gbsaObc_default.cl

#define TILE_SIZE 32

typedef struct {
    float x, y, z;
    float q;
    float fx, fy, fz, fw;
    float radius, scaledRadius;
    float bornSum;
    float bornRadius;
    float bornForce;
} AtomData;

/**
 * Compute the Born sum.
 */

__attribute__((reqd_work_group_size(64, 1, 1)))
__kernel void computeBornSum(__global float* global_bornSum, __global float4* posq, __global float2* global_params, __local AtomData* localData, __local float* tempBuffer, __global unsigned int* tiles,
#ifdef USE_CUTOFF
        __global unsigned int* interactionFlags, __global unsigned int* interactionCount) {
#else
        unsigned int numTiles) {
#endif
#ifdef USE_CUTOFF
    unsigned int numTiles = interactionCount[0];
#endif
    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);
    float energy = 0.0f;
    unsigned int lasty = 0xFFFFFFFF;

    while (pos < end) {
        // Extract the coordinates of this tile
        unsigned int x = tiles[pos];
        unsigned int y = ((x >> 2) & 0x7fff)*TILE_SIZE;
        x = (x>>17)*TILE_SIZE;
        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 + tgx;
        float bornSum = 0.0f;
        float4 posq1 = posq[atom1];
        float2 params1 = global_params[atom1];
        if (x == y) {
            // This tile is on the diagonal.

            localData[get_local_id(0)].x = posq1.x;
            localData[get_local_id(0)].y = posq1.y;
            localData[get_local_id(0)].z = posq1.z;
            localData[get_local_id(0)].q = posq1.w;
            localData[get_local_id(0)].radius = params1.x;
            localData[get_local_id(0)].scaledRadius = params1.y;
            barrier(CLK_LOCAL_MEM_FENCE);
            unsigned int xi = x/TILE_SIZE;
            unsigned int tile = xi+xi*PADDED_NUM_ATOMS/TILE_SIZE-xi*(xi+1)/2;
            for (unsigned int j = 0; j < TILE_SIZE/2; j++) {
                float4 delta = (float4) (localData[baseLocalAtom+j].x-posq1.x, localData[baseLocalAtom+j].y-posq1.y, localData[baseLocalAtom+j].z-posq1.z, 0.0f);
#ifdef USE_PERIODIC
                delta.x -= floor(delta.x*INV_PERIODIC_BOX_SIZE_X+0.5f)*PERIODIC_BOX_SIZE_X;
                delta.y -= floor(delta.y*INV_PERIODIC_BOX_SIZE_Y+0.5f)*PERIODIC_BOX_SIZE_Y;
                delta.z -= floor(delta.z*INV_PERIODIC_BOX_SIZE_Z+0.5f)*PERIODIC_BOX_SIZE_Z;
#endif
                float r2 = delta.x*delta.x + delta.y*delta.y + delta.z*delta.z;
#ifdef USE_CUTOFF
                if (atom1 < NUM_ATOMS && y+baseLocalAtom+j < NUM_ATOMS && r2 < CUTOFF_SQUARED) {
#else
                if (atom1 < NUM_ATOMS && y+baseLocalAtom+j < NUM_ATOMS) {
#endif
                    float invR = RSQRT(r2);
                    float r = RECIP(invR);
                    float2 params2 = (float2) (localData[baseLocalAtom+j].radius, localData[baseLocalAtom+j].scaledRadius);
                    float rScaledRadiusJ = r+params2.y;
                    if ((j != tgx) && (params1.x < rScaledRadiusJ)) {
                        float l_ij = 1.0f/max(params1.x, fabs(r-params2.y));
                        float u_ij = 1.0f/rScaledRadiusJ;
                        float l_ij2 = l_ij*l_ij;
                        float u_ij2 = u_ij*u_ij;
                        float ratio = log(u_ij / l_ij);
                        bornSum += l_ij - u_ij + 0.25f*r*(u_ij2-l_ij2) + (0.50f*invR*ratio) +
                                         (0.25f*params2.y*params2.y*invR)*(l_ij2-u_ij2);
                        if (params1.x < params2.x-r)
                            bornSum += 2.0f*(1.0f/params1.x-l_ij);
                    }
                }
            }

            // Sum the forces and write results.

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

            if (lasty != y && get_local_id(0) < TILE_SIZE) {
                unsigned int j = y + tgx;
                float4 tempPosq = posq[j];
                localData[get_local_id(0)].x = tempPosq.x;
                localData[get_local_id(0)].y = tempPosq.y;
                localData[get_local_id(0)].z = tempPosq.z;
                localData[get_local_id(0)].q = tempPosq.w;
                float2 tempParams = global_params[j];
                localData[get_local_id(0)].radius = tempParams.x;
                localData[get_local_id(0)].scaledRadius = tempParams.y;
            }
            localData[get_local_id(0)].bornSum = 0.0f;
            barrier(CLK_LOCAL_MEM_FENCE);

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

            unsigned int xi = x/TILE_SIZE;
            unsigned int yi = y/TILE_SIZE;
            unsigned int tile = xi+yi*PADDED_NUM_ATOMS/TILE_SIZE-yi*(yi+1)/2;
            unsigned int tj = tgx%(TILE_SIZE/2);
            for (unsigned int j = 0; j < TILE_SIZE/2; j++) {
                float4 delta = (float4) (localData[baseLocalAtom+tj].x-posq1.x, localData[baseLocalAtom+tj].y-posq1.y, localData[baseLocalAtom+tj].z-posq1.z, 0.0f);
#ifdef USE_PERIODIC
                delta.x -= floor(delta.x*INV_PERIODIC_BOX_SIZE_X+0.5f)*PERIODIC_BOX_SIZE_X;
                delta.y -= floor(delta.y*INV_PERIODIC_BOX_SIZE_Y+0.5f)*PERIODIC_BOX_SIZE_Y;
                delta.z -= floor(delta.z*INV_PERIODIC_BOX_SIZE_Z+0.5f)*PERIODIC_BOX_SIZE_Z;
#endif
                float r2 = delta.x*delta.x + delta.y*delta.y + delta.z*delta.z;
#ifdef USE_CUTOFF
                if (atom1 < NUM_ATOMS && y+baseLocalAtom+tj < NUM_ATOMS && r2 < CUTOFF_SQUARED) {
#else
                if (atom1 < NUM_ATOMS && y+baseLocalAtom+tj < NUM_ATOMS) {
#endif
                    float invR = RSQRT(r2);
                    float r = RECIP(invR);
                    float2 params2 = (float2) (localData[baseLocalAtom+tj].radius, localData[baseLocalAtom+tj].scaledRadius);
                    float rScaledRadiusJ = r+params2.y;
                    if (params1.x < rScaledRadiusJ) {
                        float l_ij = 1.0f/max(params1.x, fabs(r-params2.y));
                        float u_ij = 1.0f/rScaledRadiusJ;
                        float l_ij2 = l_ij*l_ij;
                        float u_ij2 = u_ij*u_ij;
                        float ratio = log(u_ij / l_ij);
                        bornSum += l_ij - u_ij + 0.25f*r*(u_ij2-l_ij2) + (0.50f*invR*ratio) +
                                         (0.25f*params2.y*params2.y*invR)*(l_ij2-u_ij2);
                        if (params1.x < params2.x-r)
                            bornSum += 2.0f*(1.0f/params1.x-l_ij);
                    }
                    float rScaledRadiusI = r+params1.y;
                    if (params2.x < rScaledRadiusI) {
                        float l_ij = 1.0f/max(params2.x, fabs(r-params1.y));
                        float u_ij = 1.0f/rScaledRadiusI;
                        float l_ij2 = l_ij*l_ij;
                        float u_ij2 = u_ij*u_ij;
                        float ratio = log(u_ij / l_ij);
                        float term = l_ij - u_ij + 0.25f*r*(u_ij2-l_ij2) + (0.50f*invR*ratio) +
                                         (0.25f*params1.y*params1.y*invR)*(l_ij2-u_ij2);
                        if (params2.x < params1.x-r)
                            term += 2.0f*(1.0f/params2.x-l_ij);
                        localData[baseLocalAtom+tj+forceBufferOffset].bornSum += term;
                    }
                }
                barrier(CLK_LOCAL_MEM_FENCE);
                tj = (tj+1)%(TILE_SIZE/2);
            }

            // Sum the forces and write results.

            if (get_local_id(0) >= TILE_SIZE)
                tempBuffer[get_local_id(0)] = bornSum;
            barrier(CLK_LOCAL_MEM_FENCE);
            if (get_local_id(0) < TILE_SIZE) {
#ifdef USE_OUTPUT_BUFFER_PER_BLOCK
                unsigned int offset1 = x + tgx + (y/TILE_SIZE)*PADDED_NUM_ATOMS;
                unsigned int offset2 = y + tgx + (x/TILE_SIZE)*PADDED_NUM_ATOMS;
#else
                unsigned int offset1 = x + tgx + get_group_id(0)*PADDED_NUM_ATOMS;
                unsigned int offset2 = y + tgx + get_group_id(0)*PADDED_NUM_ATOMS;
#endif
                global_bornSum[offset1] += bornSum+tempBuffer[get_local_id(0)+TILE_SIZE];
                global_bornSum[offset2] += localData[get_local_id(0)].bornSum+localData[get_local_id(0)+TILE_SIZE].bornSum;
            }
            lasty = y;
        }
        pos++;
    }
}

/**
 * First part of computing the GBSA interaction.
 */

__attribute__((reqd_work_group_size(64, 1, 1)))
__kernel void computeGBSAForce1(__global float4* forceBuffers, __global float* energyBuffer,
        __global float4* posq, __global float* global_bornRadii,
        __global float* global_bornForce, __local AtomData* localData, __local float4* tempBuffer, __global unsigned int* tiles,
#ifdef USE_CUTOFF
        __global unsigned int* interactionFlags, __global unsigned int* interactionCount) {
#else
        unsigned int numTiles) {
#endif
#ifdef USE_CUTOFF
    unsigned int numTiles = interactionCount[0];
#endif
    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);
    float energy = 0.0f;
    unsigned int lasty = 0xFFFFFFFF;

    while (pos < end) {
        // Extract the coordinates of this tile
        unsigned int x = tiles[pos];
        unsigned int y = ((x >> 2) & 0x7fff)*TILE_SIZE;
        x = (x>>17)*TILE_SIZE;
        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 + tgx;
        float4 force = 0.0f;
        float4 posq1 = posq[atom1];
        float bornRadius1 = global_bornRadii[atom1];
        if (x == y) {
            // This tile is on the diagonal.

            localData[get_local_id(0)].x = posq1.x;
            localData[get_local_id(0)].y = posq1.y;
            localData[get_local_id(0)].z = posq1.z;
            localData[get_local_id(0)].q = posq1.w;
            localData[get_local_id(0)].bornRadius = bornRadius1;
            barrier(CLK_LOCAL_MEM_FENCE);
            unsigned int xi = x/TILE_SIZE;
            unsigned int tile = xi+xi*PADDED_NUM_ATOMS/TILE_SIZE-xi*(xi+1)/2;
            for (unsigned int j = 0; j < TILE_SIZE/2; j++) {
                if (atom1 < NUM_ATOMS && y+baseLocalAtom+j < NUM_ATOMS) {
                    float4 posq2 = (float4) (localData[baseLocalAtom+j].x, localData[baseLocalAtom+j].y, localData[baseLocalAtom+j].z, localData[baseLocalAtom+j].q);
                    float4 delta = (float4) (posq2.xyz - posq1.xyz, 0.0f);
#ifdef USE_PERIODIC
                    delta.x -= floor(delta.x*INV_PERIODIC_BOX_SIZE_X+0.5f)*PERIODIC_BOX_SIZE_X;
                    delta.y -= floor(delta.y*INV_PERIODIC_BOX_SIZE_Y+0.5f)*PERIODIC_BOX_SIZE_Y;
                    delta.z -= floor(delta.z*INV_PERIODIC_BOX_SIZE_Z+0.5f)*PERIODIC_BOX_SIZE_Z;
#endif
                    float r2 = delta.x*delta.x + delta.y*delta.y + delta.z*delta.z;
                    float invR = RSQRT(r2);
                    float r = RECIP(invR);
                    float bornRadius2 = localData[baseLocalAtom+j].bornRadius;
                    float alpha2_ij = bornRadius1*bornRadius2;
                    float D_ij = r2/(4.0f*alpha2_ij);
                    float expTerm = exp(-D_ij);
                    float denominator2 = r2 + alpha2_ij*expTerm;
                    float denominator = SQRT(denominator2);
                    float tempEnergy = (PREFACTOR*posq1.w*posq2.w)/denominator;
                    float Gpol = tempEnergy/denominator2;
                    float dGpol_dalpha2_ij = -0.5f*Gpol*expTerm*(1.0f+D_ij);
                    force.w += dGpol_dalpha2_ij*bornRadius2;
                    float dEdR = Gpol*(1.0f - 0.25f*expTerm);
#ifdef USE_CUTOFF
                    if (r2 > CUTOFF_SQUARED) {
                        dEdR = 0.0f;
                        tempEnergy  = 0.0f;
                    }
#endif
                    energy += 0.5f*tempEnergy;
                    delta.xyz *= dEdR;
                    force.xyz -= delta.xyz;
                }
            }

            // 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 + tgx + (x/TILE_SIZE)*PADDED_NUM_ATOMS;
#else
                unsigned int offset = x + 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;
                global_bornForce[offset] += force.w+tempBuffer[get_local_id(0)+TILE_SIZE].w;
            }
        }
        else {
            // This is an off-diagonal tile.

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

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

            unsigned int xi = x/TILE_SIZE;
            unsigned int yi = y/TILE_SIZE;
            unsigned int tile = xi+yi*PADDED_NUM_ATOMS/TILE_SIZE-yi*(yi+1)/2;
            unsigned int tj = tgx%(TILE_SIZE/2);
            for (unsigned int j = 0; j < TILE_SIZE/2; j++) {
                if (atom1 < NUM_ATOMS && y+baseLocalAtom+tj < NUM_ATOMS) {
                    float4 posq2 = (float4) (localData[baseLocalAtom+tj].x, localData[baseLocalAtom+tj].y, localData[baseLocalAtom+tj].z, localData[baseLocalAtom+tj].q);
                    float4 delta = (float4) (posq2.xyz - posq1.xyz, 0.0f);
#ifdef USE_PERIODIC
                    delta.x -= floor(delta.x*INV_PERIODIC_BOX_SIZE_X+0.5f)*PERIODIC_BOX_SIZE_X;
                    delta.y -= floor(delta.y*INV_PERIODIC_BOX_SIZE_Y+0.5f)*PERIODIC_BOX_SIZE_Y;
                    delta.z -= floor(delta.z*INV_PERIODIC_BOX_SIZE_Z+0.5f)*PERIODIC_BOX_SIZE_Z;
#endif
                    float r2 = delta.x*delta.x + delta.y*delta.y + delta.z*delta.z;
                    float invR = RSQRT(r2);
                    float r = RECIP(invR);
                    float bornRadius2 = localData[baseLocalAtom+tj].bornRadius;
                    float alpha2_ij = bornRadius1*bornRadius2;
                    float D_ij = r2/(4.0f*alpha2_ij);
                    float expTerm = exp(-D_ij);
                    float denominator2 = r2 + alpha2_ij*expTerm;
                    float denominator = SQRT(denominator2);
                    float tempEnergy = (PREFACTOR*posq1.w*posq2.w)/denominator;
                    float Gpol = tempEnergy/denominator2;
                    float dGpol_dalpha2_ij = -0.5f*Gpol*expTerm*(1.0f+D_ij);
                    force.w += dGpol_dalpha2_ij*bornRadius2;
                    float dEdR = Gpol*(1.0f - 0.25f*expTerm);
#ifdef USE_CUTOFF
                    if (r2 > CUTOFF_SQUARED) {
                        dEdR = 0.0f;
                        tempEnergy  = 0.0f;
                    }
#endif
                    energy += tempEnergy;
                    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;
                    localData[baseLocalAtom+tj+forceBufferOffset].fw += dGpol_dalpha2_ij*bornRadius1;
                }
                barrier(CLK_LOCAL_MEM_FENCE);
                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 + tgx + (y/TILE_SIZE)*PADDED_NUM_ATOMS;
                unsigned int offset2 = y + tgx + (x/TILE_SIZE)*PADDED_NUM_ATOMS;
#else
                unsigned int offset1 = x + tgx + get_group_id(0)*PADDED_NUM_ATOMS;
                unsigned int offset2 = y + 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,
                                       localData[get_local_id(0)].fw+localData[get_local_id(0)+TILE_SIZE].fw);
                forceBuffers[offset2].xyz = forceBuffers[offset2].xyz+sum.xyz;
                global_bornForce[offset1] += force.w+tempBuffer[get_local_id(0)+TILE_SIZE].w;
                global_bornForce[offset2] += sum.w;
            }
            lasty = y;
        }
        pos++;
    }
    energyBuffer[get_global_id(0)] += energy;
}