Added documentation associated w/ mapping torques

plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaElectrostatic.h

@@ -276,14 +276,14 @@ void METHOD_NAME(kCalculateAmoebaCudaElectrostatic, Forces_kernel)(
             offset                 = (x + tgx + warp*cSim.paddedNumberOfAtoms);
             add3dArray( 3*offset, localParticle.force,  outputTorque );
 
-            offset                              = (y + tgx + warp*cSim.paddedNumberOfAtoms);
+            offset                 = (y + tgx + warp*cSim.paddedNumberOfAtoms);
             add3dArray( 3*offset, sA[threadIdx.x].force,  outputTorque );
 
 #else
             offset                 = (x + tgx + (y >> GRIDBITS) * cSim.paddedNumberOfAtoms);
             load3dArray(         3*offset, localParticle.force, outputTorque );
 
-            offset                              = (y + tgx + (x >> GRIDBITS) * cSim.paddedNumberOfAtoms);
+            offset                 = (y + tgx + (x >> GRIDBITS) * cSim.paddedNumberOfAtoms);
             load3dArray(       3*offset, sA[threadIdx.x].force, outputTorque );
 
 #endif

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

@@ -95,9 +95,9 @@ __device__ void loadKirkwoodShared( struct KirkwoodParticle* sA, unsigned int at
 }
 
 __device__ void calculateKirkwoodPairIxnOrig_kernel( KirkwoodParticle& atomI,       KirkwoodParticle& atomJ,
-                                                 float*  outputForce,           float outputTorque[2][3],
-                                                 float*  outputBorn,            float*  outputBornPolar,
-                                                 float* outputEnergy
+                                                     float*  outputForce,           float outputTorque[2][3],
+                                                     float*  outputBorn,            float*  outputBornPolar,
+                                                     float* outputEnergy
 
  ){
 
@@ -2004,7 +2004,6 @@ void kCalculateAmoebaKirkwood( amoebaGpuContext amoebaGpu )
 
     // Tinker's Born1 && E-diff
 
-    //kCalculateObcGbsaForces2( amoebaGpu->gpuContext );
     kCalculateGrycukGbsaForces2( amoebaGpu );
     kCalculateAmoebaKirkwoodEDiff( amoebaGpu );
 

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

@@ -939,8 +939,6 @@ void kCalculateAmoebaKirkwoodEDiff( amoebaGpuContext amoebaGpu )
 
     gpuContext gpu = amoebaGpu->gpuContext;
 
-    // apparently debug array can take up nontrivial no. registers
-
     static unsigned int threadsPerBlock = 0;
     if( threadsPerBlock == 0 ){
         unsigned int maxThreads;

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

@@ -456,6 +456,16 @@ void cudaComputeAmoebaMapTorqueAndAddToForce( amoebaGpuContext amoebaGpu, CUDASt
   
     gpuContext gpu    = amoebaGpu->gpuContext;
 
+    // The default is to use the Cuda force4 output buffers to collect the forces on each particle arising from the torques: a torque on
+	// particle-i will be mapped into a force on particle-j, where particle-j is one of particles defining the molecular frame axes
+	// associated w/ particle-i. 
+
+	// if amoebaGpu->amoebaSim.maxTorqueBufferIndex > amoebaGpu->gpuContext->sim.outputBuffers, then 
+	// the number of force4 output buffers is too small to accomodate the number of particles whose torques contribute to the force
+	// on at least one particle. In this case, the CUDAStream amoebaGpu->psTorqueMapForce4 is used instead to collect the forces.
+	// amoebaClearMapTorqueForce_kernel() clears these buffers; the call to amoebaAddMapTorqueForceToForce_kernel() below
+	// add the torques from the amoebaGpu->psTorqueMapForce4 buffers to the force4 CUDAStream
+
     if( amoebaGpu->amoebaSim.maxTorqueBufferIndex > amoebaGpu->gpuContext->sim.outputBuffers && amoebaGpu->psTorqueMapForce4 != amoebaGpu->gpuContext->psForce4 && amoebaGpu->psTorqueMapForce4 ){
         amoebaClearMapTorqueForce_kernel<<< gpu->sim.blocks, gpu->sim.threads_per_block>>> ( );
         LAUNCHERROR("amoebaClearMapTorqueForce");