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Commit 3db6b8ee authored by Jason Swails's avatar Jason Swails
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Merge branch 'master' into gbn-chk

parents 5d8e92ff 3a80b0f1
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Showing with 471 additions and 141 deletions
platforms/opencl/src/kernels/findInteractingBlocks.cl
View file @ 3db6b8ee
......@@ -5,15 +5,15 @@
/**
* Find a bounding box for the atoms in each block.
*/
__kernel void findBlockBounds(int numAtoms, real4 periodicBoxSize, real4 invPeriodicBoxSize, __global const real4* restrict posq,
__global real4* restrict blockCenter, __global real4* restrict blockBoundingBox, __global int* restrict rebuildNeighborList,
__kernel void findBlockBounds(int numAtoms, real4 periodicBoxSize, real4 invPeriodicBoxSize, real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ,
__global const real4* restrict posq, __global real4* restrict blockCenter, __global real4* restrict blockBoundingBox, __global int* restrict rebuildNeighborList,
__global real2* restrict sortedBlocks) {
int index = get_global_id(0);
int base = index*TILE_SIZE;
while (base < numAtoms) {
real4 pos = posq[base];
#ifdef USE_PERIODIC
pos.xyz -= floor(pos.xyz*invPeriodicBoxSize.xyz)*periodicBoxSize.xyz;
APPLY_PERIODIC_TO_POS(pos)
#endif
real4 minPos = pos;
real4 maxPos = pos;
......@@ -22,7 +22,7 @@ __kernel void findBlockBounds(int numAtoms, real4 periodicBoxSize, real4 invPeri
pos = posq[i];
#ifdef USE_PERIODIC
real4 center = 0.5f*(maxPos+minPos);
pos.xyz -= floor((pos.xyz-center.xyz)*invPeriodicBoxSize.xyz+0.5f)*periodicBoxSize.xyz;
APPLY_PERIODIC_TO_POS_WITH_CENTER(pos, center)
#endif
minPos = min(minPos, pos);
maxPos = max(maxPos, pos);
......@@ -65,9 +65,10 @@ __kernel void sortBoxData(__global const real2* restrict sortedBlock, __global c
}
}
__kernel void findBlocksWithInteractions(real4 periodicBoxSize, real4 invPeriodicBoxSize, __global unsigned int* restrict interactionCount,
__global int* restrict interactingTiles, __global unsigned int* restrict interactingAtoms, __global const real4* restrict posq, unsigned int maxTiles, unsigned int startBlockIndex,
unsigned int numBlocks, __global real2* restrict sortedBlocks, __global const real4* restrict sortedBlockCenter, __global const real4* restrict sortedBlockBoundingBox,
__kernel void findBlocksWithInteractions(real4 periodicBoxSize, real4 invPeriodicBoxSize, real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ,
__global unsigned int* restrict interactionCount, __global int* restrict interactingTiles, __global unsigned int* restrict interactingAtoms,
__global const real4* restrict posq, unsigned int maxTiles, unsigned int startBlockIndex, unsigned int numBlocks, __global real2* restrict sortedBlocks,
__global const real4* restrict sortedBlockCenter, __global const real4* restrict sortedBlockBoundingBox,
__global const unsigned int* restrict exclusionIndices, __global const unsigned int* restrict exclusionRowIndices, __global real4* restrict oldPositions,
__global const int* restrict rebuildNeighborList) {
......@@ -108,7 +109,7 @@ __kernel void findBlocksWithInteractions(real4 periodicBoxSize, real4 invPeriodi
// The box is small enough that we can just translate all the atoms into a single periodic
// box, then skip having to apply periodic boundary conditions later.
pos1.xyz -= floor((pos1.xyz-blockCenterX.xyz)*invPeriodicBoxSize.xyz+0.5f)*periodicBoxSize.xyz;
APPLY_PERIODIC_TO_POS_WITH_CENTER(pos1, blockCenterX)
}
#endif
posBuffer[get_local_id(0)] = pos1;
......@@ -136,7 +137,7 @@ __kernel void findBlocksWithInteractions(real4 periodicBoxSize, real4 invPeriodi
real4 blockSizeY = (block2 < NUM_BLOCKS ? sortedBlockBoundingBox[block2] : (real4) (0));
real4 blockDelta = blockCenterX-blockCenterY;
#ifdef USE_PERIODIC
blockDelta.xyz -= floor(blockDelta.xyz*invPeriodicBoxSize.xyz+0.5f)*periodicBoxSize.xyz;
APPLY_PERIODIC_TO_DELTA(blockDelta)
#endif
blockDelta.x = max((real) 0, fabs(blockDelta.x)-blockSizeX.x-blockSizeY.x);
blockDelta.y = max((real) 0, fabs(blockDelta.y)-blockSizeX.y-blockSizeY.y);
......@@ -166,7 +167,7 @@ __kernel void findBlocksWithInteractions(real4 periodicBoxSize, real4 invPeriodi
real3 pos2 = posq[atom2].xyz;
#ifdef USE_PERIODIC
if (singlePeriodicCopy)
pos2.xyz -= floor((pos2.xyz-blockCenterX.xyz)*invPeriodicBoxSize.xyz+0.5f)*periodicBoxSize.xyz;
APPLY_PERIODIC_TO_POS_WITH_CENTER(pos2, blockCenterX)
#endif
bool interacts = false;
if (atom2 < NUM_ATOMS) {
......@@ -174,7 +175,7 @@ __kernel void findBlocksWithInteractions(real4 periodicBoxSize, real4 invPeriodi
if (!singlePeriodicCopy) {
for (int j = 0; j < TILE_SIZE; j++) {
real3 delta = pos2-posBuffer[warpStart+j];
delta.xyz -= floor(delta.xyz*invPeriodicBoxSize.xyz+0.5f)*periodicBoxSize.xyz;
APPLY_PERIODIC_TO_DELTA(delta)
interacts |= (delta.x*delta.x+delta.y*delta.y+delta.z*delta.z < PADDED_CUTOFF_SQUARED);
}
}
......
platforms/opencl/src/kernels/gbsaObc.cl
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platforms/opencl/src/kernels/monteCarloBarostat.cl
View file @ 3db6b8ee
......@@ -2,7 +2,8 @@
* Scale the particle positions with each axis independent.
*/
__kernel void scalePositions(float scaleX, float scaleY, float scaleZ, int numMolecules, real4 periodicBoxSize, real4 invPeriodicBoxSize, __global real4* restrict posq,
__kernel void scalePositions(float scaleX, float scaleY, float scaleZ, int numMolecules, real4 periodicBoxSize, real4 invPeriodicBoxSize,
real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ, __global real4* restrict posq,
__global const int* restrict moleculeAtoms, __global const int* restrict moleculeStartIndex) {
for (int index = get_global_id(0); index < numMolecules; index += get_global_size(0)) {
int first = moleculeStartIndex[index];
......@@ -11,19 +12,17 @@ __kernel void scalePositions(float scaleX, float scaleY, float scaleZ, int numMo
// Find the center of each molecule.
real4 center = (real4) 0;
real3 center = (real3) 0;
for (int atom = first; atom < last; atom++)
center += posq[moleculeAtoms[atom]];
center += posq[moleculeAtoms[atom]].xyz;
center /= (real) numAtoms;
// Move it into the first periodic box.
int xcell = (int) floor(center.x*invPeriodicBoxSize.x);
int ycell = (int) floor(center.y*invPeriodicBoxSize.y);
int zcell = (int) floor(center.z*invPeriodicBoxSize.z);
real4 delta = (real4) (xcell*periodicBoxSize.x, ycell*periodicBoxSize.y, zcell*periodicBoxSize.z, 0);
real4 scaleXYZ = (real4) (scaleX, scaleY, scaleZ, 1);
center -= delta;
real3 oldCenter = center;
APPLY_PERIODIC_TO_POS(center)
real3 delta = oldCenter-center;;
real3 scaleXYZ = (real3) (scaleX, scaleY, scaleZ);
// Now scale the position of the molecule center.
......
platforms/opencl/src/kernels/nonbonded.cl
View file @ 3db6b8ee
......@@ -26,7 +26,8 @@ __kernel void computeNonbonded(
__global const ushort2* restrict exclusionTiles, unsigned int startTileIndex, unsigned int numTileIndices
#ifdef USE_CUTOFF
, __global const int* restrict tiles, __global const unsigned int* restrict interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize,
unsigned int maxTiles, __global const real4* restrict blockCenter, __global const real4* restrict blockSize, __global const int* restrict interactingAtoms
real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ, unsigned int maxTiles, __global const real4* restrict blockCenter,
__global const real4* restrict blockSize, __global const int* restrict interactingAtoms
#endif
PARAMETER_ARGUMENTS) {
const unsigned int totalWarps = get_global_size(0)/TILE_SIZE;
......@@ -67,7 +68,7 @@ __kernel void computeNonbonded(
real4 posq2 = (real4) (localData[atom2].x, localData[atom2].y, localData[atom2].z, localData[atom2].q);
real4 delta = (real4) (posq2.xyz - posq1.xyz, 0);
#ifdef USE_PERIODIC
delta.xyz -= floor(delta.xyz*invPeriodicBoxSize.xyz+0.5f)*periodicBoxSize.xyz;
APPLY_PERIODIC_TO_DELTA(delta)
#endif
real r2 = delta.x*delta.x + delta.y*delta.y + delta.z*delta.z;
real invR = RSQRT(r2);
......@@ -121,7 +122,7 @@ __kernel void computeNonbonded(
real4 posq2 = (real4) (localData[atom2].x, localData[atom2].y, localData[atom2].z, localData[atom2].q);
real4 delta = (real4) (posq2.xyz - posq1.xyz, 0);
#ifdef USE_PERIODIC
delta.xyz -= floor(delta.xyz*invPeriodicBoxSize.xyz+0.5f)*periodicBoxSize.xyz;
APPLY_PERIODIC_TO_DELTA(delta)
#endif
real r2 = delta.x*delta.x + delta.y*delta.y + delta.z*delta.z;
#ifdef PRUNE_BY_CUTOFF
......@@ -289,10 +290,8 @@ __kernel void computeNonbonded(
// box, then skip having to apply periodic boundary conditions later.
real4 blockCenterX = blockCenter[x];
posq1.xyz -= floor((posq1.xyz-blockCenterX.xyz)*invPeriodicBoxSize.xyz+0.5f)*periodicBoxSize.xyz;
localData[localAtomIndex].x -= floor((localData[localAtomIndex].x-blockCenterX.x)*invPeriodicBoxSize.x+0.5f)*periodicBoxSize.x;
localData[localAtomIndex].y -= floor((localData[localAtomIndex].y-blockCenterX.y)*invPeriodicBoxSize.y+0.5f)*periodicBoxSize.y;
localData[localAtomIndex].z -= floor((localData[localAtomIndex].z-blockCenterX.z)*invPeriodicBoxSize.z+0.5f)*periodicBoxSize.z;
APPLY_PERIODIC_TO_POS_WITH_CENTER(posq1, blockCenterX)
APPLY_PERIODIC_TO_POS_WITH_CENTER(localData[localAtomIndex], blockCenterX)
SYNC_WARPS;
unsigned int tj = tgx;
for (j = 0; j < TILE_SIZE; j++) {
......@@ -349,7 +348,7 @@ __kernel void computeNonbonded(
real4 posq2 = (real4) (localData[atom2].x, localData[atom2].y, localData[atom2].z, localData[atom2].q);
real4 delta = (real4) (posq2.xyz - posq1.xyz, 0);
#ifdef USE_PERIODIC
delta.xyz -= floor(delta.xyz*invPeriodicBoxSize.xyz+0.5f)*periodicBoxSize.xyz;
APPLY_PERIODIC_TO_DELTA(delta)
#endif
real r2 = delta.x*delta.x + delta.y*delta.y + delta.z*delta.z;
#ifdef PRUNE_BY_CUTOFF
......
platforms/opencl/src/kernels/pme.cl
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platforms/opencl/tests/TestOpenCLEwald.cpp
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platforms/reference/include/ObcParameters.h
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