matterviz 0.4.2 → 0.4.3

package/dist/convex-hull/StructurePopup.svelte

@@ -38,7 +38,7 @@
     popup_div?: HTMLDivElement
   } = $props()
 
-  const formula_html = $derived.by(() =>
+  const formula_html = $derived(
     sanitize_formula(get_electro_neg_formula(stats?.formula ?? structure, true)),
   )
   const context = $derived({ structure, stats, formula_html })

package/dist/convex-hull/gas-thermodynamics.js

@@ -24,47 +24,23 @@ export const GAS_STOICHIOMETRY = {
     CO2: { C: 1, O: 2 },
     H2O: { H: 2, O: 1 },
 };
-// Default T*S data for common gases (in eV/molecule)
+// Default Thermodynamic Data (abstracted - users can provide their own)
+// Temperature grid (K) shared by all tabulated T*S data below
+// oxfmt-ignore
+const TS_TEMPERATURES = [0, 298, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, 1900, 2000];
+// Default T*S values (eV/molecule) at TS_TEMPERATURES, interpolated between grid points.
 // Source: Barin Thermochemical Tables and NBS Thermochemical Tables
 // Data compiled to match PIRO (https://github.com/GENESIS-EFRC/piro)
-// Note: These values are T*S in eV/molecule
+// F2 not in Barin/NBS tables used by PIRO - approximated from similar homonuclear diatomics (O2, N2)
 // oxfmt-ignore
 const DEFAULT_TS_DATA = {
-    O2: {
-        temperatures: [0, 298, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, 1900, 2000],
-        values: [0, 0.317, 0.3192, 0.4433, 0.5718, 0.7041, 0.8396, 0.9781, 1.119, 1.2623, 1.4075, 1.5547, 1.7036, 1.8541, 2.006, 2.1594, 2.3141, 2.47, 2.6271, 2.7854],
-    },
-    H2: {
-        temperatures: [0, 298, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, 1900, 2000],
-        values: [0, 0.2019, 0.2034, 0.2886, 0.3776, 0.4697, 0.5645, 0.6614, 0.7605, 0.8614, 0.964, 1.0683, 1.1741, 1.2815, 1.3902, 1.5003, 1.6116, 1.7242, 1.838, 1.9528],
-    },
-    N2: {
-        temperatures: [0, 298, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, 1900, 2000],
-        values: [0, 0.2959, 0.2981, 0.4149, 0.5356, 0.6596, 0.7866, 0.9161, 1.0481, 1.1822, 1.3184, 1.4563, 1.596, 1.7372, 1.8799, 2.0239, 2.1693, 2.3158, 2.4634, 2.6122],
-    },
-    CO: {
-        temperatures: [0, 298, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, 1900, 2000],
-        values: [0, 0.3054, 0.3076, 0.4275, 0.5515, 0.6788, 0.8092, 0.9423, 1.0778, 1.2155, 1.3552, 1.4967, 1.64, 1.7848, 1.9311, 2.0788, 2.2277, 2.3779, 2.5291, 2.6815],
-    },
-    CO2: {
-        temperatures: [0, 298, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, 1900, 2000],
-        values: [0, 0.2202, 0.2218, 0.3113, 0.4057, 0.5042, 0.6064, 0.7116, 0.8197, 0.9303, 1.0432, 1.1582, 1.2751, 1.3938, 1.5141, 1.636, 1.7593, 1.8839, 2.0098, 2.1369],
-    },
-    H2O: {
-        temperatures: [0, 298, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, 1900, 2000],
-        values: [0, 0.1946, 0.1961, 0.2749, 0.357, 0.4419, 0.5293, 0.6189, 0.7107, 0.8045, 0.9001, 0.9975, 1.0966, 1.1972, 1.2994, 1.403, 1.5079, 1.6142, 1.7216, 1.8303],
-    },
-    F2: {
-        // F2 not in Barin/NBS tables used by PIRO - approximated from similar homonuclear diatomics (O2, N2)
-        temperatures: [
-            0, 298, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, 1300, 1400, 1500, 1600,
-            1700, 1800, 1900, 2000,
-        ],
-        values: [
-            0, 0.31, 0.312, 0.435, 0.56, 0.69, 0.82, 0.96, 1.1, 1.24, 1.38, 1.53, 1.68, 1.83,
-            1.98, 2.13, 2.29, 2.45, 2.61, 2.77,
-        ],
-    },
+    O2: [0, 0.317, 0.3192, 0.4433, 0.5718, 0.7041, 0.8396, 0.9781, 1.119, 1.2623, 1.4075, 1.5547, 1.7036, 1.8541, 2.006, 2.1594, 2.3141, 2.47, 2.6271, 2.7854],
+    H2: [0, 0.2019, 0.2034, 0.2886, 0.3776, 0.4697, 0.5645, 0.6614, 0.7605, 0.8614, 0.964, 1.0683, 1.1741, 1.2815, 1.3902, 1.5003, 1.6116, 1.7242, 1.838, 1.9528],
+    N2: [0, 0.2959, 0.2981, 0.4149, 0.5356, 0.6596, 0.7866, 0.9161, 1.0481, 1.1822, 1.3184, 1.4563, 1.596, 1.7372, 1.8799, 2.0239, 2.1693, 2.3158, 2.4634, 2.6122],
+    CO: [0, 0.3054, 0.3076, 0.4275, 0.5515, 0.6788, 0.8092, 0.9423, 1.0778, 1.2155, 1.3552, 1.4967, 1.64, 1.7848, 1.9311, 2.0788, 2.2277, 2.3779, 2.5291, 2.6815],
+    CO2: [0, 0.2202, 0.2218, 0.3113, 0.4057, 0.5042, 0.6064, 0.7116, 0.8197, 0.9303, 1.0432, 1.1582, 1.2751, 1.3938, 1.5141, 1.636, 1.7593, 1.8839, 2.0098, 2.1369],
+    H2O: [0, 0.1946, 0.1961, 0.2749, 0.357, 0.4419, 0.5293, 0.6189, 0.7107, 0.8045, 0.9001, 0.9975, 1.0966, 1.1972, 1.2994, 1.403, 1.5079, 1.6142, 1.7216, 1.8303],
+    F2: [0, 0.31, 0.312, 0.435, 0.56, 0.69, 0.82, 0.96, 1.1, 1.24, 1.38, 1.53, 1.68, 1.83, 1.98, 2.13, 2.29, 2.45, 2.61, 2.77],
 };
 // Formation enthalpies H_f at 0K in eV/molecule
 // These are the reference energies for formation from elements
@@ -76,27 +52,19 @@ const DEFAULT_ENTHALPY = {
     H2O: -0.82547,
     // O2, N2, H2, F2 are reference states with H_f = 0
 };
-// Interpolation Helpers
-// Linearly interpolate T*S value at given temperature
-function interpolate_ts(data, T) {
-    const { temperatures, values } = data;
-    // Clamp to valid range
-    if (T <= temperatures[0])
+// Linearly interpolate T*S value at given temperature (clamped to the tabulated range)
+function interpolate_ts(values, T) {
+    const temps = TS_TEMPERATURES;
+    if (T <= temps[0])
         return values[0];
-    if (T >= temperatures[temperatures.length - 1]) {
+    if (T >= temps[temps.length - 1])
         return values[values.length - 1];
-    }
     // Find bracketing indices
     let idx = 0;
-    while (idx < temperatures.length - 1 && temperatures[idx + 1] < T)
+    while (idx < temps.length - 1 && temps[idx + 1] < T)
         idx++;
-    const T_low = temperatures[idx];
-    const T_high = temperatures[idx + 1];
-    const v_low = values[idx];
-    const v_high = values[idx + 1];
-    // Linear interpolation
-    const fraction = (T - T_low) / (T_high - T_low);
-    return v_low + fraction * (v_high - v_low);
+    const fraction = (T - temps[idx]) / (temps[idx + 1] - temps[idx]);
+    return values[idx] + fraction * (values[idx + 1] - values[idx]);
 }
 // Default Provider Implementation
 // Create the default gas thermodynamics provider using built-in data

package/dist/convex-hull/helpers.js

@@ -290,13 +290,7 @@ energy_source_mode) {
         for (const el of Object.keys(entry.composition))
             elements_in_entries.add(el);
     }
-    let can_compute_e_form = true;
-    for (const el of elements_in_entries) {
-        if (!unary_refs[el]) {
-            can_compute_e_form = false;
-            break;
-        }
-    }
+    const can_compute_e_form = [...elements_in_entries].every((el) => el in unary_refs);
     // Resolve mode to avoid inconsistent states:
     // - If full precomputed available, honor user toggle
     // - Else if we can compute, use on-the-fly automatically

package/dist/convex-hull/thermodynamics.js

@@ -442,40 +442,32 @@ export function compute_lower_hull_triangles(points) {
     return compute_quickhull_triangles(points).filter((face) => face.normal.z < 0 - EPS);
 }
 export const build_lower_hull_model = (faces) => faces.map((tri) => {
-    const [p1, p2, p3] = tri.vertices;
-    const plane = (() => {
-        const x1 = p1.x, y1 = p1.y, z1 = p1.z;
-        const x2 = p2.x, y2 = p2.y, z2 = p2.z;
-        const x3 = p3.x, y3 = p3.y, z3 = p3.z;
-        const det = x1 * (y2 - y3) + x2 * (y3 - y1) + x3 * (y1 - y2);
-        if (Math.abs(det) < 1e-12)
-            return { a: 0, b: 0, c: (z1 + z2 + z3) / 3 };
-        const a = (z1 * (y2 - y3) + z2 * (y3 - y1) + z3 * (y1 - y2)) / det;
-        const b = (z1 * (x3 - x2) + z2 * (x1 - x3) + z3 * (x2 - x1)) / det;
-        const c = (z1 * (x2 * y3 - x3 * y2) + z2 * (x3 * y1 - x1 * y3) + z3 * (x1 * y2 - x2 * y1)) / det;
-        return { a, b, c };
-    })();
-    const [min_x, _mx, max_x] = [p1.x, p2.x, p3.x].sort((a, b) => a - b);
-    const [min_y, _my, max_y] = [p1.y, p2.y, p3.y].sort((a, b) => a - b);
-    const { x: x1, y: y1 } = p1;
-    const { x: x2, y: y2 } = p2;
-    const { x: x3, y: y3 } = p3;
-    const denom = (y2 - y3) * (x1 - x3) + (x3 - x2) * (y1 - y3);
+    const [{ x: x1, y: y1, z: z1 }, { x: x2, y: y2, z: z2 }, { x: x3, y: y3, z: z3 }] = tri.vertices;
+    // Fit plane z = a*x + b*y + c through the three vertices (flat fallback if degenerate)
+    const det = x1 * (y2 - y3) + x2 * (y3 - y1) + x3 * (y1 - y2);
+    const plane = Math.abs(det) < 1e-12
+        ? { a: 0, b: 0, c: (z1 + z2 + z3) / 3 }
+        : {
+            a: (z1 * (y2 - y3) + z2 * (y3 - y1) + z3 * (y1 - y2)) / det,
+            b: (z1 * (x3 - x2) + z2 * (x1 - x3) + z3 * (x2 - x1)) / det,
+            c: (z1 * (x2 * y3 - x3 * y2) +
+                z2 * (x3 * y1 - x1 * y3) +
+                z3 * (x1 * y2 - x2 * y1)) /
+                det,
+        };
     return {
-        a: plane.a,
-        b: plane.b,
-        c: plane.c,
+        ...plane,
         x1,
         y1,
         x2,
         y2,
         x3,
         y3,
-        min_x,
-        max_x,
-        min_y,
-        max_y,
-        denom,
+        min_x: Math.min(x1, x2, x3),
+        max_x: Math.max(x1, x2, x3),
+        min_y: Math.min(y1, y2, y3),
+        max_y: Math.max(y1, y2, y3),
+        denom: det,
     };
 });
 function point_in_triangle_xy(model, x, y) {

package/dist/coordination/CoordinationBarPlot.svelte

@@ -97,29 +97,21 @@
     })),
   )
 
-  // Compute appropriate ranges
-  const ranges = $derived.by(() => {
-    // CN axis should always start at 0 and show at least [0,4]
-    let max_cn = 4 // minimum max value
-    for (const entry of entries_with_data) {
-      for (const [cn] of entry.data.cn_histogram) max_cn = Math.max(max_cn, cn)
-    }
-    const cn_range: Vec2 = [-0.5, max_cn + 0.5]
-
-    return { count: [0, null] as [number, null], cn: cn_range } // Count axis should always start at 0
-  })
-
   // Derive integer CN ticks for axis labels
   const cn_ticks = $derived.by(() => {
-    const all_cns = new SvelteSet<number>()
-    // Always include minimum CN values 0-4
-    for (let idx = 0; idx <= 4; idx++) all_cns.add(idx)
-    // Add actual CN values from data
+    // Always include minimum CN values 0-4, then actual CN values from data
+    const all_cns = new SvelteSet<number>([0, 1, 2, 3, 4])
     for (const entry of entries_with_data) {
       for (const [cn] of entry.data.cn_histogram) all_cns.add(cn)
     }
     return Array.from(all_cns).sort((cn1, cn2) => cn1 - cn2)
   })
+
+  // CN axis spans all ticks with half-bar margin; count axis always starts at 0
+  const ranges = $derived({
+    count: [0, null] as [number, null],
+    cn: [-0.5, (cn_ticks.at(-1) ?? 4) + 0.5] as Vec2,
+  })
   // Build BarPlot series based on split_mode
   const bar_series = $derived.by<BarSeries<CoordinationMetadata>[]>(() => {
     if (split_mode === `by_element`) {
@@ -131,12 +123,11 @@
 
       for (const entry of entries_with_data) {
         for (const [element, cn_histogram] of entry.data.cn_histogram_by_element) {
-          if (!element_series_map.has(element)) {
-            element_series_map.set(element, new SvelteMap())
+          let element_map = element_series_map.get(element)
+          if (!element_map) {
+            element_map = new SvelteMap()
+            element_series_map.set(element, element_map)
           }
-          const element_map = element_series_map.get(element)
-          if (!element_map) continue
-
           for (const [cn, count] of cn_histogram) {
             all_cns.add(cn)
             element_map.set(cn, (element_map.get(cn) ?? 0) + count)

package/dist/element/BohrAtom.svelte

@@ -109,7 +109,6 @@
               {number_electrons(elec_idx)}
             {:else if number_electrons === `hierarchical`}
               {shell_idx + 1}.{elec_idx + 1}
-              <!-- {:else if [`sequential`, true].includes(number_electrons)} -->
             {:else}
               {@const nth_electron =
                 shells.slice(0, shell_idx).reduce((sum, count) => sum + count, 0) +

package/dist/element/ElementTile.svelte

@@ -94,57 +94,39 @@
     return !is_color(value)
   })
 
+  // CSS classes for segments and value positions, keyed by `layout-count`
+  const layout_classes: Record<string, { segments: string[]; positions: string[] }> = {
+    'diagonal-2': {
+      segments: [`diagonal-top`, `diagonal-bottom`],
+      positions: [`top-left`, `bottom-right`],
+    },
+    'horizontal-3': {
+      segments: [`horizontal-top`, `horizontal-middle`, `horizontal-bottom`],
+      positions: [`bar-top-left`, `bar-middle-right`, `bar-bottom-left`],
+    },
+    'vertical-3': {
+      segments: [`vertical-left`, `vertical-middle`, `vertical-right`],
+      positions: [`bar-left-top`, `bar-middle-bottom`, `bar-right-top`],
+    },
+    'triangular-4': {
+      segments: [`top`, `right`, `bottom`, `left`].map((pos) => `triangle-${pos}`),
+      positions: [`top`, `right`, `bottom`, `left`].map((pos) => `triangle-${pos}-pos`),
+    },
+    'quadrant-4': {
+      segments: [`tl`, `tr`, `bl`, `br`].map((pos) => `quadrant-${pos}`),
+      positions: [`tl`, `tr`, `bl`, `br`].map((pos) => `value-quadrant-${pos}`),
+    },
+  }
+
   // Get the appropriate CSS classes for segments and positions based on layout
   const layout_config = $derived.by(() => {
     if (!Array.isArray(value)) return null
-
     const count = value.length
     // Use explicit split_layout or auto-determine based on count
     const layout =
       split_layout ??
-      ({
-        2: `diagonal`,
-        3: `horizontal`,
-        4: `quadrant`,
-      }[count] as SplitLayout | undefined)
-
-    if (!layout) return null
-
-    if (layout === `diagonal` && count === 2) {
-      return {
-        segments: [`diagonal-top`, `diagonal-bottom`],
-        positions: [`top-left`, `bottom-right`],
-      }
-    }
-
-    if (layout === `horizontal` && count === 3) {
-      return {
-        segments: [`horizontal-top`, `horizontal-middle`, `horizontal-bottom`],
-        positions: [`bar-top-left`, `bar-middle-right`, `bar-bottom-left`],
-      }
-    }
-
-    if (layout === `vertical` && count === 3) {
-      return {
-        segments: [`vertical-left`, `vertical-middle`, `vertical-right`],
-        positions: [`bar-left-top`, `bar-middle-bottom`, `bar-right-top`],
-      }
-    }
-
-    if (layout === `triangular` && count === 4) {
-      return {
-        segments: [`top`, `right`, `bottom`, `left`].map((pos) => `triangle-${pos}`),
-        positions: [`top`, `right`, `bottom`, `left`].map((pos) => `triangle-${pos}-pos`),
-      }
-    }
-
-    if (layout === `quadrant` && count === 4) {
-      const segments = [`tl`, `tr`, `bl`, `br`].map((pos) => `quadrant-${pos}`)
-      const positions = [`tl`, `tr`, `bl`, `br`].map((pos) => `value-quadrant-${pos}`)
-      return { segments, positions }
-    }
-
-    return null
+      ({ 2: `diagonal`, 3: `horizontal`, 4: `quadrant` }[count] as SplitLayout | undefined)
+    return layout ? (layout_classes[`${layout}-${count}`] ?? null) : null
   })
 </script>
 

package/dist/element/data.d.ts

@@ -1 +1,3 @@
+import type { ChemicalElement, ElementSymbol } from './types';
+export declare const element_by_symbol: ReadonlyMap<ElementSymbol, ChemicalElement>;
 export { default } from './data.json.gz';