Merge remote-tracking branch 'origin/master' into charmm

platforms/cuda/src/kernels/customGBEnergyN2.cu

@@ -190,7 +190,7 @@ extern "C" __global__ void computeN2Energy(unsigned long long* __restrict__ forc
         
         // Extract the coordinates of this tile.
         
-        unsigned int x, y;
+        int x, y;
         bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
         if (numTiles <= maxTiles) {
@@ -203,7 +203,7 @@ extern "C" __global__ void computeN2Energy(unsigned long long* __restrict__ forc
         else
 #endif
         {
-            y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
+            y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
             x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
             if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
                 y += (x < y ? -1 : 1);

platforms/cuda/src/kernels/customGBValueN2.cu

@@ -166,7 +166,7 @@ extern "C" __global__ void computeN2Value(const real4* __restrict__ posq, const
         
         // Extract the coordinates of this tile.
         
-        unsigned int x, y;
+        int x, y;
         bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
         if (numTiles <= maxTiles) {
@@ -179,7 +179,7 @@ extern "C" __global__ void computeN2Value(const real4* __restrict__ posq, const
         else
 #endif
         {
-            y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
+            y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
             x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
             if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
                 y += (x < y ? -1 : 1);

platforms/cuda/src/kernels/gbsaObc1.cu

@@ -226,7 +226,7 @@ extern "C" __global__ void computeBornSum(unsigned long long* __restrict__ globa
 
         // Extract the coordinates of this tile.
         
-        unsigned int x, y;
+        int x, y;
         bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
         if (numTiles <= maxTiles) {
@@ -239,7 +239,7 @@ extern "C" __global__ void computeBornSum(unsigned long long* __restrict__ globa
         else
 #endif
         {
-            y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
+            y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
             x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
             if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
                 y += (x < y ? -1 : 1);
@@ -590,7 +590,7 @@ extern "C" __global__ void computeGBSAForce1(unsigned long long* __restrict__ fo
 
         // Extract the coordinates of this tile.
         
-        unsigned int x, y;
+        int x, y;
         bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
         if (numTiles <= maxTiles) {
@@ -603,7 +603,7 @@ extern "C" __global__ void computeGBSAForce1(unsigned long long* __restrict__ fo
         else
 #endif
         {
-            y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
+            y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
             x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
             if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
                 y += (x < y ? -1 : 1);

platforms/cuda/src/kernels/nonbonded.cu

@@ -333,7 +333,7 @@ extern "C" __global__ void computeNonbonded(
         bool includeTile = true;
 
         // Extract the coordinates of this tile.
-        unsigned int x, y;
+        int x, y;
         bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
         if (numTiles <= maxTiles) {
@@ -346,7 +346,7 @@ extern "C" __global__ void computeNonbonded(
         else
 #endif
         {
-            y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
+            y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
             x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
             if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
                 y += (x < y ? -1 : 1);

platforms/cuda/tests/TestCudaCustomIntegrator.cpp

@@ -292,6 +292,7 @@ void testWithThermostat() {
     system.addForce(forceField);
     AndersenThermostat* thermostat = new AndersenThermostat(temp, collisionFreq);
     system.addForce(thermostat);
+    integrator.setRandomNumberSeed(thermostat->getRandomNumberSeed());
     Context context(system, integrator, platform);
     vector<Vec3> positions(numParticles);
     for (int i = 0; i < numParticles; ++i)
@@ -424,6 +425,7 @@ void testParameter() {
     integrator.addGlobalVariable("temp", 0);
     integrator.addComputeGlobal("temp", "AndersenTemperature");
     integrator.addComputeGlobal("AndersenTemperature", "temp*2");
+    integrator.setRandomNumberSeed(thermostat->getRandomNumberSeed());
     Context context(system, integrator, platform);
     
     // See if the parameter is being used correctly.

platforms/cuda/tests/TestCudaMonteCarloAnisotropicBarostat.cpp

@@ -389,7 +389,7 @@ int main(int argc, char* argv[]) {
         testIdealGasAxis(1);
         testIdealGasAxis(2);
         testRandomSeed();
-        testEinsteinCrystal();
+        //testEinsteinCrystal();
     }
     catch(const exception& e) {
         cout << "exception: " << e.what() << endl;

platforms/opencl/include/OpenCLNonbondedUtilities.h

@@ -284,7 +284,8 @@ private:
     std::map<std::string, std::string> kernelDefines;
     double cutoff;
     bool useCutoff, usePeriodic, deviceIsCpu, anyExclusions, usePadding;
-    int numForceBuffers, startTileIndex, numTiles, startBlockIndex, numBlocks, numForceThreadBlocks, forceThreadBlockSize, nonbondedForceGroup;
+    int numForceBuffers, startTileIndex, numTiles, startBlockIndex, numBlocks, numForceThreadBlocks;
+    int forceThreadBlockSize, interactingBlocksThreadBlockSize, nonbondedForceGroup;
 };
 
 /**

platforms/opencl/src/OpenCLKernels.cpp

@@ -4820,7 +4820,7 @@ void OpenCLIntegrateVariableVerletStepKernel::initialize(const System& system, c
     kernel1 = cl::Kernel(program, "integrateVerletPart1");
     kernel2 = cl::Kernel(program, "integrateVerletPart2");
     selectSizeKernel = cl::Kernel(program, "selectVerletStepSize");
-    blockSize = min(min(256, system.getNumParticles()), (int) cl.getDevice().getInfo<CL_DEVICE_MAX_WORK_GROUP_SIZE>());
+    blockSize = min(min(256, system.getNumParticles()), (int) selectSizeKernel.getWorkGroupInfo<CL_KERNEL_WORK_GROUP_SIZE>(cl.getDevice()));
 }
 
 double OpenCLIntegrateVariableVerletStepKernel::execute(ContextImpl& context, const VariableVerletIntegrator& integrator, double maxTime) {
@@ -4930,7 +4930,7 @@ void OpenCLIntegrateVariableLangevinStepKernel::initialize(const System& system,
     params = new OpenCLArray(cl, 3, cl.getUseDoublePrecision() || cl.getUseMixedPrecision() ? sizeof(cl_double) : sizeof(cl_float), "langevinParams");
     blockSize = min(256, system.getNumParticles());
     blockSize = max(blockSize, params->getSize());
-    blockSize = min(blockSize, (int) cl.getDevice().getInfo<CL_DEVICE_MAX_WORK_GROUP_SIZE>());
+    blockSize = min(blockSize, (int) selectSizeKernel.getWorkGroupInfo<CL_KERNEL_WORK_GROUP_SIZE>(cl.getDevice()));
 }
 
 double OpenCLIntegrateVariableLangevinStepKernel::execute(ContextImpl& context, const VariableLangevinIntegrator& integrator, double maxTime) {

platforms/opencl/src/OpenCLNonbondedUtilities.cpp

@@ -317,42 +317,55 @@ void OpenCLNonbondedUtilities::initialize(const System& system) {
         for (int i = 0; i < (int) exclusionBlocksForBlock.size(); i++)
             maxExclusions = (maxExclusions > exclusionBlocksForBlock[i].size() ? maxExclusions : exclusionBlocksForBlock[i].size());
         defines["MAX_EXCLUSIONS"] = context.intToString(maxExclusions);
-        defines["GROUP_SIZE"] = (deviceIsCpu ? "32" : "128");
         defines["BUFFER_GROUPS"] = (deviceIsCpu ? "4" : "2");
         string file = (deviceIsCpu ? OpenCLKernelSources::findInteractingBlocks_cpu : OpenCLKernelSources::findInteractingBlocks);
-        cl::Program interactingBlocksProgram = context.createProgram(file, defines);
-        findBlockBoundsKernel = cl::Kernel(interactingBlocksProgram, "findBlockBounds");
-        findBlockBoundsKernel.setArg<cl_int>(0, context.getNumAtoms());
-        findBlockBoundsKernel.setArg<cl::Buffer>(3, context.getPosq().getDeviceBuffer());
-        findBlockBoundsKernel.setArg<cl::Buffer>(4, blockCenter->getDeviceBuffer());
-        findBlockBoundsKernel.setArg<cl::Buffer>(5, blockBoundingBox->getDeviceBuffer());
-        findBlockBoundsKernel.setArg<cl::Buffer>(6, rebuildNeighborList->getDeviceBuffer());
-        findBlockBoundsKernel.setArg<cl::Buffer>(7, sortedBlocks->getDeviceBuffer());
-        sortBoxDataKernel = cl::Kernel(interactingBlocksProgram, "sortBoxData");
-        sortBoxDataKernel.setArg<cl::Buffer>(0, sortedBlocks->getDeviceBuffer());
-        sortBoxDataKernel.setArg<cl::Buffer>(1, blockCenter->getDeviceBuffer());
-        sortBoxDataKernel.setArg<cl::Buffer>(2, blockBoundingBox->getDeviceBuffer());
-        sortBoxDataKernel.setArg<cl::Buffer>(3, sortedBlockCenter->getDeviceBuffer());
-        sortBoxDataKernel.setArg<cl::Buffer>(4, sortedBlockBoundingBox->getDeviceBuffer());
-        sortBoxDataKernel.setArg<cl::Buffer>(5, context.getPosq().getDeviceBuffer());
-        sortBoxDataKernel.setArg<cl::Buffer>(6, oldPositions->getDeviceBuffer());
-        sortBoxDataKernel.setArg<cl::Buffer>(7, interactionCount->getDeviceBuffer());
-        sortBoxDataKernel.setArg<cl::Buffer>(8, rebuildNeighborList->getDeviceBuffer());
-        findInteractingBlocksKernel = cl::Kernel(interactingBlocksProgram, "findBlocksWithInteractions");
-        findInteractingBlocksKernel.setArg<cl::Buffer>(2, interactionCount->getDeviceBuffer());
-        findInteractingBlocksKernel.setArg<cl::Buffer>(3, interactingTiles->getDeviceBuffer());
-        findInteractingBlocksKernel.setArg<cl::Buffer>(4, interactingAtoms->getDeviceBuffer());
-        findInteractingBlocksKernel.setArg<cl::Buffer>(5, context.getPosq().getDeviceBuffer());
-        findInteractingBlocksKernel.setArg<cl_uint>(6, interactingTiles->getSize());
-        findInteractingBlocksKernel.setArg<cl_uint>(7, startBlockIndex);
-        findInteractingBlocksKernel.setArg<cl_uint>(8, numBlocks);
-        findInteractingBlocksKernel.setArg<cl::Buffer>(9, sortedBlocks->getDeviceBuffer());
-        findInteractingBlocksKernel.setArg<cl::Buffer>(10, sortedBlockCenter->getDeviceBuffer());
-        findInteractingBlocksKernel.setArg<cl::Buffer>(11, sortedBlockBoundingBox->getDeviceBuffer());
-        findInteractingBlocksKernel.setArg<cl::Buffer>(12, exclusionIndices->getDeviceBuffer());
-        findInteractingBlocksKernel.setArg<cl::Buffer>(13, exclusionRowIndices->getDeviceBuffer());
-        findInteractingBlocksKernel.setArg<cl::Buffer>(14, oldPositions->getDeviceBuffer());
-        findInteractingBlocksKernel.setArg<cl::Buffer>(15, rebuildNeighborList->getDeviceBuffer());
+        int groupSize = (deviceIsCpu ? 32 : 128);
+        while (true) {
+            defines["GROUP_SIZE"] = context.intToString(groupSize);
+            cl::Program interactingBlocksProgram = context.createProgram(file, defines);
+            findBlockBoundsKernel = cl::Kernel(interactingBlocksProgram, "findBlockBounds");
+            findBlockBoundsKernel.setArg<cl_int>(0, context.getNumAtoms());
+            findBlockBoundsKernel.setArg<cl::Buffer>(3, context.getPosq().getDeviceBuffer());
+            findBlockBoundsKernel.setArg<cl::Buffer>(4, blockCenter->getDeviceBuffer());
+            findBlockBoundsKernel.setArg<cl::Buffer>(5, blockBoundingBox->getDeviceBuffer());
+            findBlockBoundsKernel.setArg<cl::Buffer>(6, rebuildNeighborList->getDeviceBuffer());
+            findBlockBoundsKernel.setArg<cl::Buffer>(7, sortedBlocks->getDeviceBuffer());
+            sortBoxDataKernel = cl::Kernel(interactingBlocksProgram, "sortBoxData");
+            sortBoxDataKernel.setArg<cl::Buffer>(0, sortedBlocks->getDeviceBuffer());
+            sortBoxDataKernel.setArg<cl::Buffer>(1, blockCenter->getDeviceBuffer());
+            sortBoxDataKernel.setArg<cl::Buffer>(2, blockBoundingBox->getDeviceBuffer());
+            sortBoxDataKernel.setArg<cl::Buffer>(3, sortedBlockCenter->getDeviceBuffer());
+            sortBoxDataKernel.setArg<cl::Buffer>(4, sortedBlockBoundingBox->getDeviceBuffer());
+            sortBoxDataKernel.setArg<cl::Buffer>(5, context.getPosq().getDeviceBuffer());
+            sortBoxDataKernel.setArg<cl::Buffer>(6, oldPositions->getDeviceBuffer());
+            sortBoxDataKernel.setArg<cl::Buffer>(7, interactionCount->getDeviceBuffer());
+            sortBoxDataKernel.setArg<cl::Buffer>(8, rebuildNeighborList->getDeviceBuffer());
+            findInteractingBlocksKernel = cl::Kernel(interactingBlocksProgram, "findBlocksWithInteractions");
+            findInteractingBlocksKernel.setArg<cl::Buffer>(2, interactionCount->getDeviceBuffer());
+            findInteractingBlocksKernel.setArg<cl::Buffer>(3, interactingTiles->getDeviceBuffer());
+            findInteractingBlocksKernel.setArg<cl::Buffer>(4, interactingAtoms->getDeviceBuffer());
+            findInteractingBlocksKernel.setArg<cl::Buffer>(5, context.getPosq().getDeviceBuffer());
+            findInteractingBlocksKernel.setArg<cl_uint>(6, interactingTiles->getSize());
+            findInteractingBlocksKernel.setArg<cl_uint>(7, startBlockIndex);
+            findInteractingBlocksKernel.setArg<cl_uint>(8, numBlocks);
+            findInteractingBlocksKernel.setArg<cl::Buffer>(9, sortedBlocks->getDeviceBuffer());
+            findInteractingBlocksKernel.setArg<cl::Buffer>(10, sortedBlockCenter->getDeviceBuffer());
+            findInteractingBlocksKernel.setArg<cl::Buffer>(11, sortedBlockBoundingBox->getDeviceBuffer());
+            findInteractingBlocksKernel.setArg<cl::Buffer>(12, exclusionIndices->getDeviceBuffer());
+            findInteractingBlocksKernel.setArg<cl::Buffer>(13, exclusionRowIndices->getDeviceBuffer());
+            findInteractingBlocksKernel.setArg<cl::Buffer>(14, oldPositions->getDeviceBuffer());
+            findInteractingBlocksKernel.setArg<cl::Buffer>(15, rebuildNeighborList->getDeviceBuffer());
+            if (findInteractingBlocksKernel.getWorkGroupInfo<CL_KERNEL_WORK_GROUP_SIZE>(context.getDevice()) < groupSize) {
+                // The device can't handle this block size, so reduce it.
+                
+                groupSize -= 32;
+                if (groupSize < 32)
+                    throw OpenMMException("Failed to create findInteractingBlocks kernel");
+                continue;
+            }
+            break;
+        }
+        interactingBlocksThreadBlockSize = (deviceIsCpu ? 1 : groupSize);
     }
 }
 
@@ -389,7 +402,7 @@ void OpenCLNonbondedUtilities::prepareInteractions() {
     context.executeKernel(sortBoxDataKernel, context.getNumAtoms());
     setPeriodicBoxSizeArg(context, findInteractingBlocksKernel, 0);
     setInvPeriodicBoxSizeArg(context, findInteractingBlocksKernel, 1);
-    context.executeKernel(findInteractingBlocksKernel, context.getNumAtoms(), deviceIsCpu ? 1 : 128);
+    context.executeKernel(findInteractingBlocksKernel, context.getNumAtoms(), interactingBlocksThreadBlockSize);
 }
 
 void OpenCLNonbondedUtilities::computeInteractions() {

platforms/opencl/src/OpenCLPlatform.cpp

@@ -32,6 +32,7 @@
 #include "openmm/Context.h"
 #include "openmm/System.h"
 #include <algorithm>
+#include <cctype>
 #include <sstream>
 #ifdef __APPLE__
 #include "sys/sysctl.h"
@@ -39,10 +40,7 @@
 
 
 using namespace OpenMM;
-using std::map;
-using std::string;
-using std::stringstream;
-using std::vector;
+using namespace std;
 
 #ifdef OPENMM_OPENCL_BUILDING_STATIC_LIBRARY
 extern "C" void registerOpenCLPlatform() {

platforms/opencl/src/OpenCLSort.cpp

@@ -56,10 +56,13 @@ OpenCLSort::OpenCLSort(OpenCLContext& context, SortTrait* trait, unsigned int le
     unsigned int maxGroupSize = std::min(256, (int) context.getDevice().getInfo<CL_DEVICE_MAX_WORK_GROUP_SIZE>());
     int maxSharedMem = context.getDevice().getInfo<CL_DEVICE_LOCAL_MEM_SIZE>();
     unsigned int maxLocalBuffer = (unsigned int) ((maxSharedMem/trait->getDataSize())/2);
-    isShortList = (length <= maxLocalBuffer);
-    for (rangeKernelSize = 1; rangeKernelSize*2 <= maxGroupSize; rangeKernelSize *= 2)
+    unsigned int maxRangeSize = std::min(maxGroupSize, (unsigned int) computeRangeKernel.getWorkGroupInfo<CL_KERNEL_WORK_GROUP_SIZE>(context.getDevice()));
+    unsigned int maxPositionsSize = std::min(maxGroupSize, (unsigned int) computeBucketPositionsKernel.getWorkGroupInfo<CL_KERNEL_WORK_GROUP_SIZE>(context.getDevice()));
+    unsigned int maxShortListSize = shortListKernel.getWorkGroupInfo<CL_KERNEL_WORK_GROUP_SIZE>(context.getDevice());
+    isShortList = (length <= maxLocalBuffer && length < maxShortListSize);
+    for (rangeKernelSize = 1; rangeKernelSize*2 <= maxRangeSize; rangeKernelSize *= 2)
         ;
-    positionsKernelSize = rangeKernelSize;
+    positionsKernelSize = std::min(rangeKernelSize, maxPositionsSize);
     sortKernelSize = (isShortList ? rangeKernelSize : rangeKernelSize/2);
     if (rangeKernelSize > length)
         rangeKernelSize = length;

platforms/opencl/src/kernels/customGBEnergyN2.cl

@@ -200,7 +200,7 @@ __kernel void computeN2Energy(
 
         // Extract the coordinates of this tile.
         
-        unsigned int x, y;
+        int x, y;
         bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
         if (numTiles <= maxTiles) {
@@ -213,7 +213,7 @@ __kernel void computeN2Energy(
         else
 #endif
         {
-            y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
+            y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
             x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
             if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
                 y += (x < y ? -1 : 1);

platforms/opencl/src/kernels/customGBEnergyN2_cpu.cl

@@ -216,7 +216,7 @@ __kernel void computeN2Energy(
         
         // Extract the coordinates of this tile.
         
-        unsigned int x, y;
+        int x, y;
         bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
         if (numTiles <= maxTiles) {
@@ -229,7 +229,7 @@ __kernel void computeN2Energy(
         else
 #endif
         {
-            y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
+            y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
             x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
             if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
                 y += (x < y ? -1 : 1);

platforms/opencl/src/kernels/customGBValueN2.cl

@@ -174,7 +174,7 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
 
         // Extract the coordinates of this tile.
         
-        unsigned int x, y;
+        int x, y;
         bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
         if (numTiles <= maxTiles) {
@@ -187,7 +187,7 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
         else
 #endif
         {
-            y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
+            y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
             x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
             if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
                 y += (x < y ? -1 : 1);

platforms/opencl/src/kernels/customGBValueN2_cpu.cl

@@ -184,7 +184,7 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
         
         // Extract the coordinates of this tile.
         
-        unsigned int x, y;
+        int x, y;
         bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
         if (numTiles <= maxTiles) {
@@ -197,7 +197,7 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
         else
 #endif
         {
-            y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
+            y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
             x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
             if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
                 y += (x < y ? -1 : 1);

platforms/opencl/src/kernels/gbsaObc.cl

@@ -186,7 +186,7 @@ __kernel void computeBornSum(
 
         // Extract the coordinates of this tile.
         
-        unsigned int x, y;
+        int x, y;
         bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
         if (numTiles <= maxTiles) {
@@ -199,7 +199,7 @@ __kernel void computeBornSum(
         else
 #endif
         {
-            y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
+            y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
             x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
             if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
                 y += (x < y ? -1 : 1);
@@ -574,7 +574,7 @@ __kernel void computeGBSAForce1(
 
         // Extract the coordinates of this tile.
         
-        unsigned int x, y;
+        int x, y;
         bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
         if (numTiles <= maxTiles) {
@@ -587,7 +587,7 @@ __kernel void computeGBSAForce1(
         else
 #endif
         {
-            y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
+            y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
             x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
             if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
                 y += (x < y ? -1 : 1);

platforms/opencl/src/kernels/gbsaObc_cpu.cl

@@ -192,7 +192,7 @@ __kernel void computeBornSum(
 
         // Extract the coordinates of this tile.
         
-        unsigned int x, y;
+        int x, y;
         bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
         if (numTiles <= maxTiles) {
@@ -205,7 +205,7 @@ __kernel void computeBornSum(
         else
 #endif
         {
-            y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
+            y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
             x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
             if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
                 y += (x < y ? -1 : 1);
@@ -607,7 +607,7 @@ __kernel void computeGBSAForce1(
 
         // Extract the coordinates of this tile.
         
-        unsigned int x, y;
+        int x, y;
         bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
         if (numTiles <= maxTiles) {
@@ -620,7 +620,7 @@ __kernel void computeGBSAForce1(
         else
 #endif
         {
-            y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
+            y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
             x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
             if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
                 y += (x < y ? -1 : 1);

platforms/opencl/src/kernels/nonbonded.cl

@@ -213,7 +213,7 @@ __kernel void computeNonbonded(
 
         // Extract the coordinates of this tile.
         
-        unsigned int x, y;
+        int x, y;
         bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
         if (numTiles <= maxTiles) {
@@ -226,7 +226,7 @@ __kernel void computeNonbonded(
         else
 #endif
         {
-            y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
+            y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
             x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
             if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
                 y += (x < y ? -1 : 1);

platforms/opencl/src/kernels/nonbonded_cpu.cl

@@ -230,7 +230,7 @@ __kernel void computeNonbonded(
         
         // Extract the coordinates of this tile.
         
-        unsigned int x, y;
+        int x, y;
         bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
         if (numTiles <= maxTiles) {
@@ -243,7 +243,7 @@ __kernel void computeNonbonded(
         else
 #endif
         {
-            y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
+            y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
             x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
             if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
                 y += (x < y ? -1 : 1);