Use C++11 style loops

platforms/cpu/src/CpuBondForce.cpp

@@ -159,8 +159,8 @@ void CpuBondForce::assignBond(int bond, int thread, vector<int>& atomThread, vec
         if (atom != -1)
             throw OpenMMException("CpuBondForce: Internal error: atoms assigned to threads incorrectly");
         atom = thread;
-        for (set<int>::const_iterator iter = atomBonds[atom].begin(); iter != atomBonds[atom].end(); ++iter)
-            candidateBonds.push_back(*iter);
+        for (int bond : atomBonds[atom])
+            candidateBonds.push_back(bond);
     }
 }
 

platforms/cpu/src/CpuNeighborList.cpp

@@ -577,10 +577,10 @@ void CpuNeighborList::threadComputeNeighborList(ThreadPool& threads, int threadI
         for (int j = 0; j < atomsInBlock; j++) {
             const set<int>& atomExclusions = (*exclusions)[sortedAtoms[firstIndex+j]];
             char mask = 1<<j;
-            for (set<int>::const_iterator iter = atomExclusions.begin(); iter != atomExclusions.end(); ++iter) {
-                map<int, char>::iterator thisAtomFlags = atomFlags.find(*iter);
+            for (int exclusion : atomExclusions) {
+                map<int, char>::iterator thisAtomFlags = atomFlags.find(exclusion);
                 if (thisAtomFlags == atomFlags.end())
-                    atomFlags[*iter] = mask;
+                    atomFlags[exclusion] = mask;
                 else
                     thisAtomFlags->second |= mask;
             }

platforms/cpu/src/CpuNonbondedForce.cpp

@@ -447,9 +447,9 @@ void CpuNonbondedForce::threadComputeDirect(ThreadPool& threads, int threadIndex
             for (int i = start; i < end; i++) {
                 fvec4 posI((float) atomCoordinates[i][0], (float) atomCoordinates[i][1], (float) atomCoordinates[i][2], 0.0f);
                 float scaledChargeI = (float) (ONE_4PI_EPS0*posq[4*i+3]);
-                for (set<int>::const_iterator iter = exclusions[i].begin(); iter != exclusions[i].end(); ++iter) {
-                    if (*iter > i) {
-                        int j = *iter;
+                for (int excluded : exclusions[i]) {
+                    if (excluded > i) {
+                        int j = excluded;
                         fvec4 deltaR;
                         fvec4 posJ((float) atomCoordinates[j][0], (float) atomCoordinates[j][1], (float) atomCoordinates[j][2], 0.0f);
                         float r2;

platforms/cuda/src/CudaExpressionUtilities.cpp

@@ -456,12 +456,12 @@ void CudaExpressionUtilities::processExpression(stringstream& out, const Express
                 vector<bool> hasAssigned(powers.size(), false);
                 exponents.push_back((int) fabs(exponent));
                 names.push_back(name);
-                for (map<int, const ExpressionTreeNode*>::const_iterator iter = powers.begin(); iter != powers.end(); ++iter) {
-                    if (iter->first != exponent) {
-                        exponents.push_back(iter->first >= 0 ? iter->first : -iter->first);
+                for (auto& power : powers) {
+                    if (power.first != exponent) {
+                        exponents.push_back(power.first >= 0 ? power.first : -power.first);
                         string name2 = prefix+context.intToString(temps.size());
                         names.push_back(name2);
-                        temps.push_back(make_pair(*iter->second, name2));
+                        temps.push_back(make_pair(*power.second, name2));
                         out << tempType << " " << name2 << " = 0.0f;\n";
                     }
                 }

platforms/opencl/src/OpenCLBondedUtilities.cpp

@@ -184,8 +184,7 @@ void OpenCLBondedUtilities::initialize(const System& system) {
 
     // Create the kernels.
 
-    for (vector<vector<int> >::const_iterator iter = forceSets.begin(); iter != forceSets.end(); ++iter) {
-        const vector<int>& set = *iter;
+    for (auto& set : forceSets) {
         int setSize = set.size();
         stringstream s;
         s<<"#ifdef SUPPORTS_64_BIT_ATOMICS\n";

platforms/opencl/src/OpenCLExpressionUtilities.cpp

@@ -448,12 +448,12 @@ void OpenCLExpressionUtilities::processExpression(stringstream& out, const Expre
                 vector<bool> hasAssigned(powers.size(), false);
                 exponents.push_back((int) fabs(exponent));
                 names.push_back(name);
-                for (map<int, const ExpressionTreeNode*>::const_iterator iter = powers.begin(); iter != powers.end(); ++iter) {
-                    if (iter->first != exponent) {
-                        exponents.push_back(iter->first >= 0 ? iter->first : -iter->first);
+                for (auto& power : powers) {
+                    if (power.first != exponent) {
+                        exponents.push_back(power.first >= 0 ? power.first : -power.first);
                         string name2 = prefix+context.intToString(temps.size());
                         names.push_back(name2);
-                        temps.push_back(make_pair(*iter->second, name2));
+                        temps.push_back(make_pair(*power.second, name2));
                         out << tempType << " " << name2 << " = 0.0f;\n";
                     }
                 }

platforms/reference/src/SimTKReference/ReferenceCCMAAlgorithm.cpp

@@ -127,8 +127,8 @@ ReferenceCCMAAlgorithm::ReferenceCCMAAlgorithm(int numberOfAtoms,
                     // We didn't find one, so look for an angle force field term.
 
                     const vector<int>& angleCandidates = atomAngles[atomb];
-                    for (vector<int>::const_iterator iter = angleCandidates.begin(); iter != angleCandidates.end(); iter++) {
-                        const AngleInfo& angle = angles[*iter];
+                    for (int candidate : angleCandidates) {
+                        const AngleInfo& angle = angles[candidate];
                         if ((angle.atom1 == atoma && angle.atom3 == atomc) || (angle.atom3 == atoma && angle.atom1 == atomc)) {
                             matrix[j].push_back(pair<int, double>(k, scale*cos(angle.angle)));
                             break;

platforms/reference/src/SimTKReference/ReferenceLJCoulombIxn.cpp

@@ -488,10 +488,10 @@ void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<Vec3>& a
     double totalExclusionEnergy = 0.0f;
     const double TWO_OVER_SQRT_PI = 2/sqrt(PI_M);
     for (int i = 0; i < numberOfAtoms; i++)
-        for (set<int>::const_iterator iter = exclusions[i].begin(); iter != exclusions[i].end(); ++iter) {
-            if (*iter > i) {
+        for (int exclusion : exclusions[i]) {
+            if (exclusion > i) {
                 int ii = i;
-                int jj = *iter;
+                int jj = exclusion;
 
                 double deltaR[2][ReferenceForce::LastDeltaRIndex];
                 ReferenceForce::getDeltaR(atomCoordinates[jj], atomCoordinates[ii], deltaR[0]);