matterviz 0.3.6 → 0.3.7
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/dist/EmptyState.svelte.d.ts +9 -0
- package/dist/FilePicker.svelte +360 -0
- package/dist/FilePicker.svelte.d.ts +17 -0
- package/dist/Icon.svelte.d.ts +13 -0
- package/dist/MillerIndexInput.svelte +66 -0
- package/dist/MillerIndexInput.svelte.d.ts +7 -0
- package/dist/api/mp.d.ts +6 -0
- package/dist/api/mp.js +22 -0
- package/dist/api/optimade.d.ts +45 -0
- package/dist/api/optimade.js +135 -0
- package/dist/brillouin/BrillouinZone.svelte +549 -0
- package/dist/brillouin/BrillouinZone.svelte.d.ts +83 -0
- package/dist/brillouin/BrillouinZoneControls.svelte +144 -0
- package/dist/brillouin/BrillouinZoneControls.svelte.d.ts +17 -0
- package/dist/brillouin/BrillouinZoneExportPane.svelte +146 -0
- package/dist/brillouin/BrillouinZoneExportPane.svelte.d.ts +15 -0
- package/dist/brillouin/BrillouinZoneInfoPane.svelte +146 -0
- package/dist/brillouin/BrillouinZoneInfoPane.svelte.d.ts +13 -0
- package/dist/brillouin/BrillouinZoneScene.svelte +476 -0
- package/dist/brillouin/BrillouinZoneScene.svelte.d.ts +48 -0
- package/dist/brillouin/BrillouinZoneTooltip.svelte +92 -0
- package/dist/brillouin/BrillouinZoneTooltip.svelte.d.ts +8 -0
- package/dist/brillouin/compute.d.ts +17 -0
- package/dist/brillouin/compute.js +426 -0
- package/dist/brillouin/index.d.ts +8 -0
- package/dist/brillouin/index.js +7 -0
- package/dist/brillouin/types.d.ts +43 -0
- package/dist/brillouin/types.js +1 -0
- package/dist/chempot-diagram/ChemPotDiagram.svelte +327 -0
- package/dist/chempot-diagram/ChemPotDiagram.svelte.d.ts +13 -0
- package/dist/chempot-diagram/ChemPotDiagram2D.svelte +846 -0
- package/dist/chempot-diagram/ChemPotDiagram2D.svelte.d.ts +16 -0
- package/dist/chempot-diagram/ChemPotDiagram3D.svelte +3193 -0
- package/dist/chempot-diagram/ChemPotDiagram3D.svelte.d.ts +16 -0
- package/dist/chempot-diagram/ChemPotScene3D.svelte.d.ts +7 -0
- package/dist/chempot-diagram/async-compute.svelte.d.ts +3 -0
- package/dist/chempot-diagram/async-compute.svelte.js +78 -0
- package/dist/chempot-diagram/chempot-worker.d.ts +1 -0
- package/dist/chempot-diagram/chempot-worker.js +11 -0
- package/dist/chempot-diagram/color.d.ts +10 -0
- package/dist/chempot-diagram/color.js +32 -0
- package/dist/chempot-diagram/compute.d.ts +48 -0
- package/dist/chempot-diagram/compute.js +806 -0
- package/dist/chempot-diagram/index.d.ts +6 -0
- package/dist/chempot-diagram/index.js +6 -0
- package/dist/chempot-diagram/pointer.d.ts +16 -0
- package/dist/chempot-diagram/pointer.js +40 -0
- package/dist/chempot-diagram/temperature.d.ts +15 -0
- package/dist/chempot-diagram/temperature.js +34 -0
- package/dist/chempot-diagram/types.d.ts +81 -0
- package/dist/chempot-diagram/types.js +28 -0
- package/dist/colors/index.d.ts +47 -0
- package/dist/colors/index.js +203 -0
- package/dist/composition/BarChart.svelte +297 -0
- package/dist/composition/BarChart.svelte.d.ts +39 -0
- package/dist/composition/BubbleChart.svelte +218 -0
- package/dist/composition/BubbleChart.svelte.d.ts +28 -0
- package/dist/composition/Composition.svelte +165 -0
- package/dist/composition/Composition.svelte.d.ts +15 -0
- package/dist/composition/Formula.svelte +268 -0
- package/dist/composition/Formula.svelte.d.ts +19 -0
- package/dist/composition/FormulaFilter.svelte +1257 -0
- package/dist/composition/FormulaFilter.svelte.d.ts +51 -0
- package/dist/composition/PieChart.svelte +323 -0
- package/dist/composition/PieChart.svelte.d.ts +37 -0
- package/dist/composition/format.d.ts +15 -0
- package/dist/composition/format.js +109 -0
- package/dist/composition/index.d.ts +20 -0
- package/dist/composition/index.js +14 -0
- package/dist/composition/parse.d.ts +56 -0
- package/dist/composition/parse.js +474 -0
- package/dist/constants.d.ts +29 -0
- package/dist/constants.js +99 -0
- package/dist/controls.d.ts +14 -0
- package/dist/controls.js +30 -0
- package/dist/convex-hull/ConvexHull.svelte +157 -0
- package/dist/convex-hull/ConvexHull.svelte.d.ts +13 -0
- package/dist/convex-hull/ConvexHull2D.svelte +825 -0
- package/dist/convex-hull/ConvexHull2D.svelte.d.ts +11 -0
- package/dist/convex-hull/ConvexHull3D.svelte +1801 -0
- package/dist/convex-hull/ConvexHull3D.svelte.d.ts +8 -0
- package/dist/convex-hull/ConvexHull4D.svelte +1398 -0
- package/dist/convex-hull/ConvexHull4D.svelte.d.ts +8 -0
- package/dist/convex-hull/ConvexHullControls.svelte +535 -0
- package/dist/convex-hull/ConvexHullControls.svelte.d.ts +48 -0
- package/dist/convex-hull/ConvexHullInfoPane.svelte +125 -0
- package/dist/convex-hull/ConvexHullInfoPane.svelte.d.ts +20 -0
- package/dist/convex-hull/ConvexHullStats.svelte +929 -0
- package/dist/convex-hull/ConvexHullStats.svelte.d.ts +17 -0
- package/dist/convex-hull/ConvexHullTooltip.svelte +131 -0
- package/dist/convex-hull/ConvexHullTooltip.svelte.d.ts +33 -0
- package/dist/convex-hull/GasPressureControls.svelte +247 -0
- package/dist/convex-hull/GasPressureControls.svelte.d.ts +11 -0
- package/dist/convex-hull/StructurePopup.svelte +151 -0
- package/dist/convex-hull/StructurePopup.svelte.d.ts +18 -0
- package/dist/convex-hull/TemperatureSlider.svelte.d.ts +8 -0
- package/dist/convex-hull/barycentric-coords.d.ts +18 -0
- package/dist/convex-hull/barycentric-coords.js +182 -0
- package/dist/convex-hull/demo-temperature.d.ts +6 -0
- package/dist/convex-hull/demo-temperature.js +40 -0
- package/dist/convex-hull/gas-thermodynamics.d.ts +16 -0
- package/dist/convex-hull/gas-thermodynamics.js +314 -0
- package/dist/convex-hull/helpers.d.ts +114 -0
- package/dist/convex-hull/helpers.js +710 -0
- package/dist/convex-hull/index.d.ts +119 -0
- package/dist/convex-hull/index.js +58 -0
- package/dist/convex-hull/thermodynamics.d.ts +67 -0
- package/dist/convex-hull/thermodynamics.js +1752 -0
- package/dist/convex-hull/types.d.ts +162 -0
- package/dist/convex-hull/types.js +36 -0
- package/dist/coordination/CoordinationBarPlot.svelte +311 -0
- package/dist/coordination/CoordinationBarPlot.svelte.d.ts +30 -0
- package/dist/coordination/calc-coordination.d.ts +15 -0
- package/dist/coordination/calc-coordination.js +63 -0
- package/dist/coordination/index.d.ts +8 -0
- package/dist/coordination/index.js +7 -0
- package/dist/effects.svelte.d.ts +12 -0
- package/dist/effects.svelte.js +37 -0
- package/dist/element/BohrAtom.svelte.d.ts +20 -0
- package/dist/element/ElementHeading.svelte +26 -0
- package/dist/element/ElementHeading.svelte.d.ts +8 -0
- package/dist/element/ElementPhoto.svelte +57 -0
- package/dist/element/ElementPhoto.svelte.d.ts +9 -0
- package/dist/element/ElementStats.svelte +80 -0
- package/dist/element/ElementStats.svelte.d.ts +8 -0
- package/dist/element/ElementTile.svelte +484 -0
- package/dist/element/ElementTile.svelte.d.ts +29 -0
- package/dist/element/Nucleus.svelte.d.ts +17 -0
- package/dist/element/data.d.ts +2 -0
- package/dist/element/data.js +2 -0
- package/dist/element/index.d.ts +8 -0
- package/dist/element/index.js +7 -0
- package/dist/element/types.d.ts +57 -0
- package/dist/element/types.js +1 -0
- package/dist/feedback/ClickFeedback.svelte +58 -0
- package/dist/feedback/ClickFeedback.svelte.d.ts +12 -0
- package/dist/feedback/DragOverlay.svelte +42 -0
- package/dist/feedback/DragOverlay.svelte.d.ts +7 -0
- package/dist/feedback/Spinner.svelte.d.ts +7 -0
- package/dist/feedback/StatusMessage.svelte.d.ts +9 -0
- package/dist/feedback/index.d.ts +4 -0
- package/dist/feedback/index.js +4 -0
- package/dist/fermi-surface/FermiSlice.svelte +189 -0
- package/dist/fermi-surface/FermiSlice.svelte.d.ts +24 -0
- package/dist/fermi-surface/FermiSurface.svelte +600 -0
- package/dist/fermi-surface/FermiSurface.svelte.d.ts +83 -0
- package/dist/fermi-surface/FermiSurfaceControls.svelte +448 -0
- package/dist/fermi-surface/FermiSurfaceControls.svelte.d.ts +35 -0
- package/dist/fermi-surface/FermiSurfaceScene.svelte +794 -0
- package/dist/fermi-surface/FermiSurfaceScene.svelte.d.ts +50 -0
- package/dist/fermi-surface/FermiSurfaceTooltip.svelte +111 -0
- package/dist/fermi-surface/FermiSurfaceTooltip.svelte.d.ts +8 -0
- package/dist/fermi-surface/compute.d.ts +5 -0
- package/dist/fermi-surface/compute.js +538 -0
- package/dist/fermi-surface/constants.d.ts +9 -0
- package/dist/fermi-surface/constants.js +27 -0
- package/dist/fermi-surface/export.d.ts +5 -0
- package/dist/fermi-surface/export.js +50 -0
- package/dist/fermi-surface/index.d.ts +12 -0
- package/dist/fermi-surface/index.js +13 -0
- package/dist/fermi-surface/marching-cubes.d.ts +2 -0
- package/dist/fermi-surface/marching-cubes.js +2 -0
- package/dist/fermi-surface/parse.d.ts +2 -0
- package/dist/fermi-surface/parse.js +491 -0
- package/dist/fermi-surface/symmetry.d.ts +3 -0
- package/dist/fermi-surface/symmetry.js +46 -0
- package/dist/fermi-surface/types.d.ts +110 -0
- package/dist/fermi-surface/types.js +4 -0
- package/dist/heatmap-matrix/HeatmapMatrix.svelte +1545 -0
- package/dist/heatmap-matrix/HeatmapMatrix.svelte.d.ts +110 -0
- package/dist/heatmap-matrix/HeatmapMatrixControls.svelte +225 -0
- package/dist/heatmap-matrix/HeatmapMatrixControls.svelte.d.ts +30 -0
- package/dist/heatmap-matrix/index.d.ts +53 -0
- package/dist/heatmap-matrix/index.js +100 -0
- package/dist/heatmap-matrix/shared.d.ts +2 -0
- package/dist/heatmap-matrix/shared.js +4 -0
- package/dist/icons.d.ts +569 -0
- package/dist/icons.js +648 -0
- package/dist/index.d.ts +39 -0
- package/dist/index.js +39 -0
- package/dist/io/decompress.d.ts +11 -0
- package/dist/io/decompress.js +74 -0
- package/dist/io/export.d.ts +16 -0
- package/dist/io/export.js +316 -0
- package/dist/io/fetch.d.ts +5 -0
- package/dist/io/fetch.js +39 -0
- package/dist/io/file-drop.d.ts +7 -0
- package/dist/io/file-drop.js +43 -0
- package/dist/io/index.d.ts +7 -0
- package/dist/io/index.js +6 -0
- package/dist/io/is-binary.d.ts +1 -0
- package/dist/io/is-binary.js +20 -0
- package/dist/io/types.d.ts +8 -0
- package/dist/io/types.js +1 -0
- package/dist/io/url-drop.d.ts +2 -0
- package/dist/io/url-drop.js +123 -0
- package/dist/isosurface/Isosurface.svelte +285 -0
- package/dist/isosurface/Isosurface.svelte.d.ts +8 -0
- package/dist/isosurface/IsosurfaceControls.svelte +277 -0
- package/dist/isosurface/IsosurfaceControls.svelte.d.ts +9 -0
- package/dist/isosurface/index.d.ts +5 -0
- package/dist/isosurface/index.js +6 -0
- package/dist/isosurface/parse.d.ts +6 -0
- package/dist/isosurface/parse.js +553 -0
- package/dist/isosurface/slice.d.ts +11 -0
- package/dist/isosurface/slice.js +140 -0
- package/dist/isosurface/types.d.ts +56 -0
- package/dist/isosurface/types.js +227 -0
- package/dist/labels.d.ts +53 -0
- package/dist/labels.js +277 -0
- package/dist/layout/FullscreenToggle.svelte +50 -0
- package/dist/layout/FullscreenToggle.svelte.d.ts +7 -0
- package/dist/layout/InfoCard.svelte +120 -0
- package/dist/layout/InfoCard.svelte.d.ts +21 -0
- package/dist/layout/InfoTag.svelte +185 -0
- package/dist/layout/InfoTag.svelte.d.ts +19 -0
- package/dist/layout/PropertyFilter.svelte +246 -0
- package/dist/layout/PropertyFilter.svelte.d.ts +24 -0
- package/dist/layout/SettingsSection.svelte +148 -0
- package/dist/layout/SettingsSection.svelte.d.ts +17 -0
- package/dist/layout/SubpageGrid.svelte +82 -0
- package/dist/layout/SubpageGrid.svelte.d.ts +14 -0
- package/dist/layout/fullscreen.d.ts +9 -0
- package/dist/layout/fullscreen.js +53 -0
- package/dist/layout/index.d.ts +10 -0
- package/dist/layout/index.js +8 -0
- package/dist/layout/json-tree/JsonNode.svelte +548 -0
- package/dist/layout/json-tree/JsonNode.svelte.d.ts +11 -0
- package/dist/layout/json-tree/JsonTree.svelte +1230 -0
- package/dist/layout/json-tree/JsonTree.svelte.d.ts +6 -0
- package/dist/layout/json-tree/JsonValue.svelte.d.ts +9 -0
- package/dist/layout/json-tree/index.d.ts +3 -0
- package/dist/layout/json-tree/index.js +3 -0
- package/dist/layout/json-tree/types.d.ts +74 -0
- package/dist/layout/json-tree/types.js +2 -0
- package/dist/layout/json-tree/utils.d.ts +29 -0
- package/dist/layout/json-tree/utils.js +641 -0
- package/dist/marching-cubes.d.ts +14 -0
- package/dist/marching-cubes.js +540 -0
- package/dist/math.d.ts +101 -0
- package/dist/math.js +905 -0
- package/dist/overlays/ContextMenu.svelte +162 -0
- package/dist/overlays/ContextMenu.svelte.d.ts +25 -0
- package/dist/overlays/CopyButton.svelte +45 -0
- package/dist/overlays/CopyButton.svelte.d.ts +8 -0
- package/dist/overlays/DragControlTab.svelte +98 -0
- package/dist/overlays/DragControlTab.svelte.d.ts +8 -0
- package/dist/overlays/DraggablePane.svelte +487 -0
- package/dist/overlays/DraggablePane.svelte.d.ts +36 -0
- package/dist/overlays/InfoPaneCards.svelte +149 -0
- package/dist/overlays/InfoPaneCards.svelte.d.ts +22 -0
- package/dist/overlays/index.d.ts +3 -0
- package/dist/overlays/index.js +3 -0
- package/dist/periodic-table/PeriodicTable.svelte +469 -0
- package/dist/periodic-table/PeriodicTable.svelte.d.ts +55 -0
- package/dist/periodic-table/PeriodicTableControls.svelte +557 -0
- package/dist/periodic-table/PeriodicTableControls.svelte.d.ts +24 -0
- package/dist/periodic-table/PropertySelect.svelte +37 -0
- package/dist/periodic-table/PropertySelect.svelte.d.ts +13 -0
- package/dist/periodic-table/TableInset.svelte.d.ts +9 -0
- package/dist/periodic-table/index.d.ts +10 -0
- package/dist/periodic-table/index.js +4 -0
- package/dist/phase-diagram/IsobaricBinaryPhaseDiagram.svelte +1086 -0
- package/dist/phase-diagram/IsobaricBinaryPhaseDiagram.svelte.d.ts +44 -0
- package/dist/phase-diagram/PhaseDiagramControls.svelte +444 -0
- package/dist/phase-diagram/PhaseDiagramControls.svelte.d.ts +30 -0
- package/dist/phase-diagram/PhaseDiagramEditorPane.svelte +126 -0
- package/dist/phase-diagram/PhaseDiagramEditorPane.svelte.d.ts +15 -0
- package/dist/phase-diagram/PhaseDiagramExportPane.svelte +184 -0
- package/dist/phase-diagram/PhaseDiagramExportPane.svelte.d.ts +19 -0
- package/dist/phase-diagram/PhaseDiagramTooltip.svelte +391 -0
- package/dist/phase-diagram/PhaseDiagramTooltip.svelte.d.ts +16 -0
- package/dist/phase-diagram/TdbInfoPanel.svelte +203 -0
- package/dist/phase-diagram/TdbInfoPanel.svelte.d.ts +12 -0
- package/dist/phase-diagram/build-diagram.d.ts +11 -0
- package/dist/phase-diagram/build-diagram.js +160 -0
- package/dist/phase-diagram/colors.d.ts +35 -0
- package/dist/phase-diagram/colors.js +51 -0
- package/dist/phase-diagram/diagram-input.d.ts +29 -0
- package/dist/phase-diagram/diagram-input.js +3 -0
- package/dist/phase-diagram/index.d.ts +13 -0
- package/dist/phase-diagram/index.js +11 -0
- package/dist/phase-diagram/parse.d.ts +55 -0
- package/dist/phase-diagram/parse.js +272 -0
- package/dist/phase-diagram/svg-to-diagram.d.ts +2 -0
- package/dist/phase-diagram/svg-to-diagram.js +867 -0
- package/dist/phase-diagram/types.d.ts +93 -0
- package/dist/phase-diagram/types.js +1 -0
- package/dist/phase-diagram/utils.d.ts +118 -0
- package/dist/phase-diagram/utils.js +604 -0
- package/dist/plot/AxisLabel.svelte +51 -0
- package/dist/plot/AxisLabel.svelte.d.ts +16 -0
- package/dist/plot/BarPlot.svelte +2113 -0
- package/dist/plot/BarPlot.svelte.d.ts +84 -0
- package/dist/plot/BarPlotControls.svelte +66 -0
- package/dist/plot/BarPlotControls.svelte.d.ts +18 -0
- package/dist/plot/BinnedScatterPlot.svelte +1114 -0
- package/dist/plot/BinnedScatterPlot.svelte.d.ts +66 -0
- package/dist/plot/ColorBar.svelte +721 -0
- package/dist/plot/ColorBar.svelte.d.ts +31 -0
- package/dist/plot/ColorScaleSelect.svelte +54 -0
- package/dist/plot/ColorScaleSelect.svelte.d.ts +15 -0
- package/dist/plot/ElementScatter.svelte +63 -0
- package/dist/plot/ElementScatter.svelte.d.ts +14 -0
- package/dist/plot/FillArea.svelte.d.ts +21 -0
- package/dist/plot/Histogram.svelte +1558 -0
- package/dist/plot/Histogram.svelte.d.ts +50 -0
- package/dist/plot/HistogramControls.svelte +212 -0
- package/dist/plot/HistogramControls.svelte.d.ts +22 -0
- package/dist/plot/InteractiveAxisLabel.svelte +96 -0
- package/dist/plot/InteractiveAxisLabel.svelte.d.ts +14 -0
- package/dist/plot/Line.svelte +84 -0
- package/dist/plot/Line.svelte.d.ts +15 -0
- package/dist/plot/PlotAxis.svelte +169 -0
- package/dist/plot/PlotAxis.svelte.d.ts +24 -0
- package/dist/plot/PlotControls.svelte +537 -0
- package/dist/plot/PlotControls.svelte.d.ts +4 -0
- package/dist/plot/PlotLegend.svelte +569 -0
- package/dist/plot/PlotLegend.svelte.d.ts +29 -0
- package/dist/plot/PlotTooltip.svelte +67 -0
- package/dist/plot/PlotTooltip.svelte.d.ts +17 -0
- package/dist/plot/PortalSelect.svelte +253 -0
- package/dist/plot/PortalSelect.svelte.d.ts +16 -0
- package/dist/plot/ReferenceLine.svelte.d.ts +20 -0
- package/dist/plot/ReferenceLine3D.svelte +156 -0
- package/dist/plot/ReferenceLine3D.svelte.d.ts +14 -0
- package/dist/plot/ReferencePlane.svelte +175 -0
- package/dist/plot/ReferencePlane.svelte.d.ts +14 -0
- package/dist/plot/ScatterPlot.svelte +2778 -0
- package/dist/plot/ScatterPlot.svelte.d.ts +96 -0
- package/dist/plot/ScatterPlot3D.svelte +529 -0
- package/dist/plot/ScatterPlot3D.svelte.d.ts +95 -0
- package/dist/plot/ScatterPlot3DControls.svelte +437 -0
- package/dist/plot/ScatterPlot3DControls.svelte.d.ts +20 -0
- package/dist/plot/ScatterPlot3DScene.svelte +912 -0
- package/dist/plot/ScatterPlot3DScene.svelte.d.ts +74 -0
- package/dist/plot/ScatterPlotControls.svelte +306 -0
- package/dist/plot/ScatterPlotControls.svelte.d.ts +17 -0
- package/dist/plot/ScatterPoint.svelte +182 -0
- package/dist/plot/ScatterPoint.svelte.d.ts +22 -0
- package/dist/plot/SpacegroupBarPlot.svelte +293 -0
- package/dist/plot/SpacegroupBarPlot.svelte.d.ts +9 -0
- package/dist/plot/Surface3D.svelte +197 -0
- package/dist/plot/Surface3D.svelte.d.ts +13 -0
- package/dist/plot/ZeroLines.svelte +97 -0
- package/dist/plot/ZeroLines.svelte.d.ts +33 -0
- package/dist/plot/ZoomRect.svelte +23 -0
- package/dist/plot/ZoomRect.svelte.d.ts +8 -0
- package/dist/plot/adaptive-density.d.ts +69 -0
- package/dist/plot/adaptive-density.js +191 -0
- package/dist/plot/auto-place.d.ts +43 -0
- package/dist/plot/auto-place.js +122 -0
- package/dist/plot/axis-utils.d.ts +19 -0
- package/dist/plot/axis-utils.js +78 -0
- package/dist/plot/binned-scatter-types.d.ts +59 -0
- package/dist/plot/binned-scatter-types.js +1 -0
- package/dist/plot/data-cleaning.d.ts +37 -0
- package/dist/plot/data-cleaning.js +855 -0
- package/dist/plot/data-transform.d.ts +16 -0
- package/dist/plot/data-transform.js +45 -0
- package/dist/plot/defaults.d.ts +19 -0
- package/dist/plot/defaults.js +9 -0
- package/dist/plot/fill-utils.d.ts +46 -0
- package/dist/plot/fill-utils.js +322 -0
- package/dist/plot/hover-lock.svelte.d.ts +14 -0
- package/dist/plot/hover-lock.svelte.js +46 -0
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- package/dist/src/lib/rdf/RdfPlot.svelte +0 -247
- package/dist/src/lib/rdf/calc-rdf.ts +0 -167
- package/dist/src/lib/rdf/index.ts +0 -27
- package/dist/src/lib/sanitize.ts +0 -126
- package/dist/src/lib/settings.ts +0 -1479
- package/dist/src/lib/spectral/Bands.svelte +0 -1040
- package/dist/src/lib/spectral/BandsAndDos.svelte +0 -134
- package/dist/src/lib/spectral/BrillouinBandsDos.svelte +0 -252
- package/dist/src/lib/spectral/Dos.svelte +0 -697
- package/dist/src/lib/spectral/helpers.ts +0 -1381
- package/dist/src/lib/spectral/index.ts +0 -8
- package/dist/src/lib/spectral/types.ts +0 -112
- package/dist/src/lib/state.svelte.ts +0 -64
- package/dist/src/lib/structure/Arrow.svelte +0 -72
- package/dist/src/lib/structure/AtomLegend.svelte +0 -815
- package/dist/src/lib/structure/Bond.svelte +0 -140
- package/dist/src/lib/structure/CanvasTooltip.svelte +0 -33
- package/dist/src/lib/structure/CellSelect.svelte +0 -349
- package/dist/src/lib/structure/Cylinder.svelte +0 -45
- package/dist/src/lib/structure/Lattice.svelte +0 -196
- package/dist/src/lib/structure/Structure.svelte +0 -2248
- package/dist/src/lib/structure/StructureControls.svelte +0 -1273
- package/dist/src/lib/structure/StructureExportPane.svelte +0 -252
- package/dist/src/lib/structure/StructureInfoPane.svelte +0 -737
- package/dist/src/lib/structure/StructureScene.svelte +0 -2255
- package/dist/src/lib/structure/atom-properties.ts +0 -316
- package/dist/src/lib/structure/bond-order-perception.ts +0 -447
- package/dist/src/lib/structure/bonding.ts +0 -944
- package/dist/src/lib/structure/export.ts +0 -861
- package/dist/src/lib/structure/index.ts +0 -291
- package/dist/src/lib/structure/label-placement.ts +0 -130
- package/dist/src/lib/structure/measure.ts +0 -45
- package/dist/src/lib/structure/parse.ts +0 -1705
- package/dist/src/lib/structure/partial-occupancy.ts +0 -183
- package/dist/src/lib/structure/pbc.ts +0 -164
- package/dist/src/lib/structure/supercell.ts +0 -226
- package/dist/src/lib/structure/validation.ts +0 -11
- package/dist/src/lib/symmetry/SymmetryStats.svelte +0 -226
- package/dist/src/lib/symmetry/WyckoffTable.svelte +0 -120
- package/dist/src/lib/symmetry/cell-transform.ts +0 -118
- package/dist/src/lib/symmetry/index.ts +0 -348
- package/dist/src/lib/symmetry/spacegroups.ts +0 -404
- package/dist/src/lib/table/HeatmapTable.svelte +0 -1833
- package/dist/src/lib/table/ToggleMenu.svelte +0 -385
- package/dist/src/lib/table/index.ts +0 -139
- package/dist/src/lib/theme/ThemeControl.svelte +0 -53
- package/dist/src/lib/theme/index.ts +0 -107
- package/dist/src/lib/time.ts +0 -71
- package/dist/src/lib/tooltip/TooltipContent.svelte +0 -58
- package/dist/src/lib/tooltip/index.ts +0 -2
- package/dist/src/lib/tooltip/types.ts +0 -13
- package/dist/src/lib/trajectory/Trajectory.svelte +0 -1545
- package/dist/src/lib/trajectory/TrajectoryError.svelte +0 -128
- package/dist/src/lib/trajectory/TrajectoryExportPane.svelte +0 -357
- package/dist/src/lib/trajectory/TrajectoryInfoPane.svelte +0 -313
- package/dist/src/lib/trajectory/constants.ts +0 -7
- package/dist/src/lib/trajectory/extract.ts +0 -196
- package/dist/src/lib/trajectory/format-detect.ts +0 -96
- package/dist/src/lib/trajectory/frame-reader.ts +0 -456
- package/dist/src/lib/trajectory/helpers.ts +0 -217
- package/dist/src/lib/trajectory/index.ts +0 -218
- package/dist/src/lib/trajectory/parse/ase.ts +0 -109
- package/dist/src/lib/trajectory/parse/hdf5.ts +0 -173
- package/dist/src/lib/trajectory/parse/index.ts +0 -411
- package/dist/src/lib/trajectory/parse/lammps.ts +0 -215
- package/dist/src/lib/trajectory/parse/vasp.ts +0 -102
- package/dist/src/lib/trajectory/parse/xyz.ts +0 -143
- package/dist/src/lib/trajectory/plotting.ts +0 -599
- package/dist/src/lib/trajectory/types.ts +0 -13
- package/dist/src/lib/utils.ts +0 -56
- package/dist/src/lib/xrd/XrdPlot.svelte +0 -615
- package/dist/src/lib/xrd/broadening.ts +0 -130
- package/dist/src/lib/xrd/calc-xrd.ts +0 -397
- package/dist/src/lib/xrd/index.ts +0 -38
- package/dist/src/lib/xrd/parse.ts +0 -858
- package/dist/webview.js +0 -29421
- package/icon.png +0 -0
- 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/scripts/sync-config.ts +0 -101
- package/src/declarations.d.ts +0 -2
- package/src/extension.ts +0 -972
- package/src/node-io.ts +0 -65
- package/src/types.ts +0 -17
- package/src/webview/JsonBrowser.svelte +0 -1079
- package/src/webview/PlotPanel.svelte +0 -346
- package/src/webview/detect.ts +0 -444
- package/src/webview/main.ts +0 -764
- package/src/webview/plot-utils.ts +0 -250
- 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 +0 -604
- package/tests/extension.test.ts +0 -2041
- package/tests/node-io.test.ts +0 -39
- package/tests/plot-utils.test.ts +0 -302
- package/tests/vite-plugin-json-gz.test.ts +0 -114
- package/tests/vscode-mock.ts +0 -18
- package/tests/webview.test.ts +0 -231
- package/tsconfig.json +0 -20
- package/vite-plugin-json-gz.ts +0 -29
- package/vite.config.ts +0 -34
- package/vite.extension.config.ts +0 -34
- /package/dist/{src/lib/EmptyState.svelte → EmptyState.svelte} +0 -0
- /package/dist/{src/lib/Icon.svelte → Icon.svelte} +0 -0
- /package/dist/{src/lib/app.css → app.css} +0 -0
- /package/dist/{src/lib/chempot-diagram → chempot-diagram}/ChemPotScene3D.svelte +0 -0
- /package/dist/{src/lib/colors → colors}/alloy-colors.json +0 -0
- /package/dist/{src/lib/colors → colors}/dark-mode-colors.json +0 -0
- /package/dist/{src/lib/colors → colors}/jmol-colors.json +0 -0
- /package/dist/{src/lib/colors → colors}/muted-colors.json +0 -0
- /package/dist/{src/lib/colors → colors}/pastel-colors.json +0 -0
- /package/dist/{src/lib/colors → colors}/vesta-colors.json +0 -0
- /package/dist/{src/lib/convex-hull → convex-hull}/TemperatureSlider.svelte +0 -0
- /package/dist/{src/lib/element → element}/BohrAtom.svelte +0 -0
- /package/dist/{src/lib/element → element}/Nucleus.svelte +0 -0
- /package/dist/{src/lib/element → element}/data.json +0 -0
- /package/dist/{src/lib/element → element}/data.json.gz +0 -0
- /package/dist/{src/lib/element → element}/data.json.gz.d.ts +0 -0
- /package/dist/{src/lib/element → element}/data.schema.json +0 -0
- /package/dist/{src/lib/element-image-urls.json → element-image-urls.json} +0 -0
- /package/dist/{src/lib/feedback → feedback}/Spinner.svelte +0 -0
- /package/dist/{src/lib/feedback → feedback}/StatusMessage.svelte +0 -0
- /package/dist/{src/lib/layout → layout}/json-tree/JsonValue.svelte +0 -0
- /package/dist/{src/lib/periodic-table → periodic-table}/TableInset.svelte +0 -0
- /package/dist/{src/lib/plot → plot}/FillArea.svelte +0 -0
- /package/dist/{src/lib/plot → plot}/ReferenceLine.svelte +0 -0
- /package/dist/{src/lib/theme → theme}/themes.mjs +0 -0
- /package/dist/{src/lib/xrd → xrd}/atomic_scattering_params.json +0 -0
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import type { CompositionType } from '../composition';
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import type { ShowControlsProp } from '../controls';
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import type { ElementSymbol } from '../element';
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import type { Point2D, Point3D, Vec3 } from '../math';
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import type { Rect, Sides } from '../plot/layout';
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import type { AnyStructure } from '../structure';
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export interface StructurePopupStats {
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id?: string;
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formula?: string;
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e_form?: number;
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}
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export interface StructurePopupContext {
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structure: AnyStructure;
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stats?: StructurePopupStats;
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formula_html: string;
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}
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export interface PhaseData {
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composition: CompositionType;
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energy: number;
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entry_id?: string;
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e_above_hull?: number;
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is_stable?: boolean;
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exclude_from_hull?: boolean;
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energy_per_atom?: number;
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reduced_formula?: string;
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name?: string;
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temperatures?: number[];
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free_energies?: number[];
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'@module'?: string;
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'@class'?: string;
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correction?: number;
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energy_adjustments?: Record<string, number>[];
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parameters?: Record<string, unknown>;
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data?: Record<string, unknown>;
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structure?: Record<string, unknown>;
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attributes?: Record<string, unknown>;
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}
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export interface ProcessedPhaseData {
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entries: PhaseData[];
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stable_entries: PhaseData[];
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unstable_entries: PhaseData[];
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elements: ElementSymbol[];
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el_refs: Record<string, PhaseData>;
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}
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export type MarkerSymbol = // Marker symbol types for convex hull entries
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`circle` | `star` | `triangle` | `cross` | `diamond` | `square` | `wye`;
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export type HullFaceColorMode = `uniform` | `formation_energy` | `dominant_element` | `facet_index`;
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export declare const HULL_FACE_COLOR_MODES: readonly HullFaceColorMode[];
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export interface ConvexHullEntry extends PhaseData, Point3D {
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is_element: boolean;
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size?: number;
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marker?: MarkerSymbol;
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}
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export interface ConvexHullConfig {
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width?: number;
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height?: number;
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margin?: Sides;
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unstable_threshold?: number;
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show_labels?: boolean;
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show_hull?: boolean;
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point_size?: number;
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line_width?: number;
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font_size?: number;
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colors?: {
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stable?: string;
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unstable?: string;
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hull_line?: string;
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background?: string;
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text?: string;
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edge?: string;
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tooltip_bg?: string;
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tooltip_text?: string;
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annotation?: string;
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};
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}
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export interface ConvexHullControlsType {
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title?: string;
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show?: ShowControlsProp;
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position?: `top-left` | `top-right` | `bottom-left` | `bottom-right`;
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width?: number;
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show_counts?: boolean;
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show_color_toggle?: boolean;
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show_label_controls?: boolean;
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}
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export interface Plane {
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normal: Point3D;
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offset: number;
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}
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export interface ConvexHullFace {
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vertices: Vec3;
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plane: Plane;
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centroid: Point3D;
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outside_points: Set<number>;
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}
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export interface ConvexHullTriangle {
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vertices: [Point3D, Point3D, Point3D];
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normal: Point3D;
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centroid: Point3D;
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}
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export interface LabelPlacement {
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x: number;
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y: number;
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rect: Rect;
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}
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export interface HoverData3D<T = ConvexHullEntry> {
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entry: T;
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position: Point2D;
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}
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export interface PhaseStats {
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total: number;
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unary: number;
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binary: number;
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ternary: number;
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quaternary: number;
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quinary_plus: number;
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stable: number;
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unstable: number;
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energy_range: {
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avg: number;
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hull_distance: {
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avg: number;
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};
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elements: number;
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chemical_system: string;
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max_arity: number;
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}
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export type PhaseArityField = Extract<keyof PhaseStats, `unary` | `binary` | `ternary` | `quaternary` | `quinary_plus`>;
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export interface HighlightStyle {
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effect?: `pulse` | `glow` | `size` | `color` | `both`;
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color?: string;
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size_multiplier?: number;
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opacity?: number;
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pulse_speed?: number;
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}
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export declare const DEFAULT_GAS_TEMP = 300;
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export type GasSpecies = `O2` | `N2` | `H2` | `CO` | `CO2` | `H2O` | `F2`;
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export declare const GAS_SPECIES: readonly GasSpecies[];
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export declare const DEFAULT_GAS_PRESSURES: Readonly<Record<GasSpecies, number>>;
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export interface GasThermodynamicsProvider {
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get_standard_chemical_potential(gas: GasSpecies, T: number): number;
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get_supported_gases(): GasSpecies[];
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get_temperature_range(): [number, number];
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}
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export interface GasThermodynamicsConfig {
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enabled_gases?: GasSpecies[];
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pressures?: Partial<Record<GasSpecies, number>>;
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provider?: GasThermodynamicsProvider;
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element_to_gas?: Partial<Record<ElementSymbol, GasSpecies>>;
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}
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export interface GasAnalysis {
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has_gas_dependent_elements: boolean;
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gas_elements: ElementSymbol[];
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relevant_gases: GasSpecies[];
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}
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export declare const GAS_CONTROL_POSITIONS: readonly ["top-left", "top-right", "bottom-left", "bottom-right"];
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export type GasControlPosition = (typeof GAS_CONTROL_POSITIONS)[number];
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export const HULL_FACE_COLOR_MODES = [
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`uniform`,
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`formation_energy`,
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`dominant_element`,
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`facet_index`,
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];
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// --- Gas Phase Thermodynamics ---
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// Default temperature (Kelvin) for gas corrections when no temperature is specified
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export const DEFAULT_GAS_TEMP = 300;
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// All supported gas species as an array (for iteration)
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export const GAS_SPECIES = [
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`O2`,
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`N2`,
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`H2`,
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`CO`,
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`CO2`,
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`H2O`,
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`F2`,
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];
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// Default atmospheric partial pressures (in bar)
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export const DEFAULT_GAS_PRESSURES = {
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O2: 0.2095, // ~21% in atmosphere
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N2: 0.7809, // ~78% in atmosphere
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H2: 0.1, // typical experimental
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CO: 1e-6, // trace
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CO2: 3.95e-4, // ~400 ppm in atmosphere
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H2O: 0.03, // ~3% humidity
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F2: 0.1, // typical experimental
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};
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// Position options for UI control panels (e.g., GasPressureControls)
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export const GAS_CONTROL_POSITIONS = [
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`top-left`,
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`top-right`,
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`bottom-left`,
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`bottom-right`,
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];
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<script lang="ts">
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import { PLOT_COLORS } from '../colors'
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import { StatusMessage } from '../feedback'
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import { create_file_drop_handler } from '../io'
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import { format_value } from '../labels'
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import { BarPlot } from '../plot'
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import type {
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AxisConfig,
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BarHandlerProps,
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BarSeries,
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11
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+
Orientation,
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12
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+
} from '../plot/types'
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13
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+
import type { AnyStructure } from '../structure'
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14
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+
import type { BondingStrategy } from '../structure/bonding'
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15
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+
import { parse_any_structure } from '../structure/parse'
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16
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+
import { is_crystal } from '../structure/validation'
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+
import type { ComponentProps } from 'svelte'
|
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18
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+
import { SvelteMap, SvelteSet } from 'svelte/reactivity'
|
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19
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+
import { calc_coordination_nums, type CoordinationData } from './calc-coordination'
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20
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+
import type { SplitMode } from './index'
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21
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+
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+
type CoordinationMetadata = {
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23
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+
element?: string
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24
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+
structure_label?: string
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25
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+
} & Record<string, unknown>
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26
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+
|
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27
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+
interface StructureEntry {
|
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+
label: string
|
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+
structure: AnyStructure
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30
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+
color?: string
|
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31
|
+
data?: CoordinationData
|
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32
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+
}
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33
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+
let {
|
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34
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+
structures,
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35
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+
strategy = `electroneg_ratio`,
|
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36
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+
split_mode = `by_element`,
|
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37
|
+
mode = $bindable(`grouped`),
|
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38
|
+
orientation = `vertical` as Orientation,
|
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39
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+
x_axis = {},
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40
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+
y_axis = {},
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41
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+
allow_file_drop = true,
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+
on_file_drop,
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43
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+
loading = $bindable(false),
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44
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+
error_msg = $bindable(),
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45
|
+
...rest
|
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+
}: Omit<ComponentProps<typeof BarPlot>, `series`> & {
|
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+
structures:
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48
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+
| AnyStructure
|
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49
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+
| Record<string, AnyStructure | { structure: AnyStructure; color?: string }>
|
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50
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+
| StructureEntry[]
|
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+
strategy?: BondingStrategy
|
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+
split_mode?: SplitMode
|
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|
+
x_axis?: AxisConfig
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|
+
y_axis?: AxisConfig
|
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|
+
allow_file_drop?: boolean
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|
+
on_file_drop?: (content: string | ArrayBuffer, filename: string) => void
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+
loading?: boolean
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+
error_msg?: string
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+
} = $props()
|
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60
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+
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+
let dragover = $state(false)
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+
let dropped_entries = $state<StructureEntry[]>([])
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+
let is_horizontal = $derived(orientation === `horizontal`)
|
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64
|
+
|
|
65
|
+
// Normalize input to consistent array of { label, structure, color }
|
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|
+
const structure_entries = $derived.by<StructureEntry[]>(() => {
|
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|
+
if (!structures) return []
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68
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+
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+
const base_entries = Array.isArray(structures)
|
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70
|
+
? (structures as StructureEntry[])
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: (is_crystal(structures)
|
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|
+
? [{ label: `Structure`, structure: structures as AnyStructure }]
|
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|
+
: Object.entries(
|
|
74
|
+
structures as Record<
|
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75
|
+
string,
|
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76
|
+
AnyStructure | { structure: AnyStructure; color?: string }
|
|
77
|
+
>,
|
|
78
|
+
).map(([label, value]) =>
|
|
79
|
+
`structure` in value
|
|
80
|
+
? { label, ...value }
|
|
81
|
+
: { label, structure: value as AnyStructure }
|
|
82
|
+
))
|
|
83
|
+
|
|
84
|
+
// Merge user-provided structures with dropped structures
|
|
85
|
+
return [...base_entries, ...dropped_entries]
|
|
86
|
+
})
|
|
87
|
+
|
|
88
|
+
// Compute coordination data for each structure
|
|
89
|
+
const entries_with_data = $derived(structure_entries.map((entry) => ({
|
|
90
|
+
...entry,
|
|
91
|
+
data: calc_coordination_nums(entry.structure, strategy),
|
|
92
|
+
})))
|
|
93
|
+
|
|
94
|
+
// Compute appropriate ranges
|
|
95
|
+
const ranges = $derived.by(() => {
|
|
96
|
+
// CN axis should always start at 0 and show at least [0,4]
|
|
97
|
+
let max_cn = 4 // minimum max value
|
|
98
|
+
for (const entry of entries_with_data) {
|
|
99
|
+
for (const [cn] of entry.data.cn_histogram) max_cn = Math.max(max_cn, cn)
|
|
100
|
+
}
|
|
101
|
+
const cn_range: [number, number] = [-0.5, max_cn + 0.5]
|
|
102
|
+
|
|
103
|
+
return { count: [0, null] as [number, null], cn: cn_range } // Count axis should always start at 0
|
|
104
|
+
})
|
|
105
|
+
|
|
106
|
+
// Derive integer CN ticks for axis labels
|
|
107
|
+
const cn_ticks = $derived.by(() => {
|
|
108
|
+
const all_cns = new SvelteSet<number>()
|
|
109
|
+
// Always include minimum CN values 0-4
|
|
110
|
+
for (let idx = 0; idx <= 4; idx++) all_cns.add(idx)
|
|
111
|
+
// Add actual CN values from data
|
|
112
|
+
for (const entry of entries_with_data) {
|
|
113
|
+
for (const [cn] of entry.data.cn_histogram) all_cns.add(cn)
|
|
114
|
+
}
|
|
115
|
+
return Array.from(all_cns).sort((cn1, cn2) => cn1 - cn2)
|
|
116
|
+
})
|
|
117
|
+
|
|
118
|
+
// Build BarPlot series based on split_mode
|
|
119
|
+
const bar_series = $derived.by<BarSeries<CoordinationMetadata>[]>(() => {
|
|
120
|
+
if (split_mode === `by_element`) {
|
|
121
|
+
// One series per element across all structures
|
|
122
|
+
const element_series_map = new SvelteMap<string, Map<number, number>>()
|
|
123
|
+
|
|
124
|
+
// Collect all unique CNs across all elements
|
|
125
|
+
const all_cns = new SvelteSet<number>()
|
|
126
|
+
|
|
127
|
+
for (const entry of entries_with_data) {
|
|
128
|
+
for (const [element, cn_histogram] of entry.data.cn_histogram_by_element) {
|
|
129
|
+
if (!element_series_map.has(element)) {
|
|
130
|
+
element_series_map.set(element, new SvelteMap())
|
|
131
|
+
}
|
|
132
|
+
const element_map = element_series_map.get(element)
|
|
133
|
+
if (!element_map) continue
|
|
134
|
+
|
|
135
|
+
for (const [cn, count] of cn_histogram) {
|
|
136
|
+
all_cns.add(cn)
|
|
137
|
+
element_map.set(cn, (element_map.get(cn) ?? 0) + count)
|
|
138
|
+
}
|
|
139
|
+
}
|
|
140
|
+
}
|
|
141
|
+
|
|
142
|
+
// Sort CNs for consistent x-axis
|
|
143
|
+
const sorted_cns = Array.from(all_cns).sort((a, b) => a - b)
|
|
144
|
+
|
|
145
|
+
// Convert map to array and ensure all series have same x-values
|
|
146
|
+
return Array.from(element_series_map.entries())
|
|
147
|
+
.sort((a, b) => a[0].localeCompare(b[0]))
|
|
148
|
+
.map(([element, cn_map], idx) => {
|
|
149
|
+
return {
|
|
150
|
+
x: sorted_cns,
|
|
151
|
+
y: sorted_cns.map((cn) => cn_map.get(cn) ?? 0),
|
|
152
|
+
label: element,
|
|
153
|
+
color: PLOT_COLORS[idx % PLOT_COLORS.length],
|
|
154
|
+
bar_width: 0.8,
|
|
155
|
+
visible: true,
|
|
156
|
+
metadata: { element },
|
|
157
|
+
}
|
|
158
|
+
})
|
|
159
|
+
} else if (split_mode === `by_structure`) {
|
|
160
|
+
// One series per structure
|
|
161
|
+
// First collect all unique CNs
|
|
162
|
+
const all_cns = new SvelteSet<number>()
|
|
163
|
+
for (const entry of entries_with_data) {
|
|
164
|
+
for (const [cn] of entry.data.cn_histogram) {
|
|
165
|
+
all_cns.add(cn)
|
|
166
|
+
}
|
|
167
|
+
}
|
|
168
|
+
const sorted_cns = Array.from(all_cns).sort((a, b) => a - b)
|
|
169
|
+
|
|
170
|
+
return entries_with_data.map((entry, idx) => {
|
|
171
|
+
return {
|
|
172
|
+
x: sorted_cns,
|
|
173
|
+
y: sorted_cns.map((cn) => entry.data.cn_histogram.get(cn) ?? 0),
|
|
174
|
+
label: entry.label,
|
|
175
|
+
color: entry.color ?? PLOT_COLORS[idx % PLOT_COLORS.length],
|
|
176
|
+
bar_width: 0.8,
|
|
177
|
+
visible: true,
|
|
178
|
+
metadata: { structure_label: entry.label },
|
|
179
|
+
}
|
|
180
|
+
})
|
|
181
|
+
} else {
|
|
182
|
+
// split_mode === 'none': combine all into single series
|
|
183
|
+
const combined_histogram = new SvelteMap<number, number>()
|
|
184
|
+
|
|
185
|
+
for (const entry of entries_with_data) {
|
|
186
|
+
for (const [cn, count] of entry.data.cn_histogram) {
|
|
187
|
+
combined_histogram.set(cn, (combined_histogram.get(cn) ?? 0) + count)
|
|
188
|
+
}
|
|
189
|
+
}
|
|
190
|
+
|
|
191
|
+
const x_vals = Array.from(combined_histogram.keys()).sort((a, b) => a - b)
|
|
192
|
+
const y_vals = x_vals.map((cn) => combined_histogram.get(cn) ?? 0)
|
|
193
|
+
|
|
194
|
+
return [
|
|
195
|
+
{
|
|
196
|
+
x: x_vals,
|
|
197
|
+
y: y_vals,
|
|
198
|
+
label: `All Sites`,
|
|
199
|
+
color: PLOT_COLORS[0],
|
|
200
|
+
bar_width: 0.8,
|
|
201
|
+
visible: true,
|
|
202
|
+
metadata: {},
|
|
203
|
+
},
|
|
204
|
+
]
|
|
205
|
+
}
|
|
206
|
+
})
|
|
207
|
+
|
|
208
|
+
const compute_and_add = (content: string | ArrayBuffer, filename: string) => {
|
|
209
|
+
try {
|
|
210
|
+
const text_content = content instanceof ArrayBuffer
|
|
211
|
+
? new TextDecoder().decode(content)
|
|
212
|
+
: content
|
|
213
|
+
const parsed_structure = parse_any_structure(text_content, filename)
|
|
214
|
+
if (is_crystal(parsed_structure)) {
|
|
215
|
+
dropped_entries = [{
|
|
216
|
+
label: filename || `Dropped structure`,
|
|
217
|
+
structure: parsed_structure,
|
|
218
|
+
}, ...dropped_entries]
|
|
219
|
+
} else {
|
|
220
|
+
error_msg = `Structure has no lattice or sites; cannot compute coordination`
|
|
221
|
+
}
|
|
222
|
+
} catch (exc) {
|
|
223
|
+
error_msg = `Failed to process structure: ${
|
|
224
|
+
exc instanceof Error ? exc.message : String(exc)
|
|
225
|
+
}`
|
|
226
|
+
}
|
|
227
|
+
}
|
|
228
|
+
|
|
229
|
+
const handle_file_drop = create_file_drop_handler({
|
|
230
|
+
allow: () => allow_file_drop,
|
|
231
|
+
on_drop: (content, filename) =>
|
|
232
|
+
(on_file_drop || compute_and_add)(content, filename),
|
|
233
|
+
on_error: (msg) => {
|
|
234
|
+
error_msg = msg
|
|
235
|
+
},
|
|
236
|
+
set_loading: (val) => {
|
|
237
|
+
loading = val
|
|
238
|
+
if (val) [error_msg, dragover] = [undefined, false]
|
|
239
|
+
},
|
|
240
|
+
})
|
|
241
|
+
|
|
242
|
+
let display = $state({ x_zero_line: false, y_zero_line: false })
|
|
243
|
+
// Update display when orientation changes
|
|
244
|
+
$effect(() => {
|
|
245
|
+
display.x_zero_line = is_horizontal
|
|
246
|
+
display.y_zero_line = !is_horizontal
|
|
247
|
+
})
|
|
248
|
+
|
|
249
|
+
const cn_axis = { label: `Coordination Number`, format: `d` }
|
|
250
|
+
const count_axis = { label: `Count`, format: `d` }
|
|
251
|
+
</script>
|
|
252
|
+
|
|
253
|
+
<StatusMessage bind:message={error_msg} type="error" dismissible />
|
|
254
|
+
|
|
255
|
+
{#if bar_series.length === 0}
|
|
256
|
+
<StatusMessage
|
|
257
|
+
message={allow_file_drop
|
|
258
|
+
? `Drag and drop structure files here to compute coordination numbers`
|
|
259
|
+
: `No coordination data to display`}
|
|
260
|
+
/>
|
|
261
|
+
{:else}
|
|
262
|
+
{#snippet tooltip(info: BarHandlerProps<CoordinationMetadata>)}
|
|
263
|
+
{@const cn = info.x}
|
|
264
|
+
{@const count = info.y}
|
|
265
|
+
{@const element = info.metadata?.element}
|
|
266
|
+
{@const structure_label = info.metadata?.structure_label}
|
|
267
|
+
{#if element}
|
|
268
|
+
{element} —
|
|
269
|
+
{/if}
|
|
270
|
+
{#if structure_label}
|
|
271
|
+
{structure_label} —
|
|
272
|
+
{/if}
|
|
273
|
+
CN: {format_value(cn, `.0f`)}
|
|
274
|
+
<br />
|
|
275
|
+
Sites: {format_value(count, `.0f`)}
|
|
276
|
+
{/snippet}
|
|
277
|
+
|
|
278
|
+
<BarPlot
|
|
279
|
+
{...rest}
|
|
280
|
+
series={bar_series}
|
|
281
|
+
bind:orientation
|
|
282
|
+
bind:mode
|
|
283
|
+
x_axis={{
|
|
284
|
+
...(is_horizontal ? count_axis : cn_axis),
|
|
285
|
+
range: is_horizontal ? ranges.count : ranges.cn,
|
|
286
|
+
ticks: is_horizontal ? undefined : cn_ticks,
|
|
287
|
+
...x_axis,
|
|
288
|
+
label_shift: { y: 20, ...(is_horizontal ? y_axis : x_axis).label_shift },
|
|
289
|
+
}}
|
|
290
|
+
y_axis={{
|
|
291
|
+
...(is_horizontal ? cn_axis : count_axis),
|
|
292
|
+
range: is_horizontal ? ranges.cn : ranges.count,
|
|
293
|
+
ticks: is_horizontal ? cn_ticks : undefined,
|
|
294
|
+
...y_axis,
|
|
295
|
+
label_shift: { x: 2, ...(is_horizontal ? x_axis : y_axis).label_shift },
|
|
296
|
+
}}
|
|
297
|
+
bind:display
|
|
298
|
+
{tooltip}
|
|
299
|
+
ondrop={handle_file_drop}
|
|
300
|
+
ondragover={(event) => {
|
|
301
|
+
event.preventDefault()
|
|
302
|
+
if (!allow_file_drop) return
|
|
303
|
+
dragover = true
|
|
304
|
+
}}
|
|
305
|
+
ondragleave={(event) => {
|
|
306
|
+
event.preventDefault()
|
|
307
|
+
dragover = false
|
|
308
|
+
}}
|
|
309
|
+
class={(rest.class ?? ``) + (dragover ? ` dragover` : ``)}
|
|
310
|
+
/>
|
|
311
|
+
{/if}
|
|
@@ -0,0 +1,30 @@
|
|
|
1
|
+
import { BarPlot } from '../plot';
|
|
2
|
+
import type { AxisConfig } from '../plot/types';
|
|
3
|
+
import type { AnyStructure } from '../structure';
|
|
4
|
+
import type { BondingStrategy } from '../structure/bonding';
|
|
5
|
+
import type { ComponentProps } from 'svelte';
|
|
6
|
+
import { type CoordinationData } from './calc-coordination';
|
|
7
|
+
import type { SplitMode } from './index';
|
|
8
|
+
interface StructureEntry {
|
|
9
|
+
label: string;
|
|
10
|
+
structure: AnyStructure;
|
|
11
|
+
color?: string;
|
|
12
|
+
data?: CoordinationData;
|
|
13
|
+
}
|
|
14
|
+
type $$ComponentProps = Omit<ComponentProps<typeof BarPlot>, `series`> & {
|
|
15
|
+
structures: AnyStructure | Record<string, AnyStructure | {
|
|
16
|
+
structure: AnyStructure;
|
|
17
|
+
color?: string;
|
|
18
|
+
}> | StructureEntry[];
|
|
19
|
+
strategy?: BondingStrategy;
|
|
20
|
+
split_mode?: SplitMode;
|
|
21
|
+
x_axis?: AxisConfig;
|
|
22
|
+
y_axis?: AxisConfig;
|
|
23
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+
allow_file_drop?: boolean;
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+
on_file_drop?: (content: string | ArrayBuffer, filename: string) => void;
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+
loading?: boolean;
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26
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+
error_msg?: string;
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+
};
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+
declare const CoordinationBarPlot: import("svelte").Component<$$ComponentProps, {}, "mode" | "loading" | "error_msg">;
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29
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+
type CoordinationBarPlot = ReturnType<typeof CoordinationBarPlot>;
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30
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+
export default CoordinationBarPlot;
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|
@@ -0,0 +1,15 @@
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1
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+
import type { AnyStructure } from '../structure';
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|
2
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+
import type { BondingStrategy } from '../structure/bonding';
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3
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+
export interface CoordinationSite {
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4
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+
site_idx: number;
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5
|
+
element: string;
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6
|
+
coordination_num: number;
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7
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+
neighbor_elements: string[];
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8
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+
}
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|
9
|
+
export interface CoordinationData {
|
|
10
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+
sites: CoordinationSite[];
|
|
11
|
+
cn_by_element: Map<string, number[]>;
|
|
12
|
+
cn_histogram: Map<number, number>;
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13
|
+
cn_histogram_by_element: Map<string, Map<number, number>>;
|
|
14
|
+
}
|
|
15
|
+
export declare function calc_coordination_nums(structure: AnyStructure, strategy?: BondingStrategy): CoordinationData;
|
|
@@ -0,0 +1,63 @@
|
|
|
1
|
+
import { BONDING_STRATEGIES } from '../structure/bonding';
|
|
2
|
+
// Calculate coordination numbers for all sites in a structure using the specified bonding strategy.
|
|
3
|
+
//
|
|
4
|
+
// Note: This function operates on the sites present in the structure. For structures with periodic
|
|
5
|
+
// boundary conditions (PBC), image atoms should be added to the structure BEFORE calling this function
|
|
6
|
+
// to ensure atoms at cell boundaries have their full coordination environment calculated correctly.
|
|
7
|
+
// Use get_pbc_image_sites() from '$lib/structure/pbc' to expand the structure with image atoms.
|
|
8
|
+
//
|
|
9
|
+
// When working with PBC-expanded structures:
|
|
10
|
+
// - Image atoms are appended after the original sites
|
|
11
|
+
// - Bonds will be calculated between original and image atoms
|
|
12
|
+
// - Caller should extract coordination numbers for only the first N sites (original atoms)
|
|
13
|
+
export function calc_coordination_nums(structure, strategy = `electroneg_ratio`) {
|
|
14
|
+
// Get bonds using the specified strategy
|
|
15
|
+
const bonds = BONDING_STRATEGIES[strategy](structure);
|
|
16
|
+
// Count neighbors for each site
|
|
17
|
+
const neighbor_counts = new Map();
|
|
18
|
+
const sites = structure.sites;
|
|
19
|
+
for (const bond of bonds) {
|
|
20
|
+
const { site_idx_1, site_idx_2 } = bond;
|
|
21
|
+
if (!neighbor_counts.has(site_idx_1)) {
|
|
22
|
+
neighbor_counts.set(site_idx_1, new Set());
|
|
23
|
+
}
|
|
24
|
+
if (!neighbor_counts.has(site_idx_2)) {
|
|
25
|
+
neighbor_counts.set(site_idx_2, new Set());
|
|
26
|
+
}
|
|
27
|
+
const neighbors_1 = neighbor_counts.get(site_idx_1);
|
|
28
|
+
const neighbors_2 = neighbor_counts.get(site_idx_2);
|
|
29
|
+
if (neighbors_1)
|
|
30
|
+
neighbors_1.add(site_idx_2);
|
|
31
|
+
if (neighbors_2)
|
|
32
|
+
neighbors_2.add(site_idx_1);
|
|
33
|
+
}
|
|
34
|
+
// Build coordination site data
|
|
35
|
+
const coordination_sites = [];
|
|
36
|
+
const cn_by_element = new Map();
|
|
37
|
+
const cn_histogram = new Map();
|
|
38
|
+
const cn_histogram_by_element = new Map();
|
|
39
|
+
for (const [site_idx, site] of sites.entries()) {
|
|
40
|
+
const element = site.species[0]?.element ?? `Unknown`;
|
|
41
|
+
const neighbors_set = neighbor_counts.get(site_idx) ?? new Set();
|
|
42
|
+
const coordination_num = neighbors_set.size;
|
|
43
|
+
// Get neighbor elements
|
|
44
|
+
const neighbor_elements = Array.from(neighbors_set).map((neighbor_idx) => sites[neighbor_idx].species[0]?.element ?? `Unknown`);
|
|
45
|
+
coordination_sites.push({ site_idx, element, coordination_num, neighbor_elements });
|
|
46
|
+
// Update cn_by_element
|
|
47
|
+
const element_array = cn_by_element.get(element) ?? [];
|
|
48
|
+
element_array.push(coordination_num);
|
|
49
|
+
cn_by_element.set(element, element_array);
|
|
50
|
+
// Update overall cn_histogram
|
|
51
|
+
cn_histogram.set(coordination_num, (cn_histogram.get(coordination_num) ?? 0) + 1);
|
|
52
|
+
// Update cn_histogram_by_element
|
|
53
|
+
const element_histogram = cn_histogram_by_element.get(element) ?? new Map();
|
|
54
|
+
element_histogram.set(coordination_num, (element_histogram.get(coordination_num) ?? 0) + 1);
|
|
55
|
+
cn_histogram_by_element.set(element, element_histogram);
|
|
56
|
+
}
|
|
57
|
+
return {
|
|
58
|
+
sites: coordination_sites,
|
|
59
|
+
cn_by_element,
|
|
60
|
+
cn_histogram,
|
|
61
|
+
cn_histogram_by_element,
|
|
62
|
+
};
|
|
63
|
+
}
|
|
@@ -0,0 +1,8 @@
|
|
|
1
|
+
export * from './calc-coordination';
|
|
2
|
+
export { default as CoordinationBarPlot } from './CoordinationBarPlot.svelte';
|
|
3
|
+
export declare const SPLIT_MODES: {
|
|
4
|
+
readonly by_element: "By Element";
|
|
5
|
+
readonly by_structure: "By Structure";
|
|
6
|
+
readonly none: "Combined";
|
|
7
|
+
};
|
|
8
|
+
export type SplitMode = keyof typeof SPLIT_MODES;
|
|
@@ -0,0 +1,12 @@
|
|
|
1
|
+
type PulseAnimationOptions = {
|
|
2
|
+
step?: number;
|
|
3
|
+
frequency?: number;
|
|
4
|
+
on_tick?: () => void;
|
|
5
|
+
reset_when_inactive?: boolean;
|
|
6
|
+
};
|
|
7
|
+
type PulseAnimation = {
|
|
8
|
+
readonly time: number;
|
|
9
|
+
readonly unit: number;
|
|
10
|
+
};
|
|
11
|
+
export declare function create_pulse_animation(active: () => boolean, options?: PulseAnimationOptions): PulseAnimation;
|
|
12
|
+
export {};
|
|
@@ -0,0 +1,37 @@
|
|
|
1
|
+
export function create_pulse_animation(active, options = {}) {
|
|
2
|
+
let time = $state(0);
|
|
3
|
+
let frame_id = null;
|
|
4
|
+
const { step = 0.02, frequency = 4, on_tick, reset_when_inactive = true } = options;
|
|
5
|
+
const cancel_frame = () => {
|
|
6
|
+
if (frame_id == null)
|
|
7
|
+
return;
|
|
8
|
+
cancelAnimationFrame(frame_id);
|
|
9
|
+
frame_id = null;
|
|
10
|
+
};
|
|
11
|
+
const stop = () => {
|
|
12
|
+
cancel_frame();
|
|
13
|
+
if (reset_when_inactive)
|
|
14
|
+
time = 0;
|
|
15
|
+
};
|
|
16
|
+
$effect(() => {
|
|
17
|
+
if (!active())
|
|
18
|
+
return stop();
|
|
19
|
+
const animate = () => {
|
|
20
|
+
time += step;
|
|
21
|
+
on_tick?.();
|
|
22
|
+
if (!active())
|
|
23
|
+
return stop();
|
|
24
|
+
frame_id = requestAnimationFrame(animate);
|
|
25
|
+
};
|
|
26
|
+
frame_id = requestAnimationFrame(animate);
|
|
27
|
+
return cancel_frame;
|
|
28
|
+
});
|
|
29
|
+
return {
|
|
30
|
+
get time() {
|
|
31
|
+
return time;
|
|
32
|
+
},
|
|
33
|
+
get unit() {
|
|
34
|
+
return 0.5 + 0.5 * Math.sin(time * frequency);
|
|
35
|
+
},
|
|
36
|
+
};
|
|
37
|
+
}
|