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Commit 047934e2 authored by Rafal P. Wiewiora's avatar Rafal P. Wiewiora
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Merge remote-tracking branch 'upstream/master'

parents ce3a5dc0 d12c9bd1
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Showing with 276 additions and 197 deletions
openmmapi/src/NonbondedForce.cpp
View file @ 047934e2
...@@ -48,7 +48,8 @@ using std::stringstream; ...@@ -48,7 +48,8 @@ using std::stringstream;
using std::vector; using std::vector;
NonbondedForce::NonbondedForce() : nonbondedMethod(NoCutoff), cutoffDistance(1.0), switchingDistance(-1.0), rfDielectric(78.3), NonbondedForce::NonbondedForce() : nonbondedMethod(NoCutoff), cutoffDistance(1.0), switchingDistance(-1.0), rfDielectric(78.3),
ewaldErrorTol(5e-4), alpha(0.0), useSwitchingFunction(false), useDispersionCorrection(true), recipForceGroup(-1), nx(0), ny(0), nz(0) { ewaldErrorTol(5e-4), alpha(0.0), dalpha(0.0), useSwitchingFunction(false), useDispersionCorrection(true), recipForceGroup(-1),
nx(0), ny(0), nz(0), dnx(0), dny(0), dnz(0) {
} }
NonbondedForce::NonbondedMethod NonbondedForce::getNonbondedMethod() const { NonbondedForce::NonbondedMethod NonbondedForce::getNonbondedMethod() const {
...@@ -106,6 +107,13 @@ void NonbondedForce::getPMEParameters(double& alpha, int& nx, int& ny, int& nz) ...@@ -106,6 +107,13 @@ void NonbondedForce::getPMEParameters(double& alpha, int& nx, int& ny, int& nz)
nz = this->nz; nz = this->nz;
} }
void NonbondedForce::getLJPMEParameters(double& alpha, int& nx, int& ny, int& nz) const {
alpha = this->dalpha;
nx = this->dnx;
ny = this->dny;
nz = this->dnz;
}
void NonbondedForce::setPMEParameters(double alpha, int nx, int ny, int nz) { void NonbondedForce::setPMEParameters(double alpha, int nx, int ny, int nz) {
this->alpha = alpha; this->alpha = alpha;
this->nx = nx; this->nx = nx;
...@@ -113,10 +121,21 @@ void NonbondedForce::setPMEParameters(double alpha, int nx, int ny, int nz) { ...@@ -113,10 +121,21 @@ void NonbondedForce::setPMEParameters(double alpha, int nx, int ny, int nz) {
this->nz = nz; this->nz = nz;
} }
void NonbondedForce::setLJPMEParameters(double alpha, int nx, int ny, int nz) {
this->dalpha = alpha;
this->dnx = nx;
this->dny = ny;
this->dnz = nz;
}
void NonbondedForce::getPMEParametersInContext(const Context& context, double& alpha, int& nx, int& ny, int& nz) const { void NonbondedForce::getPMEParametersInContext(const Context& context, double& alpha, int& nx, int& ny, int& nz) const {
dynamic_cast<const NonbondedForceImpl&>(getImplInContext(context)).getPMEParameters(alpha, nx, ny, nz); dynamic_cast<const NonbondedForceImpl&>(getImplInContext(context)).getPMEParameters(alpha, nx, ny, nz);
} }
void NonbondedForce::getLJPMEParametersInContext(const Context& context, double& alpha, int& nx, int& ny, int& nz) const {
dynamic_cast<const NonbondedForceImpl&>(getImplInContext(context)).getLJPMEParameters(alpha, nx, ny, nz);
}
int NonbondedForce::addParticle(double charge, double sigma, double epsilon) { int NonbondedForce::addParticle(double charge, double sigma, double epsilon) {
particles.push_back(ParticleInfo(charge, sigma, epsilon)); particles.push_back(ParticleInfo(charge, sigma, epsilon));
return particles.size()-1; return particles.size()-1;
......
openmmapi/src/NonbondedForceImpl.cpp
View file @ 047934e2
...@@ -90,9 +90,7 @@ void NonbondedForceImpl::initialize(ContextImpl& context) { ...@@ -90,9 +90,7 @@ void NonbondedForceImpl::initialize(ContextImpl& context) {
exceptions[particle1].insert(particle2); exceptions[particle1].insert(particle2);
exceptions[particle2].insert(particle1); exceptions[particle2].insert(particle1);
} }
if (owner.getNonbondedMethod() == NonbondedForce::CutoffPeriodic || if (owner.getNonbondedMethod() != NonbondedForce::NoCutoff && owner.getNonbondedMethod() != NonbondedForce::CutoffNonPeriodic) {
owner.getNonbondedMethod() == NonbondedForce::Ewald ||
owner.getNonbondedMethod() == NonbondedForce::PME) {
Vec3 boxVectors[3]; Vec3 boxVectors[3];
system.getDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]); system.getDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
double cutoff = owner.getCutoffDistance(); double cutoff = owner.getCutoffDistance();
...@@ -151,19 +149,29 @@ void NonbondedForceImpl::calcEwaldParameters(const System& system, const Nonbond ...@@ -151,19 +149,29 @@ void NonbondedForceImpl::calcEwaldParameters(const System& system, const Nonbond
kmaxz++; kmaxz++;
} }
void NonbondedForceImpl::calcPMEParameters(const System& system, const NonbondedForce& force, double& alpha, int& xsize, int& ysize, int& zsize) { void NonbondedForceImpl::calcPMEParameters(const System& system, const NonbondedForce& force, double& alpha, int& xsize, int& ysize, int& zsize, bool lj) {
force.getPMEParameters(alpha, xsize, ysize, zsize); if (lj)
force.getLJPMEParameters(alpha, xsize, ysize, zsize);
else
force.getPMEParameters(alpha, xsize, ysize, zsize);
if (alpha == 0.0) { if (alpha == 0.0) {
Vec3 boxVectors[3]; Vec3 boxVectors[3];
system.getDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]); system.getDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
double tol = force.getEwaldErrorTolerance(); double tol = force.getEwaldErrorTolerance();
alpha = (1.0/force.getCutoffDistance())*std::sqrt(-log(2.0*tol)); alpha = (1.0/force.getCutoffDistance())*std::sqrt(-log(2.0*tol));
xsize = (int) ceil(2*alpha*boxVectors[0][0]/(3*pow(tol, 0.2))); if (lj) {
ysize = (int) ceil(2*alpha*boxVectors[1][1]/(3*pow(tol, 0.2))); xsize = (int) ceil(alpha*boxVectors[0][0]/(3*pow(tol, 0.2)));
zsize = (int) ceil(2*alpha*boxVectors[2][2]/(3*pow(tol, 0.2))); ysize = (int) ceil(alpha*boxVectors[1][1]/(3*pow(tol, 0.2)));
xsize = max(xsize, 5); zsize = (int) ceil(alpha*boxVectors[2][2]/(3*pow(tol, 0.2)));
ysize = max(ysize, 5); }
zsize = max(zsize, 5); else {
xsize = (int) ceil(2*alpha*boxVectors[0][0]/(3*pow(tol, 0.2)));
ysize = (int) ceil(2*alpha*boxVectors[1][1]/(3*pow(tol, 0.2)));
zsize = (int) ceil(2*alpha*boxVectors[2][2]/(3*pow(tol, 0.2)));
}
xsize = max(xsize, 6);
ysize = max(ysize, 6);
zsize = max(zsize, 6);
} }
} }
...@@ -277,8 +285,13 @@ double NonbondedForceImpl::calcDispersionCorrection(const System& system, const ...@@ -277,8 +285,13 @@ double NonbondedForceImpl::calcDispersionCorrection(const System& system, const
void NonbondedForceImpl::updateParametersInContext(ContextImpl& context) { void NonbondedForceImpl::updateParametersInContext(ContextImpl& context) {
kernel.getAs<CalcNonbondedForceKernel>().copyParametersToContext(context, owner); kernel.getAs<CalcNonbondedForceKernel>().copyParametersToContext(context, owner);
context.systemChanged();
} }
void NonbondedForceImpl::getPMEParameters(double& alpha, int& nx, int& ny, int& nz) const { void NonbondedForceImpl::getPMEParameters(double& alpha, int& nx, int& ny, int& nz) const {
kernel.getAs<CalcNonbondedForceKernel>().getPMEParameters(alpha, nx, ny, nz); kernel.getAs<CalcNonbondedForceKernel>().getPMEParameters(alpha, nx, ny, nz);
} }
void NonbondedForceImpl::getLJPMEParameters(double& alpha, int& nx, int& ny, int& nz) const {
kernel.getAs<CalcNonbondedForceKernel>().getLJPMEParameters(alpha, nx, ny, nz);
}
openmmapi/src/PeriodicTorsionForceImpl.cpp
View file @ 047934e2
...@@ -63,4 +63,5 @@ std::vector<std::string> PeriodicTorsionForceImpl::getKernelNames() { ...@@ -63,4 +63,5 @@ std::vector<std::string> PeriodicTorsionForceImpl::getKernelNames() {
void PeriodicTorsionForceImpl::updateParametersInContext(ContextImpl& context) { void PeriodicTorsionForceImpl::updateParametersInContext(ContextImpl& context) {
kernel.getAs<CalcPeriodicTorsionForceKernel>().copyParametersToContext(context, owner); kernel.getAs<CalcPeriodicTorsionForceKernel>().copyParametersToContext(context, owner);
context.systemChanged();
} }
openmmapi/src/RBTorsionForceImpl.cpp
View file @ 047934e2
...@@ -63,4 +63,5 @@ std::vector<std::string> RBTorsionForceImpl::getKernelNames() { ...@@ -63,4 +63,5 @@ std::vector<std::string> RBTorsionForceImpl::getKernelNames() {
void RBTorsionForceImpl::updateParametersInContext(ContextImpl& context) { void RBTorsionForceImpl::updateParametersInContext(ContextImpl& context) {
kernel.getAs<CalcRBTorsionForceKernel>().copyParametersToContext(context, owner); kernel.getAs<CalcRBTorsionForceKernel>().copyParametersToContext(context, owner);
context.systemChanged();
} }
openmmapi/src/ThreadPool.cpp
View file @ 047934e2
...@@ -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) 2013-2017 Stanford University and the Authors. *
* Authors: Peter Eastman * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -40,10 +40,17 @@ class ThreadPool::ThreadData { ...@@ -40,10 +40,17 @@ class ThreadPool::ThreadData {
public: public:
ThreadData(ThreadPool& owner, int index) : owner(owner), index(index), isDeleted(false) { ThreadData(ThreadPool& owner, int index) : owner(owner), index(index), isDeleted(false) {
} }
void executeTask() {
if (owner.currentTask != NULL)
owner.currentTask->execute(owner, index);
else
owner.currentFunction(owner, index);
}
ThreadPool& owner; ThreadPool& owner;
int index; int index;
bool isDeleted; bool isDeleted;
Task* currentTask; Task* currentTask;
function<void (ThreadPool& pool, int)> currentFunction;
}; };
static void* threadBody(void* args) { static void* threadBody(void* args) {
...@@ -54,13 +61,13 @@ static void* threadBody(void* args) { ...@@ -54,13 +61,13 @@ static void* threadBody(void* args) {
data.owner.syncThreads(); data.owner.syncThreads();
if (data.isDeleted) if (data.isDeleted)
break; break;
data.currentTask->execute(data.owner, data.index); data.executeTask();
} }
delete &data; delete &data;
return 0; return 0;
} }
ThreadPool::ThreadPool(int numThreads) { ThreadPool::ThreadPool(int numThreads) : currentTask(NULL) {
if (numThreads <= 0) if (numThreads <= 0)
numThreads = getNumProcessors(); numThreads = getNumProcessors();
this->numThreads = numThreads; this->numThreads = numThreads;
...@@ -99,8 +106,13 @@ int ThreadPool::getNumThreads() const { ...@@ -99,8 +106,13 @@ int ThreadPool::getNumThreads() const {
} }
void ThreadPool::execute(Task& task) { void ThreadPool::execute(Task& task) {
for (int i = 0; i < (int) threadData.size(); i++) currentTask = &task;
threadData[i]->currentTask = &task; resumeThreads();
}
void ThreadPool::execute(function<void (ThreadPool&, int)> task) {
currentTask = NULL;
currentFunction = task;
resumeThreads(); resumeThreads();
} }
......
platforms/cpu/include/CpuBondForce.h
View file @ 047934e2
...@@ -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) 2014 Stanford University and the Authors. * * Portions copyright (c) 2014-2017 Stanford University and the Authors. *
* Authors: Peter Eastman * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -46,7 +46,6 @@ namespace OpenMM { ...@@ -46,7 +46,6 @@ namespace OpenMM {
*/ */
class OPENMM_EXPORT_CPU CpuBondForce { class OPENMM_EXPORT_CPU CpuBondForce {
public: public:
class ComputeForceTask;
CpuBondForce(); CpuBondForce();
/** /**
* Analyze the set of bonds and decide which to compute with each thread. * Analyze the set of bonds and decide which to compute with each thread.
...@@ -55,13 +54,13 @@ public: ...@@ -55,13 +54,13 @@ public:
/** /**
* Compute the forces from all bonds. * Compute the forces from all bonds.
*/ */
void calculateForce(std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMM** parameters, std::vector<OpenMM::RealVec>& forces, void calculateForce(std::vector<OpenMM::Vec3>& atomCoordinates, double** parameters, std::vector<OpenMM::Vec3>& forces,
RealOpenMM* totalEnergy, ReferenceBondIxn& referenceBondIxn); double* totalEnergy, ReferenceBondIxn& referenceBondIxn);
/** /**
* This routine contains the code executed by each thread. * This routine contains the code executed by each thread.
*/ */
void threadComputeForce(ThreadPool& threads, int threadIndex, std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMM** parameters, void threadComputeForce(ThreadPool& threads, int threadIndex, std::vector<OpenMM::Vec3>& atomCoordinates, double** parameters,
std::vector<OpenMM::RealVec>& forces, RealOpenMM* totalEnergy, ReferenceBondIxn& referenceBondIxn); std::vector<OpenMM::Vec3>& forces, double* totalEnergy, ReferenceBondIxn& referenceBondIxn);
private: private:
bool canAssignBond(int bond, int thread, std::vector<int>& atomThread); bool canAssignBond(int bond, int thread, std::vector<int>& atomThread);
void assignBond(int bond, int thread, std::vector<int>& atomThread, std::vector<int>& bondThread, std::vector<std::set<int> >& atomBonds, std::list<int>& candidateBonds); void assignBond(int bond, int thread, std::vector<int>& atomThread, std::vector<int>& bondThread, std::vector<std::set<int> >& atomBonds, std::list<int>& candidateBonds);
......
platforms/cpu/include/CpuCustomGBForce.h
View file @ 047934e2
/* Portions copyright (c) 2009-2016 Stanford University and Simbios. /* Portions copyright (c) 2009-2017 Stanford University and Simbios.
* Contributors: Peter Eastman * Contributors: Peter Eastman
* *
* Permission is hereby granted, free of charge, to any person obtaining * Permission is hereby granted, free of charge, to any person obtaining
...@@ -39,7 +39,6 @@ namespace OpenMM { ...@@ -39,7 +39,6 @@ namespace OpenMM {
class CpuCustomGBForce { class CpuCustomGBForce {
private: private:
class ComputeForceTask;
class ThreadData; class ThreadData;
bool cutoff; bool cutoff;
...@@ -60,7 +59,7 @@ private: ...@@ -60,7 +59,7 @@ private:
// The following variables are used to make information accessible to the individual threads. // The following variables are used to make information accessible to the individual threads.
int numberOfAtoms; int numberOfAtoms;
float* posq; float* posq;
RealOpenMM** atomParameters; double** atomParameters;
const std::map<std::string, double>* globalParameters; const std::map<std::string, double>* globalParameters;
std::vector<AlignedArray<float> >* threadForce; std::vector<AlignedArray<float> >* threadForce;
bool includeForce, includeEnergy; bool includeForce, includeEnergy;
...@@ -82,7 +81,7 @@ private: ...@@ -82,7 +81,7 @@ private:
* @param useExclusions specifies whether to use exclusions * @param useExclusions specifies whether to use exclusions
*/ */
void calculateParticlePairValue(int index, ThreadData& data, int numAtoms, float* posq, RealOpenMM** atomParameters, void calculateParticlePairValue(int index, ThreadData& data, int numAtoms, float* posq, double** atomParameters,
bool useExclusions, const fvec4& boxSize, const fvec4& invBoxSize); bool useExclusions, const fvec4& boxSize, const fvec4& invBoxSize);
/** /**
...@@ -96,7 +95,7 @@ private: ...@@ -96,7 +95,7 @@ private:
* @param atomParameters atomParameters[atomIndex][paramterIndex] * @param atomParameters atomParameters[atomIndex][paramterIndex]
*/ */
void calculateOnePairValue(int index, int atom1, int atom2, ThreadData& data, float* posq, RealOpenMM** atomParameters, void calculateOnePairValue(int index, int atom1, int atom2, ThreadData& data, float* posq, double** atomParameters,
std::vector<float>& valueArray, const fvec4& boxSize, const fvec4& invBoxSize); std::vector<float>& valueArray, const fvec4& boxSize, const fvec4& invBoxSize);
/** /**
...@@ -111,7 +110,7 @@ private: ...@@ -111,7 +110,7 @@ private:
* @param totalEnergy the energy contribution is added to this * @param totalEnergy the energy contribution is added to this
*/ */
void calculateSingleParticleEnergyTerm(int index, ThreadData& data, int numAtoms, float* posq, RealOpenMM** atomParameters, float* forces, double& totalEnergy); void calculateSingleParticleEnergyTerm(int index, ThreadData& data, int numAtoms, float* posq, double** atomParameters, float* forces, double& totalEnergy);
/** /**
* Calculate an energy term that is based on particle pairs * Calculate an energy term that is based on particle pairs
...@@ -126,7 +125,7 @@ private: ...@@ -126,7 +125,7 @@ private:
* @param totalEnergy the energy contribution is added to this * @param totalEnergy the energy contribution is added to this
*/ */
void calculateParticlePairEnergyTerm(int index, ThreadData& data, int numAtoms, float* posq, RealOpenMM** atomParameters, void calculateParticlePairEnergyTerm(int index, ThreadData& data, int numAtoms, float* posq, double** atomParameters,
bool useExclusions, float* forces, double& totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize); bool useExclusions, float* forces, double& totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize);
/** /**
...@@ -142,7 +141,7 @@ private: ...@@ -142,7 +141,7 @@ private:
* @param totalEnergy the energy contribution is added to this * @param totalEnergy the energy contribution is added to this
*/ */
void calculateOnePairEnergyTerm(int index, int atom1, int atom2, ThreadData& data, float* posq, RealOpenMM** atomParameters, void calculateOnePairEnergyTerm(int index, int atom1, int atom2, ThreadData& data, float* posq, double** atomParameters,
float* forces, double& totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize); float* forces, double& totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize);
/** /**
...@@ -155,7 +154,7 @@ private: ...@@ -155,7 +154,7 @@ private:
* @param forces forces on atoms are added to this * @param forces forces on atoms are added to this
*/ */
void calculateChainRuleForces(ThreadData& data, int numAtoms, float* posq, RealOpenMM** atomParameters, void calculateChainRuleForces(ThreadData& data, int numAtoms, float* posq, double** atomParameters,
float* forces, const fvec4& boxSize, const fvec4& invBoxSize); float* forces, const fvec4& boxSize, const fvec4& invBoxSize);
/** /**
...@@ -170,7 +169,7 @@ private: ...@@ -170,7 +169,7 @@ private:
* @param isExcluded specifies whether this is an excluded pair * @param isExcluded specifies whether this is an excluded pair
*/ */
void calculateOnePairChainRule(int atom1, int atom2, ThreadData& data, float* posq, RealOpenMM** atomParameters, void calculateOnePairChainRule(int atom1, int atom2, ThreadData& data, float* posq, double** atomParameters,
float* forces, bool isExcluded, const fvec4& boxSize, const fvec4& invBoxSize); float* forces, bool isExcluded, const fvec4& boxSize, const fvec4& invBoxSize);
/** /**
...@@ -218,7 +217,7 @@ public: ...@@ -218,7 +217,7 @@ public:
* @param boxSize the X, Y, and Z widths of the periodic box * @param boxSize the X, Y, and Z widths of the periodic box
*/ */
void setPeriodic(RealVec& boxSize); void setPeriodic(Vec3& boxSize);
/** /**
* Calculate custom GB ixn * Calculate custom GB ixn
...@@ -232,7 +231,7 @@ public: ...@@ -232,7 +231,7 @@ public:
* @param energyParamDerivs derivatives of the energy with respect to global parameters * @param energyParamDerivs derivatives of the energy with respect to global parameters
*/ */
void calculateIxn(int numberOfAtoms, float* posq, RealOpenMM** atomParameters, std::map<std::string, double>& globalParameters, void calculateIxn(int numberOfAtoms, float* posq, double** atomParameters, std::map<std::string, double>& globalParameters,
std::vector<AlignedArray<float> >& threadForce, bool includeForce, bool includeEnergy, double& totalEnergy, double* energyParamDerivs); std::vector<AlignedArray<float> >& threadForce, bool includeForce, bool includeEnergy, double& totalEnergy, double* energyParamDerivs);
}; };
......
platforms/cpu/include/CpuCustomManyParticleForce.h
View file @ 047934e2
/* Portions copyright (c) 2009-2014 Stanford University and Simbios. /* Portions copyright (c) 2009-2017 Stanford University and Simbios.
* Contributors: Peter Eastman * Contributors: Peter Eastman
* *
* Permission is hereby granted, free of charge, to any person obtaining * Permission is hereby granted, free of charge, to any person obtaining
...@@ -48,13 +48,12 @@ private: ...@@ -48,13 +48,12 @@ private:
class DistanceTermInfo; class DistanceTermInfo;
class AngleTermInfo; class AngleTermInfo;
class DihedralTermInfo; class DihedralTermInfo;
class ComputeForceTask;
class ThreadData; class ThreadData;
int numParticles, numParticlesPerSet, numPerParticleParameters, numTypes; int numParticles, numParticlesPerSet, numPerParticleParameters, numTypes;
bool useCutoff, usePeriodic, triclinic, centralParticleMode; bool useCutoff, usePeriodic, triclinic, centralParticleMode;
RealOpenMM cutoffDistance; double cutoffDistance;
float recipBoxSize[3]; float recipBoxSize[3];
RealVec periodicBoxVectors[3]; Vec3 periodicBoxVectors[3];
AlignedArray<fvec4> periodicBoxVec4; AlignedArray<fvec4> periodicBoxVec4;
CpuNeighborList* neighborList; CpuNeighborList* neighborList;
ThreadPool& threads; ThreadPool& threads;
...@@ -66,7 +65,7 @@ private: ...@@ -66,7 +65,7 @@ private:
std::vector<ThreadData*> threadData; std::vector<ThreadData*> threadData;
// The following variables are used to make information accessible to the individual threads. // The following variables are used to make information accessible to the individual threads.
float* posq; float* posq;
RealOpenMM** particleParameters; double** particleParameters;
const std::map<std::string, double>* globalParameters; const std::map<std::string, double>* globalParameters;
std::vector<AlignedArray<float> >* threadForce; std::vector<AlignedArray<float> >* threadForce;
bool includeForces, includeEnergy; bool includeForces, includeEnergy;
...@@ -82,7 +81,7 @@ private: ...@@ -82,7 +81,7 @@ private:
* interaction for each one. * interaction for each one.
*/ */
void loopOverInteractions(std::vector<int>& availableParticles, std::vector<int>& particleSet, int loopIndex, int startIndex, void loopOverInteractions(std::vector<int>& availableParticles, std::vector<int>& particleSet, int loopIndex, int startIndex,
RealOpenMM** particleParameters, float* forces, ThreadData& data, const fvec4& boxSize, const fvec4& invBoxSize); double** particleParameters, float* forces, ThreadData& data, const fvec4& boxSize, const fvec4& invBoxSize);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -105,7 +104,7 @@ private: ...@@ -105,7 +104,7 @@ private:
* @param boxSize the size of the periodic box * @param boxSize the size of the periodic box
* @param invBoxSize the inverse size of the periodic box * @param invBoxSize the inverse size of the periodic box
*/ */
void calculateOneIxn(std::vector<int>& particleSet, RealOpenMM** particleParameters, float* forces, ThreadData& data, const fvec4& boxSize, const fvec4& invBoxSize); void calculateOneIxn(std::vector<int>& particleSet, double** particleParameters, float* forces, ThreadData& data, const fvec4& boxSize, const fvec4& invBoxSize);
/** /**
* Compute the displacement and squared distance between two points, optionally using * Compute the displacement and squared distance between two points, optionally using
...@@ -133,7 +132,7 @@ public: ...@@ -133,7 +132,7 @@ public:
* *
* @param distance the cutoff distance * @param distance the cutoff distance
*/ */
void setUseCutoff(RealOpenMM distance); void setUseCutoff(double distance);
/** /**
* Set the force to use periodic boundary conditions. This requires that a cutoff has * Set the force to use periodic boundary conditions. This requires that a cutoff has
...@@ -142,7 +141,7 @@ public: ...@@ -142,7 +141,7 @@ public:
* *
* @param periodicBoxVectors the vectors defining the periodic box * @param periodicBoxVectors the vectors defining the periodic box
*/ */
void setPeriodic(RealVec* periodicBoxVectors); void setPeriodic(Vec3* periodicBoxVectors);
/** /**
* Calculate the interaction. * Calculate the interaction.
...@@ -155,7 +154,7 @@ public: ...@@ -155,7 +154,7 @@ public:
* @param includeEnergy whether to compute energy * @param includeEnergy whether to compute energy
* @param energy the total energy is added to this * @param energy the total energy is added to this
*/ */
void calculateIxn(AlignedArray<float>& posq, RealOpenMM** particleParameters, const std::map<std::string, double>& globalParameters, void calculateIxn(AlignedArray<float>& posq, double** particleParameters, const std::map<std::string, double>& globalParameters,
std::vector<AlignedArray<float> >& threadForce, bool includeForces, bool includeEnergy, double& energy); std::vector<AlignedArray<float> >& threadForce, bool includeForces, bool includeEnergy, double& energy);
}; };
......
platforms/cpu/include/CpuCustomNonbondedForce.h
View file @ 047934e2
/* Portions copyright (c) 2009-2016 Stanford University and Simbios. /* Portions copyright (c) 2009-2017 Stanford University and Simbios.
* Contributors: Peter Eastman * Contributors: Peter Eastman
* *
* Permission is hereby granted, free of charge, to any person obtaining * Permission is hereby granted, free of charge, to any person obtaining
...@@ -67,7 +67,7 @@ class CpuCustomNonbondedForce { ...@@ -67,7 +67,7 @@ class CpuCustomNonbondedForce {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void setUseCutoff(RealOpenMM distance, const CpuNeighborList& neighbors); void setUseCutoff(double distance, const CpuNeighborList& neighbors);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -88,7 +88,7 @@ class CpuCustomNonbondedForce { ...@@ -88,7 +88,7 @@ class CpuCustomNonbondedForce {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void setUseSwitchingFunction(RealOpenMM distance); void setUseSwitchingFunction(double distance);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -100,7 +100,7 @@ class CpuCustomNonbondedForce { ...@@ -100,7 +100,7 @@ class CpuCustomNonbondedForce {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void setPeriodic(RealVec* periodicBoxVectors); void setPeriodic(Vec3* periodicBoxVectors);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -118,22 +118,22 @@ class CpuCustomNonbondedForce { ...@@ -118,22 +118,22 @@ class CpuCustomNonbondedForce {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void calculatePairIxn(int numberOfAtoms, float* posq, std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMM** atomParameters, void calculatePairIxn(int numberOfAtoms, float* posq, std::vector<OpenMM::Vec3>& atomCoordinates, double** atomParameters,
RealOpenMM* fixedParameters, const std::map<std::string, double>& globalParameters, double* fixedParameters, const std::map<std::string, double>& globalParameters,
std::vector<AlignedArray<float> >& threadForce, bool includeForce, bool includeEnergy, double& totalEnergy, double* energyParamDerivs); std::vector<AlignedArray<float> >& threadForce, bool includeForce, bool includeEnergy, double& totalEnergy, double* energyParamDerivs);
private: private:
class ComputeForceTask;
class ThreadData; class ThreadData;
bool cutoff; bool cutoff;
bool useSwitch; bool useSwitch;
bool periodic; bool periodic;
bool triclinic; bool triclinic;
bool useInteractionGroups;
const CpuNeighborList* neighborList; const CpuNeighborList* neighborList;
float recipBoxSize[3]; float recipBoxSize[3];
RealVec periodicBoxVectors[3]; Vec3 periodicBoxVectors[3];
AlignedArray<fvec4> periodicBoxVec4; AlignedArray<fvec4> periodicBoxVec4;
RealOpenMM cutoffDistance, switchingDistance; double cutoffDistance, switchingDistance;
ThreadPool& threads; ThreadPool& threads;
const std::vector<std::set<int> > exclusions; const std::vector<std::set<int> > exclusions;
std::vector<ThreadData*> threadData; std::vector<ThreadData*> threadData;
...@@ -143,8 +143,8 @@ private: ...@@ -143,8 +143,8 @@ private:
// The following variables are used to make information accessible to the individual threads. // The following variables are used to make information accessible to the individual threads.
int numberOfAtoms; int numberOfAtoms;
float* posq; float* posq;
RealVec const* atomCoordinates; Vec3 const* atomCoordinates;
RealOpenMM** atomParameters; double** atomParameters;
const std::map<std::string, double>* globalParameters; const std::map<std::string, double>* globalParameters;
std::vector<AlignedArray<float> >* threadForce; std::vector<AlignedArray<float> >* threadForce;
bool includeForce, includeEnergy; bool includeForce, includeEnergy;
...@@ -185,7 +185,7 @@ public: ...@@ -185,7 +185,7 @@ public:
CompiledExpressionSet expressionSet; CompiledExpressionSet expressionSet;
std::vector<double> particleParam; std::vector<double> particleParam;
double r; double r;
std::vector<RealOpenMM> energyParamDerivs; std::vector<double> energyParamDerivs;
}; };
} // namespace OpenMM } // namespace OpenMM
......
platforms/cpu/include/CpuGBSAOBCForce.h
View file @ 047934e2
/* Portions copyright (c) 2006-2013 Stanford University and Simbios. /* Portions copyright (c) 2006-2017 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
...@@ -36,7 +36,6 @@ namespace OpenMM { ...@@ -36,7 +36,6 @@ namespace OpenMM {
class CpuGBSAOBCForce { class CpuGBSAOBCForce {
public: public:
class ComputeTask;
CpuGBSAOBCForce(); CpuGBSAOBCForce();
/** /**
......
platforms/cpu/include/CpuGayBerneForce.h
View file @ 047934e2
...@@ -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) 2016 Stanford University and the Authors. * * Portions copyright (c) 2016-2017 Stanford University and the Authors. *
* Authors: Peter Eastman * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -36,7 +36,7 @@ ...@@ -36,7 +36,7 @@
#include "openmm/internal/ThreadPool.h" #include "openmm/internal/ThreadPool.h"
#include "CpuNeighborList.h" #include "CpuNeighborList.h"
#include "CpuPlatform.h" #include "CpuPlatform.h"
#include "RealVec.h" #include "openmm/Vec3.h"
#include <set> #include <set>
#include <utility> #include <utility>
...@@ -45,7 +45,6 @@ namespace OpenMM { ...@@ -45,7 +45,6 @@ namespace OpenMM {
class CpuGayBerneForce { class CpuGayBerneForce {
public: public:
struct Matrix; struct Matrix;
class ComputeTask;
/** /**
* Constructor. * Constructor.
...@@ -62,7 +61,7 @@ public: ...@@ -62,7 +61,7 @@ public:
* @param data the platform data for the current context * @param data the platform data for the current context
* @return the energy of the interaction * @return the energy of the interaction
*/ */
RealOpenMM calculateForce(const std::vector<RealVec>& positions, std::vector<RealVec>& forces, std::vector<AlignedArray<float> >& threadForce, RealVec* boxVectors, CpuPlatform::PlatformData& data); double calculateForce(const std::vector<Vec3>& positions, std::vector<Vec3>& forces, std::vector<AlignedArray<float> >& threadForce, Vec3* boxVectors, CpuPlatform::PlatformData& data);
/** /**
* This routine contains the code executed by each thread. * This routine contains the code executed by each thread.
...@@ -82,43 +81,43 @@ private: ...@@ -82,43 +81,43 @@ private:
std::set<std::pair<int, int> > exclusions; std::set<std::pair<int, int> > exclusions;
std::vector<std::set<int> > particleExclusions; std::vector<std::set<int> > particleExclusions;
GayBerneForce::NonbondedMethod nonbondedMethod; GayBerneForce::NonbondedMethod nonbondedMethod;
RealOpenMM cutoffDistance, switchingDistance; double cutoffDistance, switchingDistance;
bool useSwitchingFunction; bool useSwitchingFunction;
std::vector<RealOpenMM> s; std::vector<double> s;
std::vector<Matrix> A, B, G; std::vector<Matrix> A, B, G;
std::vector<double> threadEnergy; std::vector<double> threadEnergy;
std::vector<std::vector<RealVec> > threadTorque; std::vector<std::vector<Vec3> > threadTorque;
// The following variables are used to make information accessible to the individual threads. // The following variables are used to make information accessible to the individual threads.
RealVec const* positions; Vec3 const* positions;
std::vector<AlignedArray<float> >* threadForce; std::vector<AlignedArray<float> >* threadForce;
RealVec* boxVectors; Vec3* boxVectors;
void* atomicCounter; void* atomicCounter;
void computeEllipsoidFrames(const std::vector<RealVec>& positions); void computeEllipsoidFrames(const std::vector<Vec3>& positions);
void applyTorques(const std::vector<RealVec>& positions, std::vector<RealVec>& forces); void applyTorques(const std::vector<Vec3>& positions, std::vector<Vec3>& forces);
RealOpenMM computeOneInteraction(int particle1, int particle2, RealOpenMM sigma, RealOpenMM epsilon, const RealVec* positions, double computeOneInteraction(int particle1, int particle2, double sigma, double epsilon, const Vec3* positions,
float* forces, std::vector<RealVec>& torques, const RealVec* boxVectors); float* forces, std::vector<Vec3>& torques, const Vec3* boxVectors);
}; };
struct CpuGayBerneForce::ParticleInfo { struct CpuGayBerneForce::ParticleInfo {
int xparticle, yparticle; int xparticle, yparticle;
RealOpenMM sigmaOver2, sqrtEpsilon, rx, ry, rz, ex, ey, ez; double sigmaOver2, sqrtEpsilon, rx, ry, rz, ex, ey, ez;
bool isPointParticle; bool isPointParticle;
}; };
struct CpuGayBerneForce::ExceptionInfo { struct CpuGayBerneForce::ExceptionInfo {
int particle1, particle2; int particle1, particle2;
RealOpenMM sigma, epsilon; double sigma, epsilon;
}; };
struct CpuGayBerneForce::Matrix { struct CpuGayBerneForce::Matrix {
RealOpenMM v[3][3]; double v[3][3];
RealVec operator*(const RealVec& r) { Vec3 operator*(const Vec3& r) {
return RealVec(v[0][0]*r[0] + v[0][1]*r[1] + v[0][2]*r[2], return Vec3(v[0][0]*r[0] + v[0][1]*r[1] + v[0][2]*r[2],
v[1][0]*r[0] + v[1][1]*r[1] + v[1][2]*r[2], v[1][0]*r[0] + v[1][1]*r[1] + v[1][2]*r[2],
v[2][0]*r[0] + v[2][1]*r[1] + v[2][2]*r[2]); v[2][0]*r[0] + v[2][1]*r[1] + v[2][2]*r[2]);
} }
Matrix operator+(const Matrix& m) { Matrix operator+(const Matrix& m) {
...@@ -129,13 +128,13 @@ struct CpuGayBerneForce::Matrix { ...@@ -129,13 +128,13 @@ struct CpuGayBerneForce::Matrix {
return result; return result;
} }
RealOpenMM determinant() { double determinant() {
return (v[0][0]*v[1][1]*v[2][2] + v[0][1]*v[1][2]*v[2][0] + v[0][2]*v[1][0]*v[2][1] - return (v[0][0]*v[1][1]*v[2][2] + v[0][1]*v[1][2]*v[2][0] + v[0][2]*v[1][0]*v[2][1] -
v[0][0]*v[1][2]*v[2][1] - v[0][1]*v[1][0]*v[2][2] - v[0][2]*v[1][1]*v[2][0]); v[0][0]*v[1][2]*v[2][1] - v[0][1]*v[1][0]*v[2][2] - v[0][2]*v[1][1]*v[2][0]);
} }
Matrix inverse() { Matrix inverse() {
RealOpenMM invDet = 1/determinant(); double invDet = 1/determinant();
Matrix result; Matrix result;
result.v[0][0] = invDet*(v[1][1]*v[2][2] - v[1][2]*v[2][1]); result.v[0][0] = invDet*(v[1][1]*v[2][2] - v[1][2]*v[2][1]);
result.v[1][0] = -invDet*(v[1][0]*v[2][2] - v[1][2]*v[2][0]); result.v[1][0] = -invDet*(v[1][0]*v[2][2] - v[1][2]*v[2][0]);
...@@ -150,10 +149,10 @@ struct CpuGayBerneForce::Matrix { ...@@ -150,10 +149,10 @@ struct CpuGayBerneForce::Matrix {
} }
}; };
static RealVec operator*(const RealVec& r, CpuGayBerneForce::Matrix& m) { static Vec3 operator*(const Vec3& r, CpuGayBerneForce::Matrix& m) {
return RealVec(m.v[0][0]*r[0] + m.v[1][0]*r[1] + m.v[2][0]*r[2], return Vec3(m.v[0][0]*r[0] + m.v[1][0]*r[1] + m.v[2][0]*r[2],
m.v[0][1]*r[0] + m.v[1][1]*r[1] + m.v[2][1]*r[2], m.v[0][1]*r[0] + m.v[1][1]*r[1] + m.v[2][1]*r[2],
m.v[0][2]*r[0] + m.v[1][2]*r[1] + m.v[2][2]*r[2]); m.v[0][2]*r[0] + m.v[1][2]*r[1] + m.v[2][2]*r[2]);
} }
} // namespace OpenMM } // namespace OpenMM
......
platforms/cpu/include/CpuKernels.h
View file @ 047934e2
...@@ -54,8 +54,6 @@ namespace OpenMM { ...@@ -54,8 +54,6 @@ namespace OpenMM {
*/ */
class CpuCalcForcesAndEnergyKernel : public CalcForcesAndEnergyKernel { class CpuCalcForcesAndEnergyKernel : public CalcForcesAndEnergyKernel {
public: public:
class InitForceTask;
class SumForceTask;
CpuCalcForcesAndEnergyKernel(std::string name, const Platform& platform, CpuPlatform::PlatformData& data, ContextImpl& context); CpuCalcForcesAndEnergyKernel(std::string name, const Platform& platform, CpuPlatform::PlatformData& data, ContextImpl& context);
/** /**
* Initialize the kernel. * Initialize the kernel.
...@@ -91,7 +89,7 @@ public: ...@@ -91,7 +89,7 @@ public:
private: private:
CpuPlatform::PlatformData& data; CpuPlatform::PlatformData& data;
Kernel referenceKernel; Kernel referenceKernel;
std::vector<RealVec> lastPositions; std::vector<Vec3> lastPositions;
}; };
/** /**
...@@ -130,7 +128,7 @@ private: ...@@ -130,7 +128,7 @@ private:
CpuPlatform::PlatformData& data; CpuPlatform::PlatformData& data;
int numAngles; int numAngles;
int **angleIndexArray; int **angleIndexArray;
RealOpenMM **angleParamArray; double **angleParamArray;
CpuBondForce bondForce; CpuBondForce bondForce;
bool usePeriodic; bool usePeriodic;
}; };
...@@ -171,7 +169,7 @@ private: ...@@ -171,7 +169,7 @@ private:
CpuPlatform::PlatformData& data; CpuPlatform::PlatformData& data;
int numTorsions; int numTorsions;
int **torsionIndexArray; int **torsionIndexArray;
RealOpenMM **torsionParamArray; double **torsionParamArray;
CpuBondForce bondForce; CpuBondForce bondForce;
bool usePeriodic; bool usePeriodic;
}; };
...@@ -212,7 +210,7 @@ private: ...@@ -212,7 +210,7 @@ private:
CpuPlatform::PlatformData& data; CpuPlatform::PlatformData& data;
int numTorsions; int numTorsions;
int **torsionIndexArray; int **torsionIndexArray;
RealOpenMM **torsionParamArray; double **torsionParamArray;
CpuBondForce bondForce; CpuBondForce bondForce;
bool usePeriodic; bool usePeriodic;
}; };
...@@ -251,27 +249,37 @@ public: ...@@ -251,27 +249,37 @@ public:
void copyParametersToContext(ContextImpl& context, const NonbondedForce& force); void copyParametersToContext(ContextImpl& context, const NonbondedForce& force);
/** /**
* Get the parameters being used for PME. * Get the parameters being used for PME.
* *
* @param alpha the separation parameter * @param alpha the separation parameter
* @param nx the number of grid points along the X axis * @param nx the number of grid points along the X axis
* @param ny the number of grid points along the Y axis * @param ny the number of grid points along the Y axis
* @param nz the number of grid points along the Z axis * @param nz the number of grid points along the Z axis
*/ */
void getPMEParameters(double& alpha, int& nx, int& ny, int& nz) const; void getPMEParameters(double& alpha, int& nx, int& ny, int& nz) const;
/**
* Get the parameters being used for the dispersion term in LJPME.
*
* @param alpha the separation parameter
* @param nx the number of grid points along the X axis
* @param ny the number of grid points along the Y axis
* @param nz the number of grid points along the Z axis
*/
void getLJPMEParameters(double& alpha, int& nx, int& ny, int& nz) const;
private: private:
class PmeIO; class PmeIO;
CpuPlatform::PlatformData& data; CpuPlatform::PlatformData& data;
int numParticles, num14; int numParticles, num14;
int **bonded14IndexArray; int **bonded14IndexArray;
double **bonded14ParamArray; double **bonded14ParamArray;
double nonbondedCutoff, switchingDistance, rfDielectric, ewaldAlpha, ewaldSelfEnergy, dispersionCoefficient; double nonbondedCutoff, switchingDistance, rfDielectric, ewaldAlpha, ewaldDispersionAlpha, ewaldSelfEnergy, dispersionCoefficient;
int kmax[3], gridSize[3]; int kmax[3], gridSize[3], dispersionGridSize[3];
bool useSwitchingFunction, useOptimizedPme, hasInitializedPme; bool useSwitchingFunction, useOptimizedPme, hasInitializedPme, hasInitializedDispersionPme;
std::vector<std::set<int> > exclusions; std::vector<std::set<int> > exclusions;
std::vector<std::pair<float, float> > particleParams; std::vector<std::pair<float, float> > particleParams;
std::vector<float> C6params;
NonbondedMethod nonbondedMethod; NonbondedMethod nonbondedMethod;
CpuNonbondedForce* nonbonded; CpuNonbondedForce* nonbonded;
Kernel optimizedPme; Kernel optimizedPme, optimizedDispersionPme;
CpuBondForce bondForce; CpuBondForce bondForce;
}; };
...@@ -395,8 +403,8 @@ private: ...@@ -395,8 +403,8 @@ private:
CpuPlatform::PlatformData& data; CpuPlatform::PlatformData& data;
int numParticles; int numParticles;
bool isPeriodic; bool isPeriodic;
RealOpenMM **particleParamArray; double **particleParamArray;
RealOpenMM nonbondedCutoff; double nonbondedCutoff;
CpuCustomGBForce* ixn; CpuCustomGBForce* ixn;
std::vector<std::set<int> > exclusions; std::vector<std::set<int> > exclusions;
std::vector<std::string> particleParameterNames, globalParameterNames, energyParamDerivNames, valueNames; std::vector<std::string> particleParameterNames, globalParameterNames, energyParamDerivNames, valueNames;
...@@ -440,8 +448,8 @@ public: ...@@ -440,8 +448,8 @@ public:
private: private:
CpuPlatform::PlatformData& data; CpuPlatform::PlatformData& data;
int numParticles; int numParticles;
RealOpenMM cutoffDistance; double cutoffDistance;
RealOpenMM **particleParamArray; double **particleParamArray;
CpuCustomManyParticleForce* ixn; CpuCustomManyParticleForce* ixn;
std::vector<std::string> globalParameterNames; std::vector<std::string> globalParameterNames;
NonbondedMethod nonbondedMethod; NonbondedMethod nonbondedMethod;
...@@ -516,7 +524,7 @@ public: ...@@ -516,7 +524,7 @@ public:
private: private:
CpuPlatform::PlatformData& data; CpuPlatform::PlatformData& data;
CpuLangevinDynamics* dynamics; CpuLangevinDynamics* dynamics;
std::vector<RealOpenMM> masses; std::vector<double> masses;
double prevTemp, prevFriction, prevStepSize; double prevTemp, prevFriction, prevStepSize;
}; };
......
platforms/cpu/include/CpuLangevinDynamics.h
View file @ 047934e2
/* Portions copyright (c) 2013-2015 Stanford University and Simbios. /* Portions copyright (c) 2013-2017 Stanford University and Simbios.
* Authors: Peter Eastman * Authors: Peter Eastman
* Contributors: * Contributors:
* *
...@@ -35,20 +35,17 @@ namespace OpenMM { ...@@ -35,20 +35,17 @@ namespace OpenMM {
class CpuLangevinDynamics : public ReferenceStochasticDynamics { class CpuLangevinDynamics : public ReferenceStochasticDynamics {
public: public:
class Update1Task;
class Update2Task;
class Update3Task;
/** /**
* Constructor. * Constructor.
* *
* @param numberOfAtoms number of atoms * @param numberOfAtoms number of atoms
* @param deltaT delta t for dynamics * @param deltaT delta t for dynamics
* @param tau viscosity * @param friction friction coefficient
* @param temperature temperature * @param temperature temperature
* @param threads thread pool for parallelizing computation * @param threads thread pool for parallelizing computation
* @param random random number generator * @param random random number generator
*/ */
CpuLangevinDynamics(int numberOfAtoms, RealOpenMM deltaT, RealOpenMM tau, RealOpenMM temperature, OpenMM::ThreadPool& threads, OpenMM::CpuRandom& random); CpuLangevinDynamics(int numberOfAtoms, double deltaT, double friction, double temperature, OpenMM::ThreadPool& threads, OpenMM::CpuRandom& random);
/** /**
* Destructor. * Destructor.
...@@ -65,8 +62,8 @@ public: ...@@ -65,8 +62,8 @@ public:
* @param inverseMasses inverse atom masses * @param inverseMasses inverse atom masses
* @param xPrime xPrime * @param xPrime xPrime
*/ */
void updatePart1(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& velocities, void updatePart1(int numberOfAtoms, std::vector<OpenMM::Vec3>& atomCoordinates, std::vector<OpenMM::Vec3>& velocities,
std::vector<OpenMM::RealVec>& forces, std::vector<RealOpenMM>& inverseMasses, std::vector<OpenMM::RealVec>& xPrime); std::vector<OpenMM::Vec3>& forces, std::vector<double>& inverseMasses, std::vector<OpenMM::Vec3>& xPrime);
/** /**
* Second update step. * Second update step.
...@@ -78,8 +75,8 @@ public: ...@@ -78,8 +75,8 @@ public:
* @param inverseMasses inverse atom masses * @param inverseMasses inverse atom masses
* @param xPrime xPrime * @param xPrime xPrime
*/ */
void updatePart2(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& velocities, void updatePart2(int numberOfAtoms, std::vector<OpenMM::Vec3>& atomCoordinates, std::vector<OpenMM::Vec3>& velocities,
std::vector<OpenMM::RealVec>& forces, std::vector<RealOpenMM>& inverseMasses, std::vector<OpenMM::RealVec>& xPrime); std::vector<OpenMM::Vec3>& forces, std::vector<double>& inverseMasses, std::vector<OpenMM::Vec3>& xPrime);
/** /**
* Third update * Third update
...@@ -89,8 +86,8 @@ public: ...@@ -89,8 +86,8 @@ public:
* @param velocities velocities * @param velocities velocities
* @param inverseMasses inverse atom masses * @param inverseMasses inverse atom masses
*/ */
void updatePart3(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& velocities, void updatePart3(int numberOfAtoms, std::vector<OpenMM::Vec3>& atomCoordinates, std::vector<OpenMM::Vec3>& velocities,
std::vector<RealOpenMM>& inverseMasses, std::vector<OpenMM::RealVec>& xPrime); std::vector<double>& inverseMasses, std::vector<OpenMM::Vec3>& xPrime);
private: private:
void threadUpdate1(int threadIndex); void threadUpdate1(int threadIndex);
...@@ -101,11 +98,11 @@ private: ...@@ -101,11 +98,11 @@ private:
std::vector<OpenMM_SFMT::SFMT> threadRandom; std::vector<OpenMM_SFMT::SFMT> threadRandom;
// The following variables are used to make information accessible to the individual threads. // The following variables are used to make information accessible to the individual threads.
int numberOfAtoms; int numberOfAtoms;
OpenMM::RealVec* atomCoordinates; OpenMM::Vec3* atomCoordinates;
OpenMM::RealVec* velocities; OpenMM::Vec3* velocities;
OpenMM::RealVec* forces; OpenMM::Vec3* forces;
RealOpenMM* inverseMasses; double* inverseMasses;
OpenMM::RealVec* xPrime; OpenMM::Vec3* xPrime;
}; };
} // namespace OpenMM } // namespace OpenMM
......
platforms/cpu/include/CpuNeighborList.h
View file @ 047934e2
...@@ -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) 2013-2016 Stanford University and the Authors. * * Portions copyright (c) 2013-2017 Stanford University and the Authors. *
* Authors: Peter Eastman * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -33,7 +33,7 @@ ...@@ -33,7 +33,7 @@
* -------------------------------------------------------------------------- */ * -------------------------------------------------------------------------- */
#include "AlignedArray.h" #include "AlignedArray.h"
#include "RealVec.h" #include "openmm/Vec3.h"
#include "windowsExportCpu.h" #include "windowsExportCpu.h"
#include "openmm/internal/gmx_atomic.h" #include "openmm/internal/gmx_atomic.h"
#include "openmm/internal/ThreadPool.h" #include "openmm/internal/ThreadPool.h"
...@@ -45,11 +45,10 @@ namespace OpenMM { ...@@ -45,11 +45,10 @@ namespace OpenMM {
class OPENMM_EXPORT_CPU CpuNeighborList { class OPENMM_EXPORT_CPU CpuNeighborList {
public: public:
class ThreadTask;
class Voxels; class Voxels;
CpuNeighborList(int blockSize); CpuNeighborList(int blockSize);
void computeNeighborList(int numAtoms, const AlignedArray<float>& atomLocations, const std::vector<std::set<int> >& exclusions, void computeNeighborList(int numAtoms, const AlignedArray<float>& atomLocations, const std::vector<std::set<int> >& exclusions,
const RealVec* periodicBoxVectors, bool usePeriodic, float maxDistance, ThreadPool& threads); const Vec3* periodicBoxVectors, bool usePeriodic, float maxDistance, ThreadPool& threads);
int getNumBlocks() const; int getNumBlocks() const;
int getBlockSize() const; int getBlockSize() const;
const std::vector<int>& getSortedAtoms() const; const std::vector<int>& getSortedAtoms() const;
...@@ -72,7 +71,7 @@ private: ...@@ -72,7 +71,7 @@ private:
Voxels* voxels; Voxels* voxels;
const std::vector<std::set<int> >* exclusions; const std::vector<std::set<int> >* exclusions;
const float* atomLocations; const float* atomLocations;
RealVec periodicBoxVectors[3]; Vec3 periodicBoxVectors[3];
int numAtoms; int numAtoms;
bool usePeriodic; bool usePeriodic;
float maxDistance; float maxDistance;
......
platforms/cpu/include/CpuNonbondedForce.h
View file @ 047934e2
/* Portions copyright (c) 2006-2015 Stanford University and Simbios. /* Portions copyright (c) 2006-2017 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
...@@ -39,7 +39,6 @@ namespace OpenMM { ...@@ -39,7 +39,6 @@ namespace OpenMM {
class CpuNonbondedForce { class CpuNonbondedForce {
public: public:
class ComputeDirectTask;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -87,7 +86,7 @@ class CpuNonbondedForce { ...@@ -87,7 +86,7 @@ class CpuNonbondedForce {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void setPeriodic(RealVec* periodicBoxVectors); void setPeriodic(Vec3* periodicBoxVectors);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -104,16 +103,27 @@ class CpuNonbondedForce { ...@@ -104,16 +103,27 @@ class CpuNonbondedForce {
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
Set the force to use Particle-Mesh Ewald (PME) summation. Set the force to use Particle-Mesh Ewald (PME) summation.
@param alpha the Ewald separation parameter @param alpha the Ewald separation parameter
@param gridSize the dimensions of the mesh @param gridSize the dimensions of the mesh
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void setUsePME(float alpha, int meshSize[3]); void setUsePME(float alpha, int meshSize[3]);
/**---------------------------------------------------------------------------------------
Set the force to use Particle-Mesh Ewald (PME) summation for dispersion.
@param alpha the Ewald separation parameter
@param gridSize the dimensions of the mesh
--------------------------------------------------------------------------------------- */
void setUseLJPME(float alpha, int meshSize[3]);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
Calculate Ewald ixn Calculate Ewald ixn
...@@ -122,16 +132,17 @@ class CpuNonbondedForce { ...@@ -122,16 +132,17 @@ class CpuNonbondedForce {
@param posq atom coordinates and charges @param posq atom coordinates and charges
@param atomCoordinates atom coordinates (in format needed by PME) @param atomCoordinates atom coordinates (in format needed by PME)
@param atomParameters atom parameters (sigma/2, 2*sqrt(epsilon)) @param atomParameters atom parameters (sigma/2, 2*sqrt(epsilon))
@param C6Paramrs C6 parameters for multiplicative representation of dispersion
@param exclusions atom exclusion indices @param exclusions atom exclusion indices
exclusions[atomIndex] contains the list of exclusions for that atom exclusions[atomIndex] contains the list of exclusions for that atom
@param forces force array (forces added) @param forces force array (forces added)
@param totalEnergy total energy @param totalEnergy total energy
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void calculateReciprocalIxn(int numberOfAtoms, float* posq, const std::vector<RealVec>& atomCoordinates, void calculateReciprocalIxn(int numberOfAtoms, float* posq, const std::vector<Vec3>& atomCoordinates,
const std::vector<std::pair<float, float> >& atomParameters, const std::vector<std::set<int> >& exclusions, const std::vector<std::pair<float, float> >& atomParameters, const std::vector<float> &C6params,
std::vector<RealVec>& forces, double* totalEnergy) const; const std::vector<std::set<int> >& exclusions, std::vector<Vec3>& forces, double* totalEnergy) const;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -149,8 +160,8 @@ class CpuNonbondedForce { ...@@ -149,8 +160,8 @@ class CpuNonbondedForce {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void calculateDirectIxn(int numberOfAtoms, float* posq, const std::vector<RealVec>& atomCoordinates, const std::vector<std::pair<float, float> >& atomParameters, void calculateDirectIxn(int numberOfAtoms, float* posq, const std::vector<Vec3>& atomCoordinates, const std::vector<std::pair<float, float> >& atomParameters,
const std::vector<std::set<int> >& exclusions, std::vector<AlignedArray<float> >& threadForce, double* totalEnergy, ThreadPool& threads); const std::vector<float>& C6params, const std::vector<std::set<int> >& exclusions, std::vector<AlignedArray<float> >& threadForce, double* totalEnergy, ThreadPool& threads);
/** /**
* This routine contains the code executed by each thread. * This routine contains the code executed by each thread.
...@@ -163,28 +174,32 @@ protected: ...@@ -163,28 +174,32 @@ protected:
bool periodic; bool periodic;
bool triclinic; bool triclinic;
bool ewald; bool ewald;
bool pme; bool ljpme, pme;
bool tableIsValid; bool tableIsValid, expTableIsValid;
const CpuNeighborList* neighborList; const CpuNeighborList* neighborList;
float recipBoxSize[3]; float recipBoxSize[3];
RealVec periodicBoxVectors[3]; Vec3 periodicBoxVectors[3];
AlignedArray<fvec4> periodicBoxVec4; AlignedArray<fvec4> periodicBoxVec4;
float cutoffDistance, switchingDistance; float cutoffDistance, switchingDistance;
float krf, crf; float krf, crf;
float alphaEwald; float alphaEwald, alphaDispersionEwald;
int numRx, numRy, numRz; int numRx, numRy, numRz;
int meshDim[3]; int meshDim[3], dispersionMeshDim[3];
std::vector<float> erfcTable, ewaldScaleTable; std::vector<float> erfcTable, ewaldScaleTable;
float ewaldDX, ewaldDXInv, erfcDXInv; std::vector<float> exptermsTable, dExptermsTable;
float ewaldDX, ewaldDXInv, erfcDXInv, exptermsDX, exptermsDXInv;
std::vector<double> threadEnergy; std::vector<double> threadEnergy;
// The following variables are used to make information accessible to the individual threads. // The following variables are used to make information accessible to the individual threads.
int numberOfAtoms; int numberOfAtoms;
float* posq; float* posq;
RealVec const* atomCoordinates; Vec3 const* atomCoordinates;
std::pair<float, float> const* atomParameters; std::pair<float, float> const* atomParameters;
float const *C6params;
std::set<int> const* exclusions; std::set<int> const* exclusions;
std::vector<AlignedArray<float> >* threadForce; std::vector<AlignedArray<float> >* threadForce;
bool includeEnergy; bool includeEnergy;
float inverseRcut6;
float inverseRcut6Expterm;
void* atomicCounter; void* atomicCounter;
static const float TWO_OVER_SQRT_PI; static const float TWO_OVER_SQRT_PI;
...@@ -238,10 +253,29 @@ protected: ...@@ -238,10 +253,29 @@ protected:
*/ */
void tabulateEwaldScaleFactor(); void tabulateEwaldScaleFactor();
/**
* Create a lookup table for the scale factor used with dispersion PME.
*/
void tabulateExpTerms();
/** /**
* Compute a fast approximation to erfc(x). * Compute a fast approximation to erfc(x).
*/ */
float erfcApprox(float x); float erfcApprox(float x);
/**
* Compute a fast approximation to (1.0 - EXP(-dar^2) * (1.0 + dar^2 + 0.5*dar^4))
* where dar = (dispersionAlpha * R)
* needed for LJPME energies.
*/
float exptermsApprox(float R);
/**
* Compute a fast approximation to (1.0 - EXP(-dar^2) * (1.0 + dar^2 + 0.5*dar^4 + dar^6/6.0))
* where dar = (dispersionAlpha * R)
* needed for LJPME forces.
*/
float dExptermsApprox(float R);
}; };
} // namespace OpenMM } // namespace OpenMM
......
platforms/cpu/include/CpuNonbondedForceVec4.h
View file @ 047934e2
...@@ -88,11 +88,25 @@ protected: ...@@ -88,11 +88,25 @@ protected:
* Compute a fast approximation to erfc(x). * Compute a fast approximation to erfc(x).
*/ */
fvec4 erfcApprox(const fvec4& x); fvec4 erfcApprox(const fvec4& x);
/** /**
* Evaluate the scale factor used with Ewald and PME: erfc(alpha*r) + 2*alpha*r*exp(-alpha*alpha*r*r)/sqrt(PI) * Evaluate the scale factor used with Ewald and PME: erfc(alpha*r) + 2*alpha*r*exp(-alpha*alpha*r*r)/sqrt(PI)
*/ */
fvec4 ewaldScaleFunction(const fvec4& x); fvec4 ewaldScaleFunction(const fvec4& x);
/**
* Compute a fast approximation to (1.0 - EXP(-dar^2) * (1.0 + dar^2 + 0.5*dar^4))
* where dar = (dispersionAlpha * R)
* needed for LJPME energies.
*/
fvec4 exptermsApprox(const fvec4& R);
/**
* Compute a fast approximation to (1.0 - EXP(-dar^2) * (1.0 + dar^2 + 0.5*dar^4 + dar^6/6.0))
* where dar = (dispersionAlpha * R)
* needed for LJPME forces.
*/
fvec4 dExptermsApprox(const fvec4& R);
}; };
} // namespace OpenMM } // namespace OpenMM
......
platforms/cpu/include/CpuNonbondedForceVec8.h
View file @ 047934e2
...@@ -92,6 +92,21 @@ protected: ...@@ -92,6 +92,21 @@ protected:
* Evaluate the scale factor used with Ewald and PME: erfc(alpha*r) + 2*alpha*r*exp(-alpha*alpha*r*r)/sqrt(PI) * Evaluate the scale factor used with Ewald and PME: erfc(alpha*r) + 2*alpha*r*exp(-alpha*alpha*r*r)/sqrt(PI)
*/ */
fvec8 ewaldScaleFunction(const fvec8& x); fvec8 ewaldScaleFunction(const fvec8& x);
/**
* Compute a fast approximation to (1.0 - EXP(-dar^2) * (1.0 + dar^2 + 0.5*dar^4))
* where dar = (dispersionAlpha * R)
* needed for LJPME energies.
*/
fvec8 exptermsApprox(const fvec8& R);
/**
* Compute a fast approximation to (1.0 - EXP(-dar^2) * (1.0 + dar^2 + 0.5*dar^4 + dar^6/6.0))
* where dar = (dispersionAlpha * R)
* needed for LJPME forces.
*/
fvec8 dExptermsApprox(const fvec8& R);
}; };
} // namespace OpenMM } // namespace OpenMM
......
platforms/cpu/include/CpuSETTLE.h
View file @ 047934e2
...@@ -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) 2013 Stanford University and the Authors. * * Portions copyright (c) 2013-2017 Stanford University and the Authors. *
* Authors: Peter Eastman * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -45,8 +45,6 @@ namespace OpenMM { ...@@ -45,8 +45,6 @@ namespace OpenMM {
*/ */
class OPENMM_EXPORT_CPU CpuSETTLE : public ReferenceConstraintAlgorithm { class OPENMM_EXPORT_CPU CpuSETTLE : public ReferenceConstraintAlgorithm {
public: public:
class ApplyToPositionsTask;
class ApplyToVelocitiesTask;
CpuSETTLE(const System& system, const ReferenceSETTLEAlgorithm& settle, ThreadPool& threads); CpuSETTLE(const System& system, const ReferenceSETTLEAlgorithm& settle, ThreadPool& threads);
~CpuSETTLE(); ~CpuSETTLE();
...@@ -58,7 +56,7 @@ public: ...@@ -58,7 +56,7 @@ public:
* @param inverseMasses 1/mass * @param inverseMasses 1/mass
* @param tolerance the constraint tolerance * @param tolerance the constraint tolerance
*/ */
void apply(std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& atomCoordinatesP, std::vector<RealOpenMM>& inverseMasses, RealOpenMM tolerance); void apply(std::vector<OpenMM::Vec3>& atomCoordinates, std::vector<OpenMM::Vec3>& atomCoordinatesP, std::vector<double>& inverseMasses, double tolerance);
/** /**
* Apply the constraint algorithm to velocities. * Apply the constraint algorithm to velocities.
...@@ -68,7 +66,7 @@ public: ...@@ -68,7 +66,7 @@ public:
* @param inverseMasses 1/mass * @param inverseMasses 1/mass
* @param tolerance the constraint tolerance * @param tolerance the constraint tolerance
*/ */
void applyToVelocities(std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& velocities, std::vector<RealOpenMM>& inverseMasses, RealOpenMM tolerance); void applyToVelocities(std::vector<OpenMM::Vec3>& atomCoordinates, std::vector<OpenMM::Vec3>& velocities, std::vector<double>& inverseMasses, double tolerance);
private: private:
std::vector<ReferenceSETTLEAlgorithm*> threadSettle; std::vector<ReferenceSETTLEAlgorithm*> threadSettle;
ThreadPool& threads; ThreadPool& threads;
......
platforms/cpu/src/CpuBondForce.cpp
View file @ 047934e2
...@@ -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) 2014-2016 Stanford University and the Authors. * * Portions copyright (c) 2014-2017 Stanford University and the Authors. *
* Authors: Peter Eastman * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -35,25 +35,6 @@ ...@@ -35,25 +35,6 @@
using namespace OpenMM; using namespace OpenMM;
using namespace std; using namespace std;
class CpuBondForce::ComputeForceTask : public ThreadPool::Task {
public:
ComputeForceTask(CpuBondForce& owner, vector<RealVec>& atomCoordinates, RealOpenMM** parameters, vector<RealVec>& forces,
vector<RealOpenMM>& threadEnergy, RealOpenMM* totalEnergy, ReferenceBondIxn& referenceBondIxn) : owner(owner), atomCoordinates(atomCoordinates),
parameters(parameters), forces(forces), threadEnergy(threadEnergy), totalEnergy(totalEnergy), referenceBondIxn(referenceBondIxn) {
}
void execute(ThreadPool& threads, int threadIndex) {
RealOpenMM* energy = (totalEnergy == NULL ? NULL : &threadEnergy[threadIndex]);
owner.threadComputeForce(threads, threadIndex, atomCoordinates, parameters, forces, energy, referenceBondIxn);
}
CpuBondForce& owner;
vector<RealVec>& atomCoordinates;
RealOpenMM** parameters;
vector<RealVec>& forces;
vector<RealOpenMM>& threadEnergy;
RealOpenMM* totalEnergy;
ReferenceBondIxn& referenceBondIxn;
};
CpuBondForce::CpuBondForce() { CpuBondForce::CpuBondForce() {
} }
...@@ -183,13 +164,15 @@ void CpuBondForce::assignBond(int bond, int thread, vector<int>& atomThread, vec ...@@ -183,13 +164,15 @@ void CpuBondForce::assignBond(int bond, int thread, vector<int>& atomThread, vec
} }
} }
void CpuBondForce::calculateForce(vector<RealVec>& atomCoordinates, RealOpenMM** parameters, vector<RealVec>& forces, void CpuBondForce::calculateForce(vector<Vec3>& atomCoordinates, double** parameters, vector<Vec3>& forces,
RealOpenMM* totalEnergy, ReferenceBondIxn& referenceBondIxn) { double* totalEnergy, ReferenceBondIxn& referenceBondIxn) {
// Have the worker threads compute their forces. // Have the worker threads compute their forces.
vector<RealOpenMM> threadEnergy(threads->getNumThreads(), 0); vector<double> threadEnergy(threads->getNumThreads(), 0);
ComputeForceTask task(*this, atomCoordinates, parameters, forces, threadEnergy, totalEnergy, referenceBondIxn); threads->execute([&] (ThreadPool& threads, int threadIndex) {
threads->execute(task); double* energy = (totalEnergy == NULL ? NULL : &threadEnergy[threadIndex]);
threadComputeForce(threads, threadIndex, atomCoordinates, parameters, forces, energy, referenceBondIxn);
});
threads->waitForThreads(); threads->waitForThreads();
// Compute any "extra" bonds. // Compute any "extra" bonds.
...@@ -206,8 +189,8 @@ void CpuBondForce::calculateForce(vector<RealVec>& atomCoordinates, RealOpenMM** ...@@ -206,8 +189,8 @@ void CpuBondForce::calculateForce(vector<RealVec>& atomCoordinates, RealOpenMM**
*totalEnergy += threadEnergy[i]; *totalEnergy += threadEnergy[i];
} }
void CpuBondForce::threadComputeForce(ThreadPool& threads, int threadIndex, vector<RealVec>& atomCoordinates, RealOpenMM** parameters, vector<RealVec>& forces, void CpuBondForce::threadComputeForce(ThreadPool& threads, int threadIndex, vector<Vec3>& atomCoordinates, double** parameters, vector<Vec3>& forces,
RealOpenMM* totalEnergy, ReferenceBondIxn& referenceBondIxn) { double* totalEnergy, ReferenceBondIxn& referenceBondIxn) {
vector<int>& bonds = threadBonds[threadIndex]; vector<int>& bonds = threadBonds[threadIndex];
int numBonds = bonds.size(); int numBonds = bonds.size();
for (int i = 0; i < numBonds; i++) { for (int i = 0; i < numBonds; i++) {
......
platforms/cpu/src/CpuCustomGBForce.cpp
View file @ 047934e2
/* Portions copyright (c) 2009-2016 Stanford University and Simbios. /* Portions copyright (c) 2009-2017 Stanford University and Simbios.
* Contributors: Peter Eastman * Contributors: Peter Eastman
* *
* Permission is hereby granted, free of charge, to any person obtaining * Permission is hereby granted, free of charge, to any person obtaining
...@@ -33,16 +33,6 @@ ...@@ -33,16 +33,6 @@
using namespace OpenMM; using namespace OpenMM;
using namespace std; using namespace std;
class CpuCustomGBForce::ComputeForceTask : public ThreadPool::Task {
public:
ComputeForceTask(CpuCustomGBForce& owner) : owner(owner) {
}
void execute(ThreadPool& threads, int threadIndex) {
owner.threadComputeForce(threads, threadIndex);
}
CpuCustomGBForce& owner;
};
CpuCustomGBForce::ThreadData::ThreadData(int numAtoms, int numThreads, int threadIndex, CpuCustomGBForce::ThreadData::ThreadData(int numAtoms, int numThreads, int threadIndex,
const vector<Lepton::CompiledExpression>& valueExpressions, const vector<Lepton::CompiledExpression>& valueExpressions,
const vector<vector<Lepton::CompiledExpression> >& valueDerivExpressions, const vector<vector<Lepton::CompiledExpression> >& valueDerivExpressions,
...@@ -176,7 +166,7 @@ void CpuCustomGBForce::setUseCutoff(float distance, const CpuNeighborList& neigh ...@@ -176,7 +166,7 @@ void CpuCustomGBForce::setUseCutoff(float distance, const CpuNeighborList& neigh
neighborList = &neighbors; neighborList = &neighbors;
} }
void CpuCustomGBForce::setPeriodic(RealVec& boxSize) { void CpuCustomGBForce::setPeriodic(Vec3& boxSize) {
if (cutoff) { if (cutoff) {
assert(boxSize[0] >= 2.0*cutoffDistance); assert(boxSize[0] >= 2.0*cutoffDistance);
assert(boxSize[1] >= 2.0*cutoffDistance); assert(boxSize[1] >= 2.0*cutoffDistance);
...@@ -188,7 +178,7 @@ void CpuCustomGBForce::setPeriodic(RealVec& boxSize) { ...@@ -188,7 +178,7 @@ void CpuCustomGBForce::setPeriodic(RealVec& boxSize) {
periodicBoxSize[2] = boxSize[2]; periodicBoxSize[2] = boxSize[2];
} }
void CpuCustomGBForce::calculateIxn(int numberOfAtoms, float* posq, RealOpenMM** atomParameters, void CpuCustomGBForce::calculateIxn(int numberOfAtoms, float* posq, double** atomParameters,
map<string, double>& globalParameters, vector<AlignedArray<float> >& threadForce, map<string, double>& globalParameters, vector<AlignedArray<float> >& threadForce,
bool includeForce, bool includeEnergy, double& totalEnergy, double* energyParamDerivs) { bool includeForce, bool includeEnergy, double& totalEnergy, double* energyParamDerivs) {
// Record the parameters for the threads. // Record the parameters for the threads.
...@@ -206,7 +196,7 @@ void CpuCustomGBForce::calculateIxn(int numberOfAtoms, float* posq, RealOpenMM** ...@@ -206,7 +196,7 @@ void CpuCustomGBForce::calculateIxn(int numberOfAtoms, float* posq, RealOpenMM**
// Calculate the first computed value. // Calculate the first computed value.
ComputeForceTask task(*this); auto task = [&] (ThreadPool& threads, int threadIndex) { threadComputeForce(threads, threadIndex); };
gmx_atomic_set(&counter, 0); gmx_atomic_set(&counter, 0);
threads.execute(task); threads.execute(task);
threads.waitForThreads(); threads.waitForThreads();
...@@ -362,7 +352,7 @@ void CpuCustomGBForce::threadComputeForce(ThreadPool& threads, int threadIndex) ...@@ -362,7 +352,7 @@ void CpuCustomGBForce::threadComputeForce(ThreadPool& threads, int threadIndex)
calculateChainRuleForces(data, numberOfAtoms, posq, atomParameters, forces, boxSize, invBoxSize); calculateChainRuleForces(data, numberOfAtoms, posq, atomParameters, forces, boxSize, invBoxSize);
} }
void CpuCustomGBForce::calculateParticlePairValue(int index, ThreadData& data, int numAtoms, float* posq, RealOpenMM** atomParameters, void CpuCustomGBForce::calculateParticlePairValue(int index, ThreadData& data, int numAtoms, float* posq, double** atomParameters,
bool useExclusions, const fvec4& boxSize, const fvec4& invBoxSize) { bool useExclusions, const fvec4& boxSize, const fvec4& invBoxSize) {
for (int i = 0; i < numAtoms; i++) for (int i = 0; i < numAtoms; i++)
values[index][i] = 0.0f; values[index][i] = 0.0f;
...@@ -409,7 +399,7 @@ void CpuCustomGBForce::calculateParticlePairValue(int index, ThreadData& data, i ...@@ -409,7 +399,7 @@ void CpuCustomGBForce::calculateParticlePairValue(int index, ThreadData& data, i
} }
} }
void CpuCustomGBForce::calculateOnePairValue(int index, int atom1, int atom2, ThreadData& data, float* posq, RealOpenMM** atomParameters, void CpuCustomGBForce::calculateOnePairValue(int index, int atom1, int atom2, ThreadData& data, float* posq, double** atomParameters,
vector<float>& valueArray, const fvec4& boxSize, const fvec4& invBoxSize) { vector<float>& valueArray, const fvec4& boxSize, const fvec4& invBoxSize) {
fvec4 deltaR; fvec4 deltaR;
fvec4 pos1(posq+4*atom1); fvec4 pos1(posq+4*atom1);
...@@ -436,7 +426,7 @@ void CpuCustomGBForce::calculateOnePairValue(int index, int atom1, int atom2, Th ...@@ -436,7 +426,7 @@ void CpuCustomGBForce::calculateOnePairValue(int index, int atom1, int atom2, Th
} }
void CpuCustomGBForce::calculateSingleParticleEnergyTerm(int index, ThreadData& data, int numAtoms, float* posq, void CpuCustomGBForce::calculateSingleParticleEnergyTerm(int index, ThreadData& data, int numAtoms, float* posq,
RealOpenMM** atomParameters, float* forces, double& totalEnergy) { double** atomParameters, float* forces, double& totalEnergy) {
for (int i = data.firstAtom; i < data.lastAtom; i++) { for (int i = data.firstAtom; i < data.lastAtom; i++) {
data.x = posq[4*i]; data.x = posq[4*i];
data.y = posq[4*i+1]; data.y = posq[4*i+1];
...@@ -460,7 +450,7 @@ void CpuCustomGBForce::calculateSingleParticleEnergyTerm(int index, ThreadData& ...@@ -460,7 +450,7 @@ void CpuCustomGBForce::calculateSingleParticleEnergyTerm(int index, ThreadData&
} }
} }
void CpuCustomGBForce::calculateParticlePairEnergyTerm(int index, ThreadData& data, int numAtoms, float* posq, RealOpenMM** atomParameters, void CpuCustomGBForce::calculateParticlePairEnergyTerm(int index, ThreadData& data, int numAtoms, float* posq, double** atomParameters,
bool useExclusions, float* forces, double& totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize) { bool useExclusions, float* forces, double& totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize) {
if (cutoff) { if (cutoff) {
// Loop over all pairs in the neighbor list. // Loop over all pairs in the neighbor list.
...@@ -502,7 +492,7 @@ void CpuCustomGBForce::calculateParticlePairEnergyTerm(int index, ThreadData& da ...@@ -502,7 +492,7 @@ void CpuCustomGBForce::calculateParticlePairEnergyTerm(int index, ThreadData& da
} }
} }
void CpuCustomGBForce::calculateOnePairEnergyTerm(int index, int atom1, int atom2, ThreadData& data, float* posq, RealOpenMM** atomParameters, void CpuCustomGBForce::calculateOnePairEnergyTerm(int index, int atom1, int atom2, ThreadData& data, float* posq, double** atomParameters,
float* forces, double& totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize) { float* forces, double& totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize) {
// Compute the displacement. // Compute the displacement.
...@@ -547,7 +537,7 @@ void CpuCustomGBForce::calculateOnePairEnergyTerm(int index, int atom1, int atom ...@@ -547,7 +537,7 @@ void CpuCustomGBForce::calculateOnePairEnergyTerm(int index, int atom1, int atom
data.energyParamDerivs[i] += data.energyParamDerivExpressions[index][i].evaluate(); data.energyParamDerivs[i] += data.energyParamDerivExpressions[index][i].evaluate();
} }
void CpuCustomGBForce::calculateChainRuleForces(ThreadData& data, int numAtoms, float* posq, RealOpenMM** atomParameters, void CpuCustomGBForce::calculateChainRuleForces(ThreadData& data, int numAtoms, float* posq, double** atomParameters,
float* forces, const fvec4& boxSize, const fvec4& invBoxSize) { float* forces, const fvec4& boxSize, const fvec4& invBoxSize) {
if (cutoff) { if (cutoff) {
// Loop over all pairs in the neighbor list. // Loop over all pairs in the neighbor list.
...@@ -624,7 +614,7 @@ void CpuCustomGBForce::calculateChainRuleForces(ThreadData& data, int numAtoms, ...@@ -624,7 +614,7 @@ void CpuCustomGBForce::calculateChainRuleForces(ThreadData& data, int numAtoms,
data.energyParamDerivs[k] += dEdV[j][i]*dValuedParam[j][k][i]; data.energyParamDerivs[k] += dEdV[j][i]*dValuedParam[j][k][i];
} }
void CpuCustomGBForce::calculateOnePairChainRule(int atom1, int atom2, ThreadData& data, float* posq, RealOpenMM** atomParameters, void CpuCustomGBForce::calculateOnePairChainRule(int atom1, int atom2, ThreadData& data, float* posq, double** atomParameters,
float* forces, bool isExcluded, const fvec4& boxSize, const fvec4& invBoxSize) { float* forces, bool isExcluded, const fvec4& boxSize, const fvec4& invBoxSize) {
// Compute the displacement. // Compute the displacement.
......
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