Fix for overwriting of CudaCalcForcesAndEnergyKernel w/ AmoebaCalcForcesAndEnergyKernel

plugins/amoeba/platforms/cuda/src/AmoebaCudaKernelFactory.cpp

@@ -56,7 +56,7 @@ extern "C" OPENMMCUDA_EXPORT void registerKernelFactories() {
              platform.registerKernelFactory(CalcAmoebaGeneralizedKirkwoodForceKernel::Name(), factory);
              platform.registerKernelFactory(CalcAmoebaVdwForceKernel::Name(), factory);
              platform.registerKernelFactory(CalcAmoebaWcaDispersionForceKernel::Name(), factory);
-             platform.registerKernelFactory(CalcAmoebaForcesAndEnergyKernel::Name(), factory);
+//             platform.registerKernelFactory(CalcAmoebaForcesAndEnergyKernel::Name(), factory);
         }
     }
 }

plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.cpp

@@ -53,7 +53,7 @@ void CalcAmoebaForcesAndEnergyKernel::beginComputation(ContextImpl& context, boo
 
     amoebaGpuContext amoebaGpu  = data.getAmoebaGpu();
     _gpuContext* gpu            = data.getAmoebaGpu()->gpuContext;
-
+/*
     if (data.cudaPlatformData.nonbondedMethod != NO_CUTOFF && data.cudaPlatformData.computeForceCount%100 == 0){
         //fprintf( stderr, "In CalcAmoebaForcesAndEnergyKernel::beginComputation reordering atoms\n" ); fflush( stderr );
         gpuReorderAtoms(gpu);
@@ -61,21 +61,32 @@ void CalcAmoebaForcesAndEnergyKernel::beginComputation(ContextImpl& context, boo
 
     data.cudaPlatformData.computeForceCount++;
 
-    if( data.getHasAmoebaGeneralizedKirkwood() ){
-        kClearBornSumAndForces(gpu);
-    } else if (includeForces){
-        kClearForces(gpu);
+    if(includeForces){
+        if( data.getHasAmoebaGeneralizedKirkwood() ){
+            kClearBornSumAndForces(gpu);
+        } else {
+            kClearForces(gpu);
+        }
     }
 
     if (includeEnergy)
         kClearEnergy(gpu);
-
+*/
+    int originalIncludeGBSA = gpu->bIncludeGBSA;
+    if(includeForces && data.getHasAmoebaGeneralizedKirkwood() ){
+        gpu->bIncludeGBSA = 1;
+    }
+    cudaCalcForcesAndEnergyKernel->beginComputation( context, includeForces, includeEnergy);
+    gpu->bIncludeGBSA = originalIncludeGBSA;
 }
 
 double CalcAmoebaForcesAndEnergyKernel::finishComputation(ContextImpl& context, bool includeForces, bool includeEnergy) {
+
     amoebaGpuContext amoebaGpu  = data.getAmoebaGpu();
     _gpuContext* gpu            = data.getAmoebaGpu()->gpuContext;
 
+    return cudaCalcForcesAndEnergyKernel->finishComputation( context, includeForces, includeEnergy);
+/*
     if( includeForces ){
         kReduceForces(gpu);
     }
@@ -85,6 +96,7 @@ double CalcAmoebaForcesAndEnergyKernel::finishComputation(ContextImpl& context,
         energy = kReduceEnergy(gpu);
     }    
     return energy;
+*/
 
 }
 

plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.h

@@ -28,6 +28,7 @@
  * -------------------------------------------------------------------------- */
 
 #include "openmm/amoebaKernels.h"
+#include "CudaKernels.h"
 #include "openmm/kernels.h"
 #include "openmm/System.h"
 #include "AmoebaCudaData.h"
@@ -42,6 +43,10 @@ namespace OpenMM {
 class CalcAmoebaForcesAndEnergyKernel : public CalcForcesAndEnergyKernel {
 public:
     CalcAmoebaForcesAndEnergyKernel(std::string name, const Platform& platform, AmoebaCudaData& data) : CalcForcesAndEnergyKernel(name, platform), data(data) {
+        cudaCalcForcesAndEnergyKernel = new CudaCalcForcesAndEnergyKernel( name, platform, data.cudaPlatformData );
+    }   
+    ~CalcAmoebaForcesAndEnergyKernel() {
+        delete cudaCalcForcesAndEnergyKernel;
     }   
     /*** 
      * Initialize the kernel.
@@ -75,6 +80,7 @@ public:
 
 private:
     AmoebaCudaData& data;
+    CudaCalcForcesAndEnergyKernel* cudaCalcForcesAndEnergyKernel;
 };
 
 /**