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Commit 61d5cc0f authored by Peter's avatar Peter
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Merge branch 'master' into applecl

parents e2999354 afae4bc8
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Showing with 1653 additions and 280 deletions
platforms/cpu/src/CpuKernelFactory.cpp
View file @ 61d5cc0f
...@@ -53,6 +53,8 @@ KernelImpl* CpuKernelFactory::createKernelImpl(std::string name, const Platform& ...@@ -53,6 +53,8 @@ KernelImpl* CpuKernelFactory::createKernelImpl(std::string name, const Platform&
return new CpuCalcCustomManyParticleForceKernel(name, platform, data); return new CpuCalcCustomManyParticleForceKernel(name, platform, data);
if (name == CalcGBSAOBCForceKernel::Name()) if (name == CalcGBSAOBCForceKernel::Name())
return new CpuCalcGBSAOBCForceKernel(name, platform, data); return new CpuCalcGBSAOBCForceKernel(name, platform, data);
if (name == CalcCustomGBForceKernel::Name())
return new CpuCalcCustomGBForceKernel(name, platform, data);
if (name == IntegrateLangevinStepKernel::Name()) if (name == IntegrateLangevinStepKernel::Name())
return new CpuIntegrateLangevinStepKernel(name, platform, data); return new CpuIntegrateLangevinStepKernel(name, platform, data);
throw OpenMMException((std::string("Tried to create kernel with illegal kernel name '") + name + "'").c_str()); throw OpenMMException((std::string("Tried to create kernel with illegal kernel name '") + name + "'").c_str());
......
platforms/cpu/src/CpuKernels.cpp
View file @ 61d5cc0f
...@@ -6,7 +6,7 @@ ...@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * Medical Research, grant U54 GM072970. See https://simtk.org. *
* * * *
* Portions copyright (c) 2013-2014 Stanford University and the Authors. * * Portions copyright (c) 2013-2015 Stanford University and the Authors. *
* Authors: Peter Eastman * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -73,6 +73,11 @@ static RealVec& extractBoxSize(ContextImpl& context) { ...@@ -73,6 +73,11 @@ static RealVec& extractBoxSize(ContextImpl& context) {
return *(RealVec*) data->periodicBoxSize; return *(RealVec*) data->periodicBoxSize;
} }
static RealVec* extractBoxVectors(ContextImpl& context) {
ReferencePlatform::PlatformData* data = reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
return (RealVec*) data->periodicBoxVectors;
}
static ReferenceConstraints& extractConstraints(ContextImpl& context) { static ReferenceConstraints& extractConstraints(ContextImpl& context) {
ReferencePlatform::PlatformData* data = reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData()); ReferencePlatform::PlatformData* data = reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
return *(ReferenceConstraints*) data->constraints; return *(ReferenceConstraints*) data->constraints;
...@@ -140,32 +145,55 @@ public: ...@@ -140,32 +145,55 @@ public:
class CpuCalcForcesAndEnergyKernel::InitForceTask : public ThreadPool::Task { class CpuCalcForcesAndEnergyKernel::InitForceTask : public ThreadPool::Task {
public: public:
InitForceTask(int numParticles, ContextImpl& context, CpuPlatform::PlatformData& data) : numParticles(numParticles), context(context), data(data) { InitForceTask(int numParticles, ContextImpl& context, CpuPlatform::PlatformData& data) : numParticles(numParticles), positionsValid(true), context(context), data(data) {
} }
void execute(ThreadPool& threads, int threadIndex) { void execute(ThreadPool& threads, int threadIndex) {
// Convert the positions to single precision and apply periodic boundary conditions // Convert the positions to single precision and apply periodic boundary conditions
AlignedArray<float>& posq = data.posq; AlignedArray<float>& posq = data.posq;
vector<RealVec>& posData = extractPositions(context); vector<RealVec>& posData = extractPositions(context);
RealVec boxSize = extractBoxSize(context); RealVec* boxVectors = extractBoxVectors(context);
double invBoxSize[3] = {1/boxSize[0], 1/boxSize[1], 1/boxSize[2]}; double boxSize[3] = {boxVectors[0][0], boxVectors[1][1], boxVectors[2][2]};
double invBoxSize[3] = {1/boxVectors[0][0], 1/boxVectors[1][1], 1/boxVectors[2][2]};
bool triclinic = (boxVectors[0][1] != 0 || boxVectors[0][2] != 0 || boxVectors[1][0] != 0 || boxVectors[1][2] != 0 || boxVectors[2][0] != 0 || boxVectors[2][1] != 0);
int numParticles = context.getSystem().getNumParticles(); int numParticles = context.getSystem().getNumParticles();
int numThreads = threads.getNumThreads(); int numThreads = threads.getNumThreads();
int start = threadIndex*numParticles/numThreads; int start = threadIndex*numParticles/numThreads;
int end = (threadIndex+1)*numParticles/numThreads; int end = (threadIndex+1)*numParticles/numThreads;
if (data.isPeriodic) if (data.isPeriodic) {
for (int i = start; i < end; i++) if (triclinic) {
for (int j = 0; j < 3; j++) { for (int i = start; i < end; i++) {
RealOpenMM x = posData[i][j]; RealVec pos = posData[i];
double base = floor(x*invBoxSize[j])*boxSize[j]; pos -= boxVectors[2]*floor(pos[2]*invBoxSize[2]);
posq[4*i+j] = (float) (x-base); pos -= boxVectors[1]*floor(pos[1]*invBoxSize[1]);
pos -= boxVectors[0]*floor(pos[0]*invBoxSize[0]);
posq[4*i] = (float) pos[0];
posq[4*i+1] = (float) pos[1];
posq[4*i+2] = (float) pos[2];
}
}
else {
for (int i = start; i < end; i++) {
for (int j = 0; j < 3; j++) {
RealOpenMM x = posData[i][j];
double base = floor(x*invBoxSize[j])*boxSize[j];
posq[4*i+j] = (float) (x-base);
}
} }
}
}
else else
for (int i = start; i < end; i++) { for (int i = start; i < end; i++) {
posq[4*i] = (float) posData[i][0]; posq[4*i] = (float) posData[i][0];
posq[4*i+1] = (float) posData[i][1]; posq[4*i+1] = (float) posData[i][1];
posq[4*i+2] = (float) posData[i][2]; posq[4*i+2] = (float) posData[i][2];
} }
// Check for invalid positions.
for (int i = 4*start; i < 4*end; i += 4)
if (posq[i] != posq[i] || posq[i+1] != posq[i+1] || posq[i+2] != posq[i+2])
positionsValid = false;
// Clear the forces. // Clear the forces.
...@@ -174,6 +202,7 @@ public: ...@@ -174,6 +202,7 @@ public:
zero.store(&data.threadForce[threadIndex][j*4]); zero.store(&data.threadForce[threadIndex][j*4]);
} }
int numParticles; int numParticles;
bool positionsValid;
ContextImpl& context; ContextImpl& context;
CpuPlatform::PlatformData& data; CpuPlatform::PlatformData& data;
}; };
...@@ -194,19 +223,21 @@ void CpuCalcForcesAndEnergyKernel::beginComputation(ContextImpl& context, bool i ...@@ -194,19 +223,21 @@ void CpuCalcForcesAndEnergyKernel::beginComputation(ContextImpl& context, bool i
referenceKernel.getAs<ReferenceCalcForcesAndEnergyKernel>().beginComputation(context, includeForce, includeEnergy, groups); referenceKernel.getAs<ReferenceCalcForcesAndEnergyKernel>().beginComputation(context, includeForce, includeEnergy, groups);
// Convert positions to single precision and clear the forces. // Convert positions to single precision and clear the forces.
InitForceTask task(context.getSystem().getNumParticles(), context, data); InitForceTask task(context.getSystem().getNumParticles(), context, data);
data.threads.execute(task); data.threads.execute(task);
data.threads.waitForThreads(); data.threads.waitForThreads();
if (!task.positionsValid)
throw OpenMMException("Particle coordinate is nan");
} }
double CpuCalcForcesAndEnergyKernel::finishComputation(ContextImpl& context, bool includeForce, bool includeEnergy, int groups) { double CpuCalcForcesAndEnergyKernel::finishComputation(ContextImpl& context, bool includeForce, bool includeEnergy, int groups, bool& valid) {
// Sum the forces from all the threads. // Sum the forces from all the threads.
SumForceTask task(context.getSystem().getNumParticles(), extractForces(context), data); SumForceTask task(context.getSystem().getNumParticles(), extractForces(context), data);
data.threads.execute(task); data.threads.execute(task);
data.threads.waitForThreads(); data.threads.waitForThreads();
return referenceKernel.getAs<ReferenceCalcForcesAndEnergyKernel>().finishComputation(context, includeForce, includeEnergy, groups); return referenceKernel.getAs<ReferenceCalcForcesAndEnergyKernel>().finishComputation(context, includeForce, includeEnergy, groups, valid);
} }
CpuCalcPeriodicTorsionForceKernel::~CpuCalcPeriodicTorsionForceKernel() { CpuCalcPeriodicTorsionForceKernel::~CpuCalcPeriodicTorsionForceKernel() {
...@@ -477,21 +508,19 @@ double CpuCalcNonbondedForceKernel::execute(ContextImpl& context, bool includeFo ...@@ -477,21 +508,19 @@ double CpuCalcNonbondedForceKernel::execute(ContextImpl& context, bool includeFo
if (nonbondedMethod == PME) { if (nonbondedMethod == PME) {
// If available, use the optimized PME implementation. // If available, use the optimized PME implementation.
try { vector<string> kernelNames;
kernelNames.push_back("CalcPmeReciprocalForce");
useOptimizedPme = getPlatform().supportsKernels(kernelNames);
if (useOptimizedPme) {
optimizedPme = getPlatform().createKernel(CalcPmeReciprocalForceKernel::Name(), context); optimizedPme = getPlatform().createKernel(CalcPmeReciprocalForceKernel::Name(), context);
optimizedPme.getAs<CalcPmeReciprocalForceKernel>().initialize(gridSize[0], gridSize[1], gridSize[2], numParticles, ewaldAlpha); optimizedPme.getAs<CalcPmeReciprocalForceKernel>().initialize(gridSize[0], gridSize[1], gridSize[2], numParticles, ewaldAlpha);
useOptimizedPme = true;
}
catch (OpenMMException& ex) {
// The CPU PME plugin isn't available.
} }
} }
} }
AlignedArray<float>& posq = data.posq; AlignedArray<float>& posq = data.posq;
vector<RealVec>& posData = extractPositions(context); vector<RealVec>& posData = extractPositions(context);
vector<RealVec>& forceData = extractForces(context); vector<RealVec>& forceData = extractForces(context);
RealVec boxSize = extractBoxSize(context); RealVec* boxVectors = extractBoxVectors(context);
float floatBoxSize[3] = {(float) boxSize[0], (float) boxSize[1], (float) boxSize[2]};
double energy = (includeReciprocal ? ewaldSelfEnergy : 0.0); double energy = (includeReciprocal ? ewaldSelfEnergy : 0.0);
bool ewald = (nonbondedMethod == Ewald); bool ewald = (nonbondedMethod == Ewald);
bool pme = (nonbondedMethod == PME); bool pme = (nonbondedMethod == PME);
...@@ -537,16 +566,17 @@ double CpuCalcNonbondedForceKernel::execute(ContextImpl& context, bool includeFo ...@@ -537,16 +566,17 @@ double CpuCalcNonbondedForceKernel::execute(ContextImpl& context, bool includeFo
} }
} }
if (needRecompute) { 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; lastPositions = posData;
} }
nonbonded->setUseCutoff(nonbondedCutoff, *neighborList, rfDielectric); nonbonded->setUseCutoff(nonbondedCutoff, *neighborList, rfDielectric);
} }
if (data.isPeriodic) { if (data.isPeriodic) {
RealVec* boxVectors = extractBoxVectors(context);
double minAllowedSize = 1.999999*nonbondedCutoff; double minAllowedSize = 1.999999*nonbondedCutoff;
if (boxSize[0] < minAllowedSize || boxSize[1] < minAllowedSize || boxSize[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."); throw OpenMMException("The periodic box size has decreased to less than twice the nonbonded cutoff.");
nonbonded->setPeriodic(floatBoxSize); nonbonded->setPeriodic(boxVectors);
} }
if (ewald) if (ewald)
nonbonded->setUseEwald(ewaldAlpha, kmax[0], kmax[1], kmax[2]); nonbonded->setUseEwald(ewaldAlpha, kmax[0], kmax[1], kmax[2]);
...@@ -560,8 +590,8 @@ double CpuCalcNonbondedForceKernel::execute(ContextImpl& context, bool includeFo ...@@ -560,8 +590,8 @@ double CpuCalcNonbondedForceKernel::execute(ContextImpl& context, bool includeFo
if (includeReciprocal) { if (includeReciprocal) {
if (useOptimizedPme) { if (useOptimizedPme) {
PmeIO io(&posq[0], &data.threadForce[0][0], numParticles); PmeIO io(&posq[0], &data.threadForce[0][0], numParticles);
Vec3 periodicBoxSize(boxSize[0], boxSize[1], boxSize[2]); Vec3 periodicBoxVectors[3] = {boxVectors[0], boxVectors[1], boxVectors[2]};
optimizedPme.getAs<CalcPmeReciprocalForceKernel>().beginComputation(io, periodicBoxSize, includeEnergy); optimizedPme.getAs<CalcPmeReciprocalForceKernel>().beginComputation(io, periodicBoxVectors, includeEnergy);
nonbondedEnergy += optimizedPme.getAs<CalcPmeReciprocalForceKernel>().finishComputation(io); nonbondedEnergy += optimizedPme.getAs<CalcPmeReciprocalForceKernel>().finishComputation(io);
} }
else else
...@@ -573,7 +603,7 @@ double CpuCalcNonbondedForceKernel::execute(ContextImpl& context, bool includeFo ...@@ -573,7 +603,7 @@ double CpuCalcNonbondedForceKernel::execute(ContextImpl& context, bool includeFo
ReferenceLJCoulomb14 nonbonded14; ReferenceLJCoulomb14 nonbonded14;
refBondForce.calculateForce(num14, bonded14IndexArray, posData, bonded14ParamArray, forceData, includeEnergy ? &energy : NULL, nonbonded14); refBondForce.calculateForce(num14, bonded14IndexArray, posData, bonded14ParamArray, forceData, includeEnergy ? &energy : NULL, nonbonded14);
if (data.isPeriodic) if (data.isPeriodic)
energy += dispersionCoefficient/(boxSize[0]*boxSize[1]*boxSize[2]); energy += dispersionCoefficient/(boxVectors[0][0]*boxVectors[1][1]*boxVectors[2][2]);
} }
return energy; return energy;
} }
...@@ -727,19 +757,18 @@ void CpuCalcCustomNonbondedForceKernel::initialize(const System& system, const C ...@@ -727,19 +757,18 @@ void CpuCalcCustomNonbondedForceKernel::initialize(const System& system, const C
double CpuCalcCustomNonbondedForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) { double CpuCalcCustomNonbondedForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
vector<RealVec>& posData = extractPositions(context); vector<RealVec>& posData = extractPositions(context);
vector<RealVec>& forceData = extractForces(context); vector<RealVec>& forceData = extractForces(context);
RealVec& box = extractBoxSize(context); RealVec* boxVectors = extractBoxVectors(context);
float floatBoxSize[3] = {(float) box[0], (float) box[1], (float) box[2]};
double energy = 0; double energy = 0;
bool periodic = (nonbondedMethod == CutoffPeriodic); bool periodic = (nonbondedMethod == CutoffPeriodic);
if (nonbondedMethod != NoCutoff) { 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); nonbonded->setUseCutoff(nonbondedCutoff, *neighborList);
} }
if (periodic) { if (periodic) {
double minAllowedSize = 2*nonbondedCutoff; 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."); throw OpenMMException("The periodic box size has decreased to less than twice the nonbonded cutoff.");
nonbonded->setPeriodic(box); nonbonded->setPeriodic(boxVectors);
} }
bool globalParamsChanged = false; bool globalParamsChanged = false;
for (int i = 0; i < (int) globalParameterNames.size(); i++) { for (int i = 0; i < (int) globalParameterNames.size(); i++) {
...@@ -758,7 +787,7 @@ double CpuCalcCustomNonbondedForceKernel::execute(ContextImpl& context, bool inc ...@@ -758,7 +787,7 @@ double CpuCalcCustomNonbondedForceKernel::execute(ContextImpl& context, bool inc
longRangeCoefficient = CustomNonbondedForceImpl::calcLongRangeCorrection(*forceCopy, context.getOwner()); longRangeCoefficient = CustomNonbondedForceImpl::calcLongRangeCorrection(*forceCopy, context.getOwner());
hasInitializedLongRangeCorrection = true; hasInitializedLongRangeCorrection = true;
} }
energy += longRangeCoefficient/(box[0]*box[1]*box[2]); energy += longRangeCoefficient/(boxVectors[0][0]*boxVectors[1][1]*boxVectors[2][2]);
return energy; return energy;
} }
...@@ -802,6 +831,7 @@ void CpuCalcGBSAOBCForceKernel::initialize(const System& system, const GBSAOBCFo ...@@ -802,6 +831,7 @@ void CpuCalcGBSAOBCForceKernel::initialize(const System& system, const GBSAOBCFo
obc.setParticleParameters(particleParams); obc.setParticleParameters(particleParams);
obc.setSolventDielectric((float) force.getSolventDielectric()); obc.setSolventDielectric((float) force.getSolventDielectric());
obc.setSoluteDielectric((float) force.getSoluteDielectric()); obc.setSoluteDielectric((float) force.getSoluteDielectric());
obc.setSurfaceAreaEnergy((float) force.getSurfaceAreaEnergy());
if (force.getNonbondedMethod() != GBSAOBCForce::NoCutoff) if (force.getNonbondedMethod() != GBSAOBCForce::NoCutoff)
obc.setUseCutoff((float) force.getCutoffDistance()); obc.setUseCutoff((float) force.getCutoffDistance());
data.isPeriodic = (force.getNonbondedMethod() == GBSAOBCForce::CutoffPeriodic); data.isPeriodic = (force.getNonbondedMethod() == GBSAOBCForce::CutoffPeriodic);
...@@ -835,6 +865,167 @@ void CpuCalcGBSAOBCForceKernel::copyParametersToContext(ContextImpl& context, co ...@@ -835,6 +865,167 @@ void CpuCalcGBSAOBCForceKernel::copyParametersToContext(ContextImpl& context, co
obc.setParticleParameters(particleParams); obc.setParticleParameters(particleParams);
} }
CpuCalcCustomGBForceKernel::~CpuCalcCustomGBForceKernel() {
if (particleParamArray != NULL) {
for (int i = 0; i < numParticles; i++)
delete[] particleParamArray[i];
delete[] particleParamArray;
}
if (neighborList != NULL)
delete neighborList;
if (ixn != NULL)
delete ixn;
}
void CpuCalcCustomGBForceKernel::initialize(const System& system, const CustomGBForce& force) {
if (force.getNumComputedValues() > 0) {
string name, expression;
CustomGBForce::ComputationType type;
force.getComputedValueParameters(0, name, expression, type);
if (type == CustomGBForce::SingleParticle)
throw OpenMMException("CpuPlatform requires that the first computed value for a CustomGBForce be of type ParticlePair or ParticlePairNoExclusions.");
for (int i = 1; i < force.getNumComputedValues(); i++) {
force.getComputedValueParameters(i, name, expression, type);
if (type != CustomGBForce::SingleParticle)
throw OpenMMException("CpuPlatform requires that a CustomGBForce only have one computed value of type ParticlePair or ParticlePairNoExclusions.");
}
}
// Record the exclusions.
numParticles = force.getNumParticles();
exclusions.resize(numParticles);
for (int i = 0; i < force.getNumExclusions(); i++) {
int particle1, particle2;
force.getExclusionParticles(i, particle1, particle2);
exclusions[particle1].insert(particle2);
exclusions[particle2].insert(particle1);
}
// Build the arrays.
int numPerParticleParameters = force.getNumPerParticleParameters();
particleParamArray = new double*[numParticles];
for (int i = 0; i < numParticles; i++)
particleParamArray[i] = new double[numPerParticleParameters];
for (int i = 0; i < numParticles; ++i) {
vector<double> parameters;
force.getParticleParameters(i, parameters);
for (int j = 0; j < numPerParticleParameters; j++)
particleParamArray[i][j] = static_cast<RealOpenMM>(parameters[j]);
}
for (int i = 0; i < numPerParticleParameters; i++)
particleParameterNames.push_back(force.getPerParticleParameterName(i));
for (int i = 0; i < force.getNumGlobalParameters(); i++)
globalParameterNames.push_back(force.getGlobalParameterName(i));
nonbondedMethod = CalcCustomGBForceKernel::NonbondedMethod(force.getNonbondedMethod());
nonbondedCutoff = (RealOpenMM) force.getCutoffDistance();
if (nonbondedMethod == NoCutoff)
neighborList = NULL;
else
neighborList = new CpuNeighborList(4);
// Create custom functions for the tabulated functions.
map<string, Lepton::CustomFunction*> functions;
for (int i = 0; i < force.getNumFunctions(); i++)
functions[force.getTabulatedFunctionName(i)] = createReferenceTabulatedFunction(force.getTabulatedFunction(i));
// Parse the expressions for computed values.
vector<vector<Lepton::CompiledExpression> > valueDerivExpressions(force.getNumComputedValues());
vector<vector<Lepton::CompiledExpression> > valueGradientExpressions(force.getNumComputedValues());
vector<Lepton::CompiledExpression> valueExpressions;
vector<Lepton::CompiledExpression> energyExpressions;
for (int i = 0; i < force.getNumComputedValues(); i++) {
string name, expression;
CustomGBForce::ComputationType type;
force.getComputedValueParameters(i, name, expression, type);
Lepton::ParsedExpression ex = Lepton::Parser::parse(expression, functions).optimize();
valueExpressions.push_back(ex.createCompiledExpression());
valueTypes.push_back(type);
valueNames.push_back(name);
if (i == 0)
valueDerivExpressions[i].push_back(ex.differentiate("r").createCompiledExpression());
else {
valueGradientExpressions[i].push_back(ex.differentiate("x").createCompiledExpression());
valueGradientExpressions[i].push_back(ex.differentiate("y").createCompiledExpression());
valueGradientExpressions[i].push_back(ex.differentiate("z").createCompiledExpression());
for (int j = 0; j < i; j++)
valueDerivExpressions[i].push_back(ex.differentiate(valueNames[j]).createCompiledExpression());
}
}
// Parse the expressions for energy terms.
vector<vector<Lepton::CompiledExpression> > energyDerivExpressions(force.getNumEnergyTerms());
vector<vector<Lepton::CompiledExpression> > energyGradientExpressions(force.getNumEnergyTerms());
for (int i = 0; i < force.getNumEnergyTerms(); i++) {
string expression;
CustomGBForce::ComputationType type;
force.getEnergyTermParameters(i, expression, type);
Lepton::ParsedExpression ex = Lepton::Parser::parse(expression, functions).optimize();
energyExpressions.push_back(ex.createCompiledExpression());
energyTypes.push_back(type);
if (type != CustomGBForce::SingleParticle)
energyDerivExpressions[i].push_back(ex.differentiate("r").createCompiledExpression());
for (int j = 0; j < force.getNumComputedValues(); j++) {
if (type == CustomGBForce::SingleParticle) {
energyDerivExpressions[i].push_back(ex.differentiate(valueNames[j]).createCompiledExpression());
energyGradientExpressions[i].push_back(ex.differentiate("x").createCompiledExpression());
energyGradientExpressions[i].push_back(ex.differentiate("y").createCompiledExpression());
energyGradientExpressions[i].push_back(ex.differentiate("z").createCompiledExpression());
}
else {
energyDerivExpressions[i].push_back(ex.differentiate(valueNames[j]+"1").createCompiledExpression());
energyDerivExpressions[i].push_back(ex.differentiate(valueNames[j]+"2").createCompiledExpression());
}
}
}
// Delete the custom functions.
for (map<string, Lepton::CustomFunction*>::iterator iter = functions.begin(); iter != functions.end(); iter++)
delete iter->second;
ixn = new CpuCustomGBForce(numParticles, exclusions, valueExpressions, valueDerivExpressions, valueGradientExpressions, valueNames, valueTypes, energyExpressions,
energyDerivExpressions, energyGradientExpressions, energyTypes, particleParameterNames, data.threads);
data.isPeriodic = (force.getNonbondedMethod() == CustomGBForce::CutoffPeriodic);
}
double CpuCalcCustomGBForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
vector<RealVec>& forceData = extractForces(context);
RealOpenMM energy = 0;
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, boxVectors, data.isPeriodic, nonbondedCutoff, data.threads);
ixn->setUseCutoff(nonbondedCutoff, *neighborList);
}
map<string, double> globalParameters;
for (int i = 0; i < (int) globalParameterNames.size(); i++)
globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
ixn->calculateIxn(numParticles, &data.posq[0], particleParamArray, globalParameters, data.threadForce, includeForces, includeEnergy, energy);
return energy;
}
void CpuCalcCustomGBForceKernel::copyParametersToContext(ContextImpl& context, const CustomGBForce& force) {
if (numParticles != force.getNumParticles())
throw OpenMMException("updateParametersInContext: The number of particles has changed");
// Record the values.
int numParameters = force.getNumPerParticleParameters();
vector<double> params;
for (int i = 0; i < numParticles; ++i) {
vector<double> parameters;
force.getParticleParameters(i, parameters);
for (int j = 0; j < numParameters; j++)
particleParamArray[i][j] = static_cast<RealOpenMM>(parameters[j]);
}
}
CpuCalcCustomManyParticleForceKernel::~CpuCalcCustomManyParticleForceKernel() { CpuCalcCustomManyParticleForceKernel::~CpuCalcCustomManyParticleForceKernel() {
if (particleParamArray != NULL) { if (particleParamArray != NULL) {
for (int i = 0; i < numParticles; i++) for (int i = 0; i < numParticles; i++)
...@@ -866,6 +1057,7 @@ void CpuCalcCustomManyParticleForceKernel::initialize(const System& system, cons ...@@ -866,6 +1057,7 @@ void CpuCalcCustomManyParticleForceKernel::initialize(const System& system, cons
ixn = new CpuCustomManyParticleForce(force, data.threads); ixn = new CpuCustomManyParticleForce(force, data.threads);
nonbondedMethod = CalcCustomManyParticleForceKernel::NonbondedMethod(force.getNonbondedMethod()); nonbondedMethod = CalcCustomManyParticleForceKernel::NonbondedMethod(force.getNonbondedMethod());
cutoffDistance = force.getCutoffDistance(); cutoffDistance = force.getCutoffDistance();
data.isPeriodic = (nonbondedMethod == CutoffPeriodic);
} }
double CpuCalcCustomManyParticleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) { double CpuCalcCustomManyParticleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
...@@ -873,11 +1065,11 @@ double CpuCalcCustomManyParticleForceKernel::execute(ContextImpl& context, bool ...@@ -873,11 +1065,11 @@ double CpuCalcCustomManyParticleForceKernel::execute(ContextImpl& context, bool
for (int i = 0; i < (int) globalParameterNames.size(); i++) for (int i = 0; i < (int) globalParameterNames.size(); i++)
globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]); globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
if (nonbondedMethod == CutoffPeriodic) { if (nonbondedMethod == CutoffPeriodic) {
RealVec& box = extractBoxSize(context); RealVec* boxVectors = extractBoxVectors(context);
double minAllowedSize = 2*cutoffDistance; 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."); throw OpenMMException("The periodic box size has decreased to less than twice the nonbonded cutoff.");
ixn->setPeriodic(box); ixn->setPeriodic(boxVectors);
} }
double energy = 0; double energy = 0;
ixn->calculateIxn(data.posq, particleParamArray, globalParameters, data.threadForce, includeForces, includeEnergy, energy); ixn->calculateIxn(data.posq, particleParamArray, globalParameters, data.threadForce, includeForces, includeEnergy, energy);
......
platforms/cpu/src/CpuLangevinDynamics.cpp
View file @ 61d5cc0f
...@@ -23,8 +23,6 @@ ...@@ -23,8 +23,6 @@
* WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. * WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/ */
#include "SimTKOpenMMCommon.h"
#include "SimTKOpenMMLog.h"
#include "SimTKOpenMMUtilities.h" #include "SimTKOpenMMUtilities.h"
#include "CpuLangevinDynamics.h" #include "CpuLangevinDynamics.h"
......
platforms/cpu/src/CpuNeighborList.cpp
View file @ 61d5cc0f
...@@ -6,7 +6,7 @@ ...@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * 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 * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -45,12 +45,12 @@ namespace OpenMM { ...@@ -45,12 +45,12 @@ namespace OpenMM {
class VoxelIndex class VoxelIndex
{ {
public: public:
VoxelIndex() : x(0), y(0) { VoxelIndex() : y(0), z(0) {
} }
VoxelIndex(int x, int y) : x(x), y(y) { VoxelIndex(int y, int z) : y(y), z(z) {
} }
int x;
int y; int y;
int z;
}; };
/** /**
...@@ -59,26 +59,35 @@ public: ...@@ -59,26 +59,35 @@ public:
*/ */
class CpuNeighborList::Voxels { class CpuNeighborList::Voxels {
public: public:
Voxels(int blockSize, float vsx, float vsy, float minx, float maxx, float miny, float maxy, const float* periodicBoxSize, bool usePeriodic) : Voxels(int blockSize, float vsy, float vsz, float miny, float maxy, float minz, float maxz, const RealVec* periodicBoxVectors, bool usePeriodic) :
blockSize(blockSize), voxelSizeX(vsx), voxelSizeY(vsy), minx(minx), maxx(maxx), miny(miny), maxy(maxy), periodicBoxSize(periodicBoxSize), usePeriodic(usePeriodic) { blockSize(blockSize), voxelSizeY(vsy), voxelSizeZ(vsz), miny(miny), maxy(maxy), minz(minz), maxz(maxz), periodicBoxVectors(periodicBoxVectors), usePeriodic(usePeriodic) {
periodicBoxSize[0] = (float) periodicBoxVectors[0][0];
periodicBoxSize[1] = (float) periodicBoxVectors[1][1];
periodicBoxSize[2] = (float) periodicBoxVectors[2][2];
recipBoxSize[0] = (float) (1/periodicBoxVectors[0][0]);
recipBoxSize[1] = (float) (1/periodicBoxVectors[1][1]);
recipBoxSize[2] = (float) (1/periodicBoxVectors[2][2]);
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);
if (usePeriodic) { if (usePeriodic) {
nx = (int) floorf(periodicBoxSize[0]/voxelSizeX+0.5f); ny = (int) floorf(periodicBoxVectors[1][1]/voxelSizeY+0.5f);
ny = (int) floorf(periodicBoxSize[1]/voxelSizeY+0.5f); nz = (int) floorf(periodicBoxVectors[2][2]/voxelSizeZ+0.5f);
voxelSizeX = periodicBoxSize[0]/nx; voxelSizeY = periodicBoxVectors[1][1]/ny;
voxelSizeY = periodicBoxSize[1]/ny; voxelSizeZ = periodicBoxVectors[2][2]/nz;
} }
else { else {
nx = max(1, (int) floorf((maxx-minx)/voxelSizeX+0.5f));
ny = max(1, (int) floorf((maxy-miny)/voxelSizeY+0.5f)); ny = max(1, (int) floorf((maxy-miny)/voxelSizeY+0.5f));
if (maxx > minx) nz = max(1, (int) floorf((maxz-minz)/voxelSizeZ+0.5f));
voxelSizeX = (maxx-minx)/nx;
if (maxy > miny) if (maxy > miny)
voxelSizeY = (maxy-miny)/ny; voxelSizeY = (maxy-miny)/ny;
if (maxz > minz)
voxelSizeZ = (maxz-minz)/nz;
} }
bins.resize(nx); bins.resize(ny);
for (int i = 0; i < nx; i++) { for (int i = 0; i < ny; i++) {
bins[i].resize(ny); bins[i].resize(nz);
for (int j = 0; j < ny; j++) for (int j = 0; j < nz; j++)
bins[i][j].resize(0); bins[i][j].resize(0);
} }
} }
...@@ -88,28 +97,28 @@ public: ...@@ -88,28 +97,28 @@ public:
*/ */
void insert(const int& atom, const float* location) { void insert(const int& atom, const float* location) {
VoxelIndex voxelIndex = getVoxelIndex(location); VoxelIndex voxelIndex = getVoxelIndex(location);
bins[voxelIndex.x][voxelIndex.y].push_back(make_pair(location[2], atom)); bins[voxelIndex.y][voxelIndex.z].push_back(make_pair(location[0], atom));
} }
/** /**
* Sort the particles in each voxel by z coordinate. * Sort the particles in each voxel by x coordinate.
*/ */
void sortItems() { void sortItems() {
for (int i = 0; i < nx; i++) for (int i = 0; i < ny; i++)
for (int j = 0; j < ny; j++) for (int j = 0; j < nz; j++)
sort(bins[i][j].begin(), bins[i][j].end()); sort(bins[i][j].begin(), bins[i][j].end());
} }
/** /**
* Find the index of the first particle in voxel (x,y) whose z coordinate in >= the specified value. * Find the index of the first particle in voxel (y,z) whose x coordinate in >= the specified value.
*/ */
int findLowerBound(int x, int y, double z) const { int findLowerBound(int y, int z, double x) const {
const vector<pair<float, int> >& bin = bins[x][y]; const vector<pair<float, int> >& bin = bins[y][z];
int lower = 0; int lower = 0;
int upper = bin.size(); int upper = bin.size();
while (lower < upper) { while (lower < upper) {
int middle = (lower+upper)/2; int middle = (lower+upper)/2;
if (bin[middle].first < z) if (bin[middle].first < x)
lower = middle+1; lower = middle+1;
else else
upper = middle; upper = middle;
...@@ -118,15 +127,15 @@ public: ...@@ -118,15 +127,15 @@ public:
} }
/** /**
* Find the index of the first particle in voxel (x,y) whose z coordinate in greater than the specified value. * Find the index of the first particle in voxel (y,z) whose x coordinate in greater than the specified value.
*/ */
int findUpperBound(int x, int y, double z) const { int findUpperBound(int y, int z, double x) const {
const vector<pair<float, int> >& bin = bins[x][y]; const vector<pair<float, int> >& bin = bins[y][z];
int lower = 0; int lower = 0;
int upper = bin.size(); int upper = bin.size();
while (lower < upper) { while (lower < upper) {
int middle = (lower+upper)/2; int middle = (lower+upper)/2;
if (bin[middle].first > z) if (bin[middle].first > x)
upper = middle; upper = middle;
else else
lower = middle+1; lower = middle+1;
...@@ -138,131 +147,167 @@ public: ...@@ -138,131 +147,167 @@ public:
* Get the voxel index containing a particular location. * Get the voxel index containing a particular location.
*/ */
VoxelIndex getVoxelIndex(const float* location) const { VoxelIndex getVoxelIndex(const float* location) const {
float xperiodic, yperiodic; float yperiodic, zperiodic;
if (!usePeriodic) { if (!usePeriodic) {
xperiodic = location[0]-minx;
yperiodic = location[1]-miny; yperiodic = location[1]-miny;
zperiodic = location[2]-minz;
} }
else { else {
xperiodic = location[0]-periodicBoxSize[0]*floorf(location[0]/periodicBoxSize[0]); float scale2 = floorf(location[2]*recipBoxSize[2]);
yperiodic = location[1]-periodicBoxSize[1]*floorf(location[1]/periodicBoxSize[1]); yperiodic = location[1]-periodicBoxVectors[2][1]*scale2;
zperiodic = location[2]-periodicBoxVectors[2][2]*scale2;
float scale1 = floorf(yperiodic*recipBoxSize[1]);
yperiodic -= periodicBoxVectors[1][0]*scale1;
} }
int x = min(nx-1, int(floorf(xperiodic / voxelSizeX)));
int y = min(ny-1, int(floorf(yperiodic / voxelSizeY))); int y = min(ny-1, int(floorf(yperiodic / voxelSizeY)));
int z = min(nz-1, int(floorf(zperiodic / voxelSizeZ)));
return VoxelIndex(x, y); 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); neighbors.resize(0);
exclusions.resize(0); exclusions.resize(0);
fvec4 boxSize(periodicBoxSize[0], periodicBoxSize[1], periodicBoxSize[2], 0); fvec4 boxSize(periodicBoxSize[0], periodicBoxSize[1], periodicBoxSize[2], 0);
fvec4 invBoxSize(1/periodicBoxSize[0], 1/periodicBoxSize[1], 1/periodicBoxSize[2], 0); fvec4 invBoxSize(recipBoxSize[0], recipBoxSize[1], recipBoxSize[2], 0);
fvec4 periodicBoxVec4[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);
float maxDistanceSquared = maxDistance * maxDistance; float maxDistanceSquared = maxDistance * maxDistance;
float refineCutoff = maxDistance-max(max(blockWidth[0], blockWidth[1]), blockWidth[2]); float refineCutoff = maxDistance-max(max(blockWidth[0], blockWidth[1]), blockWidth[2]);
float refineCutoffSquared = refineCutoff*refineCutoff; float refineCutoffSquared = refineCutoff*refineCutoff;
int dIndexX = int((maxDistance+blockWidth[0])/voxelSizeX)+1; // How may voxels away do we have to look? int dIndexY = int((maxDistance+blockWidth[1])/voxelSizeY)+1; // How may voxels away do we have to look?
int dIndexY = int((maxDistance+blockWidth[1])/voxelSizeY)+1; int dIndexZ = int((maxDistance+blockWidth[2])/voxelSizeZ)+1;
if (usePeriodic) { if (usePeriodic) {
dIndexX = min(nx/2, dIndexX);
dIndexY = min(ny/2, dIndexY); dIndexY = min(ny/2, dIndexY);
dIndexZ = min(nz/2, dIndexZ);
} }
float centerPos[4]; float centerPos[4];
blockCenter.store(centerPos); blockCenter.store(centerPos);
VoxelIndex centerVoxelIndex = getVoxelIndex(centerPos); VoxelIndex centerVoxelIndex = getVoxelIndex(centerPos);
int startx = centerVoxelIndex.x-dIndexX;
int starty = centerVoxelIndex.y-dIndexY; // Loop over voxels along the z axis.
int endx = centerVoxelIndex.x+dIndexX;
int endy = centerVoxelIndex.y+dIndexY; int startz = centerVoxelIndex.z-dIndexZ;
int numRanges; int endz = centerVoxelIndex.z+dIndexZ;
if (usePeriodic) { if (usePeriodic)
endx = min(endx, centerVoxelIndex.x-dIndexX+nx-1); endz = min(endz, startz+nz-1);
endy = min(endy, centerVoxelIndex.y-dIndexY+ny-1);
}
else { else {
startx = max(startx, 0); startz = max(startz, 0);
starty = max(starty, 0); endz = min(endz, nz-1);
endx = min(endx, nx-1);
endy = min(endy, ny-1);
} }
int lastSortedIndex = blockSize*(blockIndex+1); int lastSortedIndex = blockSize*(blockIndex+1);
VoxelIndex voxelIndex(0, 0); VoxelIndex voxelIndex(0, 0);
for (int x = startx; x <= endx; ++x) { for (int z = startz; z <= endz; ++z) {
voxelIndex.x = x; voxelIndex.z = z;
if (usePeriodic) if (usePeriodic)
voxelIndex.x = (x < 0 ? x+nx : (x >= nx ? x-nx : x)); voxelIndex.z = (z < 0 ? z+nz : (z >= nz ? z-nz : z));
// Loop over voxels along the y axis.
int boxz = (int) floor((float) z/nz);
int starty = centerVoxelIndex.y-dIndexY;
int endy = centerVoxelIndex.y+dIndexY;
float yoffset = (float) (usePeriodic ? boxz*periodicBoxVectors[2][1] : 0);
if (usePeriodic) {
starty -= (int) ceil(yoffset/voxelSizeY);
endy -= (int) floor(yoffset/voxelSizeY);
endy = min(endy, starty+ny-1);
}
else {
starty = max(starty, 0);
endy = min(endy, ny-1);
}
for (int y = starty; y <= endy; ++y) { for (int y = starty; y <= endy; ++y) {
voxelIndex.y = y; voxelIndex.y = y;
if (usePeriodic) if (usePeriodic)
voxelIndex.y = (y < 0 ? y+ny : (y >= ny ? y-ny : y)); voxelIndex.y = (y < 0 ? y+ny : (y >= ny ? y-ny : y));
int boxy = (int) floor((float) y/ny);
float xoffset = (float) (usePeriodic ? boxy*periodicBoxVectors[1][0]+boxz*periodicBoxVectors[2][0] : 0);
// Identify the range of atoms within this bin we need to search. When using periodic boundary // Identify the range of atoms within this bin we need to search. When using periodic boundary
// conditions, there may be two separate ranges. // conditions, there may be two separate ranges.
float minz = centerPos[2]; float minx = centerPos[0];
float maxz = centerPos[2]; float maxx = centerPos[0];
fvec4 offset(voxelSizeX*x+(usePeriodic ? 0.0f : minx), voxelSizeY*y+(usePeriodic ? 0.0f : miny), 0, 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++) { for (int k = 0; k < (int) blockAtoms.size(); k += 4) {
const float* atomPos = &atomLocations[4*blockAtoms[k]]; fvec4 dist2 = maxDistanceSquared;
fvec4 posVec(atomPos); if (y != atomVoxelIndex[k].y) {
fvec4 delta1 = offset-posVec; fvec4 dy1 = offset[1]-fvec4(&blockAtomY[k]);
fvec4 delta2 = delta1+fvec4(voxelSizeX, voxelSizeY, 0, 0); fvec4 dy2 = dy1+voxelSizeY;
if (usePeriodic) { if (usePeriodic) {
delta1 -= round(delta1*invBoxSize)*boxSize; dy1 -= round(dy1*invBoxSize[1])*boxSize[1];
delta2 -= round(delta2*invBoxSize)*boxSize; dy2 -= round(dy2*invBoxSize[1])*boxSize[1];
}
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 delta = min(abs(delta1), abs(delta2)); fvec4 dist = sqrt(dist2);
float dx = (x == atomVoxelIndex[k].x ? 0.0f : delta[0]); int numToCheck = min(4, (int) (blockAtoms.size()-k));
float dy = (y == atomVoxelIndex[k].y ? 0.0f : delta[1]); for (int m = 0; m < numToCheck; m++) {
float dist2 = maxDistanceSquared-dx*dx-dy*dy; minx = min(minx, blockAtomX[k+m]-dist[m]-xoffset);
if (dist2 > 0) { maxx = max(maxx, blockAtomX[k+m]+dist[m]-xoffset);
float dist = sqrtf(dist2);
minz = min(minz, atomPos[2]-dist);
maxz = max(maxz, atomPos[2]+dist);
} }
} }
if (minz == maxz) if (minx == maxx)
continue; continue;
bool needPeriodic = (centerPos[0]-blockWidth[0] < maxDistance || centerPos[0]+blockWidth[0] > periodicBoxSize[0]-maxDistance || bool needPeriodic = (centerPos[1]-blockWidth[1] < maxDistance || centerPos[1]+blockWidth[1] > periodicBoxSize[1]-maxDistance ||
centerPos[1]-blockWidth[1] < maxDistance || centerPos[1]+blockWidth[1] > periodicBoxSize[1]-maxDistance || centerPos[2]-blockWidth[2] < maxDistance || centerPos[2]+blockWidth[2] > periodicBoxSize[2]-maxDistance ||
minz < 0.0f || maxz > periodicBoxSize[2]); minx < 0.0f || maxx > periodicBoxVectors[0][0]);
int numRanges;
int rangeStart[2]; int rangeStart[2];
int rangeEnd[2]; int rangeEnd[2];
rangeStart[0] = findLowerBound(voxelIndex.x, voxelIndex.y, minz); rangeStart[0] = findLowerBound(voxelIndex.y, voxelIndex.z, minx);
if (needPeriodic) { if (needPeriodic) {
numRanges = 2; numRanges = 2;
rangeEnd[0] = findUpperBound(voxelIndex.x, voxelIndex.y, maxz); rangeEnd[0] = findUpperBound(voxelIndex.y, voxelIndex.z, maxx);
if (rangeStart[0] > 0) { if (rangeStart[0] > 0) {
rangeStart[1] = 0; rangeStart[1] = 0;
rangeEnd[1] = min(findUpperBound(voxelIndex.x, voxelIndex.y, maxz-periodicBoxSize[2]), rangeStart[0]); rangeEnd[1] = min(findUpperBound(voxelIndex.y, voxelIndex.z, maxx-periodicBoxSize[0]), rangeStart[0]);
} }
else { else {
rangeStart[1] = max(findLowerBound(voxelIndex.x, voxelIndex.y, minz+periodicBoxSize[2]), rangeEnd[0]); rangeStart[1] = max(findLowerBound(voxelIndex.y, voxelIndex.z, minx+periodicBoxSize[0]), rangeEnd[0]);
rangeEnd[1] = bins[voxelIndex.x][voxelIndex.y].size(); rangeEnd[1] = bins[voxelIndex.y][voxelIndex.z].size();
} }
} }
else { else {
numRanges = 1; numRanges = 1;
rangeEnd[0] = findUpperBound(voxelIndex.x, voxelIndex.y, maxz); rangeEnd[0] = findUpperBound(voxelIndex.y, voxelIndex.z, maxx);
} }
bool periodicRectangular = (needPeriodic && !triclinic);
// Loop over atoms and check to see if they are neighbors of this block. // Loop over atoms and check to see if they are neighbors of this block.
for (int range = 0; range < numRanges; range++) { for (int range = 0; range < numRanges; range++) {
for (int item = rangeStart[range]; item < rangeEnd[range]; item++) { for (int item = rangeStart[range]; item < rangeEnd[range]; item++) {
const int sortedIndex = bins[voxelIndex.x][voxelIndex.y][item].second; const int sortedIndex = bins[voxelIndex.y][voxelIndex.z][item].second;
// Avoid duplicate entries. // Avoid duplicate entries.
if (sortedIndex >= lastSortedIndex) if (sortedIndex >= lastSortedIndex)
continue; continue;
fvec4 atomPos(atomLocations+4*sortedAtoms[sortedIndex]); fvec4 atomPos(&sortedPositions[4*sortedIndex]);
fvec4 delta = atomPos-centerPos; fvec4 delta = atomPos-centerPos;
if (needPeriodic) { if (periodicRectangular)
fvec4 base = round(delta*invBoxSize)*boxSize; delta -= round(delta*invBoxSize)*boxSize;
delta = delta-base; 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);
} }
delta = max(0.0f, abs(delta)-blockWidth); delta = max(0.0f, abs(delta)-blockWidth);
float dSquared = dot3(delta, delta); float dSquared = dot3(delta, delta);
...@@ -273,21 +318,34 @@ public: ...@@ -273,21 +318,34 @@ public:
// The distance is large enough that there might not be any actual interactions. // The distance is large enough that there might not be any actual interactions.
// Check individual atom pairs to be sure. // Check individual atom pairs to be sure.
bool any = false; bool anyInteraction = false;
for (int k = 0; k < (int) blockAtoms.size(); k++) { for (int k = 0; k < (int) blockAtoms.size(); k += 4) {
fvec4 pos1(&atomLocations[4*blockAtoms[k]]); fvec4 dx = fvec4(&blockAtomX[k])-atomPos[0];
delta = atomPos-pos1; fvec4 dy = fvec4(&blockAtomY[k])-atomPos[1];
if (needPeriodic) { fvec4 dz = fvec4(&blockAtomZ[k])-atomPos[2];
fvec4 base = round(delta*invBoxSize)*boxSize; if (periodicRectangular) {
delta = delta-base; dx -= round(dx*invBoxSize[0])*boxSize[0];
dy -= round(dy*invBoxSize[1])*boxSize[1];
dz -= round(dz*invBoxSize[2])*boxSize[2];
} }
float r2 = dot3(delta, delta); else if (needPeriodic) {
if (r2 < maxDistanceSquared) { fvec4 scale3 = floor(dz*recipBoxSize[2]+0.5f);
any = true; 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; break;
} }
} }
if (!any) if (!anyInteraction)
continue; continue;
} }
...@@ -308,10 +366,12 @@ public: ...@@ -308,10 +366,12 @@ public:
private: private:
int blockSize; int blockSize;
float voxelSizeX, voxelSizeY; float voxelSizeY, voxelSizeZ;
float minx, maxx, miny, maxy; float miny, maxy, minz, maxz;
int nx, ny; int ny, nz;
const float* periodicBoxSize; float periodicBoxSize[3], recipBoxSize[3];
bool triclinic;
const RealVec* periodicBoxVectors;
const bool usePeriodic; const bool usePeriodic;
vector<vector<vector<pair<float, int> > > > bins; vector<vector<vector<pair<float, int> > > > bins;
}; };
...@@ -330,17 +390,20 @@ CpuNeighborList::CpuNeighborList(int blockSize) : blockSize(blockSize) { ...@@ -330,17 +390,20 @@ CpuNeighborList::CpuNeighborList(int blockSize) : blockSize(blockSize) {
} }
void CpuNeighborList::computeNeighborList(int numAtoms, const AlignedArray<float>& atomLocations, const vector<set<int> >& exclusions, void CpuNeighborList::computeNeighborList(int numAtoms, const AlignedArray<float>& atomLocations, const vector<set<int> >& exclusions,
const float* periodicBoxSize, bool usePeriodic, float maxDistance, ThreadPool& threads) { const RealVec* periodicBoxVectors, bool usePeriodic, float maxDistance, ThreadPool& threads) {
int numBlocks = (numAtoms+blockSize-1)/blockSize; int numBlocks = (numAtoms+blockSize-1)/blockSize;
blockNeighbors.resize(numBlocks); blockNeighbors.resize(numBlocks);
blockExclusions.resize(numBlocks); blockExclusions.resize(numBlocks);
sortedAtoms.resize(numAtoms); sortedAtoms.resize(numAtoms);
sortedPositions.resize(4*numAtoms);
// Record the parameters for the threads. // Record the parameters for the threads.
this->exclusions = &exclusions; this->exclusions = &exclusions;
this->atomLocations = &atomLocations[0]; this->atomLocations = &atomLocations[0];
this->periodicBoxSize = periodicBoxSize; this->periodicBoxVectors[0] = periodicBoxVectors[0];
this->periodicBoxVectors[1] = periodicBoxVectors[1];
this->periodicBoxVectors[2] = periodicBoxVectors[2];
this->numAtoms = numAtoms; this->numAtoms = numAtoms;
this->usePeriodic = usePeriodic; this->usePeriodic = usePeriodic;
this->maxDistance = maxDistance; this->maxDistance = maxDistance;
...@@ -370,23 +433,25 @@ void CpuNeighborList::computeNeighborList(int numAtoms, const AlignedArray<float ...@@ -370,23 +433,25 @@ void CpuNeighborList::computeNeighborList(int numAtoms, const AlignedArray<float
sort(atomBins.begin(), atomBins.end()); sort(atomBins.begin(), atomBins.end());
// Build the voxel hash. // Build the voxel hash.
float edgeSizeX, edgeSizeY; float edgeSizeY, edgeSizeZ;
if (!usePeriodic) if (!usePeriodic)
edgeSizeX = edgeSizeY = maxDistance; // TODO - adjust this as needed edgeSizeY = edgeSizeZ = maxDistance; // TODO - adjust this as needed
else { else {
edgeSizeX = 0.6f*periodicBoxSize[0]/floorf(periodicBoxSize[0]/maxDistance); edgeSizeY = 0.6f*periodicBoxVectors[1][1]/floorf(periodicBoxVectors[1][1]/maxDistance);
edgeSizeY = 0.6f*periodicBoxSize[1]/floorf(periodicBoxSize[1]/maxDistance); edgeSizeZ = 0.6f*periodicBoxVectors[2][2]/floorf(periodicBoxVectors[2][2]/maxDistance);
} }
Voxels voxels(blockSize, edgeSizeX, edgeSizeY, minx, maxx, miny, maxy, periodicBoxSize, usePeriodic); Voxels voxels(blockSize, edgeSizeY, edgeSizeZ, miny, maxy, minz, maxz, periodicBoxVectors, usePeriodic);
for (int i = 0; i < numAtoms; i++) { for (int i = 0; i < numAtoms; i++) {
int atomIndex = atomBins[i].second; int atomIndex = atomBins[i].second;
sortedAtoms[i] = atomIndex; sortedAtoms[i] = atomIndex;
fvec4 atomPos(&atomLocations[4*atomIndex]);
atomPos.store(&sortedPositions[4*i]);
voxels.insert(i, &atomLocations[4*atomIndex]); voxels.insert(i, &atomLocations[4*atomIndex]);
} }
voxels.sortItems(); voxels.sortItems();
this->voxels = &voxels; this->voxels = &voxels;
// Signal the threads to start running and wait for them to finish. // Signal the threads to start running and wait for them to finish.
threads.resumeThreads(); threads.resumeThreads();
...@@ -443,6 +508,7 @@ void CpuNeighborList::threadComputeNeighborList(ThreadPool& threads, int threadI ...@@ -443,6 +508,7 @@ void CpuNeighborList::threadComputeNeighborList(ThreadPool& threads, int threadI
int numBlocks = blockNeighbors.size(); int numBlocks = blockNeighbors.size();
vector<int> blockAtoms; vector<int> blockAtoms;
vector<float> blockAtomX(blockSize), blockAtomY(blockSize), blockAtomZ(blockSize);
vector<VoxelIndex> atomVoxelIndex; vector<VoxelIndex> atomVoxelIndex;
for (int i = threadIndex; i < numBlocks; i += numThreads) { for (int i = threadIndex; i < numBlocks; i += numThreads) {
// Find the atoms in this block and compute their bounding box. // Find the atoms in this block and compute their bounding box.
...@@ -455,14 +521,24 @@ void CpuNeighborList::threadComputeNeighborList(ThreadPool& threads, int threadI ...@@ -455,14 +521,24 @@ void CpuNeighborList::threadComputeNeighborList(ThreadPool& threads, int threadI
blockAtoms[j] = sortedAtoms[firstIndex+j]; blockAtoms[j] = sortedAtoms[firstIndex+j];
atomVoxelIndex[j] = voxels->getVoxelIndex(&atomLocations[4*blockAtoms[j]]); atomVoxelIndex[j] = voxels->getVoxelIndex(&atomLocations[4*blockAtoms[j]]);
} }
fvec4 minPos(&atomLocations[4*sortedAtoms[firstIndex]]); fvec4 minPos(&sortedPositions[4*firstIndex]);
fvec4 maxPos = minPos; fvec4 maxPos = minPos;
for (int j = 1; j < atomsInBlock; j++) { for (int j = 1; j < atomsInBlock; j++) {
fvec4 pos(&atomLocations[4*sortedAtoms[firstIndex+j]]); fvec4 pos(&sortedPositions[4*(firstIndex+j)]);
minPos = min(minPos, pos); minPos = min(minPos, pos);
maxPos = max(maxPos, 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. // Record the exclusions for this block.
......
platforms/cpu/src/CpuNonbondedForce.cpp
View file @ 61d5cc0f
...@@ -24,7 +24,6 @@ ...@@ -24,7 +24,6 @@
#include <complex> #include <complex>
#include "SimTKOpenMMCommon.h"
#include "SimTKOpenMMUtilities.h" #include "SimTKOpenMMUtilities.h"
#include "CpuNonbondedForce.h" #include "CpuNonbondedForce.h"
#include "ReferenceForce.h" #include "ReferenceForce.h"
...@@ -103,20 +102,30 @@ void CpuNonbondedForce::setUseSwitchingFunction(float distance) { ...@@ -103,20 +102,30 @@ void CpuNonbondedForce::setUseSwitchingFunction(float distance) {
also been set, and the smallest side of the periodic box is at least twice the cutoff also been set, and the smallest side of the periodic box is at least twice the cutoff
distance. distance.
@param boxSize the X, Y, and Z widths of the periodic box @param periodicBoxVectors the vectors defining the periodic box
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void CpuNonbondedForce::setPeriodic(float* periodicBoxSize) { void CpuNonbondedForce::setPeriodic(RealVec* periodicBoxVectors) {
assert(cutoff); assert(cutoff);
assert(periodicBoxSize[0] >= 2*cutoffDistance); assert(periodicBoxVectors[0][0] >= 2.0*cutoffDistance);
assert(periodicBoxSize[1] >= 2*cutoffDistance); assert(periodicBoxVectors[1][1] >= 2.0*cutoffDistance);
assert(periodicBoxSize[2] >= 2*cutoffDistance); assert(periodicBoxVectors[2][2] >= 2.0*cutoffDistance);
periodic = true; periodic = true;
this->periodicBoxSize[0] = periodicBoxSize[0]; this->periodicBoxVectors[0] = periodicBoxVectors[0];
this->periodicBoxSize[1] = periodicBoxSize[1]; this->periodicBoxVectors[1] = periodicBoxVectors[1];
this->periodicBoxSize[2] = periodicBoxSize[2]; 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);
} }
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -186,18 +195,16 @@ void CpuNonbondedForce::calculateReciprocalIxn(int numberOfAtoms, float* posq, c ...@@ -186,18 +195,16 @@ void CpuNonbondedForce::calculateReciprocalIxn(int numberOfAtoms, float* posq, c
int kmax = (ewald ? max(numRx, max(numRy,numRz)) : 0); int kmax = (ewald ? max(numRx, max(numRy,numRz)) : 0);
float factorEwald = -1 / (4*alphaEwald*alphaEwald); float factorEwald = -1 / (4*alphaEwald*alphaEwald);
float TWO_PI = 2.0 * PI_M; float TWO_PI = 2.0 * PI_M;
float recipCoeff = (float)(ONE_4PI_EPS0*4*PI_M/(periodicBoxSize[0] * periodicBoxSize[1] * periodicBoxSize[2]) /epsilon); float recipCoeff = (float)(ONE_4PI_EPS0*4*PI_M/(periodicBoxVectors[0][0] * periodicBoxVectors[1][1] * periodicBoxVectors[2][2]) /epsilon);
if (pme) { if (pme) {
pme_t pmedata; pme_t pmedata;
RealOpenMM virial[3][3];
pme_init(&pmedata, alphaEwald, numberOfAtoms, meshDim, 5, 1); pme_init(&pmedata, alphaEwald, numberOfAtoms, meshDim, 5, 1);
vector<RealOpenMM> charges(numberOfAtoms); vector<RealOpenMM> charges(numberOfAtoms);
for (int i = 0; i < numberOfAtoms; i++) for (int i = 0; i < numberOfAtoms; i++)
charges[i] = posq[4*i+3]; charges[i] = posq[4*i+3];
RealOpenMM boxSize[3] = {periodicBoxSize[0], periodicBoxSize[1], periodicBoxSize[2]};
RealOpenMM recipEnergy = 0.0; RealOpenMM recipEnergy = 0.0;
pme_exec(pmedata, atomCoordinates, forces, charges, boxSize, &recipEnergy, virial); pme_exec(pmedata, atomCoordinates, forces, charges, periodicBoxVectors, &recipEnergy);
if (totalEnergy) if (totalEnergy)
*totalEnergy += recipEnergy; *totalEnergy += recipEnergy;
pme_destroy(pmedata); pme_destroy(pmedata);
...@@ -209,7 +216,7 @@ void CpuNonbondedForce::calculateReciprocalIxn(int numberOfAtoms, float* posq, c ...@@ -209,7 +216,7 @@ void CpuNonbondedForce::calculateReciprocalIxn(int numberOfAtoms, float* posq, c
// setup reciprocal box // setup reciprocal box
float recipBoxSize[3] = { TWO_PI / periodicBoxSize[0], TWO_PI / periodicBoxSize[1], TWO_PI / periodicBoxSize[2]}; float recipBoxSize[3] = {(float) (TWO_PI/periodicBoxVectors[0][0]), (float) (TWO_PI/periodicBoxVectors[1][1]), (float) (TWO_PI/periodicBoxVectors[2][2])};
// setup K-vectors // setup K-vectors
...@@ -330,8 +337,8 @@ void CpuNonbondedForce::threadComputeDirect(ThreadPool& threads, int threadIndex ...@@ -330,8 +337,8 @@ void CpuNonbondedForce::threadComputeDirect(ThreadPool& threads, int threadIndex
threadEnergy[threadIndex] = 0; threadEnergy[threadIndex] = 0;
double* energyPtr = (includeEnergy ? &threadEnergy[threadIndex] : NULL); double* energyPtr = (includeEnergy ? &threadEnergy[threadIndex] : NULL);
float* forces = &(*threadForce)[threadIndex][0]; float* forces = &(*threadForce)[threadIndex][0];
fvec4 boxSize(periodicBoxSize[0], periodicBoxSize[1], periodicBoxSize[2], 0); fvec4 boxSize(periodicBoxVectors[0][0], periodicBoxVectors[1][1], periodicBoxVectors[2][2], 0);
fvec4 invBoxSize((1/periodicBoxSize[0]), (1/periodicBoxSize[1]), (1/periodicBoxSize[2]), 0); fvec4 invBoxSize(recipBoxSize[0], recipBoxSize[1], recipBoxSize[2], 0);
if (ewald || pme) { if (ewald || pme) {
// Compute the interactions from the neighbor list. // Compute the interactions from the neighbor list.
...@@ -344,8 +351,6 @@ void CpuNonbondedForce::threadComputeDirect(ThreadPool& threads, int threadIndex ...@@ -344,8 +351,6 @@ void CpuNonbondedForce::threadComputeDirect(ThreadPool& threads, int threadIndex
// Now subtract off the exclusions, since they were implicitly included in the reciprocal space sum. // Now subtract off the exclusions, since they were implicitly included in the reciprocal space sum.
fvec4 boxSize(periodicBoxSize[0], periodicBoxSize[1], periodicBoxSize[2], 0);
fvec4 invBoxSize((1/periodicBoxSize[0]), (1/periodicBoxSize[1]), (1/periodicBoxSize[2]), 0);
for (int i = threadIndex; i < numberOfAtoms; i += numThreads) { for (int i = threadIndex; i < numberOfAtoms; i += numThreads) {
fvec4 posI((float) atomCoordinates[i][0], (float) atomCoordinates[i][1], (float) atomCoordinates[i][2], 0.0f); 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) { for (set<int>::const_iterator iter = exclusions[i].begin(); iter != exclusions[i].end(); ++iter) {
...@@ -454,8 +459,15 @@ void CpuNonbondedForce::calculateOneIxn(int ii, int jj, float* forces, double* t ...@@ -454,8 +459,15 @@ void CpuNonbondedForce::calculateOneIxn(int ii, int jj, float* forces, double* t
void CpuNonbondedForce::getDeltaR(const fvec4& posI, const fvec4& posJ, fvec4& deltaR, float& r2, bool periodic, const fvec4& boxSize, const fvec4& invBoxSize) const { void CpuNonbondedForce::getDeltaR(const fvec4& posI, const fvec4& posJ, fvec4& deltaR, float& r2, bool periodic, const fvec4& boxSize, const fvec4& invBoxSize) const {
deltaR = posJ-posI; deltaR = posJ-posI;
if (periodic) { if (periodic) {
fvec4 base = round(deltaR*invBoxSize)*boxSize; if (triclinic) {
deltaR = deltaR-base; 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); r2 = dot3(deltaR, deltaR);
} }
......
platforms/cpu/src/CpuNonbondedForceVec4.cpp
View file @ 61d5cc0f
/* Portions copyright (c) 2006-2013 Stanford University and Simbios. /* Portions copyright (c) 2006-2014 Stanford University and Simbios.
* Contributors: Pande Group * Contributors: Pande Group
* *
* Permission is hereby granted, free of charge, to any person obtaining * Permission is hereby granted, free of charge, to any person obtaining
...@@ -22,7 +22,6 @@ ...@@ -22,7 +22,6 @@
* WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. * WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/ */
#include "SimTKOpenMMCommon.h"
#include "SimTKOpenMMUtilities.h" #include "SimTKOpenMMUtilities.h"
#include "CpuNonbondedForceVec4.h" #include "CpuNonbondedForceVec4.h"
...@@ -45,15 +44,68 @@ CpuNonbondedForce* createCpuNonbondedForceVec4() { ...@@ -45,15 +44,68 @@ CpuNonbondedForce* createCpuNonbondedForceVec4() {
CpuNonbondedForceVec4::CpuNonbondedForceVec4() { CpuNonbondedForceVec4::CpuNonbondedForceVec4() {
} }
enum PeriodicType {NoPeriodic, PeriodicPerAtom, PeriodicPerInteraction, PeriodicTriclinic};
void CpuNonbondedForceVec4::calculateBlockIxn(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize) { void CpuNonbondedForceVec4::calculateBlockIxn(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& 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
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 <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. // Load the positions and parameters of the atoms in the block.
int blockAtom[4]; const int* blockAtom = &neighborList->getSortedAtoms()[4*blockIndex];
fvec4 blockAtomPosq[4]; fvec4 blockAtomPosq[4];
fvec4 blockAtomForceX(0.0f), blockAtomForceY(0.0f), blockAtomForceZ(0.0f); fvec4 blockAtomForceX(0.0f), blockAtomForceY(0.0f), blockAtomForceZ(0.0f);
for (int i = 0; i < 4; i++) { for (int i = 0; i < 4; i++) {
blockAtom[i] = neighborList->getSortedAtoms()[4*blockIndex+i];
blockAtomPosq[i] = fvec4(posq+4*blockAtom[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 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 blockAtomY = fvec4(blockAtomPosq[0][1], blockAtomPosq[1][1], blockAtomPosq[2][1], blockAtomPosq[3][1]);
...@@ -61,8 +113,7 @@ void CpuNonbondedForceVec4::calculateBlockIxn(int blockIndex, float* forces, dou ...@@ -61,8 +113,7 @@ void CpuNonbondedForceVec4::calculateBlockIxn(int blockIndex, float* forces, dou
fvec4 blockAtomCharge = fvec4(ONE_4PI_EPS0)*fvec4(blockAtomPosq[0][3], blockAtomPosq[1][3], blockAtomPosq[2][3], blockAtomPosq[3][3]); 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 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); 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) || const bool needPeriodic = (PERIODIC_TYPE == PeriodicPerInteraction || PERIODIC_TYPE == PeriodicTriclinic);
any(blockAtomX > boxSize[0]-cutoffDistance) || any(blockAtomY > boxSize[1]-cutoffDistance) || any(blockAtomZ > boxSize[2]-cutoffDistance)));
const float invSwitchingInterval = 1/(cutoffDistance-switchingDistance); const float invSwitchingInterval = 1/(cutoffDistance-switchingDistance);
// Loop over neighbors for this block. // Loop over neighbors for this block.
...@@ -77,7 +128,10 @@ void CpuNonbondedForceVec4::calculateBlockIxn(int blockIndex, float* forces, dou ...@@ -77,7 +128,10 @@ void CpuNonbondedForceVec4::calculateBlockIxn(int blockIndex, float* forces, dou
// Compute the distances to the block atoms. // Compute the distances to the block atoms.
fvec4 dx, dy, dz, r2; fvec4 dx, dy, dz, r2;
getDeltaR(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; ivec4 include;
char excl = exclusions[i]; char excl = exclusions[i];
if (excl == 0) if (excl == 0)
...@@ -90,8 +144,7 @@ void CpuNonbondedForceVec4::calculateBlockIxn(int blockIndex, float* forces, dou ...@@ -90,8 +144,7 @@ void CpuNonbondedForceVec4::calculateBlockIxn(int blockIndex, float* forces, dou
// Compute the interactions. // Compute the interactions.
fvec4 r = sqrt(r2); fvec4 inverseR = rsqrt(r2);
fvec4 inverseR = fvec4(1.0f)/r;
fvec4 energy, dEdR; fvec4 energy, dEdR;
float atomEpsilon = atomParameters[atom].second; float atomEpsilon = atomParameters[atom].second;
if (atomEpsilon != 0.0f) { if (atomEpsilon != 0.0f) {
...@@ -103,6 +156,7 @@ void CpuNonbondedForceVec4::calculateBlockIxn(int blockIndex, float* forces, dou ...@@ -103,6 +156,7 @@ void CpuNonbondedForceVec4::calculateBlockIxn(int blockIndex, float* forces, dou
dEdR = epsSig6*(12.0f*sig6 - 6.0f); dEdR = epsSig6*(12.0f*sig6 - 6.0f);
energy = epsSig6*(sig6-1.0f); energy = epsSig6*(sig6-1.0f);
if (useSwitch) { if (useSwitch) {
fvec4 r = r2*inverseR;
fvec4 t = blend(0.0f, (r-switchingDistance)*invSwitchingInterval, r>switchingDistance); 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 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; fvec4 switchDeriv = t*t*(-30.0f+t*(60.0f-t*30.0f))*invSwitchingInterval;
...@@ -157,14 +211,65 @@ void CpuNonbondedForceVec4::calculateBlockIxn(int blockIndex, float* forces, dou ...@@ -157,14 +211,65 @@ void CpuNonbondedForceVec4::calculateBlockIxn(int blockIndex, float* forces, dou
} }
void CpuNonbondedForceVec4::calculateBlockEwaldIxn(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize) { void CpuNonbondedForceVec4::calculateBlockEwaldIxn(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& 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
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 <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. // Load the positions and parameters of the atoms in the block.
int blockAtom[4]; const int* blockAtom = &neighborList->getSortedAtoms()[4*blockIndex];
fvec4 blockAtomPosq[4]; fvec4 blockAtomPosq[4];
fvec4 blockAtomForceX(0.0f), blockAtomForceY(0.0f), blockAtomForceZ(0.0f); fvec4 blockAtomForceX(0.0f), blockAtomForceY(0.0f), blockAtomForceZ(0.0f);
for (int i = 0; i < 4; i++) { for (int i = 0; i < 4; i++) {
blockAtom[i] = neighborList->getSortedAtoms()[4*blockIndex+i];
blockAtomPosq[i] = fvec4(posq+4*blockAtom[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 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 blockAtomY = fvec4(blockAtomPosq[0][1], blockAtomPosq[1][1], blockAtomPosq[2][1], blockAtomPosq[3][1]);
...@@ -172,8 +277,7 @@ void CpuNonbondedForceVec4::calculateBlockEwaldIxn(int blockIndex, float* forces ...@@ -172,8 +277,7 @@ void CpuNonbondedForceVec4::calculateBlockEwaldIxn(int blockIndex, float* forces
fvec4 blockAtomCharge = fvec4(ONE_4PI_EPS0)*fvec4(blockAtomPosq[0][3], blockAtomPosq[1][3], blockAtomPosq[2][3], blockAtomPosq[3][3]); 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 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); 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) || const bool needPeriodic = (PERIODIC_TYPE == PeriodicPerInteraction || PERIODIC_TYPE == PeriodicTriclinic);
any(blockAtomX > boxSize[0]-cutoffDistance) || any(blockAtomY > boxSize[1]-cutoffDistance) || any(blockAtomZ > boxSize[2]-cutoffDistance)));
const float invSwitchingInterval = 1/(cutoffDistance-switchingDistance); const float invSwitchingInterval = 1/(cutoffDistance-switchingDistance);
// Loop over neighbors for this block. // Loop over neighbors for this block.
...@@ -188,7 +292,10 @@ void CpuNonbondedForceVec4::calculateBlockEwaldIxn(int blockIndex, float* forces ...@@ -188,7 +292,10 @@ void CpuNonbondedForceVec4::calculateBlockEwaldIxn(int blockIndex, float* forces
// Compute the distances to the block atoms. // Compute the distances to the block atoms.
fvec4 dx, dy, dz, r2; fvec4 dx, dy, dz, r2;
getDeltaR(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; ivec4 include;
char excl = exclusions[i]; char excl = exclusions[i];
if (excl == 0) if (excl == 0)
...@@ -201,8 +308,8 @@ void CpuNonbondedForceVec4::calculateBlockEwaldIxn(int blockIndex, float* forces ...@@ -201,8 +308,8 @@ void CpuNonbondedForceVec4::calculateBlockEwaldIxn(int blockIndex, float* forces
// Compute the interactions. // Compute the interactions.
fvec4 r = sqrt(r2); fvec4 inverseR = rsqrt(r2);
fvec4 inverseR = fvec4(1.0f)/r; fvec4 r = r2*inverseR;
fvec4 energy, dEdR; fvec4 energy, dEdR;
float atomEpsilon = atomParameters[atom].second; float atomEpsilon = atomParameters[atom].second;
if (atomEpsilon != 0.0f) { if (atomEpsilon != 0.0f) {
...@@ -261,11 +368,23 @@ void CpuNonbondedForceVec4::calculateBlockEwaldIxn(int blockIndex, float* forces ...@@ -261,11 +368,23 @@ void CpuNonbondedForceVec4::calculateBlockEwaldIxn(int blockIndex, float* forces
(fvec4(forces+4*blockAtom[j])+f[j]).store(forces+4*blockAtom[j]); (fvec4(forces+4*blockAtom[j])+f[j]).store(forces+4*blockAtom[j]);
} }
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]; dx = x-posI[0];
dy = y-posI[1]; dy = y-posI[1];
dz = z-posI[2]; dz = z-posI[2];
if (periodic) { if (PERIODIC_TYPE == PeriodicTriclinic) {
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];
}
else if (PERIODIC_TYPE == PeriodicPerInteraction) {
dx -= round(dx*invBoxSize[0])*boxSize[0]; dx -= round(dx*invBoxSize[0])*boxSize[0];
dy -= round(dy*invBoxSize[1])*boxSize[1]; dy -= round(dy*invBoxSize[1])*boxSize[1];
dz -= round(dz*invBoxSize[2])*boxSize[2]; dz -= round(dz*invBoxSize[2])*boxSize[2];
......
platforms/cpu/src/CpuNonbondedForceVec8.cpp
View file @ 61d5cc0f
/* Portions copyright (c) 2006-2013 Stanford University and Simbios. /* Portions copyright (c) 2006-2014 Stanford University and Simbios.
* Contributors: Pande Group * Contributors: Pande Group
* *
* Permission is hereby granted, free of charge, to any person obtaining * Permission is hereby granted, free of charge, to any person obtaining
...@@ -22,7 +22,6 @@ ...@@ -22,7 +22,6 @@
* WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. * WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/ */
#include "SimTKOpenMMCommon.h"
#include "SimTKOpenMMUtilities.h" #include "SimTKOpenMMUtilities.h"
#include "CpuNonbondedForceVec8.h" #include "CpuNonbondedForceVec8.h"
#include "openmm/OpenMMException.h" #include "openmm/OpenMMException.h"
...@@ -31,6 +30,12 @@ ...@@ -31,6 +30,12 @@
using namespace std; using namespace std;
using namespace OpenMM; using namespace OpenMM;
#ifdef _MSC_VER
// Workaround for a compiler bug in Visual Studio 10. Hopefully we can remove this
// once we move to a later version.
#undef __AVX__
#endif
#ifndef __AVX__ #ifndef __AVX__
bool isVec8Supported() { bool isVec8Supported() {
return false; return false;
...@@ -45,7 +50,7 @@ CpuNonbondedForce* createCpuNonbondedForceVec8() { ...@@ -45,7 +50,7 @@ CpuNonbondedForce* createCpuNonbondedForceVec8() {
*/ */
bool isVec8Supported() { bool isVec8Supported() {
// Make sure the CPU supports AVX. // Make sure the CPU supports AVX.
int cpuInfo[4]; int cpuInfo[4];
cpuid(cpuInfo, 0); cpuid(cpuInfo, 0);
if (cpuInfo[0] >= 1) { if (cpuInfo[0] >= 1) {
...@@ -71,23 +76,75 @@ CpuNonbondedForce* createCpuNonbondedForceVec8() { ...@@ -71,23 +76,75 @@ CpuNonbondedForce* createCpuNonbondedForceVec8() {
CpuNonbondedForceVec8::CpuNonbondedForceVec8() { CpuNonbondedForceVec8::CpuNonbondedForceVec8() {
} }
enum PeriodicType {NoPeriodic, PeriodicPerAtom, PeriodicPerInteraction, PeriodicTriclinic};
void CpuNonbondedForceVec8::calculateBlockIxn(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize) { void CpuNonbondedForceVec8::calculateBlockIxn(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& 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
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 <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. // Load the positions and parameters of the atoms in the block.
int blockAtom[8]; const int* blockAtom = &neighborList->getSortedAtoms()[8*blockIndex];
fvec4 blockAtomPosq[8]; fvec4 blockAtomPosq[8];
fvec8 blockAtomForceX(0.0f), blockAtomForceY(0.0f), blockAtomForceZ(0.0f); fvec8 blockAtomForceX(0.0f), blockAtomForceY(0.0f), blockAtomForceZ(0.0f);
fvec8 blockAtomX, blockAtomY, blockAtomZ, blockAtomCharge; fvec8 blockAtomX, blockAtomY, blockAtomZ, blockAtomCharge;
for (int i = 0; i < 8; i++) { for (int i = 0; i < 8; i++) {
blockAtom[i] = neighborList->getSortedAtoms()[8*blockIndex+i];
blockAtomPosq[i] = fvec4(posq+4*blockAtom[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); 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; 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 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); 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) || const bool needPeriodic = (PERIODIC_TYPE == PeriodicPerInteraction || PERIODIC_TYPE == PeriodicTriclinic);
any(blockAtomX > boxSize[0]-cutoffDistance) || any(blockAtomY > boxSize[1]-cutoffDistance) || any(blockAtomZ > boxSize[2]-cutoffDistance)));
const float invSwitchingInterval = 1/(cutoffDistance-switchingDistance); const float invSwitchingInterval = 1/(cutoffDistance-switchingDistance);
// Loop over neighbors for this block. // Loop over neighbors for this block.
...@@ -102,7 +159,10 @@ void CpuNonbondedForceVec8::calculateBlockIxn(int blockIndex, float* forces, dou ...@@ -102,7 +159,10 @@ void CpuNonbondedForceVec8::calculateBlockIxn(int blockIndex, float* forces, dou
// Compute the distances to the block atoms. // Compute the distances to the block atoms.
fvec8 dx, dy, dz, r2; fvec8 dx, dy, dz, r2;
getDeltaR(&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; ivec8 include;
char excl = exclusions[i]; char excl = exclusions[i];
if (excl == 0) if (excl == 0)
...@@ -115,8 +175,7 @@ void CpuNonbondedForceVec8::calculateBlockIxn(int blockIndex, float* forces, dou ...@@ -115,8 +175,7 @@ void CpuNonbondedForceVec8::calculateBlockIxn(int blockIndex, float* forces, dou
// Compute the interactions. // Compute the interactions.
fvec8 r = sqrt(r2); fvec8 inverseR = rsqrt(r2);
fvec8 inverseR = fvec8(1.0f)/r;
fvec8 energy, dEdR; fvec8 energy, dEdR;
float atomEpsilon = atomParameters[atom].second; float atomEpsilon = atomParameters[atom].second;
if (atomEpsilon != 0.0f) { if (atomEpsilon != 0.0f) {
...@@ -128,6 +187,7 @@ void CpuNonbondedForceVec8::calculateBlockIxn(int blockIndex, float* forces, dou ...@@ -128,6 +187,7 @@ void CpuNonbondedForceVec8::calculateBlockIxn(int blockIndex, float* forces, dou
dEdR = epsSig6*(12.0f*sig6 - 6.0f); dEdR = epsSig6*(12.0f*sig6 - 6.0f);
energy = epsSig6*(sig6-1.0f); energy = epsSig6*(sig6-1.0f);
if (useSwitch) { if (useSwitch) {
fvec8 r = r2*inverseR;
fvec8 t = (r>switchingDistance) & ((r-switchingDistance)*invSwitchingInterval); fvec8 t = (r>switchingDistance) & ((r-switchingDistance)*invSwitchingInterval);
fvec8 switchValue = 1+t*t*t*(-10.0f+t*(15.0f-t*6.0f)); 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; fvec8 switchDeriv = t*t*(-30.0f+t*(60.0f-t*30.0f))*invSwitchingInterval;
...@@ -182,22 +242,72 @@ void CpuNonbondedForceVec8::calculateBlockIxn(int blockIndex, float* forces, dou ...@@ -182,22 +242,72 @@ void CpuNonbondedForceVec8::calculateBlockIxn(int blockIndex, float* forces, dou
} }
void CpuNonbondedForceVec8::calculateBlockEwaldIxn(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize) { void CpuNonbondedForceVec8::calculateBlockEwaldIxn(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& 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
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 <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. // Load the positions and parameters of the atoms in the block.
int blockAtom[8]; const int* blockAtom = &neighborList->getSortedAtoms()[8*blockIndex];
fvec4 blockAtomPosq[8]; fvec4 blockAtomPosq[8];
fvec8 blockAtomForceX(0.0f), blockAtomForceY(0.0f), blockAtomForceZ(0.0f); fvec8 blockAtomForceX(0.0f), blockAtomForceY(0.0f), blockAtomForceZ(0.0f);
fvec8 blockAtomX, blockAtomY, blockAtomZ, blockAtomCharge; fvec8 blockAtomX, blockAtomY, blockAtomZ, blockAtomCharge;
for (int i = 0; i < 8; i++) { for (int i = 0; i < 8; i++) {
blockAtom[i] = neighborList->getSortedAtoms()[8*blockIndex+i];
blockAtomPosq[i] = fvec4(posq+4*blockAtom[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); 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; 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 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); 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) || const bool needPeriodic = (PERIODIC_TYPE == PeriodicPerInteraction || PERIODIC_TYPE == PeriodicTriclinic);
any(blockAtomX > boxSize[0]-cutoffDistance) || any(blockAtomY > boxSize[1]-cutoffDistance) || any(blockAtomZ > boxSize[2]-cutoffDistance)));
const float invSwitchingInterval = 1/(cutoffDistance-switchingDistance); const float invSwitchingInterval = 1/(cutoffDistance-switchingDistance);
// Loop over neighbors for this block. // Loop over neighbors for this block.
...@@ -212,7 +322,10 @@ void CpuNonbondedForceVec8::calculateBlockEwaldIxn(int blockIndex, float* forces ...@@ -212,7 +322,10 @@ void CpuNonbondedForceVec8::calculateBlockEwaldIxn(int blockIndex, float* forces
// Compute the distances to the block atoms. // Compute the distances to the block atoms.
fvec8 dx, dy, dz, r2; fvec8 dx, dy, dz, r2;
getDeltaR(&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; ivec8 include;
char excl = exclusions[i]; char excl = exclusions[i];
if (excl == 0) if (excl == 0)
...@@ -225,8 +338,8 @@ void CpuNonbondedForceVec8::calculateBlockEwaldIxn(int blockIndex, float* forces ...@@ -225,8 +338,8 @@ void CpuNonbondedForceVec8::calculateBlockEwaldIxn(int blockIndex, float* forces
// Compute the interactions. // Compute the interactions.
fvec8 r = sqrt(r2); fvec8 inverseR = rsqrt(r2);
fvec8 inverseR = fvec8(1.0f)/r; fvec8 r = r2*inverseR;
fvec8 energy, dEdR; fvec8 energy, dEdR;
float atomEpsilon = atomParameters[atom].second; float atomEpsilon = atomParameters[atom].second;
if (atomEpsilon != 0.0f) { if (atomEpsilon != 0.0f) {
...@@ -251,7 +364,7 @@ void CpuNonbondedForceVec8::calculateBlockEwaldIxn(int blockIndex, float* forces ...@@ -251,7 +364,7 @@ void CpuNonbondedForceVec8::calculateBlockEwaldIxn(int blockIndex, float* forces
} }
fvec8 chargeProd = blockAtomCharge*posq[4*atom+3]; fvec8 chargeProd = blockAtomCharge*posq[4*atom+3];
dEdR += chargeProd*inverseR*ewaldScaleFunction(r); dEdR += chargeProd*inverseR*ewaldScaleFunction(r);
dEdR *= inverseR*inverseR; dEdR *= inverseR*inverseR;
// Accumulate energies. // Accumulate energies.
...@@ -285,11 +398,23 @@ void CpuNonbondedForceVec8::calculateBlockEwaldIxn(int blockIndex, float* forces ...@@ -285,11 +398,23 @@ void CpuNonbondedForceVec8::calculateBlockEwaldIxn(int blockIndex, float* forces
(fvec4(forces+4*blockAtom[j])+f[j]).store(forces+4*blockAtom[j]); (fvec4(forces+4*blockAtom[j])+f[j]).store(forces+4*blockAtom[j]);
} }
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]; dx = x-posI[0];
dy = y-posI[1]; dy = y-posI[1];
dz = z-posI[2]; dz = z-posI[2];
if (periodic) { if (PERIODIC_TYPE == PeriodicTriclinic) {
fvec8 scale3 = floor(dz*recipBoxSize[2]+0.5f);
dx -= scale3*periodicBoxVectors[2][0];
dy -= scale3*periodicBoxVectors[2][1];
dz -= scale3*periodicBoxVectors[2][2];
fvec8 scale2 = floor(dy*recipBoxSize[1]+0.5f);
dx -= scale2*periodicBoxVectors[1][0];
dy -= scale2*periodicBoxVectors[1][1];
fvec8 scale1 = floor(dx*recipBoxSize[0]+0.5f);
dx -= scale1*periodicBoxVectors[0][0];
}
else if (PERIODIC_TYPE == PeriodicPerInteraction) {
dx -= round(dx*invBoxSize[0])*boxSize[0]; dx -= round(dx*invBoxSize[0])*boxSize[0];
dy -= round(dy*invBoxSize[1])*boxSize[1]; dy -= round(dy*invBoxSize[1])*boxSize[1];
dz -= round(dz*invBoxSize[2])*boxSize[2]; dz -= round(dz*invBoxSize[2])*boxSize[2];
......
platforms/cpu/src/CpuPlatform.cpp
View file @ 61d5cc0f
...@@ -67,6 +67,7 @@ CpuPlatform::CpuPlatform() { ...@@ -67,6 +67,7 @@ CpuPlatform::CpuPlatform() {
registerKernelFactory(CalcCustomNonbondedForceKernel::Name(), factory); registerKernelFactory(CalcCustomNonbondedForceKernel::Name(), factory);
registerKernelFactory(CalcCustomManyParticleForceKernel::Name(), factory); registerKernelFactory(CalcCustomManyParticleForceKernel::Name(), factory);
registerKernelFactory(CalcGBSAOBCForceKernel::Name(), factory); registerKernelFactory(CalcGBSAOBCForceKernel::Name(), factory);
registerKernelFactory(CalcCustomGBForceKernel::Name(), factory);
registerKernelFactory(IntegrateLangevinStepKernel::Name(), factory); registerKernelFactory(IntegrateLangevinStepKernel::Name(), factory);
platformProperties.push_back(CpuThreads()); platformProperties.push_back(CpuThreads());
int threads = getNumProcessors(); int threads = getNumProcessors();
......
platforms/cpu/src/CpuRandom.cpp
View file @ 61d5cc0f
...@@ -23,6 +23,7 @@ ...@@ -23,6 +23,7 @@
*/ */
#include "CpuRandom.h" #include "CpuRandom.h"
#include "openmm/internal/OSRngSeed.h"
#include "openmm/OpenMMException.h" #include "openmm/OpenMMException.h"
#include <cmath> #include <cmath>
...@@ -49,9 +50,13 @@ void CpuRandom::initialize(int seed, int numThreads) { ...@@ -49,9 +50,13 @@ void CpuRandom::initialize(int seed, int numThreads) {
nextGaussian.resize(numThreads); nextGaussian.resize(numThreads);
nextGaussianIsValid.resize(numThreads, false); nextGaussianIsValid.resize(numThreads, false);
// Use a quick and dirty RNG to pick seeds for the real random number generator. /* Use a quick and dirty RNG to pick seeds for the real random number generator.
* A random seed of 0 means pick a unique seed
*/
unsigned int r = (unsigned int) seed; unsigned int r = (unsigned int) seed;
if (r == 0)
r = (unsigned int) osrngseed();
for (int i = 0; i < numThreads; i++) { for (int i = 0; i < numThreads; i++) {
r = (1664525*r + 1013904223) & 0xFFFFFFFF; r = (1664525*r + 1013904223) & 0xFFFFFFFF;
threadRandom[i] = new OpenMM_SFMT::SFMT(); threadRandom[i] = new OpenMM_SFMT::SFMT();
......
platforms/cpu/tests/TestCpuCustomGBForce.cpp 0 → 100644
View file @ 61d5cc0f
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests all the different force terms in the reference implementation of CustomGBForce.
*/
#include "openmm/internal/AssertionUtilities.h"
#include "sfmt/SFMT.h"
#include "openmm/Context.h"
#include "CpuPlatform.h"
#include "openmm/CustomGBForce.h"
#include "openmm/GBSAOBCForce.h"
#include "openmm/GBVIForce.h"
#include "openmm/OpenMMException.h"
#include "openmm/System.h"
#include "openmm/VerletIntegrator.h"
#include <iostream>
#include <vector>
#include <algorithm>
using namespace OpenMM;
using namespace std;
const double TOL = 1e-5;
void testOBC(GBSAOBCForce::NonbondedMethod obcMethod, CustomGBForce::NonbondedMethod customMethod) {
const int numMolecules = 70;
const int numParticles = numMolecules*2;
const double boxSize = 10.0;
const double cutoff = 2.0;
CpuPlatform platform;
// Create two systems: one with a GBSAOBCForce, and one using a CustomGBForce to implement the same interaction.
System standardSystem;
System customSystem;
for (int i = 0; i < numParticles; i++) {
standardSystem.addParticle(1.0);
customSystem.addParticle(1.0);
}
standardSystem.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0.0, 0.0), Vec3(0.0, boxSize, 0.0), Vec3(0.0, 0.0, boxSize));
customSystem.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0.0, 0.0), Vec3(0.0, boxSize, 0.0), Vec3(0.0, 0.0, boxSize));
GBSAOBCForce* obc = new GBSAOBCForce();
CustomGBForce* custom = new CustomGBForce();
obc->setCutoffDistance(cutoff);
custom->setCutoffDistance(cutoff);
custom->addPerParticleParameter("q");
custom->addPerParticleParameter("radius");
custom->addPerParticleParameter("scale");
custom->addGlobalParameter("solventDielectric", obc->getSolventDielectric());
custom->addGlobalParameter("soluteDielectric", obc->getSoluteDielectric());
custom->addComputedValue("I", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(1/U^2-1/L^2)*(r-sr2*sr2/r)+0.5*log(L/U)/r+C);"
"U=r+sr2;"
"C=2*(1/or1-1/L)*step(sr2-r-or1);"
"L=max(or1, D);"
"D=abs(r-sr2);"
"sr2 = scale2*or2;"
"or1 = radius1-0.009; or2 = radius2-0.009", CustomGBForce::ParticlePairNoExclusions);
custom->addComputedValue("B", "1/(1/or-tanh(1*psi-0.8*psi^2+4.85*psi^3)/radius);"
"psi=I*or; or=radius-0.009", CustomGBForce::SingleParticle);
custom->addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^6-0.5*138.935485*(1/soluteDielectric-1/solventDielectric)*q^2/B", CustomGBForce::SingleParticle);
string invCutoffString = "";
if (obcMethod != GBSAOBCForce::NoCutoff) {
stringstream s;
s<<(1.0/cutoff);
invCutoffString = s.str();
}
custom->addEnergyTerm("138.935485*(1/soluteDielectric-1/solventDielectric)*q1*q2*("+invCutoffString+"-1/f);"
"f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce::ParticlePairNoExclusions);
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<double> params(3);
for (int i = 0; i < numMolecules; i++) {
if (i < numMolecules/2) {
obc->addParticle(1.0, 0.2, 0.5);
params[0] = 1.0;
params[1] = 0.2;
params[2] = 0.5;
custom->addParticle(params);
obc->addParticle(-1.0, 0.1, 0.5);
params[0] = -1.0;
params[1] = 0.1;
custom->addParticle(params);
}
else {
obc->addParticle(1.0, 0.2, 0.8);
params[0] = 1.0;
params[1] = 0.2;
params[2] = 0.8;
custom->addParticle(params);
obc->addParticle(-1.0, 0.1, 0.8);
params[0] = -1.0;
params[1] = 0.1;
custom->addParticle(params);
}
positions[2*i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
positions[2*i+1] = Vec3(positions[2*i][0]+1.0, positions[2*i][1], positions[2*i][2]);
velocities[2*i] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
velocities[2*i+1] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
}
obc->setNonbondedMethod(obcMethod);
custom->setNonbondedMethod(customMethod);
standardSystem.addForce(obc);
customSystem.addForce(custom);
VerletIntegrator integrator1(0.01);
VerletIntegrator integrator2(0.01);
Context context1(standardSystem, integrator1, platform);
context1.setPositions(positions);
context1.setVelocities(velocities);
State state1 = context1.getState(State::Forces | State::Energy);
Context context2(customSystem, integrator2, platform);
context2.setPositions(positions);
context2.setVelocities(velocities);
State state2 = context2.getState(State::Forces | State::Energy);
ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), 1e-4);
for (int i = 0; i < numParticles; i++) {
ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-4);
}
// Try changing the particle parameters and make sure it's still correct.
for (int i = 0; i < numMolecules/2; i++) {
obc->setParticleParameters(2*i, 1.1, 0.3, 0.6);
params[0] = 1.1;
params[1] = 0.3;
params[2] = 0.6;
custom->setParticleParameters(2*i, params);
obc->setParticleParameters(2*i+1, -1.1, 0.2, 0.4);
params[0] = -1.1;
params[1] = 0.2;
params[2] = 0.4;
custom->setParticleParameters(2*i+1, params);
}
obc->updateParametersInContext(context1);
custom->updateParametersInContext(context2);
state1 = context1.getState(State::Forces | State::Energy);
state2 = context2.getState(State::Forces | State::Energy);
ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), 1e-4);
for (int i = 0; i < numParticles; i++) {
ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-4);
}
}
void testMembrane() {
const int numMolecules = 70;
const int numParticles = numMolecules*2;
const double boxSize = 10.0;
CpuPlatform platform;
// Create a system with an implicit membrane.
System system;
for (int i = 0; i < numParticles; i++) {
system.addParticle(1.0);
}
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0.0, 0.0), Vec3(0.0, boxSize, 0.0), Vec3(0.0, 0.0, boxSize));
CustomGBForce* custom = new CustomGBForce();
custom->setCutoffDistance(2.0);
custom->addPerParticleParameter("q");
custom->addPerParticleParameter("radius");
custom->addPerParticleParameter("scale");
custom->addGlobalParameter("thickness", 3);
custom->addGlobalParameter("solventDielectric", 78.3);
custom->addGlobalParameter("soluteDielectric", 1);
custom->addComputedValue("Imol", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(1/U^2-1/L^2)*(r-sr2*sr2/r)+0.5*log(L/U)/r+C);"
"U=r+sr2;"
"C=2*(1/or1-1/L)*step(sr2-r-or1);"
"L=max(or1, D);"
"D=abs(r-sr2);"
"sr2 = scale2*or2;"
"or1 = radius1-0.009; or2 = radius2-0.009", CustomGBForce::ParticlePairNoExclusions);
custom->addComputedValue("Imem", "(1/radius+2*log(2)/thickness)/(1+exp(7.2*(abs(z)+radius-0.5*thickness)))", CustomGBForce::SingleParticle);
custom->addComputedValue("B", "1/(1/or-tanh(1*psi-0.8*psi^2+4.85*psi^3)/radius);"
"psi=max(Imol,Imem)*or; or=radius-0.009", CustomGBForce::SingleParticle);
custom->addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^6-0.5*138.935456*(1/soluteDielectric-1/solventDielectric)*q^2/B", CustomGBForce::SingleParticle);
custom->addEnergyTerm("-138.935456*(1/soluteDielectric-1/solventDielectric)*q1*q2/f;"
"f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce::ParticlePairNoExclusions);
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<double> params(3);
for (int i = 0; i < numMolecules; i++) {
if (i < numMolecules/2) {
params[0] = 1.0;
params[1] = 0.2;
params[2] = 0.5;
custom->addParticle(params);
params[0] = -1.0;
params[1] = 0.1;
custom->addParticle(params);
}
else {
params[0] = 1.0;
params[1] = 0.2;
params[2] = 0.8;
custom->addParticle(params);
params[0] = -1.0;
params[1] = 0.1;
custom->addParticle(params);
}
positions[2*i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
positions[2*i+1] = Vec3(positions[2*i][0]+1.0, positions[2*i][1], positions[2*i][2]);
velocities[2*i] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
velocities[2*i+1] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
}
system.addForce(custom);
VerletIntegrator integrator(0.01);
Context context(system, integrator, platform);
context.setPositions(positions);
context.setVelocities(velocities);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
// Take a small step in the direction of the energy gradient and see whether the potential energy changes by the expected amount.
double norm = 0.0;
for (int i = 0; i < (int) forces.size(); ++i)
norm += forces[i].dot(forces[i]);
norm = std::sqrt(norm);
const double stepSize = 1e-2;
double step = 0.5*stepSize/norm;
vector<Vec3> positions2(numParticles), positions3(numParticles);
for (int i = 0; i < (int) positions.size(); ++i) {
Vec3 p = positions[i];
Vec3 f = forces[i];
positions2[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
positions3[i] = Vec3(p[0]+f[0]*step, p[1]+f[1]*step, p[2]+f[2]*step);
}
context.setPositions(positions2);
State state2 = context.getState(State::Energy);
context.setPositions(positions3);
State state3 = context.getState(State::Energy);
ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state3.getPotentialEnergy())/stepSize, 1e-3);
}
void testTabulatedFunction() {
CpuPlatform platform;
System system;
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomGBForce* force = new CustomGBForce();
force->addComputedValue("a", "0", CustomGBForce::ParticlePair);
force->addEnergyTerm("fn(r)+1", CustomGBForce::ParticlePair);
force->addParticle(vector<double>());
force->addParticle(vector<double>());
vector<double> table;
for (int i = 0; i < 21; i++)
table.push_back(std::sin(0.25*i));
force->addTabulatedFunction("fn", new Continuous1DFunction(table, 1.0, 6.0));
system.addForce(force);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 0, 0);
for (int i = 1; i < 30; i++) {
double x = (7.0/30.0)*i;
positions[1] = Vec3(x, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
double force = (x < 1.0 || x > 6.0 ? 0.0 : -std::cos(x-1.0));
double energy = (x < 1.0 || x > 6.0 ? 0.0 : std::sin(x-1.0))+1.0;
ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces[0], 0.1);
ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces[1], 0.1);
ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 0.02);
}
}
void testMultipleChainRules() {
CpuPlatform platform;
System system;
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomGBForce* force = new CustomGBForce();
force->addComputedValue("a", "2*r", CustomGBForce::ParticlePair);
force->addComputedValue("b", "a+1", CustomGBForce::SingleParticle);
force->addComputedValue("c", "2*b+a", CustomGBForce::SingleParticle);
force->addEnergyTerm("0.1*a+1*b+10*c", CustomGBForce::SingleParticle); // 0.1*(2*r) + 2*r+1 + 10*(3*a+2) = 0.2*r + 2*r+1 + 40*r+20+20*r = 62.2*r+21
force->addParticle(vector<double>());
force->addParticle(vector<double>());
system.addForce(force);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 0, 0);
for (int i = 1; i < 5; i++) {
positions[1] = Vec3(i, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
ASSERT_EQUAL_VEC(Vec3(124.4, 0, 0), forces[0], 1e-4);
ASSERT_EQUAL_VEC(Vec3(-124.4, 0, 0), forces[1], 1e-4);
ASSERT_EQUAL_TOL(2*(62.2*i+21), state.getPotentialEnergy(), 0.02);
}
}
void testPositionDependence() {
CpuPlatform platform;
System system;
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomGBForce* force = new CustomGBForce();
force->addComputedValue("a", "r", CustomGBForce::ParticlePair);
force->addComputedValue("b", "a+x*y", CustomGBForce::SingleParticle);
force->addEnergyTerm("b*z", CustomGBForce::SingleParticle);
force->addEnergyTerm("b1+b2", CustomGBForce::ParticlePair); // = 2*r+x1*y1+x2*y2
force->addParticle(vector<double>());
force->addParticle(vector<double>());
system.addForce(force);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
vector<Vec3> forces(2);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < 5; i++) {
positions[0] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
positions[1] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
Vec3 delta = positions[0]-positions[1];
double r = sqrt(delta.dot(delta));
double energy = 2*r+positions[0][0]*positions[0][1]+positions[1][0]*positions[1][1];
for (int j = 0; j < 2; j++)
energy += positions[j][2]*(r+positions[j][0]*positions[j][1]);
Vec3 force1(-(1+positions[0][2])*delta[0]/r-(1+positions[0][2])*positions[0][1]-(1+positions[1][2])*delta[0]/r,
-(1+positions[0][2])*delta[1]/r-(1+positions[0][2])*positions[0][0]-(1+positions[1][2])*delta[1]/r,
-(1+positions[0][2])*delta[2]/r-(r+positions[0][0]*positions[0][1])-(1+positions[1][2])*delta[2]/r);
Vec3 force2((1+positions[0][2])*delta[0]/r+(1+positions[1][2])*delta[0]/r-(1+positions[1][2])*positions[1][1],
(1+positions[0][2])*delta[1]/r+(1+positions[1][2])*delta[1]/r-(1+positions[1][2])*positions[1][0],
(1+positions[0][2])*delta[2]/r+(1+positions[1][2])*delta[2]/r-(r+positions[1][0]*positions[1][1]));
ASSERT_EQUAL_VEC(force1, forces[0], 1e-4);
ASSERT_EQUAL_VEC(force2, forces[1], 1e-4);
ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 0.02);
// Take a small step in the direction of the energy gradient and see whether the potential energy changes by the expected amount.
double norm = 0.0;
for (int i = 0; i < (int) forces.size(); ++i)
norm += forces[i].dot(forces[i]);
norm = std::sqrt(norm);
const double stepSize = 1e-3;
double step = 0.5*stepSize/norm;
vector<Vec3> positions2(2), positions3(2);
for (int i = 0; i < (int) positions.size(); ++i) {
Vec3 p = positions[i];
Vec3 f = forces[i];
positions2[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
positions3[i] = Vec3(p[0]+f[0]*step, p[1]+f[1]*step, p[2]+f[2]*step);
}
context.setPositions(positions2);
State state2 = context.getState(State::Energy);
context.setPositions(positions3);
State state3 = context.getState(State::Energy);
ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state3.getPotentialEnergy())/stepSize, 1e-3);
}
}
void testExclusions() {
CpuPlatform platform;
for (int i = 3; i < 4; i++) {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomGBForce* force = new CustomGBForce();
force->addComputedValue("a", "r", i < 2 ? CustomGBForce::ParticlePair : CustomGBForce::ParticlePairNoExclusions);
force->addEnergyTerm("a", CustomGBForce::SingleParticle);
force->addEnergyTerm("(1+a1+a2)*r", i%2 == 0 ? CustomGBForce::ParticlePair : CustomGBForce::ParticlePairNoExclusions);
force->addParticle(vector<double>());
force->addParticle(vector<double>());
force->addExclusion(0, 1);
system.addForce(force);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(1, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
double f, energy;
switch (i)
{
case 0: // e = 0
f = 0;
energy = 0;
break;
case 1: // e = r
f = 1;
energy = 1;
break;
case 2: // e = 2r
f = 2;
energy = 2;
break;
case 3: // e = 3r + 2r^2
f = 7;
energy = 5;
break;
default:
ASSERT(false);
}
ASSERT_EQUAL_VEC(Vec3(f, 0, 0), forces[0], 1e-4);
ASSERT_EQUAL_VEC(Vec3(-f, 0, 0), forces[1], 1e-4);
ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 1e-4);
// Take a small step in the direction of the energy gradient and see whether the potential energy changes by the expected amount.
double norm = 0.0;
for (int i = 0; i < (int) forces.size(); ++i)
norm += forces[i].dot(forces[i]);
norm = std::sqrt(norm);
const double stepSize = 1e-3;
double step = stepSize/norm;
for (int i = 0; i < (int) positions.size(); ++i) {
Vec3 p = positions[i];
Vec3 f = forces[i];
positions[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
}
context.setPositions(positions);
State state2 = context.getState(State::Energy);
ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state.getPotentialEnergy())/stepSize, 1e-3*abs(state.getPotentialEnergy()));
}
}
int main() {
try {
if (!CpuPlatform::isProcessorSupported()) {
cout << "CPU is not supported. Exiting." << endl;
return 0;
}
testOBC(GBSAOBCForce::NoCutoff, CustomGBForce::NoCutoff);
testOBC(GBSAOBCForce::CutoffNonPeriodic, CustomGBForce::CutoffNonPeriodic);
testOBC(GBSAOBCForce::CutoffPeriodic, CustomGBForce::CutoffPeriodic);
testMembrane();
testTabulatedFunction();
testMultipleChainRules();
testPositionDependence();
testExclusions();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
}
platforms/cpu/tests/TestCpuCustomManyParticleForce.cpp
View file @ 61d5cc0f
...@@ -53,15 +53,36 @@ using namespace std; ...@@ -53,15 +53,36 @@ using namespace std;
const double TOL = 1e-5; 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. // Create a System and Context.
int numParticles = force->getNumParticles(); int numParticles = force->getNumParticles();
CustomManyParticleForce::NonbondedMethod nonbondedMethod = force->getNonbondedMethod(); CustomManyParticleForce::NonbondedMethod nonbondedMethod = force->getNonbondedMethod();
System system; System system;
for (int i = 0; i < numParticles; i++) for (int i = 0; i < numParticles; i++)
system.addParticle(1.0); 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); system.addForce(force);
VerletIntegrator integrator(0.001); VerletIntegrator integrator(0.001);
CpuPlatform platform; CpuPlatform platform;
...@@ -69,24 +90,18 @@ void validateAxilrodTeller(CustomManyParticleForce* force, const vector<Vec3>& p ...@@ -69,24 +90,18 @@ void validateAxilrodTeller(CustomManyParticleForce* force, const vector<Vec3>& p
context.setPositions(positions); context.setPositions(positions);
State state1 = context.getState(State::Forces | State::Energy); State state1 = context.getState(State::Forces | State::Energy);
double c = context.getParameter("C"); double c = context.getParameter("C");
// See if the energy matches the expected value. // See if the energy matches the expected value.
double expectedEnergy = 0; double expectedEnergy = 0;
bool periodic = (nonbondedMethod == CustomManyParticleForce::CutoffPeriodic);
for (int i = 0; i < (int) expectedSets.size(); i++) { for (int i = 0; i < (int) expectedSets.size(); i++) {
int p1 = expectedSets[i][0]; int p1 = expectedSets[i][0];
int p2 = expectedSets[i][1]; int p2 = expectedSets[i][1];
int p3 = expectedSets[i][2]; int p3 = expectedSets[i][2];
Vec3 d12 = positions[p2]-positions[p1]; Vec3 d12 = computeDelta(positions[p2], positions[p1], periodic, boxVectors);
Vec3 d13 = positions[p3]-positions[p1]; Vec3 d13 = computeDelta(positions[p3], positions[p1], periodic, boxVectors);
Vec3 d23 = positions[p3]-positions[p2]; Vec3 d23 = computeDelta(positions[p3], positions[p2], periodic, boxVectors);
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;
}
}
double r12 = sqrt(d12.dot(d12)); double r12 = sqrt(d12.dot(d12));
double r13 = sqrt(d13.dot(d13)); double r13 = sqrt(d13.dot(d13));
double r23 = sqrt(d23.dot(d23)); double r23 = sqrt(d23.dot(d23));
...@@ -210,7 +225,7 @@ void testNoCutoff() { ...@@ -210,7 +225,7 @@ void testNoCutoff() {
positions.push_back(Vec3(0.4, 0, -0.8)); 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}}; int sets[4][3] = {{0,1,2}, {1,2,3}, {2,3,0}, {3,0,1}};
vector<const int*> expectedSets(&sets[0], &sets[4]); vector<const int*> expectedSets(&sets[0], &sets[4]);
validateAxilrodTeller(force, positions, expectedSets, 2.0); validateAxilrodTeller(force, positions, expectedSets, 2.0, false);
} }
void testCutoff() { void testCutoff() {
...@@ -235,7 +250,7 @@ void testCutoff() { ...@@ -235,7 +250,7 @@ void testCutoff() {
positions.push_back(Vec3(0.2, 0.5, -0.1)); 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}}; 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]); vector<const int*> expectedSets(&sets[0], &sets[7]);
validateAxilrodTeller(force, positions, expectedSets, 2.0); validateAxilrodTeller(force, positions, expectedSets, 2.0, false);
} }
void testPeriodic() { void testPeriodic() {
...@@ -261,7 +276,33 @@ void testPeriodic() { ...@@ -261,7 +276,33 @@ void testPeriodic() {
double boxSize = 2.1; double boxSize = 2.1;
int sets[5][3] = {{0,1,3}, {0,1,4}, {0,2,4}, {0,3,4}, {1,3,4}}; 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]); 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() { void testExclusions() {
...@@ -286,7 +327,7 @@ void testExclusions() { ...@@ -286,7 +327,7 @@ void testExclusions() {
force->addExclusion(0, 3); force->addExclusion(0, 3);
int sets[5][3] = {{0,1,4}, {1,2,3}, {1,2,4}, {1,3,4}, {2,3,4}}; 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]); vector<const int*> expectedSets(&sets[0], &sets[5]);
validateAxilrodTeller(force, positions, expectedSets, 2.0); validateAxilrodTeller(force, positions, expectedSets, 2.0, false);
} }
void testAllTerms() { void testAllTerms() {
...@@ -673,9 +714,14 @@ void testCentralParticleModeLargeSystem() { ...@@ -673,9 +714,14 @@ void testCentralParticleModeLargeSystem() {
int main() { int main() {
try { try {
if (!CpuPlatform::isProcessorSupported()) {
cout << "CPU is not supported. Exiting." << endl;
return 0;
}
testNoCutoff(); testNoCutoff();
testCutoff(); testCutoff();
testPeriodic(); testPeriodic();
testTriclinic();
testExclusions(); testExclusions();
testAllTerms(); testAllTerms();
testParameters(); testParameters();
......
platforms/cpu/tests/TestCpuCustomNonbondedForce.cpp
View file @ 61d5cc0f
...@@ -224,6 +224,65 @@ void testPeriodic() { ...@@ -224,6 +224,65 @@ void testPeriodic() {
ASSERT_EQUAL_TOL(1.9+1+0.9, state.getPotentialEnergy(), TOL); 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() { void testContinuous1DFunction() {
System system; System system;
system.addParticle(1.0); system.addParticle(1.0);
...@@ -852,6 +911,7 @@ int main() { ...@@ -852,6 +911,7 @@ int main() {
testExclusions(); testExclusions();
testCutoff(); testCutoff();
testPeriodic(); testPeriodic();
testTriclinic();
testContinuous1DFunction(); testContinuous1DFunction();
testContinuous2DFunction(); testContinuous2DFunction();
testContinuous3DFunction(); testContinuous3DFunction();
......
platforms/cpu/tests/TestCpuEwald.cpp
View file @ 61d5cc0f
...@@ -201,6 +201,57 @@ void testEwald2Ions() { ...@@ -201,6 +201,57 @@ void testEwald2Ions() {
ASSERT_EQUAL_TOL(-217.276, state.getPotentialEnergy(), 0.01/*10*TOL*/); ASSERT_EQUAL_TOL(-217.276, state.getPotentialEnergy(), 0.01/*10*TOL*/);
} }
void testTriclinic() {
// Create a triclinic box containing eight particles.
System system;
system.setDefaultPeriodicBoxVectors(Vec3(2.5, 0, 0), Vec3(0.5, 3.0, 0), Vec3(0.7, 0.9, 3.5));
for (int i = 0; i < 8; i++)
system.addParticle(1.0);
NonbondedForce* force = new NonbondedForce();
system.addForce(force);
force->setNonbondedMethod(NonbondedForce::PME);
force->setCutoffDistance(1.0);
force->setPMEParameters(3.45891, 32, 40, 48);
for (int i = 0; i < 4; i++)
force->addParticle(-1, 0.440104, 0.4184); // Cl parameters
for (int i = 0; i < 4; i++)
force->addParticle(1, 0.332840, 0.0115897); // Na parameters
vector<Vec3> positions(8);
positions[0] = Vec3(1.744, 2.788, 3.162);
positions[1] = Vec3(1.048, 0.762, 2.340);
positions[2] = Vec3(2.489, 1.570, 2.817);
positions[3] = Vec3(1.027, 1.893, 3.271);
positions[4] = Vec3(0.937, 0.825, 0.009);
positions[5] = Vec3(2.290, 1.887, 3.352);
positions[6] = Vec3(1.266, 1.111, 2.894);
positions[7] = Vec3(0.933, 1.862, 3.490);
// Compute the forces and energy.
VerletIntegrator integ(0.001);
Context context(system, integ, platform);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
// Compare them to values computed by Gromacs.
double expectedEnergy = -963.370;
vector<Vec3> expectedForce(8);
expectedForce[0] = Vec3(4.25253e+01, -1.23503e+02, 1.22139e+02);
expectedForce[1] = Vec3(9.74752e+01, 1.68213e+02, 1.93169e+02);
expectedForce[2] = Vec3(-1.50348e+02, 1.29165e+02, 3.70435e+02);
expectedForce[3] = Vec3(9.18644e+02, -3.52571e+00, -1.34772e+03);
expectedForce[4] = Vec3(-1.61193e+02, 9.01528e+01, -7.12904e+01);
expectedForce[5] = Vec3(2.82630e+02, 2.78029e+01, -3.72864e+02);
expectedForce[6] = Vec3(-1.47454e+02, -2.14448e+02, -3.55789e+02);
expectedForce[7] = Vec3(-8.82195e+02, -7.39132e+01, 1.46202e+03);
for (int i = 0; i < 8; i++) {
ASSERT_EQUAL_VEC(expectedForce[i], state.getForces()[i], 1e-4);
}
ASSERT_EQUAL_TOL(expectedEnergy, state.getPotentialEnergy(), 1e-4);
}
void testErrorTolerance(NonbondedForce::NonbondedMethod method) { void testErrorTolerance(NonbondedForce::NonbondedMethod method) {
// Create a cloud of random point charges. // Create a cloud of random point charges.
...@@ -261,6 +312,7 @@ int main(int argc, char* argv[]) { ...@@ -261,6 +312,7 @@ int main(int argc, char* argv[]) {
testEwaldPME(false); testEwaldPME(false);
testEwaldPME(true); testEwaldPME(true);
// testEwald2Ions(); // testEwald2Ions();
testTriclinic();
testErrorTolerance(NonbondedForce::Ewald); testErrorTolerance(NonbondedForce::Ewald);
testErrorTolerance(NonbondedForce::PME); testErrorTolerance(NonbondedForce::PME);
} }
......
platforms/cpu/tests/TestCpuGBSAOBCForce.cpp
View file @ 61d5cc0f
...@@ -6,7 +6,7 @@ ...@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * Medical Research, grant U54 GM072970. See https://simtk.org. *
* * * *
* Portions copyright (c) 2008-2013 Stanford University and the Authors. * * Portions copyright (c) 2008-2014 Stanford University and the Authors. *
* Authors: Peter Eastman * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -67,7 +67,7 @@ void testSingleParticle() { ...@@ -67,7 +67,7 @@ void testSingleParticle() {
double eps0 = EPSILON0; double eps0 = EPSILON0;
double bornEnergy = (-0.5*0.5/(8*PI_M*eps0))*(1.0/forceField->getSoluteDielectric()-1.0/forceField->getSolventDielectric())/bornRadius; double bornEnergy = (-0.5*0.5/(8*PI_M*eps0))*(1.0/forceField->getSoluteDielectric()-1.0/forceField->getSolventDielectric())/bornRadius;
double extendedRadius = 0.15+0.14; // probe radius double extendedRadius = 0.15+0.14; // probe radius
double nonpolarEnergy = CAL2JOULE*PI_M*0.0216*(10*extendedRadius)*(10*extendedRadius)*std::pow(0.15/bornRadius, 6.0); // Where did this formula come from? Just copied it from CpuImplicitSolvent.cpp double nonpolarEnergy = 4*PI_M*2.25936*extendedRadius*extendedRadius*std::pow(0.15/bornRadius, 6.0);
ASSERT_EQUAL_TOL((bornEnergy+nonpolarEnergy), state.getPotentialEnergy(), 0.01); ASSERT_EQUAL_TOL((bornEnergy+nonpolarEnergy), state.getPotentialEnergy(), 0.01);
// Change the parameters and see if it is still correct. // Change the parameters and see if it is still correct.
...@@ -77,8 +77,35 @@ void testSingleParticle() { ...@@ -77,8 +77,35 @@ void testSingleParticle() {
state = context.getState(State::Energy); state = context.getState(State::Energy);
bornRadius = 0.25-0.009; // dielectric offset bornRadius = 0.25-0.009; // dielectric offset
bornEnergy = (-0.4*0.4/(8*PI_M*eps0))*(1.0/forceField->getSoluteDielectric()-1.0/forceField->getSolventDielectric())/bornRadius; bornEnergy = (-0.4*0.4/(8*PI_M*eps0))*(1.0/forceField->getSoluteDielectric()-1.0/forceField->getSolventDielectric())/bornRadius;
extendedRadius = bornRadius+0.14; extendedRadius = 0.25+0.14;
nonpolarEnergy = CAL2JOULE*PI_M*0.0216*(10*extendedRadius)*(10*extendedRadius)*std::pow(0.25/bornRadius, 6.0); nonpolarEnergy = 4*PI_M*2.25936*extendedRadius*extendedRadius*std::pow(0.25/bornRadius, 6.0);
ASSERT_EQUAL_TOL((bornEnergy+nonpolarEnergy), state.getPotentialEnergy(), 0.01);
}
void testGlobalSettings() {
CpuPlatform platform;
System system;
system.addParticle(2.0);
LangevinIntegrator integrator(0, 0.1, 0.01);
GBSAOBCForce* forceField = new GBSAOBCForce();
forceField->addParticle(0.5, 0.15, 1);
const double soluteDielectric = 2.1;
const double solventDielectric = 35.0;
const double surfaceAreaEnergy = 0.75;
forceField->setSoluteDielectric(soluteDielectric);
forceField->setSolventDielectric(solventDielectric);
forceField->setSurfaceAreaEnergy(surfaceAreaEnergy);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(1);
positions[0] = Vec3(0, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Energy);
double bornRadius = 0.15-0.009; // dielectric offset
double eps0 = EPSILON0;
double bornEnergy = (-0.5*0.5/(8*PI_M*eps0))*(1.0/soluteDielectric-1.0/solventDielectric)/bornRadius;
double extendedRadius = 0.15+0.14; // probe radius
double nonpolarEnergy = 4*PI_M*surfaceAreaEnergy*extendedRadius*extendedRadius*std::pow(0.15/bornRadius, 6.0);
ASSERT_EQUAL_TOL((bornEnergy+nonpolarEnergy), state.getPotentialEnergy(), 0.01); ASSERT_EQUAL_TOL((bornEnergy+nonpolarEnergy), state.getPotentialEnergy(), 0.01);
} }
...@@ -228,6 +255,7 @@ int main() { ...@@ -228,6 +255,7 @@ int main() {
return 0; return 0;
} }
testSingleParticle(); testSingleParticle();
testGlobalSettings();
testCutoffAndPeriodic(); testCutoffAndPeriodic();
for (int i = 5; i < 11; i++) { for (int i = 5; i < 11; i++) {
testForce(i*i*i, NonbondedForce::NoCutoff, GBSAOBCForce::NoCutoff); testForce(i*i*i, NonbondedForce::NoCutoff, GBSAOBCForce::NoCutoff);
......
platforms/cpu/tests/TestCpuNeighborList.cpp
View file @ 61d5cc0f
...@@ -48,10 +48,21 @@ ...@@ -48,10 +48,21 @@
using namespace OpenMM; using namespace OpenMM;
using namespace std; using namespace std;
void testNeighborList(bool periodic) { void testNeighborList(bool periodic, bool triclinic) {
const int numParticles = 500; const int numParticles = 500;
const float cutoff = 2.0f; const float cutoff = 2.0f;
const float boxSize[3] = {20.0f, 15.0f, 22.0f}; RealVec boxVectors[3];
if (triclinic) {
boxVectors[0] = RealVec(20, 0, 0);
boxVectors[1] = RealVec(5, 15, 0);
boxVectors[2] = RealVec(-3, -7, 22);
}
else {
boxVectors[0] = RealVec(20, 0, 0);
boxVectors[1] = RealVec(0, 15, 0);
boxVectors[2] = RealVec(0, 0, 22);
}
const float boxSize[3] = {(float) boxVectors[0][0], (float) boxVectors[1][1], (float) boxVectors[2][2]};
const int blockSize = 8; const int blockSize = 8;
OpenMM_SFMT::SFMT sfmt; OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt); init_gen_rand(0, sfmt);
...@@ -69,7 +80,7 @@ void testNeighborList(bool periodic) { ...@@ -69,7 +80,7 @@ void testNeighborList(bool periodic) {
} }
ThreadPool threads; ThreadPool threads;
CpuNeighborList neighborList(blockSize); CpuNeighborList neighborList(blockSize);
neighborList.computeNeighborList(numParticles, positions, exclusions, boxSize, periodic, cutoff, threads); neighborList.computeNeighborList(numParticles, positions, exclusions, boxVectors, periodic, cutoff, threads);
// Convert the neighbor list to a set for faster lookup. // Convert the neighbor list to a set for faster lookup.
...@@ -90,19 +101,17 @@ void testNeighborList(bool periodic) { ...@@ -90,19 +101,17 @@ void testNeighborList(bool periodic) {
} }
// Check each particle pair and figure out whether they should be in the neighbor list. // Check each particle pair and figure out whether they should be in the neighbor list.
for (int i = 0; i < numParticles; i++) for (int i = 0; i < numParticles; i++)
for (int j = 0; j <= i; j++) { for (int j = 0; j <= i; j++) {
bool shouldInclude = (exclusions[i].find(j) == exclusions[i].end()); bool shouldInclude = (exclusions[i].find(j) == exclusions[i].end());
float dx = positions[4*i]-positions[4*j]; Vec3 diff(positions[4*i]-positions[4*j], positions[4*i+1]-positions[4*j+1], positions[4*i+2]-positions[4*j+2]);
float dy = positions[4*i+1]-positions[4*j+1];
float dz = positions[4*i+2]-positions[4*j+2];
if (periodic) { if (periodic) {
dx -= floor(dx/boxSize[0]+0.5f)*boxSize[0]; diff -= boxVectors[2]*floor(diff[2]/boxSize[2]+0.5);
dy -= floor(dy/boxSize[1]+0.5f)*boxSize[1]; diff -= boxVectors[1]*floor(diff[1]/boxSize[1]+0.5);
dz -= floor(dz/boxSize[2]+0.5f)*boxSize[2]; diff -= boxVectors[0]*floor(diff[0]/boxSize[0]+0.5);
} }
if (dx*dx + dy*dy + dz*dz > cutoff*cutoff) if (diff.dot(diff) > cutoff*cutoff)
shouldInclude = false; shouldInclude = false;
bool isIncluded = (neighbors.find(make_pair(i, j)) != neighbors.end() || neighbors.find(make_pair(j, i)) != neighbors.end()); bool isIncluded = (neighbors.find(make_pair(i, j)) != neighbors.end() || neighbors.find(make_pair(j, i)) != neighbors.end());
if (shouldInclude) if (shouldInclude)
...@@ -116,8 +125,9 @@ int main() { ...@@ -116,8 +125,9 @@ int main() {
cout << "CPU is not supported. Exiting." << endl; cout << "CPU is not supported. Exiting." << endl;
return 0; return 0;
} }
testNeighborList(false); testNeighborList(false, false);
testNeighborList(true); testNeighborList(true, false);
testNeighborList(true, true);
} }
catch(const exception& e) { catch(const exception& e) {
cout << "exception: " << e.what() << endl; cout << "exception: " << e.what() << endl;
......
platforms/cpu/tests/TestCpuNonbondedForce.cpp
View file @ 61d5cc0f
...@@ -6,7 +6,7 @@ ...@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * Medical Research, grant U54 GM072970. See https://simtk.org. *
* * * *
* Portions copyright (c) 2008-2013 Stanford University and the Authors. * * Portions copyright (c) 2008-2015 Stanford University and the Authors. *
* Authors: Peter Eastman * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -353,6 +353,67 @@ void testPeriodic() { ...@@ -353,6 +353,67 @@ void testPeriodic() {
ASSERT_EQUAL_TOL(2*ONE_4PI_EPS0*(1.0)*(1.0+krf*1.0-crf), state.getPotentialEnergy(), TOL); ASSERT_EQUAL_TOL(2*ONE_4PI_EPS0*(1.0)*(1.0+krf*1.0-crf), 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);
NonbondedForce* nonbonded = new NonbondedForce();
nonbonded->addParticle(1.0, 1, 0);
nonbonded->addParticle(1.0, 1, 0);
nonbonded->setNonbondedMethod(NonbondedForce::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);
const double eps = 78.3;
const double krf = (1.0/(cutoff*cutoff*cutoff))*(eps-1.0)/(2.0*eps+1.0);
const double crf = (1.0/cutoff)*(3.0*eps)/(2.0*eps+1.0);
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*ONE_4PI_EPS0*(-1.0/(distance*distance*distance)+2.0*krf);
ASSERT_EQUAL_TOL(ONE_4PI_EPS0*(1.0/distance+krf*distance*distance-crf), state.getPotentialEnergy(), 1e-4);
ASSERT_EQUAL_VEC(force, state.getForces()[0], 2e-5);
ASSERT_EQUAL_VEC(-force, state.getForces()[1], 2e-5);
}
}
}
void testLargeSystem() { void testLargeSystem() {
const int numMolecules = 600; const int numMolecules = 600;
...@@ -635,6 +696,7 @@ int main(int argc, char* argv[]) { ...@@ -635,6 +696,7 @@ int main(int argc, char* argv[]) {
testCutoff(); testCutoff();
testCutoff14(); testCutoff14();
testPeriodic(); testPeriodic();
testTriclinic();
testLargeSystem(); testLargeSystem();
testDispersionCorrection(); testDispersionCorrection();
testChangingParameters(); testChangingParameters();
......
platforms/cuda/include/CudaContext.h
View file @ 61d5cc0f
...@@ -9,7 +9,7 @@ ...@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * Medical Research, grant U54 GM072970. See https://simtk.org. *
* * * *
* Portions copyright (c) 2009-2013 Stanford University and the Authors. * * Portions copyright (c) 2009-2015 Stanford University and the Authors. *
* Authors: Peter Eastman * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -41,6 +41,7 @@ ...@@ -41,6 +41,7 @@
#include <vector_functions.h> #include <vector_functions.h>
#include "windowsExportCuda.h" #include "windowsExportCuda.h"
#include "CudaPlatform.h" #include "CudaPlatform.h"
#include "openmm/Kernel.h"
typedef unsigned int tileflags; typedef unsigned int tileflags;
...@@ -133,6 +134,18 @@ public: ...@@ -133,6 +134,18 @@ public:
int getContextIndex() const { int getContextIndex() const {
return contextIndex; return contextIndex;
} }
/**
* Get the stream currently being used for execution.
*/
CUstream getCurrentStream();
/**
* Set the stream to use for execution.
*/
void setCurrentStream(CUstream stream);
/**
* Reset the context to using the default stream for execution.
*/
void restoreDefaultStream();
/** /**
* Get the array which contains the position (the xyz components) and charge (the w component) of each atom. * Get the array which contains the position (the xyz components) and charge (the w component) of each atom.
*/ */
...@@ -340,43 +353,62 @@ public: ...@@ -340,43 +353,62 @@ public:
/** /**
* Get whether double precision is being used. * Get whether double precision is being used.
*/ */
bool getUseDoublePrecision() { bool getUseDoublePrecision() const {
return useDoublePrecision; return useDoublePrecision;
} }
/** /**
* Get whether mixed precision is being used. * Get whether mixed precision is being used.
*/ */
bool getUseMixedPrecision() { bool getUseMixedPrecision() const {
return useMixedPrecision; return useMixedPrecision;
} }
/**
* Get whether the periodic box is triclinic.
*/
bool getBoxIsTriclinic() const {
return boxIsTriclinic;
}
/** /**
* Convert a number to a string in a format suitable for including in a kernel. * Convert a number to a string in a format suitable for including in a kernel.
* This takes into account whether the context uses single or double precision. * This takes into account whether the context uses single or double precision.
*/ */
std::string doubleToString(double value); std::string doubleToString(double value) const;
/** /**
* Convert a number to a string in a format suitable for including in a kernel. * Convert a number to a string in a format suitable for including in a kernel.
*/ */
std::string intToString(int value); std::string intToString(int value) const;
/** /**
* Convert a CUDA result code to the corresponding string description. * Convert a CUDA result code to the corresponding string description.
*/ */
static std::string getErrorString(CUresult result); static std::string getErrorString(CUresult result);
/** /**
* Get the size of the periodic box. * Get the vectors defining the periodic box.
*/ */
double4 getPeriodicBoxSize() const { void getPeriodicBoxVectors(Vec3& a, Vec3& b, Vec3& c) const {
return periodicBoxSize; a = Vec3(periodicBoxVecX.x, periodicBoxVecX.y, periodicBoxVecX.z);
b = Vec3(periodicBoxVecY.x, periodicBoxVecY.y, periodicBoxVecY.z);
c = Vec3(periodicBoxVecZ.x, periodicBoxVecZ.y, periodicBoxVecZ.z);
}
/**
* Set the vectors defining the periodic box.
*/
void setPeriodicBoxVectors(const Vec3& a, const Vec3& b, const Vec3& c) {
periodicBoxVecX = make_double4(a[0], a[1], a[2], 0.0);
periodicBoxVecY = make_double4(b[0], b[1], b[2], 0.0);
periodicBoxVecZ = make_double4(c[0], c[1], c[2], 0.0);
periodicBoxVecXFloat = make_float4((float) a[0], (float) a[1], (float) a[2], 0.0f);
periodicBoxVecYFloat = make_float4((float) b[0], (float) b[1], (float) b[2], 0.0f);
periodicBoxVecZFloat = make_float4((float) c[0], (float) c[1], (float) c[2], 0.0f);
periodicBoxSize = make_double4(a[0], b[1], c[2], 0.0);
invPeriodicBoxSize = make_double4(1.0/a[0], 1.0/b[1], 1.0/c[2], 0.0);
periodicBoxSizeFloat = make_float4((float) a[0], (float) b[1], (float) c[2], 0.0f);
invPeriodicBoxSizeFloat = make_float4(1.0f/(float) a[0], 1.0f/(float) b[1], 1.0f/(float) c[2], 0.0f);
} }
/** /**
* Set the size of the periodic box. * Get the size of the periodic box.
*/ */
void setPeriodicBoxSize(double xsize, double ysize, double zsize) { double4 getPeriodicBoxSize() const {
periodicBoxSize = make_double4(xsize, ysize, zsize, 0.0); return periodicBoxSize;
invPeriodicBoxSize = make_double4(1.0/xsize, 1.0/ysize, 1.0/zsize, 0.0);
periodicBoxSizeFloat = make_float4((float) xsize, (float) ysize, (float) zsize, 0.0f);
invPeriodicBoxSizeFloat = make_float4(1.0f/(float) xsize, 1.0f/(float) ysize, 1.0f/(float) zsize, 0.0f);
} }
/** /**
* Get the inverse of the size of the periodic box. * Get the inverse of the size of the periodic box.
...@@ -398,6 +430,27 @@ public: ...@@ -398,6 +430,27 @@ public:
void* getInvPeriodicBoxSizePointer() { void* getInvPeriodicBoxSizePointer() {
return (useDoublePrecision ? reinterpret_cast<void*>(&invPeriodicBoxSize) : reinterpret_cast<void*>(&invPeriodicBoxSizeFloat)); return (useDoublePrecision ? reinterpret_cast<void*>(&invPeriodicBoxSize) : reinterpret_cast<void*>(&invPeriodicBoxSizeFloat));
} }
/**
* Get a pointer to the first periodic box vector, represented as either a float4 or double4 depending on
* this context's precision. This value is suitable for passing to kernels as an argument.
*/
void* getPeriodicBoxVecXPointer() {
return (useDoublePrecision ? reinterpret_cast<void*>(&periodicBoxVecX) : reinterpret_cast<void*>(&periodicBoxVecXFloat));
}
/**
* Get a pointer to the second periodic box vector, represented as either a float4 or double4 depending on
* this context's precision. This value is suitable for passing to kernels as an argument.
*/
void* getPeriodicBoxVecYPointer() {
return (useDoublePrecision ? reinterpret_cast<void*>(&periodicBoxVecY) : reinterpret_cast<void*>(&periodicBoxVecYFloat));
}
/**
* Get a pointer to the third periodic box vector, represented as either a float4 or double4 depending on
* this context's precision. This value is suitable for passing to kernels as an argument.
*/
void* getPeriodicBoxVecZPointer() {
return (useDoublePrecision ? reinterpret_cast<void*>(&periodicBoxVecZ) : reinterpret_cast<void*>(&periodicBoxVecZFloat));
}
/** /**
* Get the CudaIntegrationUtilities for this context. * Get the CudaIntegrationUtilities for this context.
*/ */
...@@ -513,14 +566,15 @@ private: ...@@ -513,14 +566,15 @@ private:
int paddedNumAtoms; int paddedNumAtoms;
int numAtomBlocks; int numAtomBlocks;
int numThreadBlocks; int numThreadBlocks;
bool useBlockingSync, useDoublePrecision, useMixedPrecision, contextIsValid, atomsWereReordered; bool useBlockingSync, useDoublePrecision, useMixedPrecision, contextIsValid, atomsWereReordered, boxIsTriclinic, hasCompilerKernel;
std::string compiler, tempDir, cacheDir, gpuArchitecture; std::string compiler, tempDir, cacheDir, gpuArchitecture;
float4 periodicBoxSizeFloat, invPeriodicBoxSizeFloat; float4 periodicBoxVecXFloat, periodicBoxVecYFloat, periodicBoxVecZFloat, periodicBoxSizeFloat, invPeriodicBoxSizeFloat;
double4 periodicBoxSize, invPeriodicBoxSize; double4 periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ, periodicBoxSize, invPeriodicBoxSize;
std::string defaultOptimizationOptions; std::string defaultOptimizationOptions;
std::map<std::string, std::string> compilationDefines; std::map<std::string, std::string> compilationDefines;
CUcontext context; CUcontext context;
CUdevice device; CUdevice device;
CUstream currentStream;
CUfunction clearBufferKernel; CUfunction clearBufferKernel;
CUfunction clearTwoBuffersKernel; CUfunction clearTwoBuffersKernel;
CUfunction clearThreeBuffersKernel; CUfunction clearThreeBuffersKernel;
...@@ -549,6 +603,7 @@ private: ...@@ -549,6 +603,7 @@ private:
CudaBondedUtilities* bonded; CudaBondedUtilities* bonded;
CudaNonbondedUtilities* nonbonded; CudaNonbondedUtilities* nonbonded;
WorkThread* thread; WorkThread* thread;
Kernel compilerKernel;
}; };
struct CudaContext::Molecule { struct CudaContext::Molecule {
......
platforms/cuda/include/CudaKernels.h
View file @ 61d5cc0f
...@@ -9,7 +9,7 @@ ...@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * Medical Research, grant U54 GM072970. See https://simtk.org. *
* * * *
* Portions copyright (c) 2008-2013 Stanford University and the Authors. * * Portions copyright (c) 2008-2015 Stanford University and the Authors. *
* Authors: Peter Eastman * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -38,6 +38,27 @@ ...@@ -38,6 +38,27 @@
namespace OpenMM { namespace OpenMM {
/**
* This abstract class defines an interface for code that can compile CUDA kernels. This allows a plugin to take advantage of runtime compilation
* when running on recent versions of CUDA.
*/
class CudaCompilerKernel : public KernelImpl {
public:
static std::string Name() {
return "CudaCompilerKernel";
}
CudaCompilerKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
}
/**
* Compile a kernel to PTX.
*
* @param source the source code for the kernel
* @param options the flags to be passed to the compiler
* @param cu the CudaContext for which the kernel is being compiled
*/
virtual std::string createModule(const std::string& source, const std::string& flags, CudaContext& cu) = 0;
};
/** /**
* This kernel is invoked at the beginning and end of force and energy computations. It gives the * This kernel is invoked at the beginning and end of force and energy computations. It gives the
* Platform a chance to clear buffers and do other initialization at the beginning, and to do any * Platform a chance to clear buffers and do other initialization at the beginning, and to do any
...@@ -71,11 +92,13 @@ public: ...@@ -71,11 +92,13 @@ public:
* @param includeForce true if forces should be computed * @param includeForce true if forces should be computed
* @param includeEnergy true if potential energy should be computed * @param includeEnergy true if potential energy should be computed
* @param groups a set of bit flags for which force groups to include * @param groups a set of bit flags for which force groups to include
* @param valid the method may set this to false to indicate the results are invalid and the force/energy
* calculation should be repeated
* @return the potential energy of the system. This value is added to all values returned by ForceImpls' * @return the potential energy of the system. This value is added to all values returned by ForceImpls'
* calcForcesAndEnergy() methods. That is, each force kernel may <i>either</i> return its contribution to the * calcForcesAndEnergy() methods. That is, each force kernel may <i>either</i> return its contribution to the
* energy directly, <i>or</i> add it to an internal buffer so that it will be included here. * energy directly, <i>or</i> add it to an internal buffer so that it will be included here.
*/ */
double finishComputation(ContextImpl& context, bool includeForce, bool includeEnergy, int groups); double finishComputation(ContextImpl& context, bool includeForce, bool includeEnergy, int groups, bool& valid);
private: private:
CudaContext& cu; CudaContext& cu;
}; };
...@@ -497,11 +520,19 @@ public: ...@@ -497,11 +520,19 @@ public:
* @return the potential energy due to the force * @return the potential energy due to the force
*/ */
double execute(ContextImpl& context, bool includeForces, bool includeEnergy); double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
/**
* Copy changed parameters over to a context.
*
* @param context the context to copy parameters to
* @param force the CMAPTorsionForce to copy the parameters from
*/
void copyParametersToContext(ContextImpl& context, const CMAPTorsionForce& force);
private: private:
int numTorsions; int numTorsions;
bool hasInitializedKernel; bool hasInitializedKernel;
CudaContext& cu; CudaContext& cu;
const System& system; const System& system;
std::vector<int2> mapPositionsVec;
CudaArray* coefficients; CudaArray* coefficients;
CudaArray* mapPositions; CudaArray* mapPositions;
CudaArray* torsionMaps; CudaArray* torsionMaps;
...@@ -591,14 +622,16 @@ private: ...@@ -591,14 +622,16 @@ private:
int getKeySize() const {return 4;} int getKeySize() const {return 4;}
const char* getDataType() const {return "int2";} const char* getDataType() const {return "int2";}
const char* getKeyType() const {return "int";} const char* getKeyType() const {return "int";}
const char* getMinKey() const {return "INT_MIN";} const char* getMinKey() const {return "(-2147483647-1)";}
const char* getMaxKey() const {return "INT_MAX";} const char* getMaxKey() const {return "2147483647";}
const char* getMaxValue() const {return "make_int2(INT_MAX, INT_MAX)";} const char* getMaxValue() const {return "make_int2(2147483647, 2147483647)";}
const char* getSortKey() const {return "value.y";} const char* getSortKey() const {return "value.y";}
}; };
class PmeIO; class PmeIO;
class PmePreComputation; class PmePreComputation;
class PmePostComputation; class PmePostComputation;
class SyncStreamPreComputation;
class SyncStreamPostComputation;
CudaContext& cu; CudaContext& cu;
bool hasInitializedFFT; bool hasInitializedFFT;
CudaArray* sigmaEpsilon; CudaArray* sigmaEpsilon;
...@@ -614,6 +647,8 @@ private: ...@@ -614,6 +647,8 @@ private:
CudaSort* sort; CudaSort* sort;
Kernel cpuPme; Kernel cpuPme;
PmeIO* pmeio; PmeIO* pmeio;
CUstream pmeStream;
CUevent pmeSyncEvent;
cufftHandle fftForward; cufftHandle fftForward;
cufftHandle fftBackward; cufftHandle fftBackward;
CUfunction ewaldSumsKernel; CUfunction ewaldSumsKernel;
...@@ -628,7 +663,7 @@ private: ...@@ -628,7 +663,7 @@ private:
std::vector<std::pair<int, int> > exceptionAtoms; std::vector<std::pair<int, int> > exceptionAtoms;
double ewaldSelfEnergy, dispersionCoefficient, alpha; double ewaldSelfEnergy, dispersionCoefficient, alpha;
int interpolateForceThreads; int interpolateForceThreads;
bool hasCoulomb, hasLJ; bool hasCoulomb, hasLJ, usePmeStream;
static const int PmeOrder = 5; static const int PmeOrder = 5;
}; };
...@@ -715,7 +750,7 @@ public: ...@@ -715,7 +750,7 @@ public:
*/ */
void copyParametersToContext(ContextImpl& context, const GBSAOBCForce& force); void copyParametersToContext(ContextImpl& context, const GBSAOBCForce& force);
private: private:
double prefactor; double prefactor, surfaceAreaFactor;
bool hasCreatedKernels; bool hasCreatedKernels;
int maxTiles; int maxTiles;
CudaContext& cu; CudaContext& cu;
......
platforms/cuda/include/CudaNonbondedUtilities.h
View file @ 61d5cc0f
...@@ -278,7 +278,7 @@ private: ...@@ -278,7 +278,7 @@ private:
std::string kernelSource; std::string kernelSource;
std::map<std::string, std::string> kernelDefines; std::map<std::string, std::string> kernelDefines;
double cutoff; double cutoff;
bool useCutoff, usePeriodic, anyExclusions, usePadding; bool useCutoff, usePeriodic, anyExclusions, usePadding, forceRebuildNeighborList;
int startTileIndex, numTiles, startBlockIndex, numBlocks, maxTiles, numForceThreadBlocks, forceThreadBlockSize, nonbondedForceGroup, numAtoms; int startTileIndex, numTiles, startBlockIndex, numBlocks, maxTiles, numForceThreadBlocks, forceThreadBlockSize, nonbondedForceGroup, numAtoms;
}; };
......
platforms/cuda/include/CudaParallelKernels.h
View file @ 61d5cc0f
...@@ -9,7 +9,7 @@ ...@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * Medical Research, grant U54 GM072970. See https://simtk.org. *
* * * *
* Portions copyright (c) 2011-2013 Stanford University and the Authors. * * Portions copyright (c) 2011-2015 Stanford University and the Authors. *
* Authors: Peter Eastman * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -69,11 +69,13 @@ public: ...@@ -69,11 +69,13 @@ public:
* @param includeForce true if forces should be computed * @param includeForce true if forces should be computed
* @param includeEnergy true if potential energy should be computed * @param includeEnergy true if potential energy should be computed
* @param groups a set of bit flags for which force groups to include * @param groups a set of bit flags for which force groups to include
* @param valid the method may set this to false to indicate the results are invalid and the force/energy
* calculation should be repeated
* @return the potential energy of the system. This value is added to all values returned by ForceImpls' * @return the potential energy of the system. This value is added to all values returned by ForceImpls'
* calcForcesAndEnergy() methods. That is, each force kernel may <i>either</i> return its contribution to the * calcForcesAndEnergy() methods. That is, each force kernel may <i>either</i> return its contribution to the
* energy directly, <i>or</i> add it to an internal buffer so that it will be included here. * energy directly, <i>or</i> add it to an internal buffer so that it will be included here.
*/ */
double finishComputation(ContextImpl& context, bool includeForce, bool includeEnergy, int groups); double finishComputation(ContextImpl& context, bool includeForce, bool includeEnergy, int groups, bool& valid);
private: private:
class BeginComputationTask; class BeginComputationTask;
class FinishComputationTask; class FinishComputationTask;
...@@ -81,10 +83,13 @@ private: ...@@ -81,10 +83,13 @@ private:
std::vector<Kernel> kernels; std::vector<Kernel> kernels;
std::vector<long long> completionTimes; std::vector<long long> completionTimes;
std::vector<double> contextNonbondedFractions; std::vector<double> contextNonbondedFractions;
int* tileCounts;
CudaArray* contextForces; CudaArray* contextForces;
void* pinnedPositionBuffer; void* pinnedPositionBuffer;
long long* pinnedForceBuffer; long long* pinnedForceBuffer;
CUfunction sumKernel; CUfunction sumKernel;
CUevent event;
CUstream peerCopyStream;
}; };
/** /**
...@@ -340,6 +345,13 @@ public: ...@@ -340,6 +345,13 @@ public:
* @return the potential energy due to the force * @return the potential energy due to the force
*/ */
double execute(ContextImpl& context, bool includeForces, bool includeEnergy); double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
/**
* Copy changed parameters over to a context.
*
* @param context the context to copy parameters to
* @param force the CMAPTorsionForce to copy the parameters from
*/
void copyParametersToContext(ContextImpl& context, const CMAPTorsionForce& force);
private: private:
class Task; class Task;
CudaPlatform::PlatformData& data; CudaPlatform::PlatformData& data;
......
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