Merge pull request #107 from peastman/master

Various bug fixes

platforms/cuda/src/CudaKernels.cpp

@@ -2144,7 +2144,7 @@ void CudaCalcCustomNonbondedForceKernel::initInteractionGroups(const CustomNonbo
         }
         vector<int>& atoms1 = atomLists[tiles[tile].first];
         vector<int>& atoms2 = atomLists[tiles[tile].second];
-        vector<int> flags(atoms1.size(), (1L<<atoms2.size())-1);
+        vector<int> flags(atoms1.size(), (int) (1LL<<atoms2.size())-1);
         int numExcluded = 0;
         for (int i = 0; i < (int) atoms1.size(); i++)
             for (int j = 0; j < (int) atoms2.size(); j++) {

platforms/opencl/src/OpenCLKernels.cpp

@@ -2155,7 +2155,7 @@ void OpenCLCalcCustomNonbondedForceKernel::initInteractionGroups(const CustomNon
         }
         vector<int>& atoms1 = atomLists[tiles[tile].first];
         vector<int>& atoms2 = atomLists[tiles[tile].second];
-        vector<int> flags(atoms1.size(), (1L<<atoms2.size())-1);
+        vector<int> flags(atoms1.size(), (int) (1LL<<atoms2.size())-1);
         int numExcluded = 0;
         for (int i = 0; i < (int) atoms1.size(); i++)
             for (int j = 0; j < (int) atoms2.size(); j++) {

plugins/drude/platforms/cuda/src/CudaDrudeKernels.cpp

@@ -406,6 +406,7 @@ void CudaIntegrateDrudeSCFStepKernel::execute(ContextImpl& context, const DrudeS
     cu.setAsCurrent();
     CudaIntegrationUtilities& integration = cu.getIntegrationUtilities();
     int numAtoms = cu.getNumAtoms();
+    int paddedNumAtoms = cu.getPaddedNumAtoms();
     double dt = integrator.getStepSize();
     if (dt != prevStepSize) {
         if (cu.getUseDoublePrecision() || cu.getUseMixedPrecision()) {
@@ -424,7 +425,7 @@ void CudaIntegrateDrudeSCFStepKernel::execute(ContextImpl& context, const DrudeS
     // Call the first integration kernel.
 
     CUdeviceptr posCorrection = (cu.getUseMixedPrecision() ? cu.getPosqCorrection().getDevicePointer() : 0);
-    void* args1[] = {&cu.getIntegrationUtilities().getStepSize().getDevicePointer(), &cu.getPosq().getDevicePointer(), &posCorrection,
+    void* args1[] = {&numAtoms, &paddedNumAtoms, &cu.getIntegrationUtilities().getStepSize().getDevicePointer(), &cu.getPosq().getDevicePointer(), &posCorrection,
             &cu.getVelm().getDevicePointer(), &cu.getForce().getDevicePointer(), &integration.getPosDelta().getDevicePointer()};
     cu.executeKernel(kernel1, args1, numAtoms);
 
@@ -434,7 +435,7 @@ void CudaIntegrateDrudeSCFStepKernel::execute(ContextImpl& context, const DrudeS
 
     // Call the second integration kernel.
 
-    void* args2[] = {&cu.getIntegrationUtilities().getStepSize().getDevicePointer(), &cu.getPosq().getDevicePointer(), &posCorrection,
+    void* args2[] = {&numAtoms, &cu.getIntegrationUtilities().getStepSize().getDevicePointer(), &cu.getPosq().getDevicePointer(), &posCorrection,
             &cu.getVelm().getDevicePointer(), &integration.getPosDelta().getDevicePointer()};
     cu.executeKernel(kernel2, args2, numAtoms);
 

plugins/rpmd/platforms/cuda/tests/TestCudaRpmd.cpp

@@ -391,7 +391,7 @@ void testContractions() {
     map<int, int> contractions;
     contractions[1] = 3;
     contractions[2] = 1;
-    RPMDIntegrator integ(numCopies, temperature, 10.0, 0.001, contractions);
+    RPMDIntegrator integ(numCopies, temperature, 50.0, 0.001, contractions);
     Platform& platform = Platform::getPlatformByName("CUDA");
     Context context(system, integ, platform);
     for (int copy = 0; copy < numCopies; copy++) {

plugins/rpmd/platforms/opencl/tests/TestOpenCLRpmd.cpp

@@ -392,7 +392,7 @@ void testContractions() {
     map<int, int> contractions;
     contractions[1] = 3;
     contractions[2] = 1;
-    RPMDIntegrator integ(numCopies, temperature, 10.0, 0.001, contractions);
+    RPMDIntegrator integ(numCopies, temperature, 50.0, 0.001, contractions);
     Platform& platform = Platform::getPlatformByName("OpenCL");
     Context context(system, integ, platform);
     for (int copy = 0; copy < numCopies; copy++) {

plugins/rpmd/platforms/reference/tests/TestReferenceRpmd.cpp

@@ -273,7 +273,7 @@ void testContractions() {
     map<int, int> contractions;
     contractions[1] = 3;
     contractions[2] = 1;
-    RPMDIntegrator integ(numCopies, temperature, 10.0, 0.001, contractions);
+    RPMDIntegrator integ(numCopies, temperature, 50.0, 0.001, contractions);
     Platform& platform = Platform::getPlatformByName("Reference");
     Context context(system, integ, platform);
     for (int copy = 0; copy < numCopies; copy++) {