matterviz 0.1.12 → 0.1.13

package/dist/settings.js

@@ -1,14 +1,44 @@
 // MatterViz settings schema - single source of truth for all MatterViz settings
 // Used by both main package and VSCode extension
-import { symbol_names } from './plot/formatting';
+import { symbol_names } from './labels';
+import { merge_nested } from './utils';
 export const show_bonds_options = [`never`, `always`, `crystals`, `molecules`];
+const DISPLAY_CONFIG = {
+    x_grid: {
+        value: true,
+        description: `Show X-axis grid lines`,
+    },
+    y_grid: {
+        value: true,
+        description: `Show Y-axis grid lines`,
+    },
+    y2_grid: {
+        value: false,
+        description: `Show Y2-axis grid lines`,
+    },
+    x_zero_line: {
+        value: false,
+        description: `Show X-axis zero reference line`,
+    },
+    y_zero_line: {
+        value: false,
+        description: `Show Y-axis zero reference line`,
+    },
+};
 // Complete settings configuration with values, descriptions, and constraints
 export const SETTINGS_CONFIG = {
     // General display settings
     color_scheme: {
         value: `Vesta`,
         description: `Color scheme for atoms and bonds`,
-        enum: [`Vesta`, `Jmol`, `Alloy`, `Pastel`, `Muted`, `Dark Mode`],
+        enum: {
+            Vesta: `Vesta`,
+            Jmol: `Jmol`,
+            Alloy: `Alloy`,
+            Pastel: `Pastel`,
+            Muted: `Muted`,
+            'Dark Mode': `Dark Mode`,
+        },
     },
     background_color: {
         value: `#000000`,
@@ -48,28 +78,27 @@ export const SETTINGS_CONFIG = {
             maximum: 64,
         },
         bond_thickness: {
-            value: 0.25,
+            value: 0.07,
             description: `Thickness of bonds relative to atom radius`,
             minimum: 0.01,
             maximum: 1.0,
         },
         show_bonds: {
-            value: `molecules`,
+            value: `always`,
             description: `When to display bonds between atoms`,
-            enum: show_bonds_options,
+            enum: Object.fromEntries(show_bonds_options.map((key) => [key, key[0].toUpperCase() + key.slice(1)])),
         },
         bond_color: {
-            value: `#ffffff`,
+            value: `#666666`,
             description: `Color for bonds (hex color code)`,
         },
         bonding_strategy: {
             value: `electroneg_ratio`,
             description: `Method for determining bonds between atoms`,
-            enum: [
-                `electroneg_ratio`,
-                `max_dist`,
-                `nearest_neighbor`,
-            ],
+            enum: {
+                electroneg_ratio: `Electronegativity Ratio`,
+                solid_angle: `Solid Angle`,
+            },
         },
         // Camera & Controls
         show_gizmo: {
@@ -85,7 +114,10 @@ export const SETTINGS_CONFIG = {
         camera_projection: {
             value: `orthographic`,
             description: `Camera projection type`,
-            enum: [`perspective`, `orthographic`],
+            enum: {
+                perspective: `Perspective`,
+                orthographic: `Orthographic`,
+            },
         },
         initial_zoom: {
             value: 35,
@@ -200,21 +232,21 @@ export const SETTINGS_CONFIG = {
             description: `Color for force vectors`,
         },
         force_shaft_radius: {
-            value: 0.02,
-            description: `Radius of force vector shaft`,
-            minimum: 0.005,
+            value: -0.01,
+            description: `Radius of force vector shaft (negative = relative to length, positive = absolute)`,
+            minimum: -0.1,
             maximum: 0.1,
         },
         force_arrow_head_radius: {
-            value: 0.08,
-            description: `Radius of force vector arrow head`,
-            minimum: 0.02,
+            value: -0.025,
+            description: `Radius of force vector arrow head (negative = relative to length, positive = absolute)`,
+            minimum: -0.2,
             maximum: 0.2,
         },
         force_arrow_head_length: {
-            value: 0.2,
-            description: `Length of force vector arrow head`,
-            minimum: 0.05,
+            value: -0.1,
+            description: `Length of force vector arrow head (negative = relative to length, positive = absolute)`,
+            minimum: -0.5,
             maximum: 0.5,
         },
         show_cell: {
@@ -279,13 +311,13 @@ export const SETTINGS_CONFIG = {
         display_mode: {
             value: `structure+scatter`,
             description: `Visualization mode for trajectory data`,
-            enum: [
-                `structure+scatter`,
-                `structure`,
-                `scatter`,
-                `histogram`,
-                `structure+histogram`,
-            ],
+            enum: {
+                'structure+scatter': `Structure + Scatter`,
+                structure: `Structure`,
+                scatter: `Scatter`,
+                histogram: `Histogram`,
+                'structure+histogram': `Structure + Histogram`,
+            },
         },
         show_controls: {
             value: true,
@@ -305,7 +337,11 @@ export const SETTINGS_CONFIG = {
         layout: {
             value: `auto`,
             description: `Layout arrangement for trajectory viewer`,
-            enum: [`auto`, `horizontal`, `vertical`],
+            enum: {
+                auto: `Auto`,
+                horizontal: `Horizontal`,
+                vertical: `Vertical`,
+            },
         },
         // File handling and loading
         allow_file_drop: {
@@ -334,34 +370,6 @@ export const SETTINGS_CONFIG = {
             minimum: 10,
             maximum: 10000,
         },
-        // Histogram specific
-        histogram_mode: {
-            value: `overlay`,
-            description: `Histogram display mode. 'overlay' shows multiple histograms in the same plot, 'single' shows a single histogram`,
-            enum: [`overlay`, `single`],
-        },
-        histogram_show_legend: {
-            value: true,
-            description: `Show legend in histogram plots`,
-        },
-        histogram_bin_count: {
-            value: 100,
-            description: `Number of bins for histogram plots`,
-            minimum: 1,
-            maximum: 1000,
-        },
-        histogram_bar_opacity: {
-            value: 0.7,
-            description: `Opacity of histogram bars`,
-            minimum: 0,
-            maximum: 1,
-        },
-        histogram_bar_stroke_width: {
-            value: 1,
-            description: `Stroke width for histogram bars`,
-            minimum: 0,
-            maximum: 5,
-        },
         // Formatting
         step_label_format: {
             value: `.3~s`,
@@ -441,17 +449,106 @@ export const SETTINGS_CONFIG = {
             description: `Cache parsed trajectory data`,
         },
     },
+    // Histogram specific
+    histogram: {
+        mode: {
+            value: `overlay`,
+            description: `Histogram display mode. 'overlay' shows multiple histograms in the same plot, 'single' shows a single histogram`,
+            enum: {
+                overlay: `Overlay`,
+                single: `Single`,
+            },
+        },
+        show_legend: {
+            value: true,
+            description: `Show legend in histogram plots`,
+        },
+        bin_count: {
+            value: 100,
+            description: `Number of bins for histogram plots`,
+            minimum: 1,
+            maximum: 1000,
+        },
+        bar: {
+            color: {
+                value: `#4A9EFF`,
+                description: `Histogram bar fill color`,
+            },
+            opacity: {
+                value: 0.7,
+                description: `Histogram bar opacity`,
+                minimum: 0,
+                maximum: 1,
+            },
+            stroke_width: {
+                value: 1,
+                description: `Histogram bar stroke width`,
+                minimum: 0,
+                maximum: 5,
+            },
+            stroke_color: {
+                value: `#000000`,
+                description: `Histogram bar stroke color`,
+            },
+            stroke_opacity: {
+                value: 0.5,
+                description: `Histogram bar stroke opacity`,
+                minimum: 0,
+                maximum: 1,
+            },
+        },
+        display: DISPLAY_CONFIG,
+    },
+    // Bar plot specific
+    bar: {
+        bar: {
+            color: {
+                value: `#4A9EFF`,
+                description: `Bar plot fill color`,
+            },
+            opacity: {
+                value: 0.6,
+                description: `Bar plot opacity (overlay mode)`,
+                minimum: 0,
+                maximum: 1,
+            },
+        },
+        line: {
+            width: {
+                value: 2,
+                description: `Bar plot line width`,
+                minimum: 0.5,
+                maximum: 10,
+            },
+            color: {
+                value: `#4A9EFF`,
+                description: `Bar plot line color`,
+            },
+        },
+        display: DISPLAY_CONFIG,
+    },
     // Composition specific
     composition: {
         display_mode: {
             value: `pie`,
             description: `Display mode for composition data`,
-            enum: [`pie`, `bubble`, `bar`],
+            enum: {
+                pie: `Pie`,
+                bubble: `Bubble`,
+                bar: `Bar`,
+            },
         },
         color_scheme: {
             value: `Vesta`,
             description: `Color scheme for composition visualization`,
-            enum: [`Vesta`, `Jmol`, `Alloy`, `Pastel`, `Muted`, `Dark Mode`],
+            enum: {
+                Vesta: `Vesta`,
+                Jmol: `Jmol`,
+                Alloy: `Alloy`,
+                Pastel: `Pastel`,
+                Muted: `Muted`,
+                'Dark Mode': `Dark Mode`,
+            },
         },
     },
     // Scatter plot specific
@@ -459,70 +556,12 @@ export const SETTINGS_CONFIG = {
         symbol_type: {
             value: `Circle`,
             description: `Default symbol type for scatter plots`,
-            enum: symbol_names,
-        },
-        line_width: {
-            value: 2,
-            description: `Line width for scatter plot connections`,
-            minimum: 0.5,
-            maximum: 10,
-        },
-        point_size: {
-            value: 4,
-            description: `Point size for scatter plots`,
-            minimum: 1,
-            maximum: 20,
+            enum: Object.fromEntries(symbol_names.map((name) => [name, name])),
         },
         show_legend: {
             value: true,
             description: `Show legend in scatter plots`,
         },
-        // Scatter plot specific
-        markers: {
-            value: `line+points`,
-            description: `Scatter plot marker type`,
-            enum: [`line`, `points`, `line+points`],
-        },
-        point_color: {
-            value: `#4682b4`,
-            description: `Default color for scatter plot points`,
-        },
-        point_opacity: {
-            value: 1,
-            description: `Opacity of scatter plot points`,
-            minimum: 0,
-            maximum: 1,
-        },
-        point_stroke_width: {
-            value: 1,
-            description: `Stroke width for scatter plot points`,
-            minimum: 0,
-            maximum: 5,
-        },
-        point_stroke_color: {
-            value: `#000000`,
-            description: `Stroke color for scatter plot points`,
-        },
-        point_stroke_opacity: {
-            value: 1,
-            description: `Stroke opacity for scatter plot points`,
-            minimum: 0,
-            maximum: 1,
-        },
-        line_color: {
-            value: `#4682b4`,
-            description: `Default color for scatter plot lines`,
-        },
-        line_opacity: {
-            value: 1,
-            description: `Opacity of scatter plot lines`,
-            minimum: 0,
-            maximum: 1,
-        },
-        line_dash: {
-            value: `solid`,
-            description: `Line dash pattern for scatter plots (e.g., "4,4" for dashed)`,
-        },
         show_points: {
             value: true,
             description: `Show points in scatter plots`,
@@ -531,6 +570,63 @@ export const SETTINGS_CONFIG = {
             value: true,
             description: `Show connecting lines in scatter plots`,
         },
+        display: DISPLAY_CONFIG,
+        point: {
+            size: {
+                value: 4,
+                description: `Point size for scatter plots`,
+                minimum: 1,
+                maximum: 20,
+            },
+            color: {
+                value: `#4A9EFF`,
+                description: `Default color for scatter plot points`,
+            },
+            opacity: {
+                value: 1,
+                description: `Opacity of scatter plot points`,
+                minimum: 0,
+                maximum: 1,
+            },
+            stroke_width: {
+                value: 1,
+                description: `Stroke width for scatter plot points`,
+                minimum: 0,
+                maximum: 5,
+            },
+            stroke_color: {
+                value: `#000000`,
+                description: `Stroke color for scatter plot points`,
+            },
+            stroke_opacity: {
+                value: 1,
+                description: `Stroke opacity for scatter plot points`,
+                minimum: 0,
+                maximum: 1,
+            },
+        },
+        line: {
+            width: {
+                value: 2,
+                description: `Line width for scatter plot connections`,
+                minimum: 0.5,
+                maximum: 10,
+            },
+            color: {
+                value: `#4A9EFF`,
+                description: `Default color for scatter plot lines`,
+            },
+            opacity: {
+                value: 1,
+                description: `Opacity of scatter plot lines`,
+                minimum: 0,
+                maximum: 1,
+            },
+            dash: {
+                value: `solid`,
+                description: `Line dash pattern for scatter plots (e.g., "4,4" for dashed)`,
+            },
+        },
     },
     // Plot general
     plot: {
@@ -562,19 +658,23 @@ export const SETTINGS_CONFIG = {
             value: true,
             description: `Show axis labels in plots`,
         },
-        show_zero_lines: {
+        show_x_zero_line: {
             value: true,
-            description: `Show zero reference lines in plots`,
+            description: `Show X-axis zero reference line`,
         },
-        x_grid: {
+        show_y_zero_line: {
+            value: true,
+            description: `Show Y-axis zero reference line`,
+        },
+        show_x_grid: {
             value: true,
             description: `Show X-axis grid lines`,
         },
-        y_grid: {
+        show_y_grid: {
             value: true,
             description: `Show Y-axis grid lines`,
         },
-        y2_grid: {
+        show_y2_grid: {
             value: true,
             description: `Show secondary Y-axis grid lines`,
         },
@@ -593,12 +693,18 @@ export const SETTINGS_CONFIG = {
         x_scale_type: {
             value: `linear`,
             description: `Scale type for X-axis`,
-            enum: [`linear`, `log`],
+            enum: {
+                linear: `Linear`,
+                log: `Log`,
+            },
         },
         y_scale_type: {
             value: `linear`,
             description: `Scale type for Y-axis`,
-            enum: [`linear`, `log`],
+            enum: {
+                linear: `Linear`,
+                log: `Log`,
+            },
         },
         x_ticks: {
             value: 8,
@@ -632,7 +738,10 @@ export const SETTINGS_CONFIG = {
             color_mode: {
                 value: `energy`,
                 description: `Color mode for 2D PD points`,
-                enum: [`stability`, `energy`],
+                enum: {
+                    stability: `Stability`,
+                    energy: `Energy`,
+                },
             },
             color_scale: {
                 value: `interpolateViridis`,
@@ -654,13 +763,13 @@ export const SETTINGS_CONFIG = {
                 value: false,
                 description: `Show labels for unstable phases in 2D PD`,
             },
-            energy_threshold: {
+            max_hull_dist_show_phases: {
                 value: 0.1,
                 description: `Max eV/atom above hull for showing unstable entries in 2D PD`,
                 minimum: 0,
                 maximum: 2,
             },
-            label_energy_threshold: {
+            max_hull_dist_show_labels: {
                 value: 0.1,
                 description: `Max eV/atom above hull for labeling unstable entries in 2D PD`,
                 minimum: 0,
@@ -709,7 +818,10 @@ export const SETTINGS_CONFIG = {
             color_mode: {
                 value: `energy`,
                 description: `Color mode for 3D PD points`,
-                enum: [`stability`, `energy`],
+                enum: {
+                    stability: `Stability`,
+                    energy: `Energy`,
+                },
             },
             color_scale: {
                 value: `interpolateViridis`,
@@ -731,13 +843,13 @@ export const SETTINGS_CONFIG = {
                 value: false,
                 description: `Show labels for unstable phases in 3D PD`,
             },
-            energy_threshold: {
+            max_hull_dist_show_phases: {
                 value: 0.5,
                 description: `Max eV/atom above hull for showing unstable entries in 3D PD`,
                 minimum: 0,
                 maximum: 2,
             },
-            label_energy_threshold: {
+            max_hull_dist_show_labels: {
                 value: 0.1,
                 description: `Max eV/atom above hull for labeling unstable entries in 3D PD`,
                 minimum: 0,
@@ -800,7 +912,10 @@ export const SETTINGS_CONFIG = {
             color_mode: {
                 value: `energy`,
                 description: `Color mode for 4D PD points`,
-                enum: [`stability`, `energy`],
+                enum: {
+                    stability: `Stability`,
+                    energy: `Energy`,
+                },
             },
             color_scale: {
                 value: `interpolateViridis`,
@@ -836,13 +951,13 @@ export const SETTINGS_CONFIG = {
                 minimum: 0,
                 maximum: 1,
             },
-            energy_threshold: {
+            max_hull_dist_show_phases: {
                 value: 0.1,
                 description: `Max eV/atom above hull for showing unstable entries in 4D PD`,
                 minimum: 0,
                 maximum: 2,
             },
-            label_energy_threshold: {
+            max_hull_dist_show_labels: {
                 value: 0.1,
                 description: `Max eV/atom above hull for labeling unstable entries in 4D PD`,
                 minimum: 0,
@@ -882,27 +997,14 @@ export const DEFAULTS = extract_values(SETTINGS_CONFIG);
 export const merge = (user) => ({
     ...DEFAULTS,
     ...(user || {}),
-    structure: { ...DEFAULTS.structure, ...(user?.structure || {}) },
-    trajectory: { ...DEFAULTS.trajectory, ...(user?.trajectory || {}) },
-    composition: { ...DEFAULTS.composition, ...(user?.composition || {}) },
-    plot: { ...DEFAULTS.plot, ...(user?.plot || {}) },
-    scatter: { ...DEFAULTS.scatter, ...(user?.scatter || {}) },
-    phase_diagram: {
-        ...DEFAULTS.phase_diagram,
-        ...(user?.phase_diagram || {}),
-        binary: {
-            ...DEFAULTS.phase_diagram.binary,
-            ...(user?.phase_diagram?.binary || {}),
-        },
-        ternary: {
-            ...DEFAULTS.phase_diagram.ternary,
-            ...(user?.phase_diagram?.ternary || {}),
-        },
-        quaternary: {
-            ...DEFAULTS.phase_diagram.quaternary,
-            ...(user?.phase_diagram?.quaternary || {}),
-        },
-    },
+    structure: merge_nested(DEFAULTS.structure, user?.structure),
+    trajectory: merge_nested(DEFAULTS.trajectory, user?.trajectory),
+    composition: merge_nested(DEFAULTS.composition, user?.composition),
+    plot: merge_nested(DEFAULTS.plot, user?.plot),
+    scatter: merge_nested(DEFAULTS.scatter, user?.scatter),
+    histogram: merge_nested(DEFAULTS.histogram, user?.histogram),
+    bar: merge_nested(DEFAULTS.bar, user?.bar),
+    phase_diagram: merge_nested(DEFAULTS.phase_diagram, user?.phase_diagram),
 });
 export const PD_DEFAULTS = DEFAULTS
     .phase_diagram;