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Commit dca54ec7 authored by Saurabh Belsare's avatar Saurabh Belsare
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Merged fork with latest original master

parents cace5edf 01f9e415
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Showing with 322 additions and 302 deletions
platforms/opencl/src/kernels/cmapTorsionForce.cl
View file @ dca54ec7
......@@ -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
View file @ dca54ec7
......@@ -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
View file @ dca54ec7
......@@ -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
View file @ dca54ec7
/**
* 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
View file @ dca54ec7
......@@ -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
......@@ -204,42 +206,38 @@ __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
{
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
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
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.
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
}
}
// Skip over tiles that have exclusions, since they were already processed.
// Skip over tiles that have exclusions, since they were already processed.
SYNC_WARPS;
while (skipTiles[tbx+TILE_SIZE-1] < pos) {
SYNC_WARPS;
while (skipTiles[tbx+TILE_SIZE-1] < pos) {
SYNC_WARPS;
if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[skipBase+tgx];
skipTiles[get_local_id(0)] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
else
skipTiles[get_local_id(0)] = end;
skipBase += TILE_SIZE;
currentSkipIndex = tbx;
SYNC_WARPS;
if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[skipBase+tgx];
skipTiles[get_local_id(0)] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
while (skipTiles[currentSkipIndex] < pos)
currentSkipIndex++;
includeTile = (skipTiles[currentSkipIndex] != pos);
else
skipTiles[get_local_id(0)] = end;
skipBase += TILE_SIZE;
currentSkipIndex = tbx;
SYNC_WARPS;
}
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
View file @ dca54ec7
......@@ -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
......@@ -220,35 +222,31 @@ __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
{
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
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
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.
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
}
}
// Skip over tiles that have exclusions, since they were already processed.
// Skip over tiles that have exclusions, since they were already processed.
while (nextToSkip < pos) {
if (currentSkipIndex < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[currentSkipIndex++];
nextToSkip = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
else
nextToSkip = end;
while (nextToSkip < pos) {
if (currentSkipIndex < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[currentSkipIndex++];
nextToSkip = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
includeTile = (nextToSkip != pos);
else
nextToSkip = end;
}
includeTile = (nextToSkip != pos);
#endif
if (includeTile) {
// Load the data for this tile.
......
platforms/opencl/src/kernels/customGBValueN2.cl
View file @ dca54ec7
......@@ -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
......@@ -178,42 +180,38 @@ __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
{
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
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
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.
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
}
}
// Skip over tiles that have exclusions, since they were already processed.
// Skip over tiles that have exclusions, since they were already processed.
SYNC_WARPS;
while (skipTiles[tbx+TILE_SIZE-1] < pos) {
SYNC_WARPS;
while (skipTiles[tbx+TILE_SIZE-1] < pos) {
SYNC_WARPS;
if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[skipBase+tgx];
skipTiles[get_local_id(0)] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
else
skipTiles[get_local_id(0)] = end;
skipBase += TILE_SIZE;
currentSkipIndex = tbx;
SYNC_WARPS;
if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[skipBase+tgx];
skipTiles[get_local_id(0)] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
while (skipTiles[currentSkipIndex] < pos)
currentSkipIndex++;
includeTile = (skipTiles[currentSkipIndex] != pos);
else
skipTiles[get_local_id(0)] = end;
skipBase += TILE_SIZE;
currentSkipIndex = tbx;
SYNC_WARPS;
}
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
View file @ dca54ec7
......@@ -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
......@@ -188,35 +190,31 @@ __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
{
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
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
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.
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
}
}
// Skip over tiles that have exclusions, since they were already processed.
// Skip over tiles that have exclusions, since they were already processed.
while (nextToSkip < pos) {
if (currentSkipIndex < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[currentSkipIndex++];
nextToSkip = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
else
nextToSkip = end;
while (nextToSkip < pos) {
if (currentSkipIndex < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[currentSkipIndex++];
nextToSkip = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
includeTile = (nextToSkip != pos);
else
nextToSkip = end;
}
includeTile = (nextToSkip != pos);
#endif
if (includeTile) {
// Load the data for this tile.
......
platforms/opencl/src/kernels/customManyParticle.cl
View file @ dca54ec7
......@@ -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
}
}
}
numNeighborsForAtom[atom1] = totalNeighborsForAtom1;
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
View file @ dca54ec7
......@@ -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
......@@ -190,42 +192,38 @@ __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
{
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
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
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.
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
}
}
// Skip over tiles that have exclusions, since they were already processed.
// Skip over tiles that have exclusions, since they were already processed.
SYNC_WARPS;
while (skipTiles[tbx+TILE_SIZE-1] < pos) {
SYNC_WARPS;
while (skipTiles[tbx+TILE_SIZE-1] < pos) {
SYNC_WARPS;
if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[skipBase+tgx];
skipTiles[get_local_id(0)] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
else
skipTiles[get_local_id(0)] = end;
skipBase += TILE_SIZE;
currentSkipIndex = tbx;
SYNC_WARPS;
if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[skipBase+tgx];
skipTiles[get_local_id(0)] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
while (skipTiles[currentSkipIndex] < pos)
currentSkipIndex++;
includeTile = (skipTiles[currentSkipIndex] != pos);
else
skipTiles[get_local_id(0)] = end;
skipBase += TILE_SIZE;
currentSkipIndex = tbx;
SYNC_WARPS;
}
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
......@@ -577,42 +577,38 @@ __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
{
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
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
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.
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
}
}
// Skip over tiles that have exclusions, since they were already processed.
// Skip over tiles that have exclusions, since they were already processed.
SYNC_WARPS;
while (skipTiles[tbx+TILE_SIZE-1] < pos) {
SYNC_WARPS;
while (skipTiles[tbx+TILE_SIZE-1] < pos) {
SYNC_WARPS;
if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[skipBase+tgx];
skipTiles[get_local_id(0)] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
else
skipTiles[get_local_id(0)] = end;
skipBase += TILE_SIZE;
currentSkipIndex = tbx;
SYNC_WARPS;
if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[skipBase+tgx];
skipTiles[get_local_id(0)] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
while (skipTiles[currentSkipIndex] < pos)
currentSkipIndex++;
includeTile = (skipTiles[currentSkipIndex] != pos);
else
skipTiles[get_local_id(0)] = end;
skipBase += TILE_SIZE;
currentSkipIndex = tbx;
SYNC_WARPS;
}
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
View file @ dca54ec7
......@@ -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
......@@ -196,35 +198,31 @@ __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
{
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
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
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.
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
}
}
// Skip over tiles that have exclusions, since they were already processed.
// Skip over tiles that have exclusions, since they were already processed.
while (nextToSkip < pos) {
if (currentSkipIndex < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[currentSkipIndex++];
nextToSkip = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
else
nextToSkip = end;
while (nextToSkip < pos) {
if (currentSkipIndex < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[currentSkipIndex++];
nextToSkip = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
includeTile = (nextToSkip != pos);
else
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
......@@ -611,35 +611,31 @@ __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
{
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
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
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.
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
}
}
// Skip over tiles that have exclusions, since they were already processed.
// Skip over tiles that have exclusions, since they were already processed.
while (nextToSkip < pos) {
if (currentSkipIndex < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[currentSkipIndex++];
nextToSkip = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
else
nextToSkip = end;
while (nextToSkip < pos) {
if (currentSkipIndex < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[currentSkipIndex++];
nextToSkip = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
includeTile = (nextToSkip != pos);
else
nextToSkip = end;
}
includeTile = (nextToSkip != pos);
#endif
if (includeTile) {
// Load the data for this tile.
......
platforms/opencl/src/kernels/nonbonded.cl
View file @ dca54ec7
......@@ -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
......@@ -223,42 +225,38 @@ __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
{
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
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
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.
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
}
}
// Skip over tiles that have exclusions, since they were already processed.
// Skip over tiles that have exclusions, since they were already processed.
SYNC_WARPS;
while (skipTiles[tbx+TILE_SIZE-1] < pos) {
SYNC_WARPS;
while (skipTiles[tbx+TILE_SIZE-1] < pos) {
SYNC_WARPS;
if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[skipBase+tgx];
skipTiles[get_local_id(0)] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
else
skipTiles[get_local_id(0)] = end;
skipBase += TILE_SIZE;
currentSkipIndex = tbx;
SYNC_WARPS;
if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[skipBase+tgx];
skipTiles[get_local_id(0)] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
while (skipTiles[currentSkipIndex] < pos)
currentSkipIndex++;
includeTile = (skipTiles[currentSkipIndex] != pos);
else
skipTiles[get_local_id(0)] = end;
skipBase += TILE_SIZE;
currentSkipIndex = tbx;
SYNC_WARPS;
}
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
View file @ dca54ec7
......@@ -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
......@@ -234,35 +236,31 @@ __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
{
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
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
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.
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
}
}
// Skip over tiles that have exclusions, since they were already processed.
// Skip over tiles that have exclusions, since they were already processed.
while (nextToSkip < pos) {
if (currentSkipIndex < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[currentSkipIndex++];
nextToSkip = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
else
nextToSkip = end;
while (nextToSkip < pos) {
if (currentSkipIndex < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[currentSkipIndex++];
nextToSkip = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
includeTile = (nextToSkip != pos);
else
nextToSkip = end;
}
includeTile = (nextToSkip != pos);
#endif
if (includeTile) {
// Load the data for this tile.
......
platforms/opencl/src/kernels/pme.cl
View file @ dca54ec7
__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
View file @ dca54ec7
......@@ -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
View file @ dca54ec7
......@@ -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
View file @ dca54ec7
......@@ -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
View file @ dca54ec7
......@@ -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
View file @ dca54ec7
......@@ -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
View file @ dca54ec7
......@@ -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");
......
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