From 469542393116ebb0bfe5cb7fef95a7aba414efc8 Mon Sep 17 00:00:00 2001
From: Mike Lynch <m.lynch@sydney.edu.au>
Date: Sun, 9 Nov 2025 11:20:16 +1100
Subject: [PATCH] Weirdness - the glitchiness is coming and going depending on
 whether the clipping plane is enabled, or the cylinders added?

---
 gui.js         |  6 +++---
 polytopes.js   |  4 ++--
 taperedLink.js | 40 +++++++++++++++++++++++++++++++---------
 3 files changed, 36 insertions(+), 14 deletions(-)

diff --git a/gui.js b/gui.js
index 5c0d57e..c7fc05b 100644
--- a/gui.js
+++ b/gui.js
@@ -2,12 +2,12 @@ import { GUI } from 'lil-gui';
 
 
 const DEFAULTS = {
-	nodesize: 4,
+	nodesize: 1,
 	nodeopacity: 1,
 	linksize: 1.0,
-	linkopacity: 0.75,
+	linkopacity: 1,
 	link2opacity: 0.75,
-	shape: 'linky',
+	shape: '5-cell',
 	option: 'none',
 	visibility: 5,
 	inscribed: false,
diff --git a/polytopes.js b/polytopes.js
index fe69529..d39a834 100644
--- a/polytopes.js
+++ b/polytopes.js
@@ -865,7 +865,7 @@ export const icosahedron = () => {
 export const build_all = () => {
 	return [
 	        linkTest(),
-/*		tetrahedron(),
+		tetrahedron(),
 		octahedron(),
 		cube(),
 		icosahedron(),
@@ -879,7 +879,7 @@ export const build_all = () => {
 		cell600_layered(),
 	 	cell120_inscribed(),
 	 	cell120_layered()
-	*/ 	];
+	 	];
 }
 
 export const radii = (shape) => {
diff --git a/taperedLink.js b/taperedLink.js
index 24cb729..0d6a6f3 100644
--- a/taperedLink.js
+++ b/taperedLink.js
@@ -6,16 +6,28 @@ class TaperedLink extends THREE.Group {
 
   constructor(baseMaterial, n1, n2, r1, r2) {
     super();
-    const geometry = new THREE.ConeGeometry( 0.75, 1, 32, true );
+    const cone = new THREE.ConeGeometry( 0.75, 1, 32, true );
     const cplane = new THREE.Plane(new THREE.Vector3(0, -1, 0), 0.5);
     const material = baseMaterial.clone();
-    material.clippingPlanes = [ cplane ];
-    this.cone = new THREE.Mesh( geometry, material );
+    //material.clippingPlanes = [ cplane ];
+    this.cone = new THREE.Mesh( cone, material );
     this.add( this.cone );
+    const cylinder = new THREE.CylinderGeometry(1, 1, 1, 16, 1, true);
+    const cyl_material = baseMaterial.clone();
+    cyl_material.color = new THREE.Color(0xff0000); 
+    this.cylinder = new THREE.Mesh(cylinder, cyl_material);
+    this.add( this.cylinder );
     this.update(n1, n2, r1, r2);
-  }  
+   } 
 
-  update(n1, n2, r1, r2) {
+// mystery - commenting out the cylinder stuff makes the glitchiness return!
+
+   update(n1, n2, r1, r2) {
+       this.update_cone(n1, n2, r1, r2);
+       this.update_cylinder(n1, n2, r1, r2);
+   }
+
+  update_cone(n1, n2, r1, r2) {
     const kraw = r1 - r2;
     let k = ( kraw == 0 ) ? 0.001 : kraw;
     let nbase = n1.v3;
@@ -54,11 +66,21 @@ class TaperedLink extends THREE.Group {
     clipnorm.sub(nbase);
     clipnorm.negate();
     clipnorm.normalize();
-    this.cone.material.clippingPlanes[0].setFromNormalAndCoplanarPoint(
-      clipnorm, napex
-      );
+    //this.cone.material.clippingPlanes[0].setFromNormalAndCoplanarPoint(
+    //  clipnorm, napex
+    //  );
   }
 
+    update_cylinder(n1, n2, r1, r2) {
+        const length = n1.v3.distanceTo(n2.v3);
+        const centre = new THREE.Vector3();
+        centre.lerpVectors(n1.v3, n2.v3, 0.5);
+        const link_mean = (r1 + r2) * 0.5;		
+        this.cylinder.scale.copy(new THREE.Vector3(link_mean, link_mean, length));
+        this.cylinder.position.copy(centre);
+        this.lookAt(n2.v3);
+        this.cylinder.rotation.x = Math.PI / 2.0;
+    	
+    }
 }
-
 export { TaperedLink };