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Commit 59bccb15 authored by peastman's avatar peastman
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Merge branch 'master' into pthreads 

Conflicts:
	libraries/pthreads/include/pthread.h
parents 6cf75568 4bdbcf4d
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Showing with 445 additions and 196 deletions
openmmapi/include/openmm/internal/vectorize_neon.h
View file @ 59bccb15
......@@ -251,11 +251,15 @@ static inline fvec4 abs(const fvec4& v) {
return vabsq_f32(v);
}
static inline fvec4 sqrt(const fvec4& v) {
static inline fvec4 rsqrt(const fvec4& v) {
float32x4_t recipSqrt = vrsqrteq_f32(v);
recipSqrt = vmulq_f32(recipSqrt, vrsqrtsq_f32(vmulq_f32(recipSqrt, v), recipSqrt));
recipSqrt = vmulq_f32(recipSqrt, vrsqrtsq_f32(vmulq_f32(recipSqrt, v), recipSqrt));
return vmulq_f32(v, recipSqrt);
return recipSqrt;
}
static inline fvec4 sqrt(const fvec4& v) {
return rsqrt(v)*v;
}
static inline float dot3(const fvec4& v1, const fvec4& v2) {
......
openmmapi/include/openmm/internal/vectorize_pnacl.h
View file @ 59bccb15
......@@ -330,7 +330,7 @@ static inline fvec4 ceil(const fvec4& v) {
return truncated + blend(0.0f, 1.0f, truncated<v);
}
static inline fvec4 sqrt(const fvec4& v) {
static inline fvec4 rsqrt(const fvec4& v) {
// Initial estimate of rsqrt().
ivec4 i = (__m128i) v;
......@@ -343,7 +343,11 @@ static inline fvec4 sqrt(const fvec4& v) {
y *= 1.5f-x2*y*y;
y *= 1.5f-x2*y*y;
y *= 1.5f-x2*y*y;
return y*v;
return y;
}
static inline fvec4 sqrt(const fvec4& v) {
return rsqrt(v)*v;
}
#endif /*OPENMM_VECTORIZE_PNACL_H_*/
......
openmmapi/include/openmm/internal/vectorize_sse.h
View file @ 59bccb15
......@@ -241,6 +241,18 @@ static inline fvec4 sqrt(const fvec4& v) {
return fvec4(_mm_sqrt_ps(v.val));
}
static inline fvec4 rsqrt(const fvec4& v) {
// Initial estimate of rsqrt().
fvec4 y(_mm_rsqrt_ps(v.val));
// Perform an iteration of Newton refinement.
fvec4 x2 = v*0.5f;
y *= fvec4(1.5f)-x2*y*y;
return y;
}
static inline float dot3(const fvec4& v1, const fvec4& v2) {
return _mm_cvtss_f32(_mm_dp_ps(v1, v2, 0x71));
}
......
platforms/cpu/include/CpuNeighborList.h
View file @ 59bccb15
......@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2013 Stanford University and the Authors. *
* Portions copyright (c) 2013-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -61,6 +61,7 @@ public:
private:
int blockSize;
std::vector<int> sortedAtoms;
std::vector<float> sortedPositions;
std::vector<std::vector<int> > blockNeighbors;
std::vector<std::vector<char> > blockExclusions;
// The following variables are used to make information accessible to the individual threads.
......
platforms/cpu/include/CpuNonbondedForceVec4.h
View file @ 59bccb15
......@@ -56,8 +56,8 @@ protected:
/**
* Templatized implementation of calculateBlockIxn.
*/
template <bool TRICLINIC>
void calculateBlockIxnImpl(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize);
template <int PERIODIC_TYPE>
void calculateBlockIxnImpl(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize, const fvec4& blockCenter);
/**---------------------------------------------------------------------------------------
......@@ -74,15 +74,15 @@ protected:
/**
* Templatized implementation of calculateBlockEwaldIxn.
*/
template <bool TRICLINIC>
void calculateBlockEwaldIxnImpl(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize);
template <int PERIODIC_TYPE>
void calculateBlockEwaldIxnImpl(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize, const fvec4& blockCenter);
/**
* Compute the displacement and squared distance between a collection of points, optionally using
* periodic boundary conditions.
*/
template <bool TRICLINIC>
void getDeltaR(const float* posI, const fvec4& x, const fvec4& y, const fvec4& z, fvec4& dx, fvec4& dy, fvec4& dz, fvec4& r2, bool periodic, const fvec4& boxSize, const fvec4& invBoxSize) const;
template <int PERIODIC_TYPE>
void getDeltaR(const fvec4& posI, const fvec4& x, const fvec4& y, const fvec4& z, fvec4& dx, fvec4& dy, fvec4& dz, fvec4& r2, bool periodic, const fvec4& boxSize, const fvec4& invBoxSize) const;
/**
* Compute a fast approximation to erfc(x).
......
platforms/cpu/include/CpuNonbondedForceVec8.h
View file @ 59bccb15
......@@ -55,8 +55,8 @@ protected:
/**
* Templatized implementation of calculateBlockIxn.
*/
template <bool TRICLINIC>
void calculateBlockIxnImpl(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize);
template <int PERIODIC_TYPE>
void calculateBlockIxnImpl(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize, const fvec4& blockCenter);
/**---------------------------------------------------------------------------------------
......@@ -73,15 +73,15 @@ protected:
/**
* Templatized implementation of calculateBlockEwaldIxn.
*/
template <bool TRICLINIC>
void calculateBlockEwaldIxnImpl(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize);
template <int PERIODIC_TYPE>
void calculateBlockEwaldIxnImpl(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize, const fvec4& blockCenter);
/**
* Compute the displacement and squared distance between a collection of points, optionally using
* periodic boundary conditions.
*/
template <bool TRICLINIC>
void getDeltaR(const float* posI, const fvec8& x, const fvec8& y, const fvec8& z, fvec8& dx, fvec8& dy, fvec8& dz, fvec8& r2, bool periodic, const fvec4& boxSize, const fvec4& invBoxSize) const;
template <int PERIODIC_TYPE>
void getDeltaR(const fvec4& posI, const fvec8& x, const fvec8& y, const fvec8& z, fvec8& dx, fvec8& dy, fvec8& dz, fvec8& r2, bool periodic, const fvec4& boxSize, const fvec4& invBoxSize) const;
/**
* Compute a fast approximation to erfc(x).
......
platforms/cpu/src/CpuCustomManyParticleForce.cpp
View file @ 59bccb15
......@@ -199,7 +199,7 @@ void CpuCustomManyParticleForce::setUseCutoff(RealOpenMM distance) {
}
void CpuCustomManyParticleForce::setPeriodic(RealVec* periodicBoxVectors) {
assert(cutoff);
assert(useCutoff);
assert(periodicBoxVectors[0][0] >= 2.0*cutoffDistance);
assert(periodicBoxVectors[1][1] >= 2.0*cutoffDistance);
assert(periodicBoxVectors[2][2] >= 2.0*cutoffDistance);
......
platforms/cpu/src/CpuNeighborList.cpp
View file @ 59bccb15
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2013 Stanford University and the Authors. *
* Portions copyright (c) 2013-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -165,7 +165,7 @@ public:
return VoxelIndex(y, z);
}
void getNeighbors(vector<int>& neighbors, int blockIndex, const fvec4& blockCenter, const fvec4& blockWidth, const vector<int>& sortedAtoms, vector<char>& exclusions, float maxDistance, const vector<int>& blockAtoms, const float* atomLocations, const vector<VoxelIndex>& atomVoxelIndex) const {
void getNeighbors(vector<int>& neighbors, int blockIndex, const fvec4& blockCenter, const fvec4& blockWidth, const vector<int>& sortedAtoms, vector<char>& exclusions, float maxDistance, const vector<int>& blockAtoms, const vector<float>& blockAtomX, const vector<float>& blockAtomY, const vector<float>& blockAtomZ, const vector<float>& sortedPositions, const vector<VoxelIndex>& atomVoxelIndex) const {
neighbors.resize(0);
exclusions.resize(0);
fvec4 boxSize(periodicBoxSize[0], periodicBoxSize[1], periodicBoxSize[2], 0);
......@@ -233,24 +233,34 @@ public:
float minx = centerPos[0];
float maxx = centerPos[0];
fvec4 offset(-xoffset, -yoffset+voxelSizeY*y+(usePeriodic ? 0.0f : miny), voxelSizeZ*z+(usePeriodic ? 0.0f : minz), 0);
for (int k = 0; k < (int) blockAtoms.size(); k++) {
const float* atomPos = &atomLocations[4*blockAtoms[k]];
fvec4 posVec(atomPos);
fvec4 delta1 = offset-posVec;
fvec4 delta2 = delta1+fvec4(0, voxelSizeY, voxelSizeZ, 0);
float offset[3] = {-xoffset, -yoffset+voxelSizeY*y+(usePeriodic ? 0.0f : miny), voxelSizeZ*z+(usePeriodic ? 0.0f : minz)};
for (int k = 0; k < (int) blockAtoms.size(); k += 4) {
fvec4 dist2 = maxDistanceSquared;
if (y != atomVoxelIndex[k].y) {
fvec4 dy1 = offset[1]-fvec4(&blockAtomY[k]);
fvec4 dy2 = dy1+voxelSizeY;
if (usePeriodic) {
delta1 -= round(delta1*invBoxSize)*boxSize;
delta2 -= round(delta2*invBoxSize)*boxSize;
dy1 -= round(dy1*invBoxSize[1])*boxSize[1];
dy2 -= round(dy2*invBoxSize[1])*boxSize[1];
}
fvec4 delta = min(abs(delta1), abs(delta2));
float dy = (y == atomVoxelIndex[k].y ? 0.0f : delta[1]);
float dz = (z == atomVoxelIndex[k].z ? 0.0f : delta[2]);
float dist2 = maxDistanceSquared-dy*dy-dz*dz;
if (dist2 > 0) {
float dist = sqrtf(dist2);
minx = min(minx, atomPos[0]-dist-xoffset);
maxx = max(maxx, atomPos[0]+dist-xoffset);
fvec4 dy = min(abs(dy1), abs(dy2));
dist2 -= dy*dy;
}
if (z != atomVoxelIndex[k].z) {
fvec4 dz1 = offset[2]-fvec4(&blockAtomZ[k]);
fvec4 dz2 = dz1+voxelSizeZ;
if (usePeriodic) {
dz1 -= round(dz1*invBoxSize[2])*boxSize[2];
dz2 -= round(dz2*invBoxSize[2])*boxSize[2];
}
fvec4 dz = min(abs(dz1), abs(dz2));
dist2 -= dz*dz;
}
fvec4 dist = sqrt(dist2);
int numToCheck = min(4, (int) (blockAtoms.size()-k));
for (int m = 0; m < numToCheck; m++) {
minx = min(minx, blockAtomX[k+m]-dist[m]-xoffset);
maxx = max(maxx, blockAtomX[k+m]+dist[m]-xoffset);
}
}
if (minx == maxx)
......@@ -290,12 +300,10 @@ public:
if (sortedIndex >= lastSortedIndex)
continue;
fvec4 atomPos(atomLocations+4*sortedAtoms[sortedIndex]);
fvec4 atomPos(&sortedPositions[4*sortedIndex]);
fvec4 delta = atomPos-centerPos;
if (periodicRectangular) {
fvec4 base = round(delta*invBoxSize)*boxSize;
delta = delta-base;
}
if (periodicRectangular)
delta -= round(delta*invBoxSize)*boxSize;
else if (needPeriodic) {
delta -= periodicBoxVec4[2]*floorf(delta[2]*recipBoxSize[2]+0.5f);
delta -= periodicBoxVec4[1]*floorf(delta[1]*recipBoxSize[1]+0.5f);
......@@ -310,26 +318,34 @@ public:
// The distance is large enough that there might not be any actual interactions.
// Check individual atom pairs to be sure.
bool any = false;
for (int k = 0; k < (int) blockAtoms.size(); k++) {
fvec4 pos1(&atomLocations[4*blockAtoms[k]]);
delta = atomPos-pos1;
bool anyInteraction = false;
for (int k = 0; k < (int) blockAtoms.size(); k += 4) {
fvec4 dx = fvec4(&blockAtomX[k])-atomPos[0];
fvec4 dy = fvec4(&blockAtomY[k])-atomPos[1];
fvec4 dz = fvec4(&blockAtomZ[k])-atomPos[2];
if (periodicRectangular) {
fvec4 base = round(delta*invBoxSize)*boxSize;
delta = delta-base;
dx -= round(dx*invBoxSize[0])*boxSize[0];
dy -= round(dy*invBoxSize[1])*boxSize[1];
dz -= round(dz*invBoxSize[2])*boxSize[2];
}
else if (needPeriodic) {
delta -= periodicBoxVec4[2]*floorf(delta[2]*recipBoxSize[2]+0.5f);
delta -= periodicBoxVec4[1]*floorf(delta[1]*recipBoxSize[1]+0.5f);
delta -= periodicBoxVec4[0]*floorf(delta[0]*recipBoxSize[0]+0.5f);
}
float r2 = dot3(delta, delta);
if (r2 < maxDistanceSquared) {
any = true;
fvec4 scale3 = floor(dz*recipBoxSize[2]+0.5f);
dx -= scale3*periodicBoxVectors[2][0];
dy -= scale3*periodicBoxVectors[2][1];
dz -= scale3*periodicBoxVectors[2][2];
fvec4 scale2 = floor(dy*recipBoxSize[1]+0.5f);
dx -= scale2*periodicBoxVectors[1][0];
dy -= scale2*periodicBoxVectors[1][1];
fvec4 scale1 = floor(dx*recipBoxSize[0]+0.5f);
dx -= scale1*periodicBoxVectors[0][0];
}
fvec4 r2 = dx*dx + dy*dy + dz*dz;
if (any(r2 < maxDistanceSquared)) {
anyInteraction = true;
break;
}
}
if (!any)
if (!anyInteraction)
continue;
}
......@@ -379,6 +395,7 @@ void CpuNeighborList::computeNeighborList(int numAtoms, const AlignedArray<float
blockNeighbors.resize(numBlocks);
blockExclusions.resize(numBlocks);
sortedAtoms.resize(numAtoms);
sortedPositions.resize(4*numAtoms);
// Record the parameters for the threads.
......@@ -428,6 +445,8 @@ void CpuNeighborList::computeNeighborList(int numAtoms, const AlignedArray<float
for (int i = 0; i < numAtoms; i++) {
int atomIndex = atomBins[i].second;
sortedAtoms[i] = atomIndex;
fvec4 atomPos(&atomLocations[4*atomIndex]);
atomPos.store(&sortedPositions[4*i]);
voxels.insert(i, &atomLocations[4*atomIndex]);
}
voxels.sortItems();
......@@ -489,6 +508,7 @@ void CpuNeighborList::threadComputeNeighborList(ThreadPool& threads, int threadI
int numBlocks = blockNeighbors.size();
vector<int> blockAtoms;
vector<float> blockAtomX(blockSize), blockAtomY(blockSize), blockAtomZ(blockSize);
vector<VoxelIndex> atomVoxelIndex;
for (int i = threadIndex; i < numBlocks; i += numThreads) {
// Find the atoms in this block and compute their bounding box.
......@@ -501,14 +521,24 @@ void CpuNeighborList::threadComputeNeighborList(ThreadPool& threads, int threadI
blockAtoms[j] = sortedAtoms[firstIndex+j];
atomVoxelIndex[j] = voxels->getVoxelIndex(&atomLocations[4*blockAtoms[j]]);
}
fvec4 minPos(&atomLocations[4*sortedAtoms[firstIndex]]);
fvec4 minPos(&sortedPositions[4*firstIndex]);
fvec4 maxPos = minPos;
for (int j = 1; j < atomsInBlock; j++) {
fvec4 pos(&atomLocations[4*sortedAtoms[firstIndex+j]]);
fvec4 pos(&sortedPositions[4*(firstIndex+j)]);
minPos = min(minPos, pos);
maxPos = max(maxPos, pos);
}
voxels->getNeighbors(blockNeighbors[i], i, (maxPos+minPos)*0.5f, (maxPos-minPos)*0.5f, sortedAtoms, blockExclusions[i], maxDistance, blockAtoms, atomLocations, atomVoxelIndex);
for (int j = 0; j < atomsInBlock; j++) {
blockAtomX[j] = sortedPositions[4*(firstIndex+j)];
blockAtomY[j] = sortedPositions[4*(firstIndex+j)+1];
blockAtomZ[j] = sortedPositions[4*(firstIndex+j)+2];
}
for (int j = atomsInBlock; j < blockSize; j++) {
blockAtomX[j] = 1e10;
blockAtomY[j] = 1e10;
blockAtomZ[j] = 1e10;
}
voxels->getNeighbors(blockNeighbors[i], i, (maxPos+minPos)*0.5f, (maxPos-minPos)*0.5f, sortedAtoms, blockExclusions[i], maxDistance, blockAtoms, blockAtomX, blockAtomY, blockAtomZ, sortedPositions, atomVoxelIndex);
// Record the exclusions for this block.
......
platforms/cpu/src/CpuNonbondedForce.cpp
View file @ 59bccb15
/* Portions copyright (c) 2006-2013 Stanford University and Simbios.
/* Portions copyright (c) 2006-2015 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -364,15 +364,15 @@ void CpuNonbondedForce::threadComputeDirect(ThreadPool& threads, int threadIndex
float inverseR = 1/r;
float chargeProd = ONE_4PI_EPS0*posq[4*i+3]*posq[4*j+3];
float alphaR = alphaEwald*r;
float erfcAlphaR = erfcApprox(alphaR);
if (1-erfcAlphaR > 1e-6f) {
float erfAlphaR = erf(alphaR);
if (erfAlphaR > 1e-6f) {
float dEdR = (float) (chargeProd * inverseR * inverseR * inverseR);
dEdR = (float) (dEdR * (1.0f-erfcAlphaR-TWO_OVER_SQRT_PI*alphaR*exp(-alphaR*alphaR)));
dEdR = (float) (dEdR * (erfAlphaR-TWO_OVER_SQRT_PI*alphaR*exp(-alphaR*alphaR)));
fvec4 result = deltaR*dEdR;
(fvec4(forces+4*i)-result).store(forces+4*i);
(fvec4(forces+4*j)+result).store(forces+4*j);
if (includeEnergy)
threadEnergy[threadIndex] -= chargeProd*inverseR*(1.0f-erfcAlphaR);
threadEnergy[threadIndex] -= chargeProd*inverseR*erfAlphaR;
}
}
}
......
platforms/cpu/src/CpuNonbondedForceVec4.cpp
View file @ 59bccb15
......@@ -44,30 +44,76 @@ CpuNonbondedForce* createCpuNonbondedForceVec4() {
CpuNonbondedForceVec4::CpuNonbondedForceVec4() {
}
enum PeriodicType {NoPeriodic, PeriodicPerAtom, PeriodicPerInteraction, PeriodicTriclinic};
void CpuNonbondedForceVec4::calculateBlockIxn(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize) {
if (triclinic)
calculateBlockIxnImpl<true>(blockIndex, forces, totalEnergy, boxSize, invBoxSize);
// Determine whether we need to apply periodic boundary conditions.
PeriodicType periodicType;
fvec4 blockCenter;
if (!periodic) {
periodicType = NoPeriodic;
blockCenter = 0.0f;
}
else {
const int* blockAtom = &neighborList->getSortedAtoms()[4*blockIndex];
float minx, maxx, miny, maxy, minz, maxz;
minx = maxx = posq[4*blockAtom[0]];
miny = maxy = posq[4*blockAtom[0]+1];
minz = maxz = posq[4*blockAtom[0]+2];
for (int i = 1; i < 4; i++) {
minx = min(minx, posq[4*blockAtom[i]]);
maxx = max(maxx, posq[4*blockAtom[i]]);
miny = min(miny, posq[4*blockAtom[i]+1]);
maxy = max(maxy, posq[4*blockAtom[i]+1]);
minz = min(minz, posq[4*blockAtom[i]+2]);
maxz = max(maxz, posq[4*blockAtom[i]+2]);
}
blockCenter = fvec4(0.5f*(minx+maxx), 0.5f*(miny+maxy), 0.5f*(minz+maxz), 0.0f);
if (!(minx < cutoffDistance || miny < cutoffDistance || minz < cutoffDistance ||
maxx > boxSize[0]-cutoffDistance || maxy > boxSize[1]-cutoffDistance || maxz > boxSize[2]-cutoffDistance))
periodicType = NoPeriodic;
else if (triclinic)
periodicType = PeriodicTriclinic;
else if (0.5f*(boxSize[0]-(maxx-minx)) >= cutoffDistance &&
0.5f*(boxSize[1]-(maxy-miny)) >= cutoffDistance &&
0.5f*(boxSize[2]-(maxz-minz)) >= cutoffDistance)
periodicType = PeriodicPerAtom;
else
calculateBlockIxnImpl<false>(blockIndex, forces, totalEnergy, boxSize, invBoxSize);
periodicType = PeriodicPerInteraction;
}
// Call the appropriate version depending on what calculation is required for periodic boundary conditions.
if (periodicType == NoPeriodic)
calculateBlockIxnImpl<NoPeriodic>(blockIndex, forces, totalEnergy, boxSize, invBoxSize, blockCenter);
else if (periodicType == PeriodicPerAtom)
calculateBlockIxnImpl<PeriodicPerAtom>(blockIndex, forces, totalEnergy, boxSize, invBoxSize, blockCenter);
else if (periodicType == PeriodicPerInteraction)
calculateBlockIxnImpl<PeriodicPerInteraction>(blockIndex, forces, totalEnergy, boxSize, invBoxSize, blockCenter);
else if (periodicType == PeriodicTriclinic)
calculateBlockIxnImpl<PeriodicTriclinic>(blockIndex, forces, totalEnergy, boxSize, invBoxSize, blockCenter);
}
template <bool TRICLINIC>
void CpuNonbondedForceVec4::calculateBlockIxnImpl(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize) {
template <int PERIODIC_TYPE>
void CpuNonbondedForceVec4::calculateBlockIxnImpl(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize, const fvec4& blockCenter) {
// Load the positions and parameters of the atoms in the block.
const int* blockAtom = &neighborList->getSortedAtoms()[4*blockIndex];
fvec4 blockAtomPosq[4];
fvec4 blockAtomForceX(0.0f), blockAtomForceY(0.0f), blockAtomForceZ(0.0f);
for (int i = 0; i < 4; i++)
for (int i = 0; i < 4; i++) {
blockAtomPosq[i] = fvec4(posq+4*blockAtom[i]);
if (PERIODIC_TYPE == PeriodicPerAtom)
blockAtomPosq[i] -= floor((blockAtomPosq[i]-blockCenter)*invBoxSize+0.5f)*boxSize;
}
fvec4 blockAtomX = fvec4(blockAtomPosq[0][0], blockAtomPosq[1][0], blockAtomPosq[2][0], blockAtomPosq[3][0]);
fvec4 blockAtomY = fvec4(blockAtomPosq[0][1], blockAtomPosq[1][1], blockAtomPosq[2][1], blockAtomPosq[3][1]);
fvec4 blockAtomZ = fvec4(blockAtomPosq[0][2], blockAtomPosq[1][2], blockAtomPosq[2][2], blockAtomPosq[3][2]);
fvec4 blockAtomCharge = fvec4(ONE_4PI_EPS0)*fvec4(blockAtomPosq[0][3], blockAtomPosq[1][3], blockAtomPosq[2][3], blockAtomPosq[3][3]);
fvec4 blockAtomSigma(atomParameters[blockAtom[0]].first, atomParameters[blockAtom[1]].first, atomParameters[blockAtom[2]].first, atomParameters[blockAtom[3]].first);
fvec4 blockAtomEpsilon(atomParameters[blockAtom[0]].second, atomParameters[blockAtom[1]].second, atomParameters[blockAtom[2]].second, atomParameters[blockAtom[3]].second);
bool needPeriodic = (periodic && (any(blockAtomX < cutoffDistance) || any(blockAtomY < cutoffDistance) || any(blockAtomZ < cutoffDistance) ||
any(blockAtomX > boxSize[0]-cutoffDistance) || any(blockAtomY > boxSize[1]-cutoffDistance) || any(blockAtomZ > boxSize[2]-cutoffDistance)));
const bool needPeriodic = (PERIODIC_TYPE == PeriodicPerInteraction || PERIODIC_TYPE == PeriodicTriclinic);
const float invSwitchingInterval = 1/(cutoffDistance-switchingDistance);
// Loop over neighbors for this block.
......@@ -82,7 +128,10 @@ void CpuNonbondedForceVec4::calculateBlockIxnImpl(int blockIndex, float* forces,
// Compute the distances to the block atoms.
fvec4 dx, dy, dz, r2;
getDeltaR<TRICLINIC>(posq+4*atom, blockAtomX, blockAtomY, blockAtomZ, dx, dy, dz, r2, needPeriodic, boxSize, invBoxSize);
fvec4 atomPos(posq+4*atom);
if (PERIODIC_TYPE == PeriodicPerAtom)
atomPos -= floor((atomPos-blockCenter)*invBoxSize+0.5f)*boxSize;
getDeltaR<PERIODIC_TYPE>(atomPos, blockAtomX, blockAtomY, blockAtomZ, dx, dy, dz, r2, needPeriodic, boxSize, invBoxSize);
ivec4 include;
char excl = exclusions[i];
if (excl == 0)
......@@ -95,8 +144,7 @@ void CpuNonbondedForceVec4::calculateBlockIxnImpl(int blockIndex, float* forces,
// Compute the interactions.
fvec4 r = sqrt(r2);
fvec4 inverseR = fvec4(1.0f)/r;
fvec4 inverseR = rsqrt(r2);
fvec4 energy, dEdR;
float atomEpsilon = atomParameters[atom].second;
if (atomEpsilon != 0.0f) {
......@@ -108,6 +156,7 @@ void CpuNonbondedForceVec4::calculateBlockIxnImpl(int blockIndex, float* forces,
dEdR = epsSig6*(12.0f*sig6 - 6.0f);
energy = epsSig6*(sig6-1.0f);
if (useSwitch) {
fvec4 r = r2*inverseR;
fvec4 t = blend(0.0f, (r-switchingDistance)*invSwitchingInterval, r>switchingDistance);
fvec4 switchValue = 1+t*t*t*(-10.0f+t*(15.0f-t*6.0f));
fvec4 switchDeriv = t*t*(-30.0f+t*(60.0f-t*30.0f))*invSwitchingInterval;
......@@ -162,29 +211,73 @@ void CpuNonbondedForceVec4::calculateBlockIxnImpl(int blockIndex, float* forces,
}
void CpuNonbondedForceVec4::calculateBlockEwaldIxn(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize) {
if (triclinic)
calculateBlockEwaldIxnImpl<true>(blockIndex, forces, totalEnergy, boxSize, invBoxSize);
// Determine whether we need to apply periodic boundary conditions.
PeriodicType periodicType;
fvec4 blockCenter;
if (!periodic) {
periodicType = NoPeriodic;
blockCenter = 0.0f;
}
else {
const int* blockAtom = &neighborList->getSortedAtoms()[4*blockIndex];
float minx, maxx, miny, maxy, minz, maxz;
minx = maxx = posq[4*blockAtom[0]];
miny = maxy = posq[4*blockAtom[0]+1];
minz = maxz = posq[4*blockAtom[0]+2];
for (int i = 1; i < 4; i++) {
minx = min(minx, posq[4*blockAtom[i]]);
maxx = max(maxx, posq[4*blockAtom[i]]);
miny = min(miny, posq[4*blockAtom[i]+1]);
maxy = max(maxy, posq[4*blockAtom[i]+1]);
minz = min(minz, posq[4*blockAtom[i]+2]);
maxz = max(maxz, posq[4*blockAtom[i]+2]);
}
blockCenter = fvec4(0.5f*(minx+maxx), 0.5f*(miny+maxy), 0.5f*(minz+maxz), 0.0f);
if (!(minx < cutoffDistance || miny < cutoffDistance || minz < cutoffDistance ||
maxx > boxSize[0]-cutoffDistance || maxy > boxSize[1]-cutoffDistance || maxz > boxSize[2]-cutoffDistance))
periodicType = NoPeriodic;
else if (triclinic)
periodicType = PeriodicTriclinic;
else if (0.5f*(boxSize[0]-(maxx-minx)) >= cutoffDistance &&
0.5f*(boxSize[1]-(maxy-miny)) >= cutoffDistance &&
0.5f*(boxSize[2]-(maxz-minz)) >= cutoffDistance)
periodicType = PeriodicPerAtom;
else
calculateBlockEwaldIxnImpl<false>(blockIndex, forces, totalEnergy, boxSize, invBoxSize);
periodicType = PeriodicPerInteraction;
}
// Call the appropriate version depending on what calculation is required for periodic boundary conditions.
if (periodicType == NoPeriodic)
calculateBlockEwaldIxnImpl<NoPeriodic>(blockIndex, forces, totalEnergy, boxSize, invBoxSize, blockCenter);
else if (periodicType == PeriodicPerAtom)
calculateBlockEwaldIxnImpl<PeriodicPerAtom>(blockIndex, forces, totalEnergy, boxSize, invBoxSize, blockCenter);
else if (periodicType == PeriodicPerInteraction)
calculateBlockEwaldIxnImpl<PeriodicPerInteraction>(blockIndex, forces, totalEnergy, boxSize, invBoxSize, blockCenter);
else if (periodicType == PeriodicTriclinic)
calculateBlockEwaldIxnImpl<PeriodicTriclinic>(blockIndex, forces, totalEnergy, boxSize, invBoxSize, blockCenter);
}
template <bool TRICLINIC>
void CpuNonbondedForceVec4::calculateBlockEwaldIxnImpl(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize) {
template <int PERIODIC_TYPE>
void CpuNonbondedForceVec4::calculateBlockEwaldIxnImpl(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize, const fvec4& blockCenter) {
// Load the positions and parameters of the atoms in the block.
const int* blockAtom = &neighborList->getSortedAtoms()[4*blockIndex];
fvec4 blockAtomPosq[4];
fvec4 blockAtomForceX(0.0f), blockAtomForceY(0.0f), blockAtomForceZ(0.0f);
for (int i = 0; i < 4; i++)
for (int i = 0; i < 4; i++) {
blockAtomPosq[i] = fvec4(posq+4*blockAtom[i]);
if (PERIODIC_TYPE == PeriodicPerAtom)
blockAtomPosq[i] -= floor((blockAtomPosq[i]-blockCenter)*invBoxSize+0.5f)*boxSize;
}
fvec4 blockAtomX = fvec4(blockAtomPosq[0][0], blockAtomPosq[1][0], blockAtomPosq[2][0], blockAtomPosq[3][0]);
fvec4 blockAtomY = fvec4(blockAtomPosq[0][1], blockAtomPosq[1][1], blockAtomPosq[2][1], blockAtomPosq[3][1]);
fvec4 blockAtomZ = fvec4(blockAtomPosq[0][2], blockAtomPosq[1][2], blockAtomPosq[2][2], blockAtomPosq[3][2]);
fvec4 blockAtomCharge = fvec4(ONE_4PI_EPS0)*fvec4(blockAtomPosq[0][3], blockAtomPosq[1][3], blockAtomPosq[2][3], blockAtomPosq[3][3]);
fvec4 blockAtomSigma(atomParameters[blockAtom[0]].first, atomParameters[blockAtom[1]].first, atomParameters[blockAtom[2]].first, atomParameters[blockAtom[3]].first);
fvec4 blockAtomEpsilon(atomParameters[blockAtom[0]].second, atomParameters[blockAtom[1]].second, atomParameters[blockAtom[2]].second, atomParameters[blockAtom[3]].second);
bool needPeriodic = (periodic && (any(blockAtomX < cutoffDistance) || any(blockAtomY < cutoffDistance) || any(blockAtomZ < cutoffDistance) ||
any(blockAtomX > boxSize[0]-cutoffDistance) || any(blockAtomY > boxSize[1]-cutoffDistance) || any(blockAtomZ > boxSize[2]-cutoffDistance)));
const bool needPeriodic = (PERIODIC_TYPE == PeriodicPerInteraction || PERIODIC_TYPE == PeriodicTriclinic);
const float invSwitchingInterval = 1/(cutoffDistance-switchingDistance);
// Loop over neighbors for this block.
......@@ -199,7 +292,10 @@ void CpuNonbondedForceVec4::calculateBlockEwaldIxnImpl(int blockIndex, float* fo
// Compute the distances to the block atoms.
fvec4 dx, dy, dz, r2;
getDeltaR<TRICLINIC>(posq+4*atom, blockAtomX, blockAtomY, blockAtomZ, dx, dy, dz, r2, needPeriodic, boxSize, invBoxSize);
fvec4 atomPos(posq+4*atom);
if (PERIODIC_TYPE == PeriodicPerAtom)
atomPos -= floor((atomPos-blockCenter)*invBoxSize+0.5f)*boxSize;
getDeltaR<PERIODIC_TYPE>(atomPos, blockAtomX, blockAtomY, blockAtomZ, dx, dy, dz, r2, needPeriodic, boxSize, invBoxSize);
ivec4 include;
char excl = exclusions[i];
if (excl == 0)
......@@ -212,8 +308,8 @@ void CpuNonbondedForceVec4::calculateBlockEwaldIxnImpl(int blockIndex, float* fo
// Compute the interactions.
fvec4 r = sqrt(r2);
fvec4 inverseR = fvec4(1.0f)/r;
fvec4 inverseR = rsqrt(r2);
fvec4 r = r2*inverseR;
fvec4 energy, dEdR;
float atomEpsilon = atomParameters[atom].second;
if (atomEpsilon != 0.0f) {
......@@ -272,13 +368,12 @@ void CpuNonbondedForceVec4::calculateBlockEwaldIxnImpl(int blockIndex, float* fo
(fvec4(forces+4*blockAtom[j])+f[j]).store(forces+4*blockAtom[j]);
}
template <bool TRICLINIC>
void CpuNonbondedForceVec4::getDeltaR(const float* posI, const fvec4& x, const fvec4& y, const fvec4& z, fvec4& dx, fvec4& dy, fvec4& dz, fvec4& r2, bool periodic, const fvec4& boxSize, const fvec4& invBoxSize) const {
template <int PERIODIC_TYPE>
void CpuNonbondedForceVec4::getDeltaR(const fvec4& posI, const fvec4& x, const fvec4& y, const fvec4& z, fvec4& dx, fvec4& dy, fvec4& dz, fvec4& r2, bool periodic, const fvec4& boxSize, const fvec4& invBoxSize) const {
dx = x-posI[0];
dy = y-posI[1];
dz = z-posI[2];
if (periodic) {
if (TRICLINIC) {
if (PERIODIC_TYPE == PeriodicTriclinic) {
fvec4 scale3 = floor(dz*recipBoxSize[2]+0.5f);
dx -= scale3*periodicBoxVectors[2][0];
dy -= scale3*periodicBoxVectors[2][1];
......@@ -289,12 +384,11 @@ void CpuNonbondedForceVec4::getDeltaR(const float* posI, const fvec4& x, const f
fvec4 scale1 = floor(dx*recipBoxSize[0]+0.5f);
dx -= scale1*periodicBoxVectors[0][0];
}
else {
else if (PERIODIC_TYPE == PeriodicPerInteraction) {
dx -= round(dx*invBoxSize[0])*boxSize[0];
dy -= round(dy*invBoxSize[1])*boxSize[1];
dz -= round(dz*invBoxSize[2])*boxSize[2];
}
}
r2 = dx*dx + dy*dy + dz*dz;
}
......
platforms/cpu/src/CpuNonbondedForceVec8.cpp
View file @ 59bccb15
......@@ -76,29 +76,75 @@ CpuNonbondedForce* createCpuNonbondedForceVec8() {
CpuNonbondedForceVec8::CpuNonbondedForceVec8() {
}
enum PeriodicType {NoPeriodic, PeriodicPerAtom, PeriodicPerInteraction, PeriodicTriclinic};
void CpuNonbondedForceVec8::calculateBlockIxn(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize) {
if (triclinic)
calculateBlockIxnImpl<true>(blockIndex, forces, totalEnergy, boxSize, invBoxSize);
// Determine whether we need to apply periodic boundary conditions.
PeriodicType periodicType;
fvec4 blockCenter;
if (!periodic) {
periodicType = NoPeriodic;
blockCenter = 0.0f;
}
else {
const int* blockAtom = &neighborList->getSortedAtoms()[8*blockIndex];
float minx, maxx, miny, maxy, minz, maxz;
minx = maxx = posq[4*blockAtom[0]];
miny = maxy = posq[4*blockAtom[0]+1];
minz = maxz = posq[4*blockAtom[0]+2];
for (int i = 1; i < 8; i++) {
minx = min(minx, posq[4*blockAtom[i]]);
maxx = max(maxx, posq[4*blockAtom[i]]);
miny = min(miny, posq[4*blockAtom[i]+1]);
maxy = max(maxy, posq[4*blockAtom[i]+1]);
minz = min(minz, posq[4*blockAtom[i]+2]);
maxz = max(maxz, posq[4*blockAtom[i]+2]);
}
blockCenter = fvec4(0.5f*(minx+maxx), 0.5f*(miny+maxy), 0.5f*(minz+maxz), 0.0f);
if (!(minx < cutoffDistance || miny < cutoffDistance || minz < cutoffDistance ||
maxx > boxSize[0]-cutoffDistance || maxy > boxSize[1]-cutoffDistance || maxz > boxSize[2]-cutoffDistance))
periodicType = NoPeriodic;
else if (triclinic)
periodicType = PeriodicTriclinic;
else if (0.5f*(boxSize[0]-(maxx-minx)) >= cutoffDistance &&
0.5f*(boxSize[1]-(maxy-miny)) >= cutoffDistance &&
0.5f*(boxSize[2]-(maxz-minz)) >= cutoffDistance)
periodicType = PeriodicPerAtom;
else
calculateBlockIxnImpl<false>(blockIndex, forces, totalEnergy, boxSize, invBoxSize);
periodicType = PeriodicPerInteraction;
}
// Call the appropriate version depending on what calculation is required for periodic boundary conditions.
if (periodicType == NoPeriodic)
calculateBlockIxnImpl<NoPeriodic>(blockIndex, forces, totalEnergy, boxSize, invBoxSize, blockCenter);
else if (periodicType == PeriodicPerAtom)
calculateBlockIxnImpl<PeriodicPerAtom>(blockIndex, forces, totalEnergy, boxSize, invBoxSize, blockCenter);
else if (periodicType == PeriodicPerInteraction)
calculateBlockIxnImpl<PeriodicPerInteraction>(blockIndex, forces, totalEnergy, boxSize, invBoxSize, blockCenter);
else if (periodicType == PeriodicTriclinic)
calculateBlockIxnImpl<PeriodicTriclinic>(blockIndex, forces, totalEnergy, boxSize, invBoxSize, blockCenter);
}
template <bool TRICLINIC>
void CpuNonbondedForceVec8::calculateBlockIxnImpl(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize) {
template <int PERIODIC_TYPE>
void CpuNonbondedForceVec8::calculateBlockIxnImpl(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize, const fvec4& blockCenter) {
// Load the positions and parameters of the atoms in the block.
const int* blockAtom = &neighborList->getSortedAtoms()[8*blockIndex];
fvec4 blockAtomPosq[8];
fvec8 blockAtomForceX(0.0f), blockAtomForceY(0.0f), blockAtomForceZ(0.0f);
fvec8 blockAtomX, blockAtomY, blockAtomZ, blockAtomCharge;
for (int i = 0; i < 8; i++)
for (int i = 0; i < 8; i++) {
blockAtomPosq[i] = fvec4(posq+4*blockAtom[i]);
if (PERIODIC_TYPE == PeriodicPerAtom)
blockAtomPosq[i] -= floor((blockAtomPosq[i]-blockCenter)*invBoxSize+0.5f)*boxSize;
}
transpose(blockAtomPosq[0], blockAtomPosq[1], blockAtomPosq[2], blockAtomPosq[3], blockAtomPosq[4], blockAtomPosq[5], blockAtomPosq[6], blockAtomPosq[7], blockAtomX, blockAtomY, blockAtomZ, blockAtomCharge);
blockAtomCharge *= ONE_4PI_EPS0;
fvec8 blockAtomSigma(atomParameters[blockAtom[0]].first, atomParameters[blockAtom[1]].first, atomParameters[blockAtom[2]].first, atomParameters[blockAtom[3]].first, atomParameters[blockAtom[4]].first, atomParameters[blockAtom[5]].first, atomParameters[blockAtom[6]].first, atomParameters[blockAtom[7]].first);
fvec8 blockAtomEpsilon(atomParameters[blockAtom[0]].second, atomParameters[blockAtom[1]].second, atomParameters[blockAtom[2]].second, atomParameters[blockAtom[3]].second, atomParameters[blockAtom[4]].second, atomParameters[blockAtom[5]].second, atomParameters[blockAtom[6]].second, atomParameters[blockAtom[7]].second);
bool needPeriodic = (periodic && (any(blockAtomX < cutoffDistance) || any(blockAtomY < cutoffDistance) || any(blockAtomZ < cutoffDistance) ||
any(blockAtomX > boxSize[0]-cutoffDistance) || any(blockAtomY > boxSize[1]-cutoffDistance) || any(blockAtomZ > boxSize[2]-cutoffDistance)));
const bool needPeriodic = (PERIODIC_TYPE == PeriodicPerInteraction || PERIODIC_TYPE == PeriodicTriclinic);
const float invSwitchingInterval = 1/(cutoffDistance-switchingDistance);
// Loop over neighbors for this block.
......@@ -113,7 +159,10 @@ void CpuNonbondedForceVec8::calculateBlockIxnImpl(int blockIndex, float* forces,
// Compute the distances to the block atoms.
fvec8 dx, dy, dz, r2;
getDeltaR<TRICLINIC>(&posq[4*atom], blockAtomX, blockAtomY, blockAtomZ, dx, dy, dz, r2, needPeriodic, boxSize, invBoxSize);
fvec4 atomPos(posq+4*atom);
if (PERIODIC_TYPE == PeriodicPerAtom)
atomPos -= floor((atomPos-blockCenter)*invBoxSize+0.5f)*boxSize;
getDeltaR<PERIODIC_TYPE>(atomPos, blockAtomX, blockAtomY, blockAtomZ, dx, dy, dz, r2, needPeriodic, boxSize, invBoxSize);
ivec8 include;
char excl = exclusions[i];
if (excl == 0)
......@@ -126,8 +175,7 @@ void CpuNonbondedForceVec8::calculateBlockIxnImpl(int blockIndex, float* forces,
// Compute the interactions.
fvec8 r = sqrt(r2);
fvec8 inverseR = fvec8(1.0f)/r;
fvec8 inverseR = rsqrt(r2);
fvec8 energy, dEdR;
float atomEpsilon = atomParameters[atom].second;
if (atomEpsilon != 0.0f) {
......@@ -139,6 +187,7 @@ void CpuNonbondedForceVec8::calculateBlockIxnImpl(int blockIndex, float* forces,
dEdR = epsSig6*(12.0f*sig6 - 6.0f);
energy = epsSig6*(sig6-1.0f);
if (useSwitch) {
fvec8 r = r2*inverseR;
fvec8 t = (r>switchingDistance) & ((r-switchingDistance)*invSwitchingInterval);
fvec8 switchValue = 1+t*t*t*(-10.0f+t*(15.0f-t*6.0f));
fvec8 switchDeriv = t*t*(-30.0f+t*(60.0f-t*30.0f))*invSwitchingInterval;
......@@ -193,28 +242,72 @@ void CpuNonbondedForceVec8::calculateBlockIxnImpl(int blockIndex, float* forces,
}
void CpuNonbondedForceVec8::calculateBlockEwaldIxn(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize) {
if (triclinic)
calculateBlockEwaldIxnImpl<true>(blockIndex, forces, totalEnergy, boxSize, invBoxSize);
// Determine whether we need to apply periodic boundary conditions.
PeriodicType periodicType;
fvec4 blockCenter;
if (!periodic) {
periodicType = NoPeriodic;
blockCenter = 0.0f;
}
else {
const int* blockAtom = &neighborList->getSortedAtoms()[8*blockIndex];
float minx, maxx, miny, maxy, minz, maxz;
minx = maxx = posq[4*blockAtom[0]];
miny = maxy = posq[4*blockAtom[0]+1];
minz = maxz = posq[4*blockAtom[0]+2];
for (int i = 1; i < 8; i++) {
minx = min(minx, posq[4*blockAtom[i]]);
maxx = max(maxx, posq[4*blockAtom[i]]);
miny = min(miny, posq[4*blockAtom[i]+1]);
maxy = max(maxy, posq[4*blockAtom[i]+1]);
minz = min(minz, posq[4*blockAtom[i]+2]);
maxz = max(maxz, posq[4*blockAtom[i]+2]);
}
blockCenter = fvec4(0.5f*(minx+maxx), 0.5f*(miny+maxy), 0.5f*(minz+maxz), 0.0f);
if (!(minx < cutoffDistance || miny < cutoffDistance || minz < cutoffDistance ||
maxx > boxSize[0]-cutoffDistance || maxy > boxSize[1]-cutoffDistance || maxz > boxSize[2]-cutoffDistance))
periodicType = NoPeriodic;
else if (triclinic)
periodicType = PeriodicTriclinic;
else if (0.5f*(boxSize[0]-(maxx-minx)) >= cutoffDistance &&
0.5f*(boxSize[1]-(maxy-miny)) >= cutoffDistance &&
0.5f*(boxSize[2]-(maxz-minz)) >= cutoffDistance)
periodicType = PeriodicPerAtom;
else
calculateBlockEwaldIxnImpl<false>(blockIndex, forces, totalEnergy, boxSize, invBoxSize);
periodicType = PeriodicPerInteraction;
}
// Call the appropriate version depending on what calculation is required for periodic boundary conditions.
if (periodicType == NoPeriodic)
calculateBlockEwaldIxnImpl<NoPeriodic>(blockIndex, forces, totalEnergy, boxSize, invBoxSize, blockCenter);
else if (periodicType == PeriodicPerAtom)
calculateBlockEwaldIxnImpl<PeriodicPerAtom>(blockIndex, forces, totalEnergy, boxSize, invBoxSize, blockCenter);
else if (periodicType == PeriodicPerInteraction)
calculateBlockEwaldIxnImpl<PeriodicPerInteraction>(blockIndex, forces, totalEnergy, boxSize, invBoxSize, blockCenter);
else if (periodicType == PeriodicTriclinic)
calculateBlockEwaldIxnImpl<PeriodicTriclinic>(blockIndex, forces, totalEnergy, boxSize, invBoxSize, blockCenter);
}
template <bool TRICLINIC>
void CpuNonbondedForceVec8::calculateBlockEwaldIxnImpl(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize) {
template <int PERIODIC_TYPE>
void CpuNonbondedForceVec8::calculateBlockEwaldIxnImpl(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize, const fvec4& blockCenter) {
// Load the positions and parameters of the atoms in the block.
const int* blockAtom = &neighborList->getSortedAtoms()[8*blockIndex];
fvec4 blockAtomPosq[8];
fvec8 blockAtomForceX(0.0f), blockAtomForceY(0.0f), blockAtomForceZ(0.0f);
fvec8 blockAtomX, blockAtomY, blockAtomZ, blockAtomCharge;
for (int i = 0; i < 8; i++)
for (int i = 0; i < 8; i++) {
blockAtomPosq[i] = fvec4(posq+4*blockAtom[i]);
if (PERIODIC_TYPE == PeriodicPerAtom)
blockAtomPosq[i] -= floor((blockAtomPosq[i]-blockCenter)*invBoxSize+0.5f)*boxSize;
}
transpose(blockAtomPosq[0], blockAtomPosq[1], blockAtomPosq[2], blockAtomPosq[3], blockAtomPosq[4], blockAtomPosq[5], blockAtomPosq[6], blockAtomPosq[7], blockAtomX, blockAtomY, blockAtomZ, blockAtomCharge);
blockAtomCharge *= ONE_4PI_EPS0;
fvec8 blockAtomSigma(atomParameters[blockAtom[0]].first, atomParameters[blockAtom[1]].first, atomParameters[blockAtom[2]].first, atomParameters[blockAtom[3]].first, atomParameters[blockAtom[4]].first, atomParameters[blockAtom[5]].first, atomParameters[blockAtom[6]].first, atomParameters[blockAtom[7]].first);
fvec8 blockAtomEpsilon(atomParameters[blockAtom[0]].second, atomParameters[blockAtom[1]].second, atomParameters[blockAtom[2]].second, atomParameters[blockAtom[3]].second, atomParameters[blockAtom[4]].second, atomParameters[blockAtom[5]].second, atomParameters[blockAtom[6]].second, atomParameters[blockAtom[7]].second);
bool needPeriodic = (periodic && (any(blockAtomX < cutoffDistance) || any(blockAtomY < cutoffDistance) || any(blockAtomZ < cutoffDistance) ||
any(blockAtomX > boxSize[0]-cutoffDistance) || any(blockAtomY > boxSize[1]-cutoffDistance) || any(blockAtomZ > boxSize[2]-cutoffDistance)));
const bool needPeriodic = (PERIODIC_TYPE == PeriodicPerInteraction || PERIODIC_TYPE == PeriodicTriclinic);
const float invSwitchingInterval = 1/(cutoffDistance-switchingDistance);
// Loop over neighbors for this block.
......@@ -229,7 +322,10 @@ void CpuNonbondedForceVec8::calculateBlockEwaldIxnImpl(int blockIndex, float* fo
// Compute the distances to the block atoms.
fvec8 dx, dy, dz, r2;
getDeltaR<TRICLINIC>(&posq[4*atom], blockAtomX, blockAtomY, blockAtomZ, dx, dy, dz, r2, needPeriodic, boxSize, invBoxSize);
fvec4 atomPos(posq+4*atom);
if (PERIODIC_TYPE == PeriodicPerAtom)
atomPos -= floor((atomPos-blockCenter)*invBoxSize+0.5f)*boxSize;
getDeltaR<PERIODIC_TYPE>(atomPos, blockAtomX, blockAtomY, blockAtomZ, dx, dy, dz, r2, needPeriodic, boxSize, invBoxSize);
ivec8 include;
char excl = exclusions[i];
if (excl == 0)
......@@ -242,8 +338,8 @@ void CpuNonbondedForceVec8::calculateBlockEwaldIxnImpl(int blockIndex, float* fo
// Compute the interactions.
fvec8 r = sqrt(r2);
fvec8 inverseR = fvec8(1.0f)/r;
fvec8 inverseR = rsqrt(r2);
fvec8 r = r2*inverseR;
fvec8 energy, dEdR;
float atomEpsilon = atomParameters[atom].second;
if (atomEpsilon != 0.0f) {
......@@ -302,13 +398,12 @@ void CpuNonbondedForceVec8::calculateBlockEwaldIxnImpl(int blockIndex, float* fo
(fvec4(forces+4*blockAtom[j])+f[j]).store(forces+4*blockAtom[j]);
}
template <bool TRICLINIC>
void CpuNonbondedForceVec8::getDeltaR(const float* posI, const fvec8& x, const fvec8& y, const fvec8& z, fvec8& dx, fvec8& dy, fvec8& dz, fvec8& r2, bool periodic, const fvec4& boxSize, const fvec4& invBoxSize) const {
template <int PERIODIC_TYPE>
void CpuNonbondedForceVec8::getDeltaR(const fvec4& posI, const fvec8& x, const fvec8& y, const fvec8& z, fvec8& dx, fvec8& dy, fvec8& dz, fvec8& r2, bool periodic, const fvec4& boxSize, const fvec4& invBoxSize) const {
dx = x-posI[0];
dy = y-posI[1];
dz = z-posI[2];
if (periodic) {
if (TRICLINIC) {
if (PERIODIC_TYPE == PeriodicTriclinic) {
fvec8 scale3 = floor(dz*recipBoxSize[2]+0.5f);
dx -= scale3*periodicBoxVectors[2][0];
dy -= scale3*periodicBoxVectors[2][1];
......@@ -319,12 +414,11 @@ void CpuNonbondedForceVec8::getDeltaR(const float* posI, const fvec8& x, const f
fvec8 scale1 = floor(dx*recipBoxSize[0]+0.5f);
dx -= scale1*periodicBoxVectors[0][0];
}
else {
else if (PERIODIC_TYPE == PeriodicPerInteraction) {
dx -= round(dx*invBoxSize[0])*boxSize[0];
dy -= round(dy*invBoxSize[1])*boxSize[1];
dz -= round(dz*invBoxSize[2])*boxSize[2];
}
}
r2 = dx*dx + dy*dy + dz*dz;
}
......
platforms/cuda/include/CudaKernels.h
View file @ 59bccb15
......@@ -1282,7 +1282,8 @@ private:
void prepareForComputation(ContextImpl& context, CustomIntegrator& integrator, bool& forcesAreValid);
void recordChangedParameters(ContextImpl& context);
CudaContext& cu;
double prevStepSize;
double prevStepSize, energy;
float energyFloat;
int numGlobalVariables;
bool hasInitializedKernels, deviceValuesAreCurrent, modifiesParameters, keNeedsForce;
mutable bool localValuesAreCurrent;
......@@ -1303,7 +1304,7 @@ private:
std::vector<std::vector<CUfunction> > kernels;
std::vector<std::vector<std::vector<void*> > > kernelArgs;
std::vector<void*> kineticEnergyArgs;
CUfunction sumPotentialEnergyKernel, randomKernel, kineticEnergyKernel, sumKineticEnergyKernel;
CUfunction randomKernel, kineticEnergyKernel, sumKineticEnergyKernel;
std::vector<CustomIntegrator::ComputationType> stepType;
std::vector<bool> needsForces;
std::vector<bool> needsEnergy;
......
platforms/cuda/src/CudaExpressionUtilities.cpp
View file @ 59bccb15
......@@ -463,6 +463,9 @@ void CudaExpressionUtilities::processExpression(stringstream& out, const Express
case Operation::CEIL:
out << "ceil(" << getTempName(node.getChildren()[0], temps) << ")";
break;
case Operation::SELECT:
out << "(" << getTempName(node.getChildren()[0], temps) << " != 0 ? " << getTempName(node.getChildren()[1], temps) << " : " << getTempName(node.getChildren()[2], temps) << ")";
break;
default:
throw OpenMMException("Internal error: Unknown operation in user-defined expression: "+node.getOperation().getName());
}
......
platforms/cuda/src/CudaKernels.cpp
View file @ 59bccb15
......@@ -5731,7 +5731,7 @@ string CudaIntegrateCustomStepKernel::createGlobalComputation(const string& vari
variables["dt"] = "dt[0].y";
variables["uniform"] = "uniform";
variables["gaussian"] = "gaussian";
variables[energyName] = "energy[0]";
variables[energyName] = "energy";
for (int i = 0; i < integrator.getNumGlobalVariables(); i++)
variables[integrator.getGlobalVariableName(i)] = "globals["+cu.intToString(i)+"]";
for (int i = 0; i < (int) parameterNames.size(); i++)
......@@ -5767,7 +5767,7 @@ string CudaIntegrateCustomStepKernel::createPerDofComputation(const string& vari
variables["m"] = "mass";
variables["dt"] = "stepSize";
if (energyName != "")
variables[energyName] = "energy[0]";
variables[energyName] = "energy";
for (int i = 0; i < integrator.getNumGlobalVariables(); i++)
variables[integrator.getGlobalVariableName(i)] = "globals["+cu.intToString(i)+"]";
for (int i = 0; i < integrator.getNumPerDofVariables(); i++)
......@@ -6000,7 +6000,10 @@ void CudaIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context,
args1.push_back(NULL);
args1.push_back(NULL);
args1.push_back(NULL);
args1.push_back(&potentialEnergy->getDevicePointer());
if (cu.getUseDoublePrecision())
args1.push_back(&energy);
else
args1.push_back(&energyFloat);
for (int i = 0; i < (int) perDofValues->getBuffers().size(); i++)
args1.push_back(&perDofValues->getBuffers()[i].getMemory());
kernelArgs[step].push_back(args1);
......@@ -6049,7 +6052,10 @@ void CudaIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context,
args.push_back(&contextParameterValues->getDevicePointer());
args.push_back(NULL);
args.push_back(NULL);
args.push_back(&potentialEnergy->getDevicePointer());
if (cu.getUseDoublePrecision())
args.push_back(&energy);
else
args.push_back(&energyFloat);
kernelArgs[step].push_back(args);
}
else if (stepType[step] == CustomIntegrator::ConstrainPositions) {
......@@ -6089,13 +6095,6 @@ void CudaIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context,
CUmodule randomProgram = cu.createModule(CudaKernelSources::customIntegrator, defines);
randomKernel = cu.getKernel(randomProgram, "generateRandomNumbers");
// Create the kernel for summing the potential energy.
defines["SUM_OUTPUT_INDEX"] = "0";
defines["SUM_BUFFER_SIZE"] = cu.intToString(cu.getEnergyBuffer().getSize());
CUmodule module = cu.createModule(CudaKernelSources::customIntegrator, defines);
sumPotentialEnergyKernel = cu.getKernel(module, cu.getUseDoublePrecision() ? "computeDoubleSum" : "computeFloatSum");
// Create the kernel for computing kinetic energy.
stringstream computeKE;
......@@ -6117,10 +6116,11 @@ void CudaIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context,
args << ", " << buffer.getType() << "* __restrict__ " << valueName;
}
replacements["PARAMETER_ARGUMENTS"] = args.str();
defines["SUM_OUTPUT_INDEX"] = "0";
defines["SUM_BUFFER_SIZE"] = cu.intToString(3*numAtoms);
if (defines.find("LOAD_POS_AS_DELTA") != defines.end())
defines.erase("LOAD_POS_AS_DELTA");
module = cu.createModule(cu.replaceStrings(CudaKernelSources::customIntegratorPerDof, replacements), defines);
CUmodule module = cu.createModule(cu.replaceStrings(CudaKernelSources::customIntegratorPerDof, replacements), defines);
kineticEnergyKernel = cu.getKernel(module, "computePerDof");
kineticEnergyArgs.push_back(&cu.getPosq().getDevicePointer());
kineticEnergyArgs.push_back(NULL);
......@@ -6134,7 +6134,10 @@ void CudaIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context,
kineticEnergyArgs.push_back(NULL);
kineticEnergyArgs.push_back(NULL);
kineticEnergyArgs.push_back(&uniformRandoms->getDevicePointer());
kineticEnergyArgs.push_back(&potentialEnergy->getDevicePointer());
if (cu.getUseDoublePrecision())
kineticEnergyArgs.push_back(&energy);
else
kineticEnergyArgs.push_back(&energyFloat);
for (int i = 0; i < (int) perDofValues->getBuffers().size(); i++)
kineticEnergyArgs.push_back(&perDofValues->getBuffers()[i].getMemory());
keNeedsForce = usesVariable(keExpression, "f");
......@@ -6240,11 +6243,8 @@ void CudaIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegrat
}
else {
recordChangedParameters(context);
context.calcForcesAndEnergy(computeForce, computeEnergy, forceGroup[i]);
if (computeEnergy) {
void* args[] = {&cu.getEnergyBuffer().getDevicePointer(), &potentialEnergy->getDevicePointer()};
cu.executeKernel(sumPotentialEnergyKernel, &args[0], CudaContext::ThreadBlockSize, CudaContext::ThreadBlockSize);
}
energy = context.calcForcesAndEnergy(computeForce, computeEnergy, forceGroup[i]);
energyFloat = (float) energy;
}
forcesAreValid = true;
}
......@@ -6315,11 +6315,8 @@ double CudaIntegrateCustomStepKernel::computeKineticEnergy(ContextImpl& context,
bool willNeedEnergy = false;
for (int i = 0; i < integrator.getNumComputations(); i++)
willNeedEnergy |= needsEnergy[i];
context.calcForcesAndEnergy(true, willNeedEnergy, -1);
if (willNeedEnergy) {
void* args[] = {&cu.getEnergyBuffer().getDevicePointer(), &potentialEnergy->getDevicePointer()};
cu.executeKernel(sumPotentialEnergyKernel, &args[0], CudaContext::ThreadBlockSize, CudaContext::ThreadBlockSize);
}
energy = context.calcForcesAndEnergy(true, willNeedEnergy, -1);
energyFloat = (float) energy;
forcesAreValid = true;
}
CUdeviceptr posCorrection = (cu.getUseMixedPrecision() ? cu.getPosqCorrection().getDevicePointer() : 0);
......
platforms/cuda/src/kernels/customIntegratorGlobal.cu
View file @ 59bccb15
extern "C" __global__ void computeGlobal(mixed2* __restrict__ dt, mixed* __restrict__ globals, mixed* __restrict__ params,
float uniform, float gaussian, const real* __restrict__ energy) {
float uniform, float gaussian, const real energy) {
COMPUTE_STEP
}
platforms/cuda/src/kernels/customIntegratorPerDof.cu
View file @ 59bccb15
......@@ -34,7 +34,7 @@ inline __device__ mixed4 convertFromDouble4(double4 a) {
extern "C" __global__ void computePerDof(real4* __restrict__ posq, real4* __restrict__ posqCorrection, mixed4* __restrict__ posDelta,
mixed4* __restrict__ velm, const long long* __restrict__ force, const mixed2* __restrict__ dt, const mixed* __restrict__ globals,
const mixed* __restrict__ params, mixed* __restrict__ sum, const float4* __restrict__ gaussianValues,
unsigned int gaussianBaseIndex, const float4* __restrict__ uniformValues, const real* __restrict__ energy
unsigned int gaussianBaseIndex, const float4* __restrict__ uniformValues, const real energy
PARAMETER_ARGUMENTS) {
mixed stepSize = dt[0].y;
int index = blockIdx.x*blockDim.x+threadIdx.x;
......
platforms/cuda/tests/TestCudaCustomIntegrator.cpp
View file @ 59bccb15
......@@ -334,7 +334,7 @@ void testMonteCarlo() {
integrator.addComputePerDof("oldx", "x");
integrator.addComputePerDof("x", "x+dt*gaussian");
integrator.addComputeGlobal("accept", "step(exp((oldE-energy)/kT)-uniform)");
integrator.addComputePerDof("x", "accept*x + (1-accept)*oldx");
integrator.addComputePerDof("x", "select(accept, x, oldx)");
HarmonicBondForce* forceField = new HarmonicBondForce();
forceField->addBond(0, 1, 2.0, 10.0);
system.addForce(forceField);
......
platforms/cuda/tests/TestCudaLocalEnergyMinimizer.cpp
View file @ 59bccb15
......@@ -7,7 +7,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2010-2014 Stanford University and the Authors. *
* Portions copyright (c) 2010-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -81,7 +81,7 @@ void testLargeSystem() {
const int numParticles = numMolecules*2;
const double cutoff = 2.0;
const double boxSize = 4.0;
const double tolerance = 5;
const double tolerance = 10;
System system;
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
NonbondedForce* nonbonded = new NonbondedForce();
......@@ -114,7 +114,7 @@ void testLargeSystem() {
State finalState = context.getState(State::Forces | State::Energy | State::Positions);
ASSERT(finalState.getPotentialEnergy() < initialState.getPotentialEnergy());
// Compute the force magnitude, substracting off any component parallel to a constraint, and
// Compute the force magnitude, subtracting off any component parallel to a constraint, and
// check that it satisfies the requested tolerance.
double forceNorm = 0.0;
......@@ -129,8 +129,8 @@ void testLargeSystem() {
f -= dir*dir.dot(f);
forceNorm += f.dot(f);
}
forceNorm = sqrt(forceNorm/(4*numMolecules));
ASSERT(forceNorm < 3*tolerance);
forceNorm = sqrt(forceNorm/(5*numMolecules));
ASSERT(forceNorm < 2*tolerance);
}
void testVirtualSites() {
......@@ -138,7 +138,7 @@ void testVirtualSites() {
const int numParticles = numMolecules*3;
const double cutoff = 2.0;
const double boxSize = 4.0;
const double tolerance = 5;
const double tolerance = 10;
System system;
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
NonbondedForce* nonbonded = new NonbondedForce();
......@@ -195,8 +195,8 @@ void testVirtualSites() {
ASSERT_EQUAL_VEC((finalState.getPositions()[i+1]+finalState.getPositions()[i])*0.5, finalState.getPositions()[i+2], 1e-5);
}
forceNorm = sqrt(forceNorm/(4*numMolecules));
ASSERT(forceNorm < 3*tolerance);
forceNorm = sqrt(forceNorm/(5*numMolecules));
ASSERT(forceNorm < 2*tolerance);
}
int main(int argc, char* argv[]) {
......
platforms/opencl/include/OpenCLFFT3D.h
View file @ 59bccb15
......@@ -9,7 +9,7 @@
* 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. *
* Portions copyright (c) 2009-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -40,7 +40,7 @@ namespace OpenMM {
* 15, 207–228 (2000).
* <p>
* This class places certain restrictions on the allowed dimensions of the grid. First,
* the size of each dimension may have no prime factors other than 2, 3, and 5. You
* the size of each dimension may have no prime factors other than 2, 3, 5, and 7. You
* can call findLegalDimension() to determine the smallest size that satisfies this
* requirement and is greater than or equal to a specified minimum size. Second, the size
* of each dimension must be small enough to compute each 1D transform entirely in local
......@@ -61,12 +61,17 @@ public:
* @param xsize the first dimension of the data sets on which FFTs will be performed
* @param ysize the second dimension of the data sets on which FFTs will be performed
* @param zsize the third dimension of the data sets on which FFTs will be performed
* @param realToComplex if true, a real-to-complex transform will be done. Otherwise, it is complex-to-complex.
*/
OpenCLFFT3D(OpenCLContext& context, int xsize, int ysize, int zsize);
OpenCLFFT3D(OpenCLContext& context, int xsize, int ysize, int zsize, bool realToComplex=false);
/**
* Perform a Fourier transform. The transform cannot be done in-place: the input and output
* arrays must be different. Also, the input array is used as workspace, so its contents
* are destroyed.
* are destroyed. This also means that both arrays must be large enough to hold complex values,
* even when performing a real-to-complex transform.
* <p>
* When performing a real-to-complex transform, the output data is of size xsize*ysize*(zsize/2+1)
* and contains only the non-redundant elements.
*
* @param in the data to transform, ordered such that in[x*ysize*zsize + y*zsize + z] contains element (x, y, z)
* @param out on exit, this contains the transformed data
......@@ -75,17 +80,20 @@ public:
void execFFT(OpenCLArray& in, OpenCLArray& out, bool forward = true);
/**
* Get the smallest legal size for a dimension of the grid (that is, a size with no prime
* factors other than 2, 3, and 5).
* factors other than 2, 3, 5, and 7).
*
* @param minimum the minimum size the return value must be greater than or equal to
*/
static int findLegalDimension(int minimum);
private:
cl::Kernel createKernel(int xsize, int ysize, int zsize, int& threads);
cl::Kernel createKernel(int xsize, int ysize, int zsize, int& threads, int axis, bool forward, bool inputIsReal);
int xsize, ysize, zsize;
int xthreads, ythreads, zthreads;
bool packRealAsComplex;
OpenCLContext& context;
cl::Kernel xkernel, ykernel, zkernel;
cl::Kernel invxkernel, invykernel, invzkernel;
cl::Kernel packForwardKernel, unpackForwardKernel, packBackwardKernel, unpackBackwardKernel;
};
} // namespace OpenMM
......
platforms/opencl/include/OpenCLKernels.h
View file @ 59bccb15
......@@ -639,6 +639,7 @@ private:
cl::Kernel pmeSpreadChargeKernel;
cl::Kernel pmeFinishSpreadChargeKernel;
cl::Kernel pmeConvolutionKernel;
cl::Kernel pmeEvalEnergyKernel;
cl::Kernel pmeInterpolateForceKernel;
std::map<std::string, std::string> pmeDefines;
std::vector<std::pair<int, int> > exceptionAtoms;
......@@ -1272,7 +1273,7 @@ private:
void prepareForComputation(ContextImpl& context, CustomIntegrator& integrator, bool& forcesAreValid);
void recordChangedParameters(ContextImpl& context);
OpenCLContext& cl;
double prevStepSize;
double prevStepSize, energy;
int numGlobalVariables;
bool hasInitializedKernels, deviceValuesAreCurrent, modifiesParameters, keNeedsForce;
mutable bool localValuesAreCurrent;
......@@ -1292,7 +1293,7 @@ private:
std::vector<double> contextValuesDouble;
std::vector<float> contextValues;
std::vector<std::vector<cl::Kernel> > kernels;
cl::Kernel sumPotentialEnergyKernel, randomKernel, kineticEnergyKernel, sumKineticEnergyKernel;
cl::Kernel randomKernel, kineticEnergyKernel, sumKineticEnergyKernel;
std::vector<CustomIntegrator::ComputationType> stepType;
std::vector<bool> needsForces;
std::vector<bool> needsEnergy;
......
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