From c78f64279338b7f4c9a9d7ccbee08bd1818e6773 Mon Sep 17 00:00:00 2001
From: jessicasyu <15913767+jessicasyu@users.noreply.github.com>
Date: Tue, 6 Jun 2023 14:41:54 -0400
Subject: [PATCH] Modify junction hamiltonian delta

---
 src/arcade/potts/parameter.potts.xml          |  2 +-
 .../sim/hamiltonian/JunctionHamiltonian.java  | 28 ++++------
 .../hamiltonian/JunctionHamiltonianTest.java  | 51 +++++++++++++++----
 3 files changed, 53 insertions(+), 28 deletions(-)

diff --git a/src/arcade/potts/parameter.potts.xml b/src/arcade/potts/parameter.potts.xml
index a5496b8b..c0d66c6f 100644
--- a/src/arcade/potts/parameter.potts.xml
+++ b/src/arcade/potts/parameter.potts.xml
@@ -24,7 +24,7 @@
     <potts.term term="height" id="LAMBDA_NUCLEUS" value="1" />
     
     <!-- height term parameters -->
-    <potts.term term="junction" id="LAMBDA" value="1" />
+    <potts.term term="junction" id="LAMBDA" value="100" />
     
     <!-- substrate term parameters -->
     <potts.term term="substrate" id="HEIGHT_THRESHOLD" value="9" units="um" conversion="DS^-1" />
diff --git a/src/arcade/potts/sim/hamiltonian/JunctionHamiltonian.java b/src/arcade/potts/sim/hamiltonian/JunctionHamiltonian.java
index ca55b7c9..64a01e4a 100644
--- a/src/arcade/potts/sim/hamiltonian/JunctionHamiltonian.java
+++ b/src/arcade/potts/sim/hamiltonian/JunctionHamiltonian.java
@@ -52,28 +52,22 @@ public void deregister(PottsCell cell) {
     /**
      * {@inheritDoc}
      * <p>
-     * Junction energy is calculated only for the case where the source is media
-     * (id == 0) and the target is not media (id =/= 0).
+     * Junction energy is calculated only for the case where both the source
+     * and the target are not media (id =/= 0).
      */
     @Override
     public double getDelta(int sourceID, int targetID, int x, int y, int z) {
-        if (sourceID == 0 && targetID > 0) {
-            double lambda = configs.get(targetID).getLambda();
-            int neighbors = 0;
-            
-            for (int i = x - 1; i <= x + 1; i++) {
-                for (int j = y - 1; j <= y + 1; j++) {
-                    
-                    if (!(i == x && j == y) && ids[z][i][j] != 0) {
-                        neighbors += 1;
-                    }
-                }
-            }
-            
-            return lambda * neighbors;
+        if (sourceID == 0 || targetID == 0) {
+            return 0;
         }
         
-        return 0;
+        double lambda = configs.get(targetID).getLambda();
+        
+        if (ids[z - 1][x][y] == targetID) {
+            return -lambda;
+        }
+        
+        return lambda;
     }
     
     /**
diff --git a/test/arcade/potts/sim/hamiltonian/JunctionHamiltonianTest.java b/test/arcade/potts/sim/hamiltonian/JunctionHamiltonianTest.java
index 4507f606..a0b414bb 100644
--- a/test/arcade/potts/sim/hamiltonian/JunctionHamiltonianTest.java
+++ b/test/arcade/potts/sim/hamiltonian/JunctionHamiltonianTest.java
@@ -105,21 +105,21 @@ public void deregister_exists_removesConfig() {
     }
     
     @Test
-    public void getDelta_validIDs_calculatesValue() {
+    public void getDelta_validIDsTargetMatch_calculatesValue() {
         int id1 = randomIntBetween(1, 100);
         int id2 = id1 + randomIntBetween(1, 100);
         
         Potts potts = mock(Potts.class);
         potts.ids = new int[][][] {
                 {
-                        { id1, id1, id1, id1 },
-                        { id1, id1, id1, id1 },
-                        { id1, id1, id1, id1 },
+                        { 0, 0,   0, 0 },
+                        { 0, 0, id1, 0 },
+                        { 0, 0,   0, 0 },
                 },
                 {
-                        { id2, id2, 0,   0 },
-                        { id2,   0, 0, id1 },
-                        { id2, id2, 0,   0 },
+                        { 0, 0,   0, 0 },
+                        { 0, 0, id2, 0 },
+                        { 0, 0,   0, 0 },
                 },
         };
         
@@ -131,8 +131,39 @@ public void getDelta_validIDs_calculatesValue() {
         
         jh.configs.put(id1, config);
         
-        double delta = jh.getDelta(0, id1, 1, 2, 1);
-        assertEquals(3 * lambda, delta, EPSILON);
+        double delta = jh.getDelta(id2, id1, 1, 2, 1);
+        assertEquals(-lambda, delta, EPSILON);
+    }
+    
+    @Test
+    public void getDelta_validIDsSourceMatch_calculatesValue() {
+        int id1 = randomIntBetween(1, 100);
+        int id2 = id1 + randomIntBetween(1, 100);
+    
+        Potts potts = mock(Potts.class);
+        potts.ids = new int[][][] {
+                {
+                        { 0, 0,   0, 0 },
+                        { 0, 0, id2, 0 },
+                        { 0, 0,   0, 0 },
+                },
+                {
+                        { 0, 0,   0, 0 },
+                        { 0, 0, id2, 0 },
+                        { 0, 0,   0, 0 },
+                },
+        };
+    
+        JunctionHamiltonianConfig config = mock(JunctionHamiltonianConfig.class);
+        double lambda = randomDoubleBetween(10, 100);
+        doReturn(lambda).when(config).getLambda();
+    
+        JunctionHamiltonian jh = new JunctionHamiltonian(mock(PottsSeries.class), potts);
+    
+        jh.configs.put(id1, config);
+    
+        double delta = jh.getDelta(id2, id1, 1, 2, 1);
+        assertEquals(lambda, delta, EPSILON);
     }
     
     @Test
@@ -148,7 +179,7 @@ public void getDelta_invalidIDs_returnsZeros() {
         double delta2 = jh.getDelta(id1, 0, 0, 0, 0);
         assertEquals(0, delta2, EPSILON);
         
-        double delta3 = jh.getDelta(id1, id2, 0, 0, 0);
+        double delta3 = jh.getDelta(0, id2, 0, 0, 0);
         assertEquals(0, delta3, EPSILON);
     }