allow user to set atom_scales, sticks etc

README.md

@@ -105,6 +105,13 @@ viewer.save_image("/home/xing/filename.png")
 viewer.download_image("filename.png")
 ```
 
+### Different styles for the atoms.
+
+
+<img src="docs/source/_static/images/example-custom-model-style.png"  width="500px"/>
+
+
+
 ### Visualizing crystal structures
 For a nice visualization of a crystal, show
 - unit cell

js/widget.js

@@ -62,9 +62,6 @@ function render({ model, el }) {
         editor = new weas.WEAS({ domElement, atoms, viewerConfig, guiConfig });
         // window.editor = editor; // for debugging
         editor.avr.selectedAtomsIndices = model.get("selectedAtomsIndices");
-        // editor.avr.atomScales = model.get("atomScales");
-        // editor.avr.modelSticks = model.get("modelSticks");
-        // editor.avr.modelPolyhedras = model.get("modelPolyhedras");
         // species settings
         editor.avr.atomManager.fromSettings(model.get("speciesSettings"));
         // bond settings
@@ -82,6 +79,16 @@ function render({ model, el }) {
         // vector field
         editor.avr.VFManager.fromSettings(model.get("vectorField"));
         editor.avr.showVectorField = model.get("showVectorField");
+        // if the atomScales is not a empty array, then update the atomScales
+        if (model.get("atomScales").length > 0) {
+            editor.avr.atomScales = model.get("atomScales");
+        }
+        if (model.get("modelSticks").length > 0) {
+            editor.avr.modelSticks = model.get("modelSticks");
+        }
+        if (model.get("modelPolyhedras").length > 0) {
+            editor.avr.modelPolyhedras = model.get("modelPolyhedras");
+        }
         editor.avr.drawModels();
         // mesh primitives
         editor.instancedMeshPrimitive.fromSettings(model.get("instancedMeshPrimitive"));

package.json

@@ -7,7 +7,7 @@
 	"dependencies": {
 		"dat.gui": "^0.7.9",
 		"three": "^0.161.0",
-		"weas": ">=0.1.34"
+		"weas": ">=0.1.36"
 	},
 	"devDependencies": {
 		"esbuild": "^0.20.0"

src/weas_widget/atoms_viewer.py

@@ -67,10 +67,6 @@ def atoms(self, atoms):
         # initialize atomScales
         if isinstance(atoms, list):
             atoms = atoms[0]
-        natom = len(atoms["symbols"])
-        self._widget.atomScales = [1] * natom
-        self._widget.modelSticks = [0] * natom
-        self._widget.modelPolyhedras = [0] * natom
         # species
         self.species.update_atoms()
         # bond

src/weas_widget/base_widget.py

@@ -17,8 +17,8 @@ class BaseWidget(anywidget.AnyWidget):
     ready = tl.Bool(False).tag(sync=True)
     logLevel = tl.Unicode("info").tag(sync=True)
     # atoms can be a dictionary or a list of dictionaries
-    atoms = tl.Union([tl.Dict({}), tl.List(tl.Dict({}))]).tag(sync=True)
-    selectedAtomsIndices = tl.List([]).tag(sync=True)
+    atoms = tl.Union([tl.Dict(), tl.List(tl.Dict())]).tag(sync=True)
+    selectedAtomsIndices = tl.List().tag(sync=True)
     boundary = tl.List([[0, 1], [0, 1], [0, 1]]).tag(sync=True)
     modelStyle = tl.Int(0).tag(sync=True)
     # color
@@ -34,44 +34,44 @@ class BaseWidget(anywidget.AnyWidget):
     showBondedAtoms = tl.Bool(False).tag(sync=True)
     showHydrogenBonds = tl.Bool(False).tag(sync=True)
     hideLongBonds = tl.Bool(True).tag(sync=True)
-    atomScales = tl.List([]).tag(sync=True)
-    modelSticks = tl.List([]).tag(sync=True)
-    modelPolyhedras = tl.List([]).tag(sync=True)
+    atomScales = tl.List().tag(sync=True)
+    modelSticks = tl.List().tag(sync=True)
+    modelPolyhedras = tl.List().tag(sync=True)
     volumetricData = tl.Dict({"values": [[[]]]}).tag(sync=True)
     imageData = tl.Unicode("").tag(sync=True)
     vectorField = tl.Dict().tag(sync=True)
     showVectorField = tl.Bool(True).tag(sync=True)
-    guiConfig = tl.Dict({}).tag(sync=True)
+    guiConfig = tl.Dict().tag(sync=True)
     # animation
     currentFrame = tl.Int(0).tag(sync=True)
     # instanced mesh primitives
-    instancedMeshPrimitive = tl.List(tl.Dict({})).tag(sync=True)
+    instancedMeshPrimitive = tl.List(tl.Dict()).tag(sync=True)
     # any mesh
-    anyMesh = tl.List(tl.Dict({})).tag(sync=True)
+    anyMesh = tl.List(tl.Dict()).tag(sync=True)
     # viewer
-    viewerStyle = tl.Dict({}).tag(sync=True)
+    viewerStyle = tl.Dict().tag(sync=True)
     # camera
-    cameraSetting = tl.Dict({}).tag(sync=True)
+    cameraSetting = tl.Dict().tag(sync=True)
     cameraZoom = tl.Float().tag(sync=True)
     cameraPosition = tl.List().tag(sync=True)
     cameraRotation = tl.List().tag(sync=True)
     cameraLookAt = tl.List().tag(sync=True)
     # task
-    js_task = tl.Dict({}).tag(sync=True)
-    python_task = tl.Dict({}).tag(sync=True)
+    js_task = tl.Dict().tag(sync=True)
+    python_task = tl.Dict().tag(sync=True)
     debug = tl.Bool(False).tag(sync=True)
     # species
-    speciesSettings = tl.Dict({}).tag(sync=True)
+    speciesSettings = tl.Dict().tag(sync=True)
     # bond
-    bondSettings = tl.Dict({}).tag(sync=True)
+    bondSettings = tl.Dict().tag(sync=True)
     # isosurface
-    isoSettings = tl.Dict({}).tag(sync=True)
+    isoSettings = tl.Dict().tag(sync=True)
     # volume slice
-    sliceSettings = tl.Dict({}).tag(sync=True)
+    sliceSettings = tl.Dict().tag(sync=True)
     # phonon
-    phonon = tl.Dict({}).tag(sync=True)
+    phonon = tl.Dict().tag(sync=True)
     # highlight
-    highlightSettings = tl.Dict({}).tag(sync=True)
+    highlightSettings = tl.Dict().tag(sync=True)
     #
     showAtomLegend = tl.Bool(False).tag(sync=True)
 

tests/notebooks/tests/notebooks/widgets.ipynb

@@ -231,11 +231,32 @@
     "viewer.avr.model_style = 1\n",
     "viewer"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# set scale and style for each atom\n",
+    "from ase.build import molecule, fcc111\n",
+    "from weas_widget import WeasWidget\n",
+    "mol = molecule(\"C2H6SO\")\n",
+    "slab = fcc111(\"Pt\", size=(2, 2, 3), vacuum=5)\n",
+    "mol.translate(slab[-1].position - mol[0].position + [0, 0, 2])\n",
+    "slab += mol\n",
+    "viewer = WeasWidget()\n",
+    "viewer.from_ase(slab)\n",
+    "viewer.camera.setting = {\"direction\": [0, -1, 0], \"zoom\": 1.0}\n",
+    "viewer.avr.model_style = 1\n",
+    "viewer.avr.atom_scales = [1 if atom.symbol == \"Pt\" else 0.4 for atom in slab]\n",
+    "viewer"
+   ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "aiida",
+   "display_name": "Python 3",
    "language": "python",
    "name": "python3"
   },