Fixed bugs in OpenCL CustomHbondForce

platforms/opencl/src/OpenCLKernels.cpp

@@ -2596,10 +2596,14 @@ void OpenCLCalcCustomHbondForceKernel::initialize(const System& system, const Cu
     vector<mm_int4> acceptorBufferVector(numAcceptors);
     vector<int> donorBufferCounter(numParticles, 0);
     for (int i = 0; i < numDonors; i++)
-        donorBufferVector[i] = mm_int4(donorBufferCounter[donorVector[i].x]++, donorBufferCounter[donorVector[i].y]++, donorBufferCounter[donorVector[i].z]++, 0);
+        donorBufferVector[i] = mm_int4(donorVector[i].x > -1 ? donorBufferCounter[donorVector[i].x]++ : 0,
+                                       donorVector[i].y > -1 ? donorBufferCounter[donorVector[i].y]++ : 0,
+                                       donorVector[i].z > -1 ? donorBufferCounter[donorVector[i].z]++ : 0, 0);
     vector<int> acceptorBufferCounter(numParticles, 0);
     for (int i = 0; i < numAcceptors; i++)
-        acceptorBufferVector[i] = mm_int4(acceptorBufferCounter[acceptorVector[i].x]++, acceptorBufferCounter[acceptorVector[i].y]++, acceptorBufferCounter[acceptorVector[i].z]++, 0);
+        acceptorBufferVector[i] = mm_int4(acceptorVector[i].x > -1 ? acceptorBufferCounter[acceptorVector[i].x]++ : 0,
+                                       acceptorVector[i].y > -1 ? acceptorBufferCounter[acceptorVector[i].y]++ : 0,
+                                       acceptorVector[i].z > -1 ? acceptorBufferCounter[acceptorVector[i].z]++ : 0, 0);
     donorBufferIndices->upload(donorBufferVector);
     acceptorBufferIndices->upload(acceptorBufferVector);
     int maxBuffers = 1;

platforms/opencl/src/kernels/customHbondForce.cl

@@ -26,15 +26,15 @@ float4 deltaPeriodic(float4 vec1, float4 vec2) {
  * Compute the angle between two vectors.  The w component of each vector should contain the squared magnitude.
  */
 float computeAngle(float4 vec1, float4 vec2) {
-    float dot = vec1.x*vec2.x + vec1.y*vec2.y + vec1.z*vec2.z;
-    float cosine = dot/sqrt(vec1.w*vec2.w);
+    float dotProduct = vec1.x*vec2.x + vec1.y*vec2.y + vec1.z*vec2.z;
+    float cosine = dotProduct/sqrt(vec1.w*vec2.w);
     float angle;
     if (cosine > 0.99f || cosine < -0.99f) {
         // We're close to the singularity in acos(), so take the cross product and use asin() instead.
 
-        float4 cross_prod = cross(vec1, vec2);
+        float4 crossProduct = cross(vec1, vec2);
         float scale = vec1.w*vec2.w;
-        angle = asin(sqrt(dot(cross_prod, cross_prod)/scale));
+        angle = asin(sqrt(dot(crossProduct, crossProduct)/scale));
         if (cosine < 0.0f)
             angle = M_PI-angle;
     }