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/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.