Merge branch 'master' into master

plugins/drude/serialization/src/DrudeForceProxy.cpp

@@ -67,16 +67,12 @@ void* DrudeForceProxy::deserialize(const SerializationNode& node) const {
     DrudeForce* force = new DrudeForce();
     try {
         const SerializationNode& particles = node.getChildNode("Particles");
-        for (int i = 0; i < (int) particles.getChildren().size(); i++) {
-            const SerializationNode& particle = particles.getChildren()[i];
+        for (auto& particle : particles.getChildren())
             force->addParticle(particle.getIntProperty("p"), particle.getIntProperty("p1"), particle.getIntProperty("p2"), particle.getIntProperty("p3"), particle.getIntProperty("p4"),
                     particle.getDoubleProperty("charge"), particle.getDoubleProperty("polarizability"), particle.getDoubleProperty("a12"), particle.getDoubleProperty("a34"));
-        }
         const SerializationNode& pairs = node.getChildNode("ScreenedPairs");
-        for (int i = 0; i < (int) pairs.getChildren().size(); i++) {
-            const SerializationNode& pair = pairs.getChildren()[i];
+        for (auto& pair : pairs.getChildren())
             force->addScreenedPair(pair.getIntProperty("p1"), pair.getIntProperty("p2"), pair.getDoubleProperty("thole"));
-        }
     }
     catch (...) {
         delete force;

plugins/rpmd/openmmapi/src/RPMDIntegrator.cpp

@@ -119,13 +119,13 @@ State RPMDIntegrator::getState(int copy, int types, bool enforcePeriodicBox, int
         const vector<vector<int> >& molecules = context->getMolecules();
         Vec3 periodicBoxSize[3];
         state2.getPeriodicBoxVectors(periodicBoxSize[0], periodicBoxSize[1], periodicBoxSize[2]);
-        for (int i = 0; i < (int) molecules.size(); i++) {
+        for (auto& mol : molecules) {
             // Find the molecule center.
 
             Vec3 center;
-            for (int j = 0; j < (int) molecules[i].size(); j++)
-                center += refPos[molecules[i][j]];
-            center *= 1.0/molecules[i].size();
+            for (int j : mol)
+                center += refPos[j];
+            center *= 1.0/mol.size();
 
             // Find the displacement to move it into the first periodic box.
             Vec3 diff;
@@ -134,8 +134,8 @@ State RPMDIntegrator::getState(int copy, int types, bool enforcePeriodicBox, int
             diff += periodicBoxSize[0]*floor((center[0]-diff[0])/periodicBoxSize[0][0]);
 
             // Translate all the particles in the molecule.
-            for (int j = 0; j < (int) molecules[i].size(); j++) {
-                Vec3& pos = positions[molecules[i][j]];
+            for (int j : mol) {
+                Vec3& pos = positions[j];
                 pos -= diff;
             }
         }
@@ -188,9 +188,8 @@ void RPMDIntegrator::step(int steps) {
         context->getOwner().setPositions(p);
         isFirstStep = false;
     }
-    vector<ForceImpl*>& forceImpls = context->getForceImpls();
-    for (int i = 0; i < (int) forceImpls.size(); i++) {
-        RPMDUpdater* updater = dynamic_cast<RPMDUpdater*>(forceImpls[i]);
+    for (auto impl : context->getForceImpls()) {
+        RPMDUpdater* updater = dynamic_cast<RPMDUpdater*>(impl);
         if (updater != NULL)
             updater->updateRPMDState(*context);
     }

plugins/rpmd/platforms/cuda/src/CudaRpmdKernels.cpp

@@ -116,9 +116,9 @@ void CudaIntegrateRPMDStepKernel::initialize(const System& system, const RPMDInt
     groupsNotContracted = -1;
     const map<int, int>& contractions = integrator.getContractions();
     int maxContractedCopies = 0;
-    for (map<int, int>::const_iterator iter = contractions.begin(); iter != contractions.end(); ++iter) {
-        int group = iter->first;
-        int copies = iter->second;
+    for (auto& c : contractions) {
+        int group = c.first;
+        int copies = c.second;
         if (group < 0 || group > 31)
             throw OpenMMException("RPMDIntegrator: Force group must be between 0 and 31");
         if (copies < 0 || copies > numCopies)
@@ -166,8 +166,8 @@ void CudaIntegrateRPMDStepKernel::initialize(const System& system, const RPMDInt
     
     // Create kernels for doing contractions.
     
-    for (map<int, int>::const_iterator iter = groupsByCopies.begin(); iter != groupsByCopies.end(); ++iter) {
-        int copies = iter->first;
+    for (auto& g : groupsByCopies) {
+        int copies = g.first;
         replacements.clear();
         replacements["NUM_CONTRACTED_COPIES"] = cu.intToString(copies);
         replacements["POS_SCALE"] = cu.doubleToString(1.0/numCopies);
@@ -267,9 +267,9 @@ void CudaIntegrateRPMDStepKernel::computeForces(ContextImpl& context) {
     
     // Now loop over contractions and compute forces from them.
     
-    for (map<int, int>::const_iterator iter = groupsByCopies.begin(); iter != groupsByCopies.end(); ++iter) {
-        int copies = iter->first;
-        int groupFlags = iter->second;
+    for (auto& g : groupsByCopies) {
+        int copies = g.first;
+        int groupFlags = g.second;
         
         // Find the contracted positions.
         

plugins/rpmd/platforms/opencl/src/OpenCLRpmdKernels.cpp

@@ -96,9 +96,9 @@ void OpenCLIntegrateRPMDStepKernel::initialize(const System& system, const RPMDI
     groupsNotContracted = -1;
     const map<int, int>& contractions = integrator.getContractions();
     int maxContractedCopies = 0;
-    for (map<int, int>::const_iterator iter = contractions.begin(); iter != contractions.end(); ++iter) {
-        int group = iter->first;
-        int copies = iter->second;
+    for (auto& c : contractions) {
+        int group = c.first;
+        int copies = c.second;
         if (group < 0 || group > 31)
             throw OpenMMException("RPMDIntegrator: Force group must be between 0 and 31");
         if (copies < 0 || copies > numCopies)
@@ -146,8 +146,8 @@ void OpenCLIntegrateRPMDStepKernel::initialize(const System& system, const RPMDI
     
     // Create kernels for doing contractions.
     
-    for (map<int, int>::const_iterator iter = groupsByCopies.begin(); iter != groupsByCopies.end(); ++iter) {
-        int copies = iter->first;
+    for (auto& g : groupsByCopies) {
+        int copies = g.first;
         replacements.clear();
         replacements["NUM_CONTRACTED_COPIES"] = cl.intToString(copies);
         replacements["POS_SCALE"] = cl.doubleToString(1.0/numCopies);
@@ -182,8 +182,8 @@ void OpenCLIntegrateRPMDStepKernel::initializeKernels(ContextImpl& context) {
     copyFromContextKernel.setArg<cl::Buffer>(3, velocities->getDeviceBuffer());
     copyFromContextKernel.setArg<cl::Buffer>(4, cl.getPosq().getDeviceBuffer());
     copyFromContextKernel.setArg<cl::Buffer>(6, cl.getAtomIndexArray().getDeviceBuffer());
-    for (map<int, int>::const_iterator iter = groupsByCopies.begin(); iter != groupsByCopies.end(); ++iter) {
-        int copies = iter->first;
+    for (auto& g : groupsByCopies) {
+        int copies = g.first;
         positionContractionKernels[copies].setArg<cl::Buffer>(0, positions->getDeviceBuffer());
         positionContractionKernels[copies].setArg<cl::Buffer>(1, contractedPositions->getDeviceBuffer());
         forceContractionKernels[copies].setArg<cl::Buffer>(0, forces->getDeviceBuffer());
@@ -286,9 +286,9 @@ void OpenCLIntegrateRPMDStepKernel::computeForces(ContextImpl& context) {
         copyToContextKernel.setArg<cl::Buffer>(2, contractedPositions->getDeviceBuffer());
         copyFromContextKernel.setArg<cl::Buffer>(1, contractedForces->getDeviceBuffer());
         copyFromContextKernel.setArg<cl::Buffer>(5, contractedPositions->getDeviceBuffer());
-        for (map<int, int>::const_iterator iter = groupsByCopies.begin(); iter != groupsByCopies.end(); ++iter) {
-            int copies = iter->first;
-            int groupFlags = iter->second;
+        for (auto& g : groupsByCopies) {
+            int copies = g.first;
+            int groupFlags = g.second;
 
             // Find the contracted positions.
 

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

@@ -55,9 +55,9 @@ static vector<Vec3>& extractForces(ContextImpl& context) {
 ReferenceIntegrateRPMDStepKernel::~ReferenceIntegrateRPMDStepKernel() {
     if (fft != NULL)
         fftpack_destroy(fft);
-    for (map<int, fftpack*>::const_iterator iter = contractionFFT.begin(); iter != contractionFFT.end(); ++iter)
-        if (iter->second != NULL)
-            fftpack_destroy(iter->second);
+    for (auto& c : contractionFFT)
+        if (c.second != NULL)
+            fftpack_destroy(c.second);
 }
 
 void ReferenceIntegrateRPMDStepKernel::initialize(const System& system, const RPMDIntegrator& integrator) {
@@ -79,9 +79,9 @@ void ReferenceIntegrateRPMDStepKernel::initialize(const System& system, const RP
     groupsNotContracted = -1;
     const map<int, int>& contractions = integrator.getContractions();
     int maxContractedCopies = 0;
-    for (map<int, int>::const_iterator iter = contractions.begin(); iter != contractions.end(); ++iter) {
-        int group = iter->first;
-        int copies = iter->second;
+    for (auto& c : contractions) {
+        int group = c.first;
+        int copies = c.second;
         if (group < 0 || group > 31)
             throw OpenMMException("RPMDIntegrator: Force group must be between 0 and 31");
         if (copies < 0 || copies > numCopies)
@@ -290,9 +290,9 @@ void ReferenceIntegrateRPMDStepKernel::computeForces(ContextImpl& context, const
     
     // Now loop over contractions and compute forces from them.
     
-    for (map<int, int>::const_iterator iter = groupsByCopies.begin(); iter != groupsByCopies.end(); ++iter) {
-        int copies = iter->first;
-        int groupFlags = iter->second;
+    for (auto& g : groupsByCopies) {
+        int copies = g.first;
+        int groupFlags = g.second;
         fftpack* shortFFT = contractionFFT[copies];
         
         // Find the contracted positions.

serialization/src/CMAPTorsionForceProxy.cpp

@@ -52,8 +52,8 @@ void CMAPTorsionForceProxy::serialize(const void* object, SerializationNode& nod
         vector<double> energy;
         force.getMapParameters(i, size, energy);
         SerializationNode& map = maps.createChildNode("Map").setIntProperty("size", size);
-        for (int i = 0; i < (int) energy.size(); i++)
-            map.createChildNode("Energy").setDoubleProperty("e", energy[i]);
+        for (auto e : energy)
+            map.createChildNode("Energy").setDoubleProperty("e", e);
     }
     SerializationNode& torsions = node.createChildNode("Torsions");
     for (int i = 0; i < force.getNumTorsions(); i++) {
@@ -73,8 +73,7 @@ void* CMAPTorsionForceProxy::deserialize(const SerializationNode& node) const {
         if (version > 1)
             force->setUsesPeriodicBoundaryConditions(node.getBoolProperty("usesPeriodic"));
         const SerializationNode& maps = node.getChildNode("Maps");
-        for (int i = 0; i < (int) maps.getChildren().size(); i++) {
-            const SerializationNode& map = maps.getChildren()[i];
+        for (auto& map : maps.getChildren()) {
             int size = map.getIntProperty("size");
             if (size*size != map.getChildren().size())
                 throw OpenMMException("Wrong number of values specified for CMAP");
@@ -84,11 +83,9 @@ void* CMAPTorsionForceProxy::deserialize(const SerializationNode& node) const {
             force->addMap(size, energy);
         }
         const SerializationNode& torsions = node.getChildNode("Torsions");
-        for (int i = 0; i < (int) torsions.getChildren().size(); i++) {
-            const SerializationNode& torsion = torsions.getChildren()[i];
+        for (auto& torsion : torsions.getChildren())
             force->addTorsion(torsion.getIntProperty("map"), torsion.getIntProperty("a1"), torsion.getIntProperty("a2"), torsion.getIntProperty("a3"), torsion.getIntProperty("a4"),
                     torsion.getIntProperty("b1"), torsion.getIntProperty("b2"), torsion.getIntProperty("b3"), torsion.getIntProperty("b4"));
-        }
     }
     catch (...) {
         delete force;

serialization/src/CustomAngleForceProxy.cpp

@@ -85,26 +85,19 @@ void* CustomAngleForceProxy::deserialize(const SerializationNode& node) const {
         if (version > 1)
             force->setUsesPeriodicBoundaryConditions(node.getBoolProperty("usesPeriodic"));
         const SerializationNode& perAngleParams = node.getChildNode("PerAngleParameters");
-        for (int i = 0; i < (int) perAngleParams.getChildren().size(); i++) {
-            const SerializationNode& parameter = perAngleParams.getChildren()[i];
+        for (auto& parameter : perAngleParams.getChildren())
             force->addPerAngleParameter(parameter.getStringProperty("name"));
-        }
         const SerializationNode& globalParams = node.getChildNode("GlobalParameters");
-        for (int i = 0; i < (int) globalParams.getChildren().size(); i++) {
-            const SerializationNode& parameter = globalParams.getChildren()[i];
+        for (auto& parameter : globalParams.getChildren())
             force->addGlobalParameter(parameter.getStringProperty("name"), parameter.getDoubleProperty("default"));
-        }
         if (version > 2) {
             const SerializationNode& energyDerivs = node.getChildNode("EnergyParameterDerivatives");
-            for (int i = 0; i < (int) energyDerivs.getChildren().size(); i++) {
-                const SerializationNode& parameter = energyDerivs.getChildren()[i];
+            for (auto& parameter : energyDerivs.getChildren())
                 force->addEnergyParameterDerivative(parameter.getStringProperty("name"));
-            }
         }
         const SerializationNode& angles = node.getChildNode("Angles");
         vector<double> params(force->getNumPerAngleParameters());
-        for (int i = 0; i < (int) angles.getChildren().size(); i++) {
-            const SerializationNode& angle = angles.getChildren()[i];
+        for (auto& angle : angles.getChildren()) {
             for (int j = 0; j < (int) params.size(); j++) {
                 stringstream key;
                 key << "param";

serialization/src/CustomBondForceProxy.cpp

@@ -85,26 +85,19 @@ void* CustomBondForceProxy::deserialize(const SerializationNode& node) const {
         if (version > 1)
             force->setUsesPeriodicBoundaryConditions(node.getBoolProperty("usesPeriodic"));
         const SerializationNode& perBondParams = node.getChildNode("PerBondParameters");
-        for (int i = 0; i < (int) perBondParams.getChildren().size(); i++) {
-            const SerializationNode& parameter = perBondParams.getChildren()[i];
+        for (auto& parameter : perBondParams.getChildren())
             force->addPerBondParameter(parameter.getStringProperty("name"));
-        }
         const SerializationNode& globalParams = node.getChildNode("GlobalParameters");
-        for (int i = 0; i < (int) globalParams.getChildren().size(); i++) {
-            const SerializationNode& parameter = globalParams.getChildren()[i];
+        for (auto& parameter : globalParams.getChildren())
             force->addGlobalParameter(parameter.getStringProperty("name"), parameter.getDoubleProperty("default"));
-        }
         if (version > 2) {
             const SerializationNode& energyDerivs = node.getChildNode("EnergyParameterDerivatives");
-            for (int i = 0; i < (int) energyDerivs.getChildren().size(); i++) {
-                const SerializationNode& parameter = energyDerivs.getChildren()[i];
+            for (auto& parameter : energyDerivs.getChildren())
                 force->addEnergyParameterDerivative(parameter.getStringProperty("name"));
-            }
         }
         const SerializationNode& bonds = node.getChildNode("Bonds");
         vector<double> params(force->getNumPerBondParameters());
-        for (int i = 0; i < (int) bonds.getChildren().size(); i++) {
-            const SerializationNode& bond = bonds.getChildren()[i];
+        for (auto& bond : bonds.getChildren()) {
             for (int j = 0; j < (int) params.size(); j++) {
                 stringstream key;
                 key << "param";

serialization/src/CustomCentroidBondForceProxy.cpp

@@ -108,39 +108,31 @@ void* CustomCentroidBondForceProxy::deserialize(const SerializationNode& node) c
         if (version > 1)
             force->setUsesPeriodicBoundaryConditions(node.getBoolProperty("usesPeriodic"));
         const SerializationNode& perBondParams = node.getChildNode("PerBondParameters");
-        for (int i = 0; i < (int) perBondParams.getChildren().size(); i++) {
-            const SerializationNode& parameter = perBondParams.getChildren()[i];
+        for (auto& parameter : perBondParams.getChildren())
             force->addPerBondParameter(parameter.getStringProperty("name"));
-        }
         const SerializationNode& globalParams = node.getChildNode("GlobalParameters");
-        for (int i = 0; i < (int) globalParams.getChildren().size(); i++) {
-            const SerializationNode& parameter = globalParams.getChildren()[i];
+        for (auto& parameter : globalParams.getChildren())
             force->addGlobalParameter(parameter.getStringProperty("name"), parameter.getDoubleProperty("default"));
-        }
         if (version > 2) {
             const SerializationNode& energyDerivs = node.getChildNode("EnergyParameterDerivatives");
-            for (int i = 0; i < (int) energyDerivs.getChildren().size(); i++) {
-                const SerializationNode& parameter = energyDerivs.getChildren()[i];
+            for (auto& parameter : energyDerivs.getChildren())
                 force->addEnergyParameterDerivative(parameter.getStringProperty("name"));
-            }
         }
         const SerializationNode& groups = node.getChildNode("Groups");
-        for (int i = 0; i < (int) groups.getChildren().size(); i++) {
-            const SerializationNode& group = groups.getChildren()[i];
+        for (auto& group : groups.getChildren()) {
             vector<int> particles;
             vector<double> weights;
-            for (int j = 0; j < (int) group.getChildren().size(); j++) {
-                particles.push_back(group.getChildren()[j].getIntProperty("p"));
-                if (group.getChildren()[j].hasProperty("weight"))
-                    weights.push_back(group.getChildren()[j].getDoubleProperty("weight"));
+            for (auto& child : group.getChildren()) {
+                particles.push_back(child.getIntProperty("p"));
+                if (child.hasProperty("weight"))
+                    weights.push_back(child.getDoubleProperty("weight"));
             }
             force->addGroup(particles, weights);
         }
         const SerializationNode& bonds = node.getChildNode("Bonds");
         vector<int> bondGroups(force->getNumGroupsPerBond());
         vector<double> params(force->getNumPerBondParameters());
-        for (int i = 0; i < (int) bonds.getChildren().size(); i++) {
-            const SerializationNode& bond = bonds.getChildren()[i];
+        for (auto& bond : bonds.getChildren()) {
             for (int j = 0; j < (int) bondGroups.size(); j++) {
                 stringstream key;
                 key << "g";
@@ -156,8 +148,7 @@ void* CustomCentroidBondForceProxy::deserialize(const SerializationNode& node) c
             force->addBond(bondGroups, params);
         }
         const SerializationNode& functions = node.getChildNode("Functions");
-        for (int i = 0; i < (int) functions.getChildren().size(); i++) {
-            const SerializationNode& function = functions.getChildren()[i];
+        for (auto& function : functions.getChildren()) {
             if (function.hasProperty("type")) {
                 force->addTabulatedFunction(function.getStringProperty("name"), function.decodeObject<TabulatedFunction>());
             }
@@ -166,8 +157,8 @@ void* CustomCentroidBondForceProxy::deserialize(const SerializationNode& node) c
 
                 const SerializationNode& valuesNode = function.getChildNode("Values");
                 vector<double> values;
-                for (int j = 0; j < (int) valuesNode.getChildren().size(); j++)
-                    values.push_back(valuesNode.getChildren()[j].getDoubleProperty("v"));
+                for (auto& child : valuesNode.getChildren())
+                    values.push_back(child.getDoubleProperty("v"));
                 force->addTabulatedFunction(function.getStringProperty("name"), new Continuous1DFunction(values, function.getDoubleProperty("min"), function.getDoubleProperty("max")));
             }
         }

serialization/src/CustomCompoundBondForceProxy.cpp

@@ -95,27 +95,20 @@ void* CustomCompoundBondForceProxy::deserialize(const SerializationNode& node) c
         if (version > 1)
             force->setUsesPeriodicBoundaryConditions(node.getBoolProperty("usesPeriodic"));
         const SerializationNode& perBondParams = node.getChildNode("PerBondParameters");
-        for (int i = 0; i < (int) perBondParams.getChildren().size(); i++) {
-            const SerializationNode& parameter = perBondParams.getChildren()[i];
+        for (auto& parameter : perBondParams.getChildren())
             force->addPerBondParameter(parameter.getStringProperty("name"));
-        }
         const SerializationNode& globalParams = node.getChildNode("GlobalParameters");
-        for (int i = 0; i < (int) globalParams.getChildren().size(); i++) {
-            const SerializationNode& parameter = globalParams.getChildren()[i];
+        for (auto& parameter : globalParams.getChildren())
             force->addGlobalParameter(parameter.getStringProperty("name"), parameter.getDoubleProperty("default"));
-        }
         if (version > 2) {
             const SerializationNode& energyDerivs = node.getChildNode("EnergyParameterDerivatives");
-            for (int i = 0; i < (int) energyDerivs.getChildren().size(); i++) {
-                const SerializationNode& parameter = energyDerivs.getChildren()[i];
+            for (auto& parameter : energyDerivs.getChildren())
                 force->addEnergyParameterDerivative(parameter.getStringProperty("name"));
-            }
         }
         const SerializationNode& bonds = node.getChildNode("Bonds");
         vector<int> particles(force->getNumParticlesPerBond());
         vector<double> params(force->getNumPerBondParameters());
-        for (int i = 0; i < (int) bonds.getChildren().size(); i++) {
-            const SerializationNode& bond = bonds.getChildren()[i];
+        for (auto& bond : bonds.getChildren()) {
             for (int j = 0; j < (int) particles.size(); j++) {
                 stringstream key;
                 key << "p";
@@ -131,8 +124,7 @@ void* CustomCompoundBondForceProxy::deserialize(const SerializationNode& node) c
             force->addBond(particles, params);
         }
         const SerializationNode& functions = node.getChildNode("Functions");
-        for (int i = 0; i < (int) functions.getChildren().size(); i++) {
-            const SerializationNode& function = functions.getChildren()[i];
+        for (auto& function : functions.getChildren()) {
             if (function.hasProperty("type")) {
                 force->addTabulatedFunction(function.getStringProperty("name"), function.decodeObject<TabulatedFunction>());
             }
@@ -141,8 +133,8 @@ void* CustomCompoundBondForceProxy::deserialize(const SerializationNode& node) c
                 
                 const SerializationNode& valuesNode = function.getChildNode("Values");
                 vector<double> values;
-                for (int j = 0; j < (int) valuesNode.getChildren().size(); j++)
-                    values.push_back(valuesNode.getChildren()[j].getDoubleProperty("v"));
+                for (auto& child : valuesNode.getChildren())
+                    values.push_back(child.getDoubleProperty("v"));
                 force->addTabulatedFunction(function.getStringProperty("name"), new Continuous1DFunction(values, function.getDoubleProperty("min"), function.getDoubleProperty("max")));
             }
         }

serialization/src/CustomExternalForceProxy.cpp

@@ -77,19 +77,14 @@ void* CustomExternalForceProxy::deserialize(const SerializationNode& node) const
         CustomExternalForce* force = new CustomExternalForce(node.getStringProperty("energy"));
         force->setForceGroup(node.getIntProperty("forceGroup", 0));
         const SerializationNode& perParticleParams = node.getChildNode("PerParticleParameters");
-        for (int i = 0; i < (int) perParticleParams.getChildren().size(); i++) {
-            const SerializationNode& parameter = perParticleParams.getChildren()[i];
+        for (auto& parameter : perParticleParams.getChildren())
             force->addPerParticleParameter(parameter.getStringProperty("name"));
-        }
         const SerializationNode& globalParams = node.getChildNode("GlobalParameters");
-        for (int i = 0; i < (int) globalParams.getChildren().size(); i++) {
-            const SerializationNode& parameter = globalParams.getChildren()[i];
+        for (auto& parameter : globalParams.getChildren())
             force->addGlobalParameter(parameter.getStringProperty("name"), parameter.getDoubleProperty("default"));
-        }
         const SerializationNode& particles = node.getChildNode("Particles");
         vector<double> params(force->getNumPerParticleParameters());
-        for (int i = 0; i < (int) particles.getChildren().size(); i++) {
-            const SerializationNode& particle = particles.getChildren()[i];
+        for (auto& particle : particles.getChildren()) {
             for (int j = 0; j < (int) params.size(); j++) {
                 stringstream key;
                 key << "param";

serialization/src/CustomGBForceProxy.cpp

@@ -107,36 +107,25 @@ void* CustomGBForceProxy::deserialize(const SerializationNode& node) const {
         force->setNonbondedMethod((CustomGBForce::NonbondedMethod) node.getIntProperty("method"));
         force->setCutoffDistance(node.getDoubleProperty("cutoff"));
         const SerializationNode& perParticleParams = node.getChildNode("PerParticleParameters");
-        for (int i = 0; i < (int) perParticleParams.getChildren().size(); i++) {
-            const SerializationNode& parameter = perParticleParams.getChildren()[i];
+        for (auto& parameter : perParticleParams.getChildren())
             force->addPerParticleParameter(parameter.getStringProperty("name"));
-        }
         const SerializationNode& globalParams = node.getChildNode("GlobalParameters");
-        for (int i = 0; i < (int) globalParams.getChildren().size(); i++) {
-            const SerializationNode& parameter = globalParams.getChildren()[i];
+        for (auto& parameter : globalParams.getChildren())
             force->addGlobalParameter(parameter.getStringProperty("name"), parameter.getDoubleProperty("default"));
-        }
         if (version > 1) {
             const SerializationNode& energyDerivs = node.getChildNode("EnergyParameterDerivatives");
-            for (int i = 0; i < (int) energyDerivs.getChildren().size(); i++) {
-                const SerializationNode& parameter = energyDerivs.getChildren()[i];
+            for (auto& parameter : energyDerivs.getChildren())
                 force->addEnergyParameterDerivative(parameter.getStringProperty("name"));
-            }
         }
         const SerializationNode& computedValues = node.getChildNode("ComputedValues");
-        for (int i = 0; i < (int) computedValues.getChildren().size(); i++) {
-            const SerializationNode& value = computedValues.getChildren()[i];
+        for (auto& value : computedValues.getChildren())
             force->addComputedValue(value.getStringProperty("name"), value.getStringProperty("expression"), (CustomGBForce::ComputationType) value.getIntProperty("type"));
-        }
         const SerializationNode& energyTerms = node.getChildNode("EnergyTerms");
-        for (int i = 0; i < (int) energyTerms.getChildren().size(); i++) {
-            const SerializationNode& term = energyTerms.getChildren()[i];
+        for (auto& term : energyTerms.getChildren())
             force->addEnergyTerm(term.getStringProperty("expression"), (CustomGBForce::ComputationType) term.getIntProperty("type"));
-        }
         const SerializationNode& particles = node.getChildNode("Particles");
         vector<double> params(force->getNumPerParticleParameters());
-        for (int i = 0; i < (int) particles.getChildren().size(); i++) {
-            const SerializationNode& particle = particles.getChildren()[i];
+        for (auto& particle : particles.getChildren()) {
             for (int j = 0; j < (int) params.size(); j++) {
                 stringstream key;
                 key << "param";
@@ -146,13 +135,10 @@ void* CustomGBForceProxy::deserialize(const SerializationNode& node) const {
             force->addParticle(params);
         }
         const SerializationNode& exclusions = node.getChildNode("Exclusions");
-        for (int i = 0; i < (int) exclusions.getChildren().size(); i++) {
-            const SerializationNode& exclusion = exclusions.getChildren()[i];
+        for (auto& exclusion : exclusions.getChildren())
             force->addExclusion(exclusion.getIntProperty("p1"), exclusion.getIntProperty("p2"));
-        }
         const SerializationNode& functions = node.getChildNode("Functions");
-        for (int i = 0; i < (int) functions.getChildren().size(); i++) {
-            const SerializationNode& function = functions.getChildren()[i];
+        for (auto& function : functions.getChildren()) {
             if (function.hasProperty("type")) {
                 force->addTabulatedFunction(function.getStringProperty("name"), function.decodeObject<TabulatedFunction>());
             }
@@ -161,8 +147,8 @@ void* CustomGBForceProxy::deserialize(const SerializationNode& node) const {
                 
                 const SerializationNode& valuesNode = function.getChildNode("Values");
                 vector<double> values;
-                for (int j = 0; j < (int) valuesNode.getChildren().size(); j++)
-                    values.push_back(valuesNode.getChildren()[j].getDoubleProperty("v"));
+                for (auto& child : valuesNode.getChildren())
+                    values.push_back(child.getDoubleProperty("v"));
                 force->addTabulatedFunction(function.getStringProperty("name"), new Continuous1DFunction(values, function.getDoubleProperty("min"), function.getDoubleProperty("max")));
             }
         }

serialization/src/CustomHbondForceProxy.cpp

@@ -107,24 +107,17 @@ void* CustomHbondForceProxy::deserialize(const SerializationNode& node) const {
         force->setNonbondedMethod((CustomHbondForce::NonbondedMethod) node.getIntProperty("method"));
         force->setCutoffDistance(node.getDoubleProperty("cutoff"));
         const SerializationNode& perDonorParams = node.getChildNode("PerDonorParameters");
-        for (int i = 0; i < (int) perDonorParams.getChildren().size(); i++) {
-            const SerializationNode& parameter = perDonorParams.getChildren()[i];
+        for (auto& parameter : perDonorParams.getChildren())
             force->addPerDonorParameter(parameter.getStringProperty("name"));
-        }
         const SerializationNode& perAcceptorParams = node.getChildNode("PerAcceptorParameters");
-        for (int i = 0; i < (int) perAcceptorParams.getChildren().size(); i++) {
-            const SerializationNode& parameter = perAcceptorParams.getChildren()[i];
+        for (auto& parameter : perAcceptorParams.getChildren())
             force->addPerAcceptorParameter(parameter.getStringProperty("name"));
-        }
         const SerializationNode& globalParams = node.getChildNode("GlobalParameters");
-        for (int i = 0; i < (int) globalParams.getChildren().size(); i++) {
-            const SerializationNode& parameter = globalParams.getChildren()[i];
+        for (auto& parameter : globalParams.getChildren())
             force->addGlobalParameter(parameter.getStringProperty("name"), parameter.getDoubleProperty("default"));
-        }
         const SerializationNode& donors = node.getChildNode("Donors");
         vector<double> params(force->getNumPerDonorParameters());
-        for (int i = 0; i < (int) donors.getChildren().size(); i++) {
-            const SerializationNode& donor = donors.getChildren()[i];
+        for (auto& donor : donors.getChildren()) {
             for (int j = 0; j < (int) params.size(); j++) {
                 stringstream key;
                 key << "param";
@@ -135,8 +128,7 @@ void* CustomHbondForceProxy::deserialize(const SerializationNode& node) const {
         }
         const SerializationNode& acceptors = node.getChildNode("Acceptors");
         params.resize(force->getNumPerAcceptorParameters());
-        for (int i = 0; i < (int) acceptors.getChildren().size(); i++) {
-            const SerializationNode& acceptor = acceptors.getChildren()[i];
+        for (auto& acceptor : acceptors.getChildren()) {
             for (int j = 0; j < (int) params.size(); j++) {
                 stringstream key;
                 key << "param";
@@ -146,13 +138,10 @@ void* CustomHbondForceProxy::deserialize(const SerializationNode& node) const {
             force->addAcceptor(acceptor.getIntProperty("p1"), acceptor.getIntProperty("p2"), acceptor.getIntProperty("p3"), params);
         }
         const SerializationNode& exclusions = node.getChildNode("Exclusions");
-        for (int i = 0; i < (int) exclusions.getChildren().size(); i++) {
-            const SerializationNode& exclusion = exclusions.getChildren()[i];
+        for (auto& exclusion : exclusions.getChildren())
             force->addExclusion(exclusion.getIntProperty("donor"), exclusion.getIntProperty("acceptor"));
-        }
         const SerializationNode& functions = node.getChildNode("Functions");
-        for (int i = 0; i < (int) functions.getChildren().size(); i++) {
-            const SerializationNode& function = functions.getChildren()[i];
+        for (auto& function : functions.getChildren()) {
             if (function.hasProperty("type")) {
                 force->addTabulatedFunction(function.getStringProperty("name"), function.decodeObject<TabulatedFunction>());
             }
@@ -161,8 +150,8 @@ void* CustomHbondForceProxy::deserialize(const SerializationNode& node) const {
                 
                 const SerializationNode& valuesNode = function.getChildNode("Values");
                 vector<double> values;
-                for (int j = 0; j < (int) valuesNode.getChildren().size(); j++)
-                    values.push_back(valuesNode.getChildren()[j].getDoubleProperty("v"));
+                for (auto& child : valuesNode.getChildren())
+                    values.push_back(child.getDoubleProperty("v"));
                 force->addTabulatedFunction(function.getStringProperty("name"), new Continuous1DFunction(values, function.getDoubleProperty("min"), function.getDoubleProperty("max")));
             }
         }

serialization/src/CustomIntegratorProxy.cpp

@@ -74,45 +74,40 @@ void* CustomIntegratorProxy::deserialize(const SerializationNode& node) const {
         throw OpenMMException("Unsupported version number");
     CustomIntegrator* integrator = new CustomIntegrator(node.getDoubleProperty("stepSize"));
     const SerializationNode& globalVariablesNode = node.getChildNode("GlobalVariables");
-    const map<string, string> &globalVariableProp = globalVariablesNode.getProperties();
-    for(map<string, string>::const_iterator cit = globalVariableProp.begin(); cit != globalVariableProp.end(); cit++) {
-        integrator->addGlobalVariable(cit->first, globalVariablesNode.getDoubleProperty(cit->first));
-    }
+    for (auto& prop : globalVariablesNode.getProperties())
+        integrator->addGlobalVariable(prop.first, globalVariablesNode.getDoubleProperty(prop.first));
     const SerializationNode& perDofVariablesNode = node.getChildNode("PerDofVariables");
-    const vector<SerializationNode>& perDofVariableList = perDofVariablesNode.getChildren();
     int count = 0;
-    for(vector<SerializationNode>::const_iterator cit=perDofVariableList.begin(); cit != perDofVariableList.end(); cit++, count++) {
-        const vector<SerializationNode>& perDofVariableVector = cit->getChildren();
-        integrator->addPerDofVariable(cit->getName(),0);
+    for (auto& var : perDofVariablesNode.getChildren()) {
+        integrator->addPerDofVariable(var.getName(), 0);
         vector<Vec3> perDofValues;
-        for(vector<SerializationNode>::const_iterator dit=perDofVariableVector.begin(); dit!=perDofVariableVector.end(); dit++) {
-            perDofValues.push_back(Vec3(dit->getDoubleProperty("x"),dit->getDoubleProperty("y"),dit->getDoubleProperty("z")));
-        }
+        for (auto& child : var.getChildren())
+            perDofValues.push_back(Vec3(child.getDoubleProperty("x"), child.getDoubleProperty("y"), child.getDoubleProperty("z")));
         integrator->setPerDofVariable(count, perDofValues);
+        count++;
     }
     const SerializationNode& computationsNode = node.getChildNode("Computations");
-    const vector<SerializationNode>& computationsList = computationsNode.getChildren();
-    for(vector<SerializationNode>::const_iterator cit = computationsList.begin(); cit != computationsList.end(); cit++) {
-        CustomIntegrator::ComputationType computationType = static_cast<CustomIntegrator::ComputationType>(cit->getIntProperty("computationType"));
+    for (auto& comp : computationsNode.getChildren()) {
+        CustomIntegrator::ComputationType computationType = static_cast<CustomIntegrator::ComputationType>(comp.getIntProperty("computationType"));
         // make sure that the int casts to a valid enum
-        if(computationType == CustomIntegrator::ComputeGlobal) {
-            integrator->addComputeGlobal(cit->getStringProperty("computationVariable"), cit->getStringProperty("computationExpression"));
-        } else if(computationType == CustomIntegrator::ComputePerDof) {
-            integrator->addComputePerDof(cit->getStringProperty("computationVariable"), cit->getStringProperty("computationExpression"));
-        } else if(computationType == CustomIntegrator::ComputeSum) {
-            integrator->addComputeSum(cit->getStringProperty("computationVariable"), cit->getStringProperty("computationExpression"));
-        } else if(computationType == CustomIntegrator::ConstrainPositions) {
+        if (computationType == CustomIntegrator::ComputeGlobal) {
+            integrator->addComputeGlobal(comp.getStringProperty("computationVariable"), comp.getStringProperty("computationExpression"));
+        } else if (computationType == CustomIntegrator::ComputePerDof) {
+            integrator->addComputePerDof(comp.getStringProperty("computationVariable"), comp.getStringProperty("computationExpression"));
+        } else if (computationType == CustomIntegrator::ComputeSum) {
+            integrator->addComputeSum(comp.getStringProperty("computationVariable"), comp.getStringProperty("computationExpression"));
+        } else if (computationType == CustomIntegrator::ConstrainPositions) {
             integrator->addConstrainPositions();
-        } else if(computationType == CustomIntegrator::ConstrainVelocities) {
+        } else if (computationType == CustomIntegrator::ConstrainVelocities) {
             integrator->addConstrainVelocities();
-        } else if(computationType == CustomIntegrator::UpdateContextState) {
+        } else if (computationType == CustomIntegrator::UpdateContextState) {
             integrator->addUpdateContextState();
-        } else if(computationType == CustomIntegrator::IfBlockStart) {
-            integrator->beginIfBlock(cit->getStringProperty("computationExpression"));
-        } else if(computationType == CustomIntegrator::WhileBlockStart) {
-                  integrator->beginWhileBlock(cit->getStringProperty("computationExpression"));
-        } else if(computationType == CustomIntegrator::BlockEnd) {
-                  integrator->endBlock();
+        } else if (computationType == CustomIntegrator::IfBlockStart) {
+            integrator->beginIfBlock(comp.getStringProperty("computationExpression"));
+        } else if (computationType == CustomIntegrator::WhileBlockStart) {
+            integrator->beginWhileBlock(comp.getStringProperty("computationExpression"));
+        } else if (computationType == CustomIntegrator::BlockEnd) {
+            integrator->endBlock();
         } else {
             throw(OpenMMException("Custom Integrator Deserialization: Unknown computation type"));
         }

serialization/src/CustomManyParticleForceProxy.cpp

@@ -84,10 +84,10 @@ void CustomManyParticleForceProxy::serialize(const void* object, SerializationNo
         force.getTypeFilter(i, types);
         stringstream list;
         bool first = true;
-        for (set<int>::const_iterator iter = types.begin(); iter != types.end(); ++iter) {
+        for (int type : types) {
             if (!first)
                 list << ",";
-            list << *iter;
+            list << type;
             first = false;
         }
         filters.createChildNode("Filter").setIntProperty("index", i).setStringProperty("types", list.str());
@@ -108,19 +108,14 @@ void* CustomManyParticleForceProxy::deserialize(const SerializationNode& node) c
         force->setPermutationMode((CustomManyParticleForce::PermutationMode) node.getIntProperty("permutationMode"));
         force->setCutoffDistance(node.getDoubleProperty("cutoff"));
         const SerializationNode& perParticleParams = node.getChildNode("PerParticleParameters");
-        for (int i = 0; i < (int) perParticleParams.getChildren().size(); i++) {
-            const SerializationNode& parameter = perParticleParams.getChildren()[i];
+        for (auto& parameter : perParticleParams.getChildren())
             force->addPerParticleParameter(parameter.getStringProperty("name"));
-        }
         const SerializationNode& globalParams = node.getChildNode("GlobalParameters");
-        for (int i = 0; i < (int) globalParams.getChildren().size(); i++) {
-            const SerializationNode& parameter = globalParams.getChildren()[i];
+        for (auto& parameter : globalParams.getChildren())
             force->addGlobalParameter(parameter.getStringProperty("name"), parameter.getDoubleProperty("default"));
-        }
         const SerializationNode& particles = node.getChildNode("Particles");
         vector<double> params(force->getNumPerParticleParameters());
-        for (int i = 0; i < (int) particles.getChildren().size(); i++) {
-            const SerializationNode& particle = particles.getChildren()[i];
+        for (auto& particle : particles.getChildren()) {
             for (int j = 0; j < (int) params.size(); j++) {
                 stringstream key;
                 key << "param";
@@ -130,13 +125,10 @@ void* CustomManyParticleForceProxy::deserialize(const SerializationNode& node) c
             force->addParticle(params, particle.getIntProperty("type"));
         }
         const SerializationNode& exclusions = node.getChildNode("Exclusions");
-        for (int i = 0; i < (int) exclusions.getChildren().size(); i++) {
-            const SerializationNode& exclusion = exclusions.getChildren()[i];
+        for (auto& exclusion : exclusions.getChildren())
             force->addExclusion(exclusion.getIntProperty("p1"), exclusion.getIntProperty("p2"));
-        }
         const SerializationNode& filters = node.getChildNode("TypeFilters");
-        for (int i = 0; i < (int) filters.getChildren().size(); i++) {
-            const SerializationNode& filter = filters.getChildren()[i];
+        for (auto& filter : filters.getChildren()) {
             string typesString = filter.getStringProperty("types");
             vector<string> splitTypes;
             size_t searchPos = 0, nextPos;
@@ -146,20 +138,18 @@ void* CustomManyParticleForceProxy::deserialize(const SerializationNode& node) c
             }
             splitTypes.push_back(typesString.substr(searchPos));
             set<int> types;
-            for (int j = 0; j < (int) splitTypes.size(); j++) {
-                if (splitTypes[j].size() > 0) {
+            for (auto& t : splitTypes) {
+                if (t.size() > 0) {
                     int type;
-                    stringstream(splitTypes[j]) >> type;
+                    stringstream(t) >> type;
                     types.insert(type);
                 }
             }
             force->setTypeFilter(filter.getIntProperty("index"), types);
         }
         const SerializationNode& functions = node.getChildNode("Functions");
-        for (int i = 0; i < (int) functions.getChildren().size(); i++) {
-            const SerializationNode& function = functions.getChildren()[i];
+        for (auto& function : functions.getChildren())
             force->addTabulatedFunction(function.getStringProperty("name"), function.decodeObject<TabulatedFunction>());
-        }
         return force;
     }
     catch (...) {

serialization/src/CustomNonbondedForceProxy.cpp

@@ -92,11 +92,11 @@ void CustomNonbondedForceProxy::serialize(const void* object, SerializationNode&
         std::set<int> set2;
         force.getInteractionGroupParameters(i, set1, set2);
         SerializationNode& set1node = interactionGroup.createChildNode("Set1");
-        for (std::set<int>::iterator it = set1.begin(); it != set1.end(); ++it)
-            set1node.createChildNode("Particle").setIntProperty("index", *it);
+        for (int p : set1)
+            set1node.createChildNode("Particle").setIntProperty("index", p);
         SerializationNode& set2node = interactionGroup.createChildNode("Set2");
-        for (std::set<int>::iterator it = set2.begin(); it != set2.end(); ++it)
-            set2node.createChildNode("Particle").setIntProperty("index", *it);
+        for (int p : set2)
+            set2node.createChildNode("Particle").setIntProperty("index", p);
     }
 }
 
@@ -114,26 +114,19 @@ void* CustomNonbondedForceProxy::deserialize(const SerializationNode& node) cons
         force->setSwitchingDistance(node.getDoubleProperty("switchingDistance", -1.0));
         force->setUseLongRangeCorrection(node.getBoolProperty("useLongRangeCorrection", false));
         const SerializationNode& perParticleParams = node.getChildNode("PerParticleParameters");
-        for (int i = 0; i < (int) perParticleParams.getChildren().size(); i++) {
-            const SerializationNode& parameter = perParticleParams.getChildren()[i];
+        for (auto& parameter : perParticleParams.getChildren())
             force->addPerParticleParameter(parameter.getStringProperty("name"));
-        }
         const SerializationNode& globalParams = node.getChildNode("GlobalParameters");
-        for (int i = 0; i < (int) globalParams.getChildren().size(); i++) {
-            const SerializationNode& parameter = globalParams.getChildren()[i];
+        for (auto& parameter : globalParams.getChildren())
             force->addGlobalParameter(parameter.getStringProperty("name"), parameter.getDoubleProperty("default"));
-        }
         if (version > 1) {
             const SerializationNode& energyDerivs = node.getChildNode("EnergyParameterDerivatives");
-            for (int i = 0; i < (int) energyDerivs.getChildren().size(); i++) {
-                const SerializationNode& parameter = energyDerivs.getChildren()[i];
+            for (auto& parameter : energyDerivs.getChildren())
                 force->addEnergyParameterDerivative(parameter.getStringProperty("name"));
-            }
         }
         const SerializationNode& particles = node.getChildNode("Particles");
         vector<double> params(force->getNumPerParticleParameters());
-        for (int i = 0; i < (int) particles.getChildren().size(); i++) {
-            const SerializationNode& particle = particles.getChildren()[i];
+        for (auto& particle : particles.getChildren()) {
             for (int j = 0; j < (int) params.size(); j++) {
                 stringstream key;
                 key << "param";
@@ -143,13 +136,10 @@ void* CustomNonbondedForceProxy::deserialize(const SerializationNode& node) cons
             force->addParticle(params);
         }
         const SerializationNode& exclusions = node.getChildNode("Exclusions");
-        for (int i = 0; i < (int) exclusions.getChildren().size(); i++) {
-            const SerializationNode& exclusion = exclusions.getChildren()[i];
+        for (auto& exclusion : exclusions.getChildren())
             force->addExclusion(exclusion.getIntProperty("p1"), exclusion.getIntProperty("p2"));
-        }
         const SerializationNode& functions = node.getChildNode("Functions");
-        for (int i = 0; i < (int) functions.getChildren().size(); i++) {
-            const SerializationNode& function = functions.getChildren()[i];
+        for (auto& function : functions.getChildren()) {
             if (function.hasProperty("type")) {
                 force->addTabulatedFunction(function.getStringProperty("name"), function.decodeObject<TabulatedFunction>());
             }
@@ -158,30 +148,28 @@ void* CustomNonbondedForceProxy::deserialize(const SerializationNode& node) cons
 
                 const SerializationNode& valuesNode = function.getChildNode("Values");
                 vector<double> values;
-                for (int j = 0; j < (int) valuesNode.getChildren().size(); j++)
-                    values.push_back(valuesNode.getChildren()[j].getDoubleProperty("v"));
+                for (auto& child : valuesNode.getChildren())
+                    values.push_back(child.getDoubleProperty("v"));
                 force->addTabulatedFunction(function.getStringProperty("name"), new Continuous1DFunction(values, function.getDoubleProperty("min"), function.getDoubleProperty("max")));
             }
         }
         bool hasInteractionGroups = false; // Older files will be missing this block.
-        for (int i = 0; i < (int) node.getChildren().size(); i++) {
-            if (node.getChildren()[i].getName() == "InteractionGroups")
+        for (auto& child : node.getChildren())
+            if (child.getName() == "InteractionGroups")
                 hasInteractionGroups = true;
-        }
         if (hasInteractionGroups) {
             const SerializationNode& interactionGroups = node.getChildNode("InteractionGroups");
-            for (int i = 0; i < (int) interactionGroups.getChildren().size(); i++) {
-                const SerializationNode& interactionGroup = interactionGroups.getChildren()[i];
+            for (auto& interactionGroup : interactionGroups.getChildren()) {
                 // Get set 1.
                 const SerializationNode& set1node = interactionGroup.getChildNode("Set1");
                 std::set<int> set1;
-                for (int j = 0; j < (int) set1node.getChildren().size(); j++)
-                    set1.insert(set1node.getChildren()[j].getIntProperty("index"));
+                for (auto& child : set1node.getChildren())
+                    set1.insert(child.getIntProperty("index"));
                 // Get set 2.
                 const SerializationNode& set2node = interactionGroup.getChildNode("Set2");
                 std::set<int> set2;
-                for (int j = 0; j < (int) set2node.getChildren().size(); j++)
-                    set2.insert(set2node.getChildren()[j].getIntProperty("index"));
+                for (auto& child : set2node.getChildren())
+                    set2.insert(child.getIntProperty("index"));
                 force->addInteractionGroup(set1, set2);
             }
         }

serialization/src/CustomTorsionForceProxy.cpp

@@ -85,26 +85,19 @@ void* CustomTorsionForceProxy::deserialize(const SerializationNode& node) const
         if (version > 1)
             force->setUsesPeriodicBoundaryConditions(node.getBoolProperty("usesPeriodic"));
         const SerializationNode& perTorsionParams = node.getChildNode("PerTorsionParameters");
-        for (int i = 0; i < (int) perTorsionParams.getChildren().size(); i++) {
-            const SerializationNode& parameter = perTorsionParams.getChildren()[i];
+        for (auto& parameter : perTorsionParams.getChildren())
             force->addPerTorsionParameter(parameter.getStringProperty("name"));
-        }
         const SerializationNode& globalParams = node.getChildNode("GlobalParameters");
-        for (int i = 0; i < (int) globalParams.getChildren().size(); i++) {
-            const SerializationNode& parameter = globalParams.getChildren()[i];
+        for (auto& parameter : globalParams.getChildren())
             force->addGlobalParameter(parameter.getStringProperty("name"), parameter.getDoubleProperty("default"));
-        }
         if (version > 2) {
             const SerializationNode& energyDerivs = node.getChildNode("EnergyParameterDerivatives");
-            for (int i = 0; i < (int) energyDerivs.getChildren().size(); i++) {
-                const SerializationNode& parameter = energyDerivs.getChildren()[i];
+            for (auto& parameter : energyDerivs.getChildren())
                 force->addEnergyParameterDerivative(parameter.getStringProperty("name"));
-            }
         }
         const SerializationNode& torsions = node.getChildNode("Torsions");
         vector<double> params(force->getNumPerTorsionParameters());
-        for (int i = 0; i < (int) torsions.getChildren().size(); i++) {
-            const SerializationNode& torsion = torsions.getChildren()[i];
+        for (auto& torsion : torsions.getChildren()) {
             for (int j = 0; j < (int) params.size(); j++) {
                 stringstream key;
                 key << "param";

serialization/src/GBSAOBCForceProxy.cpp

@@ -72,10 +72,8 @@ void* GBSAOBCForceProxy::deserialize(const SerializationNode& node) const {
         if (version > 1)
             force->setSurfaceAreaEnergy(node.getDoubleProperty("surfaceAreaEnergy"));
         const SerializationNode& particles = node.getChildNode("Particles");
-        for (int i = 0; i < (int) particles.getChildren().size(); i++) {
-            const SerializationNode& particle = particles.getChildren()[i];
+        for (auto& particle : particles.getChildren())
             force->addParticle(particle.getDoubleProperty("q"), particle.getDoubleProperty("r"), particle.getDoubleProperty("scale"));
-        }
     }
     catch (...) {
         delete force;

serialization/src/GayBerneForceProxy.cpp

@@ -78,17 +78,13 @@ void* GayBerneForceProxy::deserialize(const SerializationNode& node) const {
         force->setUseSwitchingFunction(node.getBoolProperty("useSwitchingFunction", false));
         force->setSwitchingDistance(node.getDoubleProperty("switchingDistance", -1.0));
         const SerializationNode& particles = node.getChildNode("Particles");
-        for (int i = 0; i < (int) particles.getChildren().size(); i++) {
-            const SerializationNode& particle = particles.getChildren()[i];
+        for (auto& particle : particles.getChildren())
             force->addParticle(particle.getDoubleProperty("sig"), particle.getDoubleProperty("eps"), particle.getIntProperty("xparticle"),
                     particle.getIntProperty("yparticle"), particle.getDoubleProperty("sx"), particle.getDoubleProperty("sy"), particle.getDoubleProperty("sz"),
                     particle.getDoubleProperty("ex"), particle.getDoubleProperty("ey"), particle.getDoubleProperty("ez"));
-        }
         const SerializationNode& exceptions = node.getChildNode("Exceptions");
-        for (int i = 0; i < (int) exceptions.getChildren().size(); i++) {
-            const SerializationNode& exception = exceptions.getChildren()[i];
+        for (auto& exception : exceptions.getChildren())
             force->addException(exception.getIntProperty("p1"), exception.getIntProperty("p2"), exception.getDoubleProperty("sig"), exception.getDoubleProperty("eps"));
-        }
     }
     catch (...) {
         delete force;

serialization/src/HarmonicAngleForceProxy.cpp

@@ -65,10 +65,8 @@ void* HarmonicAngleForceProxy::deserialize(const SerializationNode& node) const
         if (version > 1)
             force->setUsesPeriodicBoundaryConditions(node.getBoolProperty("usesPeriodic"));
         const SerializationNode& angles = node.getChildNode("Angles");
-        for (int i = 0; i < (int) angles.getChildren().size(); i++) {
-            const SerializationNode& angle = angles.getChildren()[i];
+        for (auto& angle : angles.getChildren())
             force->addAngle(angle.getIntProperty("p1"), angle.getIntProperty("p2"), angle.getIntProperty("p3"), angle.getDoubleProperty("a"), angle.getDoubleProperty("k"));
-        }
     }
     catch (...) {
         delete force;