nonbonded_default.cl

#define TILE_SIZE 32

typedef struct {
    float x, y, z;
    float q;
    float fx, fy, fz;
    ATOM_PARAMETER_DATA
} AtomData;

/**
 * Compute nonbonded interactions.
 */

__kernel __attribute__((reqd_work_group_size(WORK_GROUP_SIZE, 1, 1)))
void computeNonbonded(__global float4* forceBuffers, __global float* energyBuffer, __global float4* posq, __global unsigned int* exclusions,
        __global unsigned int* exclusionIndices, __global unsigned int* exclusionRowIndices, __local AtomData* localData, __local float4* tempBuffer,
#ifdef USE_CUTOFF
        __global ushort2* tiles, __global unsigned int* interactionCount, float4 periodicBoxSize, float4 invPeriodicBoxSize, unsigned int maxTiles, __global unsigned int* interactionFlags
#else
        unsigned int numTiles
#endif
        PARAMETER_ARGUMENTS) {
#ifdef USE_CUTOFF
    unsigned int numTiles = interactionCount[0];
    unsigned int pos = get_group_id(0)*(numTiles > maxTiles ? NUM_BLOCKS*(NUM_BLOCKS+1)/2 : numTiles)/get_num_groups(0);
    unsigned int end = (get_group_id(0)+1)*(numTiles > maxTiles ? NUM_BLOCKS*(NUM_BLOCKS+1)/2 : numTiles)/get_num_groups(0);
#else
    unsigned int pos = get_group_id(0)*numTiles/get_num_groups(0);
    unsigned int end = (get_group_id(0)+1)*numTiles/get_num_groups(0);
#endif
    float energy = 0.0f;
    unsigned int lasty = 0xFFFFFFFF;
    __local unsigned int exclusionRange[2];
    __local int exclusionIndex[1];

    while (pos < end) {
        // Extract the coordinates of this tile
        unsigned int x, y;
#ifdef USE_CUTOFF
        if (numTiles <= maxTiles) {
            ushort2 tileIndices = tiles[pos];
            x = tileIndices.x;
            y = tileIndices.y;
        }
        else
#endif
        {
            y = (unsigned 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 >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
                y++;
                x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
            }
        }
        unsigned int baseLocalAtom = (get_local_id(0) < TILE_SIZE ? 0 : TILE_SIZE/2);
        unsigned int tgx = get_local_id(0) & (TILE_SIZE-1);
        unsigned int forceBufferOffset = (tgx < TILE_SIZE/2 ? 0 : TILE_SIZE);
        unsigned int atom1 = x*TILE_SIZE + tgx;
        float4 force = 0.0f;
        float4 posq1 = posq[atom1];
        LOAD_ATOM1_PARAMETERS

        // Locate the exclusion data for this tile.

#ifdef USE_EXCLUSIONS
        if (get_local_id(0) < 2)
            exclusionRange[get_local_id(0)] = exclusionRowIndices[x+get_local_id(0)];
        if (tgx == 0)
            exclusionIndex[0] = -1;
        barrier(CLK_LOCAL_MEM_FENCE);
        for (int i = exclusionRange[0]+tgx; i < exclusionRange[1]; i += TILE_SIZE)
            if (exclusionIndices[i] == y)
                exclusionIndex[0] = i*TILE_SIZE;
        barrier(CLK_LOCAL_MEM_FENCE);
        bool hasExclusions = (exclusionIndex[0] > -1);
#endif
        if (x == y) {
            // This tile is on the diagonal.

            const unsigned int localAtomIndex = get_local_id(0);
            localData[localAtomIndex].x = posq1.x;
            localData[localAtomIndex].y = posq1.y;
            localData[localAtomIndex].z = posq1.z;
            localData[localAtomIndex].q = posq1.w;
            LOAD_LOCAL_PARAMETERS_FROM_1
            barrier(CLK_LOCAL_MEM_FENCE);
#ifdef USE_EXCLUSIONS
            unsigned int excl = exclusions[exclusionIndex[0]+tgx] >> baseLocalAtom;
#endif
            for (unsigned int j = 0; j < TILE_SIZE/2; j++) {
#ifdef USE_EXCLUSIONS
                bool isExcluded = !(excl & 0x1);
#endif
                int atom2 = baseLocalAtom+j;
                float4 posq2 = (float4) (localData[atom2].x, localData[atom2].y, localData[atom2].z, localData[atom2].q);
                float4 delta = (float4) (posq2.xyz - posq1.xyz, 0.0f);
#ifdef USE_PERIODIC
                delta.x -= floor(delta.x*invPeriodicBoxSize.x+0.5f)*periodicBoxSize.x;
                delta.y -= floor(delta.y*invPeriodicBoxSize.y+0.5f)*periodicBoxSize.y;
                delta.z -= floor(delta.z*invPeriodicBoxSize.z+0.5f)*periodicBoxSize.z;
#endif
                float r2 = delta.x*delta.x + delta.y*delta.y + delta.z*delta.z;
                float invR = RSQRT(r2);
                float r = RECIP(invR);
                LOAD_ATOM2_PARAMETERS
                atom2 = y*TILE_SIZE+baseLocalAtom+j;
#ifdef USE_SYMMETRIC
                float dEdR = 0.0f;
#else
                float4 dEdR1 = (float4) 0.0f;
                float4 dEdR2 = (float4) 0.0f;
#endif
                float tempEnergy = 0.0f;
                COMPUTE_INTERACTION
                energy += 0.5f*tempEnergy;
#ifdef USE_SYMMETRIC
                force.xyz -= delta.xyz*dEdR;
#else
                force.xyz -= dEdR1.xyz;
#endif
                excl >>= 1;
            }

            // Sum the forces and write results.

            if (get_local_id(0) >= TILE_SIZE)
                tempBuffer[get_local_id(0)] = force;
            barrier(CLK_LOCAL_MEM_FENCE);
            if (get_local_id(0) < TILE_SIZE) {
#ifdef USE_OUTPUT_BUFFER_PER_BLOCK
                unsigned int offset = x*TILE_SIZE + tgx + x*PADDED_NUM_ATOMS;
#else
                unsigned int offset = x*TILE_SIZE + tgx + get_group_id(0)*PADDED_NUM_ATOMS;
#endif
                forceBuffers[offset].xyz = forceBuffers[offset].xyz+force.xyz+tempBuffer[get_local_id(0)+TILE_SIZE].xyz;
            }
        }
        else {
            // This is an off-diagonal tile.

            const unsigned int localAtomIndex = get_local_id(0);
            if (lasty != y && localAtomIndex < TILE_SIZE) {
                unsigned int j = y*TILE_SIZE + tgx;
                float4 tempPosq = posq[j];
                localData[localAtomIndex].x = tempPosq.x;
                localData[localAtomIndex].y = tempPosq.y;
                localData[localAtomIndex].z = tempPosq.z;
                localData[localAtomIndex].q = tempPosq.w;
                LOAD_LOCAL_PARAMETERS_FROM_GLOBAL
            }
            localData[localAtomIndex].fx = 0.0f;
            localData[localAtomIndex].fy = 0.0f;
            localData[localAtomIndex].fz = 0.0f;
            barrier(CLK_LOCAL_MEM_FENCE);

            // Compute the full set of interactions in this tile.

#ifdef USE_EXCLUSIONS
            unsigned int excl = (hasExclusions ? exclusions[exclusionIndex[0]+tgx] : 0xFFFFFFFF);
            excl = (excl >> baseLocalAtom) & 0xFFFF;
            excl += excl << 16;
            excl = (excl >> tgx) | (excl << (TILE_SIZE - tgx));
#endif
            unsigned int tj = tgx%(TILE_SIZE/2);
            for (unsigned int j = 0; j < TILE_SIZE/2; j++) {
#ifdef USE_EXCLUSIONS
                bool isExcluded = !(excl & 0x1);
#endif
                int atom2 = baseLocalAtom+tj;
                float4 posq2 = (float4) (localData[atom2].x, localData[atom2].y, localData[atom2].z, localData[atom2].q);
                float4 delta = (float4) (posq2.xyz - posq1.xyz, 0.0f);
#ifdef USE_PERIODIC
                delta.x -= floor(delta.x*invPeriodicBoxSize.x+0.5f)*periodicBoxSize.x;
                delta.y -= floor(delta.y*invPeriodicBoxSize.y+0.5f)*periodicBoxSize.y;
                delta.z -= floor(delta.z*invPeriodicBoxSize.z+0.5f)*periodicBoxSize.z;
#endif
                float r2 = delta.x*delta.x + delta.y*delta.y + delta.z*delta.z;
                float invR = RSQRT(r2);
                float r = RECIP(invR);
                LOAD_ATOM2_PARAMETERS
                atom2 = y*TILE_SIZE+baseLocalAtom+tj;
#ifdef USE_SYMMETRIC
                float dEdR = 0.0f;
#else
                float4 dEdR1 = (float4) 0.0f;
                float4 dEdR2 = (float4) 0.0f;
#endif
                float tempEnergy = 0.0f;
                COMPUTE_INTERACTION
                energy += tempEnergy;
#ifdef USE_SYMMETRIC
                delta.xyz *= dEdR;
                force.xyz -= delta.xyz;
                localData[baseLocalAtom+tj+forceBufferOffset].fx += delta.x;
                localData[baseLocalAtom+tj+forceBufferOffset].fy += delta.y;
                localData[baseLocalAtom+tj+forceBufferOffset].fz += delta.z;
#else
                force.xyz -= dEdR1.xyz;
                localData[baseLocalAtom+tj+forceBufferOffset].fx += dEdR2.x;
                localData[baseLocalAtom+tj+forceBufferOffset].fy += dEdR2.y;
                localData[baseLocalAtom+tj+forceBufferOffset].fz += dEdR2.z;
#endif
                barrier(CLK_LOCAL_MEM_FENCE);
#ifdef USE_EXCLUSIONS
                excl >>= 1;
#endif
                tj = (tj+1)%(TILE_SIZE/2);
            }

            // Sum the forces and write results.

            if (get_local_id(0) >= TILE_SIZE)
                tempBuffer[get_local_id(0)] = force;
            barrier(CLK_LOCAL_MEM_FENCE);
            if (get_local_id(0) < TILE_SIZE) {
#ifdef USE_OUTPUT_BUFFER_PER_BLOCK
                unsigned int offset1 = x*TILE_SIZE + tgx + y*PADDED_NUM_ATOMS;
                unsigned int offset2 = y*TILE_SIZE + tgx + x*PADDED_NUM_ATOMS;
#else
                unsigned int offset1 = x*TILE_SIZE + tgx + get_group_id(0)*PADDED_NUM_ATOMS;
                unsigned int offset2 = y*TILE_SIZE + tgx + get_group_id(0)*PADDED_NUM_ATOMS;
#endif
                forceBuffers[offset1].xyz = forceBuffers[offset1].xyz+force.xyz+tempBuffer[get_local_id(0)+TILE_SIZE].xyz;
                float4 sum = (float4) (localData[get_local_id(0)].fx+localData[get_local_id(0)+TILE_SIZE].fx, localData[get_local_id(0)].fy+localData[get_local_id(0)+TILE_SIZE].fy, localData[get_local_id(0)].fz+localData[get_local_id(0)+TILE_SIZE].fz, 0.0f);
                forceBuffers[offset2].xyz = forceBuffers[offset2].xyz+sum.xyz;
            }
        }
        lasty = y;
        pos++;
    }
    energyBuffer[get_global_id(0)] += energy;
}