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Commit d3469b87 authored by peastman's avatar peastman
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Merge pull request #279 from peastman/master 

Optimizations to CPU GBSA
parents 6d356ddc cf52e69f
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Showing with 42 additions and 34 deletions
platforms/cpu/src/CpuGBSAOBCForce.cpp
View file @ d3469b87
......@@ -249,7 +249,7 @@ void CpuGBSAOBCForce::threadComputeForce(ThreadPool& threads, int threadIndex) {
ivec4 blockAtomIndex(blockStart, blockStart+1, blockStart+2, blockStart+3);
float atomCharge[4], atomx[4], atomy[4], atomz[4];
int blockMask[4] = {0, 0, 0, 0};
fvec4 blockAtomForce[4];
fvec4 blockAtomForceX(0.0f), blockAtomForceY(0.0f), blockAtomForceZ(0.0f), blockAtomBornForce(0.0f);
for (int i = 0; i < numInBlock; i++) {
int atomIndex = blockStart+i;
atomx[i] = posq[4*atomIndex];
......@@ -257,7 +257,6 @@ void CpuGBSAOBCForce::threadComputeForce(ThreadPool& threads, int threadIndex) {
atomz[i] = posq[4*atomIndex+2];
atomCharge[i] = preFactor*posq[4*atomIndex+3];
blockMask[i] = 0xFFFFFFFF;
blockAtomForce[i] = 0.0f;
}
fvec4 radii(&bornRadii[blockStart]);
fvec4 x(atomx);
......@@ -277,35 +276,40 @@ void CpuGBSAOBCForce::threadComputeForce(ThreadPool& threads, int threadIndex) {
fvec4 r = sqrt(r2);
fvec4 alpha2_ij = radii*bornRadii[atomJ];
fvec4 D_ij = r2/(4.0f*alpha2_ij);
fvec4 expTerm(exp(-D_ij[0]), exp(-D_ij[1]), exp(-D_ij[2]), exp(-D_ij[3]));
fvec4 expTerm(expf(-D_ij[0]), expf(-D_ij[1]), expf(-D_ij[2]), expf(-D_ij[3]));
fvec4 denominator2 = r2 + alpha2_ij*expTerm;
fvec4 denominator = sqrt(denominator2);
fvec4 Gpol = (partialChargeI*posJ[3])/denominator;
fvec4 dGpol_dr = -Gpol*(1.0f - 0.25f*expTerm)/denominator2;
fvec4 dGpol_dalpha2_ij = -0.5f*Gpol*expTerm*(1.0f + D_ij)/denominator2;
fvec4 result[4] = {dx*dGpol_dr, dy*dGpol_dr, dz*dGpol_dr, 0.0f};
transpose(result[0], result[1], result[2], result[3]);
fvec4 atomForce(forces+4*atomJ);
for (int j = 0; j < 4; j++) {
if (include[j]) {
float termEnergy = Gpol[j];
if (blockStart+j != atomJ) {
dGpol_dr = blend(0.0f, dGpol_dr, include);
dGpol_dalpha2_ij = blend(0.0f, dGpol_dalpha2_ij, include);
fvec4 fx = dx*dGpol_dr;
fvec4 fy = dy*dGpol_dr;
fvec4 fz = dz*dGpol_dr;
blockAtomForceX -= fx;
blockAtomForceY -= fy;
blockAtomForceZ -= fz;
blockAtomBornForce += dGpol_dalpha2_ij*bornRadii[atomJ];
float* atomForce = forces+4*atomJ;
fvec4 one(1.0f);
atomForce[0] += dot4(fx, one);
atomForce[1] += dot4(fy, one);
atomForce[2] += dot4(fz, one);
ivec4 atomJMask = include & (blockAtomIndex != ivec4(atomJ));
fvec4 termEnergy = blend(0.0f, Gpol, include);
if (cutoff)
termEnergy -= partialChargeI[j]*posJ[3]/cutoffDistance;
bornForces[atomJ] += dGpol_dalpha2_ij[j]*radii[j];
blockAtomForce[j] -= result[j];
(fvec4(forces+4*atomJ)+result[j]).store(forces+4*atomJ);
}
else
termEnergy *= 0.5f;
energy += termEnergy;
bornForces[blockStart+j] += dGpol_dalpha2_ij[j]*bornRadii[atomJ];
}
}
termEnergy -= blend(0.0f, partialChargeI*posJ[3]/cutoffDistance, atomJMask);
termEnergy *= blend(0.5f, 1.0f, atomJMask);
energy += dot4(termEnergy, one);
bornForces[atomJ] += dot4(blend(0.0f, dGpol_dalpha2_ij, atomJMask), radii);
}
fvec4 f[4] = {blockAtomForceX, blockAtomForceY, blockAtomForceZ, 0.0f};
transpose(f[0], f[1], f[2], f[3]);
for (int i = 0; i < numInBlock; i++) {
int atomIndex = blockStart+i;
(fvec4(forces+4*atomIndex)+blockAtomForce[i]).store(forces+4*atomIndex);
(fvec4(forces+4*atomIndex)+f[i]).store(forces+4*atomIndex);
bornForces[atomIndex] += blockAtomBornForce[i];
}
}
threads.syncThreads();
......@@ -325,7 +329,7 @@ void CpuGBSAOBCForce::threadComputeForce(ThreadPool& threads, int threadIndex) {
ivec4 blockAtomIndex(blockStart, blockStart+1, blockStart+2, blockStart+3);
float atomRadius[4], atomx[4], atomy[4], atomz[4];
int blockMask[4] = {0, 0, 0, 0};
fvec4 blockAtomForce[4];
fvec4 blockAtomForceX(0.0f), blockAtomForceY(0.0f), blockAtomForceZ(0.0f);
for (int i = 0; i < numInBlock; i++) {
int atomIndex = blockStart+i;
atomRadius[i] = particleParams[atomIndex].first;
......@@ -333,7 +337,6 @@ void CpuGBSAOBCForce::threadComputeForce(ThreadPool& threads, int threadIndex) {
atomy[i] = posq[4*atomIndex+1];
atomz[i] = posq[4*atomIndex+2];
blockMask[i] = 0xFFFFFFFF;
blockAtomForce[i] = 0.0f;
}
fvec4 offsetRadiusI(atomRadius);
fvec4 x(atomx);
......@@ -364,18 +367,23 @@ void CpuGBSAOBCForce::threadComputeForce(ThreadPool& threads, int threadIndex) {
fvec4 t3 = 0.125f*(1.0f + scaledRadiusJ2*r2Inverse)*(l_ij2 - u_ij2) + 0.25f*logRatio*r2Inverse;
fvec4 de = bornForce*t3*rInverse;
de = blend(0.0f, de, include);
fvec4 result[4] = {dx*de, dy*de, dz*de, 0.0f};
transpose(result[0], result[1], result[2], result[3]);
fvec4 atomForce(forces+4*atomJ);
for (int j = 0; j < 4; j++) {
blockAtomForce[j] += result[j];
atomForce -= result[j];
}
atomForce.store(forces+4*atomJ);
fvec4 fx = dx*de;
fvec4 fy = dy*de;
fvec4 fz = dz*de;
blockAtomForceX += fx;
blockAtomForceY += fy;
blockAtomForceZ += fz;
float* atomForce = forces+4*atomJ;
fvec4 one(1.0f);
atomForce[0] -= dot4(fx, one);
atomForce[1] -= dot4(fy, one);
atomForce[2] -= dot4(fz, one);
}
fvec4 f[4] = {blockAtomForceX, blockAtomForceY, blockAtomForceZ, 0.0f};
transpose(f[0], f[1], f[2], f[3]);
for (int i = 0; i < numInBlock; i++) {
int atomIndex = blockStart+i;
(fvec4(forces+4*atomIndex)+blockAtomForce[i]).store(forces+4*atomIndex);
(fvec4(forces+4*atomIndex)+f[i]).store(forces+4*atomIndex);
}
}
threadEnergy[threadIndex] = energy;
......
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