Ugh... stop shadowing dot so I can use it as a function. I hate obscure compiler

errors.

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

@@ -39,9 +39,9 @@ real ym = zcp*xap - xcp*zap;
 real zm = xcp*yap - ycp*xap;
 
 real rm = max(SQRT(xm*xm + ym*ym + zm*zm), (real) 1e-6f);
-real dot = xap*xcp + yap*ycp + zap*zcp;
+real dotp = xap*xcp + yap*ycp + zap*zcp;
 real product = SQRT(rap2*rcp2);
-real cosine = (product > 0 ? (dot/product) : 0);
+real cosine = (product > 0 ? (dotp/product) : 0);
 cosine = max(min(cosine, (real) 1), (real) -1);
 real angle;
 if (cosine > 0.99f || cosine < -0.99f) {
@@ -51,7 +51,7 @@ if (cosine > 0.99f || cosine < -0.99f) {
         angle = 180-angle;
 }
 else
-    real angle = ACOS(cosine)*RAD_TO_DEG;
+    angle = ACOS(cosine)*RAD_TO_DEG;
 
 // if product == 0, set force/energy to 0
 

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

@@ -17,19 +17,20 @@ real zp = xcb*yab - ycb*xab;
 
 real rp = SQRT(xp*xp + yp*yp + zp*zp);
 
-real dot = xab*xcb + yab*ycb + zab*zcb;
-real cosine = rab*rcb > 0 ? (dot / (rab*rcb)) : (real) 1;
+real dotp = xab*xcb + yab*ycb + zab*zcb;
+real cosine = rab*rcb > 0 ? (dotp / (rab*rcb)) : (real) 1;
 cosine = (cosine > 1 ? (real) 1 : cosine);
 cosine = (cosine < -1 ? -(real) 1 : cosine);
 real angle;
 if (cosine > 0.99f || cosine < -0.99f) {
+    // Highly unlikely a stretch-bend angle will be near 0 or 180, but just in case...
     real3 cross_prod = cross(make_real3(xab, yab, zab), make_real3(xcb, ycb, zcb));
-    angle = ASIN(SQRT(dot(cross_prod, cross_prod)/(rap2*rcp2)))*RAD_TO_DEG;
+    angle = ASIN(SQRT(dot(cross_prod, cross_prod))/(rab*rcb))*RAD_TO_DEG;
     if (cosine < 0.0f)
         angle = 180-angle;
 }
 else
-    real angle = ACOS(cosine)*RAD_TO_DEG;
+    angle = ACOS(cosine)*RAD_TO_DEG;
 
 // find chain rule terms for the bond angle deviation