per_atom(entry, el_refs);
130
+ if (!Number.isFinite(e_form))
131
+ continue;
110
132
  if (best_value === undefined || e_form < best_value)
111
133
  best_value = e_form;
112
134
  }
113
135
  return best_value;
114
136
  }
137
+ // Aggregate per-formula entry count and min/max energy per atom (used for
138
+ // region coloring and hover tooltips in the 2D/3D diagram components).
139
+ export function get_energy_stats_by_formula(entries) {
140
+ const stats = new Map();
141
+ for (const entry of entries) {
142
+ const energy_per_atom = get_energy_per_atom(entry);
143
+ if (!Number.isFinite(energy_per_atom))
144
+ continue;
145
+ const formula_key = formula_key_from_composition(entry.composition);
146
+ const existing = stats.get(formula_key);
147
+ if (existing) {
148
+ existing.matching_entry_count += 1;
149
+ existing.min_energy_per_atom = Math.min(existing.min_energy_per_atom ?? energy_per_atom, energy_per_atom);
150
+ existing.max_energy_per_atom = Math.max(existing.max_energy_per_atom ?? energy_per_atom, energy_per_atom);
151
+ }
152
+ else {
153
+ stats.set(formula_key, {
154
+ matching_entry_count: 1,
155
+ min_energy_per_atom: energy_per_atom,
156
+ max_energy_per_atom: energy_per_atom,
157
+ });
158
+ }
159
+ }
160
+ return stats;
161
+ }
115
162
  // Renormalize entry energies to be relative to elemental references (formal chemical potentials).
116
163
  // For each entry, subtracts sum(x_i * E_ref_i) from its energy per atom.
117
164
  export const renormalize_entries = (entries, el_refs, elements) => entries.map((entry) => {
118
165
  const atoms = count_atoms_in_composition(entry.composition);
166
+ const base_epa = get_energy_per_atom(entry);
167
+ if (!(atoms > 0) || !Number.isFinite(base_epa))
168
+ return entry;
119
169
  let renorm_energy = 0;
120
170
  for (const el of elements) {
121
- const frac = atoms > 0 ? (entry.composition[el] ?? 0) / atoms : 0;
171
+ const frac = (entry.composition[el] ?? 0) / atoms;
122
172
  const ref = el_refs[el];
123
- if (ref)
124
- renorm_energy += frac * get_energy_per_atom(ref);
173
+ if (!ref)
174
+ continue;
175
+ const ref_epa = get_energy_per_atom(ref);
176
+ if (!Number.isFinite(ref_epa))
177
+ return entry;
178
+ renorm_energy += frac * ref_epa;
125
179
  }
126
- const new_energy_per_atom = get_energy_per_atom(entry) - renorm_energy;
180
+ const new_energy_per_atom = base_epa - renorm_energy;
127
181
  return {
128
182
  ...entry,
129
183
  energy: new_energy_per_atom * atoms,
@@ -137,7 +191,10 @@ export function build_hyperplanes(min_entries, el_refs, elements) {
137
191
  const n_elems = elements.length;
138
192
  const element_ref_energies = elements.map((element) => {
139
193
  const ref_entry = el_refs[element];
140
- return ref_entry ? get_energy_per_atom(ref_entry) : 0;
194
+ if (!ref_entry)
195
+ return 0;
196
+ const epa = get_energy_per_atom(ref_entry);
197
+ return Number.isFinite(epa) ? epa : 0;
141
198
  });
142
199
  const always_include = new Set(Object.values(el_refs));
143
200
  const tol = 1e-6; // PhaseDiagram.formation_energy_tol
@@ -148,6 +205,8 @@ export function build_hyperplanes(min_entries, el_refs, elements) {
148
205
  const atom_count = count_atoms_in_composition(entry.composition);
149
206
  const composition = entry.composition;
150
207
  const energy_per_atom = get_energy_per_atom(entry);
208
+ if (!(atom_count > 0) || !Number.isFinite(energy_per_atom))
209
+ continue;
151
210
  const row = Array(n_elems + 1).fill(0);
152
211
  let ref_energy = 0;
153
212
  for (let elem_idx = 0; elem_idx < n_elems; elem_idx++) {
@@ -670,19 +729,19 @@ export function get_ternary_combinations(elements) {
670
729
  return combos;
671
730
  }
672
731
  let nd_cache = null;
673
- // Content-based fingerprint for N-D result caching. Uses sorted formula keys
674
- // so deserialized Web Worker copies match and different compositions never collide.
675
- export function make_nd_cache_key(entries, formal_chempots, default_min_limit, limits) {
676
- const keyed = entries
677
- .map((entry) => [
732
+ // Fingerprint for N-D / async-compute cache keys (computed EPA; NaN → null).
733
+ export function entry_fingerprint(entry) {
734
+ const epa = get_energy_per_atom(entry);
735
+ return JSON.stringify([
678
736
  formula_key_from_composition(entry.composition),
679
- entry.energy,
680
- entry.is_stable ?? ``,
681
- entry.e_above_hull ?? ``,
682
- entry.exclude_from_hull ?? ``,
683
- ].join(`:`))
684
- .sort();
685
- return `${keyed.join(`,`)}|${formal_chempots}|${default_min_limit}|${JSON.stringify(limits ?? {})}`;
737
+ Number.isFinite(epa) ? epa : null,
738
+ entry.is_stable ?? null,
739
+ entry.e_above_hull ?? null,
740
+ entry.exclude_from_hull ?? null,
741
+ ]);
742
+ }
743
+ export function make_nd_cache_key(entries, formal_chempots, default_min_limit, limits) {
744
+ return `${entries.map(entry_fingerprint).sort().join(`,`)}|${formal_chempots}|${default_min_limit}|${JSON.stringify(limits ?? {})}`;
686
745
  }
687
746
  // === Main Pipeline ===
688
747
  // Compute the full chemical potential diagram from entries and config.
@@ -13,7 +13,7 @@ export function create_chempot_overrides(config, keys, custom_defaults = {}) {
13
13
  }));
14
14
  let overrides = $state({});
15
15
  return {
16
- resolve: (key) => (overrides[key] ?? config()[key] ?? defaults[key]),
16
+ resolve: (key) => overrides[key] ?? config()[key] ?? defaults[key],
17
17
  set: (key, value) => {
18
18
  overrides[key] = value;
19
19
  },
@@ -1,6 +1,7 @@
1
1
  // Export helpers for chemical potential diagrams (shared between 2D and 3D views).
2
2
  import { dpi_to_scale } from '../io/export';
3
3
  import { download } from '../io/fetch';
4
+ import { escape_html as xml_escape } from '../utils';
4
5
  import * as THREE from 'three';
5
6
  import { GLTFExporter } from 'three/examples/jsm/exporters/GLTFExporter.js';
6
7
  export const get_json_string = (payload) => JSON.stringify(payload, null, 2);
@@ -77,12 +78,6 @@ export function export_png_file(wrapper, basename, png_dpi) {
77
78
  download(blob, `${basename}.png`, `image/png`);
78
79
  }, `image/png`);
79
80
  }
80
- const xml_escape = (text) => text
81
- .replaceAll(`&`, `&amp;`)
82
- .replaceAll(`<`, `&lt;`)
83
- .replaceAll(`>`, `&gt;`)
84
- .replaceAll(`"`, `&quot;`)
85
- .replaceAll(`'`, `&#39;`);
86
81
  // SVG snapshot: rasterized canvas as embedded image + overlay labels as real text nodes
87
82
  export function export_svg_file(wrapper, basename, view_settings) {
88
83
  const gl_canvas = get_gl_canvas(wrapper);
@@ -1,21 +1,20 @@
1
1
  import { analyze_temperature_data, filter_entries_at_temperature, } from '../convex-hull/helpers';
2
2
  import { CHEMPOT_DEFAULTS } from './types';
3
3
  export const get_projection_source_entries = (entries, temp_filtered_entries) => (temp_filtered_entries.length > 0 ? temp_filtered_entries : entries);
4
- const resolve_temp_filter_options = (config, props) => ({
5
- interpolate: config.interpolate_temperature ??
6
- props.interpolate_temperature ??
7
- CHEMPOT_DEFAULTS.interpolate_temperature,
8
- max_interpolation_gap: config.max_interpolation_gap ??
9
- props.max_interpolation_gap ??
10
- CHEMPOT_DEFAULTS.max_interpolation_gap,
11
- });
12
4
  export function get_temp_filter_payload(entries, temperature, config, props) {
13
5
  const { has_temp_data, available_temperatures } = analyze_temperature_data(entries);
14
6
  if (!has_temp_data || temperature === undefined) {
15
7
  return { has_temp_data, available_temperatures, temp_filtered_entries: entries };
16
8
  }
17
- const filter_options = resolve_temp_filter_options(config, props);
18
- const temp_filtered_entries = filter_entries_at_temperature(entries, temperature, filter_options);
9
+ // Option resolution order: config beats props beats defaults
10
+ const temp_filtered_entries = filter_entries_at_temperature(entries, temperature, {
11
+ interpolate: config.interpolate_temperature ??
12
+ props.interpolate_temperature ??
13
+ CHEMPOT_DEFAULTS.interpolate_temperature,
14
+ max_interpolation_gap: config.max_interpolation_gap ??
15
+ props.max_interpolation_gap ??
16
+ CHEMPOT_DEFAULTS.max_interpolation_gap,
17
+ });
19
18
  return { has_temp_data, available_temperatures, temp_filtered_entries };
20
19
  }
21
20
  export function get_valid_temperature(temperature, has_temp_data, available_temperatures) {
@@ -1,6 +1,4 @@
1
1
  import * as d3_sc from 'd3-scale-chromatic';
2
- import type { Vec3 } from '../math';
3
- import type { ELEM_SYMBOLS } from '../labels';
4
2
  export type D3InterpolateName = keyof typeof d3_sc & `interpolate${string}`;
5
3
  export type D3ColorSchemeName = D3InterpolateName extends `interpolate${infer Name}` ? Name : never;
6
4
  export declare const get_d3_interpolator: (name: D3InterpolateName) => ((t: number) => string);
@@ -9,8 +7,6 @@ export type ColorScaleType = (typeof COLOR_SCALE_TYPES)[number];
9
7
  export declare const DEFAULT_CATEGORY_COLORS: Record<string, string>;
10
8
  export declare const AXIS_COLORS: readonly [readonly ["x", "#d75555", "#e66666"], readonly ["y", "#55b855", "#66c966"], readonly ["z", "#5555d7", "#6666e6"]];
11
9
  export declare const NEG_AXIS_COLORS: readonly [readonly ["nx", "#b84444", "#cc5555"], readonly ["ny", "#44a044", "#55b155"], readonly ["nz", "#4444b8", "#5555c9"]];
12
- export type RGBColor = Vec3;
13
- export type ElementColorScheme = Record<(typeof ELEM_SYMBOLS)[number], RGBColor>;
14
10
  export declare const vesta_hex: Record<string, string>;
15
11
  export declare const jmol_hex: Record<string, string>;
16
12
  export declare const alloy_hex: Record<string, string>;
@@ -1,5 +1,7 @@
1
1
  import { color as d3_color, rgb } from 'd3-color';
2
2
  import * as d3_sc from 'd3-scale-chromatic';
3
+ import { COLOR_THEMES, get_system_mode, get_theme_preference, is_valid_theme_name, resolve_theme_mode, THEME_STORAGE_KEY, THEME_TYPE, } from '../theme';
4
+ import { clamp01 } from '../utils';
3
5
  import alloy_colors from './alloy-colors.json' with { type: 'json' };
4
6
  import dark_mode_colors from './dark-mode-colors.json' with { type: 'json' };
5
7
  import jmol_colors from './jmol-colors.json' with { type: 'json' };
@@ -82,16 +84,17 @@ export function luminance(clr) {
82
84
  const { r: red, g: green, b: blue } = rgb(clr);
83
85
  return (0.299 * red + 0.587 * green + 0.114 * blue) / 255; // https://stackoverflow.com/a/596243
84
86
  }
87
+ // CSS color string for a fully transparent background
88
+ const NO_BG = `rgba(0, 0, 0, 0)`;
85
89
  // get background color of passed DOM node, or recurse up the DOM tree if current node is transparent
86
90
  export function get_bg_color(elem, bg_color = null) {
87
91
  if (bg_color)
88
92
  return bg_color;
89
93
  // recurse up the DOM tree to find the first non-transparent background color
90
- const transparent = `rgba(0, 0, 0, 0)`;
91
94
  if (!elem)
92
- return transparent; // if no DOM node, return transparent
95
+ return NO_BG; // if no DOM node, return transparent
93
96
  const bg = getComputedStyle(elem).backgroundColor; // get node background color
94
- if (bg !== transparent)
97
+ if (bg !== NO_BG)
95
98
  return bg; // if not transparent, return it
96
99
  return get_bg_color(elem.parentElement); // otherwise recurse up the DOM tree
97
100
  }
@@ -104,7 +107,7 @@ export function pick_contrast_color(options = {}) {
104
107
  export const contrast_color = (options = {}) => (node) => {
105
108
  node.style.color = pick_contrast_color({ ...options, bg_color: get_bg_color(node) });
106
109
  };
107
- const is_valid_bg = (bg) => bg !== `` && bg !== `rgba(0, 0, 0, 0)` && bg !== `transparent`;
110
+ const is_valid_bg = (bg) => bg !== `` && bg !== NO_BG && bg !== `transparent`;
108
111
  // Detect and return the page background color from html/body elements or user preferences
109
112
  export function get_page_background(fallback_dark = `#1a1a1a`, fallback_light = `#ffffff`) {
110
113
  if (typeof window === `undefined`)
@@ -119,25 +122,21 @@ export function get_page_background(fallback_dark = `#1a1a1a`, fallback_light =
119
122
  if (is_valid_bg(html_bg))
120
123
  return html_bg;
121
124
  // Fall back to prefers-color-scheme
122
- const prefers_dark = globalThis.matchMedia(`(prefers-color-scheme: dark)`).matches;
125
+ const prefers_dark = globalThis.matchMedia?.(`(prefers-color-scheme: dark)`)?.matches;
123
126
  return prefers_dark ? fallback_dark : fallback_light;
124
127
  }
125
- // Detect dark mode: checks data-theme attribute, localStorage, then OS preference
128
+ // Detect dark mode: checks data-theme attribute, then the persisted theme
129
+ // preference (resolving `auto` against the OS), then falls back to OS preference.
126
130
  export function is_dark_mode() {
127
131
  if (typeof document === `undefined`)
128
132
  return false;
133
+ // Prefer the resolved theme name on data-theme (light/dark/white/black), else
134
+ // fall back to the persisted preference (resolving `auto` against the OS)
129
135
  const data_theme = document.documentElement.dataset.theme;
130
- if (data_theme === `dark` || data_theme === `light`)
131
- return data_theme === `dark`;
132
- try {
133
- const stored = localStorage.getItem(`theme`);
134
- if (stored === `dark` || stored === `light`)
135
- return stored === `dark`;
136
- }
137
- catch {
138
- /* localStorage throws in private browsing mode */
139
- }
140
- return globalThis.matchMedia?.(`(prefers-color-scheme: dark)`).matches ?? false;
136
+ const theme_name = data_theme && is_valid_theme_name(data_theme)
137
+ ? data_theme
138
+ : resolve_theme_mode(get_theme_preference(), get_system_mode());
139
+ return THEME_TYPE[theme_name] === COLOR_THEMES.dark;
141
140
  }
142
141
  // Watch for dark mode changes and call callback on each change. Returns cleanup function.
143
142
  export function watch_dark_mode(on_change) {
@@ -149,8 +148,8 @@ export function watch_dark_mode(on_change) {
149
148
  attributes: true,
150
149
  attributeFilter: [`data-theme`],
151
150
  });
152
- const on_storage = (ev) => {
153
- if (ev.key === `theme`)
151
+ const on_storage = (event) => {
152
+ if (event.key === THEME_STORAGE_KEY)
154
153
  notify();
155
154
  };
156
155
  globalThis.addEventListener(`storage`, on_storage);
@@ -178,7 +177,7 @@ export function css_color_to_hex(color, fallback) {
178
177
  // Returns the color in rgba() format, or the original color if format is unsupported.
179
178
  export function add_alpha(color, alpha) {
180
179
  // Clamp alpha to valid CSS range [0, 1]
181
- const clamped_alpha = Math.max(0, Math.min(1, alpha));
180
+ const clamped_alpha = clamp01(alpha);
182
181
  // Handle hex colors (#rgb, #rgba, #rrggbb, #rrggbbaa)
183
182
  if (color.startsWith(`#`)) {
184
183
  const hex = color.slice(1);