Fixed bug in RPMD contractions

plugins/rpmd/platforms/cuda/src/CudaRpmdKernels.cpp

@@ -128,12 +128,12 @@ void CudaIntegrateRPMDStepKernel::initialize(const System& system, const RPMDInt
         if (copies != numCopies) {
             if (groupsByCopies.find(copies) == groupsByCopies.end()) {
                 groupsByCopies[copies] = 1<<group;
-                groupsNotContracted -= 1<<group;
                 if (copies > maxContractedCopies)
                     maxContractedCopies = copies;
             }
             else
                 groupsByCopies[copies] |= 1<<group;
+            groupsNotContracted -= 1<<group;
         }
     }
     if (maxContractedCopies > 0) {

plugins/rpmd/platforms/opencl/src/OpenCLRpmdKernels.cpp

@@ -108,12 +108,12 @@ void OpenCLIntegrateRPMDStepKernel::initialize(const System& system, const RPMDI
         if (copies != numCopies) {
             if (groupsByCopies.find(copies) == groupsByCopies.end()) {
                 groupsByCopies[copies] = 1<<group;
-                groupsNotContracted -= 1<<group;
                 if (copies > maxContractedCopies)
                     maxContractedCopies = copies;
             }
             else
                 groupsByCopies[copies] |= 1<<group;
+            groupsNotContracted -= 1<<group;
         }
     }
     if (maxContractedCopies > 0) {

plugins/rpmd/platforms/reference/src/ReferenceRpmdKernels.cpp

@@ -89,7 +89,6 @@ void ReferenceIntegrateRPMDStepKernel::initialize(const System& system, const RP
         if (copies != numCopies) {
             if (groupsByCopies.find(copies) == groupsByCopies.end()) {
                 groupsByCopies[copies] = 1<<group;
-                groupsNotContracted -= 1<<group;
                 contractionFFT[copies] = NULL;
                 fftpack_init_1d(&contractionFFT[copies], copies);
                 if (copies > maxContractedCopies)
@@ -97,6 +96,7 @@ void ReferenceIntegrateRPMDStepKernel::initialize(const System& system, const RP
             }
             else
                 groupsByCopies[copies] |= 1<<group;
+            groupsNotContracted -= 1<<group;
         }
     }