Removal of limitation for 'long-range in sequence' covalent bonds

Reduced memory footprint

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

@@ -217,13 +217,14 @@ void kSorUpdateMutualInducedField_kernel(
 
 static void kReduceMutualInducedFields(amoebaGpuContext amoebaGpu, CUDAStream<float>* outputArray, CUDAStream<float>* outputPolarArray )
 {
-    kReduceFields_kernel<<<amoebaGpu->nonbondBlocks, amoebaGpu->fieldReduceThreadsPerBlock>>>(
-                               amoebaGpu->paddedNumberOfAtoms*3, amoebaGpu->outputBuffers,
+    gpuContext gpu = amoebaGpu->gpuContext;
+    kReduceFields_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.bsf_reduce_threads_per_block>>>(
+                               gpu->sim.paddedNumberOfAtoms*3, gpu->sim.outputBuffers,
                                amoebaGpu->psWorkArray_3_1->_pDevData, outputArray->_pDevData );
     LAUNCHERROR("kReduceMI_Fields1");
 
-    kReduceFields_kernel<<<amoebaGpu->nonbondBlocks, amoebaGpu->fieldReduceThreadsPerBlock>>>(
-                               amoebaGpu->paddedNumberOfAtoms*3, amoebaGpu->outputBuffers,
+    kReduceFields_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.bsf_reduce_threads_per_block>>>(
+                               gpu->sim.paddedNumberOfAtoms*3, gpu->sim.outputBuffers,
                                amoebaGpu->psWorkArray_3_2->_pDevData, outputPolarArray->_pDevData );
     LAUNCHERROR("kReduceMI_Fields2");
 }
@@ -277,14 +278,14 @@ static void cudaComputeAmoebaMutualInducedFieldMatrixMultiply( amoebaGpuContext
 
 #ifdef AMOEBA_DEBUG
         (void) fprintf( amoebaGpu->log, "%s numBlocks=%u numThreads=%u bufferPerWarp=%u atm=%u shrd=%u ixnCt=%u workUnits=%u\n", methodName,
-                        amoebaGpu->nonbondBlocks, threadsPerBlock, amoebaGpu->bOutputBufferPerWarp,
+                        gpu->sim.nonbond_blocks, threadsPerBlock, gpu->bOutputBufferPerWarp,
                         sizeof(MutualInducedParticle), sizeof(MutualInducedParticle)*threadsPerBlock,
                         (*gpu->psInteractionCount)[0], gpu->sim.workUnits );
         (void) fflush( amoebaGpu->log );
 #endif
 
     if (gpu->bOutputBufferPerWarp){
-        kCalculateAmoebaMutualInducedFieldN2ByWarp_kernel<<<amoebaGpu->nonbondBlocks, threadsPerBlock, sizeof(MutualInducedParticle)*threadsPerBlock>>>(
+        kCalculateAmoebaMutualInducedFieldN2ByWarp_kernel<<<gpu->sim.nonbond_blocks, threadsPerBlock, sizeof(MutualInducedParticle)*threadsPerBlock>>>(
                                                                  amoebaGpu->psWorkUnit->_pDevData,
                                                                  amoebaGpu->psWorkArray_3_1->_pDevData,
 #ifdef AMOEBA_DEBUG
@@ -296,7 +297,7 @@ static void cudaComputeAmoebaMutualInducedFieldMatrixMultiply( amoebaGpuContext
 
     } else {
 
-        kCalculateAmoebaMutualInducedFieldN2_kernel<<<amoebaGpu->nonbondBlocks, threadsPerBlock, sizeof(MutualInducedParticle)*threadsPerBlock>>>(
+        kCalculateAmoebaMutualInducedFieldN2_kernel<<<gpu->sim.nonbond_blocks, threadsPerBlock, sizeof(MutualInducedParticle)*threadsPerBlock>>>(
                                                                  amoebaGpu->psWorkUnit->_pDevData,
                                                                  amoebaGpu->psWorkArray_3_1->_pDevData,
 #ifdef AMOEBA_DEBUG