Merge branch 'master' of github.com:SimTk/openmm

openmmapi/src/ThreadPool.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2013 Stanford University and the Authors.           *
+ * Portions copyright (c) 2013-2014 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -60,8 +60,10 @@ static void* threadBody(void* args) {
     return 0;
 }
 
-ThreadPool::ThreadPool() {
-    numThreads = getNumProcessors();
+ThreadPool::ThreadPool(int numThreads) {
+    if (numThreads <= 0)
+        numThreads = getNumProcessors();
+    this->numThreads = numThreads;
     pthread_cond_init(&startCondition, NULL);
     pthread_cond_init(&endCondition, NULL);
     pthread_mutex_init(&lock, NULL);

platforms/cpu/src/CpuSETTLE.cpp

@@ -41,7 +41,9 @@ public:
             inverseMasses(inverseMasses), tolerance(tolerance), threadSettle(threadSettle) {
     }
     void execute(ThreadPool& threads, int threadIndex) {
-        threadSettle[threadIndex]->apply(atomCoordinates, atomCoordinatesP, inverseMasses, tolerance);
+        if (threadIndex < threadSettle.size()) {
+            threadSettle[threadIndex]->apply(atomCoordinates, atomCoordinatesP, inverseMasses, tolerance);
+        }
     }
     vector<OpenMM::RealVec>& atomCoordinates;
     vector<OpenMM::RealVec>& atomCoordinatesP;

platforms/opencl/src/OpenCLFFT3D.cpp

@@ -231,7 +231,6 @@ cl::Kernel OpenCLFFT3D::createKernel(int xsize, int ysize, int zsize, int& threa
         source<<"if (index < XSIZE*YSIZE)\n";
         source<<"out[y*(ZSIZE*XSIZE)+(get_local_id(0)%ZSIZE)*XSIZE+x] = data"<<(stage%2)<<"[get_local_id(0)];\n";
     }
-    source<<"barrier(CLK_GLOBAL_MEM_FENCE);";
     map<string, string> replacements;
     replacements["XSIZE"] = context.intToString(xsize);
     replacements["YSIZE"] = context.intToString(ysize);

platforms/reference/src/SimTKReference/ReferenceCustomCompoundBondIxn.cpp

@@ -124,7 +124,7 @@ void ReferenceCustomCompoundBondIxn::calculateOneIxn(int bond, vector<RealVec>&
 
     // Compute all of the variables the energy can depend on.
 
-    const vector<int>& atoms = bondAtoms[0];
+    const vector<int>& atoms = bondAtoms[bond];
     for (int i = 0; i < (int) particleTerms.size(); i++) {
         const ParticleTermInfo& term = particleTerms[i];
         variables[term.name] = atomCoordinates[term.atom][term.component];