Changed cell specialisation calculation

src/auto-evo/simulation/SimulationCache.cs

@@ -42,6 +42,9 @@ public class SimulationCache
     private readonly CompoundDefinition oxytoxy = SimulationParameters.GetCompound(Compound.Oxytoxy);
     private readonly CompoundDefinition mucilage = SimulationParameters.GetCompound(Compound.Mucilage);
 
+    private readonly OrganelleDefinition nucleusDefinition =
+        SimulationParameters.Instance.GetOrganelleType("nucleus");
+
     private readonly WorldGenerationSettings worldSettings;
 
 #if USE_HASHED_SCORE_KEYS
@@ -141,7 +144,8 @@ public EnergyBalanceInfoSimple GetEnergyBalanceForSpecies(MicrobeSpecies species
         var cached = new EnergyBalanceInfoSimple();
 
         // Assume here that the species specialization factor may not be up to date, so recalculate here
-        var specialization = MicrobeInternalCalculations.CalculateSpecializationBonus(species.Organelles, workMemory1);
+        var specialization = MicrobeInternalCalculations.CalculateSpecializationBonus(species.Organelles, workMemory1,
+            nucleusDefinition);
 
         // Auto-evo uses the average values of compound during the course of a simulated day
         ProcessSystem.ComputeEnergyBalanceSimple(species.Organelles, biomeConditions,

src/microbe_stage/MicrobeInternalCalculations.cs

@@ -490,9 +490,11 @@ public static void GiveNearNightInitialCompoundBuff(CompoundBag compoundReceiver
         WorldGenerationSettings worldSettings)
     {
         var energyBalance = new EnergyBalanceInfoSimple();
+        var nucleusDefinition = SimulationParameters.Instance.GetOrganelleType("nucleus");
 
         // Note this assumes this is only used just for single cell types or microbe species!
-        var specialization = CalculateSpecializationBonus(organelles, new Dictionary<OrganelleDefinition, int>());
+        var specialization = CalculateSpecializationBonus(organelles, new Dictionary<OrganelleDefinition, int>(),
+            nucleusDefinition);
 
         var maximumMovementDirection = MaximumSpeedDirection(organelles);
         ProcessSystem.ComputeEnergyBalanceSimple(organelles, biomeConditions, environmentalTolerances, specialization,
@@ -591,7 +593,10 @@ public static (bool CanSurvive, Dictionary<Compound, float> RequiredStorage) Cal
         ref Dictionary<Compound, CompoundBalance>? dayCompoundBalances)
     {
         // Note this assumes this is only used just for single cell types or microbe species!
-        var specialization = CalculateSpecializationBonus(organelles, new Dictionary<OrganelleDefinition, int>());
+        var nucleusDefinition = SimulationParameters.Instance.GetOrganelleType("nucleus");
+
+        var specialization = CalculateSpecializationBonus(organelles, new Dictionary<OrganelleDefinition, int>(),
+            nucleusDefinition);
 
         if (dayCompoundBalances == null)
         {
@@ -834,9 +839,9 @@ public static void GetBindingAndSignalling(IReadOnlyList<OrganelleTemplate> orga
     /// </summary>
     /// <returns>A multiplier starting from 1 and going up as specialization improves</returns>
     public static float CalculateSpecializationBonus(IReadOnlyList<IReadOnlyOrganelleTemplate> organelles,
-        Dictionary<OrganelleDefinition, int> tempWorkMemory)
+        Dictionary<OrganelleDefinition, int> tempWorkMemory, OrganelleDefinition nucleusDefinition)
     {
-        int totalOrganelles = 0;
+        int totalHexCount = 0;
         tempWorkMemory.Clear();
 
         var count = organelles.Count;
@@ -846,33 +851,38 @@ public static float CalculateSpecializationBonus(IReadOnlyList<IReadOnlyOrganell
 
             var definition = organelle.Definition;
 
+            // Don't count the nucleus, because of its omnipresence and large size
+            if (definition == nucleusDefinition)
+            {
+                continue;
+            }
+
+            var hexCount = definition.HexCount;
+
             tempWorkMemory.TryGetValue(definition, out var existingCount);
-            tempWorkMemory[definition] = existingCount + 1;
+            tempWorkMemory[definition] = existingCount + hexCount;
 
-            ++totalOrganelles;
+            totalHexCount += hexCount;
         }
 
-        if (totalOrganelles < 1)
-            return 1;
-
-        if (totalOrganelles < Constants.CELL_SPECIALIZATION_APPLIES_AFTER_SIZE)
+        if (totalHexCount < 1)
             return 1;
 
-        int maxOrganelleCount = 0;
+        int maxHexCount = 0;
 
         foreach (var entry in tempWorkMemory)
         {
-            if (entry.Value > maxOrganelleCount)
+            if (entry.Value > maxHexCount)
             {
-                maxOrganelleCount = entry.Value;
+                maxHexCount = entry.Value;
             }
         }
 
         // The raw bonus is just the ratio of the main organelle type
-        var bonus = (float)maxOrganelleCount / totalOrganelles;
+        var bonus = (float)maxHexCount / totalHexCount;
 
         // Calculate a strength factor that adjusts things
-        var strength = Math.Min((float)totalOrganelles / Constants.CELL_SPECIALIZATION_STRENGTH_FULL_AT, 1);
+        var strength = Math.Min((float)totalHexCount / Constants.CELL_SPECIALIZATION_STRENGTH_FULL_AT, 1);
         strength *= Constants.CELL_SPECIALIZATION_STRENGTH_MULTIPLIER;
 
         // Then return the final result as the bonus being anything above 1

src/microbe_stage/MicrobeSpecies.cs

@@ -248,9 +248,12 @@ public override void OnAttemptedInAutoEvo(bool refreshCache)
 
         cachedFillTimes.Clear();
 
+        var nucleusDefinition =
+            SimulationParameters.Instance.GetOrganelleType("nucleus");
+
         SpecializationBonus =
             MicrobeInternalCalculations.CalculateSpecializationBonus(Organelles,
-                new Dictionary<OrganelleDefinition, int>());
+                new Dictionary<OrganelleDefinition, int>(), nucleusDefinition);
     }
 
     public override bool RepositionToOrigin()

src/microbe_stage/editor/CellEditorComponent.GUI.cs

@@ -478,7 +478,8 @@ private void OnUnlockedOrganellesChanged()
     private void UpdateSpecializationDisplay()
     {
         var specializationBonus =
-            MicrobeInternalCalculations.CalculateSpecializationBonus(editedMicrobeOrganelles, tempMemory3);
+            MicrobeInternalCalculations.CalculateSpecializationBonus(editedMicrobeOrganelles, tempMemory3,
+                nucleusDefinition);
 
         // Calculate the most common organelle to show what we should recommend the player place more
         var temp = tempMemory3;

src/microbe_stage/editor/CellEditorComponent.cs

@@ -45,6 +45,9 @@ public partial class CellEditorComponent :
 
     private readonly List<EditorUserOverride> ignoredEditorWarnings = new();
 
+    private readonly OrganelleDefinition nucleusDefinition =
+        SimulationParameters.Instance.GetOrganelleType("nucleus");
+
 #pragma warning disable CA2213
 
     // Selection menu tab selector buttons
@@ -2142,7 +2145,8 @@ private void CalculateEnergyAndCompoundBalance(IReadOnlyList<OrganelleTemplate>
 
         var maximumMovementDirection = MicrobeInternalCalculations.MaximumSpeedDirection(organelles);
 
-        var specialization = MicrobeInternalCalculations.CalculateSpecializationBonus(organelles, tempMemory3);
+        var specialization = MicrobeInternalCalculations.CalculateSpecializationBonus(organelles, tempMemory3,
+            nucleusDefinition);
 
         var tolerances = CalculateLatestTolerances();
         ProcessSystem.ComputeEnergyBalanceFull(organelles, conditionsData, tolerances, specialization,
@@ -2219,7 +2223,8 @@ private void HandleProcessList(EnergyBalanceInfoFull energyBalance, IBiomeCondit
         float consumptionProductionRatio = energyBalance.TotalConsumption / energyBalance.TotalProduction;
 
         var specialization =
-            MicrobeInternalCalculations.CalculateSpecializationBonus(editedMicrobeOrganelles, tempMemory3);
+            MicrobeInternalCalculations.CalculateSpecializationBonus(editedMicrobeOrganelles, tempMemory3,
+                nucleusDefinition);
 
         var speedModifier = tolerances.ProcessSpeedModifier * specialization;
 

src/microbe_stage/editor/MicrobeEditor.cs

@@ -21,6 +21,9 @@ public partial class MicrobeEditor : EditorBase<EditorAction, MicrobeStage>, IEd
     // loaded
     private readonly MicrobeSpeciesComparer speciesComparer = new();
 
+    private readonly OrganelleDefinition nucleusDefinition =
+        SimulationParameters.Instance.GetOrganelleType("nucleus");
+
 #pragma warning disable CA2213
     [Export]
     private MicrobeEditorReportComponent reportTab = null!;
@@ -631,7 +634,7 @@ private IPlayerDataSource GetPlayerDataSource()
 
         var specialization =
             MicrobeInternalCalculations.CalculateSpecializationBonus(editedSpecies.ModifiableOrganelles.Organelles,
-                tempMemory1);
+                tempMemory1, nucleusDefinition);
 
         ProcessSystem.ComputeEnergyBalanceSimple(editedSpecies.ModifiableOrganelles.Organelles,
             CurrentPatch.Biome, in tolerances, specialization, editedSpecies.MembraneType, Vector3.Zero, false, true,

src/multicellular_stage/CellType.cs

@@ -189,9 +189,11 @@ public bool IsMuscularTissueType()
 
     public void CalculateSpecialization()
     {
+        var nucleusDefinition =
+            SimulationParameters.Instance.GetOrganelleType("nucleus");
         SpecializationBonus =
             MicrobeInternalCalculations.CalculateSpecializationBonus(ModifiableOrganelles,
-                new Dictionary<OrganelleDefinition, int>());
+                new Dictionary<OrganelleDefinition, int>(), nucleusDefinition);
     }
 
     public void SetupWorldEntities(IWorldSimulation worldSimulation)

src/multicellular_stage/editor/CellBodyPlanEditorComponent.GUI.cs

@@ -59,7 +59,7 @@ private void HandleProcessList(EnergyBalanceInfoFull energyBalance, IBiomeCondit
 
             var specialization =
                 MicrobeInternalCalculations.CalculateSpecializationBonus(cellType.Key.ModifiableOrganelles,
-                    tempMemory3);
+                    tempMemory3, nucleusDefinition);
 
             for (int i = 0; i < newProcesses.Count; ++i)
             {
@@ -249,7 +249,8 @@ private void UpdateSpecializationDisplay()
             var type = GetEditedCellDataIfEdited(cells[i].Data!.ModifiableCellType);
 
             var specialization =
-                MicrobeInternalCalculations.CalculateSpecializationBonus(type.ModifiableOrganelles, tempMemory3);
+                MicrobeInternalCalculations.CalculateSpecializationBonus(type.ModifiableOrganelles, tempMemory3,
+                    nucleusDefinition);
 
             // TODO: calculate adjacency specialization values
             // https://github.com/Revolutionary-Games/Thrive/issues/6764

src/multicellular_stage/editor/CellBodyPlanEditorComponent.cs

@@ -36,6 +36,9 @@ public partial class CellBodyPlanEditorComponent :
 
     private readonly Dictionary<CellType, int> cellTypesCount = new();
 
+    private readonly OrganelleDefinition nucleusDefinition =
+        SimulationParameters.Instance.GetOrganelleType("nucleus");
+
     /// <summary>
     ///   Stores cells that end up being disconnected from the colony because of growth order
     /// </summary>
@@ -1264,7 +1267,8 @@ private void UpdateCellTypeTooltipAndWarning(CellTypeTooltip tooltip, CellTypeSe
             MicrobeInternalCalculations.MaximumSpeedDirection(cellType.ModifiableOrganelles);
 
         var specialization =
-            MicrobeInternalCalculations.CalculateSpecializationBonus(cellType.ModifiableOrganelles, tempMemory3);
+            MicrobeInternalCalculations.CalculateSpecializationBonus(cellType.ModifiableOrganelles, tempMemory3,
+                nucleusDefinition);
 
         ProcessSystem.ComputeEnergyBalanceFull(cellType.ModifiableOrganelles, Editor.CurrentPatch.Biome,
             environmentalTolerances, specialization,
@@ -1454,7 +1458,8 @@ private void CalculateEnergyAndCompoundBalance(IReadOnlyList<HexWithData<CellTem
         foreach (var hex in cells)
         {
             var specialization =
-                MicrobeInternalCalculations.CalculateSpecializationBonus(hex.Data!.ModifiableOrganelles, tempMemory3);
+                MicrobeInternalCalculations.CalculateSpecializationBonus(hex.Data!.ModifiableOrganelles, tempMemory3,
+                    nucleusDefinition);
 
             // TODO: adjacency bonuses from body plan (GetAdjacencySpecializationBonus)
 
@@ -1501,7 +1506,7 @@ private Dictionary<Compound, CompoundBalance> CalculateCompoundBalanceWithMethod
         {
             var organelles = GetEditedCellDataIfEdited(cell.Data!.ModifiableCellType).ModifiableOrganelles;
             var specialization =
-                MicrobeInternalCalculations.CalculateSpecializationBonus(organelles, tempMemory3);
+                MicrobeInternalCalculations.CalculateSpecializationBonus(organelles, tempMemory3, nucleusDefinition);
 
             // TODO: efficiency from cell layout positions (GetAdjacencySpecializationBonus)
 

src/multicellular_stage/editor/MulticellularEditor.cs

@@ -760,6 +760,8 @@ private IPlayerDataSource GetPlayerDataSource()
             throw new Exception("Tried to get player unlocks data source without an edited species being set");
         }
 
+        var nucleusDefinition = SimulationParameters.Instance.GetOrganelleType("nucleus");
+
         var energyBalance = new EnergyBalanceInfoSimple();
 
         var tolerances = MicrobeEnvironmentalToleranceCalculations.ResolveToleranceValues(
@@ -772,7 +774,7 @@ private IPlayerDataSource GetPlayerDataSource()
             // TODO: specialization from positions (GetAdjacencySpecializationBonus)
             var specialization =
                 MicrobeInternalCalculations.CalculateSpecializationBonus(cellType.ModifiableOrganelles.Organelles,
-                    tempMemory1);
+                    tempMemory1, nucleusDefinition);
 
             ProcessSystem.ComputeEnergyBalanceSimple(cellType.ModifiableOrganelles.Organelles, CurrentPatch.Biome,
                 in tolerances, specialization, cellType.MembraneType, Vector3.Zero, false, true,