Bug fixes to CustomManyParticleForce

platforms/cuda/src/kernels/customManyParticle.cu

@@ -191,7 +191,7 @@ extern "C" __global__ void findNeighbors(real4 periodicBoxSize, real4 invPeriodi
         ) {
     __shared__ real3 positionCache[FIND_NEIGHBORS_WORKGROUP_SIZE];
     int indexInWarp = threadIdx.x%32;
-    for (int atom1 = blockIdx.x*blockDim.x+threadIdx.x; atom1 < NUM_ATOMS; atom1 += blockDim.x*gridDim.x) {
+    for (int atom1 = blockIdx.x*blockDim.x+threadIdx.x; atom1 < PADDED_NUM_ATOMS; atom1 += blockDim.x*gridDim.x) {
         // Load data for this atom.  Note that all threads in a warp are processing atoms from the same block.
         
         real3 pos1 = trim(posq[atom1]);
@@ -240,6 +240,7 @@ extern "C" __global__ void findNeighbors(real4 periodicBoxSize, real4 invPeriodi
                 int included[TILE_SIZE];
                 int numIncluded = 0;
                 positionCache[threadIdx.x] = trim(posq[start+indexInWarp]);
+                if (atom1 < NUM_ATOMS) {
                     for (int j = 0; j < 32; j++) {
                         int atom2 = start+j;
                         real3 pos2 = positionCache[threadIdx.x-indexInWarp+j];
@@ -259,6 +260,7 @@ extern "C" __global__ void findNeighbors(real4 periodicBoxSize, real4 invPeriodi
                         if (includeAtom)
                             included[numIncluded++] = atom2;
                     }
+                }
 
                 // If we found any neighbors, store them to the neighbor list.
 

wrappers/python/src/swig_doxygen/swigInputConfig.py

@@ -194,6 +194,7 @@ UNITS = {
 ("*", "getWeightCross") : (None, ()),
 ("*", "getNonbondedMethod") : (None, ()),
 ("*", "getGlobalParameterDefaultValue") : (None, ()),
+("*", "getPermutationMode") : (None, ()),
 ("LocalCoordinatesSite", "getOriginWeights") : (None, ()),
 ("LocalCoordinatesSite", "getXWeights") : (None, ()),
 ("LocalCoordinatesSite", "getYWeights") : (None, ()),