Merged fork with latest original master

platforms/opencl/src/kernels/cmapTorsionForce.cl

@@ -5,6 +5,11 @@ const real PI = 3.14159265358979323846f;
 real4 v0a = (real4) (pos1.xyz-pos2.xyz, 0.0f);
 real4 v1a = (real4) (pos3.xyz-pos2.xyz, 0.0f);
 real4 v2a = (real4) (pos3.xyz-pos4.xyz, 0.0f);
+#if APPLY_PERIODIC
+APPLY_PERIODIC_TO_DELTA(v0a)
+APPLY_PERIODIC_TO_DELTA(v1a)
+APPLY_PERIODIC_TO_DELTA(v2a)
+#endif
 real4 cp0a = cross(v0a, v1a);
 real4 cp1a = cross(v1a, v2a);
 real cosangle = dot(normalize(cp0a), normalize(cp1a));
@@ -28,6 +33,11 @@ angleA = fmod(angleA+2.0f*PI, 2.0f*PI);
 real4 v0b = (real4) (pos5.xyz-pos6.xyz, 0.0f);
 real4 v1b = (real4) (pos7.xyz-pos6.xyz, 0.0f);
 real4 v2b = (real4) (pos7.xyz-pos8.xyz, 0.0f);
+#if APPLY_PERIODIC
+APPLY_PERIODIC_TO_DELTA(v0b)
+APPLY_PERIODIC_TO_DELTA(v1b)
+APPLY_PERIODIC_TO_DELTA(v2b)
+#endif
 real4 cp0b = cross(v0b, v1b);
 real4 cp1b = cross(v1b, v2b);
 cosangle = dot(normalize(cp0b), normalize(cp1b));

platforms/opencl/src/kernels/coulombLennardJones.cl

@@ -30,6 +30,10 @@
             tempForce = -prefactor*(erfAlphaR-alphaR*expAlphaRSqr*TWO_OVER_SQRT_PI);
             tempEnergy += -prefactor*erfAlphaR;
         }
+        else {
+            includeInteraction = false;
+            tempEnergy -= TWO_OVER_SQRT_PI*EWALD_ALPHA*138.935456f*posq1.w*posq2.w;
+        }
     }
     else {
 #if HAS_LENNARD_JONES

platforms/opencl/src/kernels/customCentroidBond.cl

@@ -70,8 +70,11 @@ __kernel void computeGroupCenters(__global const real4* restrict posq, __global
 /**
  * Compute the difference between two vectors, setting the fourth component to the squared magnitude.
  */
-real4 delta(real4 vec1, real4 vec2) {
+real4 delta(real4 vec1, real4 vec2, bool periodic, real4 periodicBoxSize, real4 invPeriodicBoxSize, 
+        real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ) {
     real4 result = (real4) (vec1.x-vec2.x, vec1.y-vec2.y, vec1.z-vec2.z, 0);
+    if (periodic)
+        APPLY_PERIODIC_TO_DELTA(result);
     result.w = result.x*result.x + result.y*result.y + result.z*result.z;
     return result;
 }
@@ -110,7 +113,7 @@ real4 computeCross(real4 vec1, real4 vec2) {
  * Compute the forces on groups based on the bonds.
  */
 __kernel void computeGroupForces(__global long* restrict groupForce, __global mixed* restrict energyBuffer, __global const real4* restrict centerPositions,
-        __global const int* restrict bondGroups
+        __global const int* restrict bondGroups, real4 periodicBoxSize, real4 invPeriodicBoxSize, real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ
         EXTRA_ARGS) {
     mixed energy = 0;
     for (int index = get_global_id(0); index < NUM_BONDS; index += get_global_size(0)) {

platforms/opencl/src/kernels/customCompoundBond.cl

 /**
  * Compute the difference between two vectors, setting the fourth component to the squared magnitude.
  */
-real4 ccb_delta(real4 vec1, real4 vec2) {
+real4 ccb_delta(real4 vec1, real4 vec2, bool periodic, real4 periodicBoxSize, real4 invPeriodicBoxSize, 
+        real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ) {
     real4 result = (real4) (vec1.x-vec2.x, vec1.y-vec2.y, vec1.z-vec2.z, 0);
+    if (periodic)
+        APPLY_PERIODIC_TO_DELTA(result);
     result.w = result.x*result.x + result.y*result.y + result.z*result.z;
     return result;
 }

platforms/opencl/src/kernels/customGBEnergyN2.cl

@@ -181,6 +181,8 @@ __kernel void computeN2Energy(
 
 #ifdef USE_CUTOFF
     unsigned int numTiles = interactionCount[0];
+    if (numTiles > maxTiles)
+        return; // There wasn't enough memory for the neighbor list.
     int pos = (int) (warp*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps);
     int end = (int) ((warp+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps);
 #else
@@ -204,16 +206,12 @@ __kernel void computeN2Energy(
         int x, y;
         bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
-        if (numTiles <= maxTiles) {
         x = tiles[pos];
         real4 blockSizeX = blockSize[x];
         singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
                               0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&
                               0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF);
-        }
-        else
-#endif
-        {
+#else
         y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
         x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
         if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
@@ -239,7 +237,7 @@ __kernel void computeN2Energy(
         while (skipTiles[currentSkipIndex] < pos)
             currentSkipIndex++;
         includeTile = (skipTiles[currentSkipIndex] != pos);
-        }
+#endif
         if (includeTile) {
             unsigned int atom1 = x*TILE_SIZE + tgx;
 

platforms/opencl/src/kernels/customGBEnergyN2_cpu.cl

@@ -201,6 +201,8 @@ __kernel void computeN2Energy(
 
 #ifdef USE_CUTOFF
     const unsigned int numTiles = interactionCount[0];
+    if (numTiles > maxTiles)
+        return; // There wasn't enough memory for the neighbor list.
     int pos = (int) (get_group_id(0)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : numTiles)/get_num_groups(0));
     int end = (int) ((get_group_id(0)+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : numTiles)/get_num_groups(0));
 #else
@@ -220,16 +222,12 @@ __kernel void computeN2Energy(
         int x, y;
         bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
-        if (numTiles <= maxTiles) {
         x = tiles[pos];
         real4 blockSizeX = blockSize[x];
         singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
                               0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&
                               0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF);
-        }
-        else
-#endif
-        {
+#else
         y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
         x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
         if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
@@ -248,7 +246,7 @@ __kernel void computeN2Energy(
                 nextToSkip = end;
         }
         includeTile = (nextToSkip != pos);
-        }
+#endif
         if (includeTile) {
             // Load the data for this tile.
 

platforms/opencl/src/kernels/customGBValueN2.cl

@@ -157,6 +157,8 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
 
 #ifdef USE_CUTOFF
     unsigned int numTiles = interactionCount[0];
+    if (numTiles > maxTiles)
+        return; // There wasn't enough memory for the neighbor list.
     int pos = (int) (warp*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps);
     int end = (int) ((warp+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps);
 #else
@@ -178,16 +180,12 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
         int x, y;
         bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
-        if (numTiles <= maxTiles) {
         x = tiles[pos];
         real4 blockSizeX = blockSize[x];
         singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
                               0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&
                               0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF);
-        }
-        else
-#endif
-        {
+#else
         y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
         x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
         if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
@@ -213,7 +211,7 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
         while (skipTiles[currentSkipIndex] < pos)
             currentSkipIndex++;
         includeTile = (skipTiles[currentSkipIndex] != pos);
-        }
+#endif
         if (includeTile) {
             unsigned int atom1 = x*TILE_SIZE + tgx;
 

platforms/opencl/src/kernels/customGBValueN2_cpu.cl

@@ -170,6 +170,8 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
 
 #ifdef USE_CUTOFF
     const unsigned int numTiles = interactionCount[0];
+    if (numTiles > maxTiles)
+        return; // There wasn't enough memory for the neighbor list.
     int pos = (int) (get_group_id(0)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : numTiles)/get_num_groups(0));
     int end = (int) ((get_group_id(0)+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : numTiles)/get_num_groups(0));
 #else
@@ -188,16 +190,12 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
         int x, y;
         bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
-        if (numTiles <= maxTiles) {
         x = tiles[pos];
         real4 blockSizeX = blockSize[x];
         singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
                               0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&
                               0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF);
-        }
-        else
-#endif
-        {
+#else
         y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
         x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
         if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
@@ -216,7 +214,7 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
                 nextToSkip = end;
         }
         includeTile = (nextToSkip != pos);
-        }
+#endif
         if (includeTile) {
             // Load the data for this tile.
 

platforms/opencl/src/kernels/customManyParticle.cl

@@ -55,7 +55,7 @@ inline real4 computeCross(real4 vec1, real4 vec2) {
 /**
  * Determine whether a particular interaction is in the list of exclusions.
  */
-inline bool isInteractionExcluded(int atom1, int atom2, __global int* restrict exclusions, __global int* restrict exclusionStartIndex) {
+inline bool isInteractionExcluded(int atom1, int atom2, __global const int* restrict exclusions, __global const int* restrict exclusionStartIndex) {
     int first = exclusionStartIndex[atom1];
     int last = exclusionStartIndex[atom1+1];
     for (int i = last-1; i >= first; i--) {
@@ -174,7 +174,7 @@ __kernel void findNeighbors(real4 periodicBoxSize, real4 invPeriodicBoxSize, rea
         __global const real4* restrict posq, __global const real4* restrict blockCenter, __global const real4* restrict blockBoundingBox, __global int2* restrict neighborPairs,
         __global int* restrict numNeighborPairs, __global int* restrict numNeighborsForAtom, int maxNeighborPairs
 #ifdef USE_EXCLUSIONS
-        , __global int* restrict exclusions, __global int* restrict exclusionStartIndex
+        , __global const int* restrict exclusions, __global const int* restrict exclusionStartIndex
 #endif
         ) {
     __local real4 positionCache[FIND_NEIGHBORS_WORKGROUP_SIZE];
@@ -264,7 +264,9 @@ __kernel void findNeighbors(real4 periodicBoxSize, real4 invPeriodicBoxSize, rea
                 }
             }
         }
+        if (atom1 < NUM_ATOMS)
             numNeighborsForAtom[atom1] = totalNeighborsForAtom1;
+        SYNC_WARPS;
     }
 }
 
@@ -307,6 +309,7 @@ __kernel void computeNeighborStartIndices(__global int* restrict numNeighborsFor
             numNeighborsForAtom[globalIndex] = 0; // Clear this so the next kernel can use it as a counter
         }
         globalOffset += posBuffer[get_local_size(0)-1];
+        barrier(CLK_LOCAL_MEM_FENCE);
     }
     if (get_local_id(0) == 0)
         neighborStartIndex[0] = 0;

platforms/opencl/src/kernels/gbsaObc.cl

@@ -169,6 +169,8 @@ __kernel void computeBornSum(
 
 #ifdef USE_CUTOFF
     unsigned int numTiles = interactionCount[0];
+    if (numTiles > maxTiles)
+        return; // There wasn't enough memory for the neighbor list.
     int pos = (int) (warp*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps);
     int end = (int) ((warp+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps);
 #else
@@ -190,16 +192,12 @@ __kernel void computeBornSum(
         int x, y;
         bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
-        if (numTiles <= maxTiles) {
         x = tiles[pos];
         real4 blockSizeX = blockSize[x];
         singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
                               0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&
                               0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF);
-        }
-        else
-#endif
-        {
+#else
         y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
         x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
         if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
@@ -225,7 +223,7 @@ __kernel void computeBornSum(
         while (skipTiles[currentSkipIndex] < pos)
             currentSkipIndex++;
         includeTile = (skipTiles[currentSkipIndex] != pos);
-        }
+#endif
         if (includeTile) {
             unsigned int atom1 = x*TILE_SIZE + tgx;
 
@@ -556,6 +554,8 @@ __kernel void computeGBSAForce1(
 
 #ifdef USE_CUTOFF
     unsigned int numTiles = interactionCount[0];
+    if (numTiles > maxTiles)
+        return; // There wasn't enough memory for the neighbor list.
     int pos = (int) (warp*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps);
     int end = (int) ((warp+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps);
 #else
@@ -577,16 +577,12 @@ __kernel void computeGBSAForce1(
         int x, y;
         bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
-        if (numTiles <= maxTiles) {
         x = tiles[pos];
         real4 blockSizeX = blockSize[x];
         singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
                               0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&
                               0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF);
-        }
-        else
-#endif
-        {
+#else
         y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
         x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
         if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
@@ -612,7 +608,7 @@ __kernel void computeGBSAForce1(
         while (skipTiles[currentSkipIndex] < pos)
             currentSkipIndex++;
         includeTile = (skipTiles[currentSkipIndex] != pos);
-        }
+#endif
         if (includeTile) {
             unsigned int atom1 = x*TILE_SIZE + tgx;
 

platforms/opencl/src/kernels/gbsaObc_cpu.cl

@@ -178,6 +178,8 @@ __kernel void computeBornSum(
 
 #ifdef USE_CUTOFF
     unsigned int numTiles = interactionCount[0];
+    if (numTiles > maxTiles)
+        return; // There wasn't enough memory for the neighbor list.
     int pos = (int) (get_group_id(0)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : numTiles)/get_num_groups(0));
     int end = (int) ((get_group_id(0)+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : numTiles)/get_num_groups(0));
 #else
@@ -196,16 +198,12 @@ __kernel void computeBornSum(
         int x, y;
         bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
-        if (numTiles <= maxTiles) {
         x = tiles[pos];
         real4 blockSizeX = blockSize[x];
         singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
                               0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&
                               0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF);
-        }
-        else
-#endif
-        {
+#else
         y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
         x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
         if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
@@ -224,7 +222,7 @@ __kernel void computeBornSum(
                 nextToSkip = end;
         }
         includeTile = (nextToSkip != pos);
-        }
+#endif
         if (includeTile) {
             // Load the data for this tile.
 
@@ -593,6 +591,8 @@ __kernel void computeGBSAForce1(
 
 #ifdef USE_CUTOFF
     unsigned int numTiles = interactionCount[0];
+    if (numTiles > maxTiles)
+        return; // There wasn't enough memory for the neighbor list.
     int pos = (int) (get_group_id(0)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : numTiles)/get_num_groups(0));
     int end = (int) ((get_group_id(0)+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : numTiles)/get_num_groups(0));
 #else
@@ -611,16 +611,12 @@ __kernel void computeGBSAForce1(
         int x, y;
         bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
-        if (numTiles <= maxTiles) {
         x = tiles[pos];
         real4 blockSizeX = blockSize[x];
         singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
                               0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&
                               0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF);
-        }
-        else
-#endif
-        {
+#else
         y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
         x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
         if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
@@ -639,7 +635,7 @@ __kernel void computeGBSAForce1(
                 nextToSkip = end;
         }
         includeTile = (nextToSkip != pos);
-        }
+#endif
         if (includeTile) {
             // Load the data for this tile.
 

platforms/opencl/src/kernels/nonbonded.cl

@@ -200,6 +200,8 @@ __kernel void computeNonbonded(
 
 #ifdef USE_CUTOFF
     unsigned int numTiles = interactionCount[0];
+    if (numTiles > maxTiles)
+        return; // There wasn't enough memory for the neighbor list.
     int pos = (int) (numTiles > maxTiles ? startTileIndex+warp*(long)numTileIndices/totalWarps : warp*(long)numTiles/totalWarps);
     int end = (int) (numTiles > maxTiles ? startTileIndex+(warp+1)*(long)numTileIndices/totalWarps : (warp+1)*(long)numTiles/totalWarps);
 #else
@@ -223,16 +225,12 @@ __kernel void computeNonbonded(
         int x, y;
         bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
-        if (numTiles <= maxTiles) {
         x = tiles[pos];
         real4 blockSizeX = blockSize[x];
         singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= MAX_CUTOFF &&
                               0.5f*periodicBoxSize.y-blockSizeX.y >= MAX_CUTOFF &&
                               0.5f*periodicBoxSize.z-blockSizeX.z >= MAX_CUTOFF);
-        }
-        else
-#endif
-        {
+#else
         y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
         x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
         if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
@@ -258,7 +256,7 @@ __kernel void computeNonbonded(
         while (skipTiles[currentSkipIndex] < pos)
             currentSkipIndex++;
         includeTile = (skipTiles[currentSkipIndex] != pos);
-        }
+#endif
         if (includeTile) {
             unsigned int atom1 = x*TILE_SIZE + tgx;
 

platforms/opencl/src/kernels/nonbonded_cpu.cl

@@ -214,6 +214,8 @@ __kernel void computeNonbonded(
 
 #ifdef USE_CUTOFF
     const unsigned int numTiles = interactionCount[0];
+    if (numTiles > maxTiles)
+        return; // There wasn't enough memory for the neighbor list.
     int pos = (int) (numTiles > maxTiles ? (unsigned int) (startTileIndex+get_group_id(0)*(long)numTileIndices/get_num_groups(0)) : get_group_id(0)*(long)numTiles/get_num_groups(0));
     int end = (int) (numTiles > maxTiles ? (unsigned int) (startTileIndex+(get_group_id(0)+1)*(long)numTileIndices/get_num_groups(0)) : (get_group_id(0)+1)*(long)numTiles/get_num_groups(0));
 #else
@@ -234,16 +236,12 @@ __kernel void computeNonbonded(
         int x, y;
         bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
-        if (numTiles <= maxTiles) {
         x = tiles[pos];
         real4 blockSizeX = blockSize[x];
         singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= MAX_CUTOFF &&
                               0.5f*periodicBoxSize.y-blockSizeX.y >= MAX_CUTOFF &&
                               0.5f*periodicBoxSize.z-blockSizeX.z >= MAX_CUTOFF);
-        }
-        else
-#endif
-        {
+#else
         y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
         x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
         if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
@@ -262,7 +260,7 @@ __kernel void computeNonbonded(
                 nextToSkip = end;
         }
         includeTile = (nextToSkip != pos);
-        }
+#endif
         if (includeTile) {
             // Load the data for this tile.
 

platforms/opencl/src/kernels/pme.cl

 __kernel void updateBsplines(__global const real4* restrict posq, __global real4* restrict pmeBsplineTheta, __local real4* restrict bsplinesCache,
-        __global int2* restrict pmeAtomGridIndex, real4 periodicBoxSize, real4 recipBoxVecX, real4 recipBoxVecY, real4 recipBoxVecZ) {
+        __global int2* restrict pmeAtomGridIndex, real4 periodicBoxSize, real4 invPeriodicBoxSize, real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ,
+        real4 recipBoxVecX, real4 recipBoxVecY, real4 recipBoxVecZ) {
     const real4 scale = 1/(real) (PME_ORDER-1);
     for (int i = get_global_id(0); i < NUM_ATOMS; i += get_global_size(0)) {
         __local real4* data = &bsplinesCache[get_local_id(0)*PME_ORDER];
         real4 pos = posq[i];
+        APPLY_PERIODIC_TO_POS(pos)
         real3 t = (real3) (pos.x*recipBoxVecX.x+pos.y*recipBoxVecY.x+pos.z*recipBoxVecZ.x,
                            pos.y*recipBoxVecY.y+pos.z*recipBoxVecZ.y,
                            pos.z*recipBoxVecZ.z);
@@ -83,8 +85,9 @@ __kernel void recordZIndex(__global int2* restrict pmeAtomGridIndex, __global co
 #pragma OPENCL EXTENSION cl_khr_int64_base_atomics : enable
 
 __kernel void gridSpreadCharge(__global const real4* restrict posq, __global const int2* restrict pmeAtomGridIndex, __global const int* restrict pmeAtomRange,
-        __global long* restrict pmeGrid, __global const real4* restrict pmeBsplineTheta, real4 periodicBoxSize, real4 recipBoxVecX, real4 recipBoxVecY, real4 recipBoxVecZ) {
-    const real4 scale = 1/(real) (PME_ORDER-1);
+        __global long* restrict pmeGrid, __global const real4* restrict pmeBsplineTheta, real4 periodicBoxSize, real4 invPeriodicBoxSize,
+        real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ, real4 recipBoxVecX, real4 recipBoxVecY, real4 recipBoxVecZ) {
+    const real scale = 1/(real) (PME_ORDER-1);
     real4 data[PME_ORDER];
     
     // Process the atoms in spatially sorted order.  This improves efficiency when writing
@@ -93,9 +96,7 @@ __kernel void gridSpreadCharge(__global const real4* restrict posq, __global con
     for (int i = get_global_id(0); i < NUM_ATOMS; i += get_global_size(0)) {
         int atom = pmeAtomGridIndex[i].x;
         real4 pos = posq[atom];
-        pos.x -= floor(pos.x*recipBoxVecX.x)*periodicBoxSize.x;
-        pos.y -= floor(pos.y*recipBoxVecY.y)*periodicBoxSize.y;
-        pos.z -= floor(pos.z*recipBoxVecZ.z)*periodicBoxSize.z;
+        APPLY_PERIODIC_TO_POS(pos)
         real3 t = (real3) (pos.x*recipBoxVecX.x+pos.y*recipBoxVecY.x+pos.z*recipBoxVecZ.x,
                            pos.y*recipBoxVecY.y+pos.z*recipBoxVecZ.y,
                            pos.z*recipBoxVecZ.z);
@@ -118,7 +119,7 @@ __kernel void gridSpreadCharge(__global const real4* restrict posq, __global con
             data[j-1] = div*dr*data[j-2];
             for (int k = 1; k < (j-1); k++)
                 data[j-k-1] = div*((dr+(real4) k) *data[j-k-2] + (-dr+(real4) (j-k))*data[j-k-1]);
-            data[0] = div*(- dr+1.0f)*data[0];
+            data[0] = div*(-dr+1.0f)*data[0];
         }
         data[PME_ORDER-1] = scale*dr*data[PME_ORDER-2];
         for (int j = 1; j < (PME_ORDER-1); j++)
@@ -165,7 +166,8 @@ __kernel void finishSpreadCharge(__global long* restrict fixedGrid, __global rea
 }
 #elif defined(DEVICE_IS_CPU)
 __kernel void gridSpreadCharge(__global const real4* restrict posq, __global const int2* restrict pmeAtomGridIndex, __global const int* restrict pmeAtomRange,
-        __global real* restrict pmeGrid, __global const real4* restrict pmeBsplineTheta, real4 periodicBoxSize, real4 recipBoxVecX, real4 recipBoxVecY, real4 recipBoxVecZ) {
+        __global real* restrict pmeGrid, __global const real4* restrict pmeBsplineTheta, real4 periodicBoxSize, real4 invPeriodicBoxSize,
+        real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ, real4 recipBoxVecX, real4 recipBoxVecY, real4 recipBoxVecZ) {
     const int firstx = get_global_id(0)*GRID_SIZE_X/get_global_size(0);
     const int lastx = (get_global_id(0)+1)*GRID_SIZE_X/get_global_size(0);
     if (firstx == lastx)
@@ -179,9 +181,7 @@ __kernel void gridSpreadCharge(__global const real4* restrict posq, __global con
     for (int i = 0; i < NUM_ATOMS; i++) {
         int atom = i;//pmeAtomGridIndex[i].x;
         real4 pos = posq[atom];
-        pos.x -= floor(pos.x*recipBoxVecX.x)*periodicBoxSize.x;
-        pos.y -= floor(pos.y*recipBoxVecY.y)*periodicBoxSize.y;
-        pos.z -= floor(pos.z*recipBoxVecZ.z)*periodicBoxSize.z;
+        APPLY_PERIODIC_TO_POS(pos)
         real3 t = (real3) (pos.x*recipBoxVecX.x+pos.y*recipBoxVecY.x+pos.z*recipBoxVecZ.x,
                            pos.y*recipBoxVecY.y+pos.z*recipBoxVecZ.y,
                            pos.z*recipBoxVecZ.z);
@@ -362,12 +362,17 @@ __kernel void gridEvaluateEnergy(__global real2* restrict pmeGrid, __global mixe
             energy += eterm*(grid.x*grid.x + grid.y*grid.y);
         }
     }
+#ifdef USE_PME_STREAM
     energyBuffer[get_global_id(0)] = 0.5f*energy;
+#else
+    energyBuffer[get_global_id(0)] += 0.5f*energy;
+#endif
 }
 
 __kernel void gridInterpolateForce(__global const real4* restrict posq, __global real4* restrict forceBuffers, __global const real* restrict pmeGrid,
-        real4 periodicBoxSize, real4 recipBoxVecX, real4 recipBoxVecY, real4 recipBoxVecZ, __global int2* restrict pmeAtomGridIndex) {
-    const real4 scale = 1/(real) (PME_ORDER-1);
+        real4 periodicBoxSize, real4 invPeriodicBoxSize, real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ, real4 recipBoxVecX,
+        real4 recipBoxVecY, real4 recipBoxVecZ, __global int2* restrict pmeAtomGridIndex) {
+    const real scale = 1/(real) (PME_ORDER-1);
     real4 data[PME_ORDER];
     real4 ddata[PME_ORDER];
     
@@ -378,9 +383,7 @@ __kernel void gridInterpolateForce(__global const real4* restrict posq, __global
         int atom = pmeAtomGridIndex[i].x;
         real4 force = 0.0f;
         real4 pos = posq[atom];
-        pos.x -= floor(pos.x*recipBoxVecX.x)*periodicBoxSize.x;
-        pos.y -= floor(pos.y*recipBoxVecY.y)*periodicBoxSize.y;
-        pos.z -= floor(pos.z*recipBoxVecZ.z)*periodicBoxSize.z;
+        APPLY_PERIODIC_TO_POS(pos)
         real3 t = (real3) (pos.x*recipBoxVecX.x+pos.y*recipBoxVecY.x+pos.z*recipBoxVecZ.x,
                            pos.y*recipBoxVecY.y+pos.z*recipBoxVecZ.y,
                            pos.z*recipBoxVecZ.z);
@@ -403,7 +406,7 @@ __kernel void gridInterpolateForce(__global const real4* restrict posq, __global
             data[j-1] = div*dr*data[j-2];
             for (int k = 1; k < (j-1); k++)
                 data[j-k-1] = div*((dr+(real4) k) *data[j-k-2] + (-dr+(real4) (j-k))*data[j-k-1]);
-            data[0] = div*(- dr+1.0f)*data[0];
+            data[0] = div*(-dr+1.0f)*data[0];
         }
         ddata[0] = -data[0];
         for (int j = 1; j < PME_ORDER; j++)

platforms/opencl/src/kernels/torsionForce.cl

@@ -2,6 +2,11 @@ const real PI = 3.14159265358979323846f;
 real4 v0 = (real4) (pos1.xyz-pos2.xyz, 0.0f);
 real4 v1 = (real4) (pos3.xyz-pos2.xyz, 0.0f);
 real4 v2 = (real4) (pos3.xyz-pos4.xyz, 0.0f);
+#if APPLY_PERIODIC
+APPLY_PERIODIC_TO_DELTA(v0)
+APPLY_PERIODIC_TO_DELTA(v1)
+APPLY_PERIODIC_TO_DELTA(v2)
+#endif
 real4 cp0 = cross(v0, v1);
 real4 cp1 = cross(v1, v2);
 real cosangle = dot(normalize(cp0), normalize(cp1));

platforms/opencl/tests/OpenCLTests.h

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2015 Stanford University and the Authors.           *
+ * Portions copyright (c) 2015-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -39,9 +39,9 @@ OpenMM::OpenCLPlatform platform;
 
 void initializeTests(int argc, char* argv[]) {
     if (argc > 1)
-        platform.setPropertyDefaultValue("OpenCLPrecision", std::string(argv[1]));
+        platform.setPropertyDefaultValue("Precision", std::string(argv[1]));
     if (argc > 2)
         platform.setPropertyDefaultValue("OpenCLPlatformIndex", std::string(argv[2]));
     if (argc > 3)
-        platform.setPropertyDefaultValue("OpenCLDeviceIndex", std::string(argv[3]));
+        platform.setPropertyDefaultValue("DeviceIndex", std::string(argv[3]));
 }

platforms/opencl/tests/TestOpenCLCheckpoints.cpp

@@ -120,6 +120,15 @@ void testCheckpoint() {
     integrator2.step(10);
     State s8 = context2.getState(State::Positions | State::Velocities | State::Parameters);
     compareStates(s6, s8);
+    
+    // See if a checkpoint created from one Context can be loaded into a different one.
+    
+    VerletIntegrator integrator3(0.001);
+    Context context3(system, integrator3, platform);
+    stream1.seekg(0, stream1.beg);
+    context3.loadCheckpoint(stream1);
+    State s9 = context3.getState(State::Positions | State::Velocities | State::Parameters | State::Energy);
+    compareStates(s1, s9);
 }
 
 void runPlatformTests() {

platforms/opencl/tests/TestOpenCLFFT.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2011-2015 Stanford University and the Authors.      *
+ * Portions copyright (c) 2011-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -54,7 +54,7 @@ template <class Real2>
 void testTransform(bool realToComplex, int xsize, int ysize, int zsize) {
     System system;
     system.addParticle(0.0);
-    OpenCLPlatform::PlatformData platformData(system, "", "", platform.getPropertyDefaultValue("OpenCLPrecision"), "false");
+    OpenCLPlatform::PlatformData platformData(system, "", "", platform.getPropertyDefaultValue("OpenCLPrecision"), "false", "false", 1);
     OpenCLContext& context = *platformData.contexts[0];
     context.initialize();
     OpenMM_SFMT::SFMT sfmt;

platforms/opencl/tests/TestOpenCLRandom.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2009 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -54,7 +54,7 @@ void testGaussian() {
     System system;
     for (int i = 0; i < numAtoms; i++)
         system.addParticle(1.0);
-    OpenCLPlatform::PlatformData platformData(system, "", "", platform.getPropertyDefaultValue("OpenCLPrecision"), "false");
+    OpenCLPlatform::PlatformData platformData(system, "", "", platform.getPropertyDefaultValue("OpenCLPrecision"), "false", "false", 1);
     OpenCLContext& context = *platformData.contexts[0];
     context.initialize();
     context.getIntegrationUtilities().initRandomNumberGenerator(0);

platforms/opencl/tests/TestOpenCLSort.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2009 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -64,7 +64,7 @@ void verifySorting(vector<float> array) {
 
     System system;
     system.addParticle(0.0);
-    OpenCLPlatform::PlatformData platformData(system, "", "", platform.getPropertyDefaultValue("OpenCLPrecision"), "false");
+    OpenCLPlatform::PlatformData platformData(system, "", "", platform.getPropertyDefaultValue("OpenCLPrecision"), "false", "false", 1);
     OpenCLContext& context = *platformData.contexts[0];
     context.initialize();
     OpenCLArray data(context, array.size(), sizeof(float), "sortData");