Use C++11 style loops

plugins/amoeba/openmmapi/src/AmoebaVdwForceImpl.cpp

@@ -161,14 +161,14 @@ double AmoebaVdwForceImpl::calcDispersionCorrection(const System& system, const
     // Double loop over different atom types.
     std::string sigmaCombiningRule = force.getSigmaCombiningRule();
     std::string epsilonCombiningRule = force.getEpsilonCombiningRule();
-    for (map<pair<double, double>, int>::const_iterator class1 = classCounts.begin(); class1 != classCounts.end(); ++class1) {
+    for (auto& class1 : classCounts) {
         k = 0;
-        for (map<pair<double, double>, int>::const_iterator class2 = classCounts.begin(); class2 != classCounts.end(); ++class2) { 
+        for (auto& class2 : classCounts) { 
             // AMOEBA combining rules, copied over from the CUDA code.
-            double iSigma = class1->first.first;
-            double jSigma = class2->first.first;
-            double iEpsilon = class1->first.second;
-            double jEpsilon = class2->first.second;
+            double iSigma = class1.first.first;
+            double jSigma = class2.first.first;
+            double iEpsilon = class1.first.second;
+            double jEpsilon = class2.first.second;
             // ARITHMETIC = 1
             // GEOMETRIC  = 2
             // CUBIC-MEAN = 3
@@ -207,7 +207,7 @@ double AmoebaVdwForceImpl::calcDispersionCorrection(const System& system, const
                 epsilon = 0.0;
               }
             }
-            int count = class1->second * class2->second;
+            int count = class1.second * class2.second;
             // Below is an exact copy of stuff from the previous block.
             double rv = sigma;
             double termik = 2.0 * M_PI * count; // termik is equivalent to 2 * pi * count.

plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.cpp

@@ -973,8 +973,8 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
         molecularQuadrupolesVec.push_back((float) quadrupole[5]);
     }
     hasQuadrupoles = false;
-    for (int i = 0; i < (int) molecularQuadrupolesVec.size(); i++)
-        if (molecularQuadrupolesVec[i] != 0.0)
+    for (auto q : molecularQuadrupolesVec)
+        if (q != 0.0)
             hasQuadrupoles = true;
     int paddedNumAtoms = cu.getPaddedNumAtoms();
     for (int i = numMultipoles; i < paddedNumAtoms; i++) {
@@ -1049,15 +1049,15 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
         allAtoms.insert(atoms.begin(), atoms.end());
         force.getCovalentMap(i, AmoebaMultipoleForce::Covalent13, atoms);
         allAtoms.insert(atoms.begin(), atoms.end());
-        for (set<int>::const_iterator iter = allAtoms.begin(); iter != allAtoms.end(); ++iter)
-            covalentFlagValues.push_back(make_int3(i, *iter, 0));
+        for (int atom : allAtoms)
+            covalentFlagValues.push_back(make_int3(i, atom, 0));
         force.getCovalentMap(i, AmoebaMultipoleForce::Covalent14, atoms);
         allAtoms.insert(atoms.begin(), atoms.end());
-        for (int j = 0; j < (int) atoms.size(); j++)
-            covalentFlagValues.push_back(make_int3(i, atoms[j], 1));
+        for (int atom : atoms)
+            covalentFlagValues.push_back(make_int3(i, atom, 1));
         force.getCovalentMap(i, AmoebaMultipoleForce::Covalent15, atoms);
-        for (int j = 0; j < (int) atoms.size(); j++)
-            covalentFlagValues.push_back(make_int3(i, atoms[j], 2));
+        for (int atom : atoms)
+            covalentFlagValues.push_back(make_int3(i, atom, 2));
         allAtoms.insert(atoms.begin(), atoms.end());
         force.getCovalentMap(i, AmoebaMultipoleForce::PolarizationCovalent11, atoms);
         allAtoms.insert(atoms.begin(), atoms.end());
@@ -1068,15 +1068,14 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
 
         vector<int> atoms12;
         force.getCovalentMap(i, AmoebaMultipoleForce::PolarizationCovalent12, atoms12);
-        for (int j = 0; j < (int) atoms.size(); j++)
-            if (find(atoms12.begin(), atoms12.end(), atoms[j]) == atoms12.end())
-                polarizationFlagValues.push_back(make_int2(i, atoms[j]));
+        for (int atom : atoms)
+            if (find(atoms12.begin(), atoms12.end(), atom) == atoms12.end())
+                polarizationFlagValues.push_back(make_int2(i, atom));
     }
     set<pair<int, int> > tilesWithExclusions;
     for (int atom1 = 0; atom1 < (int) exclusions.size(); ++atom1) {
         int x = atom1/CudaContext::TileSize;
-        for (int j = 0; j < (int) exclusions[atom1].size(); ++j) {
-            int atom2 = exclusions[atom1][j];
+        for (int atom2 : exclusions[atom1]) {
             int y = atom2/CudaContext::TileSize;
             tilesWithExclusions.insert(make_pair(max(x, y), min(x, y)));
         }
@@ -1412,10 +1411,10 @@ void CudaCalcAmoebaMultipoleForceKernel::initializeScaleFactors() {
     }
     covalentFlags = CudaArray::create<uint2>(cu, nb.getExclusions().getSize(), "covalentFlags");
     vector<uint2> covalentFlagsVec(nb.getExclusions().getSize(), make_uint2(0, 0));
-    for (int i = 0; i < (int) covalentFlagValues.size(); i++) {
-        int atom1 = covalentFlagValues[i].x;
-        int atom2 = covalentFlagValues[i].y;
-        int value = covalentFlagValues[i].z;
+    for (int3 values : covalentFlagValues) {
+        int atom1 = values.x;
+        int atom2 = values.y;
+        int value = values.z;
         int x = atom1/CudaContext::TileSize;
         int offset1 = atom1-x*CudaContext::TileSize;
         int y = atom2/CudaContext::TileSize;
@@ -1446,9 +1445,9 @@ void CudaCalcAmoebaMultipoleForceKernel::initializeScaleFactors() {
     
     polarizationGroupFlags = CudaArray::create<unsigned int>(cu, nb.getExclusions().getSize(), "polarizationGroupFlags");
     vector<unsigned int> polarizationGroupFlagsVec(nb.getExclusions().getSize(), 0);
-    for (int i = 0; i < (int) polarizationFlagValues.size(); i++) {
-        int atom1 = polarizationFlagValues[i].x;
-        int atom2 = polarizationFlagValues[i].y;
+    for (int2 values : polarizationFlagValues) {
+        int atom1 = values.x;
+        int atom2 = values.y;
         int x = atom1/CudaContext::TileSize;
         int offset1 = atom1-x*CudaContext::TileSize;
         int y = atom2/CudaContext::TileSize;
@@ -1473,10 +1472,12 @@ void CudaCalcAmoebaMultipoleForceKernel::initializeScaleFactors() {
 double CudaCalcAmoebaMultipoleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
     if (!hasInitializedScaleFactors) {
         initializeScaleFactors();
-        for (int i = 0; i < (int) context.getForceImpls().size() && gkKernel == NULL; i++) {
-            AmoebaGeneralizedKirkwoodForceImpl* gkImpl = dynamic_cast<AmoebaGeneralizedKirkwoodForceImpl*>(context.getForceImpls()[i]);
-            if (gkImpl != NULL)
+        for (auto impl : context.getForceImpls()) {
+            AmoebaGeneralizedKirkwoodForceImpl* gkImpl = dynamic_cast<AmoebaGeneralizedKirkwoodForceImpl*>(impl);
+            if (gkImpl != NULL) {
                 gkKernel = dynamic_cast<CudaCalcAmoebaGeneralizedKirkwoodForceKernel*>(&gkImpl->getKernel().getImpl());
+                break;
+            }
         }
     }
     CudaNonbondedUtilities& nb = cu.getNonbondedUtilities();
@@ -2232,8 +2233,8 @@ void CudaCalcAmoebaMultipoleForceKernel::copyParametersToContext(ContextImpl& co
         molecularQuadrupolesVec.push_back((float) quadrupole[5]);
     }
     if (!hasQuadrupoles) {
-        for (int i = 0; i < (int) molecularQuadrupolesVec.size(); i++)
-            if (molecularQuadrupolesVec[i] != 0.0)
+        for (auto q : molecularQuadrupolesVec)
+            if (q != 0.0)
                 throw OpenMMException("updateParametersInContext: Cannot set a non-zero quadrupole moment, because quadrupoles were excluded from the kernel");
     }
     for (int i = force.getNumMultipoles(); i < cu.getPaddedNumAtoms(); i++) {

plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaExtrapolatedPolarization.cpp

@@ -290,8 +290,8 @@ 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/cuda/tests/TestCudaAmoebaGeneralizedKirkwoodForce.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/platforms/cuda/tests/TestCudaAmoebaMultipoleForce.cpp

@@ -2919,8 +2919,8 @@ static void testNoQuadrupoles(bool usePme) {
         int axisType, atomX, atomY, atomZ;
         vector<double> dipole, quadrupole;
         amoebaMultipoleForce->getMultipoleParameters(i, charge, dipole, quadrupole, axisType, atomZ, atomX, atomY, thole, damping, polarity);
-        for (int j = 0; j < (int) quadrupole.size(); j++)
-            quadrupole[j] = 0;
+        for (auto& q : quadrupole)
+            q = 0;
         amoebaMultipoleForce->setMultipoleParameters(i, charge, dipole, quadrupole, axisType, atomZ, atomX, atomY, thole, damping, polarity);
     }
     amoebaMultipoleForce->updateParametersInContext(context);

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

@@ -206,18 +206,18 @@ void AmoebaReferenceMultipoleForce::setupScaleMaps(const vector< vector< vector<
         // pScale & mScale
 
         for (unsigned jj = 0; jj < AmoebaMultipoleForce::PolarizationCovalent11; jj++) {
-            const vector<int> covalentList    = covalentInfo[jj];
-            for (unsigned int kk = 0; kk < covalentList.size(); kk++) {
-                unsigned int covalentIndex             = static_cast<unsigned int>(covalentList[kk]);
-                if (covalentIndex < ii)continue;
+            for (int covalentIndex : covalentInfo[jj]) {
+                if (covalentIndex < ii)
+                    continue;
 
                 // handle 0.5 factor for p14
 
                 int hit = 0;
                 if (jj == AmoebaMultipoleForce::Covalent14) {
-                    for (unsigned int mm = 0; mm < covalentListP11.size() && hit == 0; mm++) {
-                        if (covalentListP11[mm]  == covalentIndex) {
+                    for (int mm : covalentListP11) {
+                        if (mm == covalentIndex) {
                             hit = 1;
+                            break;
                         }
                     }
                 }
@@ -231,9 +231,7 @@ void AmoebaReferenceMultipoleForce::setupScaleMaps(const vector< vector< vector<
         // dScale & uScale
 
         for (unsigned jj = AmoebaMultipoleForce::PolarizationCovalent11; jj < covalentInfo.size(); jj++) {
-            const vector<int> covalentList = covalentInfo[jj];
-            for (unsigned int kk = 0; kk < covalentList.size(); kk++) {
-                unsigned int covalentIndex             = static_cast<unsigned int>(covalentList[kk]);
+            for (int covalentIndex : covalentInfo[jj]) {
                 if (covalentIndex < ii)continue;
                 _scaleMaps[ii][D_SCALE][covalentIndex] = _dScale[jj-4];
                 _scaleMaps[ii][U_SCALE][covalentIndex] = _uScale[jj-4];
@@ -827,16 +825,16 @@ void AmoebaReferenceMultipoleForce::calculateInducedDipolePairIxns(const Multipo
     double rr3       = -rrI[0];
     double rr5       =  rrI[1];
 
-    for (unsigned int ii = 0; ii < updateInducedDipoleFields.size(); ii++) {
+    for (auto& field : updateInducedDipoleFields) {
         calculateInducedDipolePairIxn(particleI.particleIndex, particleJ.particleIndex, rr3, rr5, deltaR,
-                                       *updateInducedDipoleFields[ii].inducedDipoles, updateInducedDipoleFields[ii].inducedDipoleField);
+                                       *field.inducedDipoles, field.inducedDipoleField);
         if (getPolarizationType() == AmoebaReferenceMultipoleForce::Extrapolated) {
             // Compute and store the field gradient for later use.
             double dx = deltaR[0];
             double dy = deltaR[1];
             double dz = deltaR[2];
 
-            OpenMM::Vec3 &dipolesI = (*updateInducedDipoleFields[ii].inducedDipoles)[particleI.particleIndex];
+            OpenMM::Vec3 &dipolesI = (*field.inducedDipoles)[particleI.particleIndex];
             double xDipole = dipolesI[0];
             double yDipole = dipolesI[1];
             double zDipole = dipolesI[2];
@@ -848,14 +846,14 @@ void AmoebaReferenceMultipoleForce::calculateInducedDipolePairIxns(const Multipo
             double Exz = muDotR*dx*dz*rrI[2] - (xDipole*dz + zDipole*dx)*rrI[1];
             double Eyz = muDotR*dy*dz*rrI[2] - (yDipole*dz + zDipole*dy)*rrI[1];
 
-            updateInducedDipoleFields[ii].inducedDipoleFieldGradient[particleJ.particleIndex][0] -= Exx;
-            updateInducedDipoleFields[ii].inducedDipoleFieldGradient[particleJ.particleIndex][1] -= Eyy;
-            updateInducedDipoleFields[ii].inducedDipoleFieldGradient[particleJ.particleIndex][2] -= Ezz;
-            updateInducedDipoleFields[ii].inducedDipoleFieldGradient[particleJ.particleIndex][3] -= Exy;
-            updateInducedDipoleFields[ii].inducedDipoleFieldGradient[particleJ.particleIndex][4] -= Exz;
-            updateInducedDipoleFields[ii].inducedDipoleFieldGradient[particleJ.particleIndex][5] -= Eyz;
+            field.inducedDipoleFieldGradient[particleJ.particleIndex][0] -= Exx;
+            field.inducedDipoleFieldGradient[particleJ.particleIndex][1] -= Eyy;
+            field.inducedDipoleFieldGradient[particleJ.particleIndex][2] -= Ezz;
+            field.inducedDipoleFieldGradient[particleJ.particleIndex][3] -= Exy;
+            field.inducedDipoleFieldGradient[particleJ.particleIndex][4] -= Exz;
+            field.inducedDipoleFieldGradient[particleJ.particleIndex][5] -= Eyz;
 
-            OpenMM::Vec3 &dipolesJ = (*updateInducedDipoleFields[ii].inducedDipoles)[particleJ.particleIndex];
+            OpenMM::Vec3 &dipolesJ = (*field.inducedDipoles)[particleJ.particleIndex];
             xDipole = dipolesJ[0];
             yDipole = dipolesJ[1];
             zDipole = dipolesJ[2];
@@ -867,12 +865,12 @@ void AmoebaReferenceMultipoleForce::calculateInducedDipolePairIxns(const Multipo
             Exz = muDotR*dx*dz*rrI[2] - (xDipole*dz + zDipole*dx)*rrI[1];
             Eyz = muDotR*dy*dz*rrI[2] - (yDipole*dz + zDipole*dy)*rrI[1];
 
-            updateInducedDipoleFields[ii].inducedDipoleFieldGradient[particleI.particleIndex][0] += Exx;
-            updateInducedDipoleFields[ii].inducedDipoleFieldGradient[particleI.particleIndex][1] += Eyy;
-            updateInducedDipoleFields[ii].inducedDipoleFieldGradient[particleI.particleIndex][2] += Ezz;
-            updateInducedDipoleFields[ii].inducedDipoleFieldGradient[particleI.particleIndex][3] += Exy;
-            updateInducedDipoleFields[ii].inducedDipoleFieldGradient[particleI.particleIndex][4] += Exz;
-            updateInducedDipoleFields[ii].inducedDipoleFieldGradient[particleI.particleIndex][5] += Eyz;
+            field.inducedDipoleFieldGradient[particleI.particleIndex][0] += Exx;
+            field.inducedDipoleFieldGradient[particleI.particleIndex][1] += Eyy;
+            field.inducedDipoleFieldGradient[particleI.particleIndex][2] += Ezz;
+            field.inducedDipoleFieldGradient[particleI.particleIndex][3] += Exy;
+            field.inducedDipoleFieldGradient[particleI.particleIndex][4] += Exz;
+            field.inducedDipoleFieldGradient[particleI.particleIndex][5] += Eyz;
         }
     }
 }
@@ -881,8 +879,8 @@ void AmoebaReferenceMultipoleForce::calculateInducedDipoleFields(const vector<Mu
     // Initialize the fields to zero.
 
     Vec3 zeroVec(0.0, 0.0, 0.0);
-    for (unsigned int ii = 0; ii < updateInducedDipoleFields.size(); ii++)
-        std::fill(updateInducedDipoleFields[ii].inducedDipoleField.begin(), updateInducedDipoleFields[ii].inducedDipoleField.end(), zeroVec);
+    for (auto& field : updateInducedDipoleFields)
+        std::fill(field.inducedDipoleField.begin(), field.inducedDipoleField.end(), zeroVec);
 
     // Add fields from all induced dipoles.
 
@@ -901,11 +899,11 @@ double AmoebaReferenceMultipoleForce::updateInducedDipoleFields(const vector<Mul
     // Update the induced dipoles and calculate the convergence factor, maxEpsilon
 
     double maxEpsilon = 0.0;
-    for (unsigned int kk = 0; kk < updateInducedDipoleFields.size(); kk++) {
+    for (auto& field : updateInducedDipoleFields) {
         double epsilon = updateInducedDipole(particleData,
-                                             *updateInducedDipoleFields[kk].fixedMultipoleField,
-                                             updateInducedDipoleFields[kk].inducedDipoleField,
-                                             *updateInducedDipoleFields[kk].inducedDipoles);
+                                             *field.fixedMultipoleField,
+                                             field.inducedDipoleField,
+                                             *field.inducedDipoles);
 
         maxEpsilon = epsilon > maxEpsilon ? epsilon : maxEpsilon;
     }
@@ -1792,9 +1790,8 @@ double AmoebaReferenceMultipoleForce::calculateElectrostatic(const vector<Multip
 {
     double energy = 0.0;
     vector<double> scaleFactors(LAST_SCALE_TYPE_INDEX);
-    for (unsigned int kk = 0; kk < scaleFactors.size(); kk++) {
-        scaleFactors[kk] = 1.0;
-    }
+    for (auto& s : scaleFactors)
+        s = 1.0;
 
     // main loop over particle pairs
 
@@ -1971,9 +1968,7 @@ void AmoebaReferenceMultipoleForce::calculateLabFramePermanentDipoles(const vect
            multipoleAtomCovalentInfo, particleData);
     outputRotatedPermanentDipoles.resize(_numParticles);
     for (int i = 0; i < _numParticles; i++)
-      {
-      outputRotatedPermanentDipoles[i] = particleData[i].dipole;
-      }
+        outputRotatedPermanentDipoles[i] = particleData[i].dipole;
 }
 
 void AmoebaReferenceMultipoleForce::calculateTotalDipoles(const vector<Vec3>& particlePositions,
@@ -1997,12 +1992,8 @@ void AmoebaReferenceMultipoleForce::calculateTotalDipoles(const vector<Vec3>& pa
            multipoleAtomCovalentInfo, particleData);
     outputTotalDipoles.resize(_numParticles);
     for (int i = 0; i < _numParticles; i++)
-      {
-      for (int j = 0; j < 3; j++)
-        {
-        outputTotalDipoles[i][j] = particleData[i].dipole[j] + _inducedDipole[i][j];
-        }
-      }
+        for (int j = 0; j < 3; j++)
+            outputTotalDipoles[i][j] = particleData[i].dipole[j] + _inducedDipole[i][j];
 }
 
 void AmoebaReferenceMultipoleForce::calculateAmoebaSystemMultipoleMoments(const vector<double>& masses,
@@ -2173,9 +2164,8 @@ void AmoebaReferenceMultipoleForce::calculateElectrostaticPotential(const vector
            multipoleAtomCovalentInfo, particleData);
 
     potential.resize(grid.size());
-    for (unsigned int ii = 0; ii < grid.size(); ii++) {
-        potential[ii] = 0.0;
-    }
+    for (auto& p : potential)
+        p = 0.0;
 
     for (unsigned int ii = 0; ii < _numParticles; ii++) {
         for (unsigned int jj = 0; jj < grid.size(); jj++) {
@@ -2184,9 +2174,8 @@ void AmoebaReferenceMultipoleForce::calculateElectrostaticPotential(const vector
     }
 
     double term = _electric/_dielectric;
-    for (unsigned int ii = 0; ii < grid.size(); ii++) {
-        potential[ii] *= term;
-    }
+    for (auto& p : potential)
+        p *= term;
 }
 
 AmoebaReferenceMultipoleForce::UpdateInducedDipoleFieldStruct::UpdateInducedDipoleFieldStruct(vector<OpenMM::Vec3>& inputFixed_E_Field, vector<OpenMM::Vec3>& inputInducedDipoles, vector<vector<Vec3> >& extrapolatedDipoles, vector<vector<double> >& extrapolatedDipoleFieldGradient) :
@@ -4066,9 +4055,8 @@ double AmoebaReferenceGeneralizedKirkwoodMultipoleForce::calculateElectrostatic(
     // correct vacuum to SCRF derivatives (ediff1 in TINKER)
 
     vector<double> scaleFactors(LAST_SCALE_TYPE_INDEX);
-    for (unsigned int kk = 0; kk < scaleFactors.size(); kk++) {
-        scaleFactors[kk] = 1.0;
-    }
+    for (auto& s : scaleFactors)
+        s = 1.0;
 
     double eDiffEnergy = 0.0;
     for (unsigned int ii = 0; ii < particleData.size(); ii++) {
@@ -4082,9 +4070,8 @@ double AmoebaReferenceGeneralizedKirkwoodMultipoleForce::calculateElectrostatic(
                                                          scaleFactors[P_SCALE], scaleFactors[D_SCALE], forces, torques);
 
             if (jj <= _maxScaleIndex[ii]) {
-                for (unsigned int kk = 0; kk < LAST_SCALE_TYPE_INDEX; kk++) {
-                    scaleFactors[kk] = 1.0;
-                }
+                for (auto& s : scaleFactors)
+                    s = 1.0;
             }
         }
     }
@@ -5012,9 +4999,8 @@ void AmoebaReferencePmeMultipoleForce::initializePmeGrid()
     if (_pmeGrid == NULL)
         return;
 
-    for (int jj = 0; jj < _totalGridSize; jj++) {
+    for (int jj = 0; jj < _totalGridSize; jj++)
         _pmeGrid[jj].re = _pmeGrid[jj].im = 0.0;
-    }
 }
 
 void AmoebaReferencePmeMultipoleForce::getPeriodicDelta(Vec3& deltaR) const
@@ -5137,9 +5123,9 @@ void AmoebaReferencePmeMultipoleForce::initializeBSplineModuli()
             if (i > size/2)
                 k = k - size;
             double zeta;
-            if (k == 0) {
+            if (k == 0)
                 zeta = 1.0;
-            } else {
+            else {
                 double sum1 = 1.0;
                 double sum2 = 1.0;
                 factor = M_PI*k/size;
@@ -5270,9 +5256,9 @@ void AmoebaReferencePmeMultipoleForce::calculateFixedMultipoleField(const vector
 
     double term = (4.0/3.0)*(_alphaEwald*_alphaEwald*_alphaEwald)/SQRT_PI;
     for (unsigned int jj = 0; jj < _numParticles; jj++) {
-        Vec3 selfEnergy             = particleData[jj].dipole*term;
-        _fixedMultipoleField[jj]      += selfEnergy;
-        _fixedMultipoleFieldPolar[jj]  = _fixedMultipoleField[jj];
+        Vec3 selfEnergy = particleData[jj].dipole*term;
+        _fixedMultipoleField[jj] += selfEnergy;
+        _fixedMultipoleFieldPolar[jj] = _fixedMultipoleField[jj];
     }
 
     // include direct space fixed multipole fields
@@ -5307,9 +5293,8 @@ void AmoebaReferencePmeMultipoleForce::computeBSplinePoint(vector<double4>& thet
         int k = i - 1;
         double denom = 1.0 / k;
         ARRAY(i,i) = denom * w * ARRAY(k,k);
-        for (int j = 1; j <= i-2; j++) {
+        for (int j = 1; j <= i-2; j++)
             ARRAY(i,i-j) = denom * ((w+j)*ARRAY(k,i-j-1)+(i-j-w)*ARRAY(k,i-j));
-        }
         ARRAY(i,1) = denom * (1.0-w) * ARRAY(k,1);
     }
 
@@ -5351,9 +5336,8 @@ void AmoebaReferencePmeMultipoleForce::computeBSplinePoint(vector<double4>& thet
 
     // copy coefficients from temporary to permanent storage
 
-    for (int i = 1; i <= AMOEBA_PME_ORDER; i++) {
+    for (int i = 1; i <= AMOEBA_PME_ORDER; i++)
         thetai[i-1] = double4(ARRAY(AMOEBA_PME_ORDER,i), ARRAY(AMOEBA_PME_ORDER-1,i), ARRAY(AMOEBA_PME_ORDER-2,i), ARRAY(AMOEBA_PME_ORDER-3,i));
-    }
 }
 
 /**
@@ -5377,9 +5361,8 @@ void AmoebaReferencePmeMultipoleForce::computeAmoebaBsplines(const vector<Multip
             igrid[jj] += igrid[jj] < 0 ? _pmeGridDimensions[jj] : 0;
             vector<double4> thetaiTemp(AMOEBA_PME_ORDER);
             computeBSplinePoint(thetaiTemp, w);
-            for (unsigned int kk = 0; kk < AMOEBA_PME_ORDER; kk++) {
+            for (unsigned int kk = 0; kk < AMOEBA_PME_ORDER; kk++)
                 _thetai[jj][ii*AMOEBA_PME_ORDER+kk] = thetaiTemp[kk];
-            }
         }
 
         // Record the grid point.
@@ -6152,8 +6135,8 @@ void AmoebaReferencePmeMultipoleForce::calculateInducedDipoleFields(const vector
     // Initialize the fields to zero.
 
     Vec3 zeroVec(0.0, 0.0, 0.0);
-    for (unsigned int ii = 0; ii < updateInducedDipoleFields.size(); ii++)
-        std::fill(updateInducedDipoleFields[ii].inducedDipoleField.begin(), updateInducedDipoleFields[ii].inducedDipoleField.end(), zeroVec);
+    for (auto& field : updateInducedDipoleFields)
+        std::fill(field.inducedDipoleField.begin(), field.inducedDipoleField.end(), zeroVec);
 
     // Add fields from direct space interactions.
 
@@ -6232,11 +6215,11 @@ void AmoebaReferencePmeMultipoleForce::calculateInducedDipoleFields(const vector
     // self ixn
 
     double term = (4.0/3.0)*(_alphaEwald*_alphaEwald*_alphaEwald)/SQRT_PI;
-    for (unsigned int ii = 0; ii < updateInducedDipoleFields.size(); ii++) {
-        vector<Vec3>& inducedDipoles = *updateInducedDipoleFields[ii].inducedDipoles;
-        vector<Vec3>& field          = updateInducedDipoleFields[ii].inducedDipoleField;
+    for (auto& field : updateInducedDipoleFields) {
+        vector<Vec3>& inducedDipoles = *field.inducedDipoles;
+        vector<Vec3>& inducedDipoleField = field.inducedDipoleField;
         for (unsigned int jj = 0; jj < particleData.size(); jj++) {
-            field[jj] += inducedDipoles[jj]*term;
+            inducedDipoleField[jj] += inducedDipoles[jj]*term;
         }
     }
 }
@@ -6331,17 +6314,16 @@ void AmoebaReferencePmeMultipoleForce::calculateDirectInducedDipolePairIxns(cons
     double preFactor2  = bn2 - rr5;
     double preFactor3  = bn3 - rr7;
 
-    for (unsigned int ii = 0; ii < updateInducedDipoleFields.size(); ii++) {
+    for (auto& field : updateInducedDipoleFields) {
         calculateDirectInducedDipolePairIxn(particleI.particleIndex, particleJ.particleIndex, preFactor1, preFactor2, deltaR,
-                                            *updateInducedDipoleFields[ii].inducedDipoles,
-                                            updateInducedDipoleFields[ii].inducedDipoleField);
+                                            *field.inducedDipoles, field.inducedDipoleField);
         if (getPolarizationType() == AmoebaReferenceMultipoleForce::Extrapolated) {
             // Compute and store the field gradient for later use.
             double dx = deltaR[0];
             double dy = deltaR[1];
             double dz = deltaR[2];
 
-            OpenMM::Vec3 &dipolesI = (*updateInducedDipoleFields[ii].inducedDipoles)[particleI.particleIndex];
+            OpenMM::Vec3 &dipolesI = (*field.inducedDipoles)[particleI.particleIndex];
             double xDipole = dipolesI[0];
             double yDipole = dipolesI[1];
             double zDipole = dipolesI[2];
@@ -6353,14 +6335,14 @@ void AmoebaReferencePmeMultipoleForce::calculateDirectInducedDipolePairIxns(cons
             double Exz = muDotR*dx*dz*preFactor3 - (xDipole*dz + zDipole*dx)*preFactor2;
             double Eyz = muDotR*dy*dz*preFactor3 - (yDipole*dz + zDipole*dy)*preFactor2;
 
-            updateInducedDipoleFields[ii].inducedDipoleFieldGradient[particleJ.particleIndex][0] -= Exx;
-            updateInducedDipoleFields[ii].inducedDipoleFieldGradient[particleJ.particleIndex][1] -= Eyy;
-            updateInducedDipoleFields[ii].inducedDipoleFieldGradient[particleJ.particleIndex][2] -= Ezz;
-            updateInducedDipoleFields[ii].inducedDipoleFieldGradient[particleJ.particleIndex][3] -= Exy;
-            updateInducedDipoleFields[ii].inducedDipoleFieldGradient[particleJ.particleIndex][4] -= Exz;
-            updateInducedDipoleFields[ii].inducedDipoleFieldGradient[particleJ.particleIndex][5] -= Eyz;
+            field.inducedDipoleFieldGradient[particleJ.particleIndex][0] -= Exx;
+            field.inducedDipoleFieldGradient[particleJ.particleIndex][1] -= Eyy;
+            field.inducedDipoleFieldGradient[particleJ.particleIndex][2] -= Ezz;
+            field.inducedDipoleFieldGradient[particleJ.particleIndex][3] -= Exy;
+            field.inducedDipoleFieldGradient[particleJ.particleIndex][4] -= Exz;
+            field.inducedDipoleFieldGradient[particleJ.particleIndex][5] -= Eyz;
 
-            OpenMM::Vec3 &dipolesJ = (*updateInducedDipoleFields[ii].inducedDipoles)[particleJ.particleIndex];
+            OpenMM::Vec3 &dipolesJ = (*field.inducedDipoles)[particleJ.particleIndex];
             xDipole = dipolesJ[0];
             yDipole = dipolesJ[1];
             zDipole = dipolesJ[2];
@@ -6372,12 +6354,12 @@ void AmoebaReferencePmeMultipoleForce::calculateDirectInducedDipolePairIxns(cons
             Exz = muDotR*dx*dz*preFactor3 - (xDipole*dz + zDipole*dx)*preFactor2;
             Eyz = muDotR*dy*dz*preFactor3 - (yDipole*dz + zDipole*dy)*preFactor2;
 
-            updateInducedDipoleFields[ii].inducedDipoleFieldGradient[particleI.particleIndex][0] += Exx;
-            updateInducedDipoleFields[ii].inducedDipoleFieldGradient[particleI.particleIndex][1] += Eyy;
-            updateInducedDipoleFields[ii].inducedDipoleFieldGradient[particleI.particleIndex][2] += Ezz;
-            updateInducedDipoleFields[ii].inducedDipoleFieldGradient[particleI.particleIndex][3] += Exy;
-            updateInducedDipoleFields[ii].inducedDipoleFieldGradient[particleI.particleIndex][4] += Exz;
-            updateInducedDipoleFields[ii].inducedDipoleFieldGradient[particleI.particleIndex][5] += Eyz;
+            field.inducedDipoleFieldGradient[particleI.particleIndex][0] += Exx;
+            field.inducedDipoleFieldGradient[particleI.particleIndex][1] += Eyy;
+            field.inducedDipoleFieldGradient[particleI.particleIndex][2] += Ezz;
+            field.inducedDipoleFieldGradient[particleI.particleIndex][3] += Exy;
+            field.inducedDipoleFieldGradient[particleI.particleIndex][4] += Exz;
+            field.inducedDipoleFieldGradient[particleI.particleIndex][5] += Eyz;
         }
     }
 }
@@ -6846,9 +6828,8 @@ double AmoebaReferencePmeMultipoleForce::calculateElectrostatic(const vector<Mul
 {
     double energy = 0.0;
     vector<double> scaleFactors(LAST_SCALE_TYPE_INDEX);
-    for (unsigned int kk = 0; kk < scaleFactors.size(); kk++) {
-        scaleFactors[kk] = 1.0;
-    }
+    for (auto& s : scaleFactors)
+        s = 1.0;
 
     // loop over particle pairs for direct space interactions
 
@@ -6862,9 +6843,8 @@ double AmoebaReferencePmeMultipoleForce::calculateElectrostatic(const vector<Mul
             energy += calculatePmeDirectElectrostaticPairIxn(particleData[ii], particleData[jj], scaleFactors, forces, torques);
 
             if (jj <= _maxScaleIndex[ii]) {
-                for (unsigned int kk = 0; kk < LAST_SCALE_TYPE_INDEX; kk++) {
-                    scaleFactors[kk] = 1.0;
-                }
+                for (auto& s : scaleFactors)
+                    s = 1.0;
             }
         }
     }

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.