Fix velocity not updating

Cluster.cs

@@ -202,9 +202,6 @@ public class Cluster : Nucleus {
             name = this.name,
             clusterPrefab = this.clusterPrefab,
         };
-        // This cloned the prefab with the clusternuclei,
-        // but did not clone the receivers outside the cluster
-        RestoreExternalReceivers(clone, this.clusterPrefab, parent);
 
         return clone;
     }
@@ -219,8 +216,7 @@ public class Cluster : Nucleus {
             if (sourceNucleus is not Neuron sourceNeuron)
                 continue;
 
-            Nucleus clonedNucleus = clonedCluster.clusterNuclei[nucleusIx];
+            if (clonedCluster.clusterNuclei[nucleusIx] is not Neuron clonedNeuron)
-            if (clonedNucleus is not Neuron clonedNeuron)
                 continue;
 
             // copy the receivers (and thus synapses) from the source to the clone
@@ -242,46 +238,10 @@ public class Cluster : Nucleus {
                 }
 
                 clonedNeuron.AddReceiver(clonedReceiver, weight);
+                // Debug.Log($"external: {clonedReceiver.name} receives from {clonedNeuron.name} {clonedNeuron.GetHashCode()}");
             }
         }
     }
-    protected void RestoreExternalReceivers(Cluster clone, ClusterPrefab prefabParent, Cluster clonedParent) {
-        // Loop over all nuclei of this (the prefab of the clone?)
-        for (int nucleusIx = 0; nucleusIx < this.clusterNuclei.Count; nucleusIx++) {
-            Nucleus prefabNucleus = this.clusterNuclei[nucleusIx];
-            if (prefabNucleus is not Neuron prefabNeuron)
-                continue;
-
-            Nucleus clonedNucleus = clone.clusterNuclei[nucleusIx];
-            if (clonedNucleus == null || clonedNucleus is not Neuron clonedNeuron)
-                continue;
-
-            // Copy the receivers, which will also create the synapses
-            foreach (Nucleus receiver in prefabNeuron.receivers) {
-                int ix = GetNucleusIndex(prefabParent.nuclei, receiver);
-                if (ix < 0 || ix >= clonedParent.clusterNuclei.Count)
-                    continue;
-
-                //if (clone.clusterNuclei[ix] is not Nucleus clonedReceiver)
-                if (clonedParent.clusterNuclei[ix] is not Nucleus clonedReceiver)
-                    continue;
-
-                // Find the synapse for the weight
-                float weight = 1;
-                foreach (Synapse synapse in receiver.synapses) {
-                    // Find the weight for this synapse
-                    if (synapse.nucleus == prefabNucleus) {
-                        weight = synapse.weight;
-                        break;
-                    }
-                }
-
-                clonedNeuron.AddReceiver(clonedReceiver, weight);
-            }
-        }
-
-
-    }
 
     protected int GetNucleusIndex(Nucleus[] nuclei, Nucleus nucleus) {
         for (int i = 0; i < nuclei.Length; i++) {
@@ -505,21 +465,14 @@ public class Cluster : Nucleus {
         foreach (Nucleus nucleus in computeOrder) {
             nucleus.UpdateStateIsolated();
             if (startNucleus.trace)
-                Debug.Log($"   {nucleus.name} = {nucleus.outputValue}");
+                Debug.Log($"   {nucleus.name}[{nucleus.GetHashCode()}] = {nucleus.outputValue}");
         }
 
         this.outputValue = this.defaultOutput.outputValue;
         this.stale = 0;
 
-        if (this.parent != null) {
+        // continue in parent
-            // continue in parent
+        this.parent?.UpdateFromNucleus(this);
-            this.parent.UpdateFromNucleus(this);
-            // continue in parent with the receivers of the last nucleus in the compute order
-            // if (computeOrder.Last() is Neuron lastNeuron) {
-            //     foreach (Nucleus receiver in lastNeuron.receivers)
-            //         this.parent?.UpdateFromNucleus(this);
-            // }
-        }
 
         UpdateNuclei();
     }

ClusterReceptor.cs

@@ -113,15 +113,19 @@ public class ClusterReceptor : Cluster, IReceptor {
     }
 
     public override void UpdateStateIsolated() {
-        float3 sum = this.bias;
+        // Clusters don't do anything,
+        // The nuclei in them do the work
+        // and should be called directly, not from the cluster
+        
+        // float3 sum = this.bias;
 
-        foreach (Nucleus nucleus in this.sortedNuclei)
+        // foreach (Nucleus nucleus in this.sortedNuclei)
-            nucleus.UpdateStateIsolated();
+        //     nucleus.UpdateStateIsolated();
 
-        this.outputValue = this.defaultOutput.outputValue;
+        // this.outputValue = this.defaultOutput.outputValue;
-        this.stale = 0;
+        // this.stale = 0;
 
-        UpdateNuclei();
+        // UpdateNuclei();
     }
 
     public override void UpdateNuclei() {
@@ -143,6 +147,8 @@ public class ClusterReceptor : Cluster, IReceptor {
     private Dictionary<int, ClusterReceptor> thingReceivers = new();
 
     public virtual void ProcessStimulus(Neuron input, Vector3 inputValue, int thingId = 0, string thingName = null) {
+        CleanupReceivers();
+
         inputValue = input.Activator(inputValue);
 
         if (!thingReceivers.TryGetValue(thingId, out ClusterReceptor selectedReceiver))
@@ -208,4 +214,24 @@ public class ClusterReceptor : Cluster, IReceptor {
         }
         return selectedReceiver;
     }
+
+    
+    private void CleanupReceivers() {
+        // Remove a thing-receiver connection when the nucleus is inactive
+        List<int> receiversToRemove = new();
+        foreach (KeyValuePair<int, ClusterReceptor> item in thingReceivers) {
+            if (item.Value != null && item.Value.isSleeping)
+                receiversToRemove.Add(item.Key);            
+        }
+        foreach (int thingId in receiversToRemove) {
+            Nucleus selectedReceiver = thingReceivers[thingId];
+
+            thingReceivers.Remove(thingId);
+
+            int colonPos = selectedReceiver.name.IndexOf(":");
+            if (colonPos > 0)
+                selectedReceiver.name = selectedReceiver.name[..colonPos];
+
+        }
+    }
 }

Editor/ClusterInspector.cs

@@ -507,7 +507,7 @@ public class ClusterInspector : Editor {
             // Draw Cluster ring
             if (nucleus is Cluster) {
                 Handles.color = Color.white;
-                Handles.DrawWireDisc(position, Vector3.forward, size + 10);
+                Handles.DrawWireDisc(position, Vector3.forward, size + 5);
             }
 
             // Tooltip