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Commit a711ce2a authored by Peter Eastman's avatar Peter Eastman
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Refactored ForceImpl, lots of KernelImpl subclasses, and other related classes... 

Refactored ForceImpl, lots of KernelImpl subclasses, and other related classes to avoid redundant calculations when requesting a State with both forces and energies
parent 767ea1bd
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Showing with 511 additions and 1330 deletions
openmmapi/src/VariableLangevinIntegrator.cpp
View file @ a711ce2a
......@@ -64,7 +64,7 @@ vector<string> VariableLangevinIntegrator::getKernelNames() {
void VariableLangevinIntegrator::step(int steps) {
for (int i = 0; i < steps; ++i) {
context->updateContextState();
context->calcForces();
context->calcForcesAndEnergy(true, false);
dynamic_cast<IntegrateVariableLangevinStepKernel&>(kernel.getImpl()).execute(*context, *this, std::numeric_limits<double>::infinity());
}
}
......@@ -72,7 +72,7 @@ void VariableLangevinIntegrator::step(int steps) {
void VariableLangevinIntegrator::stepTo(double time) {
while (time > context->getTime()) {
context->updateContextState();
context->calcForces();
context->calcForcesAndEnergy(true, false);
dynamic_cast<IntegrateVariableLangevinStepKernel&>(kernel.getImpl()).execute(*context, *this, time);
}
}
openmmapi/src/VariableVerletIntegrator.cpp
View file @ a711ce2a
......@@ -59,7 +59,7 @@ vector<string> VariableVerletIntegrator::getKernelNames() {
void VariableVerletIntegrator::step(int steps) {
for (int i = 0; i < steps; ++i) {
context->updateContextState();
context->calcForces();
context->calcForcesAndEnergy(true, false);
dynamic_cast<IntegrateVariableVerletStepKernel&>(kernel.getImpl()).execute(*context, *this, std::numeric_limits<double>::infinity());
}
}
......@@ -67,7 +67,7 @@ void VariableVerletIntegrator::step(int steps) {
void VariableVerletIntegrator::stepTo(double time) {
while (time > context->getTime()) {
context->updateContextState();
context->calcForces();
context->calcForcesAndEnergy(true, false);
dynamic_cast<IntegrateVariableVerletStepKernel&>(kernel.getImpl()).execute(*context, *this, time);
}
}
openmmapi/src/VerletIntegrator.cpp
View file @ a711ce2a
......@@ -59,7 +59,7 @@ vector<string> VerletIntegrator::getKernelNames() {
void VerletIntegrator::step(int steps) {
for (int i = 0; i < steps; ++i) {
context->updateContextState();
context->calcForces();
context->calcForcesAndEnergy(true, false);
dynamic_cast<IntegrateVerletStepKernel&>(kernel.getImpl()).execute(*context, *this);
}
}
platforms/cuda/src/CudaKernels.cpp
View file @ a711ce2a
......@@ -44,49 +44,23 @@ using namespace std;
void CudaCalcForcesAndEnergyKernel::initialize(const System& system) {
}
void CudaCalcForcesAndEnergyKernel::beginForceComputation(ContextImpl& context) {
void CudaCalcForcesAndEnergyKernel::beginComputation(ContextImpl& context, bool includeForces, bool includeEnergy) {
_gpuContext* gpu = data.gpu;
if (data.nonbondedMethod != NO_CUTOFF && data.computeForceCount%100 == 0)
gpuReorderAtoms(gpu);
data.computeForceCount++;
if (includeForces)
data.computeForceCount++;
if (gpu->bIncludeGBSA || gpu->bIncludeGBVI)
kClearBornSumAndForces(gpu);
else
else if (includeForces)
kClearForces(gpu);
}
void CudaCalcForcesAndEnergyKernel::finishForceComputation(ContextImpl& context) {
_gpuContext* gpu = data.gpu;
if (gpu->bIncludeGBSA || gpu->bIncludeGBVI) {
gpu->bRecalculateBornRadii = true;
kCalculateCDLJObcGbsaForces1(gpu);
kReduceObcGbsaBornForces(gpu);
if (gpu->bIncludeGBSA ) {
kCalculateObcGbsaForces2(gpu);
} else {
kCalculateGBVIForces2(gpu);
}
if (includeEnergy) {
data.stepCount++;
kClearEnergy(gpu);
}
else if (data.hasNonbonded)
kCalculateCDLJForces(gpu);
if (data.hasCustomNonbonded)
kCalculateCustomNonbondedForces(gpu, data.hasNonbonded);
kCalculateLocalForces(gpu);
kReduceForces(gpu);
}
void CudaCalcForcesAndEnergyKernel::beginEnergyComputation(ContextImpl& context) {
_gpuContext* gpu = data.gpu;
if (data.nonbondedMethod != NO_CUTOFF && data.stepCount%100 == 0)
gpuReorderAtoms(gpu);
data.stepCount++;
kClearEnergy(gpu);
if (gpu->bIncludeGBSA || gpu->bIncludeGBVI)
kClearBornSumAndForces(gpu);
}
double CudaCalcForcesAndEnergyKernel::finishEnergyComputation(ContextImpl& context) {
double CudaCalcForcesAndEnergyKernel::finishComputation(ContextImpl& context, bool includeForces, bool includeEnergy) {
_gpuContext* gpu = data.gpu;
if (gpu->bIncludeGBSA || gpu->bIncludeGBVI) {
gpu->bRecalculateBornRadii = true;
......@@ -103,9 +77,14 @@ double CudaCalcForcesAndEnergyKernel::finishEnergyComputation(ContextImpl& conte
if (data.hasCustomNonbonded)
kCalculateCustomNonbondedForces(gpu, data.hasNonbonded);
kCalculateLocalForces(gpu);
double energy = kReduceEnergy(gpu)+data.ewaldSelfEnergy;
if (data.dispersionCoefficient != 0.0)
energy += data.dispersionCoefficient/(gpu->sim.periodicBoxSizeX*gpu->sim.periodicBoxSizeY*gpu->sim.periodicBoxSizeZ);
if (includeForces)
kReduceForces(gpu);
double energy = 0.0;
if (includeEnergy) {
energy = kReduceEnergy(gpu)+data.ewaldSelfEnergy;
if (data.dispersionCoefficient != 0.0)
energy += data.dispersionCoefficient/(gpu->sim.periodicBoxSizeX*gpu->sim.periodicBoxSizeY*gpu->sim.periodicBoxSizeZ);
}
return energy;
}
......@@ -226,10 +205,7 @@ void CudaCalcHarmonicBondForceKernel::initialize(const System& system, const Har
gpuSetBondParameters(data.gpu, particle1, particle2, length, k);
}
void CudaCalcHarmonicBondForceKernel::executeForces(ContextImpl& context) {
}
double CudaCalcHarmonicBondForceKernel::executeEnergy(ContextImpl& context) {
double CudaCalcHarmonicBondForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
return 0.0;
}
......@@ -257,12 +233,7 @@ void CudaCalcCustomBondForceKernel::initialize(const System& system, const Custo
SetCustomBondGlobalParams(globalParamValues);
}
void CudaCalcCustomBondForceKernel::executeForces(ContextImpl& context) {
updateGlobalParams(context);
kCalculateCustomBondForces(data.gpu);
}
double CudaCalcCustomBondForceKernel::executeEnergy(ContextImpl& context) {
double CudaCalcCustomBondForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
updateGlobalParams(context);
kCalculateCustomBondForces(data.gpu);
return 0.0;
......@@ -301,10 +272,7 @@ void CudaCalcHarmonicAngleForceKernel::initialize(const System& system, const Ha
gpuSetBondAngleParameters(data.gpu, particle1, particle2, particle3, angle, k);
}
void CudaCalcHarmonicAngleForceKernel::executeForces(ContextImpl& context) {
}
double CudaCalcHarmonicAngleForceKernel::executeEnergy(ContextImpl& context) {
double CudaCalcHarmonicAngleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
return 0.0;
}
......@@ -333,12 +301,7 @@ void CudaCalcCustomAngleForceKernel::initialize(const System& system, const Cust
SetCustomAngleGlobalParams(globalParamValues);
}
void CudaCalcCustomAngleForceKernel::executeForces(ContextImpl& context) {
updateGlobalParams(context);
kCalculateCustomAngleForces(data.gpu);
}
double CudaCalcCustomAngleForceKernel::executeEnergy(ContextImpl& context) {
double CudaCalcCustomAngleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
updateGlobalParams(context);
kCalculateCustomAngleForces(data.gpu);
return 0.0;
......@@ -379,10 +342,7 @@ void CudaCalcPeriodicTorsionForceKernel::initialize(const System& system, const
gpuSetDihedralParameters(data.gpu, particle1, particle2, particle3, particle4, k, phase, periodicity);
}
void CudaCalcPeriodicTorsionForceKernel::executeForces(ContextImpl& context) {
}
double CudaCalcPeriodicTorsionForceKernel::executeEnergy(ContextImpl& context) {
double CudaCalcPeriodicTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
return 0.0;
}
......@@ -415,10 +375,7 @@ void CudaCalcRBTorsionForceKernel::initialize(const System& system, const RBTors
gpuSetRbDihedralParameters(data.gpu, particle1, particle2, particle3, particle4, c0, c1, c2, c3, c4, c5);
}
void CudaCalcRBTorsionForceKernel::executeForces(ContextImpl& context) {
}
double CudaCalcRBTorsionForceKernel::executeEnergy(ContextImpl& context) {
double CudaCalcRBTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
return 0.0;
}
......@@ -483,11 +440,7 @@ void CudaCalcCMAPTorsionForceKernel::initialize(const System& system, const CMAP
data.gpu->sim.outputBuffers = maxBuffers;
}
void CudaCalcCMAPTorsionForceKernel::executeForces(ContextImpl& context) {
kCalculateCMAPTorsionForces(data.gpu, *coefficients, *mapPositions, *torsionIndices, *torsionMaps);
}
double CudaCalcCMAPTorsionForceKernel::executeEnergy(ContextImpl& context) {
double CudaCalcCMAPTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
kCalculateCMAPTorsionForces(data.gpu, *coefficients, *mapPositions, *torsionIndices, *torsionMaps);
return 0.0;
}
......@@ -518,12 +471,7 @@ void CudaCalcCustomTorsionForceKernel::initialize(const System& system, const Cu
SetCustomTorsionGlobalParams(globalParamValues);
}
void CudaCalcCustomTorsionForceKernel::executeForces(ContextImpl& context) {
updateGlobalParams(context);
kCalculateCustomTorsionForces(data.gpu);
}
double CudaCalcCustomTorsionForceKernel::executeEnergy(ContextImpl& context) {
double CudaCalcCustomTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
updateGlobalParams(context);
kCalculateCustomTorsionForces(data.gpu);
return 0.0;
......@@ -650,10 +598,7 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
}
}
void CudaCalcNonbondedForceKernel::executeForces(ContextImpl& context) {
}
double CudaCalcNonbondedForceKernel::executeEnergy(ContextImpl& context) {
double CudaCalcNonbondedForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
return 0.0;
}
......@@ -716,11 +661,7 @@ void CudaCalcCustomNonbondedForceKernel::initialize(const System& system, const
SetCustomNonbondedGlobalParams(globalParamValues);
}
void CudaCalcCustomNonbondedForceKernel::executeForces(ContextImpl& context) {
updateGlobalParams(context);
}
double CudaCalcCustomNonbondedForceKernel::executeEnergy(ContextImpl& context) {
double CudaCalcCustomNonbondedForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
updateGlobalParams(context);
return 0.0;
}
......@@ -757,7 +698,8 @@ void CudaCalcGBSAOBCForceKernel::initialize(const System& system, const GBSAOBCF
gpuSetObcParameters(gpu, (float) force.getSoluteDielectric(), (float) force.getSolventDielectric(), radius, scale, charge);
}
void CudaCalcGBSAOBCForceKernel::executeForces(ContextImpl& context) {
double CudaCalcGBSAOBCForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
return 0.0;
}
CudaCalcGBVIForceKernel::~CudaCalcGBVIForceKernel() {
......@@ -785,10 +727,7 @@ void CudaCalcGBVIForceKernel::initialize(const System& system, const GBVIForce&
radius, gammas, scaledRadii );
}
void CudaCalcGBVIForceKernel::executeForces(ContextImpl& context) {
}
double CudaCalcGBVIForceKernel::executeEnergy(ContextImpl& context) {
double CudaCalcGBVIForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
return 0.0;
}
......@@ -815,12 +754,7 @@ void CudaCalcCustomExternalForceKernel::initialize(const System& system, const C
SetCustomExternalGlobalParams(globalParamValues);
}
void CudaCalcCustomExternalForceKernel::executeForces(ContextImpl& context) {
updateGlobalParams(context);
kCalculateCustomExternalForces(data.gpu);
}
double CudaCalcCustomExternalForceKernel::executeEnergy(ContextImpl& context) {
double CudaCalcCustomExternalForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
updateGlobalParams(context);
kCalculateCustomExternalForces(data.gpu);
return 0.0;
......@@ -900,10 +834,6 @@ void OPENMMCUDA_EXPORT OpenMM::cudaOpenMMInitializeIntegration(const System& sys
cudaThreadSynchronize();
}
double CudaCalcGBSAOBCForceKernel::executeEnergy(ContextImpl& context) {
return 0.0;
}
CudaIntegrateVerletStepKernel::~CudaIntegrateVerletStepKernel() {
}
......
platforms/cuda/src/CudaKernels.h
View file @ a711ce2a
......@@ -59,36 +59,26 @@ public:
*/
void initialize(const System& system);
/**
* This is called at the beginning of each force computation, before calcForces() has been called on
* This is called at the beginning of each force/energy computation, before calcForcesAndEnergy() has been called on
* any ForceImpl.
*
* @param context the context in which to execute this kernel
*/
void beginForceComputation(ContextImpl& context);
/**
* This is called at the end of each force computation, after calcForces() has been called on
* every ForceImpl.
*
* @param context the context in which to execute this kernel
* @param context the context in which to execute this kernel
* @param includeForce true if forces should be computed
* @param includeEnergy true if potential energy should be computed
*/
void finishForceComputation(ContextImpl& context);
void beginComputation(ContextImpl& context, bool includeForce, bool includeEnergy);
/**
* This is called at the beginning of each energy computation, before calcEnergy() has been called on
* any ForceImpl.
*
* @param context the context in which to execute this kernel
*/
void beginEnergyComputation(ContextImpl& context);
/**
* This is called at the end of each energy computation, after calcEnergy() has been called on
* This is called at the end of each force/energy computation, after calcForcesAndEnergy() has been called on
* every ForceImpl.
*
* @param context the context in which to execute this kernel
* @param context the context in which to execute this kernel
* @param includeForce true if forces should be computed
* @param includeEnergy true if potential energy should be computed
* @return the potential energy of the system. This value is added to all values returned by ForceImpls'
* calcEnergy() 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.
*/
double finishEnergyComputation(ContextImpl& context);
double finishComputation(ContextImpl& context, bool includeForce, bool includeEnergy);
private:
CudaPlatform::PlatformData& data;
};
......@@ -209,18 +199,14 @@ public:
*/
void initialize(const System& system, const HarmonicBondForce& force);
/**
* Execute the kernel to calculate the forces.
*
* @param context the context in which to execute this kernel
*/
void executeForces(ContextImpl& context);
/**
* Execute the kernel to calculate the energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the HarmonicBondForce
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double executeEnergy(ContextImpl& context);
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
private:
int numBonds;
CudaPlatform::PlatformData& data;
......@@ -244,18 +230,14 @@ public:
*/
void initialize(const System& system, const CustomBondForce& force);
/**
* Execute the kernel to calculate the forces.
*
* @param context the context in which to execute this kernel
*/
void executeForces(ContextImpl& context);
/**
* Execute the kernel to calculate the energy.
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the CustomBondForce
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double executeEnergy(ContextImpl& context);
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
private:
void updateGlobalParams(ContextImpl& context);
int numBonds;
......@@ -281,18 +263,14 @@ public:
*/
void initialize(const System& system, const HarmonicAngleForce& force);
/**
* Execute the kernel to calculate the forces.
*
* @param context the context in which to execute this kernel
*/
void executeForces(ContextImpl& context);
/**
* Execute the kernel to calculate the energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the HarmonicAngleForce
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double executeEnergy(ContextImpl& context);
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
private:
int numAngles;
CudaPlatform::PlatformData& data;
......@@ -316,18 +294,14 @@ public:
*/
void initialize(const System& system, const CustomAngleForce& force);
/**
* Execute the kernel to calculate the forces.
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
void executeForces(ContextImpl& context);
/**
* Execute the kernel to calculate the energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the CustomAngleForce
*/
double executeEnergy(ContextImpl& context);
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
private:
void updateGlobalParams(ContextImpl& context);
int numAngles;
......@@ -353,18 +327,14 @@ public:
*/
void initialize(const System& system, const PeriodicTorsionForce& force);
/**
* Execute the kernel to calculate the forces.
*
* @param context the context in which to execute this kernel
*/
void executeForces(ContextImpl& context);
/**
* Execute the kernel to calculate the energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the PeriodicTorsionForce
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double executeEnergy(ContextImpl& context);
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
private:
int numTorsions;
CudaPlatform::PlatformData& data;
......@@ -387,18 +357,14 @@ public:
*/
void initialize(const System& system, const RBTorsionForce& force);
/**
* Execute the kernel to calculate the forces.
*
* @param context the context in which to execute this kernel
*/
void executeForces(ContextImpl& context);
/**
* Execute the kernel to calculate the energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the RBTorsionForce
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double executeEnergy(ContextImpl& context);
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
private:
int numTorsions;
CudaPlatform::PlatformData& data;
......@@ -423,18 +389,14 @@ public:
*/
void initialize(const System& system, const CMAPTorsionForce& force);
/**
* Execute the kernel to calculate the forces.
*
* @param context the context in which to execute this kernel
*/
void executeForces(ContextImpl& context);
/**
* Execute the kernel to calculate the energy.
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the CMAPTorsionForce
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double executeEnergy(ContextImpl& context);
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
private:
CudaPlatform::PlatformData& data;
System& system;
......@@ -462,18 +424,14 @@ public:
*/
void initialize(const System& system, const CustomTorsionForce& force);
/**
* Execute the kernel to calculate the forces.
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
void executeForces(ContextImpl& context);
/**
* Execute the kernel to calculate the energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the CustomTorsionForce
*/
double executeEnergy(ContextImpl& context);
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
private:
void updateGlobalParams(ContextImpl& context);
int numTorsions;
......@@ -499,18 +457,14 @@ public:
*/
void initialize(const System& system, const NonbondedForce& force);
/**
* Execute the kernel to calculate the forces.
*
* @param context the context in which to execute this kernel
*/
void executeForces(ContextImpl& context);
/**
* Execute the kernel to calculate the energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the NonbondedForce
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double executeEnergy(ContextImpl& context);
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
private:
CudaPlatform::PlatformData& data;
int numParticles;
......@@ -533,18 +487,14 @@ public:
*/
void initialize(const System& system, const CustomNonbondedForce& force);
/**
* Execute the kernel to calculate the forces.
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
void executeForces(ContextImpl& context);
/**
* Execute the kernel to calculate the energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the CustomNonbondedForce
*/
double executeEnergy(ContextImpl& context);
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
private:
void updateGlobalParams(ContextImpl& context);
CudaPlatform::PlatformData& data;
......@@ -570,18 +520,14 @@ public:
*/
void initialize(const System& system, const GBSAOBCForce& force);
/**
* Execute the kernel to calculate the forces.
*
* @param context the context in which to execute this kernel
*/
void executeForces(ContextImpl& context);
/**
* Execute the kernel to calculate the energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the GBSAOBCForce
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double executeEnergy(ContextImpl& context);
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
private:
CudaPlatform::PlatformData& data;
};
......@@ -603,18 +549,14 @@ public:
*/
void initialize(const System& system, const GBVIForce& force, const std::vector<double> & scaledRadii);
/**
* Execute the kernel to calculate the forces.
*
* @param context the context in which to execute this kernel
*/
void executeForces(ContextImpl& context);
/**
* Execute the kernel to calculate the energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the GBVIForce
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double executeEnergy(ContextImpl& context);
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
private:
CudaPlatform::PlatformData& data;
};
......@@ -636,18 +578,14 @@ public:
*/
void initialize(const System& system, const CustomExternalForce& force);
/**
* Execute the kernel to calculate the forces.
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
*/
void executeForces(ContextImpl& context);
/**
* Execute the kernel to calculate the energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the CustomExternalForce
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double executeEnergy(ContextImpl& context);
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
private:
void updateGlobalParams(ContextImpl& context);
int numParticles;
......
platforms/opencl/src/OpenCLKernels.cpp
View file @ a711ce2a
......@@ -70,7 +70,7 @@ static bool isZeroExpression(const Lepton::ParsedExpression& expression) {
void OpenCLCalcForcesAndEnergyKernel::initialize(const System& system) {
}
void OpenCLCalcForcesAndEnergyKernel::beginForceComputation(ContextImpl& context) {
void OpenCLCalcForcesAndEnergyKernel::beginComputation(ContextImpl& context, bool includeForces, bool includeEnergy) {
if (cl.getNonbondedUtilities().getUseCutoff() && cl.getComputeForceCount()%100 == 0)
cl.reorderAtoms();
cl.setComputeForceCount(cl.getComputeForceCount()+1);
......@@ -78,26 +78,17 @@ void OpenCLCalcForcesAndEnergyKernel::beginForceComputation(ContextImpl& context
cl.getNonbondedUtilities().prepareInteractions();
}
void OpenCLCalcForcesAndEnergyKernel::finishForceComputation(ContextImpl& context) {
double OpenCLCalcForcesAndEnergyKernel::finishComputation(ContextImpl& context, bool includeForces, bool includeEnergy) {
cl.getNonbondedUtilities().computeInteractions();
cl.reduceBuffer(cl.getForceBuffers(), cl.getNumForceBuffers());
}
void OpenCLCalcForcesAndEnergyKernel::beginEnergyComputation(ContextImpl& context) {
if (cl.getNonbondedUtilities().getUseCutoff() && cl.getComputeForceCount()%100 == 0)
cl.reorderAtoms();
cl.setComputeForceCount(cl.getComputeForceCount()+1);
cl.clearAutoclearBuffers();
cl.getNonbondedUtilities().prepareInteractions();
}
double OpenCLCalcForcesAndEnergyKernel::finishEnergyComputation(ContextImpl& context) {
cl.getNonbondedUtilities().computeInteractions();
OpenCLArray<cl_float>& energy = cl.getEnergyBuffer();
energy.download();
if (includeForces)
cl.reduceBuffer(cl.getForceBuffers(), cl.getNumForceBuffers());
double sum = 0.0f;
for (int i = 0; i < energy.getSize(); i++)
sum += energy[i];
if (includeEnergy) {
OpenCLArray<cl_float>& energy = cl.getEnergyBuffer();
energy.download();
for (int i = 0; i < energy.getSize(); i++)
sum += energy[i];
}
return sum;
}
......@@ -257,9 +248,9 @@ void OpenCLCalcHarmonicBondForceKernel::initialize(const System& system, const H
kernel = cl::Kernel(program, "calcHarmonicBondForce");
}
void OpenCLCalcHarmonicBondForceKernel::executeForces(ContextImpl& context) {
double OpenCLCalcHarmonicBondForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
if (numBonds == 0)
return;
return 0.0;
if (!hasInitializedKernel) {
hasInitializedKernel = true;
kernel.setArg<cl_int>(0, cl.getPaddedNumAtoms());
......@@ -271,10 +262,6 @@ void OpenCLCalcHarmonicBondForceKernel::executeForces(ContextImpl& context) {
kernel.setArg<cl::Buffer>(6, indices->getDeviceBuffer());
}
cl.executeKernel(kernel, numBonds);
}
double OpenCLCalcHarmonicBondForceKernel::executeEnergy(ContextImpl& context) {
executeForces(context);
return 0.0;
}
......@@ -390,9 +377,9 @@ void OpenCLCalcCustomBondForceKernel::initialize(const System& system, const Cus
kernel = cl::Kernel(program, "computeCustomBondForces");
}
void OpenCLCalcCustomBondForceKernel::executeForces(ContextImpl& context) {
double OpenCLCalcCustomBondForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
if (numBonds == 0)
return;
return 0.0;
if (globals != NULL) {
bool changed = false;
for (int i = 0; i < (int) globalParamNames.size(); i++) {
......@@ -421,10 +408,6 @@ void OpenCLCalcCustomBondForceKernel::executeForces(ContextImpl& context) {
}
}
cl.executeKernel(kernel, numBonds);
}
double OpenCLCalcCustomBondForceKernel::executeEnergy(ContextImpl& context) {
executeForces(context);
return 0.0;
}
......@@ -490,9 +473,9 @@ void OpenCLCalcHarmonicAngleForceKernel::initialize(const System& system, const
kernel = cl::Kernel(program, "calcHarmonicAngleForce");
}
void OpenCLCalcHarmonicAngleForceKernel::executeForces(ContextImpl& context) {
double OpenCLCalcHarmonicAngleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
if (numAngles == 0)
return;
return 0.0;
if (!hasInitializedKernel) {
hasInitializedKernel = true;
kernel.setArg<cl_int>(0, cl.getPaddedNumAtoms());
......@@ -504,10 +487,6 @@ void OpenCLCalcHarmonicAngleForceKernel::executeForces(ContextImpl& context) {
kernel.setArg<cl::Buffer>(6, indices->getDeviceBuffer());
}
cl.executeKernel(kernel, numAngles);
}
double OpenCLCalcHarmonicAngleForceKernel::executeEnergy(ContextImpl& context) {
executeForces(context);
return 0.0;
}
......@@ -625,9 +604,9 @@ void OpenCLCalcCustomAngleForceKernel::initialize(const System& system, const Cu
kernel = cl::Kernel(program, "computeCustomAngleForces");
}
void OpenCLCalcCustomAngleForceKernel::executeForces(ContextImpl& context) {
double OpenCLCalcCustomAngleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
if (numAngles == 0)
return;
return 0.0;
if (globals != NULL) {
bool changed = false;
for (int i = 0; i < (int) globalParamNames.size(); i++) {
......@@ -656,10 +635,6 @@ void OpenCLCalcCustomAngleForceKernel::executeForces(ContextImpl& context) {
}
}
cl.executeKernel(kernel, numAngles);
}
double OpenCLCalcCustomAngleForceKernel::executeEnergy(ContextImpl& context) {
executeForces(context);
return 0.0;
}
......@@ -726,9 +701,9 @@ void OpenCLCalcPeriodicTorsionForceKernel::initialize(const System& system, cons
kernel = cl::Kernel(program, "calcPeriodicTorsionForce");
}
void OpenCLCalcPeriodicTorsionForceKernel::executeForces(ContextImpl& context) {
double OpenCLCalcPeriodicTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
if (numTorsions == 0)
return;
return 0.0;
if (!hasInitializedKernel) {
hasInitializedKernel = true;
kernel.setArg<cl_int>(0, cl.getPaddedNumAtoms());
......@@ -740,10 +715,6 @@ void OpenCLCalcPeriodicTorsionForceKernel::executeForces(ContextImpl& context) {
kernel.setArg<cl::Buffer>(6, indices->getDeviceBuffer());
}
cl.executeKernel(kernel, numTorsions);
}
double OpenCLCalcPeriodicTorsionForceKernel::executeEnergy(ContextImpl& context) {
executeForces(context);
return 0.0;
}
......@@ -810,9 +781,9 @@ void OpenCLCalcRBTorsionForceKernel::initialize(const System& system, const RBTo
kernel = cl::Kernel(program, "calcRBTorsionForce");
}
void OpenCLCalcRBTorsionForceKernel::executeForces(ContextImpl& context) {
double OpenCLCalcRBTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
if (numTorsions == 0)
return;
return 0.0;
if (!hasInitializedKernel) {
hasInitializedKernel = true;
kernel.setArg<cl_int>(0, cl.getPaddedNumAtoms());
......@@ -824,10 +795,6 @@ void OpenCLCalcRBTorsionForceKernel::executeForces(ContextImpl& context) {
kernel.setArg<cl::Buffer>(6, indices->getDeviceBuffer());
}
cl.executeKernel(kernel, numTorsions);
}
double OpenCLCalcRBTorsionForceKernel::executeEnergy(ContextImpl& context) {
executeForces(context);
return 0.0;
}
......@@ -926,9 +893,9 @@ void OpenCLCalcCMAPTorsionForceKernel::initialize(const System& system, const CM
kernel = cl::Kernel(program, "computeCMAPTorsionForces");
}
void OpenCLCalcCMAPTorsionForceKernel::executeForces(ContextImpl& context) {
double OpenCLCalcCMAPTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
if (numTorsions == 0)
return;
return 0.0;
if (!hasInitializedKernel) {
hasInitializedKernel = true;
kernel.setArg<cl_int>(0, cl.getPaddedNumAtoms());
......@@ -942,10 +909,6 @@ void OpenCLCalcCMAPTorsionForceKernel::executeForces(ContextImpl& context) {
kernel.setArg<cl::Buffer>(8, torsionMaps->getDeviceBuffer());
}
cl.executeKernel(kernel, numTorsions);
}
double OpenCLCalcCMAPTorsionForceKernel::executeEnergy(ContextImpl& context) {
executeForces(context);
return 0.0;
}
......@@ -1065,9 +1028,9 @@ void OpenCLCalcCustomTorsionForceKernel::initialize(const System& system, const
kernel = cl::Kernel(program, "computeCustomTorsionForces");
}
void OpenCLCalcCustomTorsionForceKernel::executeForces(ContextImpl& context) {
double OpenCLCalcCustomTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
if (numTorsions == 0)
return;
return 0.0;
if (globals != NULL) {
bool changed = false;
for (int i = 0; i < (int) globalParamNames.size(); i++) {
......@@ -1096,10 +1059,6 @@ void OpenCLCalcCustomTorsionForceKernel::executeForces(ContextImpl& context) {
}
}
cl.executeKernel(kernel, numTorsions);
}
double OpenCLCalcCustomTorsionForceKernel::executeEnergy(ContextImpl& context) {
executeForces(context);
return 0.0;
}
......@@ -1398,7 +1357,7 @@ void OpenCLCalcNonbondedForceKernel::initialize(const System& system, const Nonb
exceptionsKernel = cl::Kernel(program, "computeNonbondedExceptions");
}
void OpenCLCalcNonbondedForceKernel::executeForces(ContextImpl& context) {
double OpenCLCalcNonbondedForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
if (!hasInitializedKernel) {
hasInitializedKernel = true;
if (exceptionIndices != NULL) {
......@@ -1484,10 +1443,6 @@ void OpenCLCalcNonbondedForceKernel::executeForces(ContextImpl& context) {
pmeInterpolateForceKernel.setArg<mm_float4>(6, invBoxSize);
cl.executeKernel(pmeInterpolateForceKernel, cl.getNumAtoms());
}
}
double OpenCLCalcNonbondedForceKernel::executeEnergy(ContextImpl& context) {
executeForces(context);
double energy = ewaldSelfEnergy;
if (dispersionCoefficient != 0.0) {
mm_float4 boxSize = cl.getPeriodicBoxSize();
......@@ -1644,7 +1599,7 @@ void OpenCLCalcCustomNonbondedForceKernel::initialize(const System& system, cons
cl.addForce(new OpenCLCustomNonbondedForceInfo(cl.getNonbondedUtilities().getNumForceBuffers(), force));
}
void OpenCLCalcCustomNonbondedForceKernel::executeForces(ContextImpl& context) {
double OpenCLCalcCustomNonbondedForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
if (globals != NULL) {
bool changed = false;
for (int i = 0; i < (int) globalParamNames.size(); i++) {
......@@ -1656,10 +1611,6 @@ void OpenCLCalcCustomNonbondedForceKernel::executeForces(ContextImpl& context) {
if (changed)
globals->upload(globalParamValues);
}
}
double OpenCLCalcCustomNonbondedForceKernel::executeEnergy(ContextImpl& context) {
executeForces(context);
return 0.0;
}
......@@ -1722,7 +1673,7 @@ void OpenCLCalcGBSAOBCForceKernel::initialize(const System& system, const GBSAOB
cl.addAutoclearBuffer(bornForce->getDeviceBuffer(), bornForce->getSize());
}
void OpenCLCalcGBSAOBCForceKernel::executeForces(ContextImpl& context) {
double OpenCLCalcGBSAOBCForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
OpenCLNonbondedUtilities& nb = cl.getNonbondedUtilities();
if (!hasCreatedKernels) {
// These Kernels cannot be created in initialize(), because the OpenCLNonbondedUtilities has not been initialized yet then.
......@@ -1805,10 +1756,6 @@ void OpenCLCalcGBSAOBCForceKernel::executeForces(ContextImpl& context) {
cl.executeKernel(reduceBornSumKernel, cl.getPaddedNumAtoms());
cl.executeKernel(force1Kernel, nb.getTiles().getSize()*OpenCLContext::TileSize);
cl.executeKernel(reduceBornForceKernel, cl.getPaddedNumAtoms());
}
double OpenCLCalcGBSAOBCForceKernel::executeEnergy(ContextImpl& context) {
executeForces(context);
return 0.0;
}
......@@ -2434,7 +2381,7 @@ void OpenCLCalcCustomGBForceKernel::initialize(const System& system, const Custo
}
}
void OpenCLCalcCustomGBForceKernel::executeForces(ContextImpl& context) {
double OpenCLCalcCustomGBForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
OpenCLNonbondedUtilities& nb = cl.getNonbondedUtilities();
if (!hasInitializedKernels) {
hasInitializedKernels = true;
......@@ -2584,10 +2531,6 @@ void OpenCLCalcCustomGBForceKernel::executeForces(ContextImpl& context) {
cl.executeKernel(perParticleEnergyKernel, cl.getPaddedNumAtoms());
if (needParameterGradient)
cl.executeKernel(gradientChainRuleKernel, cl.getPaddedNumAtoms());
}
double OpenCLCalcCustomGBForceKernel::executeEnergy(ContextImpl& context) {
executeForces(context);
return 0.0;
}
......@@ -2704,7 +2647,7 @@ void OpenCLCalcCustomExternalForceKernel::initialize(const System& system, const
kernel = cl::Kernel(program, "computeCustomExternalForces");
}
void OpenCLCalcCustomExternalForceKernel::executeForces(ContextImpl& context) {
double OpenCLCalcCustomExternalForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
if (globals != NULL) {
bool changed = false;
for (int i = 0; i < (int) globalParamNames.size(); i++) {
......@@ -2732,10 +2675,6 @@ void OpenCLCalcCustomExternalForceKernel::executeForces(ContextImpl& context) {
}
}
cl.executeKernel(kernel, numParticles);
}
double OpenCLCalcCustomExternalForceKernel::executeEnergy(ContextImpl& context) {
executeForces(context);
return 0.0;
}
......@@ -3166,7 +3105,7 @@ void OpenCLCalcCustomHbondForceKernel::initialize(const System& system, const Cu
acceptorKernel = cl::Kernel(program, "computeAcceptorForces");
}
void OpenCLCalcCustomHbondForceKernel::executeForces(ContextImpl& context) {
double OpenCLCalcCustomHbondForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
if (globals != NULL) {
bool changed = false;
for (int i = 0; i < (int) globalParamNames.size(); i++) {
......@@ -3237,10 +3176,6 @@ void OpenCLCalcCustomHbondForceKernel::executeForces(ContextImpl& context) {
acceptorKernel.setArg<mm_float4>(8, cl.getPeriodicBoxSize());
acceptorKernel.setArg<mm_float4>(9, cl.getInvPeriodicBoxSize());
cl.executeKernel(acceptorKernel, std::max(numDonors, numAcceptors));
}
double OpenCLCalcCustomHbondForceKernel::executeEnergy(ContextImpl& context) {
executeForces(context);
return 0.0;
}
......
platforms/opencl/src/OpenCLKernels.h
View file @ a711ce2a
......@@ -54,36 +54,26 @@ public:
*/
void initialize(const System& system);
/**
* This is called at the beginning of each force computation, before calcForces() has been called on
* This is called at the beginning of each force/energy computation, before calcForcesAndEnergy() has been called on
* any ForceImpl.
*
* @param context the context in which to execute this kernel
*/
void beginForceComputation(ContextImpl& context);
/**
* This is called at the end of each force computation, after calcForces() has been called on
* every ForceImpl.
*
* @param context the context in which to execute this kernel
*/
void finishForceComputation(ContextImpl& context);
/**
* This is called at the beginning of each energy computation, before calcEnergy() has been called on
* any ForceImpl.
*
* @param context the context in which to execute this kernel
* @param context the context in which to execute this kernel
* @param includeForce true if forces should be computed
* @param includeEnergy true if potential energy should be computed
*/
void beginEnergyComputation(ContextImpl& context);
void beginComputation(ContextImpl& context, bool includeForce, bool includeEnergy);
/**
* This is called at the end of each energy computation, after calcEnergy() has been called on
* This is called at the end of each force/energy computation, after calcForcesAndEnergy() has been called on
* every ForceImpl.
*
* @param context the context in which to execute this kernel
* @param context the context in which to execute this kernel
* @param includeForce true if forces should be computed
* @param includeEnergy true if potential energy should be computed
* @return the potential energy of the system. This value is added to all values returned by ForceImpls'
* calcEnergy() 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.
*/
double finishEnergyComputation(ContextImpl& context);
double finishComputation(ContextImpl& context, bool includeForce, bool includeEnergy);
private:
OpenCLContext& cl;
};
......@@ -205,18 +195,14 @@ public:
*/
void initialize(const System& system, const HarmonicBondForce& force);
/**
* Execute the kernel to calculate the forces.
*
* @param context the context in which to execute this kernel
*/
void executeForces(ContextImpl& context);
/**
* Execute the kernel to calculate the energy.
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the HarmonicBondForce
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double executeEnergy(ContextImpl& context);
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
private:
int numBonds;
bool hasInitializedKernel;
......@@ -244,18 +230,14 @@ public:
*/
void initialize(const System& system, const CustomBondForce& force);
/**
* Execute the kernel to calculate the forces.
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
void executeForces(ContextImpl& context);
/**
* Execute the kernel to calculate the energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the CustomBondForce
*/
double executeEnergy(ContextImpl& context);
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
private:
int numBonds;
bool hasInitializedKernel;
......@@ -286,18 +268,14 @@ public:
*/
void initialize(const System& system, const HarmonicAngleForce& force);
/**
* Execute the kernel to calculate the forces.
*
* @param context the context in which to execute this kernel
*/
void executeForces(ContextImpl& context);
/**
* Execute the kernel to calculate the energy.
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the HarmonicAngleForce
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double executeEnergy(ContextImpl& context);
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
private:
int numAngles;
bool hasInitializedKernel;
......@@ -325,18 +303,14 @@ public:
*/
void initialize(const System& system, const CustomAngleForce& force);
/**
* Execute the kernel to calculate the forces.
*
* @param context the context in which to execute this kernel
*/
void executeForces(ContextImpl& context);
/**
* Execute the kernel to calculate the energy.
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the CustomAngleForce
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double executeEnergy(ContextImpl& context);
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
private:
int numAngles;
bool hasInitializedKernel;
......@@ -367,18 +341,14 @@ public:
*/
void initialize(const System& system, const PeriodicTorsionForce& force);
/**
* Execute the kernel to calculate the forces.
*
* @param context the context in which to execute this kernel
*/
void executeForces(ContextImpl& context);
/**
* Execute the kernel to calculate the energy.
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the PeriodicTorsionForce
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double executeEnergy(ContextImpl& context);
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
private:
int numTorsions;
bool hasInitializedKernel;
......@@ -406,18 +376,14 @@ public:
*/
void initialize(const System& system, const RBTorsionForce& force);
/**
* Execute the kernel to calculate the forces.
*
* @param context the context in which to execute this kernel
*/
void executeForces(ContextImpl& context);
/**
* Execute the kernel to calculate the energy.
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the RBTorsionForce
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double executeEnergy(ContextImpl& context);
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
private:
int numTorsions;
bool hasInitializedKernel;
......@@ -445,18 +411,14 @@ public:
*/
void initialize(const System& system, const CMAPTorsionForce& force);
/**
* Execute the kernel to calculate the forces.
*
* @param context the context in which to execute this kernel
*/
void executeForces(ContextImpl& context);
/**
* Execute the kernel to calculate the energy.
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the CMAPTorsionForce
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double executeEnergy(ContextImpl& context);
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
private:
int numTorsions;
bool hasInitializedKernel;
......@@ -486,18 +448,14 @@ public:
*/
void initialize(const System& system, const CustomTorsionForce& force);
/**
* Execute the kernel to calculate the forces.
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
*/
void executeForces(ContextImpl& context);
/**
* Execute the kernel to calculate the energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the CustomTorsionForce
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double executeEnergy(ContextImpl& context);
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
private:
int numTorsions;
bool hasInitializedKernel;
......@@ -530,18 +488,14 @@ public:
*/
void initialize(const System& system, const NonbondedForce& force);
/**
* Execute the kernel to calculate the forces.
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
*/
void executeForces(ContextImpl& context);
/**
* Execute the kernel to calculate the energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the NonbondedForce
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double executeEnergy(ContextImpl& context);
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
private:
OpenCLContext& cl;
bool hasInitializedKernel;
......@@ -591,18 +545,14 @@ public:
*/
void initialize(const System& system, const CustomNonbondedForce& force);
/**
* Execute the kernel to calculate the forces.
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
*/
void executeForces(ContextImpl& context);
/**
* Execute the kernel to calculate the energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the CustomNonbondedForce
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double executeEnergy(ContextImpl& context);
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
private:
bool hasInitializedKernel;
OpenCLContext& cl;
......@@ -631,18 +581,14 @@ public:
*/
void initialize(const System& system, const GBSAOBCForce& force);
/**
* Execute the kernel to calculate the forces.
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
*/
void executeForces(ContextImpl& context);
/**
* Execute the kernel to calculate the energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the GBSAOBCForce
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double executeEnergy(ContextImpl& context);
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
private:
double prefactor;
bool hasCreatedKernels;
......@@ -676,18 +622,14 @@ public:
*/
void initialize(const System& system, const CustomGBForce& force);
/**
* Execute the kernel to calculate the forces.
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
*/
void executeForces(ContextImpl& context);
/**
* Execute the kernel to calculate the energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the CustomGBForce
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double executeEnergy(ContextImpl& context);
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
private:
bool hasInitializedKernels, needParameterGradient;
OpenCLContext& cl;
......@@ -721,18 +663,14 @@ public:
*/
void initialize(const System& system, const CustomExternalForce& force);
/**
* Execute the kernel to calculate the forces.
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
*/
void executeForces(ContextImpl& context);
/**
* Execute the kernel to calculate the energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the CustomExternalForce
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double executeEnergy(ContextImpl& context);
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
private:
int numParticles;
bool hasInitializedKernel;
......@@ -765,18 +703,14 @@ public:
*/
void initialize(const System& system, const CustomHbondForce& force);
/**
* Execute the kernel to calculate the forces.
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
*/
void executeForces(ContextImpl& context);
/**
* Execute the kernel to calculate the energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the CustomHbondForce
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double executeEnergy(ContextImpl& context);
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
private:
int numDonors, numAcceptors;
bool hasInitializedKernel;
......
platforms/reference/src/ReferenceKernels.h
View file @ a711ce2a
......@@ -68,36 +68,26 @@ public:
*/
void initialize(const System& system);
/**
* This is called at the beginning of each force computation, before calcForces() has been called on
* This is called at the beginning of each force/energy computation, before calcForcesAndEnergy() has been called on
* any ForceImpl.
*
* @param context the context in which to execute this kernel
* @param context the context in which to execute this kernel
* @param includeForce true if forces should be computed
* @param includeEnergy true if potential energy should be computed
*/
void beginForceComputation(ContextImpl& context);
void beginComputation(ContextImpl& context, bool includeForce, bool includeEnergy);
/**
* This is called at the end of each force computation, after calcForces() has been called on
* This is called at the end of each force/energy computation, after calcForcesAndEnergy() has been called on
* every ForceImpl.
*
* @param context the context in which to execute this kernel
*/
void finishForceComputation(ContextImpl& context);
/**
* This is called at the beginning of each energy computation, before calcEnergy() has been called on
* any ForceImpl.
*
* @param context the context in which to execute this kernel
*/
void beginEnergyComputation(ContextImpl& context);
/**
* This is called at the end of each energy computation, after calcEnergy() has been called on
* every ForceImpl.
*
* @param context the context in which to execute this kernel
* @param context the context in which to execute this kernel
* @param includeForce true if forces should be computed
* @param includeEnergy true if potential energy should be computed
* @return the potential energy of the system. This value is added to all values returned by ForceImpls'
* calcEnergy() 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.
*/
double finishEnergyComputation(ContextImpl& context);
double finishComputation(ContextImpl& context, bool includeForce, bool includeEnergy);
};
/**
......@@ -224,18 +214,14 @@ public:
*/
void initialize(const System& system, const HarmonicBondForce& force);
/**
* Execute the kernel to calculate the forces.
*
* @param context the context in which to execute this kernel
*/
void executeForces(ContextImpl& context);
/**
* Execute the kernel to calculate the energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the HarmonicBondForce
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double executeEnergy(ContextImpl& context);
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
private:
int numBonds;
int **bondIndexArray;
......@@ -258,18 +244,14 @@ public:
*/
void initialize(const System& system, const CustomBondForce& force);
/**
* Execute the kernel to calculate the forces.
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
void executeForces(ContextImpl& context);
/**
* Execute the kernel to calculate the energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the CustomBondForce
*/
double executeEnergy(ContextImpl& context);
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
private:
int numBonds;
int **bondIndexArray;
......@@ -294,18 +276,14 @@ public:
*/
void initialize(const System& system, const HarmonicAngleForce& force);
/**
* Execute the kernel to calculate the forces.
*
* @param context the context in which to execute this kernel
*/
void executeForces(ContextImpl& context);
/**
* Execute the kernel to calculate the energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the HarmonicAngleForce
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double executeEnergy(ContextImpl& context);
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
private:
int numAngles;
int **angleIndexArray;
......@@ -328,18 +306,14 @@ public:
*/
void initialize(const System& system, const CustomAngleForce& force);
/**
* Execute the kernel to calculate the forces.
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
void executeForces(ContextImpl& context);
/**
* Execute the kernel to calculate the energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the CustomAngleForce
*/
double executeEnergy(ContextImpl& context);
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
private:
int numAngles;
int **angleIndexArray;
......@@ -364,18 +338,14 @@ public:
*/
void initialize(const System& system, const PeriodicTorsionForce& force);
/**
* Execute the kernel to calculate the forces.
*
* @param context the context in which to execute this kernel
*/
void executeForces(ContextImpl& context);
/**
* Execute the kernel to calculate the energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the PeriodicTorsionForce
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double executeEnergy(ContextImpl& context);
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
private:
int numTorsions;
int **torsionIndexArray;
......@@ -398,18 +368,14 @@ public:
*/
void initialize(const System& system, const RBTorsionForce& force);
/**
* Execute the kernel to calculate the forces.
*
* @param context the context in which to execute this kernel
*/
void executeForces(ContextImpl& context);
/**
* Execute the kernel to calculate the energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the RBTorsionForce
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double executeEnergy(ContextImpl& context);
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
private:
int numTorsions;
int **torsionIndexArray;
......@@ -431,18 +397,14 @@ public:
*/
void initialize(const System& system, const CMAPTorsionForce& force);
/**
* Execute the kernel to calculate the forces.
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
void executeForces(ContextImpl& context);
/**
* Execute the kernel to calculate the energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the CMAPTorsionForce
*/
double executeEnergy(ContextImpl& context);
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
private:
std::vector<std::vector<std::vector<RealOpenMM> > > coeff;
std::vector<int> torsionMaps;
......@@ -465,18 +427,14 @@ public:
*/
void initialize(const System& system, const CustomTorsionForce& force);
/**
* Execute the kernel to calculate the forces.
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
void executeForces(ContextImpl& context);
/**
* Execute the kernel to calculate the energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the CustomTorsionForce
*/
double executeEnergy(ContextImpl& context);
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
private:
int numTorsions;
int **torsionIndexArray;
......@@ -501,18 +459,14 @@ public:
*/
void initialize(const System& system, const NonbondedForce& force);
/**
* Execute the kernel to calculate the forces.
*
* @param context the context in which to execute this kernel
*/
void executeForces(ContextImpl& context);
/**
* Execute the kernel to calculate the energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the NonbondedForce
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double executeEnergy(ContextImpl& context);
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
private:
int numParticles, num14;
int **exclusionArray, **bonded14IndexArray;
......@@ -540,18 +494,14 @@ public:
*/
void initialize(const System& system, const CustomNonbondedForce& force);
/**
* Execute the kernel to calculate the forces.
*
* @param context the context in which to execute this kernel
*/
void executeForces(ContextImpl& context);
/**
* Execute the kernel to calculate the energy.
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the CustomNonbondedForce
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double executeEnergy(ContextImpl& context);
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
private:
int numParticles;
int **exclusionArray;
......@@ -580,18 +530,14 @@ public:
*/
void initialize(const System& system, const GBSAOBCForce& force);
/**
* Execute the kernel to calculate the forces.
*
* @param context the context in which to execute this kernel
*/
void executeForces(ContextImpl& context);
/**
* Execute the kernel to calculate the energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the GBSAOBCForce
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double executeEnergy(ContextImpl& context);
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
private:
CpuObc* obc;
std::vector<RealOpenMM> charges;
......@@ -615,18 +561,14 @@ public:
*/
void initialize(const System& system, const GBVIForce& force, const std::vector<double> & scaledRadii);
/**
* Execute the kernel to calculate the forces.
*
* @param context the context in which to execute this kernel
*/
void executeForces(ContextImpl& context);
/**
* Execute the kernel to calculate the energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the GBVIForce
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double executeEnergy(ContextImpl& context);
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
private:
CpuGBVI * gbvi;
std::vector<RealOpenMM> charges;
......@@ -649,18 +591,14 @@ public:
*/
void initialize(const System& system, const CustomGBForce& force);
/**
* Execute the kernel to calculate the forces.
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
void executeForces(ContextImpl& context);
/**
* Execute the kernel to calculate the energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the CustomGBForce
*/
double executeEnergy(ContextImpl& context);
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
private:
int numParticles;
bool isPeriodic;
......@@ -696,18 +634,14 @@ public:
*/
void initialize(const System& system, const CustomExternalForce& force);
/**
* Execute the kernel to calculate the forces.
*
* @param context the context in which to execute this kernel
*/
void executeForces(ContextImpl& context);
/**
* Execute the kernel to calculate the energy.
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the CustomExternalForce
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double executeEnergy(ContextImpl& context);
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
private:
int numParticles;
std::vector<int> particles;
......@@ -732,18 +666,14 @@ public:
*/
void initialize(const System& system, const CustomHbondForce& force);
/**
* Execute the kernel to calculate the forces.
*
* @param context the context in which to execute this kernel
*/
void executeForces(ContextImpl& context);
/**
* Execute the kernel to calculate the energy.
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the CustomHbondForce
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double executeEnergy(ContextImpl& context);
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
private:
int numDonors, numAcceptors, numParticles;
bool isPeriodic;
......
plugins/amoeba/openmmapi/include/AmoebaGBSAOBCForce.h deleted 100644 → 0
View file @ 767ea1bd
#ifndef AMOEBA_OPENMM_GBSA_OBC_FORCE_FIELD_H_
#define AMOEBA_OPENMM_GBSA_OBC_FORCE_FIELD_H_
/* -------------------------------------------------------------------------- *
* 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) 2008-2009 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. *
* -------------------------------------------------------------------------- */
#include "openmm/Force.h"
#include <vector>
#include "openmm/internal/windowsExport.h"
namespace OpenMM {
/**
* This class implements an implicit solvation force using the GBSA-OBC model.
* <p>
* To use this class, create a AmoebaGBSAOBCForce object, then call addParticle() once for each particle in the
* System to define its parameters. The number of particles for which you define GBSA parameters must
* be exactly equal to the number of particles in the System, or else an exception will be thrown when you
* try to create a Context. After a particle has been added, you can modify its force field parameters
* by calling setParticleParameters().
*/
class OPENMM_EXPORT AmoebaGBSAOBCForce : public Force {
public:
/**
* This is an enumeration of the different methods that may be used for handling long range nonbonded forces.
*/
enum NonbondedMethod {
/**
* No cutoff is applied to nonbonded interactions. The full set of N^2 interactions is computed exactly.
* This necessarily means that periodic boundary conditions cannot be used. This is the default.
*/
NoCutoff = 0,
/**
* Interactions beyond the cutoff distance are ignored.
*/
CutoffNonPeriodic = 1,
/**
* Periodic boundary conditions are used, so that each particle interacts only with the nearest periodic copy of
* each other particle. Interactions beyond the cutoff distance are ignored.
*/
CutoffPeriodic = 2,
};
/*
* Create a AmoebaGBSAOBCForce.
*/
AmoebaGBSAOBCForce();
/**
* Get the number of particles in the system.
*/
int getNumParticles() const {
return particles.size();
}
/**
* Add the GBSA parameters for a particle. This should be called once for each particle
* in the System. When it is called for the i'th time, it specifies the parameters for the i'th particle.
*
* @param charge the charge of the particle, measured in units of the proton charge
* @param radius the GBSA radius of the particle, measured in nm
* @param scalingFactor the OBC scaling factor for the particle
* @return the index of the particle that was added
*/
int addParticle(double charge, double radius, double scalingFactor);
/**
* Get the force field parameters for a particle.
*
* @param index the index of the particle for which to get parameters
* @param charge the charge of the particle, measured in units of the proton charge
* @param radius the GBSA radius of the particle, measured in nm
* @param scalingFactor the OBC scaling factor for the particle
*/
void getParticleParameters(int index, double& charge, double& radius, double& scalingFactor) const;
/**
* Set the force field parameters for a particle.
*
* @param index the index of the particle for which to set parameters
* @param charge the charge of the particle, measured in units of the proton charge
* @param radius the GBSA radius of the particle, measured in nm
* @param scalingFactor the OBC scaling factor for the particle
*/
void setParticleParameters(int index, double charge, double radius, double scalingFactor);
/**
* Get the dielectric constant for the solvent.
*/
double getSolventDielectric() const {
return solventDielectric;
}
/**
* Set the dielectric constant for the solvent.
*/
void setSolventDielectric(double dielectric) {
solventDielectric = dielectric;
}
/**
* Get the dielectric constant for the solute.
*/
double getSoluteDielectric() const {
return soluteDielectric;
}
/**
* Set the dielectric constant for the solute.
*/
void setSoluteDielectric(double dielectric) {
soluteDielectric = dielectric;
}
/**
* Get the method used for handling long range nonbonded interactions.
*/
NonbondedMethod getNonbondedMethod() const;
/**
* Set the method used for handling long range nonbonded interactions.
*/
void setNonbondedMethod(NonbondedMethod method);
/**
* Get the cutoff distance (in nm) being used for nonbonded interactions. If the NonbondedMethod in use
* is NoCutoff, this value will have no effect.
*/
double getCutoffDistance() const;
/**
* Set the cutoff distance (in nm) being used for nonbonded interactions. If the NonbondedMethod in use
* is NoCutoff, this value will have no effect.
*/
void setCutoffDistance(double distance);
protected:
ForceImpl* createImpl();
private:
class ParticleInfo;
NonbondedMethod nonbondedMethod;
double cutoffDistance, solventDielectric, soluteDielectric;
std::vector<ParticleInfo> particles;
};
class AmoebaGBSAOBCForce::ParticleInfo {
public:
double charge, radius, scalingFactor;
ParticleInfo() {
charge = radius = scalingFactor = 0.0;
}
ParticleInfo(double charge, double radius, double scalingFactor) :
charge(charge), radius(radius), scalingFactor(scalingFactor) {
}
};
} // namespace OpenMM
#endif /*AMOEBA_OPENMM_GBSA_OBC_FORCE_FIELD_H_*/
plugins/amoeba/openmmapi/include/amoebaKernels.h
View file @ a711ce2a
......@@ -61,18 +61,14 @@ public:
*/
virtual void initialize(const System& system, const AmoebaHarmonicBondForce& force) = 0;
/**
* Execute the kernel to calculate the forces.
*
* @param context the context in which to execute this kernel
*/
virtual void executeForces(ContextImpl& context) = 0;
/**
* Execute the kernel to calculate the energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the HarmonicBondForce
*/
virtual double executeEnergy(ContextImpl& context) = 0;
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
virtual double execute(ContextImpl& context, bool includeForces, bool includeEnergy) = 0;
};
/**
......@@ -93,18 +89,14 @@ public:
*/
virtual void initialize(const System& system, const AmoebaHarmonicAngleForce& force) = 0;
/**
* Execute the kernel to calculate the forces.
*
* @param context the context in which to execute this kernel
*/
virtual void executeForces(ContextImpl& context) = 0;
/**
* Execute the kernel to calculate the energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the HarmonicAngleForce
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
virtual double executeEnergy(ContextImpl& context) = 0;
virtual double execute(ContextImpl& context, bool includeForces, bool includeEnergy) = 0;
};
/**
......@@ -125,18 +117,14 @@ public:
*/
virtual void initialize(const System& system, const AmoebaHarmonicInPlaneAngleForce& force) = 0;
/**
* Execute the kernel to calculate the forces.
*
* @param context the context in which to execute this kernel
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
virtual void executeForces(ContextImpl& context) = 0;
/**
* Execute the kernel to calculate the energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the HarmonicInPlaneAngleForce
*/
virtual double executeEnergy(ContextImpl& context) = 0;
virtual double execute(ContextImpl& context, bool includeForces, bool includeEnergy) = 0;
};
/**
......@@ -157,18 +145,14 @@ public:
*/
virtual void initialize(const System& system, const AmoebaTorsionForce& force) = 0;
/**
* Execute the kernel to calculate the forces.
*
* @param context the context in which to execute this kernel
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
virtual void executeForces(ContextImpl& context) = 0;
/**
* Execute the kernel to calculate the energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the TorsionForce
*/
virtual double executeEnergy(ContextImpl& context) = 0;
virtual double execute(ContextImpl& context, bool includeForces, bool includeEnergy) = 0;
};
/**
......@@ -189,18 +173,14 @@ public:
*/
virtual void initialize(const System& system, const AmoebaPiTorsionForce& force) = 0;
/**
* Execute the kernel to calculate the forces.
*
* @param context the context in which to execute this kernel
*/
virtual void executeForces(ContextImpl& context) = 0;
/**
* Execute the kernel to calculate the energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the PiTorsionForce
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
virtual double executeEnergy(ContextImpl& context) = 0;
virtual double execute(ContextImpl& context, bool includeForces, bool includeEnergy) = 0;
};
/**
......@@ -221,18 +201,14 @@ public:
*/
virtual void initialize(const System& system, const AmoebaStretchBendForce& force) = 0;
/**
* Execute the kernel to calculate the forces.
*
* @param context the context in which to execute this kernel
*/
virtual void executeForces(ContextImpl& context) = 0;
/**
* Execute the kernel to calculate the energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the StretchBendForce
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
virtual double executeEnergy(ContextImpl& context) = 0;
virtual double execute(ContextImpl& context, bool includeForces, bool includeEnergy) = 0;
};
/**
......@@ -253,18 +229,14 @@ public:
*/
virtual void initialize(const System& system, const AmoebaOutOfPlaneBendForce& force) = 0;
/**
* Execute the kernel to calculate the forces.
*
* @param context the context in which to execute this kernel
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
virtual void executeForces(ContextImpl& context) = 0;
/**
* Execute the kernel to calculate the energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the OutOfPlaneBendForce
*/
virtual double executeEnergy(ContextImpl& context) = 0;
virtual double execute(ContextImpl& context, bool includeForces, bool includeEnergy) = 0;
};
/**
......@@ -285,18 +257,14 @@ public:
*/
virtual void initialize(const System& system, const AmoebaTorsionTorsionForce& force) = 0;
/**
* Execute the kernel to calculate the forces.
*
* @param context the context in which to execute this kernel
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
virtual void executeForces(ContextImpl& context) = 0;
/**
* Execute the kernel to calculate the energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the TorsionTorsionForce
*/
virtual double executeEnergy(ContextImpl& context) = 0;
virtual double execute(ContextImpl& context, bool includeForces, bool includeEnergy) = 0;
};
/**
......@@ -317,18 +285,14 @@ public:
*/
virtual void initialize(const System& system, const AmoebaMultipoleForce& force) = 0;
/**
* Execute the kernel to calculate the forces.
*
* @param context the context in which to execute this kernel
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
virtual void executeForces(ContextImpl& context) = 0;
/**
* Execute the kernel to calculate the energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the MultipoleForce
*/
virtual double executeEnergy(ContextImpl& context) = 0;
virtual double execute(ContextImpl& context, bool includeForces, bool includeEnergy) = 0;
};
/**
......@@ -350,18 +314,14 @@ public:
*/
virtual void initialize(const System& system, const AmoebaGeneralizedKirkwoodForce& force) = 0;
/**
* Execute the kernel to calculate the forces.
*
* @param context the context in which to execute this kernel
*/
virtual void executeForces(ContextImpl& context) = 0;
/**
* Execute the kernel to calculate the energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the GBSAOBCForce
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
virtual double executeEnergy(ContextImpl& context) = 0;
virtual double execute(ContextImpl& context, bool includeForces, bool includeEnergy) = 0;
};
/**
......@@ -383,18 +343,14 @@ public:
*/
virtual void initialize(const System& system, const AmoebaSASAForce& force) = 0;
/**
* Execute the kernel to calculate the forces.
*
* @param context the context in which to execute this kernel
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
virtual void executeForces(ContextImpl& context) = 0;
/**
* Execute the kernel to calculate the energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the GBSAOBCForce
*/
virtual double executeEnergy(ContextImpl& context) = 0;
virtual double execute(ContextImpl& context, bool includeForces, bool includeEnergy) = 0;
};
/**
......@@ -416,18 +372,14 @@ public:
*/
virtual void initialize(const System& system, const AmoebaVdwForce& force) = 0;
/**
* Execute the kernel to calculate the forces.
*
* @param context the context in which to execute this kernel
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
virtual void executeForces(ContextImpl& context) = 0;
/**
* Execute the kernel to calculate the energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the GBSAOBCForce
*/
virtual double executeEnergy(ContextImpl& context) = 0;
virtual double execute(ContextImpl& context, bool includeForces, bool includeEnergy) = 0;
};
/**
......@@ -449,18 +401,14 @@ public:
*/
virtual void initialize(const System& system, const AmoebaWcaDispersionForce& force) = 0;
/**
* Execute the kernel to calculate the forces.
*
* @param context the context in which to execute this kernel
*/
virtual void executeForces(ContextImpl& context) = 0;
/**
* Execute the kernel to calculate the energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the GBSAOBCForce
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
virtual double executeEnergy(ContextImpl& context) = 0;
virtual double execute(ContextImpl& context, bool includeForces, bool includeEnergy) = 0;
};
} // namespace OpenMM
......
plugins/amoeba/openmmapi/include/internal/AmoebaGBSAOBCForceImpl.h deleted 100644 → 0
View file @ 767ea1bd
#ifndef OPENMM_AMOEBA_GBSA_OBC_FORCE_FIELD_IMPL_H_
#define OPENMM_AMOEBA_GBSA_OBC_FORCE_FIELD_IMPL_H_
/* -------------------------------------------------------------------------- *
* 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 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. *
* -------------------------------------------------------------------------- */
#include "openmm/internal/ForceImpl.h"
#include "AmoebaGBSAOBCForce.h"
#include "openmm/Kernel.h"
#include <string>
namespace OpenMM {
/**
* This is the internal implementation of AmoebaGBSAOBCForce.
*/
class AmoebaGBSAOBCForceImpl : public ForceImpl {
public:
AmoebaGBSAOBCForceImpl(AmoebaGBSAOBCForce& owner);
void initialize(ContextImpl& context);
AmoebaGBSAOBCForce& getOwner() {
return owner;
}
void updateContextState(ContextImpl& context) {
// This force field doesn't update the state directly.
}
void calcForces(ContextImpl& context);
double calcEnergy(ContextImpl& context);
std::map<std::string, double> getDefaultParameters() {
return std::map<std::string, double>(); // This force field doesn't define any parameters.
}
std::vector<std::string> getKernelNames();
private:
AmoebaGBSAOBCForce& owner;
Kernel kernel;
};
} // namespace OpenMM
#endif /*OPENMM_AMOEBA_GBSA_OBC_FORCE_FIELD_IMPL_H_*/
plugins/amoeba/openmmapi/include/internal/AmoebaGeneralizedKirkwoodForceImpl.h
View file @ a711ce2a
......@@ -53,8 +53,7 @@ public:
void updateContextState(ContextImpl& context) {
// This force field doesn't update the state directly.
}
void calcForces(ContextImpl& context);
double calcEnergy(ContextImpl& context);
double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy);
std::map<std::string, double> getDefaultParameters() {
return std::map<std::string, double>(); // This force field doesn't define any parameters.
}
......
plugins/amoeba/openmmapi/include/internal/AmoebaHarmonicAngleForceImpl.h
View file @ a711ce2a
......@@ -56,8 +56,7 @@ public:
void updateContextState(ContextImpl& context) {
// This force field doesn't update the state directly.
}
void calcForces(ContextImpl& context );
double calcEnergy(ContextImpl& context);
double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy);
std::map<std::string, double> getDefaultParameters() {
return std::map<std::string, double>(); // This force field doesn't define any parameters.
}
......
plugins/amoeba/openmmapi/include/internal/AmoebaHarmonicBondForceImpl.h
View file @ a711ce2a
......@@ -56,8 +56,7 @@ public:
void updateContextState(ContextImpl& context) {
// This force field doesn't update the state directly.
}
void calcForces(ContextImpl& context );
double calcEnergy(ContextImpl& context);
double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy);
std::map<std::string, double> getDefaultParameters() {
return std::map<std::string, double>(); // This force field doesn't define any parameters.
}
......
plugins/amoeba/openmmapi/include/internal/AmoebaHarmonicInPlaneAngleForceImpl.h
View file @ a711ce2a
......@@ -56,8 +56,7 @@ public:
void updateContextState(ContextImpl& context) {
// This force field doesn't update the state directly.
}
void calcForces(ContextImpl& context );
double calcEnergy(ContextImpl& context);
double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy);
std::map<std::string, double> getDefaultParameters() {
return std::map<std::string, double>(); // This force field doesn't define any parameters.
}
......
plugins/amoeba/openmmapi/include/internal/AmoebaMultipoleForceImpl.h
View file @ a711ce2a
......@@ -55,8 +55,7 @@ public:
void updateContextState(ContextImpl& context) {
// This force field doesn't update the state directly.
}
void calcForces(ContextImpl& context );
double calcEnergy(ContextImpl& context);
double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy);
std::map<std::string, double> getDefaultParameters() {
return std::map<std::string, double>(); // This force field doesn't define any parameters.
}
......
plugins/amoeba/openmmapi/include/internal/AmoebaOutOfPlaneBendForceImpl.h
View file @ a711ce2a
......@@ -56,8 +56,7 @@ public:
void updateContextState(ContextImpl& context) {
// This force field doesn't update the state directly.
}
void calcForces(ContextImpl& context );
double calcEnergy(ContextImpl& context);
double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy);
std::map<std::string, double> getDefaultParameters() {
return std::map<std::string, double>(); // This force field doesn't define any parameters.
}
......
plugins/amoeba/openmmapi/include/internal/AmoebaPiTorsionForceImpl.h
View file @ a711ce2a
......@@ -56,8 +56,7 @@ public:
void updateContextState(ContextImpl& context) {
// This force field doesn't update the state directly.
}
void calcForces(ContextImpl& context );
double calcEnergy(ContextImpl& context);
double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy);
std::map<std::string, double> getDefaultParameters() {
return std::map<std::string, double>(); // This force field doesn't define any parameters.
}
......
plugins/amoeba/openmmapi/include/internal/AmoebaSASAForceImpl.h
View file @ a711ce2a
......@@ -53,8 +53,7 @@ public:
void updateContextState(ContextImpl& context) {
// This force field doesn't update the state directly.
}
void calcForces(ContextImpl& context);
double calcEnergy(ContextImpl& context);
double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy);
std::map<std::string, double> getDefaultParameters() {
return std::map<std::string, double>(); // This force field doesn't define any parameters.
}
......
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