Bug fix

platforms/cpu/src/CpuNeighborList.cpp

@@ -42,8 +42,8 @@ public:
             ny = (int) floorf(periodicBoxSize[1]/voxelSizeY+0.5f);
             nz = (int) floorf(periodicBoxSize[2]/voxelSizeZ+0.5f);
             voxelSizeX = periodicBoxSize[0]/nx;
-            voxelSizeY = periodicBoxSize[0]/ny;
-            voxelSizeZ = periodicBoxSize[0]/nz;
+            voxelSizeY = periodicBoxSize[1]/ny;
+            voxelSizeZ = periodicBoxSize[2]/nz;
         }
     }
 

platforms/cpu/tests/TestCpuNeighborList.cpp

@@ -46,12 +46,13 @@ using namespace std;
 void testNeighborList(bool periodic) {
     const int numParticles = 500;
     const float cutoff = 2.0f;
-    const float boxSize = 20.0f;
+    const float boxSize[3] = {20.0f, 15.0f, 22.0f};
     OpenMM_SFMT::SFMT sfmt;
     init_gen_rand(0, sfmt);
     vector<float> positions(4*numParticles);
     for (int i = 0; i < 4*numParticles; i++)
-        positions[i] = boxSize*genrand_real2(sfmt);
+        if (i%4 < 3)
+            positions[i] = boxSize[i%4]*genrand_real2(sfmt);
     vector<set<int> > exclusions(numParticles);
     for (int i = 0; i < numParticles; i++) {
         int num = min(i+1, 10);
@@ -61,8 +62,7 @@ void testNeighborList(bool periodic) {
         }
     }
     CpuNeighborList neighborList;
-    float box[3] = {boxSize, boxSize, boxSize};
-    neighborList.computeNeighborList(numParticles, positions, exclusions, box, periodic, cutoff);
+    neighborList.computeNeighborList(numParticles, positions, exclusions, boxSize, periodic, cutoff);
     
     // Convert the neighbor list to a set for faster lookup.
     
@@ -82,9 +82,9 @@ void testNeighborList(bool periodic) {
             float dy = positions[4*i+1]-positions[4*j+1];
             float dz = positions[4*i+2]-positions[4*j+2];
             if (periodic) {
-                dx -= floor(dx/boxSize+0.5f)*boxSize;
-                dy -= floor(dy/boxSize+0.5f)*boxSize;
-                dz -= floor(dz/boxSize+0.5f)*boxSize;
+                dx -= floor(dx/boxSize[0]+0.5f)*boxSize[0];
+                dy -= floor(dy/boxSize[1]+0.5f)*boxSize[1];
+                dz -= floor(dz/boxSize[2]+0.5f)*boxSize[2];
             }
             if (dx*dx + dy*dy + dz*dz > cutoff*cutoff)
                 shouldInclude = false;

platforms/reference/src/SimTKReference/ReferenceNeighborList.cpp

@@ -101,8 +101,8 @@ public:
             ny = (int) floor(periodicBoxSize[1]/voxelSizeY+0.5);
             nz = (int) floor(periodicBoxSize[2]/voxelSizeZ+0.5);
             voxelSizeX = periodicBoxSize[0]/nx;
-            voxelSizeY = periodicBoxSize[0]/ny;
-            voxelSizeZ = periodicBoxSize[0]/nz;
+            voxelSizeY = periodicBoxSize[1]/ny;
+            voxelSizeZ = periodicBoxSize[2]/nz;
         }
     }
 

platforms/reference/tests/TestReferenceNeighborList.cpp

@@ -86,7 +86,7 @@ void verifyNeighborList(NeighborList& list, int numParticles, vector<RealVec>& p
         for (int j = i+1; j < numParticles; j++)
             if (distance2(positions[i], positions[j], periodicBoxSize) <= cutoff*cutoff)
                 count++;
-    ASSERT(count == list.size());
+    ASSERT_EQUAL(count, list.size());
 }
 
 void testPeriodic() {
@@ -112,16 +112,15 @@ void testPeriodic() {
 
 int main() 
 {
-try {
-    testNeighborList();
-    testPeriodic();
-    
-    cout << "Test Passed" << endl;
+    try {
+        testNeighborList();
+        testPeriodic();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
     return 0;
 }
-catch (...) {
-    cerr << "*** ERROR: Test Failed ***" << endl;
-    return 1;
-}
-}