Fixed error building neighbor list with triclinic boxes

platforms/cuda/src/CudaNonbondedUtilities.cpp

@@ -513,6 +513,8 @@ void CudaNonbondedUtilities::createKernelsForGroups(int groups) {
         defines["NUM_TILES_WITH_EXCLUSIONS"] = context.intToString(exclusionTiles->getSize());
         if (usePeriodic)
             defines["USE_PERIODIC"] = "1";
+        if (context.getBoxIsTriclinic())
+            defines["TRICLINIC"] = "1";
         defines["MAX_EXCLUSIONS"] = context.intToString(maxExclusions);
         defines["MAX_BITS_FOR_PAIRS"] = (canUsePairList ? "2" : "0");
         CUmodule interactingBlocksProgram = context.createModule(CudaKernelSources::vectorOps+CudaKernelSources::findInteractingBlocks, defines);

platforms/cuda/src/kernels/findInteractingBlocks.cu

@@ -255,6 +255,13 @@ extern "C" __global__ void findBlocksWithInteractions(real4 periodicBoxSize, rea
                 blockDelta.y = max(0.0f, fabs(blockDelta.y)-blockSizeX.y-blockSizeY.y);
                 blockDelta.z = max(0.0f, fabs(blockDelta.z)-blockSizeX.z-blockSizeY.z);
                 includeBlock2 &= (blockDelta.x*blockDelta.x+blockDelta.y*blockDelta.y+blockDelta.z*blockDelta.z < PADDED_CUTOFF_SQUARED);
+#ifdef TRICLINIC
+                // The calculation to find the nearest periodic copy is only guaranteed to work if the nearest copy is less than half a box width away.
+                // If there's any possibility we might have missed it, do a detailed check.
+
+                if (periodicBoxSize.z/2-blockSizeX.z-blockSizeY.z < PADDED_CUTOFF || periodicBoxSize.y/2-blockSizeX.y-blockSizeY.y < PADDED_CUTOFF)
+                    includeBlock2 = true;
+#endif
                 if (includeBlock2) {
                     unsigned short y = (unsigned short) sortedBlocks[block2].y;
                     for (int k = 0; k < numExclusions; k++)

platforms/opencl/src/OpenCLNonbondedUtilities.cpp

@@ -511,6 +511,8 @@ void OpenCLNonbondedUtilities::createKernelsForGroups(int groups) {
         defines["SIMD_WIDTH"] = context.intToString(context.getSIMDWidth());
         if (usePeriodic)
             defines["USE_PERIODIC"] = "1";
+        if (context.getBoxIsTriclinic())
+            defines["TRICLINIC"] = "1";
         defines["MAX_EXCLUSIONS"] = context.intToString(maxExclusions);
         defines["BUFFER_GROUPS"] = (deviceIsCpu ? "4" : "2");
         string file = (deviceIsCpu ? OpenCLKernelSources::findInteractingBlocks_cpu : OpenCLKernelSources::findInteractingBlocks);

platforms/opencl/src/kernels/findInteractingBlocks.cl

@@ -105,7 +105,7 @@ __kernel void findBlocksWithInteractions(real4 periodicBoxSize, real4 invPeriodi
     __local volatile int* tileStartIndex = workgroupTileIndex+(warpStart/32);
 
     // Loop over blocks.
-    
+
     for (int block1 = startBlockIndex+warpIndex; block1 < startBlockIndex+numBlocks; block1 += totalWarps) {
         // Load data for this block.  Note that all threads in a warp are processing the same block.
         
@@ -158,6 +158,13 @@ __kernel void findBlocksWithInteractions(real4 periodicBoxSize, real4 invPeriodi
                 blockDelta.y = max((real) 0, fabs(blockDelta.y)-blockSizeX.y-blockSizeY.y);
                 blockDelta.z = max((real) 0, fabs(blockDelta.z)-blockSizeX.z-blockSizeY.z);
                 includeBlock2 &= (blockDelta.x*blockDelta.x+blockDelta.y*blockDelta.y+blockDelta.z*blockDelta.z < PADDED_CUTOFF_SQUARED);
+#ifdef TRICLINIC
+                // The calculation to find the nearest periodic copy is only guaranteed to work if the nearest copy is less than half a box width away.
+                // If there's any possibility we might have missed it, do a detailed check.
+
+                if (periodicBoxSize.z/2-blockSizeX.z-blockSizeY.z < PADDED_CUTOFF || periodicBoxSize.y/2-blockSizeX.y-blockSizeY.y < PADDED_CUTOFF)
+                    includeBlock2 = true;
+#endif
                 if (includeBlock2) {
                     unsigned short y = (unsigned short) sortedBlocks[block2].y;
                     for (int k = 0; k < numExclusions; k++)