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

.travis.yml

@@ -73,6 +73,7 @@ matrix:
       addons: {apt: {packages: []}}
 
     - sudo: false
+      dist: trusty
       python: 2.7_with_system_site_packages
       env: ==STATIC_LIB==
            OPENCL=false
@@ -82,6 +83,7 @@ matrix:
            CMAKE_FLAGS="-DOPENMM_BUILD_STATIC_LIB=ON"
 
     - sudo: false
+      dist: trusty
       python: 2.7_with_system_site_packages
       env: ==PYTHON_2==
            OPENCL=false
@@ -92,6 +94,7 @@ matrix:
            CMAKE_FLAGS="-DOPENMM_GENERATE_API_DOCS=ON"
 
     - sudo: false
+      dist: trusty
       python: 3.4
       env: ==PYTHON_3==
            OPENCL=false
@@ -102,7 +105,7 @@ matrix:
 
 before_install:
   - START_TIME=$(date +%s)
-  - wget https://anaconda.org/omnia/ccache/3.2.4/download/${TRAVIS_OS_NAME}-64/ccache-3.2.4-0.tar.bz2
+  - wget http://anaconda.org/omnia/ccache/3.2.4/download/${TRAVIS_OS_NAME}-64/ccache-3.2.4-0.tar.bz2
   - mkdir -p $HOME/ccache && tar xf ccache-3.2.4-0.tar.bz2 -C $HOME/ccache
   - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
       brew install fftw;
@@ -110,7 +113,7 @@ before_install:
       sudo easy_install pytest;
     fi
   - if [[ "${TRAVIS_OS_NAME}" == "linux" ]]; then
-      CMAKE_URL="https://cmake.org/files/v3.7/cmake-3.7.2-Linux-x86_64.tar.gz";
+      CMAKE_URL="http://cmake.org/files/v3.7/cmake-3.7.2-Linux-x86_64.tar.gz";
       mkdir $HOME/cmake && travis_retry wget --no-check-certificate --quiet -O - ${CMAKE_URL} | tar --strip-components=1 -xz -C $HOME/cmake;
       export PATH=${HOME}/cmake/bin:${PATH};
     fi
@@ -131,14 +134,14 @@ before_install:
   # but this is a fast way to get an apparently functional precompiled
   # build of swig that's more modern than what's in apt.
   - if [[ "$OPENCL" == "false" && "$CUDA" == "false" && "$TRAVIS_OS_NAME" == "linux" ]]; then
-      wget https://anaconda.org/omnia/swig/3.0.7/download/linux-64/swig-3.0.7-0.tar.bz2;
+      wget http://anaconda.org/omnia/swig/3.0.7/download/linux-64/swig-3.0.7-0.tar.bz2;
       mkdir $HOME/swig;
       tar -xjvf swig-3.0.7-0.tar.bz2 -C $HOME/swig;
       export PATH=$HOME/swig/bin:$PATH;
       export SWIG_LIB=$HOME/swig/share/swig/3.0.7;
     fi
   - if [[ "$OPENCL" == "false" && "$CUDA" == "false" && "$TRAVIS_OS_NAME" == "osx" ]]; then
-      wget https://anaconda.org/omnia/swig/3.0.7/download/osx-64/swig-3.0.7-0.tar.bz2;
+      wget http://anaconda.org/omnia/swig/3.0.7/download/osx-64/swig-3.0.7-0.tar.bz2;
       mkdir $HOME/swig;
       tar -xjvf swig-3.0.7-0.tar.bz2 -C $HOME/swig;
       export PATH=$HOME/swig/bin:$PATH;

docs-source/developerguide/conf.py

@@ -185,10 +185,16 @@ latex_elements = {
     \\usepackage{caption}
     \\setcounter{tocdepth}{3}
     \\captionsetup[figure]{labelformat=empty}
+    % Backwards compatibility for sphinx < 1.5
+    \\let\\DUspan\\null % force DUspan to be defined
     \\renewcommand{\DUspan}[2]{%
         \\IfEqCase{#1}{%
-            {code}{\\small{}\\texttt{#2}\\normalsize{}}%
+            {code}{\\small{}\\texttt{#2}\\normalsize{}}
         }[\\PackageError{DUspan}{Unrecognized option passed to DUspan: #1}{}]%
+    }%
+    % Sphinx > 1.5 compatibility (github.com/sphinx-doc/sphinx/issues/2231)
+    \\newcommand{\\DUrolecode}[1]{%
+        \\small{}\\texttt{#1}\\normalsize{}%
     }%""",
 }
 

docs-source/usersguide/application.rst

@@ -775,7 +775,9 @@ File                           Force Field
 :code:`amber99sbnmr.xml`       Amber99SB with modifications to fit NMR data\ :cite:`Li2010`
 :code:`amber03.xml`            Amber03\ :cite:`Duan2003`
 :code:`amber10.xml`            Amber10 (documented in the AmberTools_ manual as `ff10`)
-:code:`amoeba2009.xml`         AMOEBA 2009\ :cite:`Ren2002`.  This force field is deprecated.  It is
+:code:`amberfb15.xml`          AMBER-FB15\ :cite:`Wang2017`. Intramolecular parameters optimized with
+                               ForceBalance using high-level ab initio data.
+:code:`amoeba2009.xml`         AMOEBA 2009\ :cite:`Ren2002`.  This force field is deprecated.  It is 
                                recommended to use AMOEBA 2013 instead.
 :code:`amoeba2013.xml`         AMOEBA 2013\ :cite:`Shi2013`
 :code:`charmm_polar_2013.xml`  CHARMM 2013 polarizable force field\ :cite:`Lopes2013`
@@ -2935,6 +2937,32 @@ need to be specified once for each class.  The atom charges, which are different
 for each type, are taken from the residue template instead.
 
 
+Including Other Files
+=====================
+
+Sometimes it is useful to split a force field definition into multiple files,
+but still be able to use the force field by specifying only a single file.  You
+can accomplish this with the :code:`<Include>` tag.  For example:
+
+.. code-block:: xml
+
+    <ForceField>
+     <Include file="definitions.xml"/>
+     ...
+    </ForceField>
+
+The :code:`file` attribute gives the path of the file to include.  It may be
+relative either to the directory containing the parent XML file (the one with
+the :code:`<Include>` tag) or the OpenMM data directory (the one containing
+built in force fields).
+
+The included file is fully processed before any other tags in the parent file
+are processed, and its definitions are added to the force field.  This means the
+parent file can refer to atom types defined in the included file, but not the
+other way around.  If there are multiple :code:`<Include>` tags, they are processed
+in the order they appear in the file.
+
+
 Using Multiple Files
 ********************
 

docs-source/usersguide/conf.py

@@ -185,10 +185,16 @@ latex_elements = {
     \\usepackage{caption}
     \\setcounter{tocdepth}{3}
     \\captionsetup[figure]{labelformat=empty}
+    % Backwards compatibility for sphinx < 1.5
+    \\let\\DUspan\\null % force DUspan to be defined
     \\renewcommand{\DUspan}[2]{%
         \\IfEqCase{#1}{%
-            {code}{\\small{}\\texttt{#2}\\normalsize{}}%
+            {code}{\\small{}\\texttt{#2}\\normalsize{}}
         }[\\PackageError{DUspan}{Unrecognized option passed to DUspan: #1}{}]%
+    }%
+    % Sphinx > 1.5 compatibility (github.com/sphinx-doc/sphinx/issues/2231)
+    \\newcommand{\\DUrolecode}[1]{%
+        \\small{}\\texttt{#1}\\normalsize{}%
     }%""",
 
 # Omit the index.

docs-source/usersguide/references.bib

@@ -518,6 +518,18 @@
    type = {Journal Article}
 }
 
+@article{Wang2017
+   author = {Wang, Lee-Ping and McKiernan, Keri A. and Gomes, Joseph and Beauchamp, Kyle A. and Head-Gordon, Teresa and Rice, Julia E. and Swope, William C. and Martínez, Todd J. and Pande, Vijay S.},
+   title = {Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15},
+   journal = {Journal of Physical Chemistry B},
+   volume = {0},
+   number = {ja},
+   pages = {null},
+   year = {2017},
+   type = {Journal Article},
+   doi = {10.1021/acs.jpcb.7b02320},
+}
+
 @article{Wennberg2015
    author = {Wennberg, Christian L. and Murtola, Teemu and Páll, Szilárd and Abraham, Mark J. and Hess, Berk and Lindahl, Erik},
    title = {Direct-Space Corrections Enable Fast and Accurate {Lorentz–Berthelot} Combination Rule {Lennard-Jones} Lattice Summation},
@@ -528,4 +540,3 @@
    year = {2015},
    type = {Journal Article}
 }
-

olla/src/Platform.cpp

@@ -70,10 +70,10 @@ static int platformInitializer = registerPlatforms();
 
 Platform::~Platform() {
     set<KernelFactory*> uniqueKernelFactories;
-    for (map<string, KernelFactory*>::const_iterator iter = kernelFactories.begin(); iter != kernelFactories.end(); ++iter)
-        uniqueKernelFactories.insert(iter->second);
-    for (set<KernelFactory*>::const_iterator iter = uniqueKernelFactories.begin(); iter != uniqueKernelFactories.end(); ++iter)
-        delete *iter;
+    for (auto& factory : kernelFactories)
+        uniqueKernelFactories.insert(factory.second);
+    for (auto factory : uniqueKernelFactories)
+        delete factory;
 }
 
 const vector<string>& Platform::getPropertyNames() const {
@@ -102,8 +102,8 @@ void Platform::setPropertyDefaultValue(const string& property, const string& val
     string propertyName = property;
     if (deprecatedPropertyReplacements.find(property) != deprecatedPropertyReplacements.end())
         propertyName = deprecatedPropertyReplacements.find(property)->second;
-    for (int i = 0; i < (int) platformProperties.size(); i++)
-        if (platformProperties[i] == propertyName) {
+    for (auto& prop : platformProperties)
+        if (prop == propertyName) {
             defaultProperties[propertyName] = value;
             return;
         }
@@ -121,8 +121,8 @@ void Platform::registerKernelFactory(const string& name, KernelFactory* factory)
 }
 
 bool Platform::supportsKernels(const vector<string>& kernelNames) const {
-    for (int i = 0; i < (int) kernelNames.size(); ++i)
-        if (kernelFactories.find(kernelNames[i]) == kernelFactories.end())
+    for (auto& name : kernelNames)
+        if (kernelFactories.find(name) == kernelFactories.end())
             return false;
     return true;
 }
@@ -167,9 +167,9 @@ Platform& Platform::findPlatform(const vector<string>& kernelNames) {
     Platform* best = 0;
     vector<Platform*>& platforms = getPlatforms();
     double speed = 0.0;
-    for (int i = 0; i < (int) platforms.size(); ++i) {
-        if (platforms[i]->supportsKernels(kernelNames) && platforms[i]->getSpeed() > speed) {
-            best = platforms[i];
+    for (auto platform : platforms) {
+        if (platform->supportsKernels(kernelNames) && platform->getSpeed() > speed) {
+            best = platform;
             speed = best->getSpeed();
         }
     }
@@ -193,15 +193,15 @@ static HMODULE loadOneLibrary(const string& file) {
 }
 
 static void initializePlugins(vector<HMODULE>& plugins) {
-    for (int i = 0; i < (int) plugins.size(); i++) {
+    for (auto plugin : plugins) {
         void (*init)();
-        *(void **)(&init) = (void *) GetProcAddress(plugins[i], "registerPlatforms");
+        *(void **)(&init) = (void *) GetProcAddress(plugin, "registerPlatforms");
         if (init != NULL)
             (*init)();
     }
-    for (int i = 0; i < (int) plugins.size(); i++) {
+    for (auto plugin : plugins) {
         void (*init)();
-        *(void **)(&init) = (void *) GetProcAddress(plugins[i], "registerKernelFactories");
+        *(void **)(&init) = (void *) GetProcAddress(plugin, "registerKernelFactories");
         if (init != NULL)
             (*init)();
     }
@@ -221,15 +221,15 @@ static void* loadOneLibrary(const string& file) {
 
 static void initializePlugins(vector<void*>& plugins) {
 #ifndef __PNACL__
-    for (int i = 0; i < (int) plugins.size(); i++) {
+    for (auto plugin : plugins) {
         void (*init)();
-        *(void **)(&init) = dlsym(plugins[i], "registerPlatforms");
+        *(void **)(&init) = dlsym(plugin, "registerPlatforms");
         if (init != NULL)
             (*init)();
     }
-    for (int i = 0; i < (int) plugins.size(); i++) {
+    for (auto plugin : plugins) {
         void (*init)();
-        *(void **)(&init) = dlsym(plugins[i], "registerKernelFactories");
+        *(void **)(&init) = dlsym(plugin, "registerKernelFactories");
         if (init != NULL)
             (*init)();
     }

openmmapi/src/AndersenThermostatImpl.cpp

@@ -94,7 +94,7 @@ void AndersenThermostatImpl::tagParticlesInGroup(int particle, int group, vector
     // Recursively tag particles as belonging to a particular group.
 
     particleGroup[particle] = group;
-    for (int i = 0; i < (int) particleConstraints[particle].size(); i++)
-        if (particleGroup[particleConstraints[particle][i]] == -1)
-            tagParticlesInGroup(particleConstraints[particle][i], group, particleGroup, particleConstraints);
+    for (int constrained : particleConstraints[particle])
+        if (particleGroup[constrained] == -1)
+            tagParticlesInGroup(constrained, group, particleGroup, particleConstraints);
 }

openmmapi/src/CompiledExpressionSet.cpp

@@ -44,15 +44,15 @@ int CompiledExpressionSet::getVariableIndex(const std::string& name) {
     int index = variables.size();
     variables.push_back(name);
     variableReferences.push_back(vector<double*>());
-    for (int i = 0; i < (int) expressions.size(); i++)
-        if (expressions[i]->getVariables().find(name) != expressions[i]->getVariables().end())
-            variableReferences[index].push_back(&expressions[i]->getVariableReference(name));
+    for (auto expression : expressions)
+        if (expression->getVariables().find(name) != expression->getVariables().end())
+            variableReferences[index].push_back(&expression->getVariableReference(name));
     return index;
 }
 
 void CompiledExpressionSet::setVariable(int index, double value) {
-    for (int i = 0; i < (int) variableReferences[index].size(); i++)
-        *variableReferences[index][i] = value;
+    for (auto ref : variableReferences[index])
+        *ref = value;
 }
 
 int CompiledExpressionSet::getNumVariables() const {

openmmapi/src/Context.cpp

@@ -97,8 +97,8 @@ State Context::getState(int types, bool enforcePeriodicBox, int groups) const {
     }
     if (types&State::Parameters) {
         map<string, double> params;
-        for (map<string, double>::const_iterator iter = impl->parameters.begin(); iter != impl->parameters.end(); iter++)
-            params[iter->first] = iter->second;
+        for (auto& param : impl->parameters)
+            params[param.first] = param.second;
         builder.setParameters(params);
     }
     if (types&State::ParameterDerivatives) {
@@ -111,13 +111,13 @@ State Context::getState(int types, bool enforcePeriodicBox, int groups) const {
         impl->getPositions(positions);
         if (enforcePeriodicBox) {
             const vector<vector<int> >& molecules = impl->getMolecules();
-            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 += positions[molecules[i][j]];
-                center *= 1.0/molecules[i].size();
+                for (int j : mol)
+                    center += positions[j];
+                center *= 1.0/mol.size();
 
                 // Find the displacement to move it into the first periodic box.
                 Vec3 diff;
@@ -126,10 +126,8 @@ State Context::getState(int types, bool enforcePeriodicBox, int groups) const {
                 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]];
-                    pos -= diff;
-                }
+                for (int j : mol)
+                    positions[j] -= diff;
             }
         }
         builder.setPositions(positions);
@@ -152,8 +150,8 @@ void Context::setState(const State& state) {
     if ((state.getDataTypes()&State::Velocities) != 0)
         setVelocities(state.getVelocities());
     if ((state.getDataTypes()&State::Parameters) != 0)
-        for (map<string, double>::const_iterator iter = state.getParameters().begin(); iter != state.getParameters().end(); ++iter)
-            setParameter(iter->first, iter->second);
+        for (auto& param : state.getParameters())
+            setParameter(param.first, param.second);
 }
 
 void Context::setTime(double time) {

openmmapi/src/ContextImpl.cpp

@@ -95,19 +95,19 @@ ContextImpl::ContextImpl(Context& owner, const System& system, Integrator& integ
 
     const vector<string>& platformProperties = platform->getPropertyNames();
     map<string, string> validatedProperties;
-    for (map<string, string>::const_iterator iter = properties.begin(); iter != properties.end(); ++iter) {
-        string property = iter->first;
+    for (auto& prop : properties) {
+        string property = prop.first;
         if (platform->deprecatedPropertyReplacements.find(property) != platform->deprecatedPropertyReplacements.end())
             property = platform->deprecatedPropertyReplacements[property];
         bool valid = false;
-        for (int i = 0; i < (int) platformProperties.size(); i++)
-            if (platformProperties[i] == property) {
+        for (auto& p : platformProperties)
+            if (p == property) {
                 valid = true;
                 break;
             }
         if (!valid)
-            throw OpenMMException("Illegal property name: "+iter->first);
-        validatedProperties[property] = iter->second;
+            throw OpenMMException("Illegal property name: "+prop.first);
+        validatedProperties[property] = prop.second;
     }
     
     // Find the list of kernels required.
@@ -184,8 +184,8 @@ ContextImpl::ContextImpl(Context& owner, const System& system, Integrator& integ
 }
 
 ContextImpl::~ContextImpl() {
-    for (int i = 0; i < (int) forceImpls.size(); ++i)
-        delete forceImpls[i];
+    for (auto force : forceImpls)
+        delete force;
     
     // Make sure all kernels get properly deleted before contextDestroyed() is called.
     
@@ -292,8 +292,8 @@ double ContextImpl::calcForcesAndEnergy(bool includeForces, bool includeEnergy,
     while (true) {
         double energy = 0.0;
         kernel.beginComputation(*this, includeForces, includeEnergy, groups);
-        for (int i = 0; i < (int) forceImpls.size(); ++i)
-            energy += forceImpls[i]->calcForcesAndEnergy(*this, includeForces, includeEnergy, groups);
+        for (auto force : forceImpls)
+            energy += force->calcForcesAndEnergy(*this, includeForces, includeEnergy, groups);
         bool valid = true;
         energy += kernel.finishComputation(*this, includeForces, includeEnergy, groups, valid);
         if (valid)
@@ -310,8 +310,8 @@ double ContextImpl::calcKineticEnergy() {
 }
 
 void ContextImpl::updateContextState() {
-    for (int i = 0; i < (int) forceImpls.size(); ++i)
-        forceImpls[i]->updateContextState(*this);
+    for (auto force : forceImpls)
+        force->updateContextState(*this);
 }
 
 const vector<ForceImpl*>& ContextImpl::getForceImpls() const {
@@ -349,8 +349,8 @@ const vector<vector<int> >& ContextImpl::getMolecules() const {
         system.getConstraintParameters(i, particle1, particle2, distance);
         bonds.push_back(std::make_pair(particle1, particle2));
     }
-    for (int i = 0; i < (int) forceImpls.size(); i++) {
-        vector<pair<int, int> > forceBonds = forceImpls[i]->getBondedParticles();
+    for (auto force : forceImpls) {
+        vector<pair<int, int> > forceBonds = force->getBondedParticles();
         bonds.insert(bonds.end(), forceBonds.begin(), forceBonds.end());
     }
     for (int i = 0; i < system.getNumParticles(); i++) {
@@ -365,9 +365,9 @@ const vector<vector<int> >& ContextImpl::getMolecules() const {
 
     int numParticles = system.getNumParticles();
     vector<vector<int> > particleBonds(numParticles);
-    for (int i = 0; i < (int) bonds.size(); i++) {
-        particleBonds[bonds[i].first].push_back(bonds[i].second);
-        particleBonds[bonds[i].second].push_back(bonds[i].first);
+    for (auto& bond : bonds) {
+        particleBonds[bond.first].push_back(bond.second);
+        particleBonds[bond.second].push_back(bond.first);
     }
 
     // Now identify particles by which molecule they belong to.
@@ -441,9 +441,9 @@ void ContextImpl::createCheckpoint(ostream& stream) {
     stream.write((char*) &numParticles, sizeof(int));
     int numParameters = parameters.size();
     stream.write((char*) &numParameters, sizeof(int));
-    for (map<string, double>::const_iterator iter = parameters.begin(); iter != parameters.end(); ++iter) {
-        writeString(stream, iter->first);
-        stream.write((char*) &iter->second, sizeof(double));
+    for (auto& param : parameters) {
+        writeString(stream, param.first);
+        stream.write((char*) &param.second, sizeof(double));
     }
     updateStateDataKernel.getAs<UpdateStateDataKernel>().createCheckpoint(*this, stream);
     stream.flush();

openmmapi/src/CustomCentroidBondForce.cpp

@@ -52,8 +52,8 @@ CustomCentroidBondForce::CustomCentroidBondForce(int numGroups, const string& en
 }
 
 CustomCentroidBondForce::~CustomCentroidBondForce() {
-    for (int i = 0; i < (int) functions.size(); i++)
-        delete functions[i].function;
+    for (auto function : functions)
+        delete function.function;
 }
 
 const string& CustomCentroidBondForce::getEnergyFunction() const {

openmmapi/src/CustomCentroidBondForceImpl.cpp

@@ -83,11 +83,11 @@ void CustomCentroidBondForceImpl::initialize(ContextImpl& context) {
     vector<double> weights;
     for (int i = 0; i < owner.getNumGroups(); i++) {
         owner.getGroupParameters(i, particles, weights);
-        for (int j = 0; j < (int) particles.size(); j++)
-            if (particles[j] < 0 || particles[j] >= system.getNumParticles()) {
+        for (int particle : particles)
+            if (particle < 0 || particle >= system.getNumParticles()) {
                 stringstream msg;
                 msg << "CustomCentroidBondForce: Illegal particle index for a group: ";
-                msg << particles[j];
+                msg << particle;
                 throw OpenMMException(msg.str());
             }
         if (weights.size() != particles.size() && weights.size() > 0) {
@@ -102,11 +102,11 @@ void CustomCentroidBondForceImpl::initialize(ContextImpl& context) {
     int numBondParameters = owner.getNumPerBondParameters();
     for (int i = 0; i < owner.getNumBonds(); i++) {
         owner.getBondParameters(i, groups, parameters);
-        for (int j = 0; j < (int) groups.size(); j++)
-            if (groups[j] < 0 || groups[j] >= owner.getNumGroups()) {
+        for (int group : groups)
+            if (group < 0 || group >= owner.getNumGroups()) {
                 stringstream msg;
                 msg << "CustomCentroidBondForce: Illegal group index for a bond: ";
-                msg << groups[j];
+                msg << group;
                 throw OpenMMException(msg.str());
             }
         if (parameters.size() != numBondParameters) {
@@ -179,8 +179,8 @@ ExpressionTreeNode CustomCentroidBondForceImpl::replaceFunctions(const Expressio
         // This is not an angle or dihedral, so process its children.
 
         vector<ExpressionTreeNode> children;
-        for (int i = 0; i < (int) node.getChildren().size(); i++)
-            children.push_back(replaceFunctions(node.getChildren()[i], groups, distances, angles, dihedrals, variables));
+        for (auto& child : node.getChildren())
+            children.push_back(replaceFunctions(child, groups, distances, angles, dihedrals, variables));
         return ExpressionTreeNode(op.clone(), children);
     }
     const Operation::Custom& custom = static_cast<const Operation::Custom&>(op);

openmmapi/src/CustomCompoundBondForce.cpp

@@ -53,8 +53,8 @@ CustomCompoundBondForce::CustomCompoundBondForce(int numParticles, const string&
 
 
 CustomCompoundBondForce::~CustomCompoundBondForce() {
-    for (int i = 0; i < (int) functions.size(); i++)
-        delete functions[i].function;
+    for (auto function : functions)
+        delete function.function;
 }
 
 const string& CustomCompoundBondForce::getEnergyFunction() const {

openmmapi/src/CustomCompoundBondForceImpl.cpp

@@ -88,11 +88,11 @@ void CustomCompoundBondForceImpl::initialize(ContextImpl& context) {
     int numBondParameters = owner.getNumPerBondParameters();
     for (int i = 0; i < owner.getNumBonds(); i++) {
         owner.getBondParameters(i, particles, parameters);
-        for (int j = 0; j < (int) particles.size(); j++)
-            if (particles[j] < 0 || particles[j] >= system.getNumParticles()) {
+        for (int particle : particles)
+            if (particle < 0 || particle >= system.getNumParticles()) {
                 stringstream msg;
                 msg << "CustomCompoundBondForce: Illegal particle index for a bond: ";
-                msg << particles[j];
+                msg << particle;
                 throw OpenMMException(msg.str());
             }
         if (parameters.size() != numBondParameters) {
@@ -165,8 +165,8 @@ ExpressionTreeNode CustomCompoundBondForceImpl::replaceFunctions(const Expressio
         // This is not an angle or dihedral, so process its children.
 
         vector<ExpressionTreeNode> children;
-        for (int i = 0; i < (int) node.getChildren().size(); i++)
-            children.push_back(replaceFunctions(node.getChildren()[i], atoms, distances, angles, dihedrals, variables));
+        for (auto& child : node.getChildren())
+            children.push_back(replaceFunctions(child, atoms, distances, angles, dihedrals, variables));
         return ExpressionTreeNode(op.clone(), children);
     }
     const Operation::Custom& custom = static_cast<const Operation::Custom&>(op);

openmmapi/src/CustomGBForce.cpp

@@ -51,8 +51,8 @@ CustomGBForce::CustomGBForce() : nonbondedMethod(NoCutoff), cutoffDistance(1.0)
 }
 
 CustomGBForce::~CustomGBForce() {
-    for (int i = 0; i < (int) functions.size(); i++)
-        delete functions[i].function;
+    for (auto function : functions)
+        delete function.function;
 }
 
 CustomGBForce::NonbondedMethod CustomGBForce::getNonbondedMethod() const {
@@ -60,6 +60,8 @@ CustomGBForce::NonbondedMethod CustomGBForce::getNonbondedMethod() const {
 }
 
 void CustomGBForce::setNonbondedMethod(NonbondedMethod method) {
+    if (method < 0 || method > 2)
+        throw OpenMMException("CustomGBForce: Illegal value for nonbonded method");
     nonbondedMethod = method;
 }
 

openmmapi/src/CustomHbondForce.cpp

@@ -52,8 +52,8 @@ CustomHbondForce::CustomHbondForce(const string& energy) : energyExpression(ener
 
 
 CustomHbondForce::~CustomHbondForce() {
-    for (int i = 0; i < (int) functions.size(); i++)
-        delete functions[i].function;
+    for (auto function : functions)
+        delete function.function;
 }
 
 const string& CustomHbondForce::getEnergyFunction() const {
@@ -69,6 +69,8 @@ CustomHbondForce::NonbondedMethod CustomHbondForce::getNonbondedMethod() const {
 }
 
 void CustomHbondForce::setNonbondedMethod(NonbondedMethod method) {
+    if (method < 0 || method > 2)
+        throw OpenMMException("CustomHbondForce: Illegal value for nonbonded method");
     nonbondedMethod = method;
 }
 

openmmapi/src/CustomHbondForceImpl.cpp

@@ -235,8 +235,8 @@ ExpressionTreeNode CustomHbondForceImpl::replaceFunctions(const ExpressionTreeNo
         // This is not an angle or dihedral, so process its children.
 
         vector<ExpressionTreeNode> children;
-        for (int i = 0; i < (int) node.getChildren().size(); i++)
-            children.push_back(replaceFunctions(node.getChildren()[i], atoms, distances, angles, dihedrals, variables));
+        for (auto& child : node.getChildren())
+            children.push_back(replaceFunctions(child, atoms, distances, angles, dihedrals, variables));
         return ExpressionTreeNode(op.clone(), children);
     }
     const Operation::Custom& custom = static_cast<const Operation::Custom&>(op);

openmmapi/src/CustomIntegrator.cpp

@@ -55,8 +55,7 @@ void CustomIntegrator::initialize(ContextImpl& contextRef) {
     set<std::string> variableSet;
     variableList.insert(variableList.end(), globalNames.begin(), globalNames.end());
     variableList.insert(variableList.end(), perDofNames.begin(), perDofNames.end());
-    for (int i = 0; i < (int) variableList.size(); i++) {
-        string& name = variableList[i];
+    for (auto& name : variableList) {
         if (variableSet.find(name) != variableSet.end())
             throw OpenMMException("The Integrator defines two variables with the same name: "+name);
         variableSet.insert(name);
@@ -66,8 +65,8 @@ void CustomIntegrator::initialize(ContextImpl& contextRef) {
     set<std::string> globalTargets;
     globalTargets.insert(globalNames.begin(), globalNames.end());
     globalTargets.insert("dt");
-    for (map<string, double>::const_iterator iter = contextRef.getParameters().begin(); iter != contextRef.getParameters().end(); ++iter)
-        globalTargets.insert(iter->first);
+    for (auto& param : contextRef.getParameters())
+        globalTargets.insert(param.first);
     for (int i = 0; i < computations.size(); i++) {
         if (computations[i].type == ComputeGlobal && globalTargets.find(computations[i].variable) == globalTargets.end())
             throw OpenMMException("Unknown global variable: "+computations[i].variable);

openmmapi/src/CustomIntegratorUtilities.cpp

@@ -59,8 +59,8 @@ bool CustomIntegratorUtilities::usesVariable(const Lepton::ExpressionTreeNode& n
     const Lepton::Operation& op = node.getOperation();
     if (op.getId() == Lepton::Operation::VARIABLE && op.getName() == variable)
         return true;
-    for (int i = 0; i < (int) node.getChildren().size(); i++)
-        if (usesVariable(node.getChildren()[i], variable))
+    for (auto& child : node.getChildren())
+        if (usesVariable(child, variable))
             return true;
     return false;
 }
@@ -107,11 +107,9 @@ void CustomIntegratorUtilities::analyzeComputations(const ContextImpl& context,
 
     set<string> affectsForce;
     affectsForce.insert("x");
-    for (vector<ForceImpl*>::const_iterator iter = context.getForceImpls().begin(); iter != context.getForceImpls().end(); ++iter) {
-        const map<string, double> params = (*iter)->getDefaultParameters();
-        for (map<string, double>::const_iterator param = params.begin(); param != params.end(); ++param)
-            affectsForce.insert(param->first);
-    }
+    for (auto force : context.getForceImpls())
+        for (auto& param : force->getDefaultParameters())
+            affectsForce.insert(param.first);
     for (int i = 0; i < numSteps; i++)
         invalidatesForces[i] = (stepType[i] == CustomIntegrator::ConstrainPositions || affectsForce.find(stepVariable[i]) != affectsForce.end());
 
@@ -253,8 +251,7 @@ void CustomIntegratorUtilities::analyzeForceComputationsForPath(vector<int>& ste
             const vector<bool>& invalidatesForces, const vector<int>& forceGroup, vector<bool>& computeBoth) {
     vector<int> candidatePoints;
     int currentGroup = -1;
-    for (int i = 0; i < (int) steps.size(); i++) {
-        int step = steps[i];
+    for (int step : steps) {
         if (invalidatesForces[step] || ((needsForces[step] || needsEnergy[step]) && forceGroup[step] != currentGroup)) {
             // Forces and energies are invalidated at this step, or it changes to a different force group,
             // so anything from this point on won't affect what we do at earlier steps.
@@ -264,11 +261,9 @@ void CustomIntegratorUtilities::analyzeForceComputationsForPath(vector<int>& ste
         if (needsForces[step] || needsEnergy[step]) {
             // See if this step affects what we do at earlier points.
 
-            for (int j = 0; j < (int) candidatePoints.size(); j++) {
-                int candidate = candidatePoints[j];
+            for (int candidate : candidatePoints)
                 if ((needsForces[candidate] && needsEnergy[step]) || (needsEnergy[candidate] && needsForces[step]))
                     computeBoth[candidate] = true;
-            }
 
             // Add this to the list of candidates that might be affected by later steps.
 

openmmapi/src/CustomManyParticleForce.cpp

@@ -48,8 +48,8 @@ CustomManyParticleForce::CustomManyParticleForce(int particlesPerSet, const stri
 }
 
 CustomManyParticleForce::~CustomManyParticleForce() {
-    for (int i = 0; i < (int) functions.size(); i++)
-        delete functions[i].function;
+    for (auto function : functions)
+        delete function.function;
 }
 
 const string& CustomManyParticleForce::getEnergyFunction() const {
@@ -65,6 +65,8 @@ CustomManyParticleForce::NonbondedMethod CustomManyParticleForce::getNonbondedMe
 }
 
 void CustomManyParticleForce::setNonbondedMethod(NonbondedMethod method) {
+    if (method < 0 || method > 2)
+        throw OpenMMException("CustomManyParticleForce: Illegal value for nonbonded method");
     nonbondedMethod = method;
 }
 
@@ -162,9 +164,9 @@ void CustomManyParticleForce::createExclusionsFromBonds(const vector<pair<int, i
         return;
     vector<set<int> > exclusions(particles.size());
     vector<set<int> > bonded12(exclusions.size());
-    for (int i = 0; i < (int) bonds.size(); ++i) {
-        int p1 = bonds[i].first;
-        int p2 = bonds[i].second;
+    for (auto& bond : bonds) {
+        int p1 = bond.first;
+        int p2 = bond.second;
         exclusions[p1].insert(p2);
         exclusions[p2].insert(p1);
         bonded12[p1].insert(p2);
@@ -172,15 +174,14 @@ void CustomManyParticleForce::createExclusionsFromBonds(const vector<pair<int, i
     }
     for (int level = 0; level < bondCutoff-1; level++) {
         vector<set<int> > currentExclusions = exclusions;
-        for (int i = 0; i < (int) particles.size(); i++) {
-            for (set<int>::const_iterator iter = currentExclusions[i].begin(); iter != currentExclusions[i].end(); ++iter)
-                exclusions[*iter].insert(bonded12[i].begin(), bonded12[i].end());
-        }
+        for (int i = 0; i < (int) particles.size(); i++)
+            for (int j : currentExclusions[i])
+                exclusions[j].insert(bonded12[i].begin(), bonded12[i].end());
     }
     for (int i = 0; i < (int) exclusions.size(); ++i)
-        for (set<int>::const_iterator iter = exclusions[i].begin(); iter != exclusions[i].end(); ++iter)
-            if (*iter < i)
-                addExclusion(*iter, i);
+        for (int j : exclusions[i])
+            if (j < i)
+                addExclusion(j, i);
 }
 
 void CustomManyParticleForce::getTypeFilter(int index, set<int>& types) const {