Merge branch 'upstream' into fork

platforms/cuda/src/CudaNonbondedUtilities.cpp

@@ -254,7 +254,7 @@ void CudaNonbondedUtilities::initialize(const System& system) {
             maxTiles = numTiles;
         if (maxTiles < 1)
             maxTiles = 1;
-        interactingTiles = CudaArray::create<ushort2>(context, maxTiles, "interactingTiles");
+        interactingTiles = CudaArray::create<int>(context, maxTiles, "interactingTiles");
         interactingAtoms = CudaArray::create<int>(context, CudaContext::TileSize*maxTiles, "interactingAtoms");
         interactionCount = CudaArray::create<unsigned int>(context, 1, "interactionCount");
         int elementSize = (context.getUseDoublePrecision() ? sizeof(double) : sizeof(float));
@@ -384,7 +384,7 @@ void CudaNonbondedUtilities::updateNeighborListSize() {
     delete interactingAtoms;
     interactingTiles = NULL; // Avoid an error in the destructor if the following allocation fails
     interactingAtoms = NULL;
-    interactingTiles = CudaArray::create<ushort2>(context, maxTiles, "interactingTiles");
+    interactingTiles = CudaArray::create<int>(context, maxTiles, "interactingTiles");
     interactingAtoms = CudaArray::create<int>(context, CudaContext::TileSize*maxTiles, "interactingAtoms");
     if (forceArgs.size() > 0)
         forceArgs[7] = &interactingTiles->getDevicePointer();

platforms/cuda/src/kernels/customGBEnergyN2.cu

@@ -16,7 +16,7 @@ typedef struct {
 extern "C" __global__ void computeN2Energy(unsigned long long* __restrict__ forceBuffers, real* __restrict__ energyBuffer,
         const real4* __restrict__ posq, const unsigned int* __restrict__ exclusions, const ushort2* __restrict__ exclusionTiles,
 #ifdef USE_CUTOFF
-        const ushort2* __restrict__ tiles, const unsigned int* __restrict__ interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize, 
+        const int* __restrict__ tiles, const unsigned int* __restrict__ interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize, 
         unsigned int maxTiles, const real4* __restrict__ blockCenter, const real4* __restrict__ blockSize, const unsigned int* __restrict__ interactingAtoms
 #else
         unsigned int numTiles
@@ -194,8 +194,7 @@ extern "C" __global__ void computeN2Energy(unsigned long long* __restrict__ forc
         bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
         if (numTiles <= maxTiles) {
-            ushort2 tileIndices = tiles[pos];
-            x = tileIndices.x;
+            x = tiles[pos];
             real4 blockSizeX = blockSize[x];
             singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
                                   0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&

platforms/cuda/src/kernels/customGBValueN2.cu

@@ -13,7 +13,7 @@ typedef struct {
 extern "C" __global__ void computeN2Value(const real4* __restrict__ posq, const unsigned int* __restrict__ exclusions,
         const ushort2* __restrict__ exclusionTiles, unsigned long long* __restrict__ global_value,
 #ifdef USE_CUTOFF
-        const ushort2* __restrict__ tiles, const unsigned int* __restrict__ interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize, 
+        const int* __restrict__ tiles, const unsigned int* __restrict__ interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize, 
         unsigned int maxTiles, const real4* __restrict__ blockCenter, const real4* __restrict__ blockSize, const unsigned int* __restrict__ interactingAtoms
 #else
         unsigned int numTiles
@@ -170,8 +170,7 @@ extern "C" __global__ void computeN2Value(const real4* __restrict__ posq, const
         bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
         if (numTiles <= maxTiles) {
-            ushort2 tileIndices = tiles[pos];
-            x = tileIndices.x;
+            x = tiles[pos];
             real4 blockSizeX = blockSize[x];
             singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
                                   0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&

platforms/cuda/src/kernels/findInteractingBlocks.cu

@@ -122,8 +122,8 @@ __device__ void prefixSum(short* sum, ushort2* temp) {
  * This is called by findBlocksWithInteractions(). It compacts the list of blocks, identifies interactions
  * in them, and writes the result to global memory.
  */
-__device__ void storeInteractionData(unsigned short x, unsigned short* buffer, short* sum, ushort2* temp, int* atoms, int& numAtoms,
-            int& baseIndex, unsigned int* interactionCount, ushort2* interactingTiles, unsigned int* interactingAtoms, real4 periodicBoxSize,
+__device__ void storeInteractionData(int x, unsigned short* buffer, short* sum, ushort2* temp, int* atoms, int& numAtoms,
+            int& baseIndex, unsigned int* interactionCount, int* interactingTiles, unsigned int* interactingAtoms, real4 periodicBoxSize,
             real4 invPeriodicBoxSize, const real4* posq, real3* posBuffer, real4 blockCenterX, real4 blockSizeX, unsigned int maxTiles, bool finish) {
     const bool singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= PADDED_CUTOFF &&
                                      0.5f*periodicBoxSize.y-blockSizeX.y >= PADDED_CUTOFF &&
@@ -223,7 +223,7 @@ __device__ void storeInteractionData(unsigned short x, unsigned short* buffer, s
                 numAtoms = atomsToStore-tilesToStore*TILE_SIZE;
             if (baseIndex+tilesToStore <= maxTiles) {
                 if (threadIdx.x < tilesToStore)
-                    interactingTiles[baseIndex+threadIdx.x] = make_ushort2(x, singlePeriodicCopy);
+                    interactingTiles[baseIndex+threadIdx.x] = x;
                 for (int i = threadIdx.x; i < tilesToStore*TILE_SIZE; i += blockDim.x)
                     interactingAtoms[baseIndex*TILE_SIZE+i] = (i < atomsToStore ? atoms[i] : NUM_ATOMS);
             }
@@ -247,7 +247,7 @@ __device__ void storeInteractionData(unsigned short x, unsigned short* buffer, s
         __syncthreads();
         if (baseIndex < maxTiles) {
             if (threadIdx.x == 0)
-                interactingTiles[baseIndex] = make_ushort2(x, singlePeriodicCopy);
+                interactingTiles[baseIndex] = x;
             if (threadIdx.x < TILE_SIZE)
                 interactingAtoms[baseIndex*TILE_SIZE+threadIdx.x] = (threadIdx.x < numAtoms ? atoms[threadIdx.x] : NUM_ATOMS);
         }
@@ -290,7 +290,7 @@ __device__ void storeInteractionData(unsigned short x, unsigned short* buffer, s
  * [in] blockCenter            - the center of each bounding box
  * [in] blockBoundingBox       - bounding box of each atom block
  * [out] interactionCount      - total number of tiles that have interactions
- * [out] interactingTiles      - set of tiles that have interactions
+ * [out] interactingTiles      - set of blocks that have interactions
  * [out] interactingAtoms      - a list of atoms that interact with each atom block
  * [in] posq                   - x,y,z coordinates of each atom and charge q
  * [in] maxTiles               - maximum number of tiles to process, used for multi-GPUs
@@ -313,7 +313,7 @@ __device__ void storeInteractionData(unsigned short x, unsigned short* buffer, s
  *
  */
 extern "C" __global__ void findBlocksWithInteractions(real4 periodicBoxSize, real4 invPeriodicBoxSize, unsigned int* __restrict__ interactionCount,
-        ushort2* __restrict__ interactingTiles, unsigned int* __restrict__ interactingAtoms, const real4* __restrict__ posq, unsigned int maxTiles, unsigned int startBlockIndex,
+        int* __restrict__ interactingTiles, unsigned int* __restrict__ interactingAtoms, const real4* __restrict__ posq, unsigned int maxTiles, unsigned int startBlockIndex,
         unsigned int numBlocks, real2* __restrict__ sortedBlocks, const real4* __restrict__ sortedBlockCenter, const real4* __restrict__ sortedBlockBoundingBox,
         const unsigned int* __restrict__ exclusionIndices, const unsigned int* __restrict__ exclusionRowIndices, real4* __restrict__ oldPositions,
         const int* __restrict__ rebuildNeighborList) {
@@ -343,7 +343,7 @@ extern "C" __global__ void findBlocksWithInteractions(real4 periodicBoxSize, rea
         if (threadIdx.x == blockDim.x-1)
             numAtoms = 0;
         real2 sortedKey = sortedBlocks[i];
-        unsigned short x = (unsigned short) sortedKey.y;
+        int x = (int) sortedKey.y;
         real4 blockCenterX = sortedBlockCenter[i];
         real4 blockSizeX = sortedBlockBoundingBox[i];
 

platforms/cuda/src/kernels/gbsaObc1.cu

@@ -69,7 +69,7 @@ typedef struct {
  */
 extern "C" __global__ void computeBornSum(unsigned long long* __restrict__ global_bornSum, const real4* __restrict__ posq, const float2* __restrict__ global_params,
 #ifdef USE_CUTOFF
-        const ushort2* __restrict__ tiles, const unsigned int* __restrict__ interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize, 
+        const int* __restrict__ tiles, const unsigned int* __restrict__ interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize, 
         unsigned int maxTiles, const real4* __restrict__ blockCenter, const real4* __restrict__ blockSize, const unsigned int* __restrict__ interactingAtoms,
 #else
         unsigned int numTiles,
@@ -230,8 +230,7 @@ extern "C" __global__ void computeBornSum(unsigned long long* __restrict__ globa
         bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
         if (numTiles <= maxTiles) {
-            ushort2 tileIndices = tiles[pos];
-            x = tileIndices.x;
+            x = tiles[pos];
             real4 blockSizeX = blockSize[x];
             singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
                                   0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&
@@ -415,7 +414,7 @@ typedef struct {
 extern "C" __global__ void computeGBSAForce1(unsigned long long* __restrict__ forceBuffers, unsigned long long* __restrict__ global_bornForce,
         real* __restrict__ energyBuffer, const real4* __restrict__ posq, const real* __restrict__ global_bornRadii,
 #ifdef USE_CUTOFF
-        const ushort2* __restrict__ tiles, const unsigned int* __restrict__ interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize, 
+        const int* __restrict__ tiles, const unsigned int* __restrict__ interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize, 
         unsigned int maxTiles, const real4* __restrict__ blockCenter, const real4* __restrict__ blockSize, const unsigned int* __restrict__ interactingAtoms,
 #else
         unsigned int numTiles,
@@ -586,8 +585,7 @@ extern "C" __global__ void computeGBSAForce1(unsigned long long* __restrict__ fo
         bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
         if (numTiles <= maxTiles) {
-            ushort2 tileIndices = tiles[pos];
-            x = tileIndices.x;
+            x = tiles[pos];
             real4 blockSizeX = blockSize[x];
             singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
                                   0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&

platforms/cuda/src/kernels/nonbonded.cu

@@ -84,8 +84,7 @@ static __inline__ __device__ long long real_shfl(long long var, int srcLane) {
  * [in]exclusionTiles   - x,y denotes the indices of tiles that have an exclusion
  * [in]startTileIndex   - index into first tile to be processed
  * [in]numTileIndices   - number of tiles this context is responsible for processing
- * [in]ushort2 tiles    - x component lists the tiles that interact with each tile
- *                      - y component not used currently
+ * [in]int tiles        - the atom block for each tile
  * [in]interactionCount - total number of tiles that have an interaction
  * [in]maxTiles         - stores the size of the neighbourlist in case it needs 
  *                      - to be expanded
@@ -104,7 +103,7 @@ extern "C" __global__ void computeNonbonded(
         unsigned long long* __restrict__ forceBuffers, real* __restrict__ energyBuffer, const real4* __restrict__ posq, const tileflags* __restrict__ exclusions,
         const ushort2* __restrict__ exclusionTiles, unsigned int startTileIndex, unsigned int numTileIndices
 #ifdef USE_CUTOFF
-        , const ushort2* __restrict__ tiles, const unsigned int* __restrict__ interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize, 
+        , const int* __restrict__ tiles, const unsigned int* __restrict__ interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize, 
         unsigned int maxTiles, const real4* __restrict__ blockCenter, const real4* __restrict__ blockSize, const unsigned int* __restrict__ interactingAtoms
 #endif
         PARAMETER_ARGUMENTS) {
@@ -338,8 +337,7 @@ extern "C" __global__ void computeNonbonded(
         bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
         if (numTiles <= maxTiles) {
-            ushort2 tileIndices = tiles[pos];
-            x = tileIndices.x;
+            x = tiles[pos];
             real4 blockSizeX = blockSize[x];
             singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
                                   0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&

platforms/opencl/src/OpenCLNonbondedUtilities.cpp

@@ -272,7 +272,7 @@ void OpenCLNonbondedUtilities::initialize(const System& system) {
         if (maxTiles < 1)
             maxTiles = 1;
         int numAtoms = context.getNumAtoms();
-        interactingTiles = OpenCLArray::create<mm_ushort2>(context, maxTiles, "interactingTiles");
+        interactingTiles = OpenCLArray::create<cl_int>(context, maxTiles, "interactingTiles");
         interactingAtoms = OpenCLArray::create<cl_int>(context, OpenCLContext::TileSize*maxTiles, "interactingAtoms");
         interactionCount = OpenCLArray::create<cl_uint>(context, 1, "interactionCount");
         int elementSize = (context.getUseDoublePrecision() ? sizeof(cl_double) : sizeof(cl_float));
@@ -423,7 +423,7 @@ void OpenCLNonbondedUtilities::updateNeighborListSize() {
     delete interactingAtoms;
     interactingTiles = NULL; // Avoid an error in the destructor if the following allocation fails
     interactingAtoms = NULL;
-    interactingTiles = OpenCLArray::create<mm_ushort2>(context, maxTiles, "interactingTiles");
+    interactingTiles = OpenCLArray::create<cl_int>(context, maxTiles, "interactingTiles");
     interactingAtoms = OpenCLArray::create<cl_int>(context, OpenCLContext::TileSize*maxTiles, "interactingAtoms");
     forceKernel.setArg<cl::Buffer>(7, interactingTiles->getDeviceBuffer());
     forceKernel.setArg<cl_uint>(11, maxTiles);

platforms/opencl/src/kernels/customGBEnergyN2.cl

@@ -20,7 +20,7 @@ __kernel void computeN2Energy(
         __global const real4* restrict posq, __local real4* restrict local_posq, __global const unsigned int* restrict exclusions,
         __global const ushort2* exclusionTiles,
 #ifdef USE_CUTOFF
-        __global const ushort2* restrict tiles, __global const unsigned int* restrict interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize, 
+        __global const int* restrict tiles, __global const unsigned int* restrict interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize, 
         unsigned int maxTiles, __global const real4* restrict blockCenter, __global const real4* restrict blockSize, __global const int* restrict interactingAtoms
 #else
         unsigned int numTiles
@@ -204,8 +204,7 @@ __kernel void computeN2Energy(
         bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
         if (numTiles <= maxTiles) {
-            ushort2 tileIndices = tiles[pos];
-            x = tileIndices.x;
+            x = tiles[pos];
             real4 blockSizeX = blockSize[x];
             singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
                                   0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&

platforms/opencl/src/kernels/customGBEnergyN2_cpu.cl

@@ -20,7 +20,7 @@ __kernel void computeN2Energy(
         __global const real4* restrict posq, __local real4* restrict local_posq, __global const unsigned int* restrict exclusions,
         __global const ushort2* exclusionTiles,
 #ifdef USE_CUTOFF
-        __global const ushort2* restrict tiles, __global const unsigned int* restrict interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize, 
+        __global const int* restrict tiles, __global const unsigned int* restrict interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize, 
         unsigned int maxTiles, __global const real4* restrict blockCenter, __global const real4* restrict blockSize, __global const int* restrict interactingAtoms
 #else
         unsigned int numTiles
@@ -220,8 +220,7 @@ __kernel void computeN2Energy(
         bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
         if (numTiles <= maxTiles) {
-            ushort2 tileIndices = tiles[pos];
-            x = tileIndices.x;
+            x = tiles[pos];
             real4 blockSizeX = blockSize[x];
             singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
                                   0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&

platforms/opencl/src/kernels/customGBValueN2.cl

@@ -14,7 +14,7 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
 #endif
         __local real* restrict local_value,
 #ifdef USE_CUTOFF
-        __global const ushort2* restrict tiles, __global const unsigned int* restrict interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize, 
+        __global const int* restrict tiles, __global const unsigned int* restrict interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize, 
         unsigned int maxTiles, __global const real4* restrict blockCenter, __global const real4* restrict blockSize, __global const int* restrict interactingAtoms
 #else
         unsigned int numTiles
@@ -178,8 +178,7 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
         bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
         if (numTiles <= maxTiles) {
-            ushort2 tileIndices = tiles[pos];
-            x = tileIndices.x;
+            x = tiles[pos];
             real4 blockSizeX = blockSize[x];
             singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
                                   0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&

platforms/opencl/src/kernels/customGBValueN2_cpu.cl

@@ -14,7 +14,7 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
 #endif
         __local real* restrict local_value,
 #ifdef USE_CUTOFF
-        __global const ushort2* restrict tiles, __global const unsigned int* restrict interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize, 
+        __global const int* restrict tiles, __global const unsigned int* restrict interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize, 
         unsigned int maxTiles, __global const real4* restrict blockCenter, __global const real4* restrict blockSize, __global const int* restrict interactingAtoms
 #else
         unsigned int numTiles
@@ -188,8 +188,7 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
         bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
         if (numTiles <= maxTiles) {
-            ushort2 tileIndices = tiles[pos];
-            x = tileIndices.x;
+            x = tiles[pos];
             real4 blockSizeX = blockSize[x];
             singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
                                   0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&

platforms/opencl/src/kernels/findInteractingBlocks.cl

@@ -98,8 +98,8 @@ void prefixSum(__local short* sum, __local ushort2* temp) {
  * This is called by findBlocksWithInteractions().  It compacts the list of blocks, identifies interactions
  * in them, and writes the result to global memory.
  */
-void storeInteractionData(unsigned short x, __local unsigned short* buffer, __local short* sum, __local ushort2* temp, __local int* atoms, __local int* numAtoms,
-            __local int* baseIndex, __global unsigned int* interactionCount, __global ushort2* interactingTiles, __global unsigned int* interactingAtoms, real4 periodicBoxSize,
+void storeInteractionData(int x, __local unsigned short* buffer, __local short* sum, __local ushort2* temp, __local int* atoms, __local int* numAtoms,
+            __local int* baseIndex, __global unsigned int* interactionCount, __global int* interactingTiles, __global unsigned int* interactingAtoms, real4 periodicBoxSize,
             real4 invPeriodicBoxSize, __global const real4* posq, __local real4* posBuffer, real4 blockCenterX, real4 blockSizeX, unsigned int maxTiles, bool finish) {
     const bool singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= PADDED_CUTOFF &&
                                      0.5f*periodicBoxSize.y-blockSizeX.y >= PADDED_CUTOFF &&
@@ -192,7 +192,7 @@ void storeInteractionData(unsigned short x, __local unsigned short* buffer, __lo
                 *numAtoms = atomsToStore-tilesToStore*TILE_SIZE;
             if (*baseIndex+tilesToStore <= maxTiles) {
                 if (get_local_id(0) < tilesToStore)
-                    interactingTiles[*baseIndex+get_local_id(0)] = (ushort2) (x, singlePeriodicCopy);
+                    interactingTiles[*baseIndex+get_local_id(0)] = x;
                 for (int i = get_local_id(0); i < tilesToStore*TILE_SIZE; i += get_local_size(0))
                     interactingAtoms[*baseIndex*TILE_SIZE+i] = (i < atomsToStore ? atoms[i] : NUM_ATOMS);
             }
@@ -216,7 +216,7 @@ void storeInteractionData(unsigned short x, __local unsigned short* buffer, __lo
         barrier(CLK_LOCAL_MEM_FENCE);
         if (*baseIndex < maxTiles) {
             if (get_local_id(0) == 0)
-                interactingTiles[*baseIndex] = (ushort2) (x, singlePeriodicCopy);
+                interactingTiles[*baseIndex] = x;
             if (get_local_id(0) < TILE_SIZE)
                 interactingAtoms[*baseIndex*TILE_SIZE+get_local_id(0)] = (get_local_id(0) < *numAtoms ? atoms[get_local_id(0)] : NUM_ATOMS);
         }
@@ -234,7 +234,7 @@ void storeInteractionData(unsigned short x, __local unsigned short* buffer, __lo
  * mark them as non-interacting.
  */
 __kernel void findBlocksWithInteractions(real4 periodicBoxSize, real4 invPeriodicBoxSize, __global unsigned int* restrict interactionCount,
-        __global ushort2* restrict interactingTiles, __global unsigned int* restrict interactingAtoms, __global const real4* restrict posq, unsigned int maxTiles, unsigned int startBlockIndex,
+        __global int* restrict interactingTiles, __global unsigned int* restrict interactingAtoms, __global const real4* restrict posq, unsigned int maxTiles, unsigned int startBlockIndex,
         unsigned int numBlocks, __global real2* restrict sortedBlocks, __global const real4* restrict sortedBlockCenter, __global const real4* restrict sortedBlockBoundingBox,
         __global const unsigned int* restrict exclusionIndices, __global const unsigned int* restrict exclusionRowIndices, __global real4* restrict oldPositions,
         __global const int* restrict rebuildNeighborList) {
@@ -272,7 +272,7 @@ __kernel void findBlocksWithInteractions(real4 periodicBoxSize, real4 invPeriodi
         if (get_local_id(0) == get_local_size(0)-1)
             numAtoms = 0;
         real2 sortedKey = sortedBlocks[i];
-        unsigned short x = (unsigned short) sortedKey.y;
+        int x = (int) sortedKey.y;
         real4 blockCenterX = sortedBlockCenter[i];
         real4 blockSizeX = sortedBlockBoundingBox[i];
 

platforms/opencl/src/kernels/gbsaObc.cl

@@ -21,7 +21,7 @@ __kernel void computeBornSum(
 #endif
         __global const real4* restrict posq, __global const float2* restrict global_params,
 #ifdef USE_CUTOFF
-        __global const ushort2* restrict tiles, __global const unsigned int* restrict interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize, 
+        __global const int* restrict tiles, __global const unsigned int* restrict interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize, 
         unsigned int maxTiles, __global const real4* restrict blockCenter, __global const real4* restrict blockSize, __global const int* restrict interactingAtoms,
 #else
         unsigned int numTiles,
@@ -190,8 +190,7 @@ __kernel void computeBornSum(
         bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
         if (numTiles <= maxTiles) {
-            ushort2 tileIndices = tiles[pos];
-            x = tileIndices.x;
+            x = tiles[pos];
             real4 blockSizeX = blockSize[x];
             singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
                                   0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&
@@ -391,7 +390,7 @@ __kernel void computeGBSAForce1(
 #endif
         __global real* restrict energyBuffer, __global const real4* restrict posq, __global const real* restrict global_bornRadii,
 #ifdef USE_CUTOFF
-        __global const ushort2* restrict tiles, __global const unsigned int* restrict interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize, 
+        __global const int* restrict tiles, __global const unsigned int* restrict interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize, 
         unsigned int maxTiles, __global const real4* restrict blockCenter, __global const real4* restrict blockSize, __global const int* restrict interactingAtoms,
 #else
         unsigned int numTiles,
@@ -568,8 +567,7 @@ __kernel void computeGBSAForce1(
         bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
         if (numTiles <= maxTiles) {
-            ushort2 tileIndices = tiles[pos];
-            x = tileIndices.x;
+            x = tiles[pos];
             real4 blockSizeX = blockSize[x];
             singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
                                   0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&

platforms/opencl/src/kernels/gbsaObc_cpu.cl

@@ -20,7 +20,7 @@ __kernel void computeBornSum(
 #endif
         __global const real4* restrict posq, __global const float2* restrict global_params,
 #ifdef USE_CUTOFF
-        __global const ushort2* restrict tiles, __global const unsigned int* restrict interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize, 
+        __global const int* restrict tiles, __global const unsigned int* restrict interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize, 
         unsigned int maxTiles, __global const real4* restrict blockCenter, __global const real4* restrict blockSize, __global const int* restrict interactingAtoms,
 #else
         unsigned int numTiles,
@@ -196,8 +196,7 @@ __kernel void computeBornSum(
         bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
         if (numTiles <= maxTiles) {
-            ushort2 tileIndices = tiles[pos];
-            x = tileIndices.x;
+            x = tiles[pos];
             real4 blockSizeX = blockSize[x];
             singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
                                   0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&
@@ -412,7 +411,7 @@ __kernel void computeGBSAForce1(
 #endif
         __global real* restrict energyBuffer, __global const real4* restrict posq, __global const real* restrict global_bornRadii,
 #ifdef USE_CUTOFF
-        __global const ushort2* restrict tiles, __global const unsigned int* restrict interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize, 
+        __global const int* restrict tiles, __global const unsigned int* restrict interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize, 
         unsigned int maxTiles, __global const real4* restrict blockCenter, __global const real4* restrict blockSize, __global const int* restrict interactingAtoms,
 #else
         unsigned int numTiles,
@@ -603,8 +602,7 @@ __kernel void computeGBSAForce1(
         bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
         if (numTiles <= maxTiles) {
-            ushort2 tileIndices = tiles[pos];
-            x = tileIndices.x;
+            x = tiles[pos];
             real4 blockSizeX = blockSize[x];
             singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
                                   0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&

platforms/opencl/src/kernels/nonbonded.cl

@@ -25,7 +25,7 @@ __kernel void computeNonbonded(
         __global real* restrict energyBuffer, __global const real4* restrict posq, __global const unsigned int* restrict exclusions,
         __global const ushort2* restrict exclusionTiles, unsigned int startTileIndex, unsigned int numTileIndices
 #ifdef USE_CUTOFF
-        , __global const ushort2* restrict tiles, __global const unsigned int* restrict interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize, 
+        , __global const int* restrict tiles, __global const unsigned int* restrict interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize, 
         unsigned int maxTiles, __global const real4* restrict blockCenter, __global const real4* restrict blockSize, __global const int* restrict interactingAtoms
 #endif
         PARAMETER_ARGUMENTS) {
@@ -217,8 +217,7 @@ __kernel void computeNonbonded(
         bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
         if (numTiles <= maxTiles) {
-            ushort2 tileIndices = tiles[pos];
-            x = tileIndices.x;
+            x = tiles[pos];
             real4 blockSizeX = blockSize[x];
             singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
                                   0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&

platforms/opencl/src/kernels/nonbonded_cpu.cl

@@ -22,7 +22,7 @@ __kernel void computeNonbonded(
         __global real* restrict energyBuffer, __global const real4* restrict posq, __global const unsigned int* restrict exclusions,
         __global const ushort2* restrict exclusionTiles, unsigned int startTileIndex, unsigned int numTileIndices
 #ifdef USE_CUTOFF
-        , __global const ushort2* restrict tiles, __global const unsigned int* restrict interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize, 
+        , __global const int* restrict tiles, __global const unsigned int* restrict interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize, 
         unsigned int maxTiles, __global const real4* restrict blockCenter, __global const real4* restrict blockSize, __global const int* restrict interactingAtoms
 #endif
         PARAMETER_ARGUMENTS) {
@@ -234,8 +234,7 @@ __kernel void computeNonbonded(
         bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
         if (numTiles <= maxTiles) {
-            ushort2 tileIndices = tiles[pos];
-            x = tileIndices.x;
+            x = tiles[pos];
             real4 blockSizeX = blockSize[x];
             singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
                                   0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&

plugins/amoeba/platforms/cuda/src/kernels/multipoleElectrostatics.cu

@@ -61,7 +61,7 @@ extern "C" __global__ void computeElectrostatics(
         const real4* __restrict__ posq, const uint2* __restrict__ covalentFlags, const unsigned int* __restrict__ polarizationGroupFlags,
         const ushort2* __restrict__ exclusionTiles, unsigned int startTileIndex, unsigned int numTileIndices,
 #ifdef USE_CUTOFF
-        const ushort2* __restrict__ tiles, const unsigned int* __restrict__ interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize, unsigned int maxTiles, const real4* __restrict__ blockCenter, const unsigned int* __restrict__ interactingAtoms,
+        const int* __restrict__ tiles, const unsigned int* __restrict__ interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize, unsigned int maxTiles, const real4* __restrict__ blockCenter, const unsigned int* __restrict__ interactingAtoms,
 #endif
         const real* __restrict__ labFrameDipole, const real* __restrict__ labFrameQuadrupole, const real* __restrict__ inducedDipole,
         const real* __restrict__ inducedDipolePolar, const float2* __restrict__ dampingAndThole) {
@@ -230,10 +230,8 @@ extern "C" __global__ void computeElectrostatics(
         
         unsigned int x, y;
 #ifdef USE_CUTOFF
-        if (numTiles <= maxTiles) {
-            ushort2 tileIndices = tiles[pos];
-            x = tileIndices.x;
-        }
+        if (numTiles <= maxTiles)
+            x = tiles[pos];
         else
 #endif
         {

plugins/amoeba/platforms/cuda/src/kernels/multipoleFixedField.cu

@@ -400,7 +400,7 @@ extern "C" __global__ void computeFixedField(
         const uint2* __restrict__ covalentFlags, const unsigned int* __restrict__ polarizationGroupFlags, const ushort2* __restrict__ exclusionTiles,
         unsigned int startTileIndex, unsigned int numTileIndices,
 #ifdef USE_CUTOFF
-        const ushort2* __restrict__ tiles, const unsigned int* __restrict__ interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize, unsigned int maxTiles, const real4* __restrict__ blockCenter, const unsigned int* __restrict__ interactingAtoms,
+        const int* __restrict__ tiles, const unsigned int* __restrict__ interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize, unsigned int maxTiles, const real4* __restrict__ blockCenter, const unsigned int* __restrict__ interactingAtoms,
 #elif defined USE_GK
         const real* __restrict__ bornRadii, unsigned long long* __restrict__ gkFieldBuffers,
 #endif
@@ -569,10 +569,8 @@ extern "C" __global__ void computeFixedField(
         
         unsigned int x, y;
 #ifdef USE_CUTOFF
-        if (numTiles <= maxTiles) {
-            ushort2 tileIndices = tiles[pos];
-            x = tileIndices.x;
-        }
+        if (numTiles <= maxTiles)
+            x = tiles[pos];
         else
 #endif
         {

plugins/amoeba/platforms/cuda/src/kernels/multipoleInducedField.cu

@@ -201,7 +201,7 @@ extern "C" __global__ void computeInducedField(
         unsigned long long* __restrict__ field, unsigned long long* __restrict__ fieldPolar, const real4* __restrict__ posq, const ushort2* __restrict__ exclusionTiles, 
         const real* __restrict__ inducedDipole, const real* __restrict__ inducedDipolePolar, unsigned int startTileIndex, unsigned int numTileIndices,
 #ifdef USE_CUTOFF
-        const ushort2* __restrict__ tiles, const unsigned int* __restrict__ interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize, unsigned int maxTiles, const real4* __restrict__ blockCenter, const unsigned int* __restrict__ interactingAtoms,
+        const int* __restrict__ tiles, const unsigned int* __restrict__ interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize, unsigned int maxTiles, const real4* __restrict__ blockCenter, const unsigned int* __restrict__ interactingAtoms,
 #elif defined USE_GK
         unsigned long long* __restrict__ fieldS, unsigned long long* __restrict__ fieldPolarS, const real* __restrict__ inducedDipoleS,
         const real* __restrict__ inducedDipolePolarS, const real* __restrict__ bornRadii,
@@ -339,10 +339,8 @@ extern "C" __global__ void computeInducedField(
         
         unsigned int x, y;
 #ifdef USE_CUTOFF
-        if (numTiles <= maxTiles) {
-            ushort2 tileIndices = tiles[pos];
-            x = tileIndices.x;
-        }
+        if (numTiles <= maxTiles)
+            x = tiles[pos];
         else
 #endif
         {

plugins/amoeba/platforms/cuda/src/kernels/pmeMultipoleElectrostatics.cu

@@ -184,7 +184,7 @@ extern "C" __global__ void computeElectrostatics(
         const real4* __restrict__ posq, const uint2* __restrict__ covalentFlags, const unsigned int* __restrict__ polarizationGroupFlags,
         const ushort2* __restrict__ exclusionTiles, unsigned int startTileIndex, unsigned int numTileIndices,
 #ifdef USE_CUTOFF
-        const ushort2* __restrict__ tiles, const unsigned int* __restrict__ interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize, unsigned int maxTiles, const real4* __restrict__ blockCenter, const unsigned int* __restrict__ interactingAtoms,
+        const int* __restrict__ tiles, const unsigned int* __restrict__ interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize, unsigned int maxTiles, const real4* __restrict__ blockCenter, const unsigned int* __restrict__ interactingAtoms,
 #endif
         const real* __restrict__ labFrameDipole, const real* __restrict__ labFrameQuadrupole, const real* __restrict__ inducedDipole,
         const real* __restrict__ inducedDipolePolar, const float2* __restrict__ dampingAndThole) {
@@ -312,10 +312,8 @@ extern "C" __global__ void computeElectrostatics(
         
         unsigned int x, y;
 #ifdef USE_CUTOFF
-        if (numTiles <= maxTiles) {
-            ushort2 tileIndices = tiles[pos];
-            x = tileIndices.x;
-        }
+        if (numTiles <= maxTiles)
+            x = tiles[pos];
         else
 #endif
         {