Context constructor now uses const System&, guaranteeing that System won't be modified.

plugins/amoeba/openmmapi/src/AmoebaMultipoleForceImpl.cpp

@@ -41,7 +41,7 @@ using std::vector;
 bool AmoebaMultipoleForceImpl::initializedCovalentDegrees = false;
 int AmoebaMultipoleForceImpl::CovalentDegrees[]           = { 1,2,3,4,0,1,2,3};
 
-AmoebaMultipoleForceImpl::AmoebaMultipoleForceImpl(AmoebaMultipoleForce& owner) : owner(owner) {
+AmoebaMultipoleForceImpl::AmoebaMultipoleForceImpl(const AmoebaMultipoleForce& owner) : owner(owner) {
 }
 
 AmoebaMultipoleForceImpl::~AmoebaMultipoleForceImpl() {
@@ -49,7 +49,7 @@ AmoebaMultipoleForceImpl::~AmoebaMultipoleForceImpl() {
 
 void AmoebaMultipoleForceImpl::initialize(ContextImpl& context) {
 
-    System& system = context.getSystem();
+    const System& system = context.getSystem();
     if (owner.getNumMultipoles() != system.getNumParticles())
         throw OpenMMException("AmoebaMultipoleForce must have exactly as many particles as the System it belongs to.");
 

plugins/amoeba/openmmapi/src/AmoebaOutOfPlaneBendForce.cpp

@@ -99,7 +99,7 @@ void AmoebaOutOfPlaneBendForce::setOutOfPlaneBendParameters(int index, int parti
     outOfPlaneBends[index].k          = k;
 }
 
-ForceImpl* AmoebaOutOfPlaneBendForce::createImpl() {
+ForceImpl* AmoebaOutOfPlaneBendForce::createImpl() const {
     return new AmoebaOutOfPlaneBendForceImpl(*this);
 }
 

plugins/amoeba/openmmapi/src/AmoebaOutOfPlaneBendForceImpl.cpp

@@ -39,7 +39,7 @@ using std::pair;
 using std::vector;
 using std::set;
 
-AmoebaOutOfPlaneBendForceImpl::AmoebaOutOfPlaneBendForceImpl(AmoebaOutOfPlaneBendForce& owner) : owner(owner) {
+AmoebaOutOfPlaneBendForceImpl::AmoebaOutOfPlaneBendForceImpl(const AmoebaOutOfPlaneBendForce& owner) : owner(owner) {
 }
 
 AmoebaOutOfPlaneBendForceImpl::~AmoebaOutOfPlaneBendForceImpl() {

plugins/amoeba/openmmapi/src/AmoebaPiTorsionForce.cpp

@@ -64,7 +64,7 @@ void AmoebaPiTorsionForce::setPiTorsionParameters(int index, int particle1, int
     piTorsions[index].k          = k;
 }
 
-ForceImpl* AmoebaPiTorsionForce::createImpl() {
+ForceImpl* AmoebaPiTorsionForce::createImpl() const {
     return new AmoebaPiTorsionForceImpl(*this);
 }
 

plugins/amoeba/openmmapi/src/AmoebaPiTorsionForceImpl.cpp

@@ -39,7 +39,7 @@ using std::pair;
 using std::vector;
 using std::set;
 
-AmoebaPiTorsionForceImpl::AmoebaPiTorsionForceImpl(AmoebaPiTorsionForce& owner) : owner(owner) {
+AmoebaPiTorsionForceImpl::AmoebaPiTorsionForceImpl(const AmoebaPiTorsionForce& owner) : owner(owner) {
 }
 
 AmoebaPiTorsionForceImpl::~AmoebaPiTorsionForceImpl() {

plugins/amoeba/openmmapi/src/AmoebaStretchBendForce.cpp

@@ -67,7 +67,7 @@ void AmoebaStretchBendForce::setStretchBendParameters(int index, int particle1,
     stretchBends[index].k          = k;
 }
 
-ForceImpl* AmoebaStretchBendForce::createImpl() {
+ForceImpl* AmoebaStretchBendForce::createImpl() const {
     return new AmoebaStretchBendForceImpl(*this);
 }
 

plugins/amoeba/openmmapi/src/AmoebaStretchBendForceImpl.cpp

@@ -39,7 +39,7 @@ using std::pair;
 using std::vector;
 using std::set;
 
-AmoebaStretchBendForceImpl::AmoebaStretchBendForceImpl(AmoebaStretchBendForce& owner) : owner(owner) {
+AmoebaStretchBendForceImpl::AmoebaStretchBendForceImpl(const AmoebaStretchBendForce& owner) : owner(owner) {
 }
 
 AmoebaStretchBendForceImpl::~AmoebaStretchBendForceImpl() {

plugins/amoeba/openmmapi/src/AmoebaTorsionTorsionForce.cpp

@@ -79,6 +79,6 @@ void AmoebaTorsionTorsionForce::setTorsionTorsionGrid(int index, const TorsionTo
    torsionTorsionGrids[index] = grid;
 }
 
-ForceImpl* AmoebaTorsionTorsionForce::createImpl() {
+ForceImpl* AmoebaTorsionTorsionForce::createImpl() const {
     return new AmoebaTorsionTorsionForceImpl(*this);
 }

plugins/amoeba/openmmapi/src/AmoebaTorsionTorsionForceImpl.cpp

@@ -40,7 +40,7 @@ using std::pair;
 using std::vector;
 using std::set;
 
-AmoebaTorsionTorsionForceImpl::AmoebaTorsionTorsionForceImpl(AmoebaTorsionTorsionForce& owner) : owner(owner) {
+AmoebaTorsionTorsionForceImpl::AmoebaTorsionTorsionForceImpl(const AmoebaTorsionTorsionForce& owner) : owner(owner) {
 }
 
 AmoebaTorsionTorsionForceImpl::~AmoebaTorsionTorsionForceImpl() {

plugins/amoeba/openmmapi/src/AmoebaVdwForce.cpp

@@ -118,7 +118,7 @@ void AmoebaVdwForce::setNonbondedMethod(NonbondedMethod method) {
     nonbondedMethod = method;
 }
 
-ForceImpl* AmoebaVdwForce::createImpl() {
+ForceImpl* AmoebaVdwForce::createImpl() const {
     return new AmoebaVdwForceImpl(*this);
 }
 

plugins/amoeba/openmmapi/src/AmoebaVdwForceImpl.cpp

@@ -45,14 +45,14 @@ using std::pair;
 using std::vector;
 using std::set;
 
-AmoebaVdwForceImpl::AmoebaVdwForceImpl(AmoebaVdwForce& owner) : owner(owner) {
+AmoebaVdwForceImpl::AmoebaVdwForceImpl(const AmoebaVdwForce& owner) : owner(owner) {
 }
 
 AmoebaVdwForceImpl::~AmoebaVdwForceImpl() {
 }
 
 void AmoebaVdwForceImpl::initialize(ContextImpl& context) {
-    System& system = context.getSystem();
+    const System& system = context.getSystem();
 
     if (owner.getNumParticles() != system.getNumParticles())
         throw OpenMMException("AmoebaVdwForce must have exactly as many particles as the System it belongs to.");

plugins/amoeba/openmmapi/src/AmoebaWcaDispersionForce.cpp

@@ -127,7 +127,7 @@ void AmoebaWcaDispersionForce::setSlevy( double inputSlevy ){
     slevy = inputSlevy;
 }
 
-ForceImpl* AmoebaWcaDispersionForce::createImpl() {
+ForceImpl* AmoebaWcaDispersionForce::createImpl() const {
     return new AmoebaWcaDispersionForceImpl(*this);
 }
 

plugins/amoeba/openmmapi/src/AmoebaWcaDispersionForceImpl.cpp

@@ -40,7 +40,7 @@ using std::pair;
 using std::vector;
 using std::set;
 
-AmoebaWcaDispersionForceImpl::AmoebaWcaDispersionForceImpl(AmoebaWcaDispersionForce& owner) : owner(owner) {
+AmoebaWcaDispersionForceImpl::AmoebaWcaDispersionForceImpl(const AmoebaWcaDispersionForce& owner) : owner(owner) {
 }
 
 AmoebaWcaDispersionForceImpl::~AmoebaWcaDispersionForceImpl() {
@@ -48,7 +48,7 @@ AmoebaWcaDispersionForceImpl::~AmoebaWcaDispersionForceImpl() {
 
 void AmoebaWcaDispersionForceImpl::initialize(ContextImpl& context) {
  
-    System& system = context.getSystem();
+    const System& system = context.getSystem();
     if (owner.getNumParticles() != system.getNumParticles())
         throw OpenMMException("AmoebaWcaDispersionForce must have exactly as many particles as the System it belongs to.");
 

plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.cpp

@@ -87,7 +87,7 @@ private:
     const AmoebaBondForce& force;
 };
 
-CudaCalcAmoebaBondForceKernel::CudaCalcAmoebaBondForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system) : 
+CudaCalcAmoebaBondForceKernel::CudaCalcAmoebaBondForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system) : 
                 CalcAmoebaBondForceKernel(name, platform), cu(cu), system(system), params(NULL) {
 }
 
@@ -184,7 +184,7 @@ private:
     const AmoebaAngleForce& force;
 };
 
-CudaCalcAmoebaAngleForceKernel::CudaCalcAmoebaAngleForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system) :
+CudaCalcAmoebaAngleForceKernel::CudaCalcAmoebaAngleForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system) :
             CalcAmoebaAngleForceKernel(name, platform), cu(cu), system(system), params(NULL) {
 }
 
@@ -285,7 +285,7 @@ private:
     const AmoebaInPlaneAngleForce& force;
 };
 
-CudaCalcAmoebaInPlaneAngleForceKernel::CudaCalcAmoebaInPlaneAngleForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system) : 
+CudaCalcAmoebaInPlaneAngleForceKernel::CudaCalcAmoebaInPlaneAngleForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system) : 
           CalcAmoebaInPlaneAngleForceKernel(name, platform), cu(cu), system(system), params(NULL) {
 }
 
@@ -387,7 +387,7 @@ private:
     const AmoebaPiTorsionForce& force;
 };
 
-CudaCalcAmoebaPiTorsionForceKernel::CudaCalcAmoebaPiTorsionForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system) :
+CudaCalcAmoebaPiTorsionForceKernel::CudaCalcAmoebaPiTorsionForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system) :
          CalcAmoebaPiTorsionForceKernel(name, platform), cu(cu), system(system), params(NULL) {
 }
 
@@ -481,7 +481,7 @@ private:
     const AmoebaStretchBendForce& force;
 };
 
-CudaCalcAmoebaStretchBendForceKernel::CudaCalcAmoebaStretchBendForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system) :
+CudaCalcAmoebaStretchBendForceKernel::CudaCalcAmoebaStretchBendForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system) :
                    CalcAmoebaStretchBendForceKernel(name, platform), cu(cu), system(system), params(NULL) {
 }
 
@@ -577,7 +577,7 @@ private:
     const AmoebaOutOfPlaneBendForce& force;
 };
 
-CudaCalcAmoebaOutOfPlaneBendForceKernel::CudaCalcAmoebaOutOfPlaneBendForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system) :
+CudaCalcAmoebaOutOfPlaneBendForceKernel::CudaCalcAmoebaOutOfPlaneBendForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system) :
           CalcAmoebaOutOfPlaneBendForceKernel(name, platform), cu(cu), system(system), params(NULL) {
 }
 
@@ -677,7 +677,7 @@ private:
     const AmoebaTorsionTorsionForce& force;
 };
 
-CudaCalcAmoebaTorsionTorsionForceKernel::CudaCalcAmoebaTorsionTorsionForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system) :
+CudaCalcAmoebaTorsionTorsionForceKernel::CudaCalcAmoebaTorsionTorsionForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system) :
                 CalcAmoebaTorsionTorsionForceKernel(name, platform), cu(cu), system(system), gridValues(NULL), gridParams(NULL), torsionParams(NULL) {
 }
 
@@ -782,7 +782,7 @@ private:
     const AmoebaMultipoleForce& force;
 };
 
-CudaCalcAmoebaMultipoleForceKernel::CudaCalcAmoebaMultipoleForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system) : 
+CudaCalcAmoebaMultipoleForceKernel::CudaCalcAmoebaMultipoleForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system) : 
         CalcAmoebaMultipoleForceKernel(name, platform), cu(cu), system(system), hasInitializedScaleFactors(false), hasInitializedFFT(false),
         multipoleParticles(NULL), molecularDipoles(NULL), molecularQuadrupoles(NULL), labFrameDipoles(NULL), labFrameQuadrupoles(NULL),
         field(NULL), fieldPolar(NULL), inducedField(NULL), inducedFieldPolar(NULL), torque(NULL), dampingAndThole(NULL),
@@ -1821,7 +1821,7 @@ private:
     const AmoebaGeneralizedKirkwoodForce& force;
 };
 
-CudaCalcAmoebaGeneralizedKirkwoodForceKernel::CudaCalcAmoebaGeneralizedKirkwoodForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system) : 
+CudaCalcAmoebaGeneralizedKirkwoodForceKernel::CudaCalcAmoebaGeneralizedKirkwoodForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system) : 
            CalcAmoebaGeneralizedKirkwoodForceKernel(name, platform), cu(cu), system(system), hasInitializedKernels(false), params(NULL), bornRadii(NULL), field(NULL),
            inducedField(NULL), inducedFieldPolar(NULL), inducedDipoleS(NULL), inducedDipolePolarS(NULL), bornSum(NULL), bornForce(NULL) {
 }
@@ -2071,7 +2071,7 @@ private:
     const AmoebaVdwForce& force;
 };
 
-CudaCalcAmoebaVdwForceKernel::CudaCalcAmoebaVdwForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system) :
+CudaCalcAmoebaVdwForceKernel::CudaCalcAmoebaVdwForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system) :
         CalcAmoebaVdwForceKernel(name, platform), cu(cu), system(system), hasInitializedNonbonded(false), sigmaEpsilon(NULL),
         bondReductionAtoms(NULL), bondReductionFactors(NULL), tempPosq(NULL), tempForces(NULL), nonbonded(NULL) {
 }
@@ -2243,7 +2243,7 @@ private:
     const AmoebaWcaDispersionForce& force;
 };
 
-CudaCalcAmoebaWcaDispersionForceKernel::CudaCalcAmoebaWcaDispersionForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system) : 
+CudaCalcAmoebaWcaDispersionForceKernel::CudaCalcAmoebaWcaDispersionForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system) : 
            CalcAmoebaWcaDispersionForceKernel(name, platform), cu(cu), system(system), radiusEpsilon(NULL) {
 }
 

plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.h

@@ -47,7 +47,7 @@ public:
     CudaCalcAmoebaBondForceKernel(std::string name, 
                                           const Platform& platform,
                                           CudaContext& cu,
-                                          System& system);
+                                          const System& system);
     ~CudaCalcAmoebaBondForceKernel();
     /**
      * Initialize the kernel.
@@ -76,7 +76,7 @@ private:
     class ForceInfo;
     int numBonds;
     CudaContext& cu;
-    System& system;
+    const System& system;
     CudaArray* params;
 };
 
@@ -85,7 +85,7 @@ private:
  */
 class CudaCalcAmoebaAngleForceKernel : public CalcAmoebaAngleForceKernel {
 public:
-    CudaCalcAmoebaAngleForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system);
+    CudaCalcAmoebaAngleForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system);
     ~CudaCalcAmoebaAngleForceKernel();
     /**
      * Initialize the kernel.
@@ -114,7 +114,7 @@ private:
     class ForceInfo;
     int numAngles;
     CudaContext& cu;
-    System& system;
+    const System& system;
     CudaArray* params;
 };
 
@@ -123,7 +123,7 @@ private:
  */
 class CudaCalcAmoebaInPlaneAngleForceKernel : public CalcAmoebaInPlaneAngleForceKernel {
 public:
-    CudaCalcAmoebaInPlaneAngleForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system);
+    CudaCalcAmoebaInPlaneAngleForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system);
     ~CudaCalcAmoebaInPlaneAngleForceKernel();
     /**
      * Initialize the kernel.
@@ -152,7 +152,7 @@ private:
     class ForceInfo;
     int numAngles;
     CudaContext& cu;
-    System& system;
+    const System& system;
     CudaArray* params;
 };
 
@@ -161,7 +161,7 @@ private:
  */
 class CudaCalcAmoebaPiTorsionForceKernel : public CalcAmoebaPiTorsionForceKernel {
 public:
-    CudaCalcAmoebaPiTorsionForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system);
+    CudaCalcAmoebaPiTorsionForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system);
     ~CudaCalcAmoebaPiTorsionForceKernel();
     /**
      * Initialize the kernel.
@@ -190,7 +190,7 @@ private:
     class ForceInfo;
     int numPiTorsions;
     CudaContext& cu;
-    System& system;
+    const System& system;
     CudaArray* params;
 };
 
@@ -199,7 +199,7 @@ private:
  */
 class CudaCalcAmoebaStretchBendForceKernel : public CalcAmoebaStretchBendForceKernel {
 public:
-    CudaCalcAmoebaStretchBendForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system);
+    CudaCalcAmoebaStretchBendForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system);
     ~CudaCalcAmoebaStretchBendForceKernel();
     /**
      * Initialize the kernel.
@@ -228,7 +228,7 @@ private:
     class ForceInfo;
     int numStretchBends;
     CudaContext& cu;
-    System& system;
+    const System& system;
     CudaArray* params;
 };
 
@@ -237,7 +237,7 @@ private:
  */
 class CudaCalcAmoebaOutOfPlaneBendForceKernel : public CalcAmoebaOutOfPlaneBendForceKernel {
 public:
-    CudaCalcAmoebaOutOfPlaneBendForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system);
+    CudaCalcAmoebaOutOfPlaneBendForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system);
     ~CudaCalcAmoebaOutOfPlaneBendForceKernel();
     /**
      * Initialize the kernel.
@@ -266,7 +266,7 @@ private:
     class ForceInfo;
     int numOutOfPlaneBends;
     CudaContext& cu;
-    System& system;
+    const System& system;
     CudaArray* params;
 };
 
@@ -275,7 +275,7 @@ private:
  */
 class CudaCalcAmoebaTorsionTorsionForceKernel : public CalcAmoebaTorsionTorsionForceKernel {
 public:
-    CudaCalcAmoebaTorsionTorsionForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system);
+    CudaCalcAmoebaTorsionTorsionForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system);
     ~CudaCalcAmoebaTorsionTorsionForceKernel();
     /**
      * Initialize the kernel.
@@ -298,7 +298,7 @@ private:
     int numTorsionTorsions;
     int numTorsionTorsionGrids;
     CudaContext& cu;
-    System& system;
+    const System& system;
     CudaArray* gridValues;
     CudaArray* gridParams;
     CudaArray* torsionParams;
@@ -309,7 +309,7 @@ private:
  */
 class CudaCalcAmoebaMultipoleForceKernel : public CalcAmoebaMultipoleForceKernel {
 public:
-    CudaCalcAmoebaMultipoleForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system);
+    CudaCalcAmoebaMultipoleForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system);
     ~CudaCalcAmoebaMultipoleForceKernel();
     /**
      * Initialize the kernel.
@@ -374,7 +374,7 @@ private:
     double inducedEpsilon;
     bool hasInitializedScaleFactors, hasInitializedFFT;
     CudaContext& cu;
-    System& system;
+    const System& system;
     std::vector<int3> covalentFlagValues;
     std::vector<int2> polarizationFlagValues;
     CudaArray* multipoleParticles;
@@ -419,7 +419,7 @@ private:
  */
 class CudaCalcAmoebaGeneralizedKirkwoodForceKernel : public CalcAmoebaGeneralizedKirkwoodForceKernel {
 public:
-    CudaCalcAmoebaGeneralizedKirkwoodForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system);
+    CudaCalcAmoebaGeneralizedKirkwoodForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system);
     ~CudaCalcAmoebaGeneralizedKirkwoodForceKernel();
     /**
      * Initialize the kernel.
@@ -473,7 +473,7 @@ public:
 private:
     class ForceInfo;
     CudaContext& cu;
-    System& system;
+    const System& system;
     bool includeSurfaceArea, hasInitializedKernels;
     int computeBornSumThreads, gkForceThreads, chainRuleThreads, ediffThreads;
     std::map<std::string, std::string> defines;
@@ -494,7 +494,7 @@ private:
  */
 class CudaCalcAmoebaVdwForceKernel : public CalcAmoebaVdwForceKernel {
 public:
-    CudaCalcAmoebaVdwForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system);
+    CudaCalcAmoebaVdwForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system);
     ~CudaCalcAmoebaVdwForceKernel();
     /**
      * Initialize the kernel.
@@ -522,7 +522,7 @@ public:
 private:
     class ForceInfo;
     CudaContext& cu;
-    System& system;
+    const System& system;
     bool hasInitializedNonbonded;
     double dispersionCoefficient;
     CudaArray* sigmaEpsilon;
@@ -539,7 +539,7 @@ private:
  */
 class CudaCalcAmoebaWcaDispersionForceKernel : public CalcAmoebaWcaDispersionForceKernel {
 public:
-    CudaCalcAmoebaWcaDispersionForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system);
+    CudaCalcAmoebaWcaDispersionForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system);
     ~CudaCalcAmoebaWcaDispersionForceKernel();
     /**
      * Initialize the kernel.
@@ -567,7 +567,7 @@ public:
 private:
     class ForceInfo;
     CudaContext& cu;
-    System& system;
+    const System& system;
     double totalMaximumDispersionEnergy;
     CudaArray* radiusEpsilon;
     CUfunction forceKernel;

plugins/amoeba/platforms/reference/src/AmoebaReferenceKernels.cpp

@@ -76,7 +76,7 @@ static RealVec& extractBoxSize(ContextImpl& context) {
 
 // ***************************************************************************
 
-ReferenceCalcAmoebaBondForceKernel::ReferenceCalcAmoebaBondForceKernel(std::string name, const Platform& platform, System& system) : 
+ReferenceCalcAmoebaBondForceKernel::ReferenceCalcAmoebaBondForceKernel(std::string name, const Platform& platform, const System& system) : 
                 CalcAmoebaBondForceKernel(name, platform), system(system) {
 }
 
@@ -130,7 +130,7 @@ void ReferenceCalcAmoebaBondForceKernel::copyParametersToContext(ContextImpl& co
 
 // ***************************************************************************
 
-ReferenceCalcAmoebaAngleForceKernel::ReferenceCalcAmoebaAngleForceKernel(std::string name, const Platform& platform, System& system) :
+ReferenceCalcAmoebaAngleForceKernel::ReferenceCalcAmoebaAngleForceKernel(std::string name, const Platform& platform, const System& system) :
             CalcAmoebaAngleForceKernel(name, platform), system(system) {
 }
 
@@ -183,7 +183,7 @@ void ReferenceCalcAmoebaAngleForceKernel::copyParametersToContext(ContextImpl& c
     }
 }
 
-ReferenceCalcAmoebaInPlaneAngleForceKernel::ReferenceCalcAmoebaInPlaneAngleForceKernel(std::string name, const Platform& platform, System& system) : 
+ReferenceCalcAmoebaInPlaneAngleForceKernel::ReferenceCalcAmoebaInPlaneAngleForceKernel(std::string name, const Platform& platform, const System& system) : 
           CalcAmoebaInPlaneAngleForceKernel(name, platform), system(system) {
 }
 
@@ -238,7 +238,7 @@ void ReferenceCalcAmoebaInPlaneAngleForceKernel::copyParametersToContext(Context
     }
 }
 
-ReferenceCalcAmoebaPiTorsionForceKernel::ReferenceCalcAmoebaPiTorsionForceKernel(std::string name, const Platform& platform, System& system) :
+ReferenceCalcAmoebaPiTorsionForceKernel::ReferenceCalcAmoebaPiTorsionForceKernel(std::string name, const Platform& platform, const System& system) :
          CalcAmoebaPiTorsionForceKernel(name, platform), system(system) {
 }
 
@@ -290,7 +290,7 @@ void ReferenceCalcAmoebaPiTorsionForceKernel::copyParametersToContext(ContextImp
     }
 }
 
-ReferenceCalcAmoebaStretchBendForceKernel::ReferenceCalcAmoebaStretchBendForceKernel(std::string name, const Platform& platform, System& system) :
+ReferenceCalcAmoebaStretchBendForceKernel::ReferenceCalcAmoebaStretchBendForceKernel(std::string name, const Platform& platform, const System& system) :
                    CalcAmoebaStretchBendForceKernel(name, platform), system(system) {
 }
 
@@ -342,7 +342,7 @@ void ReferenceCalcAmoebaStretchBendForceKernel::copyParametersToContext(ContextI
     }
 }
 
-ReferenceCalcAmoebaOutOfPlaneBendForceKernel::ReferenceCalcAmoebaOutOfPlaneBendForceKernel(std::string name, const Platform& platform, System& system) :
+ReferenceCalcAmoebaOutOfPlaneBendForceKernel::ReferenceCalcAmoebaOutOfPlaneBendForceKernel(std::string name, const Platform& platform, const System& system) :
           CalcAmoebaOutOfPlaneBendForceKernel(name, platform), system(system) {
 }
 
@@ -401,7 +401,7 @@ void ReferenceCalcAmoebaOutOfPlaneBendForceKernel::copyParametersToContext(Conte
     }
 }
 
-ReferenceCalcAmoebaTorsionTorsionForceKernel::ReferenceCalcAmoebaTorsionTorsionForceKernel(std::string name, const Platform& platform, System& system) :
+ReferenceCalcAmoebaTorsionTorsionForceKernel::ReferenceCalcAmoebaTorsionTorsionForceKernel(std::string name, const Platform& platform, const System& system) :
                 CalcAmoebaTorsionTorsionForceKernel(name, platform), system(system) {
 }
 
@@ -480,7 +480,7 @@ double ReferenceCalcAmoebaTorsionTorsionForceKernel::execute(ContextImpl& contex
  *                             AmoebaMultipole                                *
  * -------------------------------------------------------------------------- */
 
-ReferenceCalcAmoebaMultipoleForceKernel::ReferenceCalcAmoebaMultipoleForceKernel(std::string name, const Platform& platform, System& system) : 
+ReferenceCalcAmoebaMultipoleForceKernel::ReferenceCalcAmoebaMultipoleForceKernel(std::string name, const Platform& platform, const System& system) : 
          CalcAmoebaMultipoleForceKernel(name, platform), system(system), numMultipoles(0), mutualInducedMaxIterations(60), mutualInducedTargetEpsilon(1.0e-03),
                                                          usePme(false),alphaEwald(0.0), cutoffDistance(1.0) {  
 
@@ -712,7 +712,7 @@ void ReferenceCalcAmoebaMultipoleForceKernel::getSystemMultipoleMoments(ContextI
 
     // retrieve masses
 
-    System& system             = context.getSystem();
+    const System& system             = context.getSystem();
     vector<RealOpenMM> masses;
     for (int i = 0; i <  system.getNumParticles(); ++i) {
         masses.push_back( static_cast<RealOpenMM>(system.getParticleMass(i)) );
@@ -771,7 +771,7 @@ void ReferenceCalcAmoebaMultipoleForceKernel::copyParametersToContext(ContextImp
  *                       AmoebaGeneralizedKirkwood                            *
  * -------------------------------------------------------------------------- */
 
-ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel::ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel(std::string name, const Platform& platform, System& system) : 
+ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel::ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel(std::string name, const Platform& platform, const System& system) : 
            CalcAmoebaGeneralizedKirkwoodForceKernel(name, platform), system(system) {
 }
 
@@ -892,7 +892,7 @@ void ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel::copyParametersToContext(
     }
 }
 
-ReferenceCalcAmoebaVdwForceKernel::ReferenceCalcAmoebaVdwForceKernel(std::string name, const Platform& platform, System& system) :
+ReferenceCalcAmoebaVdwForceKernel::ReferenceCalcAmoebaVdwForceKernel(std::string name, const Platform& platform, const System& system) :
        CalcAmoebaVdwForceKernel(name, platform), system(system) {
     useCutoff = 0;
     usePBC = 0;
@@ -995,7 +995,7 @@ void ReferenceCalcAmoebaVdwForceKernel::copyParametersToContext(ContextImpl& con
  *                           AmoebaWcaDispersion                              *
  * -------------------------------------------------------------------------- */
 
-ReferenceCalcAmoebaWcaDispersionForceKernel::ReferenceCalcAmoebaWcaDispersionForceKernel(std::string name, const Platform& platform, System& system) : 
+ReferenceCalcAmoebaWcaDispersionForceKernel::ReferenceCalcAmoebaWcaDispersionForceKernel(std::string name, const Platform& platform, const System& system) : 
            CalcAmoebaWcaDispersionForceKernel(name, platform), system(system) {
 }
 

plugins/amoeba/platforms/reference/src/AmoebaReferenceKernels.h

@@ -43,7 +43,7 @@ class ReferenceCalcAmoebaBondForceKernel : public CalcAmoebaBondForceKernel {
 public:
     ReferenceCalcAmoebaBondForceKernel(std::string name, 
                                                const Platform& platform,
-                                               System& system);
+                                               const System& system);
     ~ReferenceCalcAmoebaBondForceKernel();
     /**
      * Initialize the kernel.
@@ -76,7 +76,7 @@ private:
     std::vector<RealOpenMM> kQuadratic;
     RealOpenMM globalBondCubic;
     RealOpenMM globalBondQuartic;
-    System& system;
+    const System& system;
 };
 
 /**
@@ -84,7 +84,7 @@ private:
  */
 class ReferenceCalcAmoebaAngleForceKernel : public CalcAmoebaAngleForceKernel {
 public:
-    ReferenceCalcAmoebaAngleForceKernel(std::string name, const Platform& platform, System& system);
+    ReferenceCalcAmoebaAngleForceKernel(std::string name, const Platform& platform, const System& system);
     ~ReferenceCalcAmoebaAngleForceKernel();
     /**
      * Initialize the kernel.
@@ -120,7 +120,7 @@ private:
     RealOpenMM globalAngleQuartic;
     RealOpenMM globalAnglePentic;
     RealOpenMM globalAngleSextic;
-    System& system;
+    const System& system;
 };
 
 /**
@@ -128,7 +128,7 @@ private:
  */
 class ReferenceCalcAmoebaInPlaneAngleForceKernel : public CalcAmoebaInPlaneAngleForceKernel {
 public:
-    ReferenceCalcAmoebaInPlaneAngleForceKernel(std::string name, const Platform& platform, System& system);
+    ReferenceCalcAmoebaInPlaneAngleForceKernel(std::string name, const Platform& platform, const System& system);
     ~ReferenceCalcAmoebaInPlaneAngleForceKernel();
     /**
      * Initialize the kernel.
@@ -165,7 +165,7 @@ private:
     RealOpenMM globalInPlaneAngleQuartic;
     RealOpenMM globalInPlaneAnglePentic;
     RealOpenMM globalInPlaneAngleSextic;
-    System& system;
+    const System& system;
 };
 
 /**
@@ -173,7 +173,7 @@ private:
  */
 class ReferenceCalcAmoebaPiTorsionForceKernel : public CalcAmoebaPiTorsionForceKernel {
 public:
-    ReferenceCalcAmoebaPiTorsionForceKernel(std::string name, const Platform& platform, System& system);
+    ReferenceCalcAmoebaPiTorsionForceKernel(std::string name, const Platform& platform, const System& system);
     ~ReferenceCalcAmoebaPiTorsionForceKernel();
     /**
      * Initialize the kernel.
@@ -207,7 +207,7 @@ private:
     std::vector<int>   particle5;
     std::vector<int>   particle6;
     std::vector<RealOpenMM> kTorsion;
-    System& system;
+    const System& system;
 };
 
 /**
@@ -215,7 +215,7 @@ private:
  */
 class ReferenceCalcAmoebaStretchBendForceKernel : public CalcAmoebaStretchBendForceKernel {
 public:
-    ReferenceCalcAmoebaStretchBendForceKernel(std::string name, const Platform& platform, System& system);
+    ReferenceCalcAmoebaStretchBendForceKernel(std::string name, const Platform& platform, const System& system);
     ~ReferenceCalcAmoebaStretchBendForceKernel();
     /**
      * Initialize the kernel.
@@ -249,7 +249,7 @@ private:
     std::vector<RealOpenMM> lengthCBParameters;
     std::vector<RealOpenMM> angleParameters;
     std::vector<RealOpenMM> kParameters;
-    System& system;
+    const System& system;
 };
 
 /**
@@ -257,7 +257,7 @@ private:
  */
 class ReferenceCalcAmoebaOutOfPlaneBendForceKernel : public CalcAmoebaOutOfPlaneBendForceKernel {
 public:
-    ReferenceCalcAmoebaOutOfPlaneBendForceKernel(std::string name, const Platform& platform, System& system);
+    ReferenceCalcAmoebaOutOfPlaneBendForceKernel(std::string name, const Platform& platform, const System& system);
     ~ReferenceCalcAmoebaOutOfPlaneBendForceKernel();
     /**
      * Initialize the kernel.
@@ -293,7 +293,7 @@ private:
     RealOpenMM globalOutOfPlaneBendAngleQuartic;
     RealOpenMM globalOutOfPlaneBendAnglePentic;
     RealOpenMM globalOutOfPlaneBendAngleSextic;
-    System& system;
+    const System& system;
 };
 
 /**
@@ -301,7 +301,7 @@ private:
  */
 class ReferenceCalcAmoebaTorsionTorsionForceKernel : public CalcAmoebaTorsionTorsionForceKernel {
 public:
-    ReferenceCalcAmoebaTorsionTorsionForceKernel(std::string name, const Platform& platform, System& system);
+    ReferenceCalcAmoebaTorsionTorsionForceKernel(std::string name, const Platform& platform, const System& system);
     ~ReferenceCalcAmoebaTorsionTorsionForceKernel();
     /**
      * Initialize the kernel.
@@ -332,7 +332,7 @@ private:
     int numTorsionTorsionGrids;
     std::vector< std::vector< std::vector< std::vector<RealOpenMM> > > > torsionTorsionGrids;
 
-    System& system;
+    const System& system;
 };
 
 /**
@@ -340,7 +340,7 @@ private:
  */
 class ReferenceCalcAmoebaMultipoleForceKernel : public CalcAmoebaMultipoleForceKernel {
 public:
-    ReferenceCalcAmoebaMultipoleForceKernel(std::string name, const Platform& platform, System& system);
+    ReferenceCalcAmoebaMultipoleForceKernel(std::string name, const Platform& platform, const System& system);
     ~ReferenceCalcAmoebaMultipoleForceKernel();
     /**
      * Initialize the kernel.
@@ -421,7 +421,7 @@ private:
     RealOpenMM cutoffDistance;
     std::vector<int> pmeGridDimension;
 
-    System& system;
+    const System& system;
 };
 
 /**
@@ -429,7 +429,7 @@ private:
  */
 class ReferenceCalcAmoebaVdwForceKernel : public CalcAmoebaVdwForceKernel {
 public:
-    ReferenceCalcAmoebaVdwForceKernel(std::string name, const Platform& platform, System& system);
+    ReferenceCalcAmoebaVdwForceKernel(std::string name, const Platform& platform, const System& system);
     ~ReferenceCalcAmoebaVdwForceKernel();
     /**
      * Initialize the kernel.
@@ -467,7 +467,7 @@ private:
     std::vector<RealOpenMM> reductions;
     std::string sigmaCombiningRule;
     std::string epsilonCombiningRule;
-    System& system;
+    const System& system;
     NeighborList* neighborList;
 };
 
@@ -476,7 +476,7 @@ private:
  */
 class ReferenceCalcAmoebaWcaDispersionForceKernel : public CalcAmoebaWcaDispersionForceKernel {
 public:
-    ReferenceCalcAmoebaWcaDispersionForceKernel(std::string name, const Platform& platform, System& system);
+    ReferenceCalcAmoebaWcaDispersionForceKernel(std::string name, const Platform& platform, const System& system);
     ~ReferenceCalcAmoebaWcaDispersionForceKernel();
     /**
      * Initialize the kernel.
@@ -515,7 +515,7 @@ private:
     RealOpenMM dispoff;
     RealOpenMM slevy;
     RealOpenMM totalMaximumDispersionEnergy;
-    System& system;
+    const System& system;
 };
 
 /**
@@ -523,7 +523,7 @@ private:
  */
 class ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel : public CalcAmoebaGeneralizedKirkwoodForceKernel {
 public:
-    ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel(std::string name, const Platform& platform, System& system);
+    ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel(std::string name, const Platform& platform, const System& system);
     ~ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel();
     /**
      * Initialize the kernel.
@@ -649,7 +649,7 @@ private:
     RealOpenMM surfaceAreaFactor;
     int includeCavityTerm;
     int directPolarization;
-    System& system;
+    const System& system;
 };
 
 } // namespace OpenMM

plugins/rpmd/platforms/reference/src/ReferenceRpmdKernels.cpp

@@ -235,7 +235,7 @@ void ReferenceIntegrateRPMDStepKernel::execute(ContextImpl& context, const RPMDI
 }
 
 double ReferenceIntegrateRPMDStepKernel::computeKineticEnergy(ContextImpl& context, const RPMDIntegrator& integrator) {
-    System& system = context.getSystem();
+    const System& system = context.getSystem();
     int numParticles = system.getNumParticles();
     vector<RealVec>& velData = extractVelocities(context);
     double energy = 0.0;