Merge branch 'master' into gayberne

openmmapi/src/CustomCentroidBondForce.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) 2015 Stanford University and the Authors.           *
+ * Portions copyright (c) 2015-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -48,7 +48,7 @@ using std::string;
 using std::stringstream;
 using std::vector;
 
-CustomCentroidBondForce::CustomCentroidBondForce(int numGroups, const string& energy) : groupsPerBond(numGroups), energyExpression(energy) {
+CustomCentroidBondForce::CustomCentroidBondForce(int numGroups, const string& energy) : groupsPerBond(numGroups), energyExpression(energy), usePeriodic(false) {
 }
 
 CustomCentroidBondForce::~CustomCentroidBondForce() {
@@ -173,3 +173,11 @@ ForceImpl* CustomCentroidBondForce::createImpl() const {
 void CustomCentroidBondForce::updateParametersInContext(Context& context) {
     dynamic_cast<CustomCentroidBondForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
 }
+
+void CustomCentroidBondForce::setUsesPeriodicBoundaryConditions(bool periodic) {
+    usePeriodic = periodic;
+}
+
+bool CustomCentroidBondForce::usesPeriodicBoundaryConditions() const {
+    return usePeriodic;
+}

openmmapi/src/CustomCompoundBondForce.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) 2008-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -48,7 +48,7 @@ using std::string;
 using std::stringstream;
 using std::vector;
 
-CustomCompoundBondForce::CustomCompoundBondForce(int numParticles, const string& energy) : particlesPerBond(numParticles), energyExpression(energy) {
+CustomCompoundBondForce::CustomCompoundBondForce(int numParticles, const string& energy) : particlesPerBond(numParticles), energyExpression(energy), usePeriodic(false) {
 }
 
 
@@ -176,3 +176,11 @@ ForceImpl* CustomCompoundBondForce::createImpl() const {
 void CustomCompoundBondForce::updateParametersInContext(Context& context) {
     dynamic_cast<CustomCompoundBondForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
 }
+
+void CustomCompoundBondForce::setUsesPeriodicBoundaryConditions(bool periodic) {
+    usePeriodic = periodic;
+}
+
+bool CustomCompoundBondForce::usesPeriodicBoundaryConditions() const {
+    return usePeriodic;
+}

openmmapi/src/CustomIntegrator.cpp

@@ -248,21 +248,21 @@ int CustomIntegrator::addUpdateContextState() {
 int CustomIntegrator::beginIfBlock(const string& expression) {
     if (owner != NULL)
         throw OpenMMException("The integrator cannot be modified after it is bound to a context");
-    computations.push_back(ComputationInfo(BeginIfBlock, "", expression));
+    computations.push_back(ComputationInfo(IfBlockStart, "", expression));
     return computations.size()-1;
 }
 
 int CustomIntegrator::beginWhileBlock(const string& expression) {
     if (owner != NULL)
         throw OpenMMException("The integrator cannot be modified after it is bound to a context");
-    computations.push_back(ComputationInfo(BeginWhileBlock, "", expression));
+    computations.push_back(ComputationInfo(WhileBlockStart, "", expression));
     return computations.size()-1;
 }
 
 int CustomIntegrator::endBlock() {
     if (owner != NULL)
         throw OpenMMException("The integrator cannot be modified after it is bound to a context");
-    computations.push_back(ComputationInfo(EndBlock, "", ""));
+    computations.push_back(ComputationInfo(BlockEnd, "", ""));
     return computations.size()-1;
 }
 

openmmapi/src/CustomIntegratorUtilities.cpp

@@ -87,7 +87,7 @@ void CustomIntegratorUtilities::analyzeComputations(const ContextImpl& context,
     for (int step = 0; step < numSteps; step++) {
         string expression;
         integrator.getComputationStep(step, stepType[step], stepVariable[step], expression);
-        if (stepType[step] == CustomIntegrator::BeginIfBlock || stepType[step] == CustomIntegrator::BeginWhileBlock) {
+        if (stepType[step] == CustomIntegrator::IfBlockStart || stepType[step] == CustomIntegrator::WhileBlockStart) {
             // This step involves a condition.
 
             string lhs, rhs;
@@ -158,9 +158,9 @@ void CustomIntegratorUtilities::analyzeComputations(const ContextImpl& context,
     vector<int> blockStart;
     blockEnd.resize(numSteps, -1);
     for (int step = 0; step < numSteps; step++) {
-        if (stepType[step] == CustomIntegrator::BeginIfBlock || stepType[step] == CustomIntegrator::BeginWhileBlock)
+        if (stepType[step] == CustomIntegrator::IfBlockStart || stepType[step] == CustomIntegrator::WhileBlockStart)
             blockStart.push_back(step);
-        else if (stepType[step] == CustomIntegrator::EndBlock) {
+        else if (stepType[step] == CustomIntegrator::BlockEnd) {
             if (blockStart.size() == 0) {
                 stringstream error("CustomIntegrator: Unexpected end of block at computation ");
                 error << step;
@@ -207,7 +207,7 @@ void CustomIntegratorUtilities::enumeratePaths(int firstStep, vector<int> steps,
             jumps[step] = -1;
             step = nextStep;
         }
-        else if (stepType[step] == CustomIntegrator::BeginIfBlock) {
+        else if (stepType[step] == CustomIntegrator::IfBlockStart) {
             // Consider skipping the block.
 
             enumeratePaths(blockEnd[step]+1, steps, jumps, blockEnd, stepType, needsForces, needsEnergy, invalidatesForces, forceGroup, computeBoth);
@@ -216,7 +216,7 @@ void CustomIntegratorUtilities::enumeratePaths(int firstStep, vector<int> steps,
 
             step++;
         }
-        else if (stepType[step] == CustomIntegrator::BeginWhileBlock && jumps[step] != -2) {
+        else if (stepType[step] == CustomIntegrator::WhileBlockStart && jumps[step] != -2) {
             // Consider skipping the block.
 
             enumeratePaths(blockEnd[step]+1, steps, jumps, blockEnd, stepType, needsForces, needsEnergy, invalidatesForces, forceGroup, computeBoth);

openmmapi/src/CustomTorsionForce.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) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -44,7 +44,7 @@ using std::string;
 using std::stringstream;
 using std::vector;
 
-CustomTorsionForce::CustomTorsionForce(const string& energy) : energyExpression(energy) {
+CustomTorsionForce::CustomTorsionForce(const string& energy) : energyExpression(energy), usePeriodic(false) {
 }
 
 const string& CustomTorsionForce::getEnergyFunction() const {
@@ -125,3 +125,11 @@ ForceImpl* CustomTorsionForce::createImpl() const {
 void CustomTorsionForce::updateParametersInContext(Context& context) {
     dynamic_cast<CustomTorsionForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
 }
+
+void CustomTorsionForce::setUsesPeriodicBoundaryConditions(bool periodic) {
+    usePeriodic = periodic;
+}
+
+bool CustomTorsionForce::usesPeriodicBoundaryConditions() const {
+    return usePeriodic;
+}

openmmapi/src/HarmonicAngleForce.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) 2008-2009 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -37,7 +37,7 @@
 
 using namespace OpenMM;
 
-HarmonicAngleForce::HarmonicAngleForce() {
+HarmonicAngleForce::HarmonicAngleForce() : usePeriodic(false) {
 }
 
 int HarmonicAngleForce::addAngle(int particle1, int particle2, int particle3, double angle, double k) {
@@ -70,3 +70,11 @@ ForceImpl* HarmonicAngleForce::createImpl() const {
 void HarmonicAngleForce::updateParametersInContext(Context& context) {
     dynamic_cast<HarmonicAngleForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
 }
+
+void HarmonicAngleForce::setUsesPeriodicBoundaryConditions(bool periodic) {
+    usePeriodic = periodic;
+}
+
+bool HarmonicAngleForce::usesPeriodicBoundaryConditions() const {
+    return usePeriodic;
+}

openmmapi/src/HarmonicBondForce.cpp

@@ -37,7 +37,7 @@
 
 using namespace OpenMM;
 
-HarmonicBondForce::HarmonicBondForce() {
+HarmonicBondForce::HarmonicBondForce() : usePeriodic(false) {
 }
 
 int HarmonicBondForce::addBond(int particle1, int particle2, double length, double k) {
@@ -68,3 +68,11 @@ ForceImpl* HarmonicBondForce::createImpl() const {
 void HarmonicBondForce::updateParametersInContext(Context& context) {
     dynamic_cast<HarmonicBondForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
 }
+
+void HarmonicBondForce::setUsesPeriodicBoundaryConditions(bool periodic) {
+    usePeriodic = periodic;
+}
+
+bool HarmonicBondForce::usesPeriodicBoundaryConditions() const {
+    return usePeriodic;
+}

openmmapi/src/LocalEnergyMinimizer.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) 2010-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -108,7 +108,8 @@ void LocalEnergyMinimizer::minimize(Context& context, double tolerance, int maxI
     if (x == NULL)
         throw OpenMMException("LocalEnergyMinimizer: Failed to allocate memory");
     double constraintTol = context.getIntegrator().getConstraintTolerance();
-    double k = tolerance/constraintTol;
+    double workingConstraintTol = max(1e-4, constraintTol);
+    double k = tolerance/workingConstraintTol;
 
     // Initialize the minimizer.
 
@@ -121,7 +122,7 @@ void LocalEnergyMinimizer::minimize(Context& context, double tolerance, int maxI
 
     // Make sure the initial configuration satisfies all constraints.
 
-    context.applyConstraints(constraintTol);
+    context.applyConstraints(workingConstraintTol);
 
     // Record the initial positions and determine a normalization constant for scaling the tolerance.
 
@@ -162,14 +163,14 @@ void LocalEnergyMinimizer::minimize(Context& context, double tolerance, int maxI
             if (error > maxError)
                 maxError = error;
         }
-        if (maxError <= constraintTol)
+        if (maxError <= workingConstraintTol)
             break; // All constraints are satisfied.
         context.setPositions(initialPos);
         if (maxError >= prevMaxError)
             break; // Further tightening the springs doesn't seem to be helping, so just give up.
         prevMaxError = maxError;
         k *= 10;
-        if (maxError > 100*constraintTol) {
+        if (maxError > 100*workingConstraintTol) {
             // We've gotten far enough from a valid state that we might have trouble getting
             // back, so reset to the original positions.
             
@@ -181,5 +182,11 @@ void LocalEnergyMinimizer::minimize(Context& context, double tolerance, int maxI
         }
     }
     lbfgs_free(x);
+    
+    // If necessary, do a final constraint projection to make sure they are satisfied
+    // to the full precision requested by the user.
+    
+    if (constraintTol < workingConstraintTol)
+        context.applyConstraints(workingConstraintTol);
 }
 

openmmapi/src/MonteCarloAnisotropicBarostat.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) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -34,8 +34,8 @@
 
 using namespace OpenMM;
 
-MonteCarloAnisotropicBarostat::MonteCarloAnisotropicBarostat(const Vec3& defaultPressure, double temperature, bool scaleX, bool scaleY, bool scaleZ, int frequency) :
-        defaultPressure(defaultPressure), temperature(temperature), scaleX(scaleX), scaleY(scaleY), scaleZ(scaleZ), frequency(frequency) {
+MonteCarloAnisotropicBarostat::MonteCarloAnisotropicBarostat(const Vec3& defaultPressure, double defaultTemperature, bool scaleX, bool scaleY, bool scaleZ, int frequency) :
+        defaultPressure(defaultPressure), defaultTemperature(defaultTemperature), scaleX(scaleX), scaleY(scaleY), scaleZ(scaleZ), frequency(frequency) {
     setRandomNumberSeed(0);
 }
 

openmmapi/src/MonteCarloAnisotropicBarostatImpl.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) 2010-2013 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman, Lee-Ping Wang                                      *
  * Contributors:                                                              *
  *                                                                            *
@@ -119,7 +119,7 @@ void MonteCarloAnisotropicBarostatImpl::updateContextState(ContextImpl& context)
     // Compute the energy of the modified system.
     
     double finalEnergy = context.getOwner().getState(State::Energy).getPotentialEnergy();
-    double kT = BOLTZ*owner.getTemperature();
+    double kT = BOLTZ*context.getParameter(MonteCarloAnisotropicBarostat::Temperature());
     double w = finalEnergy-initialEnergy + pressure*deltaVolume - context.getMolecules().size()*kT*std::log(newVolume/volume);
     if (w > 0 && genrand_real2(random) > std::exp(-w/kT)) {
         // Reject the step.
@@ -150,6 +150,7 @@ std::map<std::string, double> MonteCarloAnisotropicBarostatImpl::getDefaultParam
     parameters[MonteCarloAnisotropicBarostat::PressureX()] = getOwner().getDefaultPressure()[0];
     parameters[MonteCarloAnisotropicBarostat::PressureY()] = getOwner().getDefaultPressure()[1];
     parameters[MonteCarloAnisotropicBarostat::PressureZ()] = getOwner().getDefaultPressure()[2];
+    parameters[MonteCarloAnisotropicBarostat::Temperature()] = getOwner().getDefaultTemperature();
     return parameters;
 }
 

openmmapi/src/MonteCarloBarostat.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) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -34,8 +34,8 @@
 
 using namespace OpenMM;
 
-MonteCarloBarostat::MonteCarloBarostat(double defaultPressure, double temperature, int frequency) :
-        defaultPressure(defaultPressure), temperature(temperature), frequency(frequency) {
+MonteCarloBarostat::MonteCarloBarostat(double defaultPressure, double defaultTemperature, int frequency) :
+        defaultPressure(defaultPressure), defaultTemperature(defaultTemperature), frequency(frequency) {
     setRandomNumberSeed(0);
 }
 

openmmapi/src/MonteCarloBarostatImpl.cpp

@@ -89,7 +89,7 @@ void MonteCarloBarostatImpl::updateContextState(ContextImpl& context) {
     
     double finalEnergy = context.getOwner().getState(State::Energy).getPotentialEnergy();
     double pressure = context.getParameter(MonteCarloBarostat::Pressure())*(AVOGADRO*1e-25);
-    double kT = BOLTZ*owner.getTemperature();
+    double kT = BOLTZ*context.getParameter(MonteCarloBarostat::Temperature());
     double w = finalEnergy-initialEnergy + pressure*deltaVolume - context.getMolecules().size()*kT*std::log(newVolume/volume);
     if (w > 0 && genrand_real2(random) > std::exp(-w/kT)) {
         // Reject the step.
@@ -118,6 +118,7 @@ void MonteCarloBarostatImpl::updateContextState(ContextImpl& context) {
 std::map<std::string, double> MonteCarloBarostatImpl::getDefaultParameters() {
     std::map<std::string, double> parameters;
     parameters[MonteCarloBarostat::Pressure()] = getOwner().getDefaultPressure();
+    parameters[MonteCarloBarostat::Temperature()] = getOwner().getDefaultTemperature();
     return parameters;
 }
 

openmmapi/src/MonteCarloMembraneBarostat.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) 2010-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -34,8 +34,8 @@
 
 using namespace OpenMM;
 
-MonteCarloMembraneBarostat::MonteCarloMembraneBarostat(double defaultPressure, double defaultSurfaceTension, double temperature, XYMode xymode, ZMode zmode, int frequency) :
-        defaultPressure(defaultPressure), defaultSurfaceTension(defaultSurfaceTension), temperature(temperature),
+MonteCarloMembraneBarostat::MonteCarloMembraneBarostat(double defaultPressure, double defaultSurfaceTension, double defaultTemperature, XYMode xymode, ZMode zmode, int frequency) :
+        defaultPressure(defaultPressure), defaultSurfaceTension(defaultSurfaceTension), defaultTemperature(defaultTemperature),
         xymode(xymode), zmode(zmode), frequency(frequency) {
     setRandomNumberSeed(0);
 }

openmmapi/src/MonteCarloMembraneBarostatImpl.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) 2010-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman, Lee-Ping Wang                                      *
  * Contributors:                                                              *
  *                                                                            *
@@ -120,7 +120,7 @@ void MonteCarloMembraneBarostatImpl::updateContextState(ContextImpl& context) {
     // Compute the energy of the modified system.
     
     double finalEnergy = context.getOwner().getState(State::Energy).getPotentialEnergy();
-    double kT = BOLTZ*owner.getTemperature();
+    double kT = BOLTZ*context.getParameter(MonteCarloMembraneBarostat::Temperature());
     double w = finalEnergy-initialEnergy + pressure*deltaVolume - tension*deltaArea - context.getMolecules().size()*kT*std::log(newVolume/volume);
     if (w > 0 && genrand_real2(random) > std::exp(-w/kT)) {
         // Reject the step.
@@ -150,6 +150,7 @@ std::map<std::string, double> MonteCarloMembraneBarostatImpl::getDefaultParamete
     std::map<std::string, double> parameters;
     parameters[MonteCarloMembraneBarostat::Pressure()] = getOwner().getDefaultPressure();
     parameters[MonteCarloMembraneBarostat::SurfaceTension()] = getOwner().getDefaultSurfaceTension();
+    parameters[MonteCarloMembraneBarostat::Temperature()] = getOwner().getDefaultTemperature();
     return parameters;
 }
 

openmmapi/src/PeriodicTorsionForce.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) 2008-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -37,7 +37,7 @@
 
 using namespace OpenMM;
 
-PeriodicTorsionForce::PeriodicTorsionForce() {
+PeriodicTorsionForce::PeriodicTorsionForce() : usePeriodic(false) {
 }
 
 int PeriodicTorsionForce::addTorsion(int particle1, int particle2, int particle3, int particle4, int periodicity, double phase, double k) {
@@ -74,3 +74,11 @@ ForceImpl* PeriodicTorsionForce::createImpl() const {
 void PeriodicTorsionForce::updateParametersInContext(Context& context) {
     dynamic_cast<PeriodicTorsionForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
 }
+
+void PeriodicTorsionForce::setUsesPeriodicBoundaryConditions(bool periodic) {
+    usePeriodic = periodic;
+}
+
+bool PeriodicTorsionForce::usesPeriodicBoundaryConditions() const {
+    return usePeriodic;
+}

openmmapi/src/RBTorsionForce.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) 2008-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -37,7 +37,7 @@
 
 using namespace OpenMM;
 
-RBTorsionForce::RBTorsionForce() {
+RBTorsionForce::RBTorsionForce() : usePeriodic(false) {
 }
 
 int RBTorsionForce::addTorsion(int particle1, int particle2, int particle3, int particle4, double c0, double c1, double c2, double c3, double c4, double c5) {
@@ -80,3 +80,11 @@ ForceImpl* RBTorsionForce::createImpl() const {
 void RBTorsionForce::updateParametersInContext(Context& context) {
     dynamic_cast<RBTorsionForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
 }
+
+void RBTorsionForce::setUsesPeriodicBoundaryConditions(bool periodic) {
+    usePeriodic = periodic;
+}
+
+bool RBTorsionForce::usesPeriodicBoundaryConditions() const {
+    return usePeriodic;
+}

platforms/cpu/include/CpuKernels.h

@@ -91,6 +91,7 @@ public:
 private:
     CpuPlatform::PlatformData& data;
     Kernel referenceKernel;
+    std::vector<RealVec> lastPositions;
 };
 
 /**
@@ -99,7 +100,7 @@ private:
 class CpuCalcHarmonicAngleForceKernel : public CalcHarmonicAngleForceKernel {
 public:
     CpuCalcHarmonicAngleForceKernel(std::string name, const Platform& platform, CpuPlatform::PlatformData& data) :
-            CalcHarmonicAngleForceKernel(name, platform), data(data), angleIndexArray(NULL), angleParamArray(NULL) {
+            CalcHarmonicAngleForceKernel(name, platform), data(data), angleIndexArray(NULL), angleParamArray(NULL), usePeriodic(false) {
     }
     ~CpuCalcHarmonicAngleForceKernel();
     /**
@@ -131,6 +132,7 @@ private:
     int **angleIndexArray;
     RealOpenMM **angleParamArray;
     CpuBondForce bondForce;
+    bool usePeriodic;
 };
 
 /**
@@ -139,7 +141,7 @@ private:
 class CpuCalcPeriodicTorsionForceKernel : public CalcPeriodicTorsionForceKernel {
 public:
     CpuCalcPeriodicTorsionForceKernel(std::string name, const Platform& platform, CpuPlatform::PlatformData& data) :
-            CalcPeriodicTorsionForceKernel(name, platform), data(data), torsionIndexArray(NULL), torsionParamArray(NULL) {
+            CalcPeriodicTorsionForceKernel(name, platform), data(data), torsionIndexArray(NULL), torsionParamArray(NULL), usePeriodic(false) {
     }
     ~CpuCalcPeriodicTorsionForceKernel();
     /**
@@ -171,6 +173,7 @@ private:
     int **torsionIndexArray;
     RealOpenMM **torsionParamArray;
     CpuBondForce bondForce;
+    bool usePeriodic;
 };
 
 /**
@@ -179,7 +182,7 @@ private:
 class CpuCalcRBTorsionForceKernel : public CalcRBTorsionForceKernel {
 public:
     CpuCalcRBTorsionForceKernel(std::string name, const Platform& platform, CpuPlatform::PlatformData& data) :
-            CalcRBTorsionForceKernel(name, platform), data(data), torsionIndexArray(NULL), torsionParamArray(NULL) {
+            CalcRBTorsionForceKernel(name, platform), data(data), torsionIndexArray(NULL), torsionParamArray(NULL), usePeriodic(false) {
     }
     ~CpuCalcRBTorsionForceKernel();
     /**
@@ -211,6 +214,7 @@ private:
     int **torsionIndexArray;
     RealOpenMM **torsionParamArray;
     CpuBondForce bondForce;
+    bool usePeriodic;
 };
 
 /**
@@ -265,9 +269,7 @@ private:
     bool useSwitchingFunction, useOptimizedPme, hasInitializedPme;
     std::vector<std::set<int> > exclusions;
     std::vector<std::pair<float, float> > particleParams;
-    std::vector<RealVec> lastPositions;
     NonbondedMethod nonbondedMethod;
-    CpuNeighborList* neighborList;
     CpuNonbondedForce* nonbonded;
     Kernel optimizedPme;
     CpuBondForce bondForce;
@@ -315,7 +317,6 @@ private:
     std::vector<std::string> parameterNames, globalParameterNames;
     std::vector<std::pair<std::set<int>, std::set<int> > > interactionGroups;
     NonbondedMethod nonbondedMethod;
-    CpuNeighborList* neighborList;
     CpuCustomNonbondedForce* nonbonded;
 };
 
@@ -401,7 +402,6 @@ private:
     std::vector<OpenMM::CustomGBForce::ComputationType> valueTypes;
     std::vector<OpenMM::CustomGBForce::ComputationType> energyTypes;
     NonbondedMethod nonbondedMethod;
-    CpuNeighborList* neighborList;
 };
 
 /**

platforms/cpu/include/CpuNeighborList.h

@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2013-2015 Stanford University and the Authors.      *
+ * Portions copyright (c) 2013-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -51,6 +51,7 @@ public:
     void computeNeighborList(int numAtoms, const AlignedArray<float>& atomLocations, const std::vector<std::set<int> >& exclusions,
             const RealVec* periodicBoxVectors, bool usePeriodic, float maxDistance, ThreadPool& threads);
     int getNumBlocks() const;
+    int getBlockSize() const;
     const std::vector<int>& getSortedAtoms() const;
     const std::vector<int>& getBlockNeighbors(int blockIndex) const;
     const std::vector<char>& getBlockExclusions(int blockIndex) const;

platforms/cpu/include/CpuPlatform.h

@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2013 Stanford University and the Authors.           *
+ * Portions copyright (c) 2013-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -34,6 +34,7 @@
 
 #include "AlignedArray.h"
 #include "CpuRandom.h"
+#include "CpuNeighborList.h"
 #include "ReferencePlatform.h"
 #include "openmm/internal/ContextImpl.h"
 #include "openmm/internal/ThreadPool.h"
@@ -64,7 +65,7 @@ public:
      * This is the name of the parameter for selecting the number of threads to use.
      */
     static const std::string& CpuThreads() {
-        static const std::string key = "CpuThreads";
+        static const std::string key = "Threads";
         return key;
     }
     /**
@@ -80,12 +81,18 @@ private:
 class CpuPlatform::PlatformData {
 public:
     PlatformData(int numParticles, int numThreads);
+    ~PlatformData();
+    void requestNeighborList(double cutoffDistance, double padding, bool useExclusions, std::vector<std::set<int> >& exclusionList);
     AlignedArray<float> posq;
     std::vector<AlignedArray<float> > threadForce;
     ThreadPool threads;
     bool isPeriodic;
     CpuRandom random;
     std::map<std::string, std::string> propertyValues;
+    CpuNeighborList* neighborList;
+    double cutoff, paddedCutoff;
+    bool anyExclusions;
+    std::vector<std::set<int> > exclusions;
 };
 
 } // namespace OpenMM

platforms/cpu/src/CpuCustomGBForce.cpp

 
-/* Portions copyright (c) 2009-2014 Stanford University and Simbios.
+/* Portions copyright (c) 2009-2016 Stanford University and Simbios.
  * Contributors: Peter Eastman
  *
  * Permission is hereby granted, free of charge, to any person obtaining
@@ -294,12 +294,13 @@ void CpuCustomGBForce::calculateParticlePairValue(int index, ThreadData& data, i
             int blockIndex = gmx_atomic_fetch_add(reinterpret_cast<gmx_atomic_t*>(atomicCounter), 1);
             if (blockIndex >= neighborList->getNumBlocks())
                 break;
-            const int* blockAtom = &neighborList->getSortedAtoms()[4*blockIndex];
+            const int blockSize = neighborList->getBlockSize();
+            const int* blockAtom = &neighborList->getSortedAtoms()[blockSize*blockIndex];
             const vector<int>& neighbors = neighborList->getBlockNeighbors(blockIndex);
             const vector<char>& blockExclusions = neighborList->getBlockExclusions(blockIndex);
             for (int i = 0; i < (int) neighbors.size(); i++) {
                 int first = neighbors[i];
-                for (int k = 0; k < 4; k++) {
+                for (int k = 0; k < blockSize; k++) {
                     if ((blockExclusions[i] & (1<<k)) == 0) {
                         int second = blockAtom[k];
                         if (useExclusions && exclusions[first].find(second) != exclusions[first].end())
@@ -379,12 +380,13 @@ void CpuCustomGBForce::calculateParticlePairEnergyTerm(int index, ThreadData& da
             int blockIndex = gmx_atomic_fetch_add(reinterpret_cast<gmx_atomic_t*>(atomicCounter), 1);
             if (blockIndex >= neighborList->getNumBlocks())
                 break;
-            const int* blockAtom = &neighborList->getSortedAtoms()[4*blockIndex];
+            const int blockSize = neighborList->getBlockSize();
+            const int* blockAtom = &neighborList->getSortedAtoms()[blockSize*blockIndex];
             const vector<int>& neighbors = neighborList->getBlockNeighbors(blockIndex);
             const vector<char>& blockExclusions = neighborList->getBlockExclusions(blockIndex);
             for (int i = 0; i < (int) neighbors.size(); i++) {
                 int first = neighbors[i];
-                for (int k = 0; k < 4; k++) {
+                for (int k = 0; k < blockSize; k++) {
                     if ((blockExclusions[i] & (1<<k)) == 0) {
                         int second = blockAtom[k];
                         if (useExclusions && exclusions[first].find(second) != exclusions[first].end())
@@ -460,12 +462,13 @@ void CpuCustomGBForce::calculateChainRuleForces(ThreadData& data, int numAtoms,
             int blockIndex = gmx_atomic_fetch_add(reinterpret_cast<gmx_atomic_t*>(atomicCounter), 1);
             if (blockIndex >= neighborList->getNumBlocks())
                 break;
-            const int* blockAtom = &neighborList->getSortedAtoms()[4*blockIndex];
+            const int blockSize = neighborList->getBlockSize();
+            const int* blockAtom = &neighborList->getSortedAtoms()[blockSize*blockIndex];
             const vector<int>& neighbors = neighborList->getBlockNeighbors(blockIndex);
             const vector<char>& blockExclusions = neighborList->getBlockExclusions(blockIndex);
             for (int i = 0; i < (int) neighbors.size(); i++) {
                 int first = neighbors[i];
-                for (int k = 0; k < 4; k++) {
+                for (int k = 0; k < blockSize; k++) {
                     if ((blockExclusions[i] & (1<<k)) == 0) {
                         int second = blockAtom[k];
                         bool isExcluded = (exclusions[first].find(second) != exclusions[first].end());