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

plugins/freeEnergy/openmmapi/include/openmm/freeEnergyKernels.h

@@ -65,18 +65,14 @@ public:
      */
     virtual void initialize(const System& system, const GBSAOBCSoftcoreForce& 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 GBSAOBCSoftcoreForce
+     * 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;
 };
 
 /**
@@ -104,18 +100,14 @@ public:
      */
     virtual void initialize(const System& system, const NonbondedSoftcoreForce& 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 NonbondedSoftcoreForce
+     * 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;
 };
 
 /**
@@ -137,18 +129,14 @@ public:
      */
     virtual void initialize(const System& system, const GBVISoftcoreForce& force, const std::vector<double>& scaledRadii) = 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 GBVISoftcoreForce
+     * 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/freeEnergy/openmmapi/include/openmm/internal/GBSAOBCSoftcoreForceImpl.h

@@ -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/freeEnergy/openmmapi/include/openmm/internal/GBVISoftcoreForceImpl.h

@@ -62,8 +62,7 @@ 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/freeEnergy/openmmapi/include/openmm/internal/NonbondedSoftcoreForceImpl.h

@@ -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/freeEnergy/openmmapi/src/GBSAOBCSoftcoreForceImpl.cpp

@@ -48,12 +48,8 @@ void GBSAOBCSoftcoreForceImpl::initialize(ContextImpl& context) {
     dynamic_cast<CalcGBSAOBCSoftcoreForceKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner);
 }
 
-void GBSAOBCSoftcoreForceImpl::calcForces(ContextImpl& context ) {
-    dynamic_cast<CalcGBSAOBCSoftcoreForceKernel&>(kernel.getImpl()).executeForces(context);
-}
-
-double GBSAOBCSoftcoreForceImpl::calcEnergy(ContextImpl& context) {
-    return dynamic_cast<CalcGBSAOBCSoftcoreForceKernel&>(kernel.getImpl()).executeEnergy(context);
+double GBSAOBCSoftcoreForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy) {
+    return dynamic_cast<CalcGBSAOBCSoftcoreForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
 }
 
 std::vector<std::string> GBSAOBCSoftcoreForceImpl::getKernelNames() {

plugins/freeEnergy/openmmapi/src/GBVISoftcoreForceImpl.cpp

@@ -261,12 +261,8 @@ void GBVISoftcoreForceImpl::findScaledRadii( int numberOfParticles, const std::v
 
 }
 
-void GBVISoftcoreForceImpl::calcForces(ContextImpl& context) {
-    dynamic_cast<CalcGBVISoftcoreForceKernel&>(kernel.getImpl()).executeForces(context);
-}
-
-double GBVISoftcoreForceImpl::calcEnergy(ContextImpl& context) {
-    return dynamic_cast<CalcGBVISoftcoreForceKernel&>(kernel.getImpl()).executeEnergy(context);
+double GBVISoftcoreForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy) {
+    return dynamic_cast<CalcGBVISoftcoreForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
 }
 
 std::vector<std::string> GBVISoftcoreForceImpl::getKernelNames() {

plugins/freeEnergy/openmmapi/src/NonbondedSoftcoreForceImpl.cpp

@@ -87,12 +87,8 @@ void NonbondedSoftcoreForceImpl::initialize(ContextImpl& context) {
     dynamic_cast<CalcNonbondedSoftcoreForceKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner);
 }
 
-void NonbondedSoftcoreForceImpl::calcForces(ContextImpl& context ) {
-    dynamic_cast<CalcNonbondedSoftcoreForceKernel&>(kernel.getImpl()).executeForces(context);
-}
-
-double NonbondedSoftcoreForceImpl::calcEnergy(ContextImpl& context) {
-    return dynamic_cast<CalcNonbondedSoftcoreForceKernel&>(kernel.getImpl()).executeEnergy(context);
+double NonbondedSoftcoreForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy) {
+    return dynamic_cast<CalcNonbondedSoftcoreForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
 }
 
 std::vector<std::string> NonbondedSoftcoreForceImpl::getKernelNames() {

plugins/freeEnergy/platforms/cuda/src/CudaFreeEnergyKernels.cpp

@@ -377,7 +377,7 @@ void CudaFreeEnergyCalcNonbondedSoftcoreForceKernel::initialize(const System& sy
     }
 }
 
-void CudaFreeEnergyCalcNonbondedSoftcoreForceKernel::executeForces(ContextImpl& context) {
+double CudaFreeEnergyCalcNonbondedSoftcoreForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
 
 // ---------------------------------------------------------------------------------------
 
@@ -428,10 +428,6 @@ void CudaFreeEnergyCalcNonbondedSoftcoreForceKernel::executeForces(ContextImpl&
 //kPrintForces( gpu, "Post kCalculateLocalSoftcoreForces ", call );
 //kPrintForces(gpu, "Post kCalculateLocalSoftcoreForces", call );
 //kReduceForces(gpu);
-}
-
-double CudaFreeEnergyCalcNonbondedSoftcoreForceKernel::executeEnergy(ContextImpl& context) {
-    executeForces(context);
     return 0.0;
 }
 
@@ -519,7 +515,7 @@ void CudaFreeEnergyCalcGBSAOBCSoftcoreForceKernel::initialize(const System& syst
                                                      radius, scale, charge, nonPolarScalingFactors );
 }
 
-void CudaFreeEnergyCalcGBSAOBCSoftcoreForceKernel::executeForces(ContextImpl& context) {
+double CudaFreeEnergyCalcGBSAOBCSoftcoreForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
 
 // ---------------------------------------------------------------------------------------
 
@@ -576,11 +572,7 @@ void CudaFreeEnergyCalcGBSAOBCSoftcoreForceKernel::executeForces(ContextImpl& co
     // second loop of Obc GBSA forces
 
     kCalculateObcGbsaSoftcoreForces2(gpu);
-}
-
-double CudaFreeEnergyCalcGBSAOBCSoftcoreForceKernel::executeEnergy(ContextImpl& context) {
-    executeForces( context );
-	 return 0.0;
+    return 0.0;
 }
 
 CudaFreeEnergyCalcGBVISoftcoreForceKernel::~CudaFreeEnergyCalcGBVISoftcoreForceKernel() {
@@ -661,7 +653,7 @@ void CudaFreeEnergyCalcGBVISoftcoreForceKernel::initialize(const System& system,
 
 }
 
-void CudaFreeEnergyCalcGBVISoftcoreForceKernel::executeForces(ContextImpl& context) {
+double CudaFreeEnergyCalcGBVISoftcoreForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
 
 // ---------------------------------------------------------------------------------------
 
@@ -747,10 +739,6 @@ void CudaFreeEnergyCalcGBVISoftcoreForceKernel::executeForces(ContextImpl& conte
 
     kCalculateGBVISoftcoreForces2(gpu);
 //kPrintForces( gpu, "Post GBVISoftcoreForces2", call );
-}
-
-double CudaFreeEnergyCalcGBVISoftcoreForceKernel::executeEnergy(ContextImpl& context) {
-    executeForces( context );
     return 0.0;
 }
 

plugins/freeEnergy/platforms/cuda/src/CudaFreeEnergyKernels.h

@@ -73,18 +73,14 @@ public:
      */
     void initialize(const System& system, const NonbondedSoftcoreForce& 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);
     /**
      * Get flag signalling whether GBSA/OBC force is included
      *
@@ -177,18 +173,14 @@ public:
      */
     void initialize(const System& system, const GBSAOBCSoftcoreForce& 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;
     FILE* log;
@@ -223,18 +215,14 @@ public:
      */
     void initialize(const System& system, const GBVISoftcoreForce& 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);
 
     /**
      * Apply quintic scaling for Born radii

plugins/freeEnergy/platforms/reference/src/ReferenceFreeEnergyKernels.cpp

@@ -226,47 +226,11 @@ void ReferenceFreeEnergyCalcNonbondedSoftcoreForceKernel::initialize(const Syste
     rfDielectric = (RealOpenMM)force.getReactionFieldDielectric();
 }
 
-void ReferenceFreeEnergyCalcNonbondedSoftcoreForceKernel::executeForces(ContextImpl& context) {
+double ReferenceFreeEnergyCalcNonbondedSoftcoreForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
 
     RealOpenMM** posData   = extractPositions(context);
     RealOpenMM** forceData = extractForces(context);
 
-    ReferenceFreeEnergyLJCoulombSoftcoreIxn clj;
-    //clj.setSoftCoreLJLambda( softCoreLJLambda );
-
-    bool periodic = (nonbondedMethod == CutoffPeriodic);
-    bool ewald    = (nonbondedMethod == Ewald);
-    bool pme      = (nonbondedMethod == PME);
-
-    if (nonbondedMethod != NoCutoff) {
-        computeNeighborListVoxelHash(*neighborList, numParticles, posData, exclusions, (periodic || ewald || pme) ? periodicBoxSize : NULL, nonbondedCutoff, 0.0);
-        clj.setUseCutoff(nonbondedCutoff, *neighborList, rfDielectric);
-    }
-
-    if (periodic||ewald||pme)
-        clj.setPeriodic(periodicBoxSize);
-
-    if (ewald)
-        clj.setUseEwald(ewaldAlpha, kmax[0], kmax[1], kmax[2]);
-
-    if (pme)
-        clj.setUsePME(ewaldAlpha);
-
-    clj.calculatePairIxn(numParticles, posData, particleParamArray, exclusionArray, 0, forceData, 0, 0);
-
-    ReferenceBondForce refBondForce;
-
-    ReferenceFreeEnergyLJCoulomb14Softcore nonbonded14;
-    if (nonbondedMethod == CutoffNonPeriodic || nonbondedMethod == CutoffPeriodic)
-        nonbonded14.setUseCutoff(nonbondedCutoff, rfDielectric);
-    refBondForce.calculateForce(num14, bonded14IndexArray, posData, bonded14ParamArray, forceData, 0, nonbonded14);
-}
-
-double ReferenceFreeEnergyCalcNonbondedSoftcoreForceKernel::executeEnergy(ContextImpl& context) {
-
-    RealOpenMM** posData   = extractPositions(context);
-    RealOpenMM** forceData = allocateRealArray(numParticles, 3);
-
     RealOpenMM energy = 0;
     ReferenceFreeEnergyLJCoulombSoftcoreIxn clj;
    // clj.setSoftCoreLJLambda( softCoreLJLambda );
@@ -290,7 +254,6 @@ double ReferenceFreeEnergyCalcNonbondedSoftcoreForceKernel::executeEnergy(Contex
         nonbonded14.setUseCutoff(nonbondedCutoff, rfDielectric);
 
     refBondForce.calculateForce(num14, bonded14IndexArray, posData, bonded14ParamArray, forceData, &energy, nonbonded14);
-    disposeRealArray(forceData, numParticles);
 
     return energy;
 }
@@ -361,13 +324,7 @@ void ReferenceFreeEnergyCalcGBSAOBCSoftcoreForceKernel::initialize(const System&
     obc->setIncludeAceApproximation(true);
 }
 
-void ReferenceFreeEnergyCalcGBSAOBCSoftcoreForceKernel::executeForces(ContextImpl& context) {
-    RealOpenMM** posData   = extractPositions(context);
-    RealOpenMM** forceData = extractForces(context);
-    obc->computeImplicitSolventForces(posData, &charges[0], forceData, 1);
-}
-
-double ReferenceFreeEnergyCalcGBSAOBCSoftcoreForceKernel::executeEnergy(ContextImpl& context) {
+double ReferenceFreeEnergyCalcGBSAOBCSoftcoreForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
     RealOpenMM** posData   = extractPositions(context);
     RealOpenMM** forceData = extractForces(context);
     obc->computeImplicitSolventForces(posData, &charges[0], forceData, 1);
@@ -433,23 +390,18 @@ void ReferenceFreeEnergyCalcGBVISoftcoreForceKernel::initialize(const System& sy
     gbviSoftcore = new CpuGBVISoftcore(gBVIParameters);
 }
 
-void ReferenceFreeEnergyCalcGBVISoftcoreForceKernel::executeForces(ContextImpl& context) {
-
-    RealOpenMM** posData   = extractPositions(context);
-    RealOpenMM** forceData = extractForces(context);
-
-    RealOpenMM* bornRadii  = new RealOpenMM[context.getSystem().getNumParticles()];
-    gbviSoftcore->computeBornRadii(posData, bornRadii, NULL ); 
-    gbviSoftcore->computeBornForces(bornRadii, posData, &charges[0], forceData);
-    delete[] bornRadii;
-}
-
-double ReferenceFreeEnergyCalcGBVISoftcoreForceKernel::executeEnergy(ContextImpl& context) {
+double ReferenceFreeEnergyCalcGBVISoftcoreForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
     RealOpenMM** posData = extractPositions(context);
 
     RealOpenMM* bornRadii = new RealOpenMM[context.getSystem().getNumParticles()];
-    gbviSoftcore->computeBornRadii(posData, bornRadii, NULL ); 
-    RealOpenMM energy     = gbviSoftcore->computeBornEnergy(bornRadii ,posData, &charges[0]);
+    gbviSoftcore->computeBornRadii(posData, bornRadii, NULL );
+    if (includeForces) {
+        RealOpenMM** forceData = extractForces(context);
+        gbviSoftcore->computeBornForces(bornRadii, posData, &charges[0], forceData);
+    }
+    RealOpenMM energy = 0.0;
+    if (includeEnergy)
+        energy = gbviSoftcore->computeBornEnergy(bornRadii ,posData, &charges[0]);
     delete[] bornRadii;
     return static_cast<double>(energy);
 }

plugins/freeEnergy/platforms/reference/src/ReferenceFreeEnergyKernels.h

@@ -57,18 +57,14 @@ public:
      */
     void initialize(const System& system, const NonbondedSoftcoreForce& 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 NonbondedSoftcoreForce
+     * 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;
@@ -96,18 +92,14 @@ public:
      */
     void initialize(const System& system, const GBSAOBCSoftcoreForce& 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 GBSAOBCSoftcoreForce
+     * 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:
     CpuObcSoftcore* obc;
     std::vector<RealOpenMM> charges;
@@ -130,18 +122,14 @@ public:
      */
     void initialize(const System& system, const GBVISoftcoreForce& 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 GBVISoftcoreForce
+     * 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:
     CpuGBVISoftcore* gbviSoftcore;
     std::vector<RealOpenMM> charges;