update 3dmol; packed cell bit looser; bond radii +5%

Author: eimrek

package-lock.json

@@ -14,7 +14,7 @@
     "preview": "vite preview"
   },
   "dependencies": {
-    "3dmol": "^2.1.0",
+    "3dmol": "^2.3.0",
     "mathjs": "^12.4.1"
   },
   "peerDependencies": {

package.json

@@ -15,6 +15,7 @@ async function fetchCif3D() {
   // uuid = "a490b0ff-012a-44c8-a48a-f734dc634b3c"; // EuI4La mc3d-34858/pbe
   // uuid = "74046bff-82f1-4ced-b33e-54c09db90b78"; // "bizarre" graphite mc3d-19759/pbe
   // uuid = "f5e7395f-ecad-4227-9789-21e7e4d21124"; // Al2H4Li2O14Si4 (water molecule) mc3d-12502/pbe
+  // uuid = "ccf74efe-af52-475a-abd7-d363aa2ce63e"; // mc3d-10008/pbe
 
   const responseAiiDACif = await fetch(
     `${aiidaRestEndpoint}/nodes/${uuid}/download?download_format=cif&download=false`,

src/App.jsx

@@ -19,7 +19,7 @@ function setCustomBondLengths() {
   }
   // override the default bond lengths with covalentRadii
   Object.keys(covalentRadii).forEach((elem) => {
-    setCustomBondLength(elem, covalentRadii[elem]);
+    setCustomBondLength(elem, 1.05 * covalentRadii[elem]);
   });
 }
 
@@ -101,6 +101,10 @@ class Visualizer3dmol extends React.Component {
 
       // Build the supercell
 
+      // distance in fractional coordinates to the edge to be
+      // considered "on edge" for packed cell option
+      let edgeDelta = 0.05;
+
       let sc = this.props.viewerParams.supercell;
       for (let i = -1; i < sc[0] + 1; i++) {
         for (let j = -1; j < sc[1] + 1; j++) {
@@ -125,9 +129,9 @@ class Visualizer3dmol extends React.Component {
 
                   // prettier-ignore
                   if (
-                    frac.x > -0.0001 && frac.x < sc[0] + 0.0001 &&
-                    frac.y > -0.0001 && frac.y < sc[1] + 0.0001 &&
-                    frac.z > -0.0001 && frac.z < sc[2] + 0.0001
+                    frac.x > -edgeDelta && frac.x < sc[0] + edgeDelta &&
+                    frac.y > -edgeDelta && frac.y < sc[1] + edgeDelta &&
+                    frac.z > -edgeDelta && frac.z < sc[2] + edgeDelta
                   ) {
                     final_atoms.push({
                       elem: atom.elem,