Use C++11 style loops

openmmapi/src/AndersenThermostatImpl.cpp

@@ -94,7 +94,7 @@ void AndersenThermostatImpl::tagParticlesInGroup(int particle, int group, vector
     // Recursively tag particles as belonging to a particular group.
 
     particleGroup[particle] = group;
-    for (int i = 0; i < (int) particleConstraints[particle].size(); i++)
-        if (particleGroup[particleConstraints[particle][i]] == -1)
-            tagParticlesInGroup(particleConstraints[particle][i], group, particleGroup, particleConstraints);
+    for (int constrained : particleConstraints[particle])
+        if (particleGroup[constrained] == -1)
+            tagParticlesInGroup(constrained, group, particleGroup, particleConstraints);
 }

openmmapi/src/CompiledExpressionSet.cpp

@@ -44,15 +44,15 @@ int CompiledExpressionSet::getVariableIndex(const std::string& name) {
     int index = variables.size();
     variables.push_back(name);
     variableReferences.push_back(vector<double*>());
-    for (int i = 0; i < (int) expressions.size(); i++)
-        if (expressions[i]->getVariables().find(name) != expressions[i]->getVariables().end())
-            variableReferences[index].push_back(&expressions[i]->getVariableReference(name));
+    for (auto expression : expressions)
+        if (expression->getVariables().find(name) != expression->getVariables().end())
+            variableReferences[index].push_back(&expression->getVariableReference(name));
     return index;
 }
 
 void CompiledExpressionSet::setVariable(int index, double value) {
-    for (int i = 0; i < (int) variableReferences[index].size(); i++)
-        *variableReferences[index][i] = value;
+    for (auto ref : variableReferences[index])
+        *ref = value;
 }
 
 int CompiledExpressionSet::getNumVariables() const {

openmmapi/src/Context.cpp

@@ -97,8 +97,8 @@ State Context::getState(int types, bool enforcePeriodicBox, int groups) const {
     }
     if (types&State::Parameters) {
         map<string, double> params;
-        for (map<string, double>::const_iterator iter = impl->parameters.begin(); iter != impl->parameters.end(); iter++)
-            params[iter->first] = iter->second;
+        for (auto& param : impl->parameters)
+            params[param.first] = param.second;
         builder.setParameters(params);
     }
     if (types&State::ParameterDerivatives) {
@@ -111,13 +111,13 @@ State Context::getState(int types, bool enforcePeriodicBox, int groups) const {
         impl->getPositions(positions);
         if (enforcePeriodicBox) {
             const vector<vector<int> >& molecules = impl->getMolecules();
-            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 += positions[molecules[i][j]];
-                center *= 1.0/molecules[i].size();
+                for (int j : mol)
+                    center += positions[j];
+                center *= 1.0/mol.size();
 
                 // Find the displacement to move it into the first periodic box.
                 Vec3 diff;
@@ -126,10 +126,8 @@ State Context::getState(int types, bool enforcePeriodicBox, int groups) const {
                 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]];
-                    pos -= diff;
-                }
+                for (int j : mol)
+                    positions[j] -= diff;
             }
         }
         builder.setPositions(positions);
@@ -152,8 +150,8 @@ void Context::setState(const State& state) {
     if ((state.getDataTypes()&State::Velocities) != 0)
         setVelocities(state.getVelocities());
     if ((state.getDataTypes()&State::Parameters) != 0)
-        for (map<string, double>::const_iterator iter = state.getParameters().begin(); iter != state.getParameters().end(); ++iter)
-            setParameter(iter->first, iter->second);
+        for (auto& param : state.getParameters())
+            setParameter(param.first, param.second);
 }
 
 void Context::setTime(double time) {

openmmapi/src/ContextImpl.cpp

@@ -95,19 +95,19 @@ ContextImpl::ContextImpl(Context& owner, const System& system, Integrator& integ
 
     const vector<string>& platformProperties = platform->getPropertyNames();
     map<string, string> validatedProperties;
-    for (map<string, string>::const_iterator iter = properties.begin(); iter != properties.end(); ++iter) {
-        string property = iter->first;
+    for (auto& prop : properties) {
+        string property = prop.first;
         if (platform->deprecatedPropertyReplacements.find(property) != platform->deprecatedPropertyReplacements.end())
             property = platform->deprecatedPropertyReplacements[property];
         bool valid = false;
-        for (int i = 0; i < (int) platformProperties.size(); i++)
-            if (platformProperties[i] == property) {
+        for (auto& p : platformProperties)
+            if (p == property) {
                 valid = true;
                 break;
             }
         if (!valid)
-            throw OpenMMException("Illegal property name: "+iter->first);
-        validatedProperties[property] = iter->second;
+            throw OpenMMException("Illegal property name: "+prop.first);
+        validatedProperties[property] = prop.second;
     }
     
     // Find the list of kernels required.
@@ -184,8 +184,8 @@ ContextImpl::ContextImpl(Context& owner, const System& system, Integrator& integ
 }
 
 ContextImpl::~ContextImpl() {
-    for (int i = 0; i < (int) forceImpls.size(); ++i)
-        delete forceImpls[i];
+    for (auto force : forceImpls)
+        delete force;
     
     // Make sure all kernels get properly deleted before contextDestroyed() is called.
     
@@ -292,8 +292,8 @@ double ContextImpl::calcForcesAndEnergy(bool includeForces, bool includeEnergy,
     while (true) {
         double energy = 0.0;
         kernel.beginComputation(*this, includeForces, includeEnergy, groups);
-        for (int i = 0; i < (int) forceImpls.size(); ++i)
-            energy += forceImpls[i]->calcForcesAndEnergy(*this, includeForces, includeEnergy, groups);
+        for (auto force : forceImpls)
+            energy += force->calcForcesAndEnergy(*this, includeForces, includeEnergy, groups);
         bool valid = true;
         energy += kernel.finishComputation(*this, includeForces, includeEnergy, groups, valid);
         if (valid)
@@ -310,8 +310,8 @@ double ContextImpl::calcKineticEnergy() {
 }
 
 void ContextImpl::updateContextState() {
-    for (int i = 0; i < (int) forceImpls.size(); ++i)
-        forceImpls[i]->updateContextState(*this);
+    for (auto force : forceImpls)
+        force->updateContextState(*this);
 }
 
 const vector<ForceImpl*>& ContextImpl::getForceImpls() const {
@@ -349,8 +349,8 @@ const vector<vector<int> >& ContextImpl::getMolecules() const {
         system.getConstraintParameters(i, particle1, particle2, distance);
         bonds.push_back(std::make_pair(particle1, particle2));
     }
-    for (int i = 0; i < (int) forceImpls.size(); i++) {
-        vector<pair<int, int> > forceBonds = forceImpls[i]->getBondedParticles();
+    for (auto force : forceImpls) {
+        vector<pair<int, int> > forceBonds = force->getBondedParticles();
         bonds.insert(bonds.end(), forceBonds.begin(), forceBonds.end());
     }
     for (int i = 0; i < system.getNumParticles(); i++) {
@@ -365,9 +365,9 @@ const vector<vector<int> >& ContextImpl::getMolecules() const {
 
     int numParticles = system.getNumParticles();
     vector<vector<int> > particleBonds(numParticles);
-    for (int i = 0; i < (int) bonds.size(); i++) {
-        particleBonds[bonds[i].first].push_back(bonds[i].second);
-        particleBonds[bonds[i].second].push_back(bonds[i].first);
+    for (auto& bond : bonds) {
+        particleBonds[bond.first].push_back(bond.second);
+        particleBonds[bond.second].push_back(bond.first);
     }
 
     // Now identify particles by which molecule they belong to.
@@ -441,9 +441,9 @@ void ContextImpl::createCheckpoint(ostream& stream) {
     stream.write((char*) &numParticles, sizeof(int));
     int numParameters = parameters.size();
     stream.write((char*) &numParameters, sizeof(int));
-    for (map<string, double>::const_iterator iter = parameters.begin(); iter != parameters.end(); ++iter) {
-        writeString(stream, iter->first);
-        stream.write((char*) &iter->second, sizeof(double));
+    for (auto& param : parameters) {
+        writeString(stream, param.first);
+        stream.write((char*) &param.second, sizeof(double));
     }
     updateStateDataKernel.getAs<UpdateStateDataKernel>().createCheckpoint(*this, stream);
     stream.flush();

openmmapi/src/CustomCentroidBondForce.cpp

@@ -52,8 +52,8 @@ CustomCentroidBondForce::CustomCentroidBondForce(int numGroups, const string& en
 }
 
 CustomCentroidBondForce::~CustomCentroidBondForce() {
-    for (int i = 0; i < (int) functions.size(); i++)
-        delete functions[i].function;
+    for (auto function : functions)
+        delete function.function;
 }
 
 const string& CustomCentroidBondForce::getEnergyFunction() const {

openmmapi/src/CustomCentroidBondForceImpl.cpp

@@ -83,11 +83,11 @@ void CustomCentroidBondForceImpl::initialize(ContextImpl& context) {
     vector<double> weights;
     for (int i = 0; i < owner.getNumGroups(); i++) {
         owner.getGroupParameters(i, particles, weights);
-        for (int j = 0; j < (int) particles.size(); j++)
-            if (particles[j] < 0 || particles[j] >= system.getNumParticles()) {
+        for (int particle : particles)
+            if (particle < 0 || particle >= system.getNumParticles()) {
                 stringstream msg;
                 msg << "CustomCentroidBondForce: Illegal particle index for a group: ";
-                msg << particles[j];
+                msg << particle;
                 throw OpenMMException(msg.str());
             }
         if (weights.size() != particles.size() && weights.size() > 0) {
@@ -102,11 +102,11 @@ void CustomCentroidBondForceImpl::initialize(ContextImpl& context) {
     int numBondParameters = owner.getNumPerBondParameters();
     for (int i = 0; i < owner.getNumBonds(); i++) {
         owner.getBondParameters(i, groups, parameters);
-        for (int j = 0; j < (int) groups.size(); j++)
-            if (groups[j] < 0 || groups[j] >= owner.getNumGroups()) {
+        for (int group : groups)
+            if (group < 0 || group >= owner.getNumGroups()) {
                 stringstream msg;
                 msg << "CustomCentroidBondForce: Illegal group index for a bond: ";
-                msg << groups[j];
+                msg << group;
                 throw OpenMMException(msg.str());
             }
         if (parameters.size() != numBondParameters) {
@@ -179,8 +179,8 @@ ExpressionTreeNode CustomCentroidBondForceImpl::replaceFunctions(const Expressio
         // This is not an angle or dihedral, so process its children.
 
         vector<ExpressionTreeNode> children;
-        for (int i = 0; i < (int) node.getChildren().size(); i++)
-            children.push_back(replaceFunctions(node.getChildren()[i], groups, distances, angles, dihedrals, variables));
+        for (auto& child : node.getChildren())
+            children.push_back(replaceFunctions(child, groups, distances, angles, dihedrals, variables));
         return ExpressionTreeNode(op.clone(), children);
     }
     const Operation::Custom& custom = static_cast<const Operation::Custom&>(op);

openmmapi/src/CustomCompoundBondForce.cpp

@@ -53,8 +53,8 @@ CustomCompoundBondForce::CustomCompoundBondForce(int numParticles, const string&
 
 
 CustomCompoundBondForce::~CustomCompoundBondForce() {
-    for (int i = 0; i < (int) functions.size(); i++)
-        delete functions[i].function;
+    for (auto function : functions)
+        delete function.function;
 }
 
 const string& CustomCompoundBondForce::getEnergyFunction() const {

openmmapi/src/CustomCompoundBondForceImpl.cpp

@@ -88,11 +88,11 @@ void CustomCompoundBondForceImpl::initialize(ContextImpl& context) {
     int numBondParameters = owner.getNumPerBondParameters();
     for (int i = 0; i < owner.getNumBonds(); i++) {
         owner.getBondParameters(i, particles, parameters);
-        for (int j = 0; j < (int) particles.size(); j++)
-            if (particles[j] < 0 || particles[j] >= system.getNumParticles()) {
+        for (int particle : particles)
+            if (particle < 0 || particle >= system.getNumParticles()) {
                 stringstream msg;
                 msg << "CustomCompoundBondForce: Illegal particle index for a bond: ";
-                msg << particles[j];
+                msg << particle;
                 throw OpenMMException(msg.str());
             }
         if (parameters.size() != numBondParameters) {
@@ -165,8 +165,8 @@ ExpressionTreeNode CustomCompoundBondForceImpl::replaceFunctions(const Expressio
         // This is not an angle or dihedral, so process its children.
 
         vector<ExpressionTreeNode> children;
-        for (int i = 0; i < (int) node.getChildren().size(); i++)
-            children.push_back(replaceFunctions(node.getChildren()[i], atoms, distances, angles, dihedrals, variables));
+        for (auto& child : node.getChildren())
+            children.push_back(replaceFunctions(child, atoms, distances, angles, dihedrals, variables));
         return ExpressionTreeNode(op.clone(), children);
     }
     const Operation::Custom& custom = static_cast<const Operation::Custom&>(op);

openmmapi/src/CustomGBForce.cpp

@@ -51,8 +51,8 @@ CustomGBForce::CustomGBForce() : nonbondedMethod(NoCutoff), cutoffDistance(1.0)
 }
 
 CustomGBForce::~CustomGBForce() {
-    for (int i = 0; i < (int) functions.size(); i++)
-        delete functions[i].function;
+    for (auto function : functions)
+        delete function.function;
 }
 
 CustomGBForce::NonbondedMethod CustomGBForce::getNonbondedMethod() const {

openmmapi/src/CustomHbondForce.cpp

@@ -52,8 +52,8 @@ CustomHbondForce::CustomHbondForce(const string& energy) : energyExpression(ener
 
 
 CustomHbondForce::~CustomHbondForce() {
-    for (int i = 0; i < (int) functions.size(); i++)
-        delete functions[i].function;
+    for (auto function : functions)
+        delete function.function;
 }
 
 const string& CustomHbondForce::getEnergyFunction() const {

openmmapi/src/CustomHbondForceImpl.cpp

@@ -235,8 +235,8 @@ ExpressionTreeNode CustomHbondForceImpl::replaceFunctions(const ExpressionTreeNo
         // This is not an angle or dihedral, so process its children.
 
         vector<ExpressionTreeNode> children;
-        for (int i = 0; i < (int) node.getChildren().size(); i++)
-            children.push_back(replaceFunctions(node.getChildren()[i], atoms, distances, angles, dihedrals, variables));
+        for (auto& child : node.getChildren())
+            children.push_back(replaceFunctions(child, atoms, distances, angles, dihedrals, variables));
         return ExpressionTreeNode(op.clone(), children);
     }
     const Operation::Custom& custom = static_cast<const Operation::Custom&>(op);

openmmapi/src/CustomIntegrator.cpp

@@ -55,8 +55,7 @@ void CustomIntegrator::initialize(ContextImpl& contextRef) {
     set<std::string> variableSet;
     variableList.insert(variableList.end(), globalNames.begin(), globalNames.end());
     variableList.insert(variableList.end(), perDofNames.begin(), perDofNames.end());
-    for (int i = 0; i < (int) variableList.size(); i++) {
-        string& name = variableList[i];
+    for (auto& name : variableList) {
         if (variableSet.find(name) != variableSet.end())
             throw OpenMMException("The Integrator defines two variables with the same name: "+name);
         variableSet.insert(name);
@@ -66,8 +65,8 @@ void CustomIntegrator::initialize(ContextImpl& contextRef) {
     set<std::string> globalTargets;
     globalTargets.insert(globalNames.begin(), globalNames.end());
     globalTargets.insert("dt");
-    for (map<string, double>::const_iterator iter = contextRef.getParameters().begin(); iter != contextRef.getParameters().end(); ++iter)
-        globalTargets.insert(iter->first);
+    for (auto& param : contextRef.getParameters())
+        globalTargets.insert(param.first);
     for (int i = 0; i < computations.size(); i++) {
         if (computations[i].type == ComputeGlobal && globalTargets.find(computations[i].variable) == globalTargets.end())
             throw OpenMMException("Unknown global variable: "+computations[i].variable);

openmmapi/src/CustomIntegratorUtilities.cpp

@@ -59,8 +59,8 @@ bool CustomIntegratorUtilities::usesVariable(const Lepton::ExpressionTreeNode& n
     const Lepton::Operation& op = node.getOperation();
     if (op.getId() == Lepton::Operation::VARIABLE && op.getName() == variable)
         return true;
-    for (int i = 0; i < (int) node.getChildren().size(); i++)
-        if (usesVariable(node.getChildren()[i], variable))
+    for (auto& child : node.getChildren())
+        if (usesVariable(child, variable))
             return true;
     return false;
 }
@@ -107,11 +107,9 @@ void CustomIntegratorUtilities::analyzeComputations(const ContextImpl& context,
 
     set<string> affectsForce;
     affectsForce.insert("x");
-    for (vector<ForceImpl*>::const_iterator iter = context.getForceImpls().begin(); iter != context.getForceImpls().end(); ++iter) {
-        const map<string, double> params = (*iter)->getDefaultParameters();
-        for (map<string, double>::const_iterator param = params.begin(); param != params.end(); ++param)
-            affectsForce.insert(param->first);
-    }
+    for (auto force : context.getForceImpls())
+        for (auto& param : force->getDefaultParameters())
+            affectsForce.insert(param.first);
     for (int i = 0; i < numSteps; i++)
         invalidatesForces[i] = (stepType[i] == CustomIntegrator::ConstrainPositions || affectsForce.find(stepVariable[i]) != affectsForce.end());
 
@@ -253,8 +251,7 @@ void CustomIntegratorUtilities::analyzeForceComputationsForPath(vector<int>& ste
             const vector<bool>& invalidatesForces, const vector<int>& forceGroup, vector<bool>& computeBoth) {
     vector<int> candidatePoints;
     int currentGroup = -1;
-    for (int i = 0; i < (int) steps.size(); i++) {
-        int step = steps[i];
+    for (int step : steps) {
         if (invalidatesForces[step] || ((needsForces[step] || needsEnergy[step]) && forceGroup[step] != currentGroup)) {
             // Forces and energies are invalidated at this step, or it changes to a different force group,
             // so anything from this point on won't affect what we do at earlier steps.
@@ -264,11 +261,9 @@ void CustomIntegratorUtilities::analyzeForceComputationsForPath(vector<int>& ste
         if (needsForces[step] || needsEnergy[step]) {
             // See if this step affects what we do at earlier points.
 
-            for (int j = 0; j < (int) candidatePoints.size(); j++) {
-                int candidate = candidatePoints[j];
+            for (int candidate : candidatePoints)
                 if ((needsForces[candidate] && needsEnergy[step]) || (needsEnergy[candidate] && needsForces[step]))
                     computeBoth[candidate] = true;
-            }
 
             // Add this to the list of candidates that might be affected by later steps.
 

openmmapi/src/CustomManyParticleForce.cpp

@@ -48,8 +48,8 @@ CustomManyParticleForce::CustomManyParticleForce(int particlesPerSet, const stri
 }
 
 CustomManyParticleForce::~CustomManyParticleForce() {
-    for (int i = 0; i < (int) functions.size(); i++)
-        delete functions[i].function;
+    for (auto function : functions)
+        delete function.function;
 }
 
 const string& CustomManyParticleForce::getEnergyFunction() const {
@@ -162,9 +162,9 @@ void CustomManyParticleForce::createExclusionsFromBonds(const vector<pair<int, i
         return;
     vector<set<int> > exclusions(particles.size());
     vector<set<int> > bonded12(exclusions.size());
-    for (int i = 0; i < (int) bonds.size(); ++i) {
-        int p1 = bonds[i].first;
-        int p2 = bonds[i].second;
+    for (auto& bond : bonds) {
+        int p1 = bond.first;
+        int p2 = bond.second;
         exclusions[p1].insert(p2);
         exclusions[p2].insert(p1);
         bonded12[p1].insert(p2);
@@ -172,15 +172,14 @@ void CustomManyParticleForce::createExclusionsFromBonds(const vector<pair<int, i
     }
     for (int level = 0; level < bondCutoff-1; level++) {
         vector<set<int> > currentExclusions = exclusions;
-        for (int i = 0; i < (int) particles.size(); i++) {
-            for (set<int>::const_iterator iter = currentExclusions[i].begin(); iter != currentExclusions[i].end(); ++iter)
-                exclusions[*iter].insert(bonded12[i].begin(), bonded12[i].end());
-        }
+        for (int i = 0; i < (int) particles.size(); i++)
+            for (int j : currentExclusions[i])
+                exclusions[j].insert(bonded12[i].begin(), bonded12[i].end());
     }
     for (int i = 0; i < (int) exclusions.size(); ++i)
-        for (set<int>::const_iterator iter = exclusions[i].begin(); iter != exclusions[i].end(); ++iter)
-            if (*iter < i)
-                addExclusion(*iter, i);
+        for (int j : exclusions[i])
+            if (j < i)
+                addExclusion(j, i);
 }
 
 void CustomManyParticleForce::getTypeFilter(int index, set<int>& types) const {

openmmapi/src/CustomManyParticleForceImpl.cpp

@@ -197,8 +197,8 @@ ExpressionTreeNode CustomManyParticleForceImpl::replaceFunctions(const Expressio
         // This is not an angle or dihedral, so process its children.
 
         vector<ExpressionTreeNode> children;
-        for (int i = 0; i < (int) node.getChildren().size(); i++)
-            children.push_back(replaceFunctions(node.getChildren()[i], atoms, distances, angles, dihedrals, variables));
+        for (auto& child : node.getChildren())
+            children.push_back(replaceFunctions(child, atoms, distances, angles, dihedrals, variables));
         return ExpressionTreeNode(op.clone(), children);
     }
     const Operation::Custom& custom = static_cast<const Operation::Custom&>(op);
@@ -280,9 +280,9 @@ void CustomManyParticleForceImpl::buildFilterArrays(const CustomManyParticleForc
             for (int j = 0; j < numTypes; j++)
                 allowedTypes[i].insert(j);
         else {
-            for (set<int>::const_iterator iter = types.begin(); iter != types.end(); ++iter)
-                if (typeMap.find(*iter) != typeMap.end())
-                    allowedTypes[i].insert(typeMap[*iter]);
+            for (int type : types)
+                if (typeMap.find(type) != typeMap.end())
+                    allowedTypes[i].insert(typeMap[type]);
             if (allowedTypes[i].size() < numTypes)
                 anyFilters = true;
         }

openmmapi/src/CustomNonbondedForce.cpp

@@ -70,8 +70,8 @@ CustomNonbondedForce::CustomNonbondedForce(const CustomNonbondedForce& rhs) {
 }
 
 CustomNonbondedForce::~CustomNonbondedForce() {
-    for (int i = 0; i < (int) functions.size(); i++)
-        delete functions[i].function;
+    for (auto function : functions)
+        delete function.function;
 }
 
 const string& CustomNonbondedForce::getEnergyFunction() const {
@@ -210,14 +210,14 @@ void CustomNonbondedForce::setExclusionParticles(int index, int particle1, int p
 void CustomNonbondedForce::createExclusionsFromBonds(const vector<pair<int, int> >& bonds, int bondCutoff) {
     if (bondCutoff < 1)
         return;
-    for (int i = 0; i < (int) bonds.size(); ++i)
-        if (bonds[i].first < 0 || bonds[i].second < 0 || bonds[i].first >= particles.size() || bonds[i].second >= particles.size())
+    for (auto& bond : bonds)
+        if (bond.first < 0 || bond.second < 0 || bond.first >= particles.size() || bond.second >= particles.size())
             throw OpenMMException("createExclusionsFromBonds: Illegal particle index in list of bonds");
     vector<set<int> > exclusions(particles.size());
     vector<set<int> > bonded12(exclusions.size());
-    for (int i = 0; i < (int) bonds.size(); ++i) {
-        int p1 = bonds[i].first;
-        int p2 = bonds[i].second;
+    for (auto& bond : bonds) {
+        int p1 = bond.first;
+        int p2 = bond.second;
         exclusions[p1].insert(p2);
         exclusions[p2].insert(p1);
         bonded12[p1].insert(p2);
@@ -225,15 +225,14 @@ void CustomNonbondedForce::createExclusionsFromBonds(const vector<pair<int, int>
     }
     for (int level = 0; level < bondCutoff-1; level++) {
         vector<set<int> > currentExclusions = exclusions;
-        for (int i = 0; i < (int) particles.size(); i++) {
-            for (set<int>::const_iterator iter = currentExclusions[i].begin(); iter != currentExclusions[i].end(); ++iter)
-                exclusions[*iter].insert(bonded12[i].begin(), bonded12[i].end());
-        }
+        for (int i = 0; i < (int) particles.size(); i++)
+            for (int j : currentExclusions[i])
+                exclusions[j].insert(bonded12[i].begin(), bonded12[i].end());
     }
     for (int i = 0; i < (int) exclusions.size(); ++i)
-        for (set<int>::const_iterator iter = exclusions[i].begin(); iter != exclusions[i].end(); ++iter)
-            if (*iter < i)
-                addExclusion(*iter, i);
+        for (int j : exclusions[i])
+            if (j < i)
+                addExclusion(j, i);
 }
 
 int CustomNonbondedForce::addTabulatedFunction(const std::string& name, TabulatedFunction* function) {

openmmapi/src/Force.cpp

@@ -54,18 +54,16 @@ bool Force::usesPeriodicBoundaryConditions() const {
 }
 
 ForceImpl& Force::getImplInContext(Context& context) {
-    const vector<ForceImpl*>& impls = context.getImpl().getForceImpls();
-    for (int i = 0; i < (int) impls.size(); i++)
-        if (&impls[i]->getOwner() == this)
-            return *impls[i];
+    for (auto impl : context.getImpl().getForceImpls())
+        if (&impl->getOwner() == this)
+            return *impl;
     throw OpenMMException("getImplInContext: This Force is not present in the Context");
 }
 
 const ForceImpl& Force::getImplInContext(const Context& context) const {
-    const vector<ForceImpl*>& impls = context.getImpl().getForceImpls();
-    for (int i = 0; i < (int) impls.size(); i++)
-        if (&impls[i]->getOwner() == this)
-            return *impls[i];
+    for (auto impl : context.getImpl().getForceImpls())
+        if (&impl->getOwner() == this)
+            return *impl;
     throw OpenMMException("getImplInContext: This Force is not present in the Context");
 }
 

openmmapi/src/NonbondedForce.cpp

@@ -203,17 +203,17 @@ ForceImpl* NonbondedForce::createImpl() const {
 }
 
 void NonbondedForce::createExceptionsFromBonds(const vector<pair<int, int> >& bonds, double coulomb14Scale, double lj14Scale) {
-    for (int i = 0; i < (int) bonds.size(); ++i)
-        if (bonds[i].first < 0 || bonds[i].second < 0 || bonds[i].first >= particles.size() || bonds[i].second >= particles.size())
+    for (auto& bond : bonds)
+        if (bond.first < 0 || bond.second < 0 || bond.first >= particles.size() || bond.second >= particles.size())
             throw OpenMMException("createExceptionsFromBonds: Illegal particle index in list of bonds");
 
     // Find particles separated by 1, 2, or 3 bonds.
 
     vector<set<int> > exclusions(particles.size());
     vector<set<int> > bonded12(exclusions.size());
-    for (int i = 0; i < (int) bonds.size(); ++i) {
-        bonded12[bonds[i].first].insert(bonds[i].second);
-        bonded12[bonds[i].second].insert(bonds[i].first);
+    for (auto& bond : bonds) {
+        bonded12[bond.first].insert(bond.second);
+        bonded12[bond.second].insert(bond.first);
     }
     for (int i = 0; i < (int) exclusions.size(); ++i)
         addExclusionsToSet(bonded12, exclusions[i], i, i, 2);
@@ -223,33 +223,34 @@ void NonbondedForce::createExceptionsFromBonds(const vector<pair<int, int> >& bo
     for (int i = 0; i < (int) exclusions.size(); ++i) {
         set<int> bonded13;
         addExclusionsToSet(bonded12, bonded13, i, i, 1);
-        for (set<int>::const_iterator iter = exclusions[i].begin(); iter != exclusions[i].end(); ++iter)
-            if (*iter < i) {
-                if (bonded13.find(*iter) == bonded13.end()) {
+        for (int j : exclusions[i]) {
+            if (j < i) {
+                if (bonded13.find(j) == bonded13.end()) {
                     // This is a 1-4 interaction.
 
-                    const ParticleInfo& particle1 = particles[*iter];
+                    const ParticleInfo& particle1 = particles[j];
                     const ParticleInfo& particle2 = particles[i];
                     const double chargeProd = coulomb14Scale*particle1.charge*particle2.charge;
                     const double sigma = 0.5*(particle1.sigma+particle2.sigma);
                     const double epsilon = lj14Scale*std::sqrt(particle1.epsilon*particle2.epsilon);
-                    addException(*iter, i, chargeProd, sigma, epsilon);
+                    addException(j, i, chargeProd, sigma, epsilon);
                 }
                 else {
                     // This interaction should be completely excluded.
 
-                    addException(*iter, i, 0.0, 1.0, 0.0);
+                    addException(j, i, 0.0, 1.0, 0.0);
+                }
             }
         }
     }
 }
 
 void NonbondedForce::addExclusionsToSet(const vector<set<int> >& bonded12, set<int>& exclusions, int baseParticle, int fromParticle, int currentLevel) const {
-    for (set<int>::const_iterator iter = bonded12[fromParticle].begin(); iter != bonded12[fromParticle].end(); ++iter) {
-        if (*iter != baseParticle)
-            exclusions.insert(*iter);
+    for (int i : bonded12[fromParticle]) {
+        if (i != baseParticle)
+            exclusions.insert(i);
         if (currentLevel > 0)
-            addExclusionsToSet(bonded12, exclusions, baseParticle, *iter, currentLevel-1);
+            addExclusionsToSet(bonded12, exclusions, baseParticle, i, currentLevel-1);
     }
 }
 

openmmapi/src/System.cpp

@@ -45,10 +45,10 @@ System::System() {
 }
 
 System::~System() {
-    for (int i = 0; i < (int) forces.size(); ++i)
-        delete forces[i];
-    for (int i = 0; i < (int) virtualSites.size(); ++i)
-        delete virtualSites[i];
+    for (auto force : forces)
+        delete force;
+    for (auto site : virtualSites)
+        delete site;
 }
 
 double System::getParticleMass(int index) const {

openmmapi/src/ThreadPool.cpp

@@ -89,13 +89,13 @@ ThreadPool::ThreadPool(int numThreads) : currentTask(NULL) {
 }
 
 ThreadPool::~ThreadPool() {
-    for (int i = 0; i < (int) threadData.size(); i++)
-        threadData[i]->isDeleted = true;
+    for (auto data : threadData)
+        data->isDeleted = true;
     pthread_mutex_lock(&lock);
     pthread_cond_broadcast(&startCondition);
     pthread_mutex_unlock(&lock);
-    for (int i = 0; i < (int) thread.size(); i++)
-        pthread_join(thread[i], NULL);
+    for (auto t : thread)
+        pthread_join(t, NULL);
     pthread_mutex_destroy(&lock);
     pthread_cond_destroy(&startCondition);
     pthread_cond_destroy(&endCondition);