From 7c23377348b0e02c6fb22de3c4f2ddea8df9b8fc Mon Sep 17 00:00:00 2001
From: Cursor Agent <cursoragent@cursor.com>
Date: Sat, 1 Nov 2025 11:25:11 +0000
Subject: [PATCH 1/5] refactor: Improve base Modifier class design

- Convert Modifier class to abstract class
- Make run() method abstract to enforce implementation in subclasses
- All 6 modifier subclasses already override run(), so this is safe
- Improves API clarity and TypeScript type safety

Closes #187
---
 src/modifiers/modifier.ts | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/modifiers/modifier.ts b/src/modifiers/modifier.ts
index 4c0e43bf..474d26be 100644
--- a/src/modifiers/modifier.ts
+++ b/src/modifiers/modifier.ts
@@ -5,7 +5,7 @@ interface ModifierProps {
   active: boolean;
 }
 
-class Modifier {
+abstract class Modifier {
   public name: string;
   public key: string;
   public active: boolean;
@@ -16,10 +16,10 @@ class Modifier {
     this.active = active;
   }
 
-  run = (
+  abstract run(
     input: ModifierInput,
     output: ModifierOutput,
-    everything: boolean = false,
-  ) => {};
+    everything?: boolean
+  ): void;
 }
 export default Modifier;

From b21686c7558f3a4d5b393dc4e4ea88f2d15038f6 Mon Sep 17 00:00:00 2001
From: Cursor Agent <cursoragent@cursor.com>
Date: Sat, 1 Nov 2025 11:39:36 +0000
Subject: [PATCH 2/5] refactor: Update Modifier subclasses to implement
 abstract run() method

- Convert arrow function properties to method declarations in all subclasses
- Add missing 'everything' parameter to SyncBondsModifier and ColorModifier
- Remove semicolons after method declarations for consistency
- All 6 modifier subclasses now properly implement the abstract run() method

Addresses PR review feedback about breaking changes
---
 src/modifiers/colormodifier.ts         | 8 ++++++--
 src/modifiers/syncbondsmodifier.ts     | 8 ++++++--
 src/modifiers/synccomputesmodifier.ts  | 6 +++---
 src/modifiers/syncfixesmodifier.ts     | 6 +++---
 src/modifiers/syncparticlesmodifier.ts | 6 +++---
 src/modifiers/syncvariablesmodifier.ts | 6 +++---
 6 files changed, 24 insertions(+), 16 deletions(-)

diff --git a/src/modifiers/colormodifier.ts b/src/modifiers/colormodifier.ts
index a6ac6be9..1a0854ea 100644
--- a/src/modifiers/colormodifier.ts
+++ b/src/modifiers/colormodifier.ts
@@ -214,13 +214,17 @@ class ColorModifier extends Modifier {
     this.previousColoringMethod = "type";
   };
 
-  run = (input: ModifierInput, output: ModifierOutput) => {
+  run(
+    input: ModifierInput,
+    output: ModifierOutput,
+    everything: boolean = false,
+  ): void {
     if (this.computeName) {
       this.runByProperty(input, output);
     } else {
       this.runByType(input, output);
     }
-  };
+  }
 }
 
 export default ColorModifier;
diff --git a/src/modifiers/syncbondsmodifier.ts b/src/modifiers/syncbondsmodifier.ts
index 16257a2c..f29c3d80 100644
--- a/src/modifiers/syncbondsmodifier.ts
+++ b/src/modifiers/syncbondsmodifier.ts
@@ -12,7 +12,11 @@ class SyncBondsModifier extends Modifier {
     super({ name, active });
   }
 
-  run = (input: ModifierInput, output: ModifierOutput) => {
+  run(
+    input: ModifierInput,
+    output: ModifierOutput,
+    everything: boolean = false,
+  ): void {
     if (!this.active) {
       if (output.bonds) {
         output.bonds.count = 0;
@@ -64,7 +68,7 @@ class SyncBondsModifier extends Modifier {
       newBonds.mesh.count = numBonds;
     }
     newBonds.markNeedsUpdate();
-  };
+  }
 }
 
 export default SyncBondsModifier;
diff --git a/src/modifiers/synccomputesmodifier.ts b/src/modifiers/synccomputesmodifier.ts
index 069df3c9..f40e867e 100644
--- a/src/modifiers/synccomputesmodifier.ts
+++ b/src/modifiers/synccomputesmodifier.ts
@@ -11,11 +11,11 @@ class SyncComputesModifier extends Modifier {
     super({ name, active });
   }
 
-  run = (
+  run(
     input: ModifierInput,
     output: ModifierOutput,
     everything: boolean = false,
-  ) => {
+  ): void {
     if (!this.active || !input.hasSynchronized) {
       return;
     }
@@ -121,7 +121,7 @@ class SyncComputesModifier extends Modifier {
       }
       output.computes[name] = compute;
     }
-  };
+  }
 }
 
 export default SyncComputesModifier;
diff --git a/src/modifiers/syncfixesmodifier.ts b/src/modifiers/syncfixesmodifier.ts
index d1d54716..857993ec 100644
--- a/src/modifiers/syncfixesmodifier.ts
+++ b/src/modifiers/syncfixesmodifier.ts
@@ -11,11 +11,11 @@ class SyncFixesModifier extends Modifier {
     super({ name, active });
   }
 
-  run = (
+  run(
     input: ModifierInput,
     output: ModifierOutput,
     everything: boolean = false,
-  ) => {
+  ): void {
     if (!this.active || !input.hasSynchronized) {
       return;
     }
@@ -116,7 +116,7 @@ class SyncFixesModifier extends Modifier {
       }
       output.fixes[name] = fix;
     }
-  };
+  }
 }
 
 export default SyncFixesModifier;
diff --git a/src/modifiers/syncparticlesmodifier.ts b/src/modifiers/syncparticlesmodifier.ts
index 7a4ad840..e5a92e22 100644
--- a/src/modifiers/syncparticlesmodifier.ts
+++ b/src/modifiers/syncparticlesmodifier.ts
@@ -12,11 +12,11 @@ class SyncParticlesModifier extends Modifier {
     super({ name, active });
   }
 
-  run = (
+  run(
     input: ModifierInput,
     output: ModifierOutput,
     everything: boolean = false,
-  ) => {
+  ): void {
     if (!this.active) {
       if (output.particles) {
         output.particles.count = 0;
@@ -76,7 +76,7 @@ class SyncParticlesModifier extends Modifier {
 
     newParticles.markNeedsUpdate();
     return newParticles;
-  };
+  }
 }
 
 export default SyncParticlesModifier;
diff --git a/src/modifiers/syncvariablesmodifier.ts b/src/modifiers/syncvariablesmodifier.ts
index f84923d6..1773201c 100644
--- a/src/modifiers/syncvariablesmodifier.ts
+++ b/src/modifiers/syncvariablesmodifier.ts
@@ -11,11 +11,11 @@ class SyncVariablesModifier extends Modifier {
     super({ name, active });
   }
 
-  run = (
+  run(
     input: ModifierInput,
     output: ModifierOutput,
     everything: boolean = false,
-  ) => {
+  ): void {
     if (!this.active || !input.hasSynchronized) {
       return;
     }
@@ -118,7 +118,7 @@ class SyncVariablesModifier extends Modifier {
       }
       output.variables[name] = variable;
     }
-  };
+  }
 }
 
 export default SyncVariablesModifier;

From 1bdcb29b452b914ec705917a1f568db88f2a02b0 Mon Sep 17 00:00:00 2001
From: Cursor Agent <cursoragent@cursor.com>
Date: Sat, 1 Nov 2025 11:46:56 +0000
Subject: [PATCH 3/5] fix: Remove return statements to match void return type

- Remove return newParticles from SyncParticlesModifier.run()
- Change return newBonds to return in SyncBondsModifier.run()
- Both methods now correctly return void to match abstract method signature
---
 src/modifiers/syncbondsmodifier.ts     | 2 +-
 src/modifiers/syncparticlesmodifier.ts | 1 -
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/modifiers/syncbondsmodifier.ts b/src/modifiers/syncbondsmodifier.ts
index f29c3d80..28c7bcdb 100644
--- a/src/modifiers/syncbondsmodifier.ts
+++ b/src/modifiers/syncbondsmodifier.ts
@@ -47,7 +47,7 @@ class SyncBondsModifier extends Modifier {
       if (newBonds.mesh) {
         newBonds.mesh.count = numBonds;
       }
-      return newBonds;
+      return;
     }
 
     const bonds1Ptr = input.lammps.getBondsPosition1Pointer() / 4;
diff --git a/src/modifiers/syncparticlesmodifier.ts b/src/modifiers/syncparticlesmodifier.ts
index e5a92e22..fed8a44b 100644
--- a/src/modifiers/syncparticlesmodifier.ts
+++ b/src/modifiers/syncparticlesmodifier.ts
@@ -75,7 +75,6 @@ class SyncParticlesModifier extends Modifier {
     }
 
     newParticles.markNeedsUpdate();
-    return newParticles;
   }
 }
 

From 37194c6ff3e9b818fe4660d179d8798e69f9aaa3 Mon Sep 17 00:00:00 2001
From: Cursor Agent <cursoragent@cursor.com>
Date: Sat, 1 Nov 2025 11:52:35 +0000
Subject: [PATCH 4/5] fix: Pass everything parameter to runByType in
 ColorModifier

- Pass everything parameter from run() to runByType()
- Update runByType to use everything to bypass caching logic
- When everything=true, forces runByType to execute even if previousColoringMethod matches and colorsDirty is false

Addresses PR review feedback about missing parameter propagation
---
 src/modifiers/colormodifier.ts | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/modifiers/colormodifier.ts b/src/modifiers/colormodifier.ts
index 1a0854ea..614b164f 100644
--- a/src/modifiers/colormodifier.ts
+++ b/src/modifiers/colormodifier.ts
@@ -187,7 +187,9 @@ class ColorModifier extends Modifier {
     everything: boolean = false,
   ) => {
     if (
-      (this.previousColoringMethod === "type" && !output.colorsDirty) ||
+      (!everything &&
+        this.previousColoringMethod === "type" &&
+        !output.colorsDirty) ||
       !input.renderState.visualizer
     ) {
       return;
@@ -222,7 +224,7 @@ class ColorModifier extends Modifier {
     if (this.computeName) {
       this.runByProperty(input, output);
     } else {
-      this.runByType(input, output);
+      this.runByType(input, output, everything);
     }
   }
 }

From ed1e00a37a53ba27e4e23a4dd02fbfd8ca6041f2 Mon Sep 17 00:00:00 2001
From: Cursor Agent <cursoragent@cursor.com>
Date: Sat, 1 Nov 2025 11:59:35 +0000
Subject: [PATCH 5/5] fix: Address PR review comments for modifier
 implementations

- Pass everything parameter to runByProperty in ColorModifier for consistency
- Update runByProperty signature to accept everything parameter
- Prefix unused everything parameters with underscore in SyncBondsModifier and SyncParticlesModifier to signal intentional non-use

Addresses medium-priority review feedback
---
 src/modifiers/colormodifier.ts         | 8 ++++++--
 src/modifiers/syncbondsmodifier.ts     | 2 +-
 src/modifiers/syncparticlesmodifier.ts | 2 +-
 3 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/src/modifiers/colormodifier.ts b/src/modifiers/colormodifier.ts
index 614b164f..48224fe6 100644
--- a/src/modifiers/colormodifier.ts
+++ b/src/modifiers/colormodifier.ts
@@ -129,7 +129,11 @@ class ColorModifier extends Modifier {
     this.computeName = undefined;
   }
 
-  runByProperty = (input: ModifierInput, output: ModifierOutput) => {
+  runByProperty = (
+    input: ModifierInput,
+    output: ModifierOutput,
+    everything: boolean = false,
+  ) => {
     if (!input.renderState.visualizer) {
       return;
     }
@@ -222,7 +226,7 @@ class ColorModifier extends Modifier {
     everything: boolean = false,
   ): void {
     if (this.computeName) {
-      this.runByProperty(input, output);
+      this.runByProperty(input, output, everything);
     } else {
       this.runByType(input, output, everything);
     }
diff --git a/src/modifiers/syncbondsmodifier.ts b/src/modifiers/syncbondsmodifier.ts
index 28c7bcdb..f9400dd7 100644
--- a/src/modifiers/syncbondsmodifier.ts
+++ b/src/modifiers/syncbondsmodifier.ts
@@ -15,7 +15,7 @@ class SyncBondsModifier extends Modifier {
   run(
     input: ModifierInput,
     output: ModifierOutput,
-    everything: boolean = false,
+    _everything: boolean = false,
   ): void {
     if (!this.active) {
       if (output.bonds) {
diff --git a/src/modifiers/syncparticlesmodifier.ts b/src/modifiers/syncparticlesmodifier.ts
index fed8a44b..047bf5d6 100644
--- a/src/modifiers/syncparticlesmodifier.ts
+++ b/src/modifiers/syncparticlesmodifier.ts
@@ -15,7 +15,7 @@ class SyncParticlesModifier extends Modifier {
   run(
     input: ModifierInput,
     output: ModifierOutput,
-    everything: boolean = false,
+    _everything: boolean = false,
   ): void {
     if (!this.active) {
       if (output.particles) {