Created architecture for multiple time step integrators and completed reference implementation

plugins/amoeba/openmmapi/src/AmoebaWcaDispersionForceImpl.cpp

@@ -56,8 +56,9 @@ void AmoebaWcaDispersionForceImpl::initialize(ContextImpl& context) {
     dynamic_cast<CalcAmoebaWcaDispersionForceKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner);
 }
 
-double AmoebaWcaDispersionForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy) {
-    return dynamic_cast<CalcAmoebaWcaDispersionForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
+double AmoebaWcaDispersionForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
+    if ((groups&(1<<owner.getForceGroup())) != 0)
+        return dynamic_cast<CalcAmoebaWcaDispersionForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
 }
 void AmoebaWcaDispersionForceImpl::getMaximumDispersionEnergy( const AmoebaWcaDispersionForce& force, int particleIndex, double& maxDispersionEnergy ) {
 

plugins/freeEnergy/openmmapi/include/openmm/internal/GBSAOBCSoftcoreForceImpl.h

@@ -53,7 +53,7 @@ public:
     void updateContextState(ContextImpl& context) {
         // This force field doesn't update the state directly.
     }
-    double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy);
+    double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups);
     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

@@ -62,7 +62,7 @@ public:
     void updateContextState(ContextImpl& context) {
         // This force field doesn't update the state directly.
     }
-    double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy);
+    double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups);
     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

@@ -56,7 +56,7 @@ public:
     void updateContextState(ContextImpl& context) {
         // This force field doesn't update the state directly.
     }
-    double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy);
+    double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups);
     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

@@ -48,8 +48,9 @@ void GBSAOBCSoftcoreForceImpl::initialize(ContextImpl& context) {
     dynamic_cast<CalcGBSAOBCSoftcoreForceKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner);
 }
 
-double GBSAOBCSoftcoreForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy) {
-    return dynamic_cast<CalcGBSAOBCSoftcoreForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
+double GBSAOBCSoftcoreForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
+    if ((groups&(1<<owner.getForceGroup())) != 0)
+        return dynamic_cast<CalcGBSAOBCSoftcoreForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
 }
 
 std::vector<std::string> GBSAOBCSoftcoreForceImpl::getKernelNames() {

plugins/freeEnergy/openmmapi/src/GBVISoftcoreForceImpl.cpp

@@ -261,8 +261,9 @@ void GBVISoftcoreForceImpl::findScaledRadii( int numberOfParticles, const std::v
 
 }
 
-double GBVISoftcoreForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy) {
-    return dynamic_cast<CalcGBVISoftcoreForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
+double GBVISoftcoreForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
+    if ((groups&(1<<owner.getForceGroup())) != 0)
+        return dynamic_cast<CalcGBVISoftcoreForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
 }
 
 std::vector<std::string> GBVISoftcoreForceImpl::getKernelNames() {

plugins/freeEnergy/openmmapi/src/NonbondedSoftcoreForceImpl.cpp

@@ -87,8 +87,9 @@ void NonbondedSoftcoreForceImpl::initialize(ContextImpl& context) {
     dynamic_cast<CalcNonbondedSoftcoreForceKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner);
 }
 
-double NonbondedSoftcoreForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy) {
-    return dynamic_cast<CalcNonbondedSoftcoreForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
+double NonbondedSoftcoreForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
+    if ((groups&(1<<owner.getForceGroup())) != 0)
+        return dynamic_cast<CalcNonbondedSoftcoreForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
 }
 
 std::vector<std::string> NonbondedSoftcoreForceImpl::getKernelNames() {