Improve Fermi surface

README.md

@@ -109,7 +109,7 @@ Press the keyboard shortcut, and move your mouse.
 
 ### Rotate selected atoms
 
-To rotate around a custom axis, press ``r`` then ``a`` and click one or two atoms.
+To rotate around a custom axis, press ``r`` then ``a`` and click one or two atoms, then press ``a`` again to exit axis picking.
 Rotation defaults to the camera axis through the selection center.
 One atom sets the rotation center (camera axis), two atoms define the bond axis.
 The axis is shown with orange crosses and a long orange line (for two atoms).
@@ -118,6 +118,8 @@ Press ``r`` then ``x``, ``y``, or ``z`` to lock rotation to a world axis (press
 
 ### Translate along one axis
 To translate along one axis, press ``g`` then ``x``, ``y``, or ``z`` to lock movement.
+To translate along an atom-defined axis, press ``g`` then ``a`` and click two atoms, then press ``a`` again to exit axis picking.
+To translate in an atom-defined plane, press ``g`` then ``a`` and click three atoms, press ``a`` again to exit axis picking, then press ``p`` for plane or ``n`` for normal.
 
 
 ### Delete selected atoms

docs/source/edit.rst

@@ -34,7 +34,7 @@ and click to confirm.
 - ``s`` scale
 - ``d`` duplicate and move
 Rotation defaults to the camera axis through the selection center.
-To rotate around a custom axis, press ``r`` to enter rotate mode, then press ``a`` and click one or two atoms.
+To rotate around a custom axis, press ``r`` to enter rotate mode, then press ``a`` and click one or two atoms, then press ``a`` again to exit axis picking.
 One atom sets the rotation center (camera axis), two atoms define the bond axis.
 The axis is shown with orange crosses and a long orange line (for two atoms), and stays active until you redefine it.
 Press ``a`` again to exit axis picking and rotate; click an axis atom again to deselect it.
@@ -43,6 +43,8 @@ Press ``r`` then ``x``, ``y``, or ``z`` to lock rotation to a world axis (press
 Translate Axis Lock
 =======================
 Press ``g`` to translate, then press ``x``, ``y``, or ``z`` to lock movement to that axis.
+To translate along an atom-defined axis, press ``g`` then ``a`` and click two atoms, then press ``a`` again to exit axis picking.
+To translate in an atom-defined plane, press ``g`` then ``a`` and click three atoms, press ``a`` again to exit axis picking, then press ``p`` for plane or ``n`` for normal.
 
 +-----------+----------+
 | Operation | Shortcut |

docs/source/fermi_surface.ipynb

@@ -7,6 +7,7 @@
    "source": [
     "# Fermi Surface\n",
     "Generate and visualize Fermi surfaces from BXSF files.\n",
+    "The Fermi surface mesh is generated in the frontend (JavaScript marching cubes); Python prepares the volumetric data and optional Brillouin-zone mesh via seekpath.\n\n",
     "\n",
     "Requires the optional `fermi-surface` dependencies (includes `seekpath`):\n",
     "\n",
@@ -44,21 +45,21 @@
     "- `file_path`: Path to the `.bxsf` file.\n",
     "- `fermi_energy`: Override the Fermi energy (default: use value in file).\n",
     "- `drop_periodic`: Drop the duplicated periodic end points (default: `True`).\n",
-    "- `clip_bz`: Clip to the first Brillouin zone (default: `False`, requires `seekpath`).\n",
+    "- `clip_bz`: Clip to the first Brillouin zone (default: `True`, requires `seekpath`).\n",
     "- `show_bz`: Add the Brillouin zone mesh (default: `True`).\n",
     "- `show_reciprocal_axes`: Add reciprocal axes vectors (default: `True`).\n",
     "- `band_index`: Render a single band by index (default: `None`).\n",
-    "- `combine_bands`: Merge all Fermi-crossing bands into one mesh (default: `True`).\n",
+    "- `combine_bands`: Merge all Fermi-crossing bands into one mesh (default: `False`).\n",
     "- `name`: Mesh name override.\n",
     "- `color`: RGB list for the mesh color or hex color string.\n",
     "- `opacity`: Alpha channel applied to the mesh.\n",
     "- `material_type`: Material type for the mesh (default: `\"Standard\"`).\n",
-    "- `supercell_size`: Tuple for band replication in reciprocal space (default: `(2, 2, 2)`).\n",
     "- `brillouin_zone_options`: Extra keyword arguments forwarded to `add_brillouin_zone` (e.g., custom color/opacity).\n",
     "- `reciprocal_axes_options`: Extra keyword arguments forwarded to `add_reciprocal_axes`.\n",
     "\n",
     "Notes:\n",
     "\n",
+    "- The Fermi surface mesh is generated in the frontend (JavaScript marching cubes).\n",
     "- If `band_index` is `None`, all Fermi-crossing bands are used.\n",
     "- If `combine_bands=False`, each band is added as a separate mesh.\n",
     "- A `ValueError` is raised when no Fermi-crossing bands are found.\n",

js/widget.js

@@ -96,6 +96,8 @@ function render({ model, el }) {
         window.editor = editor; // for debugging
         // volumetric data
         setVolumetricData(editor, model.get("volumetricData"), atoms.cell);
+        // fermi surface data
+        setFermiSurfaceData(editor, model.get("fermiData"), atoms.cell);
         editor.avr.transaction(() => {
             const initialState = {
                 modelStyle: model.get("modelStyle"),
@@ -131,6 +133,7 @@ function render({ model, el }) {
             const showOutBoundaryBonds = model.get("showOutBoundaryBonds");
             const highlightSettings = model.get("highlightSettings") || {};
             const isoSettings = model.get("isoSettings") || {};
+            const fermiSettings = model.get("fermiSettings") || {};
             const sliceSettings = model.get("sliceSettings") || {};
             const vectorField = model.get("vectorField") || {};
             const showVectorField = model.get("showVectorField");
@@ -152,6 +155,7 @@ function render({ model, el }) {
                     vectorField: { settings: vectorField, show: showVectorField },
                     instancedMeshPrimitive: { settings: model.get("instancedMeshPrimitive") || [] },
                     anyMesh: { settings: model.get("anyMesh") || [] },
+                    fermiSurface: { settings: fermiSettings },
                     text: { settings: model.get("text") || [] },
                     species: { settings: model.get("speciesSettings") || {} },
                 },
@@ -288,10 +292,20 @@ function render({ model, el }) {
         setVolumetricData(editor, data, editor.avr.atoms.cell);
         console.log("volumeData: ", editor.avr.volumetricData);
     });
+    model.on("change:fermiData", () => {
+        const data = model.get("fermiData");
+        console.log("fermiData: ", data);
+        setFermiSurfaceData(editor, data, editor.avr.atoms.cell);
+        console.log("fermiSurfaceData: ", editor.avr.fermiSurfaceData);
+    });
     model.on("change:isoSettings", () => {
         const isoSettings = model.get("isoSettings") || {};
         editor.state.set({ plugins: { isosurface: { settings: isoSettings } } });
     });
+    model.on("change:fermiSettings", () => {
+        const fermiSettings = model.get("fermiSettings") || {};
+        editor.state.set({ plugins: { fermiSurface: { settings: fermiSettings } } });
+    });
     // volume slice
     model.on("change:sliceSettings", () => {
         const data = model.get("sliceSettings") || {};
@@ -418,14 +432,24 @@ function render({ model, el }) {
     });
 }
 function createVolumeData(data, cell=[[1, 0, 0], [0, 1, 0], [0, 0, 1]]) {
-    if (!data || !data.values || !Array.isArray(data.values) || data.values.length === 0) {
+    if (!data) {
         return null;
     }
-    // get the dimensions
-    const dims = [data.values.length, data.values[0].length, data.values[0][0].length];
-    // flatten the 3d data to 1d
-    const values = [].concat.apply([], [].concat.apply([], data.values));
-    return {dims, values, cell: cell, origin: [0, 0, 0]};
+    if (Array.isArray(data.values) && data.values.length === 0) {
+        return null;
+    }
+    if (Array.isArray(data.values) && Array.isArray(data.values[0]) && Array.isArray(data.values[0][0])) {
+        const dims = [data.values.length, data.values[0].length, data.values[0][0].length];
+        const values = [].concat.apply([], [].concat.apply([], data.values));
+        return {dims, values, cell: data.cell || cell, origin: data.origin || [0, 0, 0], bzPlanes: data.bzPlanes, bzMesh: data.bzMesh};
+    }
+    if (Array.isArray(data.values) && Array.isArray(data.dims)) {
+        return {dims: data.dims, values: data.values, cell: data.cell || cell, origin: data.origin || [0, 0, 0], bzPlanes: data.bzPlanes, bzMesh: data.bzMesh, datasets: data.datasets};
+    }
+    if (Array.isArray(data.datasets)) {
+        return {datasets: data.datasets, cell: data.cell || cell, origin: data.origin || [0, 0, 0], bzPlanes: data.bzPlanes, bzMesh: data.bzMesh};
+    }
+    return null;
 }
 
 function setVolumetricData(editor, data, cell) {
@@ -452,6 +476,27 @@ function setVolumetricData(editor, data, cell) {
     }
 }
 
+function setFermiSurfaceData(editor, data, cell) {
+    if (!editor || !editor.avr) {
+        return;
+    }
+    const fermiData = createVolumeData(data, cell);
+    if (!fermiData) {
+        return;
+    }
+    if (typeof editor.avr.setFermiSurfaceData === "function") {
+        editor.avr.setFermiSurfaceData(fermiData);
+        return;
+    }
+    editor.avr.fermiSurfaceData = fermiData;
+    if (editor.avr.fermiSurfaceManager && typeof editor.avr.fermiSurfaceManager.drawFermiSurfaces === "function") {
+        editor.avr.fermiSurfaceManager.drawFermiSurfaces();
+    }
+    if (typeof editor.avr.requestRedraw === "function") {
+        editor.avr.requestRedraw("render");
+    }
+}
+
 function preventEventPropagation(element) {
     const stopPropagation = (e) => e.stopPropagation();
     ["click", "keydown", "keyup", "keypress"].forEach((eventType) => {

package.json

@@ -7,7 +7,7 @@
 	"dependencies": {
 		"dat.gui": "^0.7.9",
 		"three": "^0.169.0",
-		"weas": "^0.2.8"
+		"weas": "^0.2.10"
 	},
 	"devDependencies": {
 		"esbuild": "^0.20.0"

src/weas_widget/atoms_viewer.py

@@ -1,6 +1,7 @@
 from .base_class import WidgetWrapper
 from .plugins.vector_field import VectorField
 from .plugins.isosurface import Isosurface
+from .plugins.fermi_surface_plugin import FermiSurface
 from .plugins.volume_slice import VolumeSlice
 from .plugins.lattice_plane import LatticePlane
 from .plugins.cell import CellManager
@@ -39,6 +40,7 @@ class AtomsViewer(WidgetWrapper):
         "species",
         "vf",
         "iso",
+        "fermi",
         "volume_slice",
         "lp",
         "atoms",
@@ -54,6 +56,7 @@ def __init__(self, _widget):
         # Initialize plugins
         setattr(self, "vf", VectorField(_widget))
         setattr(self, "iso", Isosurface(_widget))
+        setattr(self, "fermi", FermiSurface(_widget))
         setattr(self, "lp", LatticePlane(_widget))
         setattr(self, "cell", CellManager(_widget))
         setattr(self, "bond", BondManager(_widget))

src/weas_widget/base_widget.py

@@ -38,6 +38,7 @@ class BaseWidget(anywidget.AnyWidget):
     modelSticks = tl.List().tag(sync=True)
     modelPolyhedras = tl.List().tag(sync=True)
     volumetricData = tl.Dict({"values": [[[]]]}).tag(sync=True)
+    fermiData = tl.Dict().tag(sync=True)
     imageData = tl.Unicode("").tag(sync=True)
     vectorField = tl.Dict().tag(sync=True)
     showVectorField = tl.Bool(True).tag(sync=True)
@@ -71,6 +72,7 @@ class BaseWidget(anywidget.AnyWidget):
     bondSettings = tl.Dict().tag(sync=True)
     # isosurface
     isoSettings = tl.Dict().tag(sync=True)
+    fermiSettings = tl.Dict().tag(sync=True)
     # volume slice
     sliceSettings = tl.Dict().tag(sync=True)
     # phonon