matterviz 0.3.5 → 0.3.6
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.
- package/.vscode/launch.json +13 -0
- package/.vscodeignore +7 -0
- package/dist/assets/STLExporter-BpTH3YHE.js +8 -0
- package/dist/assets/browser-DdDecX_W.js +1 -0
- package/dist/assets/export-qgn-H9y6.js +2 -0
- package/dist/assets/main-DiKYzti2.css +1 -0
- package/dist/assets/moyo_wasm_bg-0ocwg7xY.wasm +0 -0
- package/dist/extension.js +31293 -0
- package/dist/src/lib/FilePicker.svelte +360 -0
- package/dist/src/lib/MillerIndexInput.svelte +66 -0
- package/dist/src/lib/api/mp.ts +26 -0
- package/dist/src/lib/api/optimade.ts +204 -0
- package/dist/src/lib/brillouin/BrillouinZone.svelte +549 -0
- package/dist/src/lib/brillouin/BrillouinZoneControls.svelte +144 -0
- package/dist/src/lib/brillouin/BrillouinZoneExportPane.svelte +146 -0
- package/dist/src/lib/brillouin/BrillouinZoneInfoPane.svelte +146 -0
- package/dist/src/lib/brillouin/BrillouinZoneScene.svelte +476 -0
- package/dist/src/lib/brillouin/BrillouinZoneTooltip.svelte +92 -0
- package/dist/src/lib/brillouin/compute.ts +529 -0
- package/dist/src/lib/brillouin/index.ts +8 -0
- package/dist/src/lib/brillouin/types.ts +51 -0
- package/dist/src/lib/chempot-diagram/ChemPotDiagram.svelte +327 -0
- package/dist/src/lib/chempot-diagram/ChemPotDiagram2D.svelte +846 -0
- package/dist/src/lib/chempot-diagram/ChemPotDiagram3D.svelte +3193 -0
- package/dist/src/lib/chempot-diagram/async-compute.svelte.ts +94 -0
- package/dist/src/lib/chempot-diagram/chempot-worker.ts +11 -0
- package/dist/src/lib/chempot-diagram/color.ts +42 -0
- package/dist/src/lib/chempot-diagram/compute.ts +1014 -0
- package/dist/src/lib/chempot-diagram/index.ts +6 -0
- package/dist/src/lib/chempot-diagram/pointer.ts +56 -0
- package/dist/src/lib/chempot-diagram/temperature.ts +77 -0
- package/dist/src/lib/chempot-diagram/types.ts +130 -0
- package/dist/src/lib/colors/index.ts +249 -0
- package/dist/src/lib/composition/BarChart.svelte +297 -0
- package/dist/src/lib/composition/BubbleChart.svelte +218 -0
- package/dist/src/lib/composition/Composition.svelte +165 -0
- package/dist/src/lib/composition/Formula.svelte +268 -0
- package/dist/src/lib/composition/FormulaFilter.svelte +1257 -0
- package/dist/src/lib/composition/PieChart.svelte +323 -0
- package/dist/src/lib/composition/format.ts +155 -0
- package/dist/src/lib/composition/index.ts +37 -0
- package/dist/src/lib/composition/parse.ts +605 -0
- package/dist/src/lib/constants.ts +134 -0
- package/dist/src/lib/controls.ts +42 -0
- package/dist/src/lib/convex-hull/ConvexHull.svelte +157 -0
- package/dist/src/lib/convex-hull/ConvexHull2D.svelte +825 -0
- package/dist/src/lib/convex-hull/ConvexHull3D.svelte +1801 -0
- package/dist/src/lib/convex-hull/ConvexHull4D.svelte +1398 -0
- package/dist/src/lib/convex-hull/ConvexHullControls.svelte +535 -0
- package/dist/src/lib/convex-hull/ConvexHullInfoPane.svelte +125 -0
- package/dist/src/lib/convex-hull/ConvexHullStats.svelte +929 -0
- package/dist/src/lib/convex-hull/ConvexHullTooltip.svelte +131 -0
- package/dist/src/lib/convex-hull/GasPressureControls.svelte +247 -0
- package/dist/src/lib/convex-hull/StructurePopup.svelte +151 -0
- package/dist/src/lib/convex-hull/TemperatureSlider.svelte +140 -0
- package/dist/src/lib/convex-hull/barycentric-coords.ts +246 -0
- package/dist/src/lib/convex-hull/demo-temperature.ts +63 -0
- package/dist/src/lib/convex-hull/gas-thermodynamics.ts +405 -0
- package/dist/src/lib/convex-hull/helpers.ts +932 -0
- package/dist/src/lib/convex-hull/index.ts +202 -0
- package/dist/src/lib/convex-hull/thermodynamics.ts +2192 -0
- package/dist/src/lib/convex-hull/types.ts +267 -0
- package/dist/src/lib/coordination/CoordinationBarPlot.svelte +311 -0
- package/dist/src/lib/coordination/calc-coordination.ts +93 -0
- package/dist/src/lib/coordination/index.ts +9 -0
- package/dist/src/lib/effects.svelte.ts +48 -0
- package/dist/src/lib/element/BohrAtom.svelte +147 -0
- package/dist/src/lib/element/ElementHeading.svelte +26 -0
- package/dist/src/lib/element/ElementPhoto.svelte +57 -0
- package/dist/src/lib/element/ElementStats.svelte +80 -0
- package/dist/src/lib/element/ElementTile.svelte +484 -0
- package/dist/src/lib/element/data.json.gz.d.ts +4 -0
- package/dist/src/lib/element/data.ts +14 -0
- package/dist/src/lib/element/index.ts +8 -0
- package/dist/src/lib/element/types.ts +62 -0
- package/dist/src/lib/feedback/ClickFeedback.svelte +58 -0
- package/dist/src/lib/feedback/DragOverlay.svelte +42 -0
- package/dist/src/lib/feedback/index.ts +4 -0
- package/dist/src/lib/fermi-surface/FermiSlice.svelte +189 -0
- package/dist/src/lib/fermi-surface/FermiSurface.svelte +600 -0
- package/dist/src/lib/fermi-surface/FermiSurfaceControls.svelte +448 -0
- package/dist/src/lib/fermi-surface/FermiSurfaceScene.svelte +794 -0
- package/dist/src/lib/fermi-surface/FermiSurfaceTooltip.svelte +111 -0
- package/dist/src/lib/fermi-surface/compute.ts +728 -0
- package/dist/src/lib/fermi-surface/constants.ts +32 -0
- package/dist/src/lib/fermi-surface/export.ts +64 -0
- package/dist/src/lib/fermi-surface/index.ts +14 -0
- package/dist/src/lib/fermi-surface/marching-cubes.ts +3 -0
- package/dist/src/lib/fermi-surface/parse.ts +574 -0
- package/dist/src/lib/fermi-surface/symmetry.ts +56 -0
- package/dist/src/lib/fermi-surface/types.ts +159 -0
- package/dist/src/lib/heatmap-matrix/HeatmapMatrix.svelte +1545 -0
- package/dist/src/lib/heatmap-matrix/HeatmapMatrixControls.svelte +225 -0
- package/dist/src/lib/heatmap-matrix/index.ts +167 -0
- package/dist/src/lib/heatmap-matrix/shared.ts +7 -0
- package/dist/src/lib/icons.ts +650 -0
- package/dist/src/lib/index.ts +61 -0
- package/dist/src/lib/io/decompress.ts +92 -0
- package/dist/src/lib/io/export.ts +385 -0
- package/dist/src/lib/io/fetch.ts +46 -0
- package/dist/src/lib/io/file-drop.ts +51 -0
- package/dist/src/lib/io/index.ts +7 -0
- package/dist/src/lib/io/is-binary.ts +24 -0
- package/dist/src/lib/io/types.ts +8 -0
- package/dist/src/lib/io/url-drop.ts +141 -0
- package/dist/src/lib/isosurface/Isosurface.svelte +285 -0
- package/dist/src/lib/isosurface/IsosurfaceControls.svelte +277 -0
- package/dist/src/lib/isosurface/index.ts +7 -0
- package/dist/src/lib/isosurface/parse.ts +656 -0
- package/dist/src/lib/isosurface/slice.ts +175 -0
- package/dist/src/lib/isosurface/types.ts +309 -0
- package/dist/src/lib/labels.ts +320 -0
- package/dist/src/lib/layout/FullscreenToggle.svelte +50 -0
- package/dist/src/lib/layout/InfoCard.svelte +120 -0
- package/dist/src/lib/layout/InfoTag.svelte +185 -0
- package/dist/src/lib/layout/PropertyFilter.svelte +246 -0
- package/dist/src/lib/layout/SettingsSection.svelte +148 -0
- package/dist/src/lib/layout/SubpageGrid.svelte +82 -0
- package/dist/src/lib/layout/fullscreen.ts +65 -0
- package/dist/src/lib/layout/index.ts +11 -0
- package/dist/src/lib/layout/json-tree/JsonNode.svelte +548 -0
- package/dist/src/lib/layout/json-tree/JsonTree.svelte +1230 -0
- package/dist/src/lib/layout/json-tree/JsonValue.svelte +334 -0
- package/dist/src/lib/layout/json-tree/index.ts +3 -0
- package/dist/src/lib/layout/json-tree/types.ts +126 -0
- package/dist/src/lib/layout/json-tree/utils.ts +682 -0
- package/dist/src/lib/marching-cubes.ts +614 -0
- package/dist/src/lib/math.ts +1081 -0
- package/dist/src/lib/overlays/ContextMenu.svelte +162 -0
- package/dist/src/lib/overlays/CopyButton.svelte +45 -0
- package/dist/src/lib/overlays/DragControlTab.svelte +98 -0
- package/dist/src/lib/overlays/DraggablePane.svelte +487 -0
- package/dist/src/lib/overlays/InfoPaneCards.svelte +149 -0
- package/dist/src/lib/overlays/index.ts +3 -0
- package/dist/src/lib/periodic-table/PeriodicTable.svelte +469 -0
- package/dist/src/lib/periodic-table/PeriodicTableControls.svelte +557 -0
- package/dist/src/lib/periodic-table/PropertySelect.svelte +37 -0
- package/dist/src/lib/periodic-table/index.ts +12 -0
- package/dist/src/lib/phase-diagram/IsobaricBinaryPhaseDiagram.svelte +1086 -0
- package/dist/src/lib/phase-diagram/PhaseDiagramControls.svelte +444 -0
- package/dist/src/lib/phase-diagram/PhaseDiagramEditorPane.svelte +126 -0
- package/dist/src/lib/phase-diagram/PhaseDiagramExportPane.svelte +184 -0
- package/dist/src/lib/phase-diagram/PhaseDiagramTooltip.svelte +391 -0
- package/dist/src/lib/phase-diagram/TdbInfoPanel.svelte +203 -0
- package/dist/src/lib/phase-diagram/build-diagram.ts +186 -0
- package/dist/src/lib/phase-diagram/colors.ts +58 -0
- package/dist/src/lib/phase-diagram/diagram-input.ts +40 -0
- package/dist/src/lib/phase-diagram/index.ts +13 -0
- package/dist/src/lib/phase-diagram/parse.ts +348 -0
- package/dist/src/lib/phase-diagram/svg-to-diagram.ts +1023 -0
- package/dist/src/lib/phase-diagram/types.ts +144 -0
- package/dist/src/lib/phase-diagram/utils.ts +775 -0
- package/dist/src/lib/plot/AxisLabel.svelte +51 -0
- package/dist/src/lib/plot/BarPlot.svelte +2113 -0
- package/dist/src/lib/plot/BarPlotControls.svelte +66 -0
- package/dist/src/lib/plot/BinnedScatterPlot.svelte +1114 -0
- package/dist/src/lib/plot/ColorBar.svelte +721 -0
- package/dist/src/lib/plot/ColorScaleSelect.svelte +54 -0
- package/dist/src/lib/plot/ElementScatter.svelte +63 -0
- package/dist/src/lib/plot/FillArea.svelte +223 -0
- package/dist/src/lib/plot/Histogram.svelte +1558 -0
- package/dist/src/lib/plot/HistogramControls.svelte +212 -0
- package/dist/src/lib/plot/InteractiveAxisLabel.svelte +96 -0
- package/dist/src/lib/plot/Line.svelte +84 -0
- package/dist/src/lib/plot/PlotAxis.svelte +169 -0
- package/dist/src/lib/plot/PlotControls.svelte +537 -0
- package/dist/src/lib/plot/PlotLegend.svelte +569 -0
- package/dist/src/lib/plot/PlotTooltip.svelte +67 -0
- package/dist/src/lib/plot/PortalSelect.svelte +253 -0
- package/dist/src/lib/plot/ReferenceLine3D.svelte +156 -0
- package/dist/src/lib/plot/ReferencePlane.svelte +175 -0
- package/dist/src/lib/plot/ScatterPlot.svelte +2778 -0
- package/dist/src/lib/plot/ScatterPlot3D.svelte +529 -0
- package/dist/src/lib/plot/ScatterPlot3DControls.svelte +437 -0
- package/dist/src/lib/plot/ScatterPlot3DScene.svelte +912 -0
- package/dist/src/lib/plot/ScatterPlotControls.svelte +306 -0
- package/dist/src/lib/plot/ScatterPoint.svelte +182 -0
- package/dist/src/lib/plot/SpacegroupBarPlot.svelte +293 -0
- package/dist/src/lib/plot/Surface3D.svelte +197 -0
- package/dist/src/lib/plot/ZeroLines.svelte +97 -0
- package/dist/src/lib/plot/ZoomRect.svelte +23 -0
- package/dist/src/lib/plot/adaptive-density.ts +316 -0
- package/dist/src/lib/plot/auto-place.ts +184 -0
- package/dist/src/lib/plot/axis-utils.ts +122 -0
- package/dist/src/lib/plot/binned-scatter-types.ts +83 -0
- package/dist/src/lib/plot/data-cleaning.ts +1069 -0
- package/dist/src/lib/plot/data-transform.ts +69 -0
- package/dist/src/lib/plot/defaults.ts +9 -0
- package/dist/src/lib/plot/fill-utils.ts +494 -0
- package/dist/src/lib/plot/hover-lock.svelte.ts +60 -0
- package/dist/src/lib/plot/index.ts +53 -0
- package/dist/src/lib/plot/interactions.ts +119 -0
- package/dist/src/lib/plot/layout.ts +425 -0
- package/dist/src/lib/plot/reference-line.ts +426 -0
- package/dist/src/lib/plot/scales.ts +654 -0
- package/dist/src/lib/plot/svg.ts +23 -0
- package/dist/src/lib/plot/types.ts +1144 -0
- package/dist/src/lib/plot/utils/label-placement.ts +541 -0
- package/dist/src/lib/plot/utils/series-visibility.ts +140 -0
- package/dist/src/lib/plot/utils.ts +11 -0
- package/dist/src/lib/rdf/RdfPlot.svelte +247 -0
- package/dist/src/lib/rdf/calc-rdf.ts +167 -0
- package/dist/src/lib/rdf/index.ts +27 -0
- package/dist/src/lib/sanitize.ts +126 -0
- package/dist/src/lib/settings.ts +1479 -0
- package/dist/src/lib/spectral/Bands.svelte +1040 -0
- package/dist/src/lib/spectral/BandsAndDos.svelte +134 -0
- package/dist/src/lib/spectral/BrillouinBandsDos.svelte +252 -0
- package/dist/src/lib/spectral/Dos.svelte +697 -0
- package/dist/src/lib/spectral/helpers.ts +1381 -0
- package/dist/src/lib/spectral/index.ts +8 -0
- package/dist/src/lib/spectral/types.ts +112 -0
- package/dist/src/lib/state.svelte.ts +64 -0
- package/dist/src/lib/structure/Arrow.svelte +72 -0
- package/dist/src/lib/structure/AtomLegend.svelte +815 -0
- package/dist/src/lib/structure/Bond.svelte +140 -0
- package/dist/src/lib/structure/CanvasTooltip.svelte +33 -0
- package/dist/src/lib/structure/CellSelect.svelte +349 -0
- package/dist/src/lib/structure/Cylinder.svelte +45 -0
- package/dist/src/lib/structure/Lattice.svelte +196 -0
- package/dist/src/lib/structure/Structure.svelte +2248 -0
- package/dist/src/lib/structure/StructureControls.svelte +1273 -0
- package/dist/src/lib/structure/StructureExportPane.svelte +252 -0
- package/dist/src/lib/structure/StructureInfoPane.svelte +737 -0
- package/dist/src/lib/structure/StructureScene.svelte +2255 -0
- package/dist/src/lib/structure/atom-properties.ts +316 -0
- package/dist/src/lib/structure/bond-order-perception.ts +447 -0
- package/dist/src/lib/structure/bonding.ts +944 -0
- package/dist/src/lib/structure/export.ts +861 -0
- package/dist/src/lib/structure/index.ts +291 -0
- package/dist/src/lib/structure/label-placement.ts +130 -0
- package/dist/src/lib/structure/measure.ts +45 -0
- package/dist/src/lib/structure/parse.ts +1705 -0
- package/dist/src/lib/structure/partial-occupancy.ts +183 -0
- package/dist/src/lib/structure/pbc.ts +164 -0
- package/dist/src/lib/structure/supercell.ts +226 -0
- package/dist/src/lib/structure/validation.ts +11 -0
- package/dist/src/lib/symmetry/SymmetryStats.svelte +226 -0
- package/dist/src/lib/symmetry/WyckoffTable.svelte +120 -0
- package/dist/src/lib/symmetry/cell-transform.ts +118 -0
- package/dist/src/lib/symmetry/index.ts +348 -0
- package/dist/src/lib/symmetry/spacegroups.ts +404 -0
- package/dist/src/lib/table/HeatmapTable.svelte +1833 -0
- package/dist/src/lib/table/ToggleMenu.svelte +385 -0
- package/dist/src/lib/table/index.ts +139 -0
- package/dist/src/lib/theme/ThemeControl.svelte +53 -0
- package/dist/src/lib/theme/index.ts +107 -0
- package/dist/src/lib/theme/themes.mjs +297 -0
- package/dist/src/lib/time.ts +71 -0
- package/dist/src/lib/tooltip/TooltipContent.svelte +58 -0
- package/dist/src/lib/tooltip/index.ts +2 -0
- package/dist/src/lib/tooltip/types.ts +13 -0
- package/dist/src/lib/trajectory/Trajectory.svelte +1545 -0
- package/dist/src/lib/trajectory/TrajectoryError.svelte +128 -0
- package/dist/src/lib/trajectory/TrajectoryExportPane.svelte +357 -0
- package/dist/src/lib/trajectory/TrajectoryInfoPane.svelte +313 -0
- package/dist/src/lib/trajectory/constants.ts +7 -0
- package/dist/src/lib/trajectory/extract.ts +196 -0
- package/dist/src/lib/trajectory/format-detect.ts +96 -0
- package/dist/src/lib/trajectory/frame-reader.ts +456 -0
- package/dist/src/lib/trajectory/helpers.ts +217 -0
- package/dist/src/lib/trajectory/index.ts +218 -0
- package/dist/src/lib/trajectory/parse/ase.ts +109 -0
- package/dist/src/lib/trajectory/parse/hdf5.ts +173 -0
- package/dist/src/lib/trajectory/parse/index.ts +411 -0
- package/dist/src/lib/trajectory/parse/lammps.ts +215 -0
- package/dist/src/lib/trajectory/parse/vasp.ts +102 -0
- package/dist/src/lib/trajectory/parse/xyz.ts +143 -0
- package/dist/src/lib/trajectory/plotting.ts +599 -0
- package/dist/src/lib/trajectory/types.ts +13 -0
- package/dist/src/lib/utils.ts +56 -0
- package/dist/src/lib/xrd/XrdPlot.svelte +615 -0
- package/dist/src/lib/xrd/broadening.ts +130 -0
- package/dist/src/lib/xrd/calc-xrd.ts +397 -0
- package/dist/src/lib/xrd/index.ts +38 -0
- package/dist/src/lib/xrd/parse.ts +858 -0
- package/dist/webview.js +29421 -0
- package/icon.png +0 -0
- package/license +1 -1
- package/matterviz-0.3.2.vsix +0 -0
- package/matterviz-0.3.4.vsix +0 -0
- package/matterviz-0.3.5.vsix +0 -0
- package/package.json +1460 -215
- package/readme.md +171 -98
- package/scripts/sync-config.ts +101 -0
- package/src/declarations.d.ts +2 -0
- package/src/extension.ts +972 -0
- package/src/node-io.ts +65 -0
- package/src/types.ts +17 -0
- package/src/webview/JsonBrowser.svelte +1079 -0
- package/src/webview/PlotPanel.svelte +346 -0
- package/src/webview/detect.ts +444 -0
- package/src/webview/main.ts +764 -0
- package/src/webview/plot-utils.ts +250 -0
- package/test-fixtures/all-viz-types.json.gz +0 -0
- package/test-fixtures/plot-demo-data.json.gz +0 -0
- package/tests/detect.test.ts +604 -0
- package/tests/extension.test.ts +2041 -0
- package/tests/node-io.test.ts +39 -0
- package/tests/plot-utils.test.ts +302 -0
- package/tests/vite-plugin-json-gz.test.ts +114 -0
- package/tests/vscode-mock.ts +18 -0
- package/tests/webview.test.ts +231 -0
- package/tsconfig.json +20 -0
- package/vite-plugin-json-gz.ts +29 -0
- package/vite.config.ts +34 -0
- package/vite.extension.config.ts +34 -0
- package/dist/EmptyState.svelte.d.ts +0 -9
- package/dist/FilePicker.svelte +0 -360
- package/dist/FilePicker.svelte.d.ts +0 -17
- package/dist/Icon.svelte.d.ts +0 -13
- package/dist/MillerIndexInput.svelte +0 -66
- package/dist/MillerIndexInput.svelte.d.ts +0 -7
- package/dist/api/mp.d.ts +0 -6
- package/dist/api/mp.js +0 -22
- package/dist/api/optimade.d.ts +0 -45
- package/dist/api/optimade.js +0 -135
- package/dist/brillouin/BrillouinZone.svelte +0 -546
- package/dist/brillouin/BrillouinZone.svelte.d.ts +0 -83
- package/dist/brillouin/BrillouinZoneControls.svelte +0 -144
- package/dist/brillouin/BrillouinZoneControls.svelte.d.ts +0 -17
- package/dist/brillouin/BrillouinZoneExportPane.svelte +0 -148
- package/dist/brillouin/BrillouinZoneExportPane.svelte.d.ts +0 -15
- package/dist/brillouin/BrillouinZoneInfoPane.svelte +0 -146
- package/dist/brillouin/BrillouinZoneInfoPane.svelte.d.ts +0 -13
- package/dist/brillouin/BrillouinZoneScene.svelte +0 -476
- package/dist/brillouin/BrillouinZoneScene.svelte.d.ts +0 -48
- package/dist/brillouin/BrillouinZoneTooltip.svelte +0 -92
- package/dist/brillouin/BrillouinZoneTooltip.svelte.d.ts +0 -8
- package/dist/brillouin/compute.d.ts +0 -17
- package/dist/brillouin/compute.js +0 -426
- package/dist/brillouin/index.d.ts +0 -8
- package/dist/brillouin/index.js +0 -8
- package/dist/brillouin/types.d.ts +0 -48
- package/dist/brillouin/types.js +0 -1
- package/dist/chempot-diagram/ChemPotDiagram.svelte +0 -327
- package/dist/chempot-diagram/ChemPotDiagram.svelte.d.ts +0 -13
- package/dist/chempot-diagram/ChemPotDiagram2D.svelte +0 -847
- package/dist/chempot-diagram/ChemPotDiagram2D.svelte.d.ts +0 -16
- package/dist/chempot-diagram/ChemPotDiagram3D.svelte +0 -3194
- package/dist/chempot-diagram/ChemPotDiagram3D.svelte.d.ts +0 -16
- package/dist/chempot-diagram/ChemPotScene3D.svelte.d.ts +0 -7
- package/dist/chempot-diagram/async-compute.svelte.d.ts +0 -3
- package/dist/chempot-diagram/async-compute.svelte.js +0 -78
- package/dist/chempot-diagram/chempot-worker.d.ts +0 -1
- package/dist/chempot-diagram/chempot-worker.js +0 -11
- package/dist/chempot-diagram/color.d.ts +0 -10
- package/dist/chempot-diagram/color.js +0 -32
- package/dist/chempot-diagram/compute.d.ts +0 -48
- package/dist/chempot-diagram/compute.js +0 -812
- package/dist/chempot-diagram/index.d.ts +0 -6
- package/dist/chempot-diagram/index.js +0 -6
- package/dist/chempot-diagram/pointer.d.ts +0 -16
- package/dist/chempot-diagram/pointer.js +0 -40
- package/dist/chempot-diagram/temperature.d.ts +0 -15
- package/dist/chempot-diagram/temperature.js +0 -36
- package/dist/chempot-diagram/types.d.ts +0 -86
- package/dist/chempot-diagram/types.js +0 -28
- package/dist/colors/index.d.ts +0 -47
- package/dist/colors/index.js +0 -203
- package/dist/composition/BarChart.svelte +0 -297
- package/dist/composition/BarChart.svelte.d.ts +0 -39
- package/dist/composition/BubbleChart.svelte +0 -218
- package/dist/composition/BubbleChart.svelte.d.ts +0 -28
- package/dist/composition/Composition.svelte +0 -164
- package/dist/composition/Composition.svelte.d.ts +0 -15
- package/dist/composition/Formula.svelte +0 -265
- package/dist/composition/Formula.svelte.d.ts +0 -19
- package/dist/composition/FormulaFilter.svelte +0 -1259
- package/dist/composition/FormulaFilter.svelte.d.ts +0 -51
- package/dist/composition/PieChart.svelte +0 -323
- package/dist/composition/PieChart.svelte.d.ts +0 -37
- package/dist/composition/format.d.ts +0 -15
- package/dist/composition/format.js +0 -109
- package/dist/composition/index.d.ts +0 -20
- package/dist/composition/index.js +0 -14
- package/dist/composition/parse.d.ts +0 -55
- package/dist/composition/parse.js +0 -459
- package/dist/constants.d.ts +0 -29
- package/dist/constants.js +0 -99
- package/dist/controls.d.ts +0 -14
- package/dist/controls.js +0 -30
- package/dist/convex-hull/ConvexHull.svelte +0 -157
- package/dist/convex-hull/ConvexHull.svelte.d.ts +0 -13
- package/dist/convex-hull/ConvexHull2D.svelte +0 -814
- package/dist/convex-hull/ConvexHull2D.svelte.d.ts +0 -11
- package/dist/convex-hull/ConvexHull3D.svelte +0 -1790
- package/dist/convex-hull/ConvexHull3D.svelte.d.ts +0 -8
- package/dist/convex-hull/ConvexHull4D.svelte +0 -1386
- package/dist/convex-hull/ConvexHull4D.svelte.d.ts +0 -8
- package/dist/convex-hull/ConvexHullControls.svelte +0 -546
- package/dist/convex-hull/ConvexHullControls.svelte.d.ts +0 -48
- package/dist/convex-hull/ConvexHullInfoPane.svelte +0 -122
- package/dist/convex-hull/ConvexHullInfoPane.svelte.d.ts +0 -18
- package/dist/convex-hull/ConvexHullStats.svelte +0 -922
- package/dist/convex-hull/ConvexHullStats.svelte.d.ts +0 -15
- package/dist/convex-hull/ConvexHullTooltip.svelte +0 -131
- package/dist/convex-hull/ConvexHullTooltip.svelte.d.ts +0 -33
- package/dist/convex-hull/GasPressureControls.svelte +0 -247
- package/dist/convex-hull/GasPressureControls.svelte.d.ts +0 -11
- package/dist/convex-hull/StructurePopup.svelte +0 -116
- package/dist/convex-hull/StructurePopup.svelte.d.ts +0 -18
- package/dist/convex-hull/TemperatureSlider.svelte +0 -137
- package/dist/convex-hull/TemperatureSlider.svelte.d.ts +0 -8
- package/dist/convex-hull/barycentric-coords.d.ts +0 -18
- package/dist/convex-hull/barycentric-coords.js +0 -182
- package/dist/convex-hull/demo-temperature.d.ts +0 -6
- package/dist/convex-hull/demo-temperature.js +0 -40
- package/dist/convex-hull/gas-thermodynamics.d.ts +0 -16
- package/dist/convex-hull/gas-thermodynamics.js +0 -316
- package/dist/convex-hull/helpers.d.ts +0 -103
- package/dist/convex-hull/helpers.js +0 -689
- package/dist/convex-hull/index.d.ts +0 -118
- package/dist/convex-hull/index.js +0 -57
- package/dist/convex-hull/thermodynamics.d.ts +0 -66
- package/dist/convex-hull/thermodynamics.js +0 -1752
- package/dist/convex-hull/types.d.ts +0 -162
- package/dist/convex-hull/types.js +0 -36
- package/dist/coordination/CoordinationBarPlot.svelte +0 -311
- package/dist/coordination/CoordinationBarPlot.svelte.d.ts +0 -30
- package/dist/coordination/calc-coordination.d.ts +0 -15
- package/dist/coordination/calc-coordination.js +0 -63
- package/dist/coordination/index.d.ts +0 -8
- package/dist/coordination/index.js +0 -7
- package/dist/element/BohrAtom.svelte +0 -147
- package/dist/element/BohrAtom.svelte.d.ts +0 -20
- package/dist/element/ElementHeading.svelte +0 -26
- package/dist/element/ElementHeading.svelte.d.ts +0 -8
- package/dist/element/ElementPhoto.svelte +0 -57
- package/dist/element/ElementPhoto.svelte.d.ts +0 -9
- package/dist/element/ElementStats.svelte +0 -80
- package/dist/element/ElementStats.svelte.d.ts +0 -8
- package/dist/element/ElementTile.svelte +0 -484
- package/dist/element/ElementTile.svelte.d.ts +0 -29
- package/dist/element/Nucleus.svelte.d.ts +0 -17
- package/dist/element/data.d.ts +0 -2
- package/dist/element/data.js +0 -2
- package/dist/element/data.json.gz.d.ts +0 -2
- package/dist/element/index.d.ts +0 -8
- package/dist/element/index.js +0 -8
- package/dist/element/types.d.ts +0 -57
- package/dist/element/types.js +0 -1
- package/dist/feedback/ClickFeedback.svelte +0 -58
- package/dist/feedback/ClickFeedback.svelte.d.ts +0 -12
- package/dist/feedback/DragOverlay.svelte +0 -42
- package/dist/feedback/DragOverlay.svelte.d.ts +0 -7
- package/dist/feedback/Spinner.svelte.d.ts +0 -7
- package/dist/feedback/StatusMessage.svelte.d.ts +0 -9
- package/dist/feedback/index.d.ts +0 -4
- package/dist/feedback/index.js +0 -4
- package/dist/fermi-surface/FermiSlice.svelte +0 -189
- package/dist/fermi-surface/FermiSlice.svelte.d.ts +0 -24
- package/dist/fermi-surface/FermiSurface.svelte +0 -600
- package/dist/fermi-surface/FermiSurface.svelte.d.ts +0 -83
- package/dist/fermi-surface/FermiSurfaceControls.svelte +0 -452
- package/dist/fermi-surface/FermiSurfaceControls.svelte.d.ts +0 -35
- package/dist/fermi-surface/FermiSurfaceScene.svelte +0 -792
- package/dist/fermi-surface/FermiSurfaceScene.svelte.d.ts +0 -50
- package/dist/fermi-surface/FermiSurfaceTooltip.svelte +0 -111
- package/dist/fermi-surface/FermiSurfaceTooltip.svelte.d.ts +0 -8
- package/dist/fermi-surface/compute.d.ts +0 -5
- package/dist/fermi-surface/compute.js +0 -538
- package/dist/fermi-surface/constants.d.ts +0 -9
- package/dist/fermi-surface/constants.js +0 -27
- package/dist/fermi-surface/export.d.ts +0 -5
- package/dist/fermi-surface/export.js +0 -63
- package/dist/fermi-surface/index.d.ts +0 -12
- package/dist/fermi-surface/index.js +0 -13
- package/dist/fermi-surface/marching-cubes.d.ts +0 -2
- package/dist/fermi-surface/marching-cubes.js +0 -2
- package/dist/fermi-surface/parse.d.ts +0 -2
- package/dist/fermi-surface/parse.js +0 -495
- package/dist/fermi-surface/symmetry.d.ts +0 -3
- package/dist/fermi-surface/symmetry.js +0 -46
- package/dist/fermi-surface/types.d.ts +0 -113
- package/dist/fermi-surface/types.js +0 -4
- package/dist/heatmap-matrix/HeatmapMatrix.svelte +0 -1527
- package/dist/heatmap-matrix/HeatmapMatrix.svelte.d.ts +0 -110
- package/dist/heatmap-matrix/HeatmapMatrixControls.svelte +0 -225
- package/dist/heatmap-matrix/HeatmapMatrixControls.svelte.d.ts +0 -30
- package/dist/heatmap-matrix/index.d.ts +0 -53
- package/dist/heatmap-matrix/index.js +0 -100
- package/dist/heatmap-matrix/shared.d.ts +0 -2
- package/dist/heatmap-matrix/shared.js +0 -4
- package/dist/icons.d.ts +0 -569
- package/dist/icons.js +0 -648
- package/dist/index.d.ts +0 -39
- package/dist/index.js +0 -39
- package/dist/io/decompress.d.ts +0 -10
- package/dist/io/decompress.js +0 -74
- package/dist/io/export.d.ts +0 -16
- package/dist/io/export.js +0 -316
- package/dist/io/fetch.d.ts +0 -5
- package/dist/io/fetch.js +0 -39
- package/dist/io/file-drop.d.ts +0 -7
- package/dist/io/file-drop.js +0 -43
- package/dist/io/index.d.ts +0 -7
- package/dist/io/index.js +0 -7
- package/dist/io/is-binary.d.ts +0 -1
- package/dist/io/is-binary.js +0 -20
- package/dist/io/types.d.ts +0 -8
- package/dist/io/types.js +0 -1
- package/dist/io/url-drop.d.ts +0 -2
- package/dist/io/url-drop.js +0 -117
- package/dist/isosurface/Isosurface.svelte +0 -285
- package/dist/isosurface/Isosurface.svelte.d.ts +0 -8
- package/dist/isosurface/IsosurfaceControls.svelte +0 -291
- package/dist/isosurface/IsosurfaceControls.svelte.d.ts +0 -9
- package/dist/isosurface/index.d.ts +0 -5
- package/dist/isosurface/index.js +0 -6
- package/dist/isosurface/parse.d.ts +0 -6
- package/dist/isosurface/parse.js +0 -553
- package/dist/isosurface/slice.d.ts +0 -11
- package/dist/isosurface/slice.js +0 -140
- package/dist/isosurface/types.d.ts +0 -56
- package/dist/isosurface/types.js +0 -227
- package/dist/labels.d.ts +0 -53
- package/dist/labels.js +0 -274
- package/dist/layout/FullscreenToggle.svelte +0 -50
- package/dist/layout/FullscreenToggle.svelte.d.ts +0 -7
- package/dist/layout/InfoCard.svelte +0 -120
- package/dist/layout/InfoCard.svelte.d.ts +0 -21
- package/dist/layout/InfoTag.svelte +0 -183
- package/dist/layout/InfoTag.svelte.d.ts +0 -19
- package/dist/layout/PropertyFilter.svelte +0 -244
- package/dist/layout/PropertyFilter.svelte.d.ts +0 -24
- package/dist/layout/SettingsSection.svelte +0 -148
- package/dist/layout/SettingsSection.svelte.d.ts +0 -17
- package/dist/layout/SubpageGrid.svelte +0 -82
- package/dist/layout/SubpageGrid.svelte.d.ts +0 -14
- package/dist/layout/fullscreen.d.ts +0 -9
- package/dist/layout/fullscreen.js +0 -53
- package/dist/layout/index.d.ts +0 -10
- package/dist/layout/index.js +0 -8
- package/dist/layout/json-tree/JsonNode.svelte +0 -548
- package/dist/layout/json-tree/JsonNode.svelte.d.ts +0 -11
- package/dist/layout/json-tree/JsonTree.svelte +0 -1222
- package/dist/layout/json-tree/JsonTree.svelte.d.ts +0 -6
- package/dist/layout/json-tree/JsonValue.svelte +0 -334
- package/dist/layout/json-tree/JsonValue.svelte.d.ts +0 -9
- package/dist/layout/json-tree/index.d.ts +0 -3
- package/dist/layout/json-tree/index.js +0 -3
- package/dist/layout/json-tree/types.d.ts +0 -73
- package/dist/layout/json-tree/types.js +0 -3
- package/dist/layout/json-tree/utils.d.ts +0 -29
- package/dist/layout/json-tree/utils.js +0 -649
- package/dist/marching-cubes.d.ts +0 -14
- package/dist/marching-cubes.js +0 -542
- package/dist/math.d.ts +0 -91
- package/dist/math.js +0 -896
- package/dist/overlays/ContextMenu.svelte +0 -162
- package/dist/overlays/ContextMenu.svelte.d.ts +0 -25
- package/dist/overlays/CopyButton.svelte +0 -45
- package/dist/overlays/CopyButton.svelte.d.ts +0 -8
- package/dist/overlays/DraggablePane.svelte +0 -564
- package/dist/overlays/DraggablePane.svelte.d.ts +0 -36
- package/dist/overlays/InfoPaneCards.svelte +0 -149
- package/dist/overlays/InfoPaneCards.svelte.d.ts +0 -22
- package/dist/overlays/index.d.ts +0 -2
- package/dist/overlays/index.js +0 -2
- package/dist/periodic-table/PeriodicTable.svelte +0 -469
- package/dist/periodic-table/PeriodicTable.svelte.d.ts +0 -55
- package/dist/periodic-table/PeriodicTableControls.svelte +0 -557
- package/dist/periodic-table/PeriodicTableControls.svelte.d.ts +0 -24
- package/dist/periodic-table/PropertySelect.svelte +0 -37
- package/dist/periodic-table/PropertySelect.svelte.d.ts +0 -13
- package/dist/periodic-table/TableInset.svelte.d.ts +0 -9
- package/dist/periodic-table/index.d.ts +0 -10
- package/dist/periodic-table/index.js +0 -4
- package/dist/phase-diagram/IsobaricBinaryPhaseDiagram.svelte +0 -1084
- package/dist/phase-diagram/IsobaricBinaryPhaseDiagram.svelte.d.ts +0 -44
- package/dist/phase-diagram/PhaseDiagramControls.svelte +0 -449
- package/dist/phase-diagram/PhaseDiagramControls.svelte.d.ts +0 -30
- package/dist/phase-diagram/PhaseDiagramEditorPane.svelte +0 -126
- package/dist/phase-diagram/PhaseDiagramEditorPane.svelte.d.ts +0 -15
- package/dist/phase-diagram/PhaseDiagramExportPane.svelte +0 -192
- package/dist/phase-diagram/PhaseDiagramExportPane.svelte.d.ts +0 -19
- package/dist/phase-diagram/PhaseDiagramTooltip.svelte +0 -392
- package/dist/phase-diagram/PhaseDiagramTooltip.svelte.d.ts +0 -16
- package/dist/phase-diagram/TdbInfoPanel.svelte +0 -203
- package/dist/phase-diagram/TdbInfoPanel.svelte.d.ts +0 -12
- package/dist/phase-diagram/build-diagram.d.ts +0 -11
- package/dist/phase-diagram/build-diagram.js +0 -167
- package/dist/phase-diagram/colors.d.ts +0 -35
- package/dist/phase-diagram/colors.js +0 -51
- package/dist/phase-diagram/diagram-input.d.ts +0 -33
- package/dist/phase-diagram/diagram-input.js +0 -3
- package/dist/phase-diagram/index.d.ts +0 -13
- package/dist/phase-diagram/index.js +0 -13
- package/dist/phase-diagram/parse.d.ts +0 -55
- package/dist/phase-diagram/parse.js +0 -276
- package/dist/phase-diagram/svg-to-diagram.d.ts +0 -2
- package/dist/phase-diagram/svg-to-diagram.js +0 -867
- package/dist/phase-diagram/types.d.ts +0 -99
- package/dist/phase-diagram/types.js +0 -1
- package/dist/phase-diagram/utils.d.ts +0 -118
- package/dist/phase-diagram/utils.js +0 -606
- package/dist/plot/AxisLabel.svelte +0 -51
- package/dist/plot/AxisLabel.svelte.d.ts +0 -16
- package/dist/plot/BarPlot.svelte +0 -2265
- package/dist/plot/BarPlot.svelte.d.ts +0 -83
- package/dist/plot/BarPlotControls.svelte +0 -66
- package/dist/plot/BarPlotControls.svelte.d.ts +0 -18
- package/dist/plot/ColorBar.svelte +0 -719
- package/dist/plot/ColorBar.svelte.d.ts +0 -31
- package/dist/plot/ColorScaleSelect.svelte +0 -54
- package/dist/plot/ColorScaleSelect.svelte.d.ts +0 -15
- package/dist/plot/ElementScatter.svelte +0 -63
- package/dist/plot/ElementScatter.svelte.d.ts +0 -14
- package/dist/plot/FillArea.svelte +0 -225
- package/dist/plot/FillArea.svelte.d.ts +0 -21
- package/dist/plot/Histogram.svelte +0 -1672
- package/dist/plot/Histogram.svelte.d.ts +0 -50
- package/dist/plot/HistogramControls.svelte +0 -212
- package/dist/plot/HistogramControls.svelte.d.ts +0 -22
- package/dist/plot/InteractiveAxisLabel.svelte +0 -94
- package/dist/plot/InteractiveAxisLabel.svelte.d.ts +0 -14
- package/dist/plot/Line.svelte +0 -84
- package/dist/plot/Line.svelte.d.ts +0 -15
- package/dist/plot/PlotControls.svelte +0 -537
- package/dist/plot/PlotControls.svelte.d.ts +0 -4
- package/dist/plot/PlotLegend.svelte +0 -569
- package/dist/plot/PlotLegend.svelte.d.ts +0 -29
- package/dist/plot/PlotTooltip.svelte +0 -67
- package/dist/plot/PlotTooltip.svelte.d.ts +0 -17
- package/dist/plot/PortalSelect.svelte +0 -253
- package/dist/plot/PortalSelect.svelte.d.ts +0 -16
- package/dist/plot/ReferenceLine.svelte.d.ts +0 -20
- package/dist/plot/ReferenceLine3D.svelte +0 -154
- package/dist/plot/ReferenceLine3D.svelte.d.ts +0 -14
- package/dist/plot/ReferencePlane.svelte +0 -178
- package/dist/plot/ReferencePlane.svelte.d.ts +0 -14
- package/dist/plot/ScatterPlot.svelte +0 -2845
- package/dist/plot/ScatterPlot.svelte.d.ts +0 -93
- package/dist/plot/ScatterPlot3D.svelte +0 -502
- package/dist/plot/ScatterPlot3D.svelte.d.ts +0 -94
- package/dist/plot/ScatterPlot3DControls.svelte +0 -437
- package/dist/plot/ScatterPlot3DControls.svelte.d.ts +0 -20
- package/dist/plot/ScatterPlot3DScene.svelte +0 -912
- package/dist/plot/ScatterPlot3DScene.svelte.d.ts +0 -74
- package/dist/plot/ScatterPlotControls.svelte +0 -307
- package/dist/plot/ScatterPlotControls.svelte.d.ts +0 -17
- package/dist/plot/ScatterPoint.svelte +0 -191
- package/dist/plot/ScatterPoint.svelte.d.ts +0 -21
- package/dist/plot/SpacegroupBarPlot.svelte +0 -293
- package/dist/plot/SpacegroupBarPlot.svelte.d.ts +0 -9
- package/dist/plot/Surface3D.svelte +0 -200
- package/dist/plot/Surface3D.svelte.d.ts +0 -13
- package/dist/plot/ZeroLines.svelte +0 -96
- package/dist/plot/ZeroLines.svelte.d.ts +0 -32
- package/dist/plot/ZoomRect.svelte +0 -23
- package/dist/plot/ZoomRect.svelte.d.ts +0 -8
- package/dist/plot/axis-utils.d.ts +0 -19
- package/dist/plot/axis-utils.js +0 -80
- package/dist/plot/data-cleaning.d.ts +0 -37
- package/dist/plot/data-cleaning.js +0 -855
- package/dist/plot/data-transform.d.ts +0 -16
- package/dist/plot/data-transform.js +0 -45
- package/dist/plot/defaults.d.ts +0 -19
- package/dist/plot/defaults.js +0 -9
- package/dist/plot/fill-utils.d.ts +0 -51
- package/dist/plot/fill-utils.js +0 -337
- package/dist/plot/hover-lock.svelte.d.ts +0 -14
- package/dist/plot/hover-lock.svelte.js +0 -46
- package/dist/plot/index.d.ts +0 -37
- package/dist/plot/index.js +0 -37
- package/dist/plot/interactions.d.ts +0 -12
- package/dist/plot/interactions.js +0 -100
- package/dist/plot/layout.d.ts +0 -60
- package/dist/plot/layout.js +0 -230
- package/dist/plot/reference-line.d.ts +0 -60
- package/dist/plot/reference-line.js +0 -316
- package/dist/plot/scales.d.ts +0 -48
- package/dist/plot/scales.js +0 -484
- package/dist/plot/svg.d.ts +0 -1
- package/dist/plot/svg.js +0 -11
- package/dist/plot/types.d.ts +0 -859
- package/dist/plot/types.js +0 -103
- package/dist/plot/utils/label-placement.d.ts +0 -47
- package/dist/plot/utils/label-placement.js +0 -256
- package/dist/plot/utils/series-visibility.d.ts +0 -9
- package/dist/plot/utils/series-visibility.js +0 -67
- package/dist/plot/utils.d.ts +0 -1
- package/dist/plot/utils.js +0 -14
- package/dist/rdf/RdfPlot.svelte +0 -247
- package/dist/rdf/RdfPlot.svelte.d.ts +0 -27
- package/dist/rdf/calc-rdf.d.ts +0 -4
- package/dist/rdf/calc-rdf.js +0 -111
- package/dist/rdf/index.d.ts +0 -23
- package/dist/rdf/index.js +0 -2
- package/dist/sanitize.d.ts +0 -4
- package/dist/sanitize.js +0 -114
- package/dist/settings.d.ts +0 -255
- package/dist/settings.js +0 -1132
- package/dist/spectral/Bands.svelte +0 -1040
- package/dist/spectral/Bands.svelte.d.ts +0 -40
- package/dist/spectral/BandsAndDos.svelte +0 -128
- package/dist/spectral/BandsAndDos.svelte.d.ts +0 -18
- package/dist/spectral/BrillouinBandsDos.svelte +0 -248
- package/dist/spectral/BrillouinBandsDos.svelte.d.ts +0 -20
- package/dist/spectral/Dos.svelte +0 -697
- package/dist/spectral/Dos.svelte.d.ts +0 -29
- package/dist/spectral/helpers.d.ts +0 -117
- package/dist/spectral/helpers.js +0 -1023
- package/dist/spectral/index.d.ts +0 -6
- package/dist/spectral/index.js +0 -7
- package/dist/spectral/types.d.ts +0 -84
- package/dist/spectral/types.js +0 -2
- package/dist/state.svelte.d.ts +0 -25
- package/dist/state.svelte.js +0 -45
- package/dist/structure/Arrow.svelte +0 -72
- package/dist/structure/Arrow.svelte.d.ts +0 -15
- package/dist/structure/AtomLegend.svelte +0 -798
- package/dist/structure/AtomLegend.svelte.d.ts +0 -34
- package/dist/structure/Bond.svelte +0 -140
- package/dist/structure/Bond.svelte.d.ts +0 -9
- package/dist/structure/CanvasTooltip.svelte +0 -33
- package/dist/structure/CanvasTooltip.svelte.d.ts +0 -12
- package/dist/structure/CellSelect.svelte +0 -351
- package/dist/structure/CellSelect.svelte.d.ts +0 -13
- package/dist/structure/Cylinder.svelte +0 -45
- package/dist/structure/Cylinder.svelte.d.ts +0 -10
- package/dist/structure/Lattice.svelte +0 -196
- package/dist/structure/Lattice.svelte.d.ts +0 -17
- package/dist/structure/Structure.svelte +0 -1999
- package/dist/structure/Structure.svelte.d.ts +0 -87
- package/dist/structure/StructureControls.svelte +0 -1298
- package/dist/structure/StructureControls.svelte.d.ts +0 -31
- package/dist/structure/StructureExportPane.svelte +0 -251
- package/dist/structure/StructureExportPane.svelte.d.ts +0 -17
- package/dist/structure/StructureInfoPane.svelte +0 -735
- package/dist/structure/StructureInfoPane.svelte.d.ts +0 -19
- package/dist/structure/StructureScene.svelte +0 -1905
- package/dist/structure/StructureScene.svelte.d.ts +0 -108
- package/dist/structure/atom-properties.d.ts +0 -37
- package/dist/structure/atom-properties.js +0 -200
- package/dist/structure/bond-order-perception.d.ts +0 -13
- package/dist/structure/bond-order-perception.js +0 -367
- package/dist/structure/bonding.d.ts +0 -42
- package/dist/structure/bonding.js +0 -525
- package/dist/structure/export.d.ts +0 -20
- package/dist/structure/export.js +0 -727
- package/dist/structure/index.d.ts +0 -125
- package/dist/structure/index.js +0 -171
- package/dist/structure/label-placement.d.ts +0 -14
- package/dist/structure/label-placement.js +0 -72
- package/dist/structure/measure.d.ts +0 -6
- package/dist/structure/measure.js +0 -29
- package/dist/structure/parse.d.ts +0 -66
- package/dist/structure/parse.js +0 -1363
- package/dist/structure/partial-occupancy.d.ts +0 -25
- package/dist/structure/partial-occupancy.js +0 -99
- package/dist/structure/pbc.d.ts +0 -9
- package/dist/structure/pbc.js +0 -123
- package/dist/structure/supercell.d.ts +0 -8
- package/dist/structure/supercell.js +0 -170
- package/dist/structure/validation.d.ts +0 -2
- package/dist/structure/validation.js +0 -10
- package/dist/symmetry/SymmetryStats.svelte +0 -226
- package/dist/symmetry/SymmetryStats.svelte.d.ts +0 -21
- package/dist/symmetry/WyckoffTable.svelte +0 -113
- package/dist/symmetry/WyckoffTable.svelte.d.ts +0 -11
- package/dist/symmetry/cell-transform.d.ts +0 -12
- package/dist/symmetry/cell-transform.js +0 -91
- package/dist/symmetry/index.d.ts +0 -43
- package/dist/symmetry/index.js +0 -229
- package/dist/symmetry/spacegroups.d.ts +0 -9
- package/dist/symmetry/spacegroups.js +0 -394
- package/dist/table/HeatmapTable.svelte +0 -1854
- package/dist/table/HeatmapTable.svelte.d.ts +0 -49
- package/dist/table/ToggleMenu.svelte +0 -376
- package/dist/table/ToggleMenu.svelte.d.ts +0 -11
- package/dist/table/index.d.ts +0 -74
- package/dist/table/index.js +0 -38
- package/dist/theme/ThemeControl.svelte +0 -53
- package/dist/theme/ThemeControl.svelte.d.ts +0 -9
- package/dist/theme/index.d.ts +0 -29
- package/dist/theme/index.js +0 -79
- package/dist/theme/themes.mjs +0 -285
- package/dist/time.d.ts +0 -4
- package/dist/time.js +0 -70
- package/dist/tooltip/TooltipContent.svelte +0 -58
- package/dist/tooltip/TooltipContent.svelte.d.ts +0 -31
- package/dist/tooltip/index.d.ts +0 -2
- package/dist/tooltip/index.js +0 -2
- package/dist/tooltip/types.d.ts +0 -8
- package/dist/tooltip/types.js +0 -1
- package/dist/trajectory/Trajectory.svelte +0 -1517
- package/dist/trajectory/Trajectory.svelte.d.ts +0 -77
- package/dist/trajectory/TrajectoryError.svelte +0 -128
- package/dist/trajectory/TrajectoryError.svelte.d.ts +0 -13
- package/dist/trajectory/TrajectoryExportPane.svelte +0 -357
- package/dist/trajectory/TrajectoryExportPane.svelte.d.ts +0 -17
- package/dist/trajectory/TrajectoryInfoPane.svelte +0 -313
- package/dist/trajectory/TrajectoryInfoPane.svelte.d.ts +0 -17
- package/dist/trajectory/constants.d.ts +0 -6
- package/dist/trajectory/constants.js +0 -7
- package/dist/trajectory/extract.d.ts +0 -5
- package/dist/trajectory/extract.js +0 -162
- package/dist/trajectory/format-detect.d.ts +0 -9
- package/dist/trajectory/format-detect.js +0 -76
- package/dist/trajectory/frame-reader.d.ts +0 -17
- package/dist/trajectory/frame-reader.js +0 -332
- package/dist/trajectory/helpers.d.ts +0 -14
- package/dist/trajectory/helpers.js +0 -172
- package/dist/trajectory/index.d.ts +0 -63
- package/dist/trajectory/index.js +0 -126
- package/dist/trajectory/parse/ase.d.ts +0 -2
- package/dist/trajectory/parse/ase.js +0 -73
- package/dist/trajectory/parse/hdf5.d.ts +0 -2
- package/dist/trajectory/parse/hdf5.js +0 -127
- package/dist/trajectory/parse/index.d.ts +0 -12
- package/dist/trajectory/parse/index.js +0 -299
- package/dist/trajectory/parse/lammps.d.ts +0 -5
- package/dist/trajectory/parse/lammps.js +0 -179
- package/dist/trajectory/parse/vasp.d.ts +0 -2
- package/dist/trajectory/parse/vasp.js +0 -68
- package/dist/trajectory/parse/xyz.d.ts +0 -2
- package/dist/trajectory/parse/xyz.js +0 -110
- package/dist/trajectory/plotting.d.ts +0 -28
- package/dist/trajectory/plotting.js +0 -423
- package/dist/trajectory/types.d.ts +0 -11
- package/dist/trajectory/types.js +0 -1
- package/dist/utils.d.ts +0 -5
- package/dist/utils.js +0 -36
- package/dist/xrd/XrdPlot.svelte +0 -615
- package/dist/xrd/XrdPlot.svelte.d.ts +0 -28
- package/dist/xrd/broadening.d.ts +0 -20
- package/dist/xrd/broadening.js +0 -97
- package/dist/xrd/calc-xrd.d.ts +0 -37
- package/dist/xrd/calc-xrd.js +0 -337
- package/dist/xrd/index.d.ts +0 -37
- package/dist/xrd/index.js +0 -4
- package/dist/xrd/parse.d.ts +0 -13
- package/dist/xrd/parse.js +0 -749
- /package/dist/{EmptyState.svelte → src/lib/EmptyState.svelte} +0 -0
- /package/dist/{Icon.svelte → src/lib/Icon.svelte} +0 -0
- /package/dist/{app.css → src/lib/app.css} +0 -0
- /package/dist/{chempot-diagram → src/lib/chempot-diagram}/ChemPotScene3D.svelte +0 -0
- /package/dist/{colors → src/lib/colors}/alloy-colors.json +0 -0
- /package/dist/{colors → src/lib/colors}/dark-mode-colors.json +0 -0
- /package/dist/{colors → src/lib/colors}/jmol-colors.json +0 -0
- /package/dist/{colors → src/lib/colors}/muted-colors.json +0 -0
- /package/dist/{colors → src/lib/colors}/pastel-colors.json +0 -0
- /package/dist/{colors → src/lib/colors}/vesta-colors.json +0 -0
- /package/dist/{element → src/lib/element}/Nucleus.svelte +0 -0
- /package/dist/{element → src/lib/element}/data.json +0 -0
- /package/dist/{element → src/lib/element}/data.json.gz +0 -0
- /package/dist/{element → src/lib/element}/data.schema.json +0 -0
- /package/dist/{element-image-urls.json → src/lib/element-image-urls.json} +0 -0
- /package/dist/{feedback → src/lib/feedback}/Spinner.svelte +0 -0
- /package/dist/{feedback → src/lib/feedback}/StatusMessage.svelte +0 -0
- /package/dist/{periodic-table → src/lib/periodic-table}/TableInset.svelte +0 -0
- /package/dist/{plot → src/lib/plot}/ReferenceLine.svelte +0 -0
- /package/dist/{xrd → src/lib/xrd}/atomic_scattering_params.json +0 -0
|
@@ -0,0 +1,656 @@
|
|
|
1
|
+
// Parsers for volumetric data file formats (VASP CHGCAR, Gaussian .cube)
|
|
2
|
+
import { COMPRESSION_EXTENSIONS_REGEX, VASP_VOLUMETRIC_REGEX } from '$lib/constants'
|
|
3
|
+
import type { ElementSymbol } from '$lib/element'
|
|
4
|
+
import { ELEM_SYMBOLS } from '$lib/labels'
|
|
5
|
+
import type { Matrix3x3, Vec3 } from '$lib/math'
|
|
6
|
+
import * as math from '$lib/math'
|
|
7
|
+
import type { Site } from '$lib/structure'
|
|
8
|
+
import { wrap_to_unit_cell } from '$lib/structure/pbc'
|
|
9
|
+
import type { ParsedStructure } from '$lib/structure/parse'
|
|
10
|
+
import type { DataRange, VolumetricData, VolumetricFileData } from './types'
|
|
11
|
+
|
|
12
|
+
// Bohr radius in Angstroms (for Gaussian .cube unit conversion)
|
|
13
|
+
const BOHR_TO_ANGSTROM = 0.529177249
|
|
14
|
+
|
|
15
|
+
// === Fast number parsing utilities ===
|
|
16
|
+
|
|
17
|
+
// Parse whitespace-separated numbers directly from a string, starting at `pos`.
|
|
18
|
+
// Writes into a pre-allocated Float64Array and returns { count, end_pos }.
|
|
19
|
+
// Stops at `max_count` numbers, end of string, or when encountering a line
|
|
20
|
+
// starting with a letter (e.g. "augmentation" in CHGCAR).
|
|
21
|
+
function parse_float_block(
|
|
22
|
+
text: string,
|
|
23
|
+
pos: number,
|
|
24
|
+
max_count: number,
|
|
25
|
+
data: Float64Array,
|
|
26
|
+
data_offset: number = 0,
|
|
27
|
+
): { count: number; end_pos: number } {
|
|
28
|
+
let idx = data_offset
|
|
29
|
+
const target = data_offset + max_count
|
|
30
|
+
const len = text.length
|
|
31
|
+
|
|
32
|
+
while (idx < target && pos < len) {
|
|
33
|
+
// Skip whitespace
|
|
34
|
+
let char_code = text.charCodeAt(pos)
|
|
35
|
+
while (pos < len && char_code <= 32) {
|
|
36
|
+
// After a newline, check if the next non-space char is a letter (section break)
|
|
37
|
+
if (char_code === 10 || char_code === 13) {
|
|
38
|
+
let peek = pos + 1
|
|
39
|
+
// Skip \r\n combo
|
|
40
|
+
if (char_code === 13 && peek < len && text.charCodeAt(peek) === 10) peek++
|
|
41
|
+
// Skip leading spaces on the new line
|
|
42
|
+
while (peek < len && text.charCodeAt(peek) === 32) peek++
|
|
43
|
+
if (peek < len) {
|
|
44
|
+
const next_char = text.charCodeAt(peek)
|
|
45
|
+
// Letter a-z or A-Z signals a non-numeric line (e.g. "augmentation")
|
|
46
|
+
if ((next_char >= 65 && next_char <= 90) || (next_char >= 97 && next_char <= 122)) {
|
|
47
|
+
return { count: idx - data_offset, end_pos: pos }
|
|
48
|
+
}
|
|
49
|
+
}
|
|
50
|
+
}
|
|
51
|
+
char_code = text.charCodeAt(++pos)
|
|
52
|
+
}
|
|
53
|
+
if (pos >= len) break
|
|
54
|
+
|
|
55
|
+
// Find end of token
|
|
56
|
+
const start = pos
|
|
57
|
+
while (pos < len && text.charCodeAt(pos) > 32) pos++
|
|
58
|
+
|
|
59
|
+
// Parse number using unary + (handles scientific notation)
|
|
60
|
+
const num = +text.substring(start, pos)
|
|
61
|
+
if (!Number.isNaN(num)) {
|
|
62
|
+
data[idx++] = num
|
|
63
|
+
}
|
|
64
|
+
}
|
|
65
|
+
return { count: idx - data_offset, end_pos: pos }
|
|
66
|
+
}
|
|
67
|
+
|
|
68
|
+
// Find the character offset for line N in a string (0-indexed).
|
|
69
|
+
// Much faster than splitting the entire string into lines.
|
|
70
|
+
function find_line_offset(text: string, target_line: number): number {
|
|
71
|
+
let line = 0
|
|
72
|
+
let pos = 0
|
|
73
|
+
while (line < target_line && pos < text.length) {
|
|
74
|
+
if (text.charCodeAt(pos) === 10) line++
|
|
75
|
+
pos++
|
|
76
|
+
}
|
|
77
|
+
return pos
|
|
78
|
+
}
|
|
79
|
+
|
|
80
|
+
// Read a single line from text at the given offset, returning the line and next offset
|
|
81
|
+
function read_line(text: string, pos: number): { line: string; next: number } {
|
|
82
|
+
let end = pos
|
|
83
|
+
while (end < text.length && text.charCodeAt(end) !== 10 && text.charCodeAt(end) !== 13) end++
|
|
84
|
+
const line = text.substring(pos, end)
|
|
85
|
+
let next = end
|
|
86
|
+
if (next < text.length && text.charCodeAt(next) === 13) next++ // skip \r
|
|
87
|
+
if (next < text.length && text.charCodeAt(next) === 10) next++ // skip \n
|
|
88
|
+
return { line, next }
|
|
89
|
+
}
|
|
90
|
+
|
|
91
|
+
// Read N lines starting from pos, returning array of trimmed lines and final offset
|
|
92
|
+
function read_lines(
|
|
93
|
+
text: string,
|
|
94
|
+
pos: number,
|
|
95
|
+
count: number,
|
|
96
|
+
): { lines: string[]; next: number } {
|
|
97
|
+
const result: string[] = []
|
|
98
|
+
for (let idx = 0; idx < count; idx++) {
|
|
99
|
+
const { line, next } = read_line(text, pos)
|
|
100
|
+
result.push(line.trim())
|
|
101
|
+
pos = next
|
|
102
|
+
}
|
|
103
|
+
return { lines: result, next: pos }
|
|
104
|
+
}
|
|
105
|
+
|
|
106
|
+
// Build 3D grid directly from Float64Array, computing data_range in the same pass.
|
|
107
|
+
type BuildGridOptions = {
|
|
108
|
+
data: Float64Array
|
|
109
|
+
nx: number
|
|
110
|
+
ny: number
|
|
111
|
+
nz: number
|
|
112
|
+
divisor?: number
|
|
113
|
+
data_order?: `x_fastest` | `z_fastest`
|
|
114
|
+
}
|
|
115
|
+
|
|
116
|
+
function build_grid({
|
|
117
|
+
data,
|
|
118
|
+
nx,
|
|
119
|
+
ny,
|
|
120
|
+
nz,
|
|
121
|
+
divisor = 1,
|
|
122
|
+
data_order = `z_fastest`,
|
|
123
|
+
}: BuildGridOptions): { grid: number[][][]; data_range: DataRange } {
|
|
124
|
+
const grid: number[][][] = Array(nx)
|
|
125
|
+
let [min_val, max_val, sum] = [Infinity, -Infinity, 0]
|
|
126
|
+
const total = nx * ny * nz
|
|
127
|
+
const data_len = Math.min(data.length, total)
|
|
128
|
+
|
|
129
|
+
if (data_len === 0) {
|
|
130
|
+
// Empty data: return zeroed grid with neutral data_range
|
|
131
|
+
for (let ix = 0; ix < nx; ix++) {
|
|
132
|
+
const plane: number[][] = Array(ny)
|
|
133
|
+
for (let iy = 0; iy < ny; iy++) plane[iy] = Array(nz).fill(0)
|
|
134
|
+
grid[ix] = plane
|
|
135
|
+
}
|
|
136
|
+
return { grid, data_range: { min: 0, max: 0, abs_max: 0, mean: 0 } }
|
|
137
|
+
}
|
|
138
|
+
|
|
139
|
+
if (data_order === `z_fastest`) {
|
|
140
|
+
// .cube convention: z varies fastest, then y, then x.
|
|
141
|
+
const ny_nz = ny * nz
|
|
142
|
+
for (let ix = 0; ix < nx; ix++) {
|
|
143
|
+
const plane: number[][] = Array(ny)
|
|
144
|
+
for (let iy = 0; iy < ny; iy++) {
|
|
145
|
+
const row = Array(nz).fill(0)
|
|
146
|
+
const base = ix * ny_nz + iy * nz
|
|
147
|
+
const row_end = Math.min(base + nz, data_len)
|
|
148
|
+
for (let flat_idx = base; flat_idx < row_end; flat_idx++) {
|
|
149
|
+
const val = data[flat_idx] / divisor
|
|
150
|
+
row[flat_idx - base] = val
|
|
151
|
+
if (val < min_val) min_val = val
|
|
152
|
+
if (val > max_val) max_val = val
|
|
153
|
+
sum += val
|
|
154
|
+
}
|
|
155
|
+
plane[iy] = row
|
|
156
|
+
}
|
|
157
|
+
grid[ix] = plane
|
|
158
|
+
}
|
|
159
|
+
} else {
|
|
160
|
+
// VASP CHGCAR/ELFCAR/LOCPOT convention: x varies fastest, then y, then z.
|
|
161
|
+
for (let ix = 0; ix < nx; ix++) {
|
|
162
|
+
const plane: number[][] = Array(ny)
|
|
163
|
+
for (let iy = 0; iy < ny; iy++) plane[iy] = Array(nz).fill(0)
|
|
164
|
+
grid[ix] = plane
|
|
165
|
+
}
|
|
166
|
+
let [flat_idx, data_exhausted] = [0, false]
|
|
167
|
+
for (let iz = 0; iz < nz; iz++) {
|
|
168
|
+
for (let iy = 0; iy < ny; iy++) {
|
|
169
|
+
for (let ix = 0; ix < nx; ix++) {
|
|
170
|
+
if (flat_idx >= data_len) {
|
|
171
|
+
data_exhausted = true
|
|
172
|
+
break
|
|
173
|
+
}
|
|
174
|
+
const val = data[flat_idx] / divisor
|
|
175
|
+
grid[ix][iy][iz] = val
|
|
176
|
+
if (val < min_val) min_val = val
|
|
177
|
+
if (val > max_val) max_val = val
|
|
178
|
+
sum += val
|
|
179
|
+
flat_idx++
|
|
180
|
+
}
|
|
181
|
+
if (data_exhausted) break
|
|
182
|
+
}
|
|
183
|
+
if (data_exhausted) break
|
|
184
|
+
}
|
|
185
|
+
}
|
|
186
|
+
|
|
187
|
+
const abs_max = Math.max(Math.abs(min_val), Math.abs(max_val))
|
|
188
|
+
const data_range = { min: min_val, max: max_val, abs_max, mean: sum / data_len }
|
|
189
|
+
return { grid, data_range }
|
|
190
|
+
}
|
|
191
|
+
|
|
192
|
+
// === CHGCAR Parser ===
|
|
193
|
+
|
|
194
|
+
// Parse VASP CHGCAR/AECCAR/ELFCAR/LOCPOT/PARCHG file format.
|
|
195
|
+
// CHGCAR/PARCHG consists of a POSCAR header followed by volumetric data on a 3D grid.
|
|
196
|
+
// Spin-polarized files contain two data blocks (total charge + magnetization).
|
|
197
|
+
export function parse_chgcar(content: string): VolumetricFileData | null {
|
|
198
|
+
// Strip leading whitespace
|
|
199
|
+
let pos = 0
|
|
200
|
+
while (pos < content.length && content.charCodeAt(pos) <= 32) pos++
|
|
201
|
+
|
|
202
|
+
// Parse header line by line (only the first ~20 lines, not the whole file)
|
|
203
|
+
// Line 0: comment
|
|
204
|
+
let cur = read_line(content, pos)
|
|
205
|
+
pos = cur.next
|
|
206
|
+
|
|
207
|
+
// Line 1: scale factor
|
|
208
|
+
cur = read_line(content, pos)
|
|
209
|
+
const scale_factor = parseFloat(cur.line)
|
|
210
|
+
if (isNaN(scale_factor)) {
|
|
211
|
+
console.error(`Invalid scaling factor in CHGCAR`)
|
|
212
|
+
return null
|
|
213
|
+
}
|
|
214
|
+
pos = cur.next
|
|
215
|
+
|
|
216
|
+
// Lines 2-4: lattice vectors
|
|
217
|
+
const parse_vector = (line: string): Vec3 =>
|
|
218
|
+
math.scale(line.trim().split(/\s+/).slice(0, 3).map(Number) as Vec3, scale_factor)
|
|
219
|
+
|
|
220
|
+
const lat_lines = read_lines(content, pos, 3)
|
|
221
|
+
const lattice: Matrix3x3 = [
|
|
222
|
+
parse_vector(lat_lines.lines[0]),
|
|
223
|
+
parse_vector(lat_lines.lines[1]),
|
|
224
|
+
parse_vector(lat_lines.lines[2]),
|
|
225
|
+
]
|
|
226
|
+
pos = lat_lines.next
|
|
227
|
+
|
|
228
|
+
// Lines 5+: element symbols and atom counts
|
|
229
|
+
let element_symbols: string[] = []
|
|
230
|
+
let atom_counts: number[] = []
|
|
231
|
+
|
|
232
|
+
cur = read_line(content, pos)
|
|
233
|
+
if (pos >= content.length) {
|
|
234
|
+
console.error(`CHGCAR: file ends before element/count lines`)
|
|
235
|
+
return null
|
|
236
|
+
}
|
|
237
|
+
|
|
238
|
+
// Detect VASP 5+ format (has element symbols before counts)
|
|
239
|
+
const first_token = cur.line.trim().split(/\s+/)[0]
|
|
240
|
+
const has_element_symbols = isNaN(parseInt(first_token))
|
|
241
|
+
|
|
242
|
+
if (has_element_symbols) {
|
|
243
|
+
element_symbols = cur.line.trim().split(/\s+/)
|
|
244
|
+
pos = cur.next
|
|
245
|
+
cur = read_line(content, pos)
|
|
246
|
+
if (pos >= content.length) {
|
|
247
|
+
console.error(`CHGCAR: file ends before atom counts line`)
|
|
248
|
+
return null
|
|
249
|
+
}
|
|
250
|
+
atom_counts = cur.line.trim().split(/\s+/).map(Number)
|
|
251
|
+
pos = cur.next
|
|
252
|
+
} else {
|
|
253
|
+
atom_counts = cur.line.trim().split(/\s+/).map(Number)
|
|
254
|
+
const fallback_elements = [`H`, `He`, `Li`, `Be`, `B`, `C`, `N`, `O`, `F`, `Ne`]
|
|
255
|
+
element_symbols = atom_counts.map(
|
|
256
|
+
(_count, idx) => fallback_elements[idx % fallback_elements.length],
|
|
257
|
+
)
|
|
258
|
+
pos = cur.next
|
|
259
|
+
}
|
|
260
|
+
|
|
261
|
+
if (pos >= content.length) {
|
|
262
|
+
console.error(`CHGCAR: file ends before coordinate mode line`)
|
|
263
|
+
return null
|
|
264
|
+
}
|
|
265
|
+
|
|
266
|
+
// Check for selective dynamics line
|
|
267
|
+
cur = read_line(content, pos)
|
|
268
|
+
if (cur.line.trim().toUpperCase().startsWith(`S`)) {
|
|
269
|
+
pos = cur.next // skip selective dynamics line
|
|
270
|
+
cur = read_line(content, pos)
|
|
271
|
+
}
|
|
272
|
+
|
|
273
|
+
if (pos >= content.length) {
|
|
274
|
+
console.error(`CHGCAR: file ends before coordinate mode line`)
|
|
275
|
+
return null
|
|
276
|
+
}
|
|
277
|
+
|
|
278
|
+
// Coordinate mode line
|
|
279
|
+
const is_direct = cur.line.trim().toUpperCase().startsWith(`D`)
|
|
280
|
+
pos = cur.next
|
|
281
|
+
|
|
282
|
+
// Parse atomic positions
|
|
283
|
+
let cart_to_frac: (v: Vec3) => Vec3
|
|
284
|
+
let frac_to_cart: (v: Vec3) => Vec3
|
|
285
|
+
try {
|
|
286
|
+
;({ cart_to_frac, frac_to_cart } = math.create_lattice_converters(lattice))
|
|
287
|
+
} catch {
|
|
288
|
+
console.error(`CHGCAR: lattice matrix is singular; cannot convert coordinates`)
|
|
289
|
+
return null
|
|
290
|
+
}
|
|
291
|
+
const sites: Site[] = []
|
|
292
|
+
let atom_idx = 0
|
|
293
|
+
|
|
294
|
+
for (let elem_idx = 0; elem_idx < element_symbols.length; elem_idx++) {
|
|
295
|
+
const symbol = element_symbols[elem_idx].split(/[_/]/)[0]
|
|
296
|
+
const element = (
|
|
297
|
+
ELEM_SYMBOLS.includes(symbol as ElementSymbol) ? symbol : `H`
|
|
298
|
+
) as ElementSymbol
|
|
299
|
+
const count = atom_counts[elem_idx]
|
|
300
|
+
|
|
301
|
+
for (let count_idx = 0; count_idx < count; count_idx++) {
|
|
302
|
+
if (pos >= content.length) {
|
|
303
|
+
console.error(`CHGCAR: file ends before all atom coordinates are read`)
|
|
304
|
+
return null
|
|
305
|
+
}
|
|
306
|
+
cur = read_line(content, pos)
|
|
307
|
+
const coords = cur.line.trim().split(/\s+/).slice(0, 3).map(Number) as Vec3
|
|
308
|
+
pos = cur.next
|
|
309
|
+
|
|
310
|
+
let abc: Vec3
|
|
311
|
+
let xyz: Vec3
|
|
312
|
+
|
|
313
|
+
if (is_direct) {
|
|
314
|
+
abc = wrap_to_unit_cell(coords)
|
|
315
|
+
xyz = frac_to_cart(abc)
|
|
316
|
+
} else {
|
|
317
|
+
xyz = math.scale(coords, scale_factor)
|
|
318
|
+
const raw = cart_to_frac(xyz)
|
|
319
|
+
abc = wrap_to_unit_cell(raw)
|
|
320
|
+
}
|
|
321
|
+
|
|
322
|
+
sites.push({
|
|
323
|
+
species: [{ element, occu: 1, oxidation_state: 0 }],
|
|
324
|
+
abc,
|
|
325
|
+
xyz,
|
|
326
|
+
label: `${element}${atom_idx + count_idx + 1}`,
|
|
327
|
+
properties: {},
|
|
328
|
+
})
|
|
329
|
+
}
|
|
330
|
+
atom_idx += count
|
|
331
|
+
}
|
|
332
|
+
|
|
333
|
+
// Build the structure (volumetric files are always periodic)
|
|
334
|
+
const lattice_params = math.calc_lattice_params(lattice)
|
|
335
|
+
const structure: ParsedStructure = {
|
|
336
|
+
sites,
|
|
337
|
+
lattice: { matrix: lattice, pbc: [true, true, true], ...lattice_params },
|
|
338
|
+
}
|
|
339
|
+
|
|
340
|
+
// Parse volumetric data blocks
|
|
341
|
+
const volumes: VolumetricData[] = []
|
|
342
|
+
const volume_labels = [`charge density`, `magnetization density`]
|
|
343
|
+
|
|
344
|
+
for (let vol_idx = 0; vol_idx < 2; vol_idx++) {
|
|
345
|
+
// Skip blank lines
|
|
346
|
+
while (pos < content.length) {
|
|
347
|
+
cur = read_line(content, pos)
|
|
348
|
+
if (cur.line.trim() !== ``) break
|
|
349
|
+
pos = cur.next
|
|
350
|
+
}
|
|
351
|
+
|
|
352
|
+
if (pos >= content.length) break
|
|
353
|
+
|
|
354
|
+
// Parse grid dimensions: NGX NGY NGZ
|
|
355
|
+
cur = read_line(content, pos)
|
|
356
|
+
const grid_tokens = cur.line.trim().split(/\s+/).map(Number)
|
|
357
|
+
if (grid_tokens.length < 3 || grid_tokens.some(isNaN)) break
|
|
358
|
+
|
|
359
|
+
const [ngx, ngy, ngz] = grid_tokens
|
|
360
|
+
pos = cur.next
|
|
361
|
+
|
|
362
|
+
// Fast-parse volumetric data directly from the string
|
|
363
|
+
const total_points = ngx * ngy * ngz
|
|
364
|
+
const data = new Float64Array(total_points)
|
|
365
|
+
const { count: parsed_count, end_pos } = parse_float_block(
|
|
366
|
+
content,
|
|
367
|
+
pos,
|
|
368
|
+
total_points,
|
|
369
|
+
data,
|
|
370
|
+
)
|
|
371
|
+
pos = end_pos
|
|
372
|
+
|
|
373
|
+
if (parsed_count < total_points) {
|
|
374
|
+
console.warn(
|
|
375
|
+
`CHGCAR volume ${vol_idx}: expected ${total_points} values, got ${parsed_count}`,
|
|
376
|
+
)
|
|
377
|
+
if (parsed_count === 0) break
|
|
378
|
+
}
|
|
379
|
+
|
|
380
|
+
// CHGCAR stores rho * V_cell, so normalize by dividing by cell volume.
|
|
381
|
+
// Use Math.abs to guard against negative determinant (left-handed lattice).
|
|
382
|
+
const cell_volume = Math.abs(lattice_params.volume)
|
|
383
|
+
const divisor = cell_volume > 1e-30 ? cell_volume : 1
|
|
384
|
+
const { grid, data_range } = build_grid({
|
|
385
|
+
data: data.subarray(0, parsed_count),
|
|
386
|
+
nx: ngx,
|
|
387
|
+
ny: ngy,
|
|
388
|
+
nz: ngz,
|
|
389
|
+
divisor,
|
|
390
|
+
data_order: `x_fastest`,
|
|
391
|
+
})
|
|
392
|
+
|
|
393
|
+
volumes.push({
|
|
394
|
+
grid,
|
|
395
|
+
grid_dims: [ngx, ngy, ngz],
|
|
396
|
+
lattice,
|
|
397
|
+
origin: [0, 0, 0],
|
|
398
|
+
data_range,
|
|
399
|
+
data_order: `x_fastest`,
|
|
400
|
+
periodic: true, // VASP grids span [0,1) with N points, wrapping at boundaries
|
|
401
|
+
label: volume_labels[vol_idx],
|
|
402
|
+
})
|
|
403
|
+
|
|
404
|
+
// Skip augmentation occupancies and any remaining non-numeric lines
|
|
405
|
+
while (pos < content.length) {
|
|
406
|
+
cur = read_line(content, pos)
|
|
407
|
+
const trimmed = cur.line.trim()
|
|
408
|
+
if (trimmed === `` || /^\d+\s+\d+\s+\d+$/.test(trimmed)) break
|
|
409
|
+
pos = cur.next
|
|
410
|
+
}
|
|
411
|
+
}
|
|
412
|
+
|
|
413
|
+
if (volumes.length === 0) {
|
|
414
|
+
console.error(`No volumetric data found in CHGCAR`)
|
|
415
|
+
return null
|
|
416
|
+
}
|
|
417
|
+
|
|
418
|
+
return { structure, volumes }
|
|
419
|
+
}
|
|
420
|
+
|
|
421
|
+
// === Gaussian .cube Parser ===
|
|
422
|
+
|
|
423
|
+
// Parse Gaussian .cube file format.
|
|
424
|
+
// Contains atomic structure and volumetric data in a single file.
|
|
425
|
+
// Units: if grid dimensions are positive, coordinates are in Bohr; if negative, in Angstrom.
|
|
426
|
+
export function parse_cube(
|
|
427
|
+
content: string,
|
|
428
|
+
options: { periodic?: boolean } = {},
|
|
429
|
+
): VolumetricFileData | null {
|
|
430
|
+
// Quick line count check: need at least 7 lines (2 title + 1 header + 3 voxel + 1 atom)
|
|
431
|
+
let line_count = 0
|
|
432
|
+
for (let idx = 0; idx < content.length && line_count < 7; idx++) {
|
|
433
|
+
if (content.charCodeAt(idx) === 10) line_count++
|
|
434
|
+
}
|
|
435
|
+
if (line_count < 6) {
|
|
436
|
+
console.error(`.cube file too short`)
|
|
437
|
+
return null
|
|
438
|
+
}
|
|
439
|
+
|
|
440
|
+
// Parse header (first 6 lines + atom lines)
|
|
441
|
+
let pos = 0
|
|
442
|
+
const header = read_lines(content, pos, 6)
|
|
443
|
+
pos = header.next
|
|
444
|
+
|
|
445
|
+
// Line 2: n_atoms, origin_x, origin_y, origin_z
|
|
446
|
+
// (negative n_atoms indicates orbital data with extra header line)
|
|
447
|
+
const line2 = header.lines[2].split(/\s+/).map(Number)
|
|
448
|
+
if (line2.length < 4 || line2.some(isNaN)) {
|
|
449
|
+
console.error(`.cube header line 3 malformed: expected 4 numbers`)
|
|
450
|
+
return null
|
|
451
|
+
}
|
|
452
|
+
const n_atoms = Math.abs(line2[0])
|
|
453
|
+
const has_orbital_header = line2[0] < 0
|
|
454
|
+
const raw_origin: Vec3 = [line2[1], line2[2], line2[3]]
|
|
455
|
+
|
|
456
|
+
// Lines 3-5: grid dimensions and voxel vectors
|
|
457
|
+
// Positive N means coordinates in Bohr, negative N means Angstrom
|
|
458
|
+
const voxel_lines = [
|
|
459
|
+
header.lines[3].split(/\s+/).map(Number),
|
|
460
|
+
header.lines[4].split(/\s+/).map(Number),
|
|
461
|
+
header.lines[5].split(/\s+/).map(Number),
|
|
462
|
+
]
|
|
463
|
+
if (voxel_lines.some((line) => line.length < 4 || line.some(isNaN))) {
|
|
464
|
+
console.error(`.cube voxel lines malformed: expected 4 numbers per line`)
|
|
465
|
+
return null
|
|
466
|
+
}
|
|
467
|
+
|
|
468
|
+
const n_grid: Vec3 = [
|
|
469
|
+
Math.abs(voxel_lines[0][0]),
|
|
470
|
+
Math.abs(voxel_lines[1][0]),
|
|
471
|
+
Math.abs(voxel_lines[2][0]),
|
|
472
|
+
]
|
|
473
|
+
|
|
474
|
+
// Per Gaussian .cube convention, the sign of the first axis N determines units
|
|
475
|
+
const is_bohr = voxel_lines[0][0] > 0
|
|
476
|
+
const unit_scale = is_bohr ? BOHR_TO_ANGSTROM : 1.0
|
|
477
|
+
|
|
478
|
+
// Voxel vectors (convert to Angstrom if needed)
|
|
479
|
+
const [voxel_a, voxel_b, voxel_c] = voxel_lines.map((line) =>
|
|
480
|
+
math.scale(line.slice(1, 4) as Vec3, unit_scale),
|
|
481
|
+
)
|
|
482
|
+
|
|
483
|
+
// Lattice vectors = grid_dim * voxel_vector
|
|
484
|
+
const lattice: Matrix3x3 = [
|
|
485
|
+
math.scale(voxel_a, n_grid[0]),
|
|
486
|
+
math.scale(voxel_b, n_grid[1]),
|
|
487
|
+
math.scale(voxel_c, n_grid[2]),
|
|
488
|
+
]
|
|
489
|
+
|
|
490
|
+
const origin = math.scale(raw_origin, unit_scale)
|
|
491
|
+
|
|
492
|
+
// Periodicity: use explicit override if provided, else heuristic based on origin.
|
|
493
|
+
// Molecular .cube files have a non-zero origin (bounding box offset); periodic
|
|
494
|
+
// systems (QE, CP2K) have origin at (0,0,0). Pass { periodic: true/false } to
|
|
495
|
+
// override when the heuristic is wrong (e.g. molecule centered at origin).
|
|
496
|
+
const is_periodic = options.periodic ?? Math.hypot(...origin) < 1e-6
|
|
497
|
+
|
|
498
|
+
// Parse atomic positions
|
|
499
|
+
const sites: Site[] = []
|
|
500
|
+
let cube_cart_to_frac: (v: Vec3) => Vec3
|
|
501
|
+
try {
|
|
502
|
+
cube_cart_to_frac = math.create_cart_to_frac(lattice)
|
|
503
|
+
} catch {
|
|
504
|
+
// Non-periodic system (molecule), use identity
|
|
505
|
+
cube_cart_to_frac = (v: Vec3): Vec3 => [v[0], v[1], v[2]]
|
|
506
|
+
}
|
|
507
|
+
|
|
508
|
+
for (let atom_idx = 0; atom_idx < n_atoms; atom_idx++) {
|
|
509
|
+
const cur = read_line(content, pos)
|
|
510
|
+
const atom_line = cur.line.trim().split(/\s+/).map(Number)
|
|
511
|
+
pos = cur.next
|
|
512
|
+
|
|
513
|
+
// Validate: need atomic_number, charge, x, y, z (5 tokens, indices 2-4 finite)
|
|
514
|
+
if (
|
|
515
|
+
atom_line.length < 5 ||
|
|
516
|
+
!isFinite(atom_line[2]) ||
|
|
517
|
+
!isFinite(atom_line[3]) ||
|
|
518
|
+
!isFinite(atom_line[4])
|
|
519
|
+
) {
|
|
520
|
+
console.warn(`.cube atom ${atom_idx}: malformed line "${cur.line.trim()}", skipping`)
|
|
521
|
+
continue
|
|
522
|
+
}
|
|
523
|
+
|
|
524
|
+
// atom_line[1] is the charge (often 0)
|
|
525
|
+
const raw_xyz = math.scale([atom_line[2], atom_line[3], atom_line[4]] as Vec3, unit_scale)
|
|
526
|
+
|
|
527
|
+
// Convert Cartesian to fractional, accounting for origin offset.
|
|
528
|
+
// Store lattice-frame xyz (shifted) so abc and xyz stay consistent.
|
|
529
|
+
const xyz = math.subtract(raw_xyz, origin)
|
|
530
|
+
const abc = cube_cart_to_frac(xyz)
|
|
531
|
+
|
|
532
|
+
const element = atomic_number_to_symbol(atom_line[0])
|
|
533
|
+
sites.push({
|
|
534
|
+
species: [{ element, occu: 1, oxidation_state: 0 }],
|
|
535
|
+
abc,
|
|
536
|
+
xyz,
|
|
537
|
+
label: `${element}${atom_idx + 1}`,
|
|
538
|
+
properties: {},
|
|
539
|
+
})
|
|
540
|
+
}
|
|
541
|
+
|
|
542
|
+
// Build structure
|
|
543
|
+
const lattice_params = math.calc_lattice_params(lattice)
|
|
544
|
+
const structure: ParsedStructure = {
|
|
545
|
+
sites,
|
|
546
|
+
lattice: {
|
|
547
|
+
matrix: lattice,
|
|
548
|
+
pbc: [is_periodic, is_periodic, is_periodic],
|
|
549
|
+
...lattice_params,
|
|
550
|
+
},
|
|
551
|
+
}
|
|
552
|
+
|
|
553
|
+
// Skip orbital header line if present
|
|
554
|
+
if (has_orbital_header && pos < content.length) {
|
|
555
|
+
const cur = read_line(content, pos)
|
|
556
|
+
pos = cur.next
|
|
557
|
+
}
|
|
558
|
+
|
|
559
|
+
// Fast-parse volumetric data directly from the string
|
|
560
|
+
const total_points = n_grid[0] * n_grid[1] * n_grid[2]
|
|
561
|
+
const data = new Float64Array(total_points)
|
|
562
|
+
const { count: parsed_count } = parse_float_block(content, pos, total_points, data)
|
|
563
|
+
|
|
564
|
+
if (parsed_count < total_points) {
|
|
565
|
+
console.warn(`.cube: expected ${total_points} data values, got ${parsed_count}`)
|
|
566
|
+
if (parsed_count === 0) {
|
|
567
|
+
console.error(`No volumetric data found in .cube file`)
|
|
568
|
+
return null
|
|
569
|
+
}
|
|
570
|
+
}
|
|
571
|
+
|
|
572
|
+
const { grid, data_range } = build_grid({
|
|
573
|
+
data: data.subarray(0, parsed_count),
|
|
574
|
+
nx: n_grid[0],
|
|
575
|
+
ny: n_grid[1],
|
|
576
|
+
nz: n_grid[2],
|
|
577
|
+
data_order: `z_fastest`,
|
|
578
|
+
})
|
|
579
|
+
|
|
580
|
+
const volumes: VolumetricData[] = [
|
|
581
|
+
{
|
|
582
|
+
grid,
|
|
583
|
+
grid_dims: n_grid,
|
|
584
|
+
lattice,
|
|
585
|
+
origin,
|
|
586
|
+
data_range,
|
|
587
|
+
data_order: `z_fastest`,
|
|
588
|
+
periodic: is_periodic, // periodic systems wrap; molecular .cube files include both endpoints
|
|
589
|
+
label: `volumetric data`,
|
|
590
|
+
},
|
|
591
|
+
]
|
|
592
|
+
|
|
593
|
+
return { structure, volumes }
|
|
594
|
+
}
|
|
595
|
+
|
|
596
|
+
// Convert atomic number to element symbol using ELEM_SYMBOLS (1-indexed: H=1, He=2, ...)
|
|
597
|
+
function atomic_number_to_symbol(atomic_number: number): ElementSymbol {
|
|
598
|
+
// ELEM_SYMBOLS is 0-indexed (H at index 0), atomic numbers are 1-indexed
|
|
599
|
+
const idx = atomic_number - 1
|
|
600
|
+
return idx >= 0 && idx < ELEM_SYMBOLS.length ? ELEM_SYMBOLS[idx] : `H`
|
|
601
|
+
}
|
|
602
|
+
|
|
603
|
+
// Auto-detect and parse volumetric file format based on filename and content
|
|
604
|
+
export function parse_volumetric_file(
|
|
605
|
+
content: string,
|
|
606
|
+
filename?: string,
|
|
607
|
+
): VolumetricFileData | null {
|
|
608
|
+
// Strip compression suffixes so "CHGCAR.gz" and "molecule.cube.bz2" match correctly
|
|
609
|
+
const lower_name = (filename ?? ``).toLowerCase().replace(COMPRESSION_EXTENSIONS_REGEX, ``)
|
|
610
|
+
|
|
611
|
+
// Extension-based detection
|
|
612
|
+
if (lower_name.endsWith(`.cube`)) return parse_cube(content)
|
|
613
|
+
|
|
614
|
+
// VASP volumetric file detection by filename
|
|
615
|
+
if (VASP_VOLUMETRIC_REGEX.test(lower_name)) return parse_chgcar(content)
|
|
616
|
+
|
|
617
|
+
// Content-based detection (only parse first few lines, not the whole file)
|
|
618
|
+
// Find enough lines for detection without splitting the entire string
|
|
619
|
+
const detection_end = find_line_offset(content, 10)
|
|
620
|
+
const detection_text = content.substring(0, detection_end)
|
|
621
|
+
const lines = detection_text.split(/\r?\n/)
|
|
622
|
+
|
|
623
|
+
// .cube detection: line 3 has 4 numbers (n_atoms + origin), line 4 has 4 numbers (grid dim + voxel)
|
|
624
|
+
if (lines.length > 4) {
|
|
625
|
+
const line2_tokens = lines[2].trim().split(/\s+/)
|
|
626
|
+
const line3_tokens = lines[3].trim().split(/\s+/)
|
|
627
|
+
if (
|
|
628
|
+
line2_tokens.length === 4 &&
|
|
629
|
+
line3_tokens.length === 4 &&
|
|
630
|
+
line2_tokens.every((tok) => !isNaN(Number(tok))) &&
|
|
631
|
+
line3_tokens.every((tok) => !isNaN(Number(tok)))
|
|
632
|
+
) {
|
|
633
|
+
return parse_cube(content)
|
|
634
|
+
}
|
|
635
|
+
}
|
|
636
|
+
|
|
637
|
+
// CHGCAR detection: requires POSCAR-like header (scale factor on line 2) AND
|
|
638
|
+
// a grid dimensions line (3 integers) somewhere after the header. This distinguishes
|
|
639
|
+
// CHGCAR from plain POSCAR/CONTCAR files which share the same header format.
|
|
640
|
+
if (lines.length > 2 && !isNaN(parseFloat(lines[1].trim()))) {
|
|
641
|
+
// Scan for grid dimensions line (3 integers) starting from ~line 7
|
|
642
|
+
let scan_pos = find_line_offset(content, 7)
|
|
643
|
+
// Only scan a limited window, not the entire file
|
|
644
|
+
// Scan enough to cover large atom blocks (~100 chars/atom × ~200 atoms max)
|
|
645
|
+
const scan_end = Math.min(content.length, scan_pos + 25000)
|
|
646
|
+
while (scan_pos < scan_end) {
|
|
647
|
+
const { line, next } = read_line(content, scan_pos)
|
|
648
|
+
if (/^\s*\d+\s+\d+\s+\d+\s*$/.test(line)) {
|
|
649
|
+
return parse_chgcar(content)
|
|
650
|
+
}
|
|
651
|
+
scan_pos = next
|
|
652
|
+
}
|
|
653
|
+
}
|
|
654
|
+
|
|
655
|
+
return null
|
|
656
|
+
}
|