#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. */ __kernel __attribute__((reqd_work_group_size(WORK_GROUP_SIZE, 1, 1))) 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 totalWarps = get_global_size(0)/TILE_SIZE; unsigned int warp = get_global_id(0)/TILE_SIZE; unsigned int pos = warp*numTiles/totalWarps; unsigned int end = (warp+1)*numTiles/totalWarps; 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 tgx = get_local_id(0) & (TILE_SIZE-1); unsigned int tbx = get_local_id(0) - tgx; 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; 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; j++) { float4 delta = (float4) (localData[tbx+j].x-posq1.x, localData[tbx+j].y-posq1.y, localData[tbx+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+j < NUM_ATOMS && r2 < CUTOFF_SQUARED) { #else if (atom1 < NUM_ATOMS && y+j < NUM_ATOMS) { #endif float invR = RSQRT(r2); float r = RECIP(invR); float2 params2 = (float2) (localData[tbx+j].radius, localData[tbx+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); } } } // Write results #ifdef USE_OUTPUT_BUFFER_PER_BLOCK unsigned int offset = x + tgx + (x/TILE_SIZE)*PADDED_NUM_ATOMS; #else unsigned int offset = x + tgx + warp*PADDED_NUM_ATOMS; #endif global_bornSum[offset] += bornSum; } else { // This is an off-diagonal tile. if (lasty != y) { 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; #ifdef USE_CUTOFF unsigned int flags = interactionFlags[pos]; if (flags != 0xFFFFFFFF) { if (flags == 0) { // No interactions in this tile. } else { // Compute only a subset of the interactions in this tile. for (unsigned int j = 0; j < TILE_SIZE; j++) { if ((flags&(1<> 2) & 0x7fff)*TILE_SIZE; x = (x>>17)*TILE_SIZE; unsigned int tgx = get_local_id(0) & (TILE_SIZE-1); unsigned int tbx = get_local_id(0) - tgx; 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; 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; j++) { if (atom1 < NUM_ATOMS && y+j < NUM_ATOMS) { float4 posq2 = (float4) (localData[tbx+j].x, localData[tbx+j].y, localData[tbx+j].z, localData[tbx+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[tbx+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; } } // Write results #ifdef USE_OUTPUT_BUFFER_PER_BLOCK unsigned int offset = x + tgx + (x/TILE_SIZE)*PADDED_NUM_ATOMS; #else unsigned int offset = x + tgx + warp*PADDED_NUM_ATOMS; #endif forceBuffers[offset].xyz += force.xyz; global_bornForce[offset] += force.w; } else { // This is an off-diagonal tile. if (lasty != y) { 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; #ifdef USE_CUTOFF unsigned int flags = interactionFlags[pos]; if (flags != 0xFFFFFFFF) { if (flags == 0) { // No interactions in this tile. } else { // Compute only a subset of the interactions in this tile. for (unsigned int j = 0; j < TILE_SIZE; j++) { if ((flags&(1<= NUM_ATOMS || y+j >= NUM_ATOMS || r2 > CUTOFF_SQUARED) { #else if (atom1 >= NUM_ATOMS || y+j >= NUM_ATOMS) { #endif dEdR = 0.0f; tempEnergy = 0.0f; } energy += tempEnergy; delta.xyz *= dEdR; force.xyz -= delta.xyz; tempBuffer[get_local_id(0)] = (float4) (delta.xyz, dGpol_dalpha2_ij*bornRadius1); // Sum the forces on atom j. if (tgx % 2 == 0) tempBuffer[get_local_id(0)] += tempBuffer[get_local_id(0)+1]; if (tgx % 4 == 0) tempBuffer[get_local_id(0)] += tempBuffer[get_local_id(0)+2]; if (tgx % 8 == 0) tempBuffer[get_local_id(0)] += tempBuffer[get_local_id(0)+4]; if (tgx % 16 == 0) tempBuffer[get_local_id(0)] += tempBuffer[get_local_id(0)+8]; if (tgx == 0) { float4 sum = tempBuffer[get_local_id(0)] + tempBuffer[get_local_id(0)+16]; localData[tbx+j].fx += sum.x; localData[tbx+j].fy += sum.y; localData[tbx+j].fz += sum.z; localData[tbx+j].fw += sum.w; } } } } } else #endif { // 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; for (unsigned int j = 0; j < TILE_SIZE; j++) { if (atom1 < NUM_ATOMS && y+tj < NUM_ATOMS) { float4 posq2 = (float4) (localData[tbx+tj].x, localData[tbx+tj].y, localData[tbx+tj].z, localData[tbx+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[tbx+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[tbx+tj].fx += delta.x; localData[tbx+tj].fy += delta.y; localData[tbx+tj].fz += delta.z; localData[tbx+tj].fw += dGpol_dalpha2_ij*bornRadius1; } tj = (tj + 1) & (TILE_SIZE - 1); } } // Write results #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 + warp*PADDED_NUM_ATOMS; unsigned int offset2 = y + tgx + warp*PADDED_NUM_ATOMS; #endif forceBuffers[offset1].xyz += force.xyz; forceBuffers[offset2] += (float4) (localData[get_local_id(0)].fx, localData[get_local_id(0)].fy, localData[get_local_id(0)].fz, 0); global_bornForce[offset1] += force.w; global_bornForce[offset2] += localData[get_local_id(0)].fw; lasty = y; } pos++; } energyBuffer[get_global_id(0)] += energy; }