Use C++11 style loops

platforms/cpu/src/CpuKernels.cpp

@@ -98,8 +98,8 @@ static void validateVariables(const Lepton::ExpressionTreeNode& node, const set<
     const Lepton::Operation& op = node.getOperation();
     if (op.getId() == Lepton::Operation::VARIABLE && variables.find(op.getName()) == variables.end())
         throw OpenMMException("Unknown variable in expression: "+op.getName());
-    for (int i = 0; i < (int) node.getChildren().size(); i++)
-        validateVariables(node.getChildren()[i], variables);
+    for (auto& child : node.getChildren())
+        validateVariables(child, variables);
 }
 
 /**
@@ -867,8 +867,8 @@ void CpuCalcCustomNonbondedForceKernel::initialize(const System& system, const C
 
     // Delete the custom functions.
 
-    for (map<string, Lepton::CustomFunction*>::iterator iter = functions.begin(); iter != functions.end(); iter++)
-        delete iter->second;
+    for (auto& function : functions)
+        delete function.second;
     
     // Record information for the long range correction.
     
@@ -909,11 +909,11 @@ double CpuCalcCustomNonbondedForceKernel::execute(ContextImpl& context, bool inc
         nonbonded->setPeriodic(boxVectors);
     }
     bool globalParamsChanged = false;
-    for (int i = 0; i < (int) globalParameterNames.size(); i++) {
-        double value = context.getParameter(globalParameterNames[i]);
-        if (globalParamValues[globalParameterNames[i]] != value)
+    for (auto& name : globalParameterNames) {
+        double value = context.getParameter(name);
+        if (globalParamValues[name] != value)
             globalParamsChanged = true;
-        globalParamValues[globalParameterNames[i]] = value;
+        globalParamValues[name] = value;
     }
     if (useSwitchingFunction)
         nonbonded->setUseSwitchingFunction(switchingDistance);
@@ -1155,8 +1155,8 @@ void CpuCalcCustomGBForceKernel::initialize(const System& system, const CustomGB
 
     // Delete the custom functions.
 
-    for (map<string, Lepton::CustomFunction*>::iterator iter = functions.begin(); iter != functions.end(); iter++)
-        delete iter->second;
+    for (auto& function : functions)
+        delete function.second;
     ixn = new CpuCustomGBForce(numParticles, exclusions, valueExpressions, valueDerivExpressions, valueGradientExpressions, valueParamDerivExpressions,
         valueNames, valueTypes, energyExpressions, energyDerivExpressions, energyGradientExpressions, energyParamDerivExpressions, energyTypes,
         particleParameterNames, data.threads);
@@ -1174,8 +1174,8 @@ double CpuCalcCustomGBForceKernel::execute(ContextImpl& context, bool includeFor
         ixn->setUseCutoff(nonbondedCutoff, *data.neighborList);
     }
     map<string, double> globalParameters;
-    for (int i = 0; i < (int) globalParameterNames.size(); i++)
-        globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
+    for (auto& name : globalParameterNames)
+        globalParameters[name] = context.getParameter(name);
     vector<double> energyParamDerivValues(energyParamDerivNames.size()+1, 0.0);
     ixn->calculateIxn(numParticles, &data.posq[0], particleParamArray, globalParameters, data.threadForce, includeForces, includeEnergy, energy, &energyParamDerivValues[0]);
     map<string, double>& energyParamDerivs = extractEnergyParameterDerivatives(context);
@@ -1236,8 +1236,8 @@ void CpuCalcCustomManyParticleForceKernel::initialize(const System& system, cons
 
 double CpuCalcCustomManyParticleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
     map<string, double> globalParameters;
-    for (int i = 0; i < (int) globalParameterNames.size(); i++)
-        globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
+    for (auto& name : globalParameterNames)
+        globalParameters[name] = context.getParameter(name);
     if (nonbondedMethod == CutoffPeriodic) {
         Vec3* boxVectors = extractBoxVectors(context);
         double minAllowedSize = 2*cutoffDistance;

platforms/cuda/src/CudaContext.cpp

@@ -385,14 +385,14 @@ CudaContext::CudaContext(const System& system, int deviceIndex, bool useBlocking
 
 CudaContext::~CudaContext() {
     setAsCurrent();
-    for (int i = 0; i < (int) forces.size(); i++)
-        delete forces[i];
-    for (int i = 0; i < (int) reorderListeners.size(); i++)
-        delete reorderListeners[i];
-    for (int i = 0; i < (int) preComputations.size(); i++)
-        delete preComputations[i];
-    for (int i = 0; i < (int) postComputations.size(); i++)
-        delete postComputations[i];
+    for (auto force : forces)
+        delete force;
+    for (auto listener : reorderListeners)
+        delete listener;
+    for (auto computation : preComputations)
+        delete computation;
+    for (auto computation : postComputations)
+        delete computation;
     if (pinnedBuffer != NULL)
         cuMemFreeHost(pinnedBuffer);
     if (posq != NULL)
@@ -498,17 +498,17 @@ string CudaContext::replaceStrings(const string& input, const std::map<std::stri
             symbolChars.insert(c);
     }
     string result = input;
-    for (map<string, string>::const_iterator iter = replacements.begin(); iter != replacements.end(); iter++) {
+    for (auto& pair : replacements) {
         int index = 0;
-        int size = iter->first.size();
+        int size = pair.first.size();
         do {
-            index = result.find(iter->first, index);
+            index = result.find(pair.first, index);
             if (index != result.npos) {
                 if ((index == 0 || symbolChars.find(result[index-1]) == symbolChars.end()) && (index == result.size()-size || symbolChars.find(result[index+size]) == symbolChars.end())) {
                     // We have found a complete symbol, not part of a longer symbol.
 
-                    result.replace(index, size, iter->second);
-                    index += iter->second.size();
+                    result.replace(index, size, pair.second);
+                    index += pair.second.size();
                 }
                 else
                     index++;
@@ -528,10 +528,10 @@ CUmodule CudaContext::createModule(const string source, const map<string, string
     stringstream src;
     if (!options.empty())
         src << "// Compilation Options: " << options << endl << endl;
-    for (map<string, string>::const_iterator iter = compilationDefines.begin(); iter != compilationDefines.end(); ++iter) {
-        src << "#define " << iter->first;
-        if (!iter->second.empty())
-            src << " " << iter->second;
+    for (auto& pair : compilationDefines) {
+        src << "#define " << pair.first;
+        if (!pair.second.empty())
+            src << " " << pair.second;
         src << endl;
     }
     if (!compilationDefines.empty())
@@ -561,10 +561,10 @@ CUmodule CudaContext::createModule(const string source, const map<string, string
         src << "typedef float4 mixed4;\n";
     }
     src << "typedef unsigned int tileflags;\n";
-    for (map<string, string>::const_iterator iter = defines.begin(); iter != defines.end(); ++iter) {
-        src << "#define " << iter->first;
-        if (!iter->second.empty())
-            src << " " << iter->second;
+    for (auto& pair : defines) {
+        src << "#define " << pair.first;
+        if (!pair.second.empty())
+            src << " " << pair.second;
         src << endl;
     }
     if (!defines.empty())
@@ -966,10 +966,10 @@ void CudaContext::findMoleculeGroups() {
             atomBonds[particle1].push_back(particle2);
             atomBonds[particle2].push_back(particle1);
         }
-        for (int i = 0; i < (int) forces.size(); i++) {
-            for (int j = 0; j < forces[i]->getNumParticleGroups(); j++) {
+        for (auto force : forces) {
+            for (int j = 0; j < force->getNumParticleGroups(); j++) {
                 vector<int> particles;
-                forces[i]->getParticlesInGroup(j, particles);
+                force->getParticlesInGroup(j, particles);
                 for (int k = 0; k < (int) particles.size(); k++)
                     for (int m = 0; m < (int) particles.size(); m++)
                         if (k != m)
@@ -1187,8 +1187,8 @@ bool CudaContext::invalidateMolecules(CudaForceInfo* force) {
     }
     atomIndexDevice->upload(atomIndex);
     findMoleculeGroups();
-    for (int i = 0; i < (int) reorderListeners.size(); i++)
-        reorderListeners[i]->execute();
+    for (auto listener : reorderListeners)
+        listener->execute();
     reorderAtoms();
     return true;
 }
@@ -1250,10 +1250,9 @@ void CudaContext::reorderAtomsImpl() {
     vector<Real4> newPosqCorrection(paddedNumAtoms);
     vector<Mixed4> newVelm(paddedNumAtoms);
     vector<int4> newCellOffsets(numAtoms);
-    for (int group = 0; group < (int) moleculeGroups.size(); group++) {
+    for (auto& mol : moleculeGroups) {
         // Find the center of each molecule.
 
-        MoleculeGroup& mol = moleculeGroups[group];
         int numMolecules = mol.offsets.size();
         vector<int>& atoms = mol.atoms;
         vector<Real4> molPos(numMolecules);
@@ -1347,9 +1346,9 @@ void CudaContext::reorderAtomsImpl() {
         // Reorder the atoms.
 
         for (int i = 0; i < numMolecules; i++) {
-            for (int j = 0; j < (int)atoms.size(); j++) {
-                int oldIndex = mol.offsets[molBins[i].second]+atoms[j];
-                int newIndex = mol.offsets[i]+atoms[j];
+            for (int atom : atoms) {
+                int oldIndex = mol.offsets[molBins[i].second]+atom;
+                int newIndex = mol.offsets[i]+atom;
                 originalIndex[newIndex] = atomIndex[oldIndex];
                 newPosq[newIndex] = oldPosq[oldIndex];
                 if (useMixedPrecision)
@@ -1371,8 +1370,8 @@ void CudaContext::reorderAtomsImpl() {
         posqCorrection->upload(newPosqCorrection);
     velm->upload(newVelm);
     atomIndexDevice->upload(atomIndex);
-    for (int i = 0; i < (int) reorderListeners.size(); i++)
-        reorderListeners[i]->execute();
+    for (auto listener : reorderListeners)
+        listener->execute();
 }
 
 void CudaContext::addReorderListener(ReorderListener* listener) {

platforms/opencl/src/OpenCLContext.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2009-2016 Stanford University and the Authors.      *
+ * Portions copyright (c) 2009-2017 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -318,8 +318,8 @@ OpenCLContext::OpenCLContext(const System& system, int platformIndex, int device
         OpenCLArray valuesArray(*this, 20, sizeof(mm_float8), "values");
         vector<mm_float8> values(valuesArray.getSize());
         float nextValue = 1e-4f;
-        for (int i = 0; i < (int) values.size(); ++i) {
-            values[i].s0 = nextValue;
+        for (auto& val : values) {
+            val.s0 = nextValue;
             nextValue *= (float) M_PI;
         }
         valuesArray.upload(values);
@@ -328,14 +328,14 @@ OpenCLContext::OpenCLContext(const System& system, int platformIndex, int device
         executeKernel(accuracyKernel, values.size());
         valuesArray.download(values);
         double maxSqrtError = 0.0, maxRsqrtError = 0.0, maxRecipError = 0.0, maxExpError = 0.0, maxLogError = 0.0;
-        for (int i = 0; i < (int) values.size(); ++i) {
-            double v = values[i].s0;
+        for (auto& val : values) {
+            double v = val.s0;
             double correctSqrt = sqrt(v);
-            maxSqrtError = max(maxSqrtError, fabs(correctSqrt-values[i].s1)/correctSqrt);
-            maxRsqrtError = max(maxRsqrtError, fabs(1.0/correctSqrt-values[i].s2)*correctSqrt);
-            maxRecipError = max(maxRecipError, fabs(1.0/v-values[i].s3)/values[i].s3);
-            maxExpError = max(maxExpError, fabs(exp(v)-values[i].s4)/values[i].s4);
-            maxLogError = max(maxLogError, fabs(log(v)-values[i].s5)/values[i].s5);
+            maxSqrtError = max(maxSqrtError, fabs(correctSqrt-val.s1)/correctSqrt);
+            maxRsqrtError = max(maxRsqrtError, fabs(1.0/correctSqrt-val.s2)*correctSqrt);
+            maxRecipError = max(maxRecipError, fabs(1.0/v-val.s3)/val.s3);
+            maxExpError = max(maxExpError, fabs(exp(v)-val.s4)/val.s4);
+            maxLogError = max(maxLogError, fabs(log(v)-val.s5)/val.s5);
         }
         compilationDefines["SQRT"] = (maxSqrtError < 1e-6) ? "native_sqrt" : "sqrt";
         compilationDefines["RSQRT"] = (maxRsqrtError < 1e-6) ? "native_rsqrt" : "rsqrt";
@@ -412,14 +412,14 @@ OpenCLContext::OpenCLContext(const System& system, int platformIndex, int device
 }
 
 OpenCLContext::~OpenCLContext() {
-    for (int i = 0; i < (int) forces.size(); i++)
-        delete forces[i];
-    for (int i = 0; i < (int) reorderListeners.size(); i++)
-        delete reorderListeners[i];
-    for (int i = 0; i < (int) preComputations.size(); i++)
-        delete preComputations[i];
-    for (int i = 0; i < (int) postComputations.size(); i++)
-        delete postComputations[i];
+    for (auto force : forces)
+        delete force;
+    for (auto listener : reorderListeners)
+        delete listener;
+    for (auto computation : preComputations)
+        delete computation;
+    for (auto computation : postComputations)
+        delete computation;
     if (pinnedBuffer != NULL)
         delete pinnedBuffer;
     if (posq != NULL)
@@ -458,8 +458,8 @@ void OpenCLContext::initialize() {
     bonded->initialize(system);
     numForceBuffers = platformData.contexts.size();
     numForceBuffers = std::max(numForceBuffers, bonded->getNumForceBuffers());
-    for (int i = 0; i < (int) forces.size(); i++)
-        numForceBuffers = std::max(numForceBuffers, forces[i]->getRequiredForceBuffers());
+    for (auto force : forces)
+        numForceBuffers = std::max(numForceBuffers, force->getRequiredForceBuffers());
     int energyBufferSize = max(numThreadBlocks*ThreadBlockSize, nonbonded->getNumEnergyBuffers());
     if (useDoublePrecision) {
         forceBuffers = OpenCLArray::create<mm_double4>(*this, paddedNumAtoms*numForceBuffers, "forceBuffers");
@@ -525,17 +525,17 @@ string OpenCLContext::replaceStrings(const string& input, const std::map<std::st
             symbolChars.insert(c);
     }
     string result = input;
-    for (map<string, string>::const_iterator iter = replacements.begin(); iter != replacements.end(); iter++) {
+    for (auto& pair : replacements) {
         int index = 0;
-        int size = iter->first.size();
+        int size = pair.first.size();
         do {
-            index = result.find(iter->first, index);
+            index = result.find(pair.first, index);
             if (index != result.npos) {
                 if ((index == 0 || symbolChars.find(result[index-1]) == symbolChars.end()) && (index == result.size()-size || symbolChars.find(result[index+size]) == symbolChars.end())) {
                     // We have found a complete symbol, not part of a longer symbol.
 
-                    result.replace(index, size, iter->second);
-                    index += iter->second.size();
+                    result.replace(index, size, pair.second);
+                    index += pair.second.size();
                 }
                 else
                     index++;
@@ -554,10 +554,10 @@ cl::Program OpenCLContext::createProgram(const string source, const map<string,
     stringstream src;
     if (!options.empty())
         src << "// Compilation Options: " << options << endl << endl;
-    for (map<string, string>::const_iterator iter = compilationDefines.begin(); iter != compilationDefines.end(); ++iter) {
-        src << "#define " << iter->first;
-        if (!iter->second.empty())
-            src << " " << iter->second;
+    for (auto& pair : compilationDefines) {
+        src << "#define " << pair.first;
+        if (!pair.second.empty())
+            src << " " << pair.second;
         src << endl;
     }
     if (!compilationDefines.empty())
@@ -588,10 +588,10 @@ cl::Program OpenCLContext::createProgram(const string source, const map<string,
         src << "typedef float3 mixed3;\n";
         src << "typedef float4 mixed4;\n";
     }
-    for (map<string, string>::const_iterator iter = defines.begin(); iter != defines.end(); ++iter) {
-        src << "#define " << iter->first;
-        if (!iter->second.empty())
-            src << " " << iter->second;
+    for (auto& pair : defines) {
+        src << "#define " << pair.first;
+        if (!pair.second.empty())
+            src << " " << pair.second;
         src << endl;
     }
     if (!defines.empty())
@@ -856,10 +856,10 @@ void OpenCLContext::findMoleculeGroups() {
             atomBonds[particle1].push_back(particle2);
             atomBonds[particle2].push_back(particle1);
         }
-        for (int i = 0; i < (int) forces.size(); i++) {
-            for (int j = 0; j < forces[i]->getNumParticleGroups(); j++) {
+        for (auto force : forces) {
+            for (int j = 0; j < force->getNumParticleGroups(); j++) {
                 vector<int> particles;
-                forces[i]->getParticlesInGroup(j, particles);
+                force->getParticlesInGroup(j, particles);
                 for (int k = 0; k < (int) particles.size(); k++)
                     for (int m = 0; m < (int) particles.size(); m++)
                         if (k != m)
@@ -1076,8 +1076,8 @@ bool OpenCLContext::invalidateMolecules(OpenCLForceInfo* force) {
     }
     atomIndexDevice->upload(atomIndex);
     findMoleculeGroups();
-    for (int i = 0; i < (int) reorderListeners.size(); i++)
-        reorderListeners[i]->execute();
+    for (auto listener : reorderListeners)
+        listener->execute();
     reorderAtoms();
     return true;
 }
@@ -1138,10 +1138,9 @@ void OpenCLContext::reorderAtomsImpl() {
     vector<Real4> newPosqCorrection(paddedNumAtoms, Real4(0,0,0,0));
     vector<Mixed4> newVelm(paddedNumAtoms, Mixed4(0,0,0,0));
     vector<mm_int4> newCellOffsets(numAtoms);
-    for (int group = 0; group < (int) moleculeGroups.size(); group++) {
+    for (auto& mol : moleculeGroups) {
         // Find the center of each molecule.
 
-        MoleculeGroup& mol = moleculeGroups[group];
         int numMolecules = mol.offsets.size();
         vector<int>& atoms = mol.atoms;
         vector<Real4> molPos(numMolecules);
@@ -1235,9 +1234,9 @@ void OpenCLContext::reorderAtomsImpl() {
         // Reorder the atoms.
 
         for (int i = 0; i < numMolecules; i++) {
-            for (int j = 0; j < (int)atoms.size(); j++) {
-                int oldIndex = mol.offsets[molBins[i].second]+atoms[j];
-                int newIndex = mol.offsets[i]+atoms[j];
+            for (int atom : atoms) {
+                int oldIndex = mol.offsets[molBins[i].second]+atom;
+                int newIndex = mol.offsets[i]+atom;
                 originalIndex[newIndex] = atomIndex[oldIndex];
                 newPosq[newIndex] = oldPosq[oldIndex];
                 if (useMixedPrecision)
@@ -1259,8 +1258,8 @@ void OpenCLContext::reorderAtomsImpl() {
         posqCorrection->upload(newPosqCorrection);
     velm->upload(newVelm);
     atomIndexDevice->upload(atomIndex);
-    for (int i = 0; i < (int) reorderListeners.size(); i++)
-        reorderListeners[i]->execute();
+    for (auto listener : reorderListeners)
+        listener->execute();
 }
 
 void OpenCLContext::addReorderListener(ReorderListener* listener) {

platforms/reference/src/ReferenceKernels.cpp

@@ -159,8 +159,8 @@ static void validateVariables(const Lepton::ExpressionTreeNode& node, const set<
     const Lepton::Operation& op = node.getOperation();
     if (op.getId() == Lepton::Operation::VARIABLE && variables.find(op.getName()) == variables.end())
         throw OpenMMException("Unknown variable in expression: "+op.getName());
-    for (int i = 0; i < (int) node.getChildren().size(); i++)
-        validateVariables(node.getChildren()[i], variables);
+    for (auto& child : node.getChildren())
+        validateVariables(child, variables);
 }
 
 /**
@@ -214,8 +214,8 @@ void ReferenceCalcForcesAndEnergyKernel::beginComputation(ContextImpl& context,
     }
     else
         savedForces = forceData;
-    for (map<string, double>::const_iterator iter = context.getParameters().begin(); iter != context.getParameters().end(); ++iter)
-        extractEnergyParameterDerivatives(context)[iter->first] = 0;
+    for (auto& param : context.getParameters())
+        extractEnergyParameterDerivatives(context)[param.first] = 0;
 }
 
 double ReferenceCalcForcesAndEnergyKernel::finishComputation(ContextImpl& context, bool includeForces, bool includeEnergy, int groups, bool& valid) {
@@ -466,8 +466,8 @@ double ReferenceCalcCustomBondForceKernel::execute(ContextImpl& context, bool in
     vector<Vec3>& forceData = extractForces(context);
     double energy = 0;
     map<string, double> globalParameters;
-    for (int i = 0; i < (int) globalParameterNames.size(); i++)
-        globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
+    for (auto& name : globalParameterNames)
+        globalParameters[name] = context.getParameter(name);
     ReferenceCustomBondIxn bond(energyExpression, forceExpression, parameterNames, globalParameters, energyParamDerivExpressions);
     if (usePeriodic)
         bond.setPeriodic(extractBoxVectors(context));
@@ -600,8 +600,8 @@ double ReferenceCalcCustomAngleForceKernel::execute(ContextImpl& context, bool i
     vector<Vec3>& forceData = extractForces(context);
     double energy = 0;
     map<string, double> globalParameters;
-    for (int i = 0; i < (int) globalParameterNames.size(); i++)
-        globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
+    for (auto& name : globalParameterNames)
+        globalParameters[name] = context.getParameter(name);
     ReferenceCustomAngleIxn customAngle(energyExpression, forceExpression, parameterNames, globalParameters, energyParamDerivExpressions);
     if (usePeriodic)
         customAngle.setPeriodic(extractBoxVectors(context));
@@ -870,8 +870,8 @@ double ReferenceCalcCustomTorsionForceKernel::execute(ContextImpl& context, bool
     vector<Vec3>& forceData = extractForces(context);
     double energy = 0;
     map<string, double> globalParameters;
-    for (int i = 0; i < (int) globalParameterNames.size(); i++)
-        globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
+    for (auto& name : globalParameterNames)
+        globalParameters[name] = context.getParameter(name);
     ReferenceCustomTorsionIxn customTorsion(energyExpression, forceExpression, parameterNames, globalParameters, energyParamDerivExpressions);
     if (usePeriodic)
         customTorsion.setPeriodic(extractBoxVectors(context));
@@ -1165,8 +1165,8 @@ void ReferenceCalcCustomNonbondedForceKernel::initialize(const System& system, c
 
     // Delete the custom functions.
 
-    for (map<string, Lepton::CustomFunction*>::iterator iter = functions.begin(); iter != functions.end(); iter++)
-        delete iter->second;
+    for (auto& function : functions)
+        delete function.second;
     
     // Record information for the long range correction.
     
@@ -1208,11 +1208,11 @@ double ReferenceCalcCustomNonbondedForceKernel::execute(ContextImpl& context, bo
     if (interactionGroups.size() > 0)
         ixn.setInteractionGroups(interactionGroups);
     bool globalParamsChanged = false;
-    for (int i = 0; i < (int) globalParameterNames.size(); i++) {
-        double value = context.getParameter(globalParameterNames[i]);
-        if (globalParamValues[globalParameterNames[i]] != value)
+    for (auto& name : globalParameterNames) {
+        double value = context.getParameter(name);
+        if (globalParamValues[name] != value)
             globalParamsChanged = true;
-        globalParamValues[globalParameterNames[i]] = value;
+        globalParamValues[name] = value;
     }
     if (useSwitchingFunction)
         ixn.setUseSwitchingFunction(switchingDistance);
@@ -1459,8 +1459,8 @@ void ReferenceCalcCustomGBForceKernel::initialize(const System& system, const Cu
 
     // Delete the custom functions.
 
-    for (map<string, Lepton::CustomFunction*>::iterator iter = functions.begin(); iter != functions.end(); iter++)
-        delete iter->second;
+    for (auto& function : functions)
+        delete function.second;
 }
 
 double ReferenceCalcCustomGBForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
@@ -1477,8 +1477,8 @@ double ReferenceCalcCustomGBForceKernel::execute(ContextImpl& context, bool incl
         ixn.setUseCutoff(nonbondedCutoff, *neighborList);
     }
     map<string, double> globalParameters;
-    for (int i = 0; i < (int) globalParameterNames.size(); i++)
-        globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
+    for (auto& name : globalParameterNames)
+        globalParameters[name] = context.getParameter(name);
     vector<double> energyParamDerivValues(energyParamDerivNames.size()+1, 0.0);
     ixn.calculateIxn(numParticles, posData, particleParamArray, exclusions, globalParameters, forceData, includeEnergy ? &energy : NULL, &energyParamDerivValues[0]);
     map<string, double>& energyParamDerivs = extractEnergyParameterDerivatives(context);
@@ -1593,8 +1593,8 @@ double ReferenceCalcCustomExternalForceKernel::execute(ContextImpl& context, boo
     boxVectors = extractBoxVectors(context);
     double energy = 0;
     map<string, double> globalParameters;
-    for (int i = 0; i < (int) globalParameterNames.size(); i++)
-        globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
+    for (auto& name : globalParameterNames)
+        globalParameters[name] = context.getParameter(name);
     ReferenceCustomExternalIxn force(energyExpression, forceExpressionX, forceExpressionY, forceExpressionZ, parameterNames, globalParameters);
     for (int i = 0; i < numParticles; ++i)
         force.calculateForce(particles[i], posData, particleParamArray[i], forceData, includeEnergy ? &energy : NULL);
@@ -1699,8 +1699,8 @@ void ReferenceCalcCustomHbondForceKernel::initialize(const System& system, const
 
     // Delete the custom functions.
 
-    for (map<string, Lepton::CustomFunction*>::iterator iter = functions.begin(); iter != functions.end(); iter++)
-        delete iter->second;
+    for (auto& function : functions)
+        delete function.second;
 }
 
 double ReferenceCalcCustomHbondForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
@@ -1710,8 +1710,8 @@ double ReferenceCalcCustomHbondForceKernel::execute(ContextImpl& context, bool i
         ixn->setPeriodic(extractBoxVectors(context));
     double energy = 0;
     map<string, double> globalParameters;
-    for (int i = 0; i < (int) globalParameterNames.size(); i++)
-        globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
+    for (auto& name : globalParameterNames)
+        globalParameters[name] = context.getParameter(name);
     ixn->calculatePairIxn(posData, donorParamArray, acceptorParamArray, exclusions, globalParameters, forceData, includeEnergy ? &energy : NULL);
     return energy;
 }
@@ -1803,8 +1803,8 @@ void ReferenceCalcCustomCentroidBondForceKernel::initialize(const System& system
 
     // Delete the custom functions.
 
-    for (map<string, Lepton::CustomFunction*>::iterator iter = functions.begin(); iter != functions.end(); iter++)
-        delete iter->second;
+    for (auto& function : functions)
+        delete function.second;
 }
 
 double ReferenceCalcCustomCentroidBondForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
@@ -1812,8 +1812,8 @@ double ReferenceCalcCustomCentroidBondForceKernel::execute(ContextImpl& context,
     vector<Vec3>& forceData = extractForces(context);
     double energy = 0;
     map<string, double> globalParameters;
-    for (int i = 0; i < (int) globalParameterNames.size(); i++)
-        globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
+    for (auto& name : globalParameterNames)
+        globalParameters[name] = context.getParameter(name);
     if (usePeriodic)
         ixn->setPeriodic(extractBoxVectors(context));
     vector<double> energyParamDerivValues(energyParamDerivNames.size()+1, 0.0);
@@ -1893,8 +1893,8 @@ void ReferenceCalcCustomCompoundBondForceKernel::initialize(const System& system
 
     // Delete the custom functions.
 
-    for (map<string, Lepton::CustomFunction*>::iterator iter = functions.begin(); iter != functions.end(); iter++)
-        delete iter->second;
+    for (auto& function : functions)
+        delete function.second;
 }
 
 double ReferenceCalcCustomCompoundBondForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
@@ -1902,8 +1902,8 @@ double ReferenceCalcCustomCompoundBondForceKernel::execute(ContextImpl& context,
     vector<Vec3>& forceData = extractForces(context);
     double energy = 0;
     map<string, double> globalParameters;
-    for (int i = 0; i < (int) globalParameterNames.size(); i++)
-        globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
+    for (auto& name : globalParameterNames)
+        globalParameters[name] = context.getParameter(name);
     if (usePeriodic)
         ixn->setPeriodic(extractBoxVectors(context));
     vector<double> energyParamDerivValues(energyParamDerivNames.size()+1, 0.0);
@@ -1966,8 +1966,8 @@ double ReferenceCalcCustomManyParticleForceKernel::execute(ContextImpl& context,
     vector<Vec3>& forceData = extractForces(context);
     double energy = 0;
     map<string, double> globalParameters;
-    for (int i = 0; i < (int) globalParameterNames.size(); i++)
-        globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
+    for (auto& name : globalParameterNames)
+        globalParameters[name] = context.getParameter(name);
     if (nonbondedMethod == CutoffPeriodic) {
         Vec3* boxVectors = extractBoxVectors(context);
         double minAllowedSize = 2*cutoffDistance;
@@ -2232,8 +2232,8 @@ void ReferenceIntegrateCustomStepKernel::initialize(const System& system, const
     for (int i = 0; i < numParticles; ++i)
         masses[i] = system.getParticleMass(i);
     perDofValues.resize(integrator.getNumPerDofVariables());
-    for (int i = 0; i < (int) perDofValues.size(); i++)
-        perDofValues[i].resize(numParticles);
+    for (auto& values : perDofValues)
+        values.resize(numParticles);
 
     // Create the computation objects.