Created architecture for multiple time step integrators and completed reference implementation

plugins/amoeba/openmmapi/include/openmm/internal/AmoebaOutOfPlaneBendForceImpl.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/amoeba/openmmapi/include/openmm/internal/AmoebaPiTorsionForceImpl.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/amoeba/openmmapi/include/openmm/internal/AmoebaStretchBendForceImpl.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/amoeba/openmmapi/include/openmm/internal/AmoebaTorsionForceImpl.h

@@ -57,7 +57,7 @@ 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/amoeba/openmmapi/include/openmm/internal/AmoebaTorsionTorsionForceImpl.h

@@ -55,7 +55,7 @@ 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/amoeba/openmmapi/include/openmm/internal/AmoebaUreyBradleyForceImpl.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/amoeba/openmmapi/include/openmm/internal/AmoebaVdwForceImpl.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/amoeba/openmmapi/include/openmm/internal/AmoebaWcaDispersionForceImpl.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/amoeba/openmmapi/src/AmoebaGeneralizedKirkwoodForceImpl.cpp

@@ -52,8 +52,9 @@ void AmoebaGeneralizedKirkwoodForceImpl::initialize(ContextImpl& context) {
     dynamic_cast<CalcAmoebaGeneralizedKirkwoodForceKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner);
 }
 
-double AmoebaGeneralizedKirkwoodForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy) {
-    return dynamic_cast<CalcAmoebaGeneralizedKirkwoodForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
+double AmoebaGeneralizedKirkwoodForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
+    if ((groups&(1<<owner.getForceGroup())) != 0)
+        return dynamic_cast<CalcAmoebaGeneralizedKirkwoodForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
 }
 
 std::vector<std::string> AmoebaGeneralizedKirkwoodForceImpl::getKernelNames() {

plugins/amoeba/openmmapi/src/AmoebaHarmonicAngleForceImpl.cpp

@@ -50,8 +50,9 @@ void AmoebaHarmonicAngleForceImpl::initialize(ContextImpl& context) {
     dynamic_cast<CalcAmoebaHarmonicAngleForceKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner);
 }
 
-double AmoebaHarmonicAngleForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy) {
-    return dynamic_cast<CalcAmoebaHarmonicAngleForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
+double AmoebaHarmonicAngleForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
+    if ((groups&(1<<owner.getForceGroup())) != 0)
+        return dynamic_cast<CalcAmoebaHarmonicAngleForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
 }
 
 std::vector<std::string> AmoebaHarmonicAngleForceImpl::getKernelNames() {

plugins/amoeba/openmmapi/src/AmoebaHarmonicBondForceImpl.cpp

@@ -51,8 +51,9 @@ void AmoebaHarmonicBondForceImpl::initialize(ContextImpl& context) {
     dynamic_cast<CalcAmoebaHarmonicBondForceKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner);
 }
 
-double AmoebaHarmonicBondForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy) {
-    return dynamic_cast<CalcAmoebaHarmonicBondForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
+double AmoebaHarmonicBondForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
+    if ((groups&(1<<owner.getForceGroup())) != 0)
+        return dynamic_cast<CalcAmoebaHarmonicBondForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
 }
 
 std::vector<std::string> AmoebaHarmonicBondForceImpl::getKernelNames() {

plugins/amoeba/openmmapi/src/AmoebaHarmonicInPlaneAngleForceImpl.cpp

@@ -50,8 +50,9 @@ void AmoebaHarmonicInPlaneAngleForceImpl::initialize(ContextImpl& context) {
     dynamic_cast<CalcAmoebaHarmonicInPlaneAngleForceKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner);
 }
 
-double AmoebaHarmonicInPlaneAngleForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy) {
-    return dynamic_cast<CalcAmoebaHarmonicInPlaneAngleForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
+double AmoebaHarmonicInPlaneAngleForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
+    if ((groups&(1<<owner.getForceGroup())) != 0)
+        return dynamic_cast<CalcAmoebaHarmonicInPlaneAngleForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
 }
 
 std::vector<std::string> AmoebaHarmonicInPlaneAngleForceImpl::getKernelNames() {

plugins/amoeba/openmmapi/src/AmoebaMultipoleForceImpl.cpp

@@ -81,8 +81,9 @@ void AmoebaMultipoleForceImpl::initialize(ContextImpl& context) {
     dynamic_cast<CalcAmoebaMultipoleForceKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner);
 }
 
-double AmoebaMultipoleForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy) {
-    return dynamic_cast<CalcAmoebaMultipoleForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
+double AmoebaMultipoleForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
+    if ((groups&(1<<owner.getForceGroup())) != 0)
+        return dynamic_cast<CalcAmoebaMultipoleForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
 }
 
 std::vector<std::string> AmoebaMultipoleForceImpl::getKernelNames() {

plugins/amoeba/openmmapi/src/AmoebaOutOfPlaneBendForceImpl.cpp

@@ -50,8 +50,9 @@ void AmoebaOutOfPlaneBendForceImpl::initialize(ContextImpl& context) {
     dynamic_cast<CalcAmoebaOutOfPlaneBendForceKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner);
 }
 
-double AmoebaOutOfPlaneBendForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy) {
-    return dynamic_cast<CalcAmoebaOutOfPlaneBendForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
+double AmoebaOutOfPlaneBendForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
+    if ((groups&(1<<owner.getForceGroup())) != 0)
+        return dynamic_cast<CalcAmoebaOutOfPlaneBendForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
 }
 
 std::vector<std::string> AmoebaOutOfPlaneBendForceImpl::getKernelNames() {

plugins/amoeba/openmmapi/src/AmoebaPiTorsionForceImpl.cpp

@@ -50,8 +50,9 @@ void AmoebaPiTorsionForceImpl::initialize(ContextImpl& context) {
     dynamic_cast<CalcAmoebaPiTorsionForceKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner);
 }
 
-double AmoebaPiTorsionForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy) {
-    return dynamic_cast<CalcAmoebaPiTorsionForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
+double AmoebaPiTorsionForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
+    if ((groups&(1<<owner.getForceGroup())) != 0)
+        return dynamic_cast<CalcAmoebaPiTorsionForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
 }
 
 std::vector<std::string> AmoebaPiTorsionForceImpl::getKernelNames() {

plugins/amoeba/openmmapi/src/AmoebaStretchBendForceImpl.cpp

@@ -50,8 +50,9 @@ void AmoebaStretchBendForceImpl::initialize(ContextImpl& context) {
     dynamic_cast<CalcAmoebaStretchBendForceKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner);
 }
 
-double AmoebaStretchBendForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy) {
-    return dynamic_cast<CalcAmoebaStretchBendForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
+double AmoebaStretchBendForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
+    if ((groups&(1<<owner.getForceGroup())) != 0)
+        return dynamic_cast<CalcAmoebaStretchBendForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
 }
 
 std::vector<std::string> AmoebaStretchBendForceImpl::getKernelNames() {

plugins/amoeba/openmmapi/src/AmoebaTorsionForceImpl.cpp

@@ -50,8 +50,9 @@ void AmoebaTorsionForceImpl::initialize(ContextImpl& context) {
     dynamic_cast<CalcAmoebaTorsionForceKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner);
 }
 
-double AmoebaTorsionForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy) {
-    return dynamic_cast<CalcAmoebaTorsionForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
+double AmoebaTorsionForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
+    if ((groups&(1<<owner.getForceGroup())) != 0)
+        return dynamic_cast<CalcAmoebaTorsionForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
 }
 
 std::vector<std::string> AmoebaTorsionForceImpl::getKernelNames() {

plugins/amoeba/openmmapi/src/AmoebaTorsionTorsionForceImpl.cpp

@@ -51,8 +51,9 @@ void AmoebaTorsionTorsionForceImpl::initialize(ContextImpl& context) {
     dynamic_cast<CalcAmoebaTorsionTorsionForceKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner);
 }
 
-double AmoebaTorsionTorsionForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy) {
-    return dynamic_cast<CalcAmoebaTorsionTorsionForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
+double AmoebaTorsionTorsionForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
+    if ((groups&(1<<owner.getForceGroup())) != 0)
+        return dynamic_cast<CalcAmoebaTorsionTorsionForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
 }
 
 struct IntPair {

plugins/amoeba/openmmapi/src/AmoebaUreyBradleyForceImpl.cpp

@@ -51,8 +51,9 @@ void AmoebaUreyBradleyForceImpl::initialize(ContextImpl& context) {
     dynamic_cast<CalcAmoebaUreyBradleyForceKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner);
 }
 
-double AmoebaUreyBradleyForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy) {
-    return dynamic_cast<CalcAmoebaUreyBradleyForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
+double AmoebaUreyBradleyForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
+    if ((groups&(1<<owner.getForceGroup())) != 0)
+        return dynamic_cast<CalcAmoebaUreyBradleyForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
 }
 
 std::vector<std::string> AmoebaUreyBradleyForceImpl::getKernelNames() {

plugins/amoeba/openmmapi/src/AmoebaVdwForceImpl.cpp

@@ -55,8 +55,9 @@ void AmoebaVdwForceImpl::initialize(ContextImpl& context) {
     dynamic_cast<CalcAmoebaVdwForceKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner);
 }
 
-double AmoebaVdwForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy) {
-    return dynamic_cast<CalcAmoebaVdwForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
+double AmoebaVdwForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
+    if ((groups&(1<<owner.getForceGroup())) != 0)
+        return dynamic_cast<CalcAmoebaVdwForceKernel&>(kernel.getImpl()).execute(context, includeForces, includeEnergy);
 }
 
 std::vector<std::string> AmoebaVdwForceImpl::getKernelNames() {