Merge pull request #609 from peastman/nb

Rewrote the neighbor list generation kernel to be simpler and (slightly) faster

platforms/opencl/src/OpenCLContext.cpp

@@ -471,21 +471,25 @@ cl::Program OpenCLContext::createProgram(const string source, const map<string,
     if (useDoublePrecision) {
         src << "typedef double real;\n";
         src << "typedef double2 real2;\n";
+        src << "typedef double3 real3;\n";
         src << "typedef double4 real4;\n";
     }
     else {
         src << "typedef float real;\n";
         src << "typedef float2 real2;\n";
+        src << "typedef float3 real3;\n";
         src << "typedef float4 real4;\n";
     }
     if (useDoublePrecision || useMixedPrecision) {
         src << "typedef double mixed;\n";
         src << "typedef double2 mixed2;\n";
+        src << "typedef double3 mixed3;\n";
         src << "typedef double4 mixed4;\n";
     }
     else {
         src << "typedef float mixed;\n";
         src << "typedef float2 mixed2;\n";
+        src << "typedef float3 mixed3;\n";
         src << "typedef float4 mixed4;\n";
     }
     for (map<string, string>::const_iterator iter = defines.begin(); iter != defines.end(); ++iter) {

platforms/opencl/src/OpenCLNonbondedUtilities.cpp

@@ -319,7 +319,7 @@ void OpenCLNonbondedUtilities::initialize(const System& system) {
         defines["MAX_EXCLUSIONS"] = context.intToString(maxExclusions);
         defines["BUFFER_GROUPS"] = (deviceIsCpu ? "4" : "2");
         string file = (deviceIsCpu ? OpenCLKernelSources::findInteractingBlocks_cpu : OpenCLKernelSources::findInteractingBlocks);
-        int groupSize = (deviceIsCpu ? 32 : 128);
+        int groupSize = (deviceIsCpu || context.getSIMDWidth() < 32 ? 32 : 256);
         while (true) {
             defines["GROUP_SIZE"] = context.intToString(groupSize);
             cl::Program interactingBlocksProgram = context.createProgram(file, defines);