Merge pull request #1769 from peastman/loops

Use C++11 style loops

plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceVdwForce.cpp

@@ -277,9 +277,8 @@ double AmoebaReferenceVdwForce::calculateForceAndEnergy(int numParticles,
  
         double sigmaI      = sigmas[ii];
         double epsilonI    = epsilons[ii];
-        for (std::set<int>::const_iterator jj = allExclusions[ii].begin(); jj != allExclusions[ii].end(); jj++) {
-            exclusions[*jj] = 1;
-        }
+        for (int jj : allExclusions[ii])
+            exclusions[jj] = 1;
 
         for (unsigned int jj = ii+1; jj < static_cast<unsigned int>(numParticles); jj++) {
             if (exclusions[jj] == 0) {
@@ -310,9 +309,8 @@ double AmoebaReferenceVdwForce::calculateForceAndEnergy(int numParticles,
             }
         }
 
-        for (std::set<int>::const_iterator jj = allExclusions[ii].begin(); jj != allExclusions[ii].end(); jj++) {
-            exclusions[*jj] = 0;
-        }
+        for (int jj : allExclusions[ii])
+            exclusions[jj] = 0;
     }
 
     return energy;

plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaExtrapolatedPolarization.cpp

@@ -287,8 +287,8 @@ static void check_finite_differences(vector<Vec3> analytic_forces, Context &cont
     // Take a small step in the direction of the energy gradient and see whether the potential energy changes by the expected amount.
 
     double norm = 0.0;
-    for (int i = 0; i < (int) analytic_forces.size(); ++i)
-        norm += analytic_forces[i].dot(analytic_forces[i]);
+    for (auto& f : analytic_forces)
+        norm += f.dot(f);
     norm = std::sqrt(norm);
     const double stepSize = 1e-3;
     double step = 0.5*stepSize/norm;

plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaGeneralizedKirkwoodForce.cpp

@@ -61,8 +61,8 @@ static void checkFiniteDifferences(vector<Vec3> forces, Context &context, vector
     // Take a small step in the direction of the energy gradient and see whether the potential energy changes by the expected amount.
     double norm = 0.0;
-    for (int i = 0; i < (int) forces.size(); ++i)
-        norm += forces[i].dot(forces[i]);
+    for (auto& f : forces)
+        norm += f.dot(f);
     norm = std::sqrt(norm);
     const double stepSize = 1e-3;
     double step = 0.5*stepSize/norm;

plugins/amoeba/serialization/src/AmoebaBondForceProxy.cpp

@@ -72,10 +72,8 @@ void* AmoebaBondForceProxy::deserialize(const SerializationNode& node) const {
         force->setAmoebaGlobalBondCubic(node.getDoubleProperty("cubic"));
         force->setAmoebaGlobalBondQuartic(node.getDoubleProperty("quartic"));
         const SerializationNode& bonds = node.getChildNode("Bonds");
-        for (unsigned int ii = 0; ii < (int) bonds.getChildren().size(); ii++) {
-            const SerializationNode& bond = bonds.getChildren()[ii];
+        for (auto& bond : bonds.getChildren())
             force->addBond(bond.getIntProperty("p1"), bond.getIntProperty("p2"), bond.getDoubleProperty("d"), bond.getDoubleProperty("k"));
-        }
     }
     catch (...) {
         delete force;

plugins/amoeba/serialization/src/AmoebaStretchBendForceProxy.cpp

@@ -67,8 +67,7 @@ void* AmoebaStretchBendForceProxy::deserialize(const SerializationNode& node) co
         if (version > 3)
             force->setUsesPeriodicBoundaryConditions(node.getBoolProperty("usesPeriodic"));
         const SerializationNode& bonds = node.getChildNode("StretchBendAngles");
-        for (unsigned int ii = 0; ii < (int) bonds.getChildren().size(); ii++) {
-            const SerializationNode& bond = bonds.getChildren()[ii];
+        for (auto& bond : bonds.getChildren()) {
             double k1, k2;
             if (version == 1)
                 k1 = k2 = bond.getDoubleProperty("k");

plugins/cpupme/src/CpuPmeKernels.cpp

@@ -515,8 +515,8 @@ CpuCalcPmeReciprocalForceKernel::~CpuCalcPmeReciprocalForceKernel() {
     pthread_mutex_destroy(&lock);
     pthread_cond_destroy(&startCondition);
     pthread_cond_destroy(&endCondition);
-    for (int i = 0; i < (int) tempGrid.size(); i++)
-        fftwf_free(tempGrid[i]);
+    for (auto grid : tempGrid)
+        fftwf_free(grid);
     if (complexGrid != NULL)
         fftwf_free(complexGrid);
     if (hasCreatedPlan) {
@@ -552,8 +552,8 @@ void CpuCalcPmeReciprocalForceKernel::runMainThread() {
         if (includeEnergy) {
             threads.resumeThreads(); // Signal threads to compute energy.
             threads.waitForThreads();
-            for (int i = 0; i < (int) threadEnergy.size(); i++)
-                energy += threadEnergy[i];
+            for (auto e : threadEnergy)
+                energy += e;
         }
         threads.resumeThreads(); // Signal threads to perform reciprocal convolution.
         threads.waitForThreads();
@@ -805,8 +805,8 @@ CpuCalcDispersionPmeReciprocalForceKernel::~CpuCalcDispersionPmeReciprocalForceK
     pthread_mutex_destroy(&lock);
     pthread_cond_destroy(&startCondition);
     pthread_cond_destroy(&endCondition);
-    for (int i = 0; i < (int) tempGrid.size(); i++)
-        fftwf_free(tempGrid[i]);
+    for (auto grid : tempGrid)
+        fftwf_free(grid);
     if (complexGrid != NULL)
         fftwf_free(complexGrid);
     if (hasCreatedPlan) {
@@ -843,8 +843,8 @@ void CpuCalcDispersionPmeReciprocalForceKernel::runMainThread() {
         if (includeEnergy) {
             threads.resumeThreads(); // Signal threads to compute energy.
             threads.waitForThreads();
-            for (int i = 0; i < (int) threadEnergy.size(); i++)
-                energy += threadEnergy[i];
+            for (auto e : threadEnergy)
+                energy += e;
         }
         threads.resumeThreads(); // Signal threads to perform reciprocal convolution.
         threads.waitForThreads();

plugins/drude/platforms/reference/src/ReferenceDrudeKernels.cpp

@@ -267,8 +267,7 @@ void ReferenceIntegrateDrudeLangevinStepKernel::execute(ContextImpl& context, co
     const double fscale = (1-vscale)/integrator.getFriction();
     const double kT = BOLTZ*integrator.getTemperature();
     const double noisescale = sqrt(2*kT*integrator.getFriction())*sqrt(0.5*(1-vscale*vscale)/integrator.getFriction());
-    for (int i = 0; i < (int) normalParticles.size(); i++) {
-        int index = normalParticles[i];
+    for (int index : normalParticles) {
         double invMass = particleInvMass[index];
         if (invMass != 0.0) {
             double sqrtInvMass = sqrt(invMass);

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")));
             }
         }