/* -------------------------------------------------------------------------- * * OpenMM * * -------------------------------------------------------------------------- * * This is part of the OpenMM molecular simulation toolkit originating from * * Simbios, the NIH National Center for Physics-Based Simulation of * * Biological Structures at Stanford, funded under the NIH Roadmap for * * Medical Research, grant U54 GM072970. See https://simtk.org. * * * * Portions copyright (c) 2009 Stanford University and the Authors. * * Authors: Scott Le Grand, Peter Eastman * * Contributors: * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU Lesser General Public License as published * * by the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU Lesser General Public License for more details. * * * * You should have received a copy of the GNU Lesser General Public License * * along with this program. If not, see . * * -------------------------------------------------------------------------- */ #include "amoebaScaleFactors.h" __global__ #if (__CUDA_ARCH__ >= 200) __launch_bounds__(256, 1) #elif (__CUDA_ARCH__ >= 130) __launch_bounds__(128, 1) #else __launch_bounds__(64, 1) #endif void METHOD_NAME(kCalculateAmoebaCudaKirkwood, Forces_kernel)( unsigned int* workUnit #ifdef AMOEBA_DEBUG , float4* debugArray, unsigned int targetAtom #endif ){ #ifdef AMOEBA_DEBUG float4 pullBack[20]; #endif extern __shared__ KirkwoodParticle sA[]; unsigned int totalWarps = gridDim.x*blockDim.x/GRID; unsigned int warp = (blockIdx.x*blockDim.x+threadIdx.x)/GRID; unsigned int numWorkUnits = cSim.pInteractionCount[0]; unsigned int pos = warp*numWorkUnits/totalWarps; unsigned int end = (warp+1)*numWorkUnits/totalWarps; unsigned int lasty = 0xFFFFFFFF; // pWorkArray_3_1 == force // pWorkArray_3_2 == torque // pWorkArray_1_1 == dBorn // pWorkArray_1_2 == dBornPolar float4 jCoord; float jDipole[3]; float jQuadrupole[9]; float jInducedDipole[3]; float jInducedDipolePolar[3]; float jBornRadius; float energySum = 0.0f; while (pos < end) { unsigned int x; unsigned int y; bool bExclusionFlag; // extract cell coordinates decodeCell( workUnit[pos], &x, &y, &bExclusionFlag ); unsigned int tgx = threadIdx.x & (GRID - 1); unsigned int tbx = threadIdx.x - tgx; unsigned int tj = tgx; KirkwoodParticle* psA = &sA[tbx]; unsigned int atomI = x + tgx; float4 iCoord = cSim.pPosq[atomI]; float forceSum[3]; float torqueSum[3]; float dBornSum; float dBornPolarSum; forceSum[0] = 0.0f; forceSum[1] = 0.0f; forceSum[2] = 0.0f; torqueSum[0] = 0.0f; torqueSum[1] = 0.0f; torqueSum[2] = 0.0f; dBornSum = 0.0f; dBornPolarSum = 0.0f; // handle diagonals uniquely at 50% efficiency if (x == y) { // load shared data loadKirkwoodShared( &(sA[threadIdx.x]), atomI, cSim.pPosq, cAmoebaSim.pLabFrameDipole, cAmoebaSim.pLabFrameQuadrupole, cAmoebaSim.pInducedDipoleS, cAmoebaSim.pInducedDipolePolarS, cSim.pBornRadii ); // this branch is never exercised since it includes the // interaction between atomI and itself which is always excluded for (unsigned int j = 0; j < GRID; j++) { float force[3]; float torque[2][3]; float dBorn[2]; float dBornPolar[2]; float energy; unsigned int atomJ = y + j; unsigned int sameAtom = atomI == atomJ ? 1 : 0; // load coords, charge, ... loadKirkwoodData( &(psA[j]), &jCoord, jDipole, jQuadrupole, jInducedDipole, jInducedDipolePolar, &jBornRadius ); calculateKirkwoodPairIxn_kernel( sameAtom, iCoord, jCoord, &(cAmoebaSim.pLabFrameDipole[3*atomI]), jDipole, &(cAmoebaSim.pLabFrameQuadrupole[9*atomI]), jQuadrupole, &(cAmoebaSim.pInducedDipoleS[3*atomI]), jInducedDipole, &(cAmoebaSim.pInducedDipolePolarS[3*atomI]),jInducedDipolePolar, cSim.pBornRadii[atomI], jBornRadius, force, torque, dBorn, dBornPolar, &energy #ifdef AMOEBA_DEBUG , pullBack #endif ); unsigned int mask = ( (atomI >= cAmoebaSim.numberOfAtoms) || (atomJ >= cAmoebaSim.numberOfAtoms) ) ? 0 : 1; // torques include i == j contribution torqueSum[0] += mask ? torque[0][0] : 0.0f; torqueSum[1] += mask ? torque[0][1] : 0.0f; torqueSum[2] += mask ? torque[0][2] : 0.0f; dBornSum += mask ? dBorn[0] : 0.0f; dBornPolarSum += mask ? dBornPolar[0] : 0.0f; energySum += mask ? 0.5f*energy : 0.0f; // add to field at atomI the field due atomJ's charge/dipole/quadrupole mask = (atomI == atomJ) ? 0 : mask; forceSum[0] += mask ? force[0] : 0.0f; forceSum[1] += mask ? force[1] : 0.0f; forceSum[2] += mask ? force[2] : 0.0f; #ifdef AMOEBA_DEBUG if( atomI == targetAtom || atomJ == targetAtom ){ unsigned int index = (atomI == targetAtom) ? atomJ : atomI; unsigned int indexI = (atomI == targetAtom) ? 0 : 1; unsigned int indexJ = (atomI == targetAtom) ? 1 : 0; //float forceSign = (atomI == targetAtom) ? 1.0f : -1.0f; debugArray[index].x = (float) atomI; debugArray[index].y = (float) atomJ; debugArray[index].z = (float) (mask + 1); //debugArray[index].z = cSim.pBornRadii[atomI]; //debugArray[index].z = energy; //debugArray[index].w = (float) (blockIdx.x*blockDim.x+threadIdx.x); debugArray[index].w = jBornRadius; index = debugAccumulate( index, debugArray, force, mask, 1.0f ); mask = ( (atomI >= cAmoebaSim.numberOfAtoms) || (atomJ >= cAmoebaSim.numberOfAtoms) ) ? 0 : 1; index = debugAccumulate( index, debugArray, torque[indexI], mask, 2.0f ); index = debugAccumulate( index, debugArray, torque[indexJ], mask, 3.0f ); index += cAmoebaSim.paddedNumberOfAtoms; debugArray[index].x = pullBack[0].x; debugArray[index].y = pullBack[0].y; debugArray[index].z = pullBack[0].z; debugArray[index].w = pullBack[0].w; index += cAmoebaSim.paddedNumberOfAtoms; debugArray[index].x = pullBack[1].x; debugArray[index].y = pullBack[1].y; debugArray[index].z = pullBack[1].z; debugArray[index].w = pullBack[1].w; index += cAmoebaSim.paddedNumberOfAtoms; debugArray[index].x = pullBack[2].x; debugArray[index].y = pullBack[2].y; debugArray[index].z = pullBack[2].z; debugArray[index].w = pullBack[2].w; /* index += cAmoebaSim.paddedNumberOfAtoms; debugArray[index].x = dBorn[0]; debugArray[index].y = dBornPolar[0]; debugArray[index].z = dBorn[1]; debugArray[index].w = dBornPolar[1]; */ } #endif } // end of j-loop // write results #ifdef USE_OUTPUT_BUFFER_PER_WARP float of; unsigned int offset = x + tgx + warp*cAmoebaSim.paddedNumberOfAtoms; of = cAmoebaSim.pWorkArray_1_1[offset]; of += dBornSum; cAmoebaSim.pWorkArray_1_1[offset] = of; of = cAmoebaSim.pWorkArray_1_2[offset]; of += dBornPolarSum; cAmoebaSim.pWorkArray_1_2[offset] = of; offset *= 3; load3dArrayBufferPerWarp( offset, forceSum, cAmoebaSim.pWorkArray_3_1 ); load3dArrayBufferPerWarp( offset, torqueSum, cAmoebaSim.pWorkArray_3_2 ); #else unsigned int offset = x + tgx + (x >> GRIDBITS) * cAmoebaSim.paddedNumberOfAtoms; cAmoebaSim.pWorkArray_1_1[offset] = dBornSum; cAmoebaSim.pWorkArray_1_2[offset] = dBornPolarSum; offset *= 3; load3dArray( offset, forceSum, cAmoebaSim.pWorkArray_3_1 ); load3dArray( offset, torqueSum, cAmoebaSim.pWorkArray_3_2 ); #endif } else // 100% utilization { // Read fixed atom data into registers and GRF if (lasty != y) { // load shared data loadKirkwoodShared( &(sA[threadIdx.x]), (y+tgx), cSim.pPosq, cAmoebaSim.pLabFrameDipole, cAmoebaSim.pLabFrameQuadrupole, cAmoebaSim.pInducedDipoleS, cAmoebaSim.pInducedDipolePolarS, cSim.pBornRadii); } // zero j-atom output fields zeroKirkwoodParticleSharedField( &(sA[threadIdx.x]) ); for (unsigned int j = 0; j < GRID; j++) { float force[3]; float torque[2][3]; float dBorn[2]; float dBornPolar[2]; float energy; unsigned int atomJ = y + tj; unsigned int sameAtom = 0; // load coords, charge, ... loadKirkwoodData( &(psA[tj]), &jCoord, jDipole, jQuadrupole, jInducedDipole, jInducedDipolePolar, &jBornRadius ); calculateKirkwoodPairIxn_kernel( sameAtom, iCoord, jCoord, &(cAmoebaSim.pLabFrameDipole[3*atomI]), jDipole, &(cAmoebaSim.pLabFrameQuadrupole[9*atomI]), jQuadrupole, &(cAmoebaSim.pInducedDipoleS[3*atomI]), jInducedDipole, &(cAmoebaSim.pInducedDipolePolarS[3*atomI]), jInducedDipolePolar, cSim.pBornRadii[atomI], jBornRadius, force, torque, dBorn, dBornPolar, &energy #ifdef AMOEBA_DEBUG , pullBack #endif ); unsigned int mask = ( (atomI >= cAmoebaSim.numberOfAtoms) || ( atomJ >= cAmoebaSim.numberOfAtoms) ) ? 0 : 1; // add force and torque to atom I due atom J forceSum[0] += mask ? force[0] : 0.0f; forceSum[1] += mask ? force[1] : 0.0f; forceSum[2] += mask ? force[2] : 0.0f; torqueSum[0] += mask ? torque[0][0] : 0.0f; torqueSum[1] += mask ? torque[0][1] : 0.0f; torqueSum[2] += mask ? torque[0][2] : 0.0f; dBornSum += mask ? dBorn[0] : 0.0f; dBornPolarSum += mask ? dBornPolar[0] : 0.0f; energySum += mask ? energy : 0.0f; // add force and torque to atom J due atom I psA[tj].force[0] -= mask ? force[0] : 0.0f; psA[tj].force[1] -= mask ? force[1] : 0.0f; psA[tj].force[2] -= mask ? force[2] : 0.0f; psA[tj].torque[0] += mask ? torque[1][0] : 0.0f; psA[tj].torque[1] += mask ? torque[1][1] : 0.0f; psA[tj].torque[2] += mask ? torque[1][2] : 0.0f; psA[tj].dBornRadius += mask ? dBorn[1] : 0.0f; psA[tj].dBornRadiusPolar += mask ? dBornPolar[1] : 0.0f; #ifdef AMOEBA_DEBUG if( atomI == targetAtom || atomJ == targetAtom ){ unsigned int index = (atomI == targetAtom) ? atomJ : atomI; unsigned int indexI = (atomI == targetAtom) ? 0 : 1; unsigned int indexJ = (atomI == targetAtom) ? 1 : 0; // float forceSign = (atomI == targetAtom) ? 1.0f : -1.0f; debugArray[index].x = (float) atomI; debugArray[index].y = (float) atomJ; debugArray[index].z = (float) (mask+1); //debugArray[index].z = cSim.pBornRadii[atomI]; //debugArray[index].z = energy; debugArray[index].w = (float) (blockIdx.x*blockDim.x+threadIdx.x); index = debugAccumulate( index, debugArray, force, mask, -1.0f ); index = debugAccumulate( index, debugArray, torque[indexI], mask, -2.0f ); index = debugAccumulate( index, debugArray, torque[indexJ], mask, -3.0f ); index += cAmoebaSim.paddedNumberOfAtoms; debugArray[index].x = pullBack[0].x; debugArray[index].y = pullBack[0].y; debugArray[index].z = pullBack[0].z; debugArray[index].w = -1.0f; index += cAmoebaSim.paddedNumberOfAtoms; debugArray[index].x = pullBack[1].x; debugArray[index].y = pullBack[1].y; debugArray[index].z = pullBack[1].z; debugArray[index].w = pullBack[1].w; index += cAmoebaSim.paddedNumberOfAtoms; debugArray[index].x = pullBack[2].x; debugArray[index].y = pullBack[2].y; debugArray[index].z = pullBack[2].z; debugArray[index].w = pullBack[2].w; /* index += cAmoebaSim.paddedNumberOfAtoms; debugArray[index].x = dBorn[0]; debugArray[index].y = dBornPolar[0]; debugArray[index].z = dBorn[1]; debugArray[index].w = dBornPolar[1]; */ } #endif //#ifdef AMOEBA_DEBUG #if 0 if( mask || !mask ){ unsigned int index = atomJ + atomI*cAmoebaSim.paddedNumberOfAtoms; debugArray[index].x = (float) atomI; debugArray[index].y = (float) atomJ; debugArray[index].z = energy; debugArray[index].w = jBornRadius; } #endif tj = (tj + 1) & (GRID - 1); } // Write results #ifdef USE_OUTPUT_BUFFER_PER_WARP float of; unsigned int offset = x + tgx + warp*cAmoebaSim.paddedNumberOfAtoms; of = cAmoebaSim.pWorkArray_1_1[offset]; of += dBornSum; cAmoebaSim.pWorkArray_1_1[offset] = of; of = cAmoebaSim.pWorkArray_1_2[offset]; of += dBornPolarSum; cAmoebaSim.pWorkArray_1_2[offset] = of; offset *= 3; load3dArrayBufferPerWarp( offset, forceSum, cAmoebaSim.pWorkArray_3_1 ); load3dArrayBufferPerWarp( offset, torqueSum, cAmoebaSim.pWorkArray_3_2 ); offset = y + tgx + warp*cAmoebaSim.paddedNumberOfAtoms; of = cAmoebaSim.pWorkArray_1_1[offset]; of += dBornSum; cAmoebaSim.pWorkArray_1_1[offset] = of; of = cAmoebaSim.pWorkArray_1_2[offset]; of += dBornPolarSum; cAmoebaSim.pWorkArray_1_2[offset] = of; offset *= 3; load3dArrayBufferPerWarp( offset, sA[threadIdx.x].force, cAmoebaSim.pWorkArray_3_1 ); load3dArrayBufferPerWarp( offset, sA[threadIdx.x].torque, cAmoebaSim.pWorkArray_3_2 ); #else unsigned int offset = x + tgx + (y >> GRIDBITS) * cAmoebaSim.paddedNumberOfAtoms; cAmoebaSim.pWorkArray_1_1[offset] = dBornSum; cAmoebaSim.pWorkArray_1_2[offset] = dBornPolarSum; offset *= 3; load3dArray( offset, forceSum, cAmoebaSim.pWorkArray_3_1 ); load3dArray( offset, torqueSum, cAmoebaSim.pWorkArray_3_2 ); offset = y + tgx + (x >> GRIDBITS) * cAmoebaSim.paddedNumberOfAtoms; cAmoebaSim.pWorkArray_1_1[offset] = sA[threadIdx.x].dBornRadius; cAmoebaSim.pWorkArray_1_2[offset] = sA[threadIdx.x].dBornRadiusPolar; offset *= 3; load3dArray( offset, sA[threadIdx.x].force, cAmoebaSim.pWorkArray_3_1 ); load3dArray( offset, sA[threadIdx.x].torque, cAmoebaSim.pWorkArray_3_2 ); #endif lasty = y; } pos++; } cSim.pEnergy[blockIdx.x*blockDim.x+threadIdx.x] += energySum; }