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Commit be0d5cbe authored by peastman's avatar peastman
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Began vectorizing CustomManyParticleForce

parent 0e2ffb4b
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Showing with 57 additions and 51 deletions
openmmapi/include/openmm/internal/vectorize_neon.h
View file @ be0d5cbe
......@@ -268,6 +268,12 @@ static inline float dot4(const fvec4& v1, const fvec4& v2) {
return vgetq_lane_f32(result, 0) + vgetq_lane_f32(result, 1) + vgetq_lane_f32(result, 2) + vgetq_lane_f32(result,3);
}
static inline fvec4 cross(const fvec4& v1, const fvec4& v2) {
return fvec4(v1[1]*v2[2] - v1[2]*v2[1],
v1[2]*v2[0] - v1[0]*v2[2],
v1[0]*v2[1] - v1[1]*v2[0], 0);
}
static inline void transpose(fvec4& v1, fvec4& v2, fvec4& v3, fvec4& v4) {
float32x4x2_t t1 = vuzpq_f32(v1, v3);
float32x4x2_t t2 = vuzpq_f32(v2, v4);
......
openmmapi/include/openmm/internal/vectorize_pnacl.h
View file @ be0d5cbe
......@@ -255,6 +255,12 @@ static inline float dot4(const fvec4& v1, const fvec4& v2) {
return r[0]+r[1]+r[2]+r[3];
}
static inline fvec4 cross(const fvec4& v1, const fvec4& v2) {
__m128 temp = v2.val*__builtin_shufflevector(v1.val, v1.val, 2, 0, 1, 3) -
v1.val*__builtin_shufflevector(v2.val, v2.val, 2, 0, 1, 3);
return __builtin_shufflevector(temp, temp, 2, 0, 1, 3);
}
static inline void transpose(fvec4& v1, fvec4& v2, fvec4& v3, fvec4& v4) {
__m128 a1 = __builtin_shufflevector(v1.val, v2.val, 0, 4, 2, 6);
__m128 a2 = __builtin_shufflevector(v1.val, v2.val, 1, 5, 3, 7);
......
openmmapi/include/openmm/internal/vectorize_sse.h
View file @ be0d5cbe
......@@ -249,6 +249,12 @@ static inline float dot4(const fvec4& v1, const fvec4& v2) {
return _mm_cvtss_f32(_mm_dp_ps(v1, v2, 0xF1));
}
static inline fvec4 cross(const fvec4& v1, const fvec4& v2) {
fvec4 temp = _mm_mul_ps(v2, _mm_shuffle_ps(v1, v1, _MM_SHUFFLE(3, 0, 2, 1))) -
_mm_mul_ps(v1, _mm_shuffle_ps(v2, v2, _MM_SHUFFLE(3, 0, 2, 1)));
return _mm_shuffle_ps(temp, temp, _MM_SHUFFLE(3, 0, 2, 1));
}
static inline void transpose(fvec4& v1, fvec4& v2, fvec4& v3, fvec4& v4) {
_MM_TRANSPOSE4_PS(v1, v2, v3, v4);
}
......
platforms/cpu/src/CpuCustomManyParticleForce.cpp
View file @ be0d5cbe
......@@ -207,7 +207,7 @@ void CpuCustomManyParticleForce::setPeriodic(RealVec& boxSize) {
void CpuCustomManyParticleForce::loopOverInteractions(vector<int>& availableParticles, vector<int>& particleSet, int loopIndex, int startIndex,
RealOpenMM** particleParameters, float* forces, ThreadData& data, const fvec4& boxSize, const fvec4& invBoxSize) {
int numParticles = availableParticles.size();
// double cutoff2 = cutoffDistance*cutoffDistance;
double cutoff2 = cutoffDistance*cutoffDistance;
for (int i = startIndex; i < numParticles; i++) {
int particle = availableParticles[i];
......@@ -215,18 +215,13 @@ void CpuCustomManyParticleForce::loopOverInteractions(vector<int>& availablePart
bool include = true;
if (useCutoff) {
// fvec4 deltaR;
// fvec4 pos1(posq+4*particle);
// float r2;
// for (int j = 0; j < loopIndex && include; j++) {
// fvec4 pos2(posq+4*particleSet[j]);
// getDeltaR(pos1, pos2, deltaR, r2, boxSize, invBoxSize);
// include &= (r2 < cutoff2);
// }
RealOpenMM delta[ReferenceForce::LastDeltaRIndex];
fvec4 deltaR;
fvec4 pos1(posq+4*particle);
float r2;
for (int j = 0; j < loopIndex && include; j++) {
computeDelta(particle, particleSet[j], delta, atomCoordinates);
include &= (delta[ReferenceForce::RIndex] < cutoffDistance);
fvec4 pos2(posq+4*particleSet[j]);
getDeltaR(pos1, pos2, deltaR, r2, boxSize, invBoxSize);
include &= (r2 < cutoff2);
}
}
for (int j = 0; j < loopIndex && include; j++)
......@@ -299,10 +294,15 @@ void CpuCustomManyParticleForce::calculateOneIxn(vector<int>& particleSet, RealO
if (includeForces) {
// Apply forces based on individual particle coordinates.
vector<RealVec> f(numParticlesPerSet);
AlignedArray<fvec4> f(numParticlesPerSet);
for (int i = 0; i < numParticlesPerSet; i++)
f[i] = fvec4(0.0f);
for (int i = 0; i < (int) data.particleTerms.size(); i++) {
const ParticleTermInfo& term = data.particleTerms[i];
f[term.atom][term.component] -= term.forceExpression.evaluate();
float temp[4];
f[term.atom].store(temp);
temp[term.component] -= term.forceExpression.evaluate();
f[term.atom] = fvec4(temp);
}
// Apply forces based on distances.
......@@ -310,11 +310,9 @@ void CpuCustomManyParticleForce::calculateOneIxn(vector<int>& particleSet, RealO
for (int i = 0; i < (int) data.distanceTerms.size(); i++) {
const DistanceTermInfo& term = data.distanceTerms[i];
RealOpenMM dEdR = (RealOpenMM) (term.forceExpression.evaluate()*term.deltaSign/(delta[term.delta][ReferenceForce::RIndex]));
for (int i = 0; i < 3; i++) {
RealOpenMM force = -dEdR*delta[term.delta][i];
f[term.p1][i] -= force;
f[term.p2][i] += force;
}
fvec4 force = -dEdR*fvec4((float) delta[term.delta][0], (float) delta[term.delta][1], (float) delta[term.delta][2], 0.0f);
f[term.p1] -= force;
f[term.p2] += force;
}
// Apply forces based on angles.
......@@ -322,26 +320,22 @@ void CpuCustomManyParticleForce::calculateOneIxn(vector<int>& particleSet, RealO
for (int i = 0; i < (int) data.angleTerms.size(); i++) {
const AngleTermInfo& term = data.angleTerms[i];
RealOpenMM dEdTheta = (RealOpenMM) term.forceExpression.evaluate();
RealOpenMM thetaCross[ReferenceForce::LastDeltaRIndex];
SimTKOpenMMUtilities::crossProductVector3(delta[term.delta1], delta[term.delta2], thetaCross);
RealOpenMM lengthThetaCross = SQRT(DOT3(thetaCross, thetaCross));
if (lengthThetaCross < 1.0e-06)
lengthThetaCross = (RealOpenMM) 1.0e-06;
fvec4 delta1((float) delta[term.delta1][0], (float) delta[term.delta1][1], (float) delta[term.delta1][2], 0.0f);
fvec4 delta2((float) delta[term.delta2][0], (float) delta[term.delta2][1], (float) delta[term.delta2][2], 0.0f);
fvec4 thetaCross = cross(delta1, delta2);
float lengthThetaCross = sqrtf(dot3(thetaCross, thetaCross));
if (lengthThetaCross < 1.0e-6f)
lengthThetaCross = 1.0e-6f;
RealOpenMM termA = dEdTheta*term.delta2Sign/(delta[term.delta1][ReferenceForce::R2Index]*lengthThetaCross);
RealOpenMM termC = -dEdTheta*term.delta1Sign/(delta[term.delta2][ReferenceForce::R2Index]*lengthThetaCross);
RealOpenMM deltaCrossP[3][3];
SimTKOpenMMUtilities::crossProductVector3(delta[term.delta1], thetaCross, deltaCrossP[0]);
SimTKOpenMMUtilities::crossProductVector3(delta[term.delta2], thetaCross, deltaCrossP[2]);
for (int i = 0; i < 3; i++) {
deltaCrossP[0][i] *= termA;
deltaCrossP[2][i] *= termC;
deltaCrossP[1][i] = -(deltaCrossP[0][i]+deltaCrossP[2][i]);
}
for (int i = 0; i < 3; i++) {
f[term.p1][i] += deltaCrossP[0][i];
f[term.p2][i] += deltaCrossP[1][i];
f[term.p3][i] += deltaCrossP[2][i];
}
fvec4 deltaCross1 = cross(delta1, thetaCross);
fvec4 deltaCross2 = cross(delta2, thetaCross);
fvec4 force1 = termA*deltaCross1;
fvec4 force3 = termC*deltaCross2;
fvec4 force2 = -(force1+force3);
f[term.p1] += force1;
f[term.p2] += force2;
f[term.p3] += force3;
}
// Apply forces based on dihedrals.
......@@ -360,26 +354,20 @@ void CpuCustomManyParticleForce::calculateOneIxn(vector<int>& particleSet, RealO
forceFactors[1] /= delta[term.delta2][ReferenceForce::R2Index];
forceFactors[2] = DOT3(delta[term.delta3], delta[term.delta2]);
forceFactors[2] /= delta[term.delta2][ReferenceForce::R2Index];
for (int i = 0; i < 3; i++) {
internalF[0][i] = forceFactors[0]*term.cross1[i];
internalF[3][i] = forceFactors[3]*term.cross2[i];
RealOpenMM s = forceFactors[1]*internalF[0][i] - forceFactors[2]*internalF[3][i];
internalF[1][i] = internalF[0][i] - s;
internalF[2][i] = internalF[3][i] + s;
}
for (int i = 0; i < 3; i++) {
f[term.p1][i] += internalF[0][i];
f[term.p2][i] -= internalF[1][i];
f[term.p3][i] -= internalF[2][i];
f[term.p4][i] += internalF[3][i];
}
fvec4 force1 = forceFactors[0]*fvec4((float) term.cross1[0], (float) term.cross1[1], (float) term.cross1[2], 0.0f);
fvec4 force4 = forceFactors[3]*fvec4((float) term.cross2[0], (float) term.cross2[1], (float) term.cross2[2], 0.0f);
fvec4 s = forceFactors[1]*force1 - forceFactors[2]*force4;
f[term.p1] += force1;
f[term.p2] -= force1-s;
f[term.p3] -= force4+s;
f[term.p4] += force4;
}
// Store the forces.
for (int i = 0; i < numParticlesPerSet; i++) {
int index = permutedParticles[i];
(fvec4(forces+4*index)+fvec4((float) f[i][0], (float) f[i][1], (float) f[i][2], 0.0f)).store(forces+4*index);
(fvec4(forces+4*index)+f[i]).store(forces+4*index);
}
}
......
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