Merge branch 'master' of https://github.com/rafwiewiora/openmm

platforms/cuda/src/kernels/customHbondForce.cu

@@ -105,8 +105,8 @@ extern "C" __global__ void computeDonorForces(unsigned long long* __restrict__ f
             __syncthreads();
             if (donorIndex < NUM_DONORS) {
                 for (int index = 0; index < blockSize; index++) {
-#ifdef USE_EXCLUSIONS
                     int acceptorIndex = acceptorStart+index;
+#ifdef USE_EXCLUSIONS
                     if (acceptorIndex == exclusionIndices.x || acceptorIndex == exclusionIndices.y || acceptorIndex == exclusionIndices.z || acceptorIndex == exclusionIndices.w)
                         continue;
 #endif
@@ -193,8 +193,8 @@ extern "C" __global__ void computeAcceptorForces(unsigned long long* __restrict_
             __syncthreads();
             if (acceptorIndex < NUM_ACCEPTORS) {
                 for (int index = 0; index < blockSize; index++) {
-#ifdef USE_EXCLUSIONS
                     int donorIndex = donorStart+index;
+#ifdef USE_EXCLUSIONS
                     if (donorIndex == exclusionIndices.x || donorIndex == exclusionIndices.y || donorIndex == exclusionIndices.z || donorIndex == exclusionIndices.w)
                         continue;
 #endif

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/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/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/opencl/src/kernels/customHbondForce.cl

@@ -91,8 +91,8 @@ __kernel void computeDonorForces(__global real4* restrict forceBuffers, __global
             barrier(CLK_LOCAL_MEM_FENCE);
             if (donorIndex < NUM_DONORS) {
                 for (int index = 0; index < blockSize; index++) {
-#ifdef USE_EXCLUSIONS
                     int acceptorIndex = acceptorStart+index;
+#ifdef USE_EXCLUSIONS
                     if (acceptorIndex == exclusionIndices.x || acceptorIndex == exclusionIndices.y || acceptorIndex == exclusionIndices.z || acceptorIndex == exclusionIndices.w)
                         continue;
 #endif
@@ -179,8 +179,8 @@ __kernel void computeAcceptorForces(__global real4* restrict forceBuffers, __glo
             barrier(CLK_LOCAL_MEM_FENCE);
             if (acceptorIndex < NUM_ACCEPTORS) {
                 for (int index = 0; index < blockSize; index++) {
-#ifdef USE_EXCLUSIONS
                     int donorIndex = donorStart+index;
+#ifdef USE_EXCLUSIONS
                     if (donorIndex == exclusionIndices.x || donorIndex == exclusionIndices.y || donorIndex == exclusionIndices.z || donorIndex == exclusionIndices.w)
                         continue;
 #endif

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.
 

platforms/reference/src/SimTKReference/ReferenceAndersenThermostat.cpp

@@ -66,13 +66,12 @@ using namespace OpenMM;
               double temperature, double collisionFrequency, double stepSize) const {
           
           const double collisionProbability = 1.0f - exp(-collisionFrequency*stepSize);
-          for (int i = 0; i < (int) atomGroups.size(); ++i) {
+          for (auto& group : atomGroups) {
               if (SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber() < collisionProbability) {
                   
                   // A collision occurred, so set the velocities to new values chosen from a Boltzmann distribution.
 
-                  for (int j = 0; j < (int) atomGroups[i].size(); j++) {
-                      int atom = atomGroups[i][j];
+                  for (int atom : group) {
                       if (atomMasses[atom] != 0) {
                           const double velocityScale = static_cast<double>(sqrt(BOLTZ*temperature/atomMasses[atom]));
                           atomVelocities[atom][0] = velocityScale*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();

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;
@@ -145,8 +145,7 @@ ReferenceCCMAAlgorithm::ReferenceCCMAAlgorithm(int numberOfAtoms,
         vector<double> matrixValue;
         for (int i = 0; i < numberOfConstraints; i++) {
             matrixRowStart.push_back(matrixValue.size());
-            for (int j = 0; j < (int) matrix[i].size(); j++) {
-                pair<int, double> element = matrix[i][j];
+            for (auto& element : matrix[i]) {
                 matrixColIndex.push_back(element.first);
                 matrixValue.push_back(element.second);
             }
@@ -292,10 +291,8 @@ void ReferenceCCMAAlgorithm::applyConstraints(vector<Vec3>& atomCoordinates,
         if (_matrix.size() > 0) {
             for (int i = 0; i < _numberOfConstraints; i++) {
                 double sum = 0.0;
-                for (int j = 0; j < (int) _matrix[i].size(); j++) {
-                    pair<int, double> element = _matrix[i][j];
+                for (auto& element : _matrix[i])
                     sum += element.second*constraintDelta[element.first];
-                }
                 tempDelta[i] = sum;
             }
             constraintDelta = tempDelta;

platforms/reference/src/SimTKReference/ReferenceCustomAngleIxn.cpp

@@ -47,10 +47,10 @@ ReferenceCustomAngleIxn::ReferenceCustomAngleIxn(const Lepton::CompiledExpressio
         expressionSet.registerExpression(this->energyParamDerivExpressions[i]);
     thetaIndex = expressionSet.getVariableIndex("theta");
     numParameters = parameterNames.size();
-    for (int i = 0; i < (int) numParameters; i++)
-        angleParamIndex.push_back(expressionSet.getVariableIndex(parameterNames[i]));
-    for (map<string, double>::const_iterator iter = globalParameters.begin(); iter != globalParameters.end(); ++iter)
-        expressionSet.setVariable(expressionSet.getVariableIndex(iter->first), iter->second);
+    for (auto& param : parameterNames)
+        angleParamIndex.push_back(expressionSet.getVariableIndex(param));
+    for (auto& param : globalParameters)
+        expressionSet.setVariable(expressionSet.getVariableIndex(param.first), param.second);
 }
 
 /**---------------------------------------------------------------------------------------

platforms/reference/src/SimTKReference/ReferenceCustomBondIxn.cpp

@@ -48,10 +48,10 @@ ReferenceCustomBondIxn::ReferenceCustomBondIxn(const Lepton::CompiledExpression&
         expressionSet.registerExpression(this->energyParamDerivExpressions[i]);
     rIndex = expressionSet.getVariableIndex("r");
     numParameters = parameterNames.size();
-    for (int i = 0; i < (int) numParameters; i++)
-        bondParamIndex.push_back(expressionSet.getVariableIndex(parameterNames[i]));
-    for (map<string, double>::const_iterator iter = globalParameters.begin(); iter != globalParameters.end(); ++iter)
-        expressionSet.setVariable(expressionSet.getVariableIndex(iter->first), iter->second);
+    for (auto& param : parameterNames)
+        bondParamIndex.push_back(expressionSet.getVariableIndex(param));
+    for (auto& param : globalParameters)
+        expressionSet.setVariable(expressionSet.getVariableIndex(param.first), param.second);
 }
 
 /**---------------------------------------------------------------------------------------

platforms/reference/src/SimTKReference/ReferenceCustomCentroidBondIxn.cpp

@@ -56,12 +56,12 @@ ReferenceCustomCentroidBondIxn::ReferenceCustomCentroidBondIxn(int numGroupsPerB
         positionTerms.push_back(ReferenceCustomCentroidBondIxn::PositionTermInfo(yname.str(), i, 1, energyExpression.differentiate(yname.str()).createCompiledExpression()));
         positionTerms.push_back(ReferenceCustomCentroidBondIxn::PositionTermInfo(zname.str(), i, 2, energyExpression.differentiate(zname.str()).createCompiledExpression()));
     }
-    for (map<string, vector<int> >::const_iterator iter = distances.begin(); iter != distances.end(); ++iter)
-        distanceTerms.push_back(ReferenceCustomCentroidBondIxn::DistanceTermInfo(iter->first, iter->second, energyExpression.differentiate(iter->first).createCompiledExpression()));
-    for (map<string, vector<int> >::const_iterator iter = angles.begin(); iter != angles.end(); ++iter)
-        angleTerms.push_back(ReferenceCustomCentroidBondIxn::AngleTermInfo(iter->first, iter->second, energyExpression.differentiate(iter->first).createCompiledExpression()));
-    for (map<string, vector<int> >::const_iterator iter = dihedrals.begin(); iter != dihedrals.end(); ++iter)
-        dihedralTerms.push_back(ReferenceCustomCentroidBondIxn::DihedralTermInfo(iter->first, iter->second, energyExpression.differentiate(iter->first).createCompiledExpression()));
+    for (auto& term : distances)
+        distanceTerms.push_back(ReferenceCustomCentroidBondIxn::DistanceTermInfo(term.first, term.second, energyExpression.differentiate(term.first).createCompiledExpression()));
+    for (auto& term : angles)
+        angleTerms.push_back(ReferenceCustomCentroidBondIxn::AngleTermInfo(term.first, term.second, energyExpression.differentiate(term.first).createCompiledExpression()));
+    for (auto& term : dihedrals)
+        dihedralTerms.push_back(ReferenceCustomCentroidBondIxn::DihedralTermInfo(term.first, term.second, energyExpression.differentiate(term.first).createCompiledExpression()));
     for (int i = 0; i < positionTerms.size(); i++) {
         expressionSet.registerExpression(positionTerms[i].forceExpression);
         positionTerms[i].index = expressionSet.getVariableIndex(positionTerms[i].name);
@@ -108,8 +108,8 @@ void ReferenceCustomCentroidBondIxn::calculatePairIxn(vector<Vec3>& atomCoordina
 
     // Compute the forces on groups.
 
-    for (map<string, double>::const_iterator iter = globalParameters.begin(); iter != globalParameters.end(); ++iter)
-        expressionSet.setVariable(expressionSet.getVariableIndex(iter->first), iter->second);
+    for (auto& param : globalParameters)
+        expressionSet.setVariable(expressionSet.getVariableIndex(param.first), param.second);
     vector<Vec3> groupForces(numGroups);
     int numBonds = bondGroups.size();
     for (int bond = 0; bond < numBonds; bond++) {
@@ -131,23 +131,18 @@ void ReferenceCustomCentroidBondIxn::calculateOneIxn(int bond, vector<Vec3>& gro
     // Compute all of the variables the energy can depend on.
 
     const vector<int>& groups = bondGroups[bond];
-    for (int i = 0; i < (int) positionTerms.size(); i++) {
-        const PositionTermInfo& term = positionTerms[i];
+    for (auto& term : positionTerms)
         expressionSet.setVariable(term.index, groupCenters[groups[term.group]][term.component]);
-    }
-    for (int i = 0; i < (int) distanceTerms.size(); i++) {
-        const DistanceTermInfo& term = distanceTerms[i];
+    for (auto& term : distanceTerms) {
         computeDelta(groups[term.g1], groups[term.g2], term.delta, groupCenters);
         expressionSet.setVariable(term.index, term.delta[ReferenceForce::RIndex]);
     }
-    for (int i = 0; i < (int) angleTerms.size(); i++) {
-        const AngleTermInfo& term = angleTerms[i];
+    for (auto& term : angleTerms) {
         computeDelta(groups[term.g1], groups[term.g2], term.delta1, groupCenters);
         computeDelta(groups[term.g3], groups[term.g2], term.delta2, groupCenters);
         expressionSet.setVariable(term.index, computeAngle(term.delta1, term.delta2));
     }
-    for (int i = 0; i < (int) dihedralTerms.size(); i++) {
-        const DihedralTermInfo& term = dihedralTerms[i];
+    for (auto& term : dihedralTerms) {
         computeDelta(groups[term.g2], groups[term.g1], term.delta1, groupCenters);
         computeDelta(groups[term.g2], groups[term.g3], term.delta2, groupCenters);
         computeDelta(groups[term.g4], groups[term.g3], term.delta3, groupCenters);
@@ -158,15 +153,12 @@ void ReferenceCustomCentroidBondIxn::calculateOneIxn(int bond, vector<Vec3>& gro
 
     // Apply forces based on individual particle coordinates.
 
-    for (int i = 0; i < (int) positionTerms.size(); i++) {
-        const PositionTermInfo& term = positionTerms[i];
+    for (auto& term : positionTerms)
         forces[groups[term.group]][term.component] -= term.forceExpression.evaluate();
-    }
 
     // Apply forces based on distances.
 
-    for (int i = 0; i < (int) distanceTerms.size(); i++) {
-        const DistanceTermInfo& term = distanceTerms[i];
+    for (auto& term : distanceTerms) {
         double dEdR = term.forceExpression.evaluate()/(term.delta[ReferenceForce::RIndex]);
         for (int i = 0; i < 3; i++) {
            double force  = -dEdR*term.delta[i];
@@ -177,8 +169,7 @@ void ReferenceCustomCentroidBondIxn::calculateOneIxn(int bond, vector<Vec3>& gro
 
     // Apply forces based on angles.
 
-    for (int i = 0; i < (int) angleTerms.size(); i++) {
-        const AngleTermInfo& term = angleTerms[i];
+    for (auto& term : angleTerms) {
         double dEdTheta = term.forceExpression.evaluate();
         double thetaCross[ReferenceForce::LastDeltaRIndex];
         SimTKOpenMMUtilities::crossProductVector3(term.delta1, term.delta2, thetaCross);
@@ -204,8 +195,7 @@ void ReferenceCustomCentroidBondIxn::calculateOneIxn(int bond, vector<Vec3>& gro
 
     // Apply forces based on dihedrals.
 
-    for (int i = 0; i < (int) dihedralTerms.size(); i++) {
-        const DihedralTermInfo& term = dihedralTerms[i];
+    for (auto& term : dihedralTerms) {
         double dEdTheta = term.forceExpression.evaluate();
         double internalF[4][3];
         double forceFactors[4];

platforms/reference/src/SimTKReference/ReferenceCustomCompoundBondIxn.cpp

@@ -61,12 +61,12 @@ ReferenceCustomCompoundBondIxn::ReferenceCustomCompoundBondIxn(int numParticlesP
         particleTerms.push_back(ReferenceCustomCompoundBondIxn::ParticleTermInfo(yname.str(), i, 1, energyExpression.differentiate(yname.str()).createCompiledExpression()));
         particleTerms.push_back(ReferenceCustomCompoundBondIxn::ParticleTermInfo(zname.str(), i, 2, energyExpression.differentiate(zname.str()).createCompiledExpression()));
     }
-    for (map<string, vector<int> >::const_iterator iter = distances.begin(); iter != distances.end(); ++iter)
-        distanceTerms.push_back(ReferenceCustomCompoundBondIxn::DistanceTermInfo(iter->first, iter->second, energyExpression.differentiate(iter->first).createCompiledExpression()));
-    for (map<string, vector<int> >::const_iterator iter = angles.begin(); iter != angles.end(); ++iter)
-        angleTerms.push_back(ReferenceCustomCompoundBondIxn::AngleTermInfo(iter->first, iter->second, energyExpression.differentiate(iter->first).createCompiledExpression()));
-    for (map<string, vector<int> >::const_iterator iter = dihedrals.begin(); iter != dihedrals.end(); ++iter)
-        dihedralTerms.push_back(ReferenceCustomCompoundBondIxn::DihedralTermInfo(iter->first, iter->second, energyExpression.differentiate(iter->first).createCompiledExpression()));
+    for (auto& term : distances)
+        distanceTerms.push_back(ReferenceCustomCompoundBondIxn::DistanceTermInfo(term.first, term.second, energyExpression.differentiate(term.first).createCompiledExpression()));
+    for (auto& term : angles)
+        angleTerms.push_back(ReferenceCustomCompoundBondIxn::AngleTermInfo(term.first, term.second, energyExpression.differentiate(term.first).createCompiledExpression()));
+    for (auto& term : dihedrals)
+        dihedralTerms.push_back(ReferenceCustomCompoundBondIxn::DihedralTermInfo(term.first, term.second, energyExpression.differentiate(term.first).createCompiledExpression()));
     for (int i = 0; i < particleTerms.size(); i++) {
         expressionSet.registerExpression(particleTerms[i].forceExpression);
         particleTerms[i].index = expressionSet.getVariableIndex(particleTerms[i].name);
@@ -119,8 +119,8 @@ void ReferenceCustomCompoundBondIxn::setPeriodic(OpenMM::Vec3* vectors) {
 void ReferenceCustomCompoundBondIxn::calculatePairIxn(vector<Vec3>& atomCoordinates, double** bondParameters,
                                              const map<string, double>& globalParameters, vector<Vec3>& forces,
                                              double* totalEnergy, double* energyParamDerivs) {
-    for (map<string, double>::const_iterator iter = globalParameters.begin(); iter != globalParameters.end(); ++iter)
-        expressionSet.setVariable(expressionSet.getVariableIndex(iter->first), iter->second);
+    for (auto& param : globalParameters)
+        expressionSet.setVariable(expressionSet.getVariableIndex(param.first), param.second);
     int numBonds = bondAtoms.size();
     for (int bond = 0; bond < numBonds; bond++) {
         for (int i = 0; i < numParameters; i++)
@@ -146,23 +146,18 @@ void ReferenceCustomCompoundBondIxn::calculateOneIxn(int bond, vector<Vec3>& ato
     // Compute all of the variables the energy can depend on.
 
     const vector<int>& atoms = bondAtoms[bond];
-    for (int i = 0; i < (int) particleTerms.size(); i++) {
-        const ParticleTermInfo& term = particleTerms[i];
+    for (auto& term : particleTerms)
         expressionSet.setVariable(term.index, atomCoordinates[atoms[term.atom]][term.component]);
-    }
-    for (int i = 0; i < (int) distanceTerms.size(); i++) {
-        const DistanceTermInfo& term = distanceTerms[i];
+    for (auto& term : distanceTerms) {
         computeDelta(atoms[term.p1], atoms[term.p2], term.delta, atomCoordinates);
         expressionSet.setVariable(term.index, term.delta[ReferenceForce::RIndex]);
     }
-    for (int i = 0; i < (int) angleTerms.size(); i++) {
-        const AngleTermInfo& term = angleTerms[i];
+    for (auto& term : angleTerms) {
         computeDelta(atoms[term.p1], atoms[term.p2], term.delta1, atomCoordinates);
         computeDelta(atoms[term.p3], atoms[term.p2], term.delta2, atomCoordinates);
         expressionSet.setVariable(term.index, computeAngle(term.delta1, term.delta2));
     }
-    for (int i = 0; i < (int) dihedralTerms.size(); i++) {
-        const DihedralTermInfo& term = dihedralTerms[i];
+    for (auto& term : dihedralTerms) {
         computeDelta(atoms[term.p2], atoms[term.p1], term.delta1, atomCoordinates);
         computeDelta(atoms[term.p2], atoms[term.p3], term.delta2, atomCoordinates);
         computeDelta(atoms[term.p4], atoms[term.p3], term.delta3, atomCoordinates);
@@ -173,15 +168,12 @@ void ReferenceCustomCompoundBondIxn::calculateOneIxn(int bond, vector<Vec3>& ato
     
     // Apply forces based on individual particle coordinates.
     
-    for (int i = 0; i < (int) particleTerms.size(); i++) {
-        const ParticleTermInfo& term = particleTerms[i];
+    for (auto& term : particleTerms)
         forces[atoms[term.atom]][term.component] -= term.forceExpression.evaluate();
-    }
 
     // Apply forces based on distances.
 
-    for (int i = 0; i < (int) distanceTerms.size(); i++) {
-        const DistanceTermInfo& term = distanceTerms[i];
+    for (auto& term : distanceTerms) {
         double dEdR = term.forceExpression.evaluate()/(term.delta[ReferenceForce::RIndex]);
         for (int i = 0; i < 3; i++) {
            double force  = -dEdR*term.delta[i];
@@ -192,8 +184,7 @@ void ReferenceCustomCompoundBondIxn::calculateOneIxn(int bond, vector<Vec3>& ato
 
     // Apply forces based on angles.
 
-    for (int i = 0; i < (int) angleTerms.size(); i++) {
-        const AngleTermInfo& term = angleTerms[i];
+    for (auto& term : angleTerms) {
         double dEdTheta = term.forceExpression.evaluate();
         double thetaCross[ReferenceForce::LastDeltaRIndex];
         SimTKOpenMMUtilities::crossProductVector3(term.delta1, term.delta2, thetaCross);
@@ -219,8 +210,7 @@ void ReferenceCustomCompoundBondIxn::calculateOneIxn(int bond, vector<Vec3>& ato
 
     // Apply forces based on dihedrals.
 
-    for (int i = 0; i < (int) dihedralTerms.size(); i++) {
-        const DihedralTermInfo& term = dihedralTerms[i];
+    for (auto& term : dihedralTerms) {
         double dEdTheta = term.forceExpression.evaluate();
         double internalF[4][3];
         double forceFactors[4];

platforms/reference/src/SimTKReference/ReferenceCustomDynamics.cpp

@@ -175,8 +175,8 @@ ExpressionTreeNode ReferenceCustomDynamics::replaceDerivFunctions(const Expressi
     }
     else {
         vector<ExpressionTreeNode> children;
-        for (int i = 0; i < (int) node.getChildren().size(); i++)
-            children.push_back(replaceDerivFunctions(node.getChildren()[i], context));
+        for (auto& child : node.getChildren())
+            children.push_back(replaceDerivFunctions(child, context));
         return ExpressionTreeNode(op.clone(), children);
     }
 }
@@ -204,8 +204,8 @@ void ReferenceCustomDynamics::update(ContextImpl& context, int numberOfAtoms, ve
         initialize(context, masses, globals);
     int numSteps = stepType.size();
     globals.insert(context.getParameters().begin(), context.getParameters().end());
-    for (map<string, double>::const_iterator iter = globals.begin(); iter != globals.end(); ++iter)
-        expressionSet.setVariable(expressionSet.getVariableIndex(iter->first), iter->second);
+    for (auto& global : globals)
+        expressionSet.setVariable(expressionSet.getVariableIndex(global.first), global.second);
     oldPos = atomCoordinates;
     
     // Loop over steps and execute them.
@@ -276,8 +276,8 @@ void ReferenceCustomDynamics::update(ContextImpl& context, int numberOfAtoms, ve
                 recordChangedParameters(context, globals);
                 context.updateContextState();
                 globals.insert(context.getParameters().begin(), context.getParameters().end());
-                for (map<string, double>::const_iterator iter = globals.begin(); iter != globals.end(); ++iter)
-                    expressionSet.setVariable(expressionSet.getVariableIndex(iter->first), iter->second);
+                for (auto& global : globals)
+                    expressionSet.setVariable(expressionSet.getVariableIndex(global.first), global.second);
                 break;
             }
             case CustomIntegrator::IfBlockStart: {
@@ -355,10 +355,10 @@ bool ReferenceCustomDynamics::evaluateCondition(int step) {
  * Check which context parameters have changed and register them with the context.
  */
 void ReferenceCustomDynamics::recordChangedParameters(OpenMM::ContextImpl& context, std::map<std::string, double>& globals) {
-    for (map<string, double>::const_iterator iter = context.getParameters().begin(); iter != context.getParameters().end(); ++iter) {
-        string name = iter->first;
+    for (auto& param : context.getParameters()) {
+        string name = param.first;
         double value = globals[name];
-        if (value != iter->second)
+        if (value != param.second)
             context.setParameter(name, globals[name]);
     }
 }
@@ -385,8 +385,8 @@ double ReferenceCustomDynamics::computeKineticEnergy(OpenMM::ContextImpl& contex
     if (invalidatesForces.size() == 0)
         initialize(context, masses, globals);
     globals.insert(context.getParameters().begin(), context.getParameters().end());
-    for (map<string, double>::const_iterator iter = globals.begin(); iter != globals.end(); ++iter)
-        expressionSet.setVariable(expressionSet.getVariableIndex(iter->first), iter->second);
+    for (auto& global : globals)
+        expressionSet.setVariable(expressionSet.getVariableIndex(global.first), global.second);
     if (kineticEnergyNeedsForce) {
         energy = context.calcForcesAndEnergy(true, true, -1);
         forcesAreValid = true;

platforms/reference/src/SimTKReference/ReferenceCustomExternalIxn.cpp

@@ -57,17 +57,17 @@ ReferenceCustomExternalIxn::ReferenceCustomExternalIxn(const Lepton::CompiledExp
     forceZY = ReferenceForce::getVariablePointer(this->forceExpressionZ, "y");
     forceZZ = ReferenceForce::getVariablePointer(this->forceExpressionZ, "z");
     numParameters = parameterNames.size();
-    for (int i = 0; i < (int) numParameters; i++) {
-        energyParams.push_back(ReferenceForce::getVariablePointer(this->energyExpression, parameterNames[i]));
-        forceXParams.push_back(ReferenceForce::getVariablePointer(this->forceExpressionX, parameterNames[i]));
-        forceYParams.push_back(ReferenceForce::getVariablePointer(this->forceExpressionY, parameterNames[i]));
-        forceZParams.push_back(ReferenceForce::getVariablePointer(this->forceExpressionZ, parameterNames[i]));
+    for (auto& param : parameterNames) {
+        energyParams.push_back(ReferenceForce::getVariablePointer(this->energyExpression, param));
+        forceXParams.push_back(ReferenceForce::getVariablePointer(this->forceExpressionX, param));
+        forceYParams.push_back(ReferenceForce::getVariablePointer(this->forceExpressionY, param));
+        forceZParams.push_back(ReferenceForce::getVariablePointer(this->forceExpressionZ, param));
     }
-    for (map<string, double>::const_iterator iter = globalParameters.begin(); iter != globalParameters.end(); ++iter) {
-        ReferenceForce::setVariable(ReferenceForce::getVariablePointer(this->energyExpression, iter->first), iter->second);
-        ReferenceForce::setVariable(ReferenceForce::getVariablePointer(this->forceExpressionX, iter->first), iter->second);
-        ReferenceForce::setVariable(ReferenceForce::getVariablePointer(this->forceExpressionY, iter->first), iter->second);
-        ReferenceForce::setVariable(ReferenceForce::getVariablePointer(this->forceExpressionZ, iter->first), iter->second);
+    for (auto& param : globalParameters) {
+        ReferenceForce::setVariable(ReferenceForce::getVariablePointer(this->energyExpression, param.first), param.second);
+        ReferenceForce::setVariable(ReferenceForce::getVariablePointer(this->forceExpressionX, param.first), param.second);
+        ReferenceForce::setVariable(ReferenceForce::getVariablePointer(this->forceExpressionY, param.first), param.second);
+        ReferenceForce::setVariable(ReferenceForce::getVariablePointer(this->forceExpressionZ, param.first), param.second);
     }
 }
 

platforms/reference/src/SimTKReference/ReferenceCustomGBIxn.cpp

@@ -84,19 +84,19 @@ ReferenceCustomGBIxn::ReferenceCustomGBIxn(const vector<Lepton::CompiledExpressi
     xIndex = expressionSet.getVariableIndex("x");
     yIndex = expressionSet.getVariableIndex("y");
     zIndex = expressionSet.getVariableIndex("z");
-    for (int i = 0; i < (int) parameterNames.size(); i++) {
-        paramIndex.push_back(expressionSet.getVariableIndex(parameterNames[i]));
+    for (auto& param : parameterNames) {
+        paramIndex.push_back(expressionSet.getVariableIndex(param));
         for (int j = 1; j < 3; j++) {
             stringstream name;
-            name << parameterNames[i] << j;
+            name << param << j;
             particleParamIndex.push_back(expressionSet.getVariableIndex(name.str()));
         }
     }
-    for (int i = 0; i < (int) valueNames.size(); i++) {
-        valueIndex.push_back(expressionSet.getVariableIndex(valueNames[i]));
+    for (auto& value : valueNames) {
+        valueIndex.push_back(expressionSet.getVariableIndex(value));
         for (int j = 1; j < 3; j++) {
             stringstream name;
-            name << valueNames[i] << j;
+            name << value << j;
             particleValueIndex.push_back(expressionSet.getVariableIndex(name.str()));
         }
     }
@@ -153,8 +153,8 @@ ReferenceCustomGBIxn::~ReferenceCustomGBIxn() {
 void ReferenceCustomGBIxn::calculateIxn(int numberOfAtoms, vector<Vec3>& atomCoordinates, double** atomParameters,
                                            const vector<set<int> >& exclusions, map<string, double>& globalParameters, vector<Vec3>& forces,
                                            double* totalEnergy, double* energyParamDerivs) {
-    for (map<string, double>::const_iterator iter = globalParameters.begin(); iter != globalParameters.end(); ++iter)
-        expressionSet.setVariable(expressionSet.getVariableIndex(iter->first), iter->second);
+    for (auto& param : globalParameters)
+        expressionSet.setVariable(expressionSet.getVariableIndex(param.first), param.second);
     
     // Initialize arrays for storing values.
     
@@ -225,8 +225,7 @@ void ReferenceCustomGBIxn::calculateParticlePairValue(int index, int numAtoms, v
     if (cutoff) {
         // Loop over all pairs in the neighbor list.
 
-        for (int i = 0; i < (int) neighborList->size(); i++) {
-            OpenMM::AtomPair pair = (*neighborList)[i];
+        for (auto& pair : *neighborList) {
             if (useExclusions && exclusions[pair.first].find(pair.second) != exclusions[pair.first].end())
                 continue;
             calculateOnePairValue(index, pair.first, pair.second, atomCoordinates, atomParameters);
@@ -306,8 +305,7 @@ void ReferenceCustomGBIxn::calculateParticlePairEnergyTerm(int index, int numAto
     if (cutoff) {
         // Loop over all pairs in the neighbor list.
 
-        for (int i = 0; i < (int) neighborList->size(); i++) {
-            OpenMM::AtomPair pair = (*neighborList)[i];
+        for (auto& pair : *neighborList) {
             if (useExclusions && exclusions[pair.first].find(pair.second) != exclusions[pair.first].end())
                 continue;
             calculateOnePairEnergyTerm(index, pair.first, pair.second, atomCoordinates, atomParameters, forces, totalEnergy, energyParamDerivs);
@@ -377,8 +375,7 @@ void ReferenceCustomGBIxn::calculateChainRuleForces(int numAtoms, vector<Vec3>&
     if (cutoff) {
         // Loop over all pairs in the neighbor list.
 
-        for (int i = 0; i < (int) neighborList->size(); i++) {
-            OpenMM::AtomPair pair = (*neighborList)[i];
+        for (auto& pair : *neighborList) {
             bool isExcluded = (exclusions[pair.first].find(pair.second) != exclusions[pair.first].end());
             calculateOnePairChainRule(pair.first, pair.second, atomCoordinates, atomParameters, forces, isExcluded);
             calculateOnePairChainRule(pair.second, pair.first, atomCoordinates, atomParameters, forces, isExcluded);

platforms/reference/src/SimTKReference/ReferenceCustomHbondIxn.cpp

@@ -49,12 +49,12 @@ ReferenceCustomHbondIxn::ReferenceCustomHbondIxn(const vector<vector<int> >& don
             const map<string, vector<int> >& distances, const map<string, vector<int> >& angles, const map<string, vector<int> >& dihedrals) :
             cutoff(false), periodic(false), donorAtoms(donorAtoms), acceptorAtoms(acceptorAtoms), energyExpression(energyExpression.createProgram()),
             donorParamNames(donorParameterNames), acceptorParamNames(acceptorParameterNames) {
-    for (map<string, vector<int> >::const_iterator iter = distances.begin(); iter != distances.end(); ++iter)
-        distanceTerms.push_back(ReferenceCustomHbondIxn::DistanceTermInfo(iter->first, iter->second, energyExpression.differentiate(iter->first).optimize().createProgram()));
-    for (map<string, vector<int> >::const_iterator iter = angles.begin(); iter != angles.end(); ++iter)
-        angleTerms.push_back(ReferenceCustomHbondIxn::AngleTermInfo(iter->first, iter->second, energyExpression.differentiate(iter->first).optimize().createProgram()));
-    for (map<string, vector<int> >::const_iterator iter = dihedrals.begin(); iter != dihedrals.end(); ++iter)
-        dihedralTerms.push_back(ReferenceCustomHbondIxn::DihedralTermInfo(iter->first, iter->second, energyExpression.differentiate(iter->first).optimize().createProgram()));
+    for (auto& term : distances)
+        distanceTerms.push_back(ReferenceCustomHbondIxn::DistanceTermInfo(term.first, term.second, energyExpression.differentiate(term.first).optimize().createProgram()));
+    for (auto& term : angles)
+        angleTerms.push_back(ReferenceCustomHbondIxn::AngleTermInfo(term.first, term.second, energyExpression.differentiate(term.first).optimize().createProgram()));
+    for (auto& term : dihedrals)
+        dihedralTerms.push_back(ReferenceCustomHbondIxn::DihedralTermInfo(term.first, term.second, energyExpression.differentiate(term.first).optimize().createProgram()));
 }
 
 /**---------------------------------------------------------------------------------------

platforms/reference/src/SimTKReference/ReferenceCustomManyParticleIxn.cpp

@@ -60,8 +60,8 @@ ReferenceCustomManyParticleIxn::ReferenceCustomManyParticleIxn(const CustomManyP
 
     // 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;
 
     // Differentiate the energy to get expressions for the force.
 
@@ -80,12 +80,12 @@ ReferenceCustomManyParticleIxn::ReferenceCustomManyParticleIxn(const CustomManyP
             particleParamNames[i].push_back(paramname.str());
         }
     }
-    for (map<string, vector<int> >::const_iterator iter = distances.begin(); iter != distances.end(); ++iter)
-        distanceTerms.push_back(ReferenceCustomManyParticleIxn::DistanceTermInfo(iter->first, iter->second, energyExpr.differentiate(iter->first).optimize().createProgram()));
-    for (map<string, vector<int> >::const_iterator iter = angles.begin(); iter != angles.end(); ++iter)
-        angleTerms.push_back(ReferenceCustomManyParticleIxn::AngleTermInfo(iter->first, iter->second, energyExpr.differentiate(iter->first).optimize().createProgram()));
-    for (map<string, vector<int> >::const_iterator iter = dihedrals.begin(); iter != dihedrals.end(); ++iter)
-        dihedralTerms.push_back(ReferenceCustomManyParticleIxn::DihedralTermInfo(iter->first, iter->second, energyExpr.differentiate(iter->first).optimize().createProgram()));
+    for (auto& term : distances)
+        distanceTerms.push_back(ReferenceCustomManyParticleIxn::DistanceTermInfo(term.first, term.second, energyExpr.differentiate(term.first).optimize().createProgram()));
+    for (auto& term : angles)
+        angleTerms.push_back(ReferenceCustomManyParticleIxn::AngleTermInfo(term.first, term.second, energyExpr.differentiate(term.first).optimize().createProgram()));
+    for (auto& term : dihedrals)
+        dihedralTerms.push_back(ReferenceCustomManyParticleIxn::DihedralTermInfo(term.first, term.second, energyExpr.differentiate(term.first).optimize().createProgram()));
     
     // Record exclusions.
     
@@ -192,23 +192,18 @@ void ReferenceCustomManyParticleIxn::calculateOneIxn(const vector<int>& particle
     
     // Compute all of the variables the energy can depend on.
 
-    for (int i = 0; i < (int) particleTerms.size(); i++) {
-        const ParticleTermInfo& term = particleTerms[i];
+    for (auto& term : particleTerms)
         variables[term.name] = atomCoordinates[permutedParticles[term.atom]][term.component];
-    }
-    for (int i = 0; i < (int) distanceTerms.size(); i++) {
-        const DistanceTermInfo& term = distanceTerms[i];
+    for (auto& term : distanceTerms) {
         computeDelta(permutedParticles[term.p1], permutedParticles[term.p2], term.delta, atomCoordinates);
         variables[term.name] = term.delta[ReferenceForce::RIndex];
     }
-    for (int i = 0; i < (int) angleTerms.size(); i++) {
-        const AngleTermInfo& term = angleTerms[i];
+    for (auto& term : angleTerms) {
         computeDelta(permutedParticles[term.p1], permutedParticles[term.p2], term.delta1, atomCoordinates);
         computeDelta(permutedParticles[term.p3], permutedParticles[term.p2], term.delta2, atomCoordinates);
         variables[term.name] = computeAngle(term.delta1, term.delta2);
     }
-    for (int i = 0; i < (int) dihedralTerms.size(); i++) {
-        const DihedralTermInfo& term = dihedralTerms[i];
+    for (auto& term : dihedralTerms) {
         computeDelta(permutedParticles[term.p2], permutedParticles[term.p1], term.delta1, atomCoordinates);
         computeDelta(permutedParticles[term.p2], permutedParticles[term.p3], term.delta2, atomCoordinates);
         computeDelta(permutedParticles[term.p4], permutedParticles[term.p3], term.delta3, atomCoordinates);
@@ -219,15 +214,12 @@ void ReferenceCustomManyParticleIxn::calculateOneIxn(const vector<int>& particle
     
     // Apply forces based on individual particle coordinates.
     
-    for (int i = 0; i < (int) particleTerms.size(); i++) {
-        const ParticleTermInfo& term = particleTerms[i];
+    for (auto& term : particleTerms)
         forces[permutedParticles[term.atom]][term.component] -= term.forceExpression.evaluate(variables);
-    }
 
     // Apply forces based on distances.
 
-    for (int i = 0; i < (int) distanceTerms.size(); i++) {
-        const DistanceTermInfo& term = distanceTerms[i];
+    for (auto& term : distanceTerms) {
         double dEdR = term.forceExpression.evaluate(variables)/(term.delta[ReferenceForce::RIndex]);
         for (int i = 0; i < 3; i++) {
            double force  = -dEdR*term.delta[i];
@@ -238,8 +230,7 @@ void ReferenceCustomManyParticleIxn::calculateOneIxn(const vector<int>& particle
 
     // Apply forces based on angles.
 
-    for (int i = 0; i < (int) angleTerms.size(); i++) {
-        const AngleTermInfo& term = angleTerms[i];
+    for (auto& term : angleTerms) {
         double dEdTheta = term.forceExpression.evaluate(variables);
         double thetaCross[ReferenceForce::LastDeltaRIndex];
         SimTKOpenMMUtilities::crossProductVector3(term.delta1, term.delta2, thetaCross);
@@ -265,8 +256,7 @@ void ReferenceCustomManyParticleIxn::calculateOneIxn(const vector<int>& particle
 
     // Apply forces based on dihedrals.
 
-    for (int i = 0; i < (int) dihedralTerms.size(); i++) {
-        const DihedralTermInfo& term = dihedralTerms[i];
+    for (auto& term : dihedralTerms) {
         double dEdTheta = term.forceExpression.evaluate(variables);
         double internalF[4][3];
         double forceFactors[4];

platforms/reference/src/SimTKReference/ReferenceCustomNonbondedIxn.cpp

@@ -53,10 +53,10 @@ ReferenceCustomNonbondedIxn::ReferenceCustomNonbondedIxn(const Lepton::CompiledE
     for (int i = 0; i < this->energyParamDerivExpressions.size(); i++)
         expressionSet.registerExpression(this->energyParamDerivExpressions[i]);
     rIndex = expressionSet.getVariableIndex("r");
-    for (int i = 0; i < (int) paramNames.size(); i++) {
+    for (auto& param : paramNames) {
         for (int j = 1; j < 3; j++) {
             stringstream name;
-            name << paramNames[i] << j;
+            name << param << j;
             particleParamIndex.push_back(expressionSet.getVariableIndex(name.str()));
         }
     }
@@ -159,14 +159,14 @@ void ReferenceCustomNonbondedIxn::calculatePairIxn(int numberOfAtoms, vector<Vec
                                              double* fixedParameters, const map<string, double>& globalParameters, vector<Vec3>& forces,
                                              double* energyByAtom, double* totalEnergy, double* energyParamDerivs) {
 
-    for (map<string, double>::const_iterator iter = globalParameters.begin(); iter != globalParameters.end(); ++iter)
-        expressionSet.setVariable(expressionSet.getVariableIndex(iter->first), iter->second);
+    for (auto& param : globalParameters)
+        expressionSet.setVariable(expressionSet.getVariableIndex(param.first), param.second);
     if (interactionGroups.size() > 0) { 
         // The user has specified interaction groups, so compute only the requested interactions.
         
-        for (int group = 0; group < (int) interactionGroups.size(); group++) {
-            const set<int>& set1 = interactionGroups[group].first;
-            const set<int>& set2 = interactionGroups[group].second;
+        for (auto& group : interactionGroups) {
+            const set<int>& set1 = group.first;
+            const set<int>& set2 = group.second;
             for (set<int>::const_iterator atom1 = set1.begin(); atom1 != set1.end(); ++atom1) {
                 for (set<int>::const_iterator atom2 = set2.begin(); atom2 != set2.end(); ++atom2) {
                     if (*atom1 == *atom2 || exclusions[*atom1].find(*atom2) != exclusions[*atom1].end())
@@ -185,8 +185,7 @@ void ReferenceCustomNonbondedIxn::calculatePairIxn(int numberOfAtoms, vector<Vec
     else if (cutoff) {
         // We are using a cutoff, so get the interactions from the neighbor list.
         
-        for (int i = 0; i < (int) neighborList->size(); i++) {
-            OpenMM::AtomPair pair = (*neighborList)[i];
+        for (auto& pair : *neighborList) {
             for (int j = 0; j < (int) paramNames.size(); j++) {
                 expressionSet.setVariable(particleParamIndex[j*2], atomParameters[pair.first][j]);
                 expressionSet.setVariable(particleParamIndex[j*2+1], atomParameters[pair.second][j]);

platforms/reference/src/SimTKReference/ReferenceCustomTorsionIxn.cpp

@@ -47,10 +47,10 @@ ReferenceCustomTorsionIxn::ReferenceCustomTorsionIxn(const Lepton::CompiledExpre
         expressionSet.registerExpression(this->energyParamDerivExpressions[i]);
     thetaIndex = expressionSet.getVariableIndex("theta");
     numParameters = parameterNames.size();
-    for (int i = 0; i < (int) numParameters; i++)
-        torsionParamIndex.push_back(expressionSet.getVariableIndex(parameterNames[i]));
-    for (map<string, double>::const_iterator iter = globalParameters.begin(); iter != globalParameters.end(); ++iter)
-        expressionSet.setVariable(expressionSet.getVariableIndex(iter->first), iter->second);
+    for (auto& param : parameterNames)
+        torsionParamIndex.push_back(expressionSet.getVariableIndex(param));
+    for (auto& param : globalParameters)
+        expressionSet.setVariable(expressionSet.getVariableIndex(param.first), param.second);
 }
 
 /**---------------------------------------------------------------------------------------