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Commit 78e5f13a authored by peastman's avatar peastman
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Continuing to implement triclinic boxes in CPU platform

parent 4193a416
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Showing with 266 additions and 99 deletions
platforms/cpu/include/CpuCustomManyParticleForce.h
View file @ 78e5f13a
......@@ -51,9 +51,11 @@ private:
class ComputeForceTask;
class ThreadData;
int numParticles, numParticlesPerSet, numPerParticleParameters, numTypes;
bool useCutoff, usePeriodic, centralParticleMode;
bool useCutoff, usePeriodic, triclinic, centralParticleMode;
RealOpenMM cutoffDistance;
RealOpenMM periodicBoxSize[3];
float recipBoxSize[3];
RealVec periodicBoxVectors[3];
AlignedArray<fvec4> periodicBoxVec4;
CpuNeighborList* neighborList;
ThreadPool& threads;
std::vector<std::set<int> > exclusions;
......@@ -138,9 +140,9 @@ public:
* already been set, and the smallest side of the periodic box is at least twice the cutoff
* distance.
*
* @param boxSize the X, Y, and Z widths of the periodic box
* @param periodicBoxVectors the vectors defining the periodic box
*/
void setPeriodic(OpenMM::RealVec& boxSize);
void setPeriodic(RealVec* periodicBoxVectors);
/**
* Calculate the interaction.
......
platforms/cpu/include/CpuCustomNonbondedForce.h
View file @ 78e5f13a
......@@ -95,11 +95,11 @@ class CpuCustomNonbondedForce {
already been set, and the smallest side of the periodic box is at least twice the cutoff
distance.
@param boxSize the X, Y, and Z widths of the periodic box
@param periodicBoxVectors the vectors defining the periodic box
--------------------------------------------------------------------------------------- */
void setPeriodic(OpenMM::RealVec& boxSize);
void setPeriodic(RealVec* periodicBoxVectors);
/**---------------------------------------------------------------------------------------
......@@ -127,8 +127,11 @@ private:
bool cutoff;
bool useSwitch;
bool periodic;
bool triclinic;
const CpuNeighborList* neighborList;
RealOpenMM periodicBoxSize[3];
float recipBoxSize[3];
RealVec periodicBoxVectors[3];
AlignedArray<fvec4> periodicBoxVec4;
RealOpenMM cutoffDistance, switchingDistance;
ThreadPool& threads;
const std::vector<std::set<int> > exclusions;
......
platforms/cpu/include/CpuNeighborList.h
View file @ 78e5f13a
......@@ -49,8 +49,6 @@ public:
CpuNeighborList(int blockSize);
void computeNeighborList(int numAtoms, const AlignedArray<float>& atomLocations, const std::vector<std::set<int> >& exclusions,
const RealVec* periodicBoxVectors, bool usePeriodic, float maxDistance, ThreadPool& threads);
void computeNeighborList(int numAtoms, const AlignedArray<float>& atomLocations, const std::vector<std::set<int> >& exclusions,
const float* periodicBoxSize, bool usePeriodic, float maxDistance, ThreadPool& threads);
int getNumBlocks() const;
const std::vector<int>& getSortedAtoms() const;
const std::vector<int>& getBlockNeighbors(int blockIndex) const;
......
platforms/cpu/src/CpuCustomManyParticleForce.cpp
View file @ 78e5f13a
......@@ -122,8 +122,7 @@ void CpuCustomManyParticleForce::calculateIxn(AlignedArray<float>& posq, RealOpe
particleNeighbors.resize(numParticles);
for (int i = 0; i < numParticles; i++)
particleNeighbors[i].clear();
float boxSizeFloat[] = {(float) periodicBoxSize[0], (float) periodicBoxSize[1], (float) periodicBoxSize[2]};
neighborList->computeNeighborList(numParticles, posq, exclusions, boxSizeFloat, usePeriodic, cutoffDistance, threads);
neighborList->computeNeighborList(numParticles, posq, exclusions, periodicBoxVectors, usePeriodic, cutoffDistance, threads);
for (int blockIndex = 0; blockIndex < neighborList->getNumBlocks(); blockIndex++) {
const vector<int>& neighbors = neighborList->getBlockNeighbors(blockIndex);
const vector<char>& exclusions = neighborList->getBlockExclusions(blockIndex);
......@@ -159,8 +158,8 @@ void CpuCustomManyParticleForce::calculateIxn(AlignedArray<float>& posq, RealOpe
void CpuCustomManyParticleForce::threadComputeForce(ThreadPool& threads, int threadIndex) {
vector<int> particleIndices(numParticlesPerSet);
fvec4 boxSize(periodicBoxSize[0], periodicBoxSize[1], periodicBoxSize[2], 0);
fvec4 invBoxSize((1/periodicBoxSize[0]), (1/periodicBoxSize[1]), (1/periodicBoxSize[2]), 0);
fvec4 boxSize(periodicBoxVectors[0][0], periodicBoxVectors[1][1], periodicBoxVectors[2][2], 0);
fvec4 invBoxSize(recipBoxSize[0], recipBoxSize[1], recipBoxSize[2], 0);
float* forces = &(*threadForce)[threadIndex][0];
ThreadData& data = *threadData[threadIndex];
data.energy = 0;
......@@ -201,15 +200,25 @@ void CpuCustomManyParticleForce::setUseCutoff(RealOpenMM distance) {
neighborList = new CpuNeighborList(4);
}
void CpuCustomManyParticleForce::setPeriodic(RealVec& boxSize) {
assert(useCutoff);
assert(boxSize[0] >= 2.0*cutoffDistance);
assert(boxSize[1] >= 2.0*cutoffDistance);
assert(boxSize[2] >= 2.0*cutoffDistance);
void CpuCustomManyParticleForce::setPeriodic(RealVec* periodicBoxVectors) {
assert(cutoff);
assert(periodicBoxVectors[0][0] >= 2.0*cutoffDistance);
assert(periodicBoxVectors[1][1] >= 2.0*cutoffDistance);
assert(periodicBoxVectors[2][2] >= 2.0*cutoffDistance);
usePeriodic = true;
periodicBoxSize[0] = boxSize[0];
periodicBoxSize[1] = boxSize[1];
periodicBoxSize[2] = boxSize[2];
this->periodicBoxVectors[0] = periodicBoxVectors[0];
this->periodicBoxVectors[1] = periodicBoxVectors[1];
this->periodicBoxVectors[2] = periodicBoxVectors[2];
recipBoxSize[0] = (float) (1.0/periodicBoxVectors[0][0]);
recipBoxSize[1] = (float) (1.0/periodicBoxVectors[1][1]);
recipBoxSize[2] = (float) (1.0/periodicBoxVectors[2][2]);
periodicBoxVec4.resize(3);
periodicBoxVec4[0] = fvec4(periodicBoxVectors[0][0], periodicBoxVectors[0][1], periodicBoxVectors[0][2], 0);
periodicBoxVec4[1] = fvec4(periodicBoxVectors[1][0], periodicBoxVectors[1][1], periodicBoxVectors[1][2], 0);
periodicBoxVec4[2] = fvec4(periodicBoxVectors[2][0], periodicBoxVectors[2][1], periodicBoxVectors[2][2], 0);
triclinic = (periodicBoxVectors[0][1] != 0.0 || periodicBoxVectors[0][2] != 0.0 ||
periodicBoxVectors[1][0] != 0.0 || periodicBoxVectors[1][2] != 0.0 ||
periodicBoxVectors[2][0] != 0.0 || periodicBoxVectors[2][1] != 0.0);
}
void CpuCustomManyParticleForce::loopOverInteractions(vector<int>& availableParticles, vector<int>& particleSet, int loopIndex, int startIndex,
......@@ -394,8 +403,15 @@ void CpuCustomManyParticleForce::calculateOneIxn(vector<int>& particleSet, RealO
void CpuCustomManyParticleForce::computeDelta(const fvec4& posI, const fvec4& posJ, fvec4& deltaR, float& r2, const fvec4& boxSize, const fvec4& invBoxSize) const {
deltaR = posJ-posI;
if (usePeriodic) {
fvec4 base = round(deltaR*invBoxSize)*boxSize;
deltaR = deltaR-base;
if (triclinic) {
deltaR -= periodicBoxVec4[2]*floorf(deltaR[2]*recipBoxSize[2]+0.5f);
deltaR -= periodicBoxVec4[1]*floorf(deltaR[1]*recipBoxSize[1]+0.5f);
deltaR -= periodicBoxVec4[0]*floorf(deltaR[0]*recipBoxSize[0]+0.5f);
}
else {
fvec4 base = round(deltaR*invBoxSize)*boxSize;
deltaR = deltaR-base;
}
}
r2 = dot3(deltaR, deltaR);
}
......
platforms/cpu/src/CpuCustomNonbondedForce.cpp
View file @ 78e5f13a
......@@ -98,15 +98,25 @@ void CpuCustomNonbondedForce::setUseSwitchingFunction(RealOpenMM distance) {
switchingDistance = distance;
}
void CpuCustomNonbondedForce::setPeriodic(RealVec& boxSize) {
void CpuCustomNonbondedForce::setPeriodic(RealVec* periodicBoxVectors) {
assert(cutoff);
assert(boxSize[0] >= 2.0*cutoffDistance);
assert(boxSize[1] >= 2.0*cutoffDistance);
assert(boxSize[2] >= 2.0*cutoffDistance);
assert(periodicBoxVectors[0][0] >= 2.0*cutoffDistance);
assert(periodicBoxVectors[1][1] >= 2.0*cutoffDistance);
assert(periodicBoxVectors[2][2] >= 2.0*cutoffDistance);
periodic = true;
periodicBoxSize[0] = boxSize[0];
periodicBoxSize[1] = boxSize[1];
periodicBoxSize[2] = boxSize[2];
this->periodicBoxVectors[0] = periodicBoxVectors[0];
this->periodicBoxVectors[1] = periodicBoxVectors[1];
this->periodicBoxVectors[2] = periodicBoxVectors[2];
recipBoxSize[0] = (float) (1.0/periodicBoxVectors[0][0]);
recipBoxSize[1] = (float) (1.0/periodicBoxVectors[1][1]);
recipBoxSize[2] = (float) (1.0/periodicBoxVectors[2][2]);
periodicBoxVec4.resize(3);
periodicBoxVec4[0] = fvec4(periodicBoxVectors[0][0], periodicBoxVectors[0][1], periodicBoxVectors[0][2], 0);
periodicBoxVec4[1] = fvec4(periodicBoxVectors[1][0], periodicBoxVectors[1][1], periodicBoxVectors[1][2], 0);
periodicBoxVec4[2] = fvec4(periodicBoxVectors[2][0], periodicBoxVectors[2][1], periodicBoxVectors[2][2], 0);
triclinic = (periodicBoxVectors[0][1] != 0.0 || periodicBoxVectors[0][2] != 0.0 ||
periodicBoxVectors[1][0] != 0.0 || periodicBoxVectors[1][2] != 0.0 ||
periodicBoxVectors[2][0] != 0.0 || periodicBoxVectors[2][1] != 0.0);
}
......@@ -155,8 +165,8 @@ void CpuCustomNonbondedForce::threadComputeForce(ThreadPool& threads, int thread
ReferenceForce::setVariable(ReferenceForce::getVariablePointer(data.energyExpression, iter->first), iter->second);
ReferenceForce::setVariable(ReferenceForce::getVariablePointer(data.forceExpression, iter->first), iter->second);
}
fvec4 boxSize(periodicBoxSize[0], periodicBoxSize[1], periodicBoxSize[2], 0);
fvec4 invBoxSize((1/periodicBoxSize[0]), (1/periodicBoxSize[1]), (1/periodicBoxSize[2]), 0);
fvec4 boxSize(periodicBoxVectors[0][0], periodicBoxVectors[1][1], periodicBoxVectors[2][2], 0);
fvec4 invBoxSize(recipBoxSize[0], recipBoxSize[1], recipBoxSize[2], 0);
if (groupInteractions.size() > 0) {
// The user has specified interaction groups, so compute only the requested interactions.
......@@ -266,8 +276,15 @@ void CpuCustomNonbondedForce::calculateOneIxn(int ii, int jj, ThreadData& data,
void CpuCustomNonbondedForce::getDeltaR(const fvec4& posI, const fvec4& posJ, fvec4& deltaR, float& r2, const fvec4& boxSize, const fvec4& invBoxSize) const {
deltaR = posJ-posI;
if (periodic) {
fvec4 base = round(deltaR*invBoxSize)*boxSize;
deltaR = deltaR-base;
if (triclinic) {
deltaR -= periodicBoxVec4[2]*floorf(deltaR[2]*recipBoxSize[2]+0.5f);
deltaR -= periodicBoxVec4[1]*floorf(deltaR[1]*recipBoxSize[1]+0.5f);
deltaR -= periodicBoxVec4[0]*floorf(deltaR[0]*recipBoxSize[0]+0.5f);
}
else {
fvec4 base = round(deltaR*invBoxSize)*boxSize;
deltaR = deltaR-base;
}
}
r2 = dot3(deltaR, deltaR);
}
platforms/cpu/src/CpuKernels.cpp
View file @ 78e5f13a
......@@ -216,7 +216,7 @@ void CpuCalcForcesAndEnergyKernel::beginComputation(ContextImpl& context, bool i
referenceKernel.getAs<ReferenceCalcForcesAndEnergyKernel>().beginComputation(context, includeForce, includeEnergy, groups);
// Convert positions to single precision and clear the forces.
InitForceTask task(context.getSystem().getNumParticles(), context, data);
data.threads.execute(task);
data.threads.waitForThreads();
......@@ -512,8 +512,7 @@ double CpuCalcNonbondedForceKernel::execute(ContextImpl& context, bool includeFo
AlignedArray<float>& posq = data.posq;
vector<RealVec>& posData = extractPositions(context);
vector<RealVec>& forceData = extractForces(context);
RealVec boxSize = extractBoxSize(context);
float floatBoxSize[3] = {(float) boxSize[0], (float) boxSize[1], (float) boxSize[2]};
RealVec* boxVectors = extractBoxVectors(context);
double energy = (includeReciprocal ? ewaldSelfEnergy : 0.0);
bool ewald = (nonbondedMethod == Ewald);
bool pme = (nonbondedMethod == PME);
......@@ -559,7 +558,7 @@ double CpuCalcNonbondedForceKernel::execute(ContextImpl& context, bool includeFo
}
}
if (needRecompute) {
neighborList->computeNeighborList(numParticles, posq, exclusions, floatBoxSize, data.isPeriodic, nonbondedCutoff+padding, data.threads);
neighborList->computeNeighborList(numParticles, posq, exclusions, boxVectors, data.isPeriodic, nonbondedCutoff+padding, data.threads);
lastPositions = posData;
}
nonbonded->setUseCutoff(nonbondedCutoff, *neighborList, rfDielectric);
......@@ -583,7 +582,7 @@ double CpuCalcNonbondedForceKernel::execute(ContextImpl& context, bool includeFo
if (includeReciprocal) {
if (useOptimizedPme) {
PmeIO io(&posq[0], &data.threadForce[0][0], numParticles);
Vec3 periodicBoxSize(boxSize[0], boxSize[1], boxSize[2]);
Vec3 periodicBoxSize(boxVectors[0][0], boxVectors[1][1], boxVectors[2][2]);
optimizedPme.getAs<CalcPmeReciprocalForceKernel>().beginComputation(io, periodicBoxSize, includeEnergy);
nonbondedEnergy += optimizedPme.getAs<CalcPmeReciprocalForceKernel>().finishComputation(io);
}
......@@ -596,7 +595,7 @@ double CpuCalcNonbondedForceKernel::execute(ContextImpl& context, bool includeFo
ReferenceLJCoulomb14 nonbonded14;
refBondForce.calculateForce(num14, bonded14IndexArray, posData, bonded14ParamArray, forceData, includeEnergy ? &energy : NULL, nonbonded14);
if (data.isPeriodic)
energy += dispersionCoefficient/(boxSize[0]*boxSize[1]*boxSize[2]);
energy += dispersionCoefficient/(boxVectors[0][0]*boxVectors[1][1]*boxVectors[2][2]);
}
return energy;
}
......@@ -750,19 +749,18 @@ void CpuCalcCustomNonbondedForceKernel::initialize(const System& system, const C
double CpuCalcCustomNonbondedForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
vector<RealVec>& posData = extractPositions(context);
vector<RealVec>& forceData = extractForces(context);
RealVec& box = extractBoxSize(context);
float floatBoxSize[3] = {(float) box[0], (float) box[1], (float) box[2]};
RealVec* boxVectors = extractBoxVectors(context);
double energy = 0;
bool periodic = (nonbondedMethod == CutoffPeriodic);
if (nonbondedMethod != NoCutoff) {
neighborList->computeNeighborList(numParticles, data.posq, exclusions, floatBoxSize, data.isPeriodic, nonbondedCutoff, data.threads);
neighborList->computeNeighborList(numParticles, data.posq, exclusions, boxVectors, data.isPeriodic, nonbondedCutoff, data.threads);
nonbonded->setUseCutoff(nonbondedCutoff, *neighborList);
}
if (periodic) {
double minAllowedSize = 2*nonbondedCutoff;
if (box[0] < minAllowedSize || box[1] < minAllowedSize || box[2] < minAllowedSize)
if (boxVectors[0][0] < minAllowedSize || boxVectors[1][1] < minAllowedSize || boxVectors[2][2] < minAllowedSize)
throw OpenMMException("The periodic box size has decreased to less than twice the nonbonded cutoff.");
nonbonded->setPeriodic(box);
nonbonded->setPeriodic(boxVectors);
}
bool globalParamsChanged = false;
for (int i = 0; i < (int) globalParameterNames.size(); i++) {
......@@ -781,7 +779,7 @@ double CpuCalcCustomNonbondedForceKernel::execute(ContextImpl& context, bool inc
longRangeCoefficient = CustomNonbondedForceImpl::calcLongRangeCorrection(*forceCopy, context.getOwner());
hasInitializedLongRangeCorrection = true;
}
energy += longRangeCoefficient/(box[0]*box[1]*box[2]);
energy += longRangeCoefficient/(boxVectors[0][0]*boxVectors[1][1]*boxVectors[2][2]);
return energy;
}
......@@ -989,13 +987,12 @@ void CpuCalcCustomGBForceKernel::initialize(const System& system, const CustomGB
double CpuCalcCustomGBForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
vector<RealVec>& forceData = extractForces(context);
RealOpenMM energy = 0;
RealVec& box = extractBoxSize(context);
float floatBoxSize[3] = {(float) box[0], (float) box[1], (float) box[2]};
RealVec* boxVectors = extractBoxVectors(context);
if (data.isPeriodic)
ixn->setPeriodic(extractBoxSize(context));
if (nonbondedMethod != NoCutoff) {
vector<set<int> > noExclusions(numParticles);
neighborList->computeNeighborList(numParticles, data.posq, exclusions, floatBoxSize, data.isPeriodic, nonbondedCutoff, data.threads);
neighborList->computeNeighborList(numParticles, data.posq, exclusions, boxVectors, data.isPeriodic, nonbondedCutoff, data.threads);
ixn->setUseCutoff(nonbondedCutoff, *neighborList);
}
map<string, double> globalParameters;
......@@ -1052,6 +1049,7 @@ void CpuCalcCustomManyParticleForceKernel::initialize(const System& system, cons
ixn = new CpuCustomManyParticleForce(force, data.threads);
nonbondedMethod = CalcCustomManyParticleForceKernel::NonbondedMethod(force.getNonbondedMethod());
cutoffDistance = force.getCutoffDistance();
data.isPeriodic = (nonbondedMethod == CutoffPeriodic);
}
double CpuCalcCustomManyParticleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
......@@ -1059,11 +1057,11 @@ double CpuCalcCustomManyParticleForceKernel::execute(ContextImpl& context, bool
for (int i = 0; i < (int) globalParameterNames.size(); i++)
globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
if (nonbondedMethod == CutoffPeriodic) {
RealVec& box = extractBoxSize(context);
RealVec* boxVectors = extractBoxVectors(context);
double minAllowedSize = 2*cutoffDistance;
if (box[0] < minAllowedSize || box[1] < minAllowedSize || box[2] < minAllowedSize)
if (boxVectors[0][0] < minAllowedSize || boxVectors[1][1] < minAllowedSize || boxVectors[2][2] < minAllowedSize)
throw OpenMMException("The periodic box size has decreased to less than twice the nonbonded cutoff.");
ixn->setPeriodic(box);
ixn->setPeriodic(boxVectors);
}
double energy = 0;
ixn->calculateIxn(data.posq, particleParamArray, globalParameters, data.threadForce, includeForces, includeEnergy, energy);
......
platforms/cpu/src/CpuNeighborList.cpp
View file @ 78e5f13a
......@@ -373,15 +373,6 @@ public:
CpuNeighborList::CpuNeighborList(int blockSize) : blockSize(blockSize) {
}
void CpuNeighborList::computeNeighborList(int numAtoms, const AlignedArray<float>& atomLocations, const vector<set<int> >& exclusions,
const float* periodicBoxSize, bool usePeriodic, float maxDistance, ThreadPool& threads) {
RealVec vectors[3];
vectors[0] = RealVec(periodicBoxSize[0], 0, 0);
vectors[1] = RealVec(0, periodicBoxSize[1], 0);
vectors[2] = RealVec(0, 0, periodicBoxSize[2]);
computeNeighborList(numAtoms, atomLocations, exclusions, vectors, usePeriodic, maxDistance, threads);
}
void CpuNeighborList::computeNeighborList(int numAtoms, const AlignedArray<float>& atomLocations, const vector<set<int> >& exclusions,
const RealVec* periodicBoxVectors, bool usePeriodic, float maxDistance, ThreadPool& threads) {
int numBlocks = (numAtoms+blockSize-1)/blockSize;
......@@ -425,7 +416,7 @@ void CpuNeighborList::computeNeighborList(int numAtoms, const AlignedArray<float
sort(atomBins.begin(), atomBins.end());
// Build the voxel hash.
float edgeSizeY, edgeSizeZ;
if (!usePeriodic)
edgeSizeY = edgeSizeZ = maxDistance; // TODO - adjust this as needed
......
platforms/cpu/src/CpuNonbondedForce.cpp
View file @ 78e5f13a
......@@ -352,8 +352,6 @@ void CpuNonbondedForce::threadComputeDirect(ThreadPool& threads, int threadIndex
// Now subtract off the exclusions, since they were implicitly included in the reciprocal space sum.
fvec4 boxSize(periodicBoxVectors[0][0], periodicBoxVectors[1][1], periodicBoxVectors[2][2], 0);
fvec4 invBoxSize(recipBoxSize[0], recipBoxSize[1], recipBoxSize[2], 0);
for (int i = threadIndex; i < numberOfAtoms; i += numThreads) {
fvec4 posI((float) atomCoordinates[i][0], (float) atomCoordinates[i][1], (float) atomCoordinates[i][2], 0.0f);
for (set<int>::const_iterator iter = exclusions[i].begin(); iter != exclusions[i].end(); ++iter) {
......
platforms/cpu/tests/TestCpuCustomManyParticleForce.cpp
View file @ 78e5f13a
......@@ -53,15 +53,36 @@ using namespace std;
const double TOL = 1e-5;
void validateAxilrodTeller(CustomManyParticleForce* force, const vector<Vec3>& positions, const vector<const int*>& expectedSets, double boxSize) {
Vec3 computeDelta(const Vec3& pos1, const Vec3& pos2, bool periodic, const Vec3* periodicBoxVectors) {
Vec3 diff = pos1-pos2;
if (periodic) {
diff -= periodicBoxVectors[2]*floor(diff[2]/periodicBoxVectors[2][2]+0.5);
diff -= periodicBoxVectors[1]*floor(diff[1]/periodicBoxVectors[1][1]+0.5);
diff -= periodicBoxVectors[0]*floor(diff[0]/periodicBoxVectors[0][0]+0.5);
}
return diff;
}
void validateAxilrodTeller(CustomManyParticleForce* force, const vector<Vec3>& positions, const vector<const int*>& expectedSets, double boxSize, bool triclinic) {
// Create a System and Context.
int numParticles = force->getNumParticles();
CustomManyParticleForce::NonbondedMethod nonbondedMethod = force->getNonbondedMethod();
System system;
for (int i = 0; i < numParticles; i++)
system.addParticle(1.0);
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
Vec3 boxVectors[3];
if (triclinic) {
boxVectors[0] = Vec3(boxSize, 0, 0);
boxVectors[1] = Vec3(0.2*boxSize, boxSize, 0);
boxVectors[2] = Vec3(-0.3*boxSize, -0.1*boxSize, boxSize);
}
else {
boxVectors[0] = Vec3(boxSize, 0, 0);
boxVectors[1] = Vec3(0, boxSize, 0);
boxVectors[2] = Vec3(0, 0, boxSize);
}
system.setDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
system.addForce(force);
VerletIntegrator integrator(0.001);
CpuPlatform platform;
......@@ -69,24 +90,18 @@ void validateAxilrodTeller(CustomManyParticleForce* force, const vector<Vec3>& p
context.setPositions(positions);
State state1 = context.getState(State::Forces | State::Energy);
double c = context.getParameter("C");
// See if the energy matches the expected value.
double expectedEnergy = 0;
bool periodic = (nonbondedMethod == CustomManyParticleForce::CutoffPeriodic);
for (int i = 0; i < (int) expectedSets.size(); i++) {
int p1 = expectedSets[i][0];
int p2 = expectedSets[i][1];
int p3 = expectedSets[i][2];
Vec3 d12 = positions[p2]-positions[p1];
Vec3 d13 = positions[p3]-positions[p1];
Vec3 d23 = positions[p3]-positions[p2];
if (nonbondedMethod == CustomManyParticleForce::CutoffPeriodic) {
for (int j = 0; j < 3; j++) {
d12[j] -= floor(d12[j]/boxSize+0.5f)*boxSize;
d13[j] -= floor(d13[j]/boxSize+0.5f)*boxSize;
d23[j] -= floor(d23[j]/boxSize+0.5f)*boxSize;
}
}
Vec3 d12 = computeDelta(positions[p2], positions[p1], periodic, boxVectors);
Vec3 d13 = computeDelta(positions[p3], positions[p1], periodic, boxVectors);
Vec3 d23 = computeDelta(positions[p3], positions[p2], periodic, boxVectors);
double r12 = sqrt(d12.dot(d12));
double r13 = sqrt(d13.dot(d13));
double r23 = sqrt(d23.dot(d23));
......@@ -210,7 +225,7 @@ void testNoCutoff() {
positions.push_back(Vec3(0.4, 0, -0.8));
int sets[4][3] = {{0,1,2}, {1,2,3}, {2,3,0}, {3,0,1}};
vector<const int*> expectedSets(&sets[0], &sets[4]);
validateAxilrodTeller(force, positions, expectedSets, 2.0);
validateAxilrodTeller(force, positions, expectedSets, 2.0, false);
}
void testCutoff() {
......@@ -235,7 +250,7 @@ void testCutoff() {
positions.push_back(Vec3(0.2, 0.5, -0.1));
int sets[7][3] = {{0,1,2}, {0,1,3}, {0,1,4}, {0,2,4}, {0,3,4}, {1,2,4}, {1,3,4}};
vector<const int*> expectedSets(&sets[0], &sets[7]);
validateAxilrodTeller(force, positions, expectedSets, 2.0);
validateAxilrodTeller(force, positions, expectedSets, 2.0, false);
}
void testPeriodic() {
......@@ -261,7 +276,33 @@ void testPeriodic() {
double boxSize = 2.1;
int sets[5][3] = {{0,1,3}, {0,1,4}, {0,2,4}, {0,3,4}, {1,3,4}};
vector<const int*> expectedSets(&sets[0], &sets[5]);
validateAxilrodTeller(force, positions, expectedSets, boxSize);
validateAxilrodTeller(force, positions, expectedSets, boxSize, false);
}
void testTriclinic() {
CustomManyParticleForce* force = new CustomManyParticleForce(3,
"C*(1+3*cos(theta1)*cos(theta2)*cos(theta3))/(r12*r13*r23)^3;"
"theta1=angle(p1,p2,p3); theta2=angle(p2,p3,p1); theta3=angle(p3,p1,p2);"
"r12=distance(p1,p2); r13=distance(p1,p3); r23=distance(p2,p3)");
force->addGlobalParameter("C", 1.5);
force->setNonbondedMethod(CustomManyParticleForce::CutoffPeriodic);
force->setCutoffDistance(1.05);
vector<double> params;
force->addParticle(params);
force->addParticle(params);
force->addParticle(params);
force->addParticle(params);
force->addParticle(params);
vector<Vec3> positions;
positions.push_back(Vec3(0, 0, 0));
positions.push_back(Vec3(1, 0, 0));
positions.push_back(Vec3(0, 1.1, 0.3));
positions.push_back(Vec3(0.4, 0, -0.8));
positions.push_back(Vec3(0.2, 0.5, -0.1));
double boxSize = 2.1;
int sets[4][3] = {{0,1,3}, {0,1,4}, {0,3,4}, {1,3,4}};
vector<const int*> expectedSets(&sets[0], &sets[4]);
validateAxilrodTeller(force, positions, expectedSets, boxSize, true);
}
void testExclusions() {
......@@ -286,7 +327,7 @@ void testExclusions() {
force->addExclusion(0, 3);
int sets[5][3] = {{0,1,4}, {1,2,3}, {1,2,4}, {1,3,4}, {2,3,4}};
vector<const int*> expectedSets(&sets[0], &sets[5]);
validateAxilrodTeller(force, positions, expectedSets, 2.0);
validateAxilrodTeller(force, positions, expectedSets, 2.0, false);
}
void testAllTerms() {
......@@ -680,6 +721,7 @@ int main() {
testNoCutoff();
testCutoff();
testPeriodic();
testTriclinic();
testExclusions();
testAllTerms();
testParameters();
......
platforms/cpu/tests/TestCpuCustomNonbondedForce.cpp
View file @ 78e5f13a
......@@ -224,6 +224,65 @@ void testPeriodic() {
ASSERT_EQUAL_TOL(1.9+1+0.9, state.getPotentialEnergy(), TOL);
}
void testTriclinic() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
Vec3 a(3.1, 0, 0);
Vec3 b(0.4, 3.5, 0);
Vec3 c(-0.1, -0.5, 4.0);
system.setDefaultPeriodicBoxVectors(a, b, c);
VerletIntegrator integrator(0.01);
CustomNonbondedForce* nonbonded = new CustomNonbondedForce("r");
nonbonded->addParticle(vector<double>());
nonbonded->addParticle(vector<double>());
nonbonded->setNonbondedMethod(CustomNonbondedForce::CutoffPeriodic);
const double cutoff = 1.5;
nonbonded->setCutoffDistance(cutoff);
system.addForce(nonbonded);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int iteration = 0; iteration < 50; iteration++) {
// Generate random positions for the two particles.
positions[0] = a*genrand_real2(sfmt) + b*genrand_real2(sfmt) + c*genrand_real2(sfmt);
positions[1] = a*genrand_real2(sfmt) + b*genrand_real2(sfmt) + c*genrand_real2(sfmt);
context.setPositions(positions);
// Loop over all possible periodic copies and find the nearest one.
Vec3 delta;
double distance2 = 100.0;
for (int i = -1; i < 2; i++)
for (int j = -1; j < 2; j++)
for (int k = -1; k < 2; k++) {
Vec3 d = positions[1]-positions[0]+a*i+b*j+c*k;
if (d.dot(d) < distance2) {
delta = d;
distance2 = d.dot(d);
}
}
double distance = sqrt(distance2);
// See if the force and energy are correct.
State state = context.getState(State::Forces | State::Energy);
if (distance >= cutoff) {
ASSERT_EQUAL(0.0, state.getPotentialEnergy());
ASSERT_EQUAL_VEC(Vec3(0, 0, 0), state.getForces()[0], 0);
ASSERT_EQUAL_VEC(Vec3(0, 0, 0), state.getForces()[1], 0);
}
else {
const Vec3 force = delta/sqrt(delta.dot(delta));
ASSERT_EQUAL_TOL(distance, state.getPotentialEnergy(), TOL);
ASSERT_EQUAL_VEC(force, state.getForces()[0], TOL);
ASSERT_EQUAL_VEC(-force, state.getForces()[1], TOL);
}
}
}
void testContinuous1DFunction() {
System system;
system.addParticle(1.0);
......@@ -852,6 +911,7 @@ int main() {
testExclusions();
testCutoff();
testPeriodic();
testTriclinic();
testContinuous1DFunction();
testContinuous2DFunction();
testContinuous3DFunction();
......
platforms/reference/tests/TestReferenceCustomManyParticleForce.cpp
View file @ 78e5f13a
......@@ -53,7 +53,17 @@ using namespace std;
const double TOL = 1e-5;
void validateAxilrodTeller(CustomManyParticleForce* force, const vector<Vec3>& positions, const vector<const int*>& expectedSets, double boxSize) {
Vec3 computeDelta(const Vec3& pos1, const Vec3& pos2, bool periodic, const Vec3* periodicBoxVectors) {
Vec3 diff = pos1-pos2;
if (periodic) {
diff -= periodicBoxVectors[2]*floor(diff[2]/periodicBoxVectors[2][2]+0.5);
diff -= periodicBoxVectors[1]*floor(diff[1]/periodicBoxVectors[1][1]+0.5);
diff -= periodicBoxVectors[0]*floor(diff[0]/periodicBoxVectors[0][0]+0.5);
}
return diff;
}
void validateAxilrodTeller(CustomManyParticleForce* force, const vector<Vec3>& positions, const vector<const int*>& expectedSets, double boxSize, bool triclinic) {
// Create a System and Context.
int numParticles = force->getNumParticles();
......@@ -61,7 +71,18 @@ void validateAxilrodTeller(CustomManyParticleForce* force, const vector<Vec3>& p
System system;
for (int i = 0; i < numParticles; i++)
system.addParticle(1.0);
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
Vec3 boxVectors[3];
if (triclinic) {
boxVectors[0] = Vec3(boxSize, 0, 0);
boxVectors[1] = Vec3(0.2*boxSize, boxSize, 0);
boxVectors[2] = Vec3(-0.3*boxSize, -0.1*boxSize, boxSize);
}
else {
boxVectors[0] = Vec3(boxSize, 0, 0);
boxVectors[1] = Vec3(0, boxSize, 0);
boxVectors[2] = Vec3(0, 0, boxSize);
}
system.setDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
system.addForce(force);
VerletIntegrator integrator(0.001);
ReferencePlatform platform;
......@@ -73,20 +94,14 @@ void validateAxilrodTeller(CustomManyParticleForce* force, const vector<Vec3>& p
// See if the energy matches the expected value.
double expectedEnergy = 0;
bool periodic = (nonbondedMethod == CustomManyParticleForce::CutoffPeriodic);
for (int i = 0; i < (int) expectedSets.size(); i++) {
int p1 = expectedSets[i][0];
int p2 = expectedSets[i][1];
int p3 = expectedSets[i][2];
Vec3 d12 = positions[p2]-positions[p1];
Vec3 d13 = positions[p3]-positions[p1];
Vec3 d23 = positions[p3]-positions[p2];
if (nonbondedMethod == CustomManyParticleForce::CutoffPeriodic) {
for (int j = 0; j < 3; j++) {
d12[j] -= floor(d12[j]/boxSize+0.5f)*boxSize;
d13[j] -= floor(d13[j]/boxSize+0.5f)*boxSize;
d23[j] -= floor(d23[j]/boxSize+0.5f)*boxSize;
}
}
Vec3 d12 = computeDelta(positions[p2], positions[p1], periodic, boxVectors);
Vec3 d13 = computeDelta(positions[p3], positions[p1], periodic, boxVectors);
Vec3 d23 = computeDelta(positions[p3], positions[p2], periodic, boxVectors);
double r12 = sqrt(d12.dot(d12));
double r13 = sqrt(d13.dot(d13));
double r23 = sqrt(d23.dot(d23));
......@@ -210,7 +225,7 @@ void testNoCutoff() {
positions.push_back(Vec3(0.4, 0, -0.8));
int sets[4][3] = {{0,1,2}, {1,2,3}, {2,3,0}, {3,0,1}};
vector<const int*> expectedSets(&sets[0], &sets[4]);
validateAxilrodTeller(force, positions, expectedSets, 2.0);
validateAxilrodTeller(force, positions, expectedSets, 2.0, false);
}
void testCutoff() {
......@@ -235,7 +250,7 @@ void testCutoff() {
positions.push_back(Vec3(0.2, 0.5, -0.1));
int sets[7][3] = {{0,1,2}, {0,1,3}, {0,1,4}, {0,2,4}, {0,3,4}, {1,2,4}, {1,3,4}};
vector<const int*> expectedSets(&sets[0], &sets[7]);
validateAxilrodTeller(force, positions, expectedSets, 2.0);
validateAxilrodTeller(force, positions, expectedSets, 2.0, false);
}
void testPeriodic() {
......@@ -261,7 +276,33 @@ void testPeriodic() {
double boxSize = 2.1;
int sets[5][3] = {{0,1,3}, {0,1,4}, {0,2,4}, {0,3,4}, {1,3,4}};
vector<const int*> expectedSets(&sets[0], &sets[5]);
validateAxilrodTeller(force, positions, expectedSets, boxSize);
validateAxilrodTeller(force, positions, expectedSets, boxSize, false);
}
void testTriclinic() {
CustomManyParticleForce* force = new CustomManyParticleForce(3,
"C*(1+3*cos(theta1)*cos(theta2)*cos(theta3))/(r12*r13*r23)^3;"
"theta1=angle(p1,p2,p3); theta2=angle(p2,p3,p1); theta3=angle(p3,p1,p2);"
"r12=distance(p1,p2); r13=distance(p1,p3); r23=distance(p2,p3)");
force->addGlobalParameter("C", 1.5);
force->setNonbondedMethod(CustomManyParticleForce::CutoffPeriodic);
force->setCutoffDistance(1.05);
vector<double> params;
force->addParticle(params);
force->addParticle(params);
force->addParticle(params);
force->addParticle(params);
force->addParticle(params);
vector<Vec3> positions;
positions.push_back(Vec3(0, 0, 0));
positions.push_back(Vec3(1, 0, 0));
positions.push_back(Vec3(0, 1.1, 0.3));
positions.push_back(Vec3(0.4, 0, -0.8));
positions.push_back(Vec3(0.2, 0.5, -0.1));
double boxSize = 2.1;
int sets[4][3] = {{0,1,3}, {0,1,4}, {0,3,4}, {1,3,4}};
vector<const int*> expectedSets(&sets[0], &sets[4]);
validateAxilrodTeller(force, positions, expectedSets, boxSize, true);
}
void testExclusions() {
......@@ -286,7 +327,7 @@ void testExclusions() {
force->addExclusion(0, 3);
int sets[5][3] = {{0,1,4}, {1,2,3}, {1,2,4}, {1,3,4}, {2,3,4}};
vector<const int*> expectedSets(&sets[0], &sets[5]);
validateAxilrodTeller(force, positions, expectedSets, 2.0);
validateAxilrodTeller(force, positions, expectedSets, 2.0, false);
}
void testAllTerms() {
......@@ -592,6 +633,7 @@ int main() {
testNoCutoff();
testCutoff();
testPeriodic();
testTriclinic();
testExclusions();
testAllTerms();
testParameters();
......
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