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

openmmapi/include/openmm/internal/PeriodicTorsionForceImpl.h

@@ -47,10 +47,10 @@ namespace OpenMM {
 
 class PeriodicTorsionForceImpl : public ForceImpl {
 public:
-    PeriodicTorsionForceImpl(PeriodicTorsionForce& owner);
+    PeriodicTorsionForceImpl(const PeriodicTorsionForce& owner);
     ~PeriodicTorsionForceImpl();
     void initialize(ContextImpl& context);
-    PeriodicTorsionForce& getOwner() {
+    const PeriodicTorsionForce& getOwner() const {
         return owner;
     }
     void updateContextState(ContextImpl& context) {
@@ -63,7 +63,7 @@ public:
     std::vector<std::string> getKernelNames();
     void updateParametersInContext(ContextImpl& context);
 private:
-    PeriodicTorsionForce& owner;
+    const PeriodicTorsionForce& owner;
     Kernel kernel;
 };
 

openmmapi/include/openmm/internal/RBTorsionForceImpl.h

@@ -47,10 +47,10 @@ namespace OpenMM {
 
 class RBTorsionForceImpl : public ForceImpl {
 public:
-    RBTorsionForceImpl(RBTorsionForce& owner);
+    RBTorsionForceImpl(const RBTorsionForce& owner);
     ~RBTorsionForceImpl();
     void initialize(ContextImpl& context);
-    RBTorsionForce& getOwner() {
+    const RBTorsionForce& getOwner() const {
         return owner;
     }
     void updateContextState(ContextImpl& context) {
@@ -63,7 +63,7 @@ public:
     std::vector<std::string> getKernelNames();
     void updateParametersInContext(ContextImpl& context);
 private:
-    RBTorsionForce& owner;
+    const RBTorsionForce& owner;
     Kernel kernel;
 };
 

openmmapi/src/AndersenThermostat.cpp

@@ -40,6 +40,6 @@ AndersenThermostat::AndersenThermostat(double defaultTemperature, double default
     setRandomNumberSeed((int) time(NULL));
 }
 
-ForceImpl* AndersenThermostat::createImpl() {
+ForceImpl* AndersenThermostat::createImpl() const {
     return new AndersenThermostatImpl(*this);
 }

openmmapi/src/AndersenThermostatImpl.cpp

@@ -39,7 +39,7 @@
 using namespace OpenMM;
 using std::vector;
 
-AndersenThermostatImpl::AndersenThermostatImpl(AndersenThermostat& owner) : owner(owner) {
+AndersenThermostatImpl::AndersenThermostatImpl(const AndersenThermostat& owner) : owner(owner) {
 }
 
 void AndersenThermostatImpl::initialize(ContextImpl& context) {

openmmapi/src/CMAPTorsionForce.cpp

@@ -92,7 +92,7 @@ void CMAPTorsionForce::setTorsionParameters(int index, int map, int a1, int a2,
     torsions[index].b4 = b4;
 }
 
-ForceImpl* CMAPTorsionForce::createImpl() {
+ForceImpl* CMAPTorsionForce::createImpl() const {
     return new CMAPTorsionForceImpl(*this);
 }
 

openmmapi/src/CMAPTorsionForceImpl.cpp

@@ -41,7 +41,7 @@
 using namespace OpenMM;
 using namespace std;
 
-CMAPTorsionForceImpl::CMAPTorsionForceImpl(CMAPTorsionForce& owner) : owner(owner) {
+CMAPTorsionForceImpl::CMAPTorsionForceImpl(const CMAPTorsionForce& owner) : owner(owner) {
 }
 
 CMAPTorsionForceImpl::~CMAPTorsionForceImpl() {

openmmapi/src/CMMotionRemover.cpp

@@ -37,6 +37,6 @@ using namespace OpenMM;
 CMMotionRemover::CMMotionRemover(int frequency) : frequency(frequency) {
 }
 
-ForceImpl* CMMotionRemover::createImpl() {
+ForceImpl* CMMotionRemover::createImpl() const {
     return new CMMotionRemoverImpl(*this);
 }

openmmapi/src/CMMotionRemoverImpl.cpp

@@ -39,7 +39,7 @@
 using namespace OpenMM;
 using std::vector;
 
-CMMotionRemoverImpl::CMMotionRemoverImpl(CMMotionRemover& owner) : owner(owner) {
+CMMotionRemoverImpl::CMMotionRemoverImpl(const CMMotionRemover& owner) : owner(owner) {
 }
 
 void CMMotionRemoverImpl::initialize(ContextImpl& context) {

openmmapi/src/Context.cpp

@@ -40,15 +40,15 @@
 using namespace OpenMM;
 using namespace std;
 
-Context::Context(System& system, Integrator& integrator) : properties(map<string, string>()) {
+Context::Context(const System& system, Integrator& integrator) : properties(map<string, string>()) {
     impl = new ContextImpl(*this, system, integrator, 0, properties);
 }
 
-Context::Context(System& system, Integrator& integrator, Platform& platform) : properties(map<string, string>()) {
+Context::Context(const System& system, Integrator& integrator, Platform& platform) : properties(map<string, string>()) {
     impl = new ContextImpl(*this, system, integrator, &platform, properties);
 }
 
-Context::Context(System& system, Integrator& integrator, Platform& platform, const map<string, string>& properties) : properties(properties) {
+Context::Context(const System& system, Integrator& integrator, Platform& platform, const map<string, string>& properties) : properties(properties) {
     impl = new ContextImpl(*this, system, integrator, &platform, properties);
 }
 
@@ -61,10 +61,6 @@ const System& Context::getSystem() const {
 
 }
 
-System& Context::getSystem() {
-    return impl->getSystem();
-}
-
 const Integrator& Context::getIntegrator() const {
     return impl->getIntegrator();
 }
@@ -204,7 +200,7 @@ void Context::setVelocities(const vector<Vec3>& velocities) {
 }
 
 void Context::setVelocitiesToTemperature(double temperature, int randomSeed) {
-    System& system = impl->getSystem();
+    const System& system = impl->getSystem();
     
     // Generate the list of Gaussian random numbers.
     
@@ -263,7 +259,7 @@ void Context::computeVirtualSites() {
 }
 
 void Context::reinitialize() {
-    System& system = impl->getSystem();
+    const System& system = impl->getSystem();
     Integrator& integrator = impl->getIntegrator();
     Platform& platform = impl->getPlatform();
     integrator.cleanup();

openmmapi/src/ContextImpl.cpp

@@ -47,7 +47,7 @@
 using namespace OpenMM;
 using namespace std;
 
-ContextImpl::ContextImpl(Context& owner, System& system, Integrator& integrator, Platform* platform, const map<string, string>& properties) :
+ContextImpl::ContextImpl(Context& owner, const System& system, Integrator& integrator, Platform* platform, const map<string, string>& properties) :
         owner(owner), system(system), integrator(integrator), hasInitializedForces(false), hasSetPositions(false), integratorIsDeleted(false),
         lastForceGroups(-1), platform(platform), platformData(NULL) {
     if (system.getNumParticles() == 0)

openmmapi/src/CustomAngleForce.cpp

@@ -116,7 +116,7 @@ void CustomAngleForce::setAngleParameters(int index, int particle1, int particle
     angles[index].particle3 = particle3;
 }
 
-ForceImpl* CustomAngleForce::createImpl() {
+ForceImpl* CustomAngleForce::createImpl() const {
     return new CustomAngleForceImpl(*this);
 }
 

openmmapi/src/CustomAngleForceImpl.cpp

@@ -43,7 +43,7 @@ using std::set;
 using std::string;
 using std::stringstream;
 
-CustomAngleForceImpl::CustomAngleForceImpl(CustomAngleForce& owner) : owner(owner) {
+CustomAngleForceImpl::CustomAngleForceImpl(const CustomAngleForce& owner) : owner(owner) {
 }
 
 CustomAngleForceImpl::~CustomAngleForceImpl() {
@@ -53,8 +53,7 @@ void CustomAngleForceImpl::initialize(ContextImpl& context) {
     kernel = context.getPlatform().createKernel(CalcCustomAngleForceKernel::Name(), context);
 
     // Check for errors in the specification of bonds.
-
-    System& system = context.getSystem();
+    const System& system = context.getSystem();
     vector<double> parameters;
     int numParameters = owner.getNumPerAngleParameters();
     for (int i = 0; i < owner.getNumAngles(); i++) {

openmmapi/src/CustomBondForce.cpp

@@ -114,7 +114,7 @@ void CustomBondForce::setBondParameters(int index, int particle1, int particle2,
     bonds[index].particle2 = particle2;
 }
 
-ForceImpl* CustomBondForce::createImpl() {
+ForceImpl* CustomBondForce::createImpl() const {
     return new CustomBondForceImpl(*this);
 }
 

openmmapi/src/CustomBondForceImpl.cpp

@@ -43,7 +43,7 @@ using std::set;
 using std::string;
 using std::stringstream;
 
-CustomBondForceImpl::CustomBondForceImpl(CustomBondForce& owner) : owner(owner) {
+CustomBondForceImpl::CustomBondForceImpl(const CustomBondForce& owner) : owner(owner) {
 }
 
 CustomBondForceImpl::~CustomBondForceImpl() {
@@ -54,7 +54,7 @@ void CustomBondForceImpl::initialize(ContextImpl& context) {
 
     // Check for errors in the specification of bonds.
 
-    System& system = context.getSystem();
+    const System& system = context.getSystem();
     vector<double> parameters;
     int numParameters = owner.getNumPerBondParameters();
     for (int i = 0; i < owner.getNumBonds(); i++) {

openmmapi/src/CustomCompoundBondForce.cpp

@@ -149,7 +149,7 @@ void CustomCompoundBondForce::setFunctionParameters(int index, const std::string
     functions[index].max = max;
 }
 
-ForceImpl* CustomCompoundBondForce::createImpl() {
+ForceImpl* CustomCompoundBondForce::createImpl() const {
     return new CustomCompoundBondForceImpl(*this);
 }
 

openmmapi/src/CustomCompoundBondForceImpl.cpp

@@ -71,7 +71,7 @@ public:
     }
 };
 
-CustomCompoundBondForceImpl::CustomCompoundBondForceImpl(CustomCompoundBondForce& owner) : owner(owner) {
+CustomCompoundBondForceImpl::CustomCompoundBondForceImpl(const CustomCompoundBondForce& owner) : owner(owner) {
 }
 
 CustomCompoundBondForceImpl::~CustomCompoundBondForceImpl() {
@@ -82,7 +82,7 @@ void CustomCompoundBondForceImpl::initialize(ContextImpl& context) {
 
     // Check for errors in the specification of parameters and exclusions.
 
-    System& system = context.getSystem();
+    const System& system = context.getSystem();
     vector<int> particles;
     vector<double> parameters;
     int numBondParameters = owner.getNumPerBondParameters();

openmmapi/src/CustomExternalForce.cpp

@@ -112,7 +112,7 @@ void CustomExternalForce::setParticleParameters(int index, int particle, const v
     particles[index].particle = particle;
 }
 
-ForceImpl* CustomExternalForce::createImpl() {
+ForceImpl* CustomExternalForce::createImpl() const {
     return new CustomExternalForceImpl(*this);
 }
 

openmmapi/src/CustomExternalForceImpl.cpp

@@ -43,7 +43,7 @@ using std::set;
 using std::string;
 using std::stringstream;
 
-CustomExternalForceImpl::CustomExternalForceImpl(CustomExternalForce& owner) : owner(owner) {
+CustomExternalForceImpl::CustomExternalForceImpl(const CustomExternalForce& owner) : owner(owner) {
 }
 
 CustomExternalForceImpl::~CustomExternalForceImpl() {
@@ -54,7 +54,7 @@ void CustomExternalForceImpl::initialize(ContextImpl& context) {
 
     // Check for errors in the specification of bonds.
 
-    System& system = context.getSystem();
+    const System& system = context.getSystem();
     vector<double> parameters;
     int numParameters = owner.getNumPerParticleParameters();
     for (int i = 0; i < owner.getNumParticles(); i++) {

openmmapi/src/CustomGBForce.cpp

@@ -202,7 +202,7 @@ void CustomGBForce::setFunctionParameters(int index, const std::string& name, co
     functions[index].max = max;
 }
 
-ForceImpl* CustomGBForce::createImpl() {
+ForceImpl* CustomGBForce::createImpl() const {
     return new CustomGBForceImpl(*this);
 }
 

openmmapi/src/CustomGBForceImpl.cpp

@@ -43,7 +43,7 @@ using std::set;
 using std::string;
 using std::stringstream;
 
-CustomGBForceImpl::CustomGBForceImpl(CustomGBForce& owner) : owner(owner) {
+CustomGBForceImpl::CustomGBForceImpl(const CustomGBForce& owner) : owner(owner) {
 }
 
 CustomGBForceImpl::~CustomGBForceImpl() {
@@ -54,7 +54,7 @@ void CustomGBForceImpl::initialize(ContextImpl& context) {
 
     // Check for errors in the specification of parameters and exclusions.
 
-    System& system = context.getSystem();
+    const System& system = context.getSystem();
     if (owner.getNumParticles() != system.getNumParticles())
         throw OpenMMException("CustomGBForce must have exactly as many particles as the System it belongs to.");
     vector<set<int> > exclusions(owner.getNumParticles());