Optimzations and bug fix for mapping of torque to force for small molecules

plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaMutualInducedField.cu

@@ -558,9 +558,11 @@ static void cudaComputeAmoebaMutualInducedFieldBySOR( amoebaGpuContext amoebaGpu
            amoebaGpu->psCurrentEpsilon->_pDevData );
         LAUNCHERROR("kReduceMutualInducedFieldDelta");
 
+#ifdef AMOEBA_DEBUG
         if( 0 && amoebaGpu->log ){ // trackMutualInducedIterations
             trackMutualInducedIterations( amoebaGpu, iteration);
         }
+#endif
 
         // Debye=48.033324f
         amoebaGpu->psCurrentEpsilon->Download();

plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaUtilities.cu

@@ -118,7 +118,7 @@ void kClearFields_3( amoebaGpuContext amoebaGpu, unsigned int numberToClear )
 {
 
     gpuContext gpu = amoebaGpu->gpuContext;
-    kClearFields_kernel<<<gpu->sim.nonbond_blocks, 384>>>( gpu->sim.paddedNumberOfAtoms*3*gpu->sim.outputBuffers, amoebaGpu->psWorkArray_3_1->_pDevData );
+    kClearFields_kernel<<<gpu->sim.blocks, gpu->sim.threads_per_block>>>( gpu->sim.paddedNumberOfAtoms*3*gpu->sim.outputBuffers, amoebaGpu->psWorkArray_3_1->_pDevData );
     LAUNCHERROR("kClearFields_3_1");
 
     if( numberToClear > 1 ){