Merged fork with latest original master

platforms/reference/include/ReferenceAngleBondIxn.h

@@ -33,6 +33,9 @@ class OPENMM_EXPORT ReferenceAngleBondIxn : public ReferenceBondIxn {
 
    private:
 
+        bool usePeriodic;
+        RealVec boxVectors[3];
+
    public:
 
       /**---------------------------------------------------------------------------------------
@@ -51,6 +54,16 @@ class OPENMM_EXPORT ReferenceAngleBondIxn : public ReferenceBondIxn {
 
        ~ReferenceAngleBondIxn();
 
+       /**---------------------------------------------------------------------------------------
+      
+         Set the force to use periodic boundary conditions.
+      
+         @param vectors    the vectors defining the periodic box
+      
+         --------------------------------------------------------------------------------------- */
+      
+      void setPeriodic(OpenMM::RealVec* vectors);
+
       /**---------------------------------------------------------------------------------------
 
          Get dEdR and energy term for angle bond

platforms/reference/include/ReferenceCMAPTorsionIxn.h

@@ -38,6 +38,8 @@ private:
     std::vector<std::vector<std::vector<RealOpenMM> > > coeff;
     std::vector<int> torsionMaps;
     std::vector<std::vector<int> > torsionIndices;
+    bool usePeriodic;
+    RealVec boxVectors[3];
 
     /**---------------------------------------------------------------------------------------
 
@@ -65,6 +67,16 @@ public:
                             const std::vector<int>& torsionMaps,
                             const std::vector<std::vector<int> >& torsionIndices);
 
+       /**---------------------------------------------------------------------------------------
+      
+         Set the force to use periodic boundary conditions.
+      
+         @param vectors    the vectors defining the periodic box
+      
+         --------------------------------------------------------------------------------------- */
+      
+       void setPeriodic(OpenMM::RealVec* vectors);
+
     /**---------------------------------------------------------------------------------------
 
        Calculate torsion interaction

platforms/reference/include/ReferenceCustomAngleIxn.h

-/* Portions copyright (c) 2010-2013 Stanford University and Simbios.
+/* Portions copyright (c) 2010-2016 Stanford University and Simbios.
  * Contributors: Peter Eastman
  *
  * Permission is hereby granted, free of charge, to any person obtaining
@@ -39,6 +39,8 @@ class ReferenceCustomAngleIxn : public ReferenceBondIxn {
       double* energyTheta;
       double* forceTheta;
       int numParameters;
+      bool usePeriodic;
+      RealVec boxVectors[3];
 
    public:
 
@@ -59,6 +61,16 @@ class ReferenceCustomAngleIxn : public ReferenceBondIxn {
 
        ~ReferenceCustomAngleIxn();
 
+       /**---------------------------------------------------------------------------------------
+      
+         Set the force to use periodic boundary conditions.
+      
+         @param vectors    the vectors defining the periodic box
+      
+         --------------------------------------------------------------------------------------- */
+      
+      void setPeriodic(OpenMM::RealVec* vectors);
+
       /**---------------------------------------------------------------------------------------
 
          Calculate Custom Angle Ixn

platforms/reference/include/ReferenceCustomBondIxn.h

 
-/* Portions copyright (c) 2009-2013 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
@@ -40,6 +40,8 @@ class ReferenceCustomBondIxn : public ReferenceBondIxn {
       double* energyR;
       double* forceR;
       int numParameters;
+      bool usePeriodic;
+      RealVec boxVectors[3];
 
    public:
 
@@ -60,6 +62,16 @@ class ReferenceCustomBondIxn : public ReferenceBondIxn {
 
        ~ReferenceCustomBondIxn();
 
+       /**---------------------------------------------------------------------------------------
+      
+         Set the force to use periodic boundary conditions.
+      
+         @param vectors    the vectors defining the periodic box
+      
+         --------------------------------------------------------------------------------------- */
+      
+      void setPeriodic(OpenMM::RealVec* vectors);
+
       /**---------------------------------------------------------------------------------------
 
          Calculate Custom Bond Ixn

platforms/reference/include/ReferenceCustomCentroidBondIxn.h

 
-/* Portions copyright (c) 2009-2015 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
@@ -50,6 +50,8 @@ class ReferenceCustomCentroidBondIxn : public ReferenceBondIxn {
       std::vector<DistanceTermInfo> distanceTerms;
       std::vector<AngleTermInfo> angleTerms;
       std::vector<DihedralTermInfo> dihedralTerms;
+      bool usePeriodic;
+      RealVec boxVectors[3];
 
 
       /**---------------------------------------------------------------------------------------
@@ -94,6 +96,16 @@ class ReferenceCustomCentroidBondIxn : public ReferenceBondIxn {
 
        ~ReferenceCustomCentroidBondIxn();
 
+       /**---------------------------------------------------------------------------------------
+      
+         Set the force to use periodic boundary conditions.
+      
+         @param vectors    the vectors defining the periodic box
+      
+         --------------------------------------------------------------------------------------- */
+      
+       void setPeriodic(OpenMM::RealVec* vectors);
+
       /**---------------------------------------------------------------------------------------
 
          Get the list of groups in each bond.

platforms/reference/include/ReferenceCustomCompoundBondIxn.h

 
-/* Portions copyright (c) 2009-2012 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
@@ -48,6 +48,8 @@ class ReferenceCustomCompoundBondIxn : public ReferenceBondIxn {
       std::vector<DistanceTermInfo> distanceTerms;
       std::vector<AngleTermInfo> angleTerms;
       std::vector<DihedralTermInfo> dihedralTerms;
+      bool usePeriodic;
+      RealVec boxVectors[3];
 
 
       /**---------------------------------------------------------------------------------------
@@ -91,6 +93,16 @@ class ReferenceCustomCompoundBondIxn : public ReferenceBondIxn {
 
        ~ReferenceCustomCompoundBondIxn();
 
+       /**---------------------------------------------------------------------------------------
+      
+         Set the force to use periodic boundary conditions.
+      
+         @param vectors    the vectors defining the periodic box
+      
+         --------------------------------------------------------------------------------------- */
+      
+       void setPeriodic(OpenMM::RealVec* vectors);
+
       /**---------------------------------------------------------------------------------------
 
          Get the list atoms in each bond.

platforms/reference/include/ReferenceCustomDynamics.h

 
-/* Portions copyright (c) 2011-2015 Stanford University and Simbios.
+/* Portions copyright (c) 2011-2016 Stanford University and Simbios.
  * Contributors: Peter Eastman
  *
  * Permission is hereby granted, free of charge, to any person obtaining
@@ -29,7 +29,8 @@
 #include "openmm/CustomIntegrator.h"
 #include "openmm/internal/ContextImpl.h"
 #include "openmm/internal/CustomIntegratorUtilities.h"
-#include "lepton/ExpressionProgram.h"
+#include "openmm/internal/CompiledExpressionSet.h"
+#include "lepton/CompiledExpression.h"
 
 #include <map>
 #include <string>
@@ -44,23 +45,27 @@ private:
     std::vector<RealOpenMM> inverseMasses;
     std::vector<OpenMM::RealVec> sumBuffer, oldPos;
     std::vector<OpenMM::CustomIntegrator::ComputationType> stepType;
-    std::vector<std::string> stepVariable, forceName, energyName;
-    std::vector<std::vector<Lepton::ExpressionProgram> > stepExpressions;
+    std::vector<std::string> stepVariable;
+    std::vector<std::vector<Lepton::CompiledExpression> > stepExpressions;
     std::vector<CustomIntegratorUtilities::Comparison> comparisons;
     std::vector<bool> invalidatesForces, needsForces, needsEnergy, computeBothForceAndEnergy;
     std::vector<int> forceGroupFlags, blockEnd;
     RealOpenMM energy;
-    Lepton::ExpressionProgram kineticEnergyExpression;
+    Lepton::CompiledExpression kineticEnergyExpression;
     bool kineticEnergyNeedsForce;
+    CompiledExpressionSet expressionSet;
+    int xIndex, vIndex, mIndex, fIndex, energyIndex, gaussianIndex, uniformIndex;
+    std::vector<int> forceVariableIndex, energyVariableIndex, perDofVariableIndex, stepVariableIndex;
+
+    void initialize(OpenMM::ContextImpl& context, std::vector<RealOpenMM>& masses, std::map<std::string, RealOpenMM>& globals);
     
     void computePerDof(int numberOfAtoms, std::vector<OpenMM::RealVec>& results, const std::vector<OpenMM::RealVec>& atomCoordinates,
                   const std::vector<OpenMM::RealVec>& velocities, const std::vector<OpenMM::RealVec>& forces, const std::vector<RealOpenMM>& masses,
-                  const std::map<std::string, RealOpenMM>& globals, const std::vector<std::vector<OpenMM::RealVec> >& perDof,
-                  const Lepton::ExpressionProgram& expression, const std::string& forceName);
+                  const std::vector<std::vector<OpenMM::RealVec> >& perDof, const Lepton::CompiledExpression& expression, int forceIndex);
     
     void recordChangedParameters(OpenMM::ContextImpl& context, std::map<std::string, RealOpenMM>& globals);
 
-    bool evaluateCondition(int step, std::map<std::string, RealOpenMM>& globals);
+    bool evaluateCondition(int step);
       
 public:
 

platforms/reference/include/ReferenceCustomTorsionIxn.h

-/* Portions copyright (c) 2010-2013 Stanford University and Simbios.
+/* Portions copyright (c) 2010-2016 Stanford University and Simbios.
  * Contributors: Peter Eastman
  *
  * Permission is hereby granted, free of charge, to any person obtaining
@@ -39,6 +39,8 @@ class ReferenceCustomTorsionIxn : public ReferenceBondIxn {
       double* energyTheta;
       double* forceTheta;
       int numParameters;
+      bool usePeriodic;
+      RealVec boxVectors[3];
 
    public:
 
@@ -59,6 +61,16 @@ class ReferenceCustomTorsionIxn : public ReferenceBondIxn {
 
        ~ReferenceCustomTorsionIxn();
 
+       /**---------------------------------------------------------------------------------------
+      
+         Set the force to use periodic boundary conditions.
+      
+         @param vectors    the vectors defining the periodic box
+      
+         --------------------------------------------------------------------------------------- */
+      
+       void setPeriodic(OpenMM::RealVec* vectors);
+
       /**---------------------------------------------------------------------------------------
 
          Calculate Custom Torsion Ixn

platforms/reference/include/ReferenceForce.h

@@ -83,6 +83,19 @@ class OPENMM_EXPORT  ReferenceForce {
       static void getDeltaR(const OpenMM::RealVec& atomCoordinatesI, const OpenMM::RealVec& atomCoordinatesJ,
                             RealOpenMM* deltaR);
       
+      /**---------------------------------------------------------------------------------------
+      
+         Get deltaR between atomI and atomJ (static method)
+         deltaR: j - i
+      
+         @param atomCoordinatesI    atom i coordinates
+         @param atomCoordinatesI    atom j coordinates
+         @return the displacement
+      
+         --------------------------------------------------------------------------------------- */
+      
+      static RealVec getDeltaR(const OpenMM::RealVec& atomCoordinatesI, const OpenMM::RealVec& atomCoordinatesJ);
+      
       /**---------------------------------------------------------------------------------------
 
          Get deltaR and distance and distance**2 between atomI and atomJ, assuming periodic
@@ -113,6 +126,21 @@ class OPENMM_EXPORT  ReferenceForce {
       static void getDeltaRPeriodic(const OpenMM::RealVec& atomCoordinatesI, const OpenMM::RealVec& atomCoordinatesJ,
                                     const OpenMM::RealVec* boxVectors, RealOpenMM* deltaR);
 
+      /**---------------------------------------------------------------------------------------
+
+         Get deltaR between atomI and atomJ, assuming periodic boundary conditions (static method);
+         deltaR: j - i
+
+         @param atomCoordinatesI    atom i coordinates
+         @param atomCoordinatesI    atom j coordinates
+         @param boxVectors          the vectors defining the periodic box
+         @return the displacement
+
+         --------------------------------------------------------------------------------------- */
+
+      static RealVec getDeltaRPeriodic(const OpenMM::RealVec& atomCoordinatesI, const OpenMM::RealVec& atomCoordinatesJ,
+                                    const OpenMM::RealVec* boxVectors);
+
       /**
        * Get a pointer to the memory for setting a variable in a CompiledExpression.  If the expression
        * does not use the specified variable, return NULL.

platforms/reference/include/ReferenceHarmonicBondIxn.h

 
-/* Portions copyright (c) 2006 Stanford University and Simbios.
+/* Portions copyright (c) 2006-2016 Stanford University and Simbios.
  * Contributors: Pande Group
  *
  * Permission is hereby granted, free of charge, to any person obtaining
@@ -32,6 +32,9 @@ namespace OpenMM {
 class ReferenceHarmonicBondIxn : public ReferenceBondIxn {
 
    private:
+       
+        bool usePeriodic;
+        RealVec boxVectors[3];
 
    public:
 
@@ -51,6 +54,16 @@ class ReferenceHarmonicBondIxn : public ReferenceBondIxn {
 
        ~ReferenceHarmonicBondIxn();
 
+       /**---------------------------------------------------------------------------------------
+      
+         Set the force to use periodic boundary conditions.
+      
+         @param vectors    the vectors defining the periodic box
+      
+         --------------------------------------------------------------------------------------- */
+      
+      void setPeriodic(OpenMM::RealVec* vectors);
+
       /**---------------------------------------------------------------------------------------
       
          Calculate Harmonic Bond Ixn

platforms/reference/include/ReferenceKernels.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) 2008-2015 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -172,7 +172,7 @@ public:
      * @param b      the vector defining the second edge of the periodic box
      * @param c      the vector defining the third edge of the periodic box
      */
-    void setPeriodicBoxVectors(ContextImpl& context, const Vec3& a, const Vec3& b, const Vec3& c) const;
+    void setPeriodicBoxVectors(ContextImpl& context, const Vec3& a, const Vec3& b, const Vec3& c);
     /**
      * Create a checkpoint recording the current state of the Context.
      * 
@@ -280,6 +280,7 @@ private:
     int numBonds;
     int **bondIndexArray;
     RealOpenMM **bondParamArray;
+    bool usePeriodic;
 };
 
 /**
@@ -319,6 +320,7 @@ private:
     RealOpenMM **bondParamArray;
     Lepton::CompiledExpression energyExpression, forceExpression;
     std::vector<std::string> parameterNames, globalParameterNames;
+    bool usePeriodic;
 };
 
 /**
@@ -356,6 +358,7 @@ private:
     int numAngles;
     int **angleIndexArray;
     RealOpenMM **angleParamArray;
+    bool usePeriodic;
 };
 
 /**
@@ -395,6 +398,7 @@ private:
     RealOpenMM **angleParamArray;
     Lepton::CompiledExpression energyExpression, forceExpression;
     std::vector<std::string> parameterNames, globalParameterNames;
+    bool usePeriodic;
 };
 
 /**
@@ -432,6 +436,7 @@ private:
     int numTorsions;
     int **torsionIndexArray;
     RealOpenMM **torsionParamArray;
+    bool usePeriodic;
 };
 
 /**
@@ -469,6 +474,7 @@ private:
     int numTorsions;
     int **torsionIndexArray;
     RealOpenMM **torsionParamArray;
+    bool usePeriodic;
 };
 
 /**
@@ -505,6 +511,7 @@ private:
     std::vector<std::vector<std::vector<RealOpenMM> > > coeff;
     std::vector<int> torsionMaps;
     std::vector<std::vector<int> > torsionIndices;
+    bool usePeriodic;
 };
 
 /**
@@ -544,6 +551,7 @@ private:
     RealOpenMM **torsionParamArray;
     Lepton::CompiledExpression energyExpression, forceExpression;
     std::vector<std::string> parameterNames, globalParameterNames;
+    bool usePeriodic;
 };
 
 /**
@@ -860,6 +868,7 @@ private:
     RealOpenMM **bondParamArray;
     ReferenceCustomCentroidBondIxn* ixn;
     std::vector<std::string> globalParameterNames;
+    bool usePeriodic;
 };
 
 /**
@@ -898,6 +907,7 @@ private:
     RealOpenMM **bondParamArray;
     ReferenceCustomCompoundBondIxn* ixn;
     std::vector<std::string> globalParameterNames;
+    bool usePeriodic;
 };
 
 /**

platforms/reference/include/ReferenceProperDihedralBond.h

 
-/* Portions copyright (c) 2006 Stanford University and Simbios.
+/* Portions copyright (c) 2006-2016 Stanford University and Simbios.
  * Contributors: Pande Group
  *
  * Permission is hereby granted, free of charge, to any person obtaining
@@ -33,6 +33,9 @@ class OPENMM_EXPORT ReferenceProperDihedralBond : public ReferenceBondIxn {
 
    private:
 
+        bool usePeriodic;
+        RealVec boxVectors[3];
+       
    public:
 
       /**---------------------------------------------------------------------------------------
@@ -51,6 +54,16 @@ class OPENMM_EXPORT ReferenceProperDihedralBond : public ReferenceBondIxn {
 
        ~ReferenceProperDihedralBond();
 
+       /**---------------------------------------------------------------------------------------
+      
+         Set the force to use periodic boundary conditions.
+      
+         @param vectors    the vectors defining the periodic box
+      
+         --------------------------------------------------------------------------------------- */
+      
+       void setPeriodic(OpenMM::RealVec* vectors);
+
       /**---------------------------------------------------------------------------------------
       
         Calculate proper dihedral bond ixn

platforms/reference/include/ReferenceRbDihedralBond.h

 
-/* Portions copyright (c) 2006 Stanford University and Simbios.
+/* Portions copyright (c) 2006-2016 Stanford University and Simbios.
  * Contributors: Pande Group
  *
  * Permission is hereby granted, free of charge, to any person obtaining
@@ -33,6 +33,9 @@ class OPENMM_EXPORT ReferenceRbDihedralBond : public ReferenceBondIxn {
 
    private:
 
+        bool usePeriodic;
+        RealVec boxVectors[3];
+       
    public:
 
       /**---------------------------------------------------------------------------------------
@@ -51,6 +54,16 @@ class OPENMM_EXPORT ReferenceRbDihedralBond : public ReferenceBondIxn {
 
        ~ReferenceRbDihedralBond();
 
+       /**---------------------------------------------------------------------------------------
+      
+         Set the force to use periodic boundary conditions.
+      
+         @param vectors    the vectors defining the periodic box
+      
+         --------------------------------------------------------------------------------------- */
+      
+       void setPeriodic(OpenMM::RealVec* vectors);
+
       /**---------------------------------------------------------------------------------------
       
          Calculate Ryckaert-Bellemans bond ixn

platforms/reference/include/ReferenceTabulatedFunction.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) 2014 Stanford University and the Authors.           *
+ * Portions copyright (c) 2014-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -55,6 +55,7 @@ public:
     double evaluateDerivative(const double* arguments, const int* derivOrder) const;
     CustomFunction* clone() const;
 private:
+    ReferenceContinuous1DFunction(const ReferenceContinuous1DFunction& other);
     const Continuous1DFunction& function;
     double min, max;
     std::vector<double> x, values, derivs;
@@ -71,6 +72,7 @@ public:
     double evaluateDerivative(const double* arguments, const int* derivOrder) const;
     CustomFunction* clone() const;
 private:
+    ReferenceContinuous2DFunction(const ReferenceContinuous2DFunction& other);
     const Continuous2DFunction& function;
     int xsize, ysize;
     double xmin, xmax, ymin, ymax;
@@ -89,6 +91,7 @@ public:
     double evaluateDerivative(const double* arguments, const int* derivOrder) const;
     CustomFunction* clone() const;
 private:
+    ReferenceContinuous3DFunction(const ReferenceContinuous3DFunction& other);
     const Continuous3DFunction& function;
     int xsize, ysize, zsize;
     double xmin, xmax, ymin, ymax, zmin, zmax;

platforms/reference/src/ReferenceKernels.cpp

@@ -280,7 +280,7 @@ void ReferenceUpdateStateDataKernel::getPeriodicBoxVectors(ContextImpl& context,
     c = vectors[2];
 }
 
-void ReferenceUpdateStateDataKernel::setPeriodicBoxVectors(ContextImpl& context, const Vec3& a, const Vec3& b, const Vec3& c) const {
+void ReferenceUpdateStateDataKernel::setPeriodicBoxVectors(ContextImpl& context, const Vec3& a, const Vec3& b, const Vec3& c) {
     RealVec& box = extractBoxSize(context);
     box[0] = (RealOpenMM) a[0];
     box[1] = (RealOpenMM) b[1];
@@ -370,6 +370,7 @@ void ReferenceCalcHarmonicBondForceKernel::initialize(const System& system, cons
         bondParamArray[i][0] = (RealOpenMM) length;
         bondParamArray[i][1] = (RealOpenMM) k;
     }
+    usePeriodic = force.usesPeriodicBoundaryConditions();
 }
 
 double ReferenceCalcHarmonicBondForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
@@ -378,6 +379,8 @@ double ReferenceCalcHarmonicBondForceKernel::execute(ContextImpl& context, bool
     RealOpenMM energy = 0;
     ReferenceBondForce refBondForce;
     ReferenceHarmonicBondIxn harmonicBond;
+    if (usePeriodic)
+        harmonicBond.setPeriodic(extractBoxVectors(context));
     refBondForce.calculateForce(numBonds, bondIndexArray, posData, bondParamArray, forceData, includeEnergy ? &energy : NULL, harmonicBond);
     return energy;
 }
@@ -409,6 +412,7 @@ ReferenceCalcCustomBondForceKernel::~ReferenceCalcCustomBondForceKernel() {
 void ReferenceCalcCustomBondForceKernel::initialize(const System& system, const CustomBondForce& force) {
     numBonds = force.getNumBonds();
     int numParameters = force.getNumPerBondParameters();
+    usePeriodic = force.usesPeriodicBoundaryConditions();
 
     // Build the arrays.
 
@@ -448,8 +452,10 @@ double ReferenceCalcCustomBondForceKernel::execute(ContextImpl& context, bool in
     for (int i = 0; i < (int) globalParameterNames.size(); i++)
         globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
     ReferenceBondForce refBondForce;
-    ReferenceCustomBondIxn harmonicBond(energyExpression, forceExpression, parameterNames, globalParameters);
-    refBondForce.calculateForce(numBonds, bondIndexArray, posData, bondParamArray, forceData, includeEnergy ? &energy : NULL, harmonicBond);
+    ReferenceCustomBondIxn bond(energyExpression, forceExpression, parameterNames, globalParameters);
+    if (usePeriodic)
+        bond.setPeriodic(extractBoxVectors(context));
+    refBondForce.calculateForce(numBonds, bondIndexArray, posData, bondParamArray, forceData, includeEnergy ? &energy : NULL, bond);
     return energy;
 }
 
@@ -490,6 +496,7 @@ void ReferenceCalcHarmonicAngleForceKernel::initialize(const System& system, con
         angleParamArray[i][0] = (RealOpenMM) angle;
         angleParamArray[i][1] = (RealOpenMM) k;
     }
+    usePeriodic = force.usesPeriodicBoundaryConditions();
 }
 
 double ReferenceCalcHarmonicAngleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
@@ -498,6 +505,8 @@ double ReferenceCalcHarmonicAngleForceKernel::execute(ContextImpl& context, bool
     RealOpenMM energy = 0;
     ReferenceBondForce refBondForce;
     ReferenceAngleBondIxn angleBond;
+    if (usePeriodic)
+        angleBond.setPeriodic(extractBoxVectors(context));
     refBondForce.calculateForce(numAngles, angleIndexArray, posData, angleParamArray, forceData, includeEnergy ? &energy : NULL, angleBond);
     return energy;
 }
@@ -527,6 +536,7 @@ ReferenceCalcCustomAngleForceKernel::~ReferenceCalcCustomAngleForceKernel() {
 void ReferenceCalcCustomAngleForceKernel::initialize(const System& system, const CustomAngleForce& force) {
     numAngles = force.getNumAngles();
     int numParameters = force.getNumPerAngleParameters();
+    usePeriodic = force.usesPeriodicBoundaryConditions();
 
     // Build the arrays.
 
@@ -568,6 +578,8 @@ double ReferenceCalcCustomAngleForceKernel::execute(ContextImpl& context, bool i
         globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
     ReferenceBondForce refBondForce;
     ReferenceCustomAngleIxn customAngle(energyExpression, forceExpression, parameterNames, globalParameters);
+    if (usePeriodic)
+        customAngle.setPeriodic(extractBoxVectors(context));
     refBondForce.calculateForce(numAngles, angleIndexArray, posData, angleParamArray, forceData, includeEnergy ? &energy : NULL, customAngle);
     return energy;
 }
@@ -611,6 +623,7 @@ void ReferenceCalcPeriodicTorsionForceKernel::initialize(const System& system, c
         torsionParamArray[i][1] = (RealOpenMM) phase;
         torsionParamArray[i][2] = (RealOpenMM) periodicity;
     }
+    usePeriodic = force.usesPeriodicBoundaryConditions();
 }
 
 double ReferenceCalcPeriodicTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
@@ -619,6 +632,8 @@ double ReferenceCalcPeriodicTorsionForceKernel::execute(ContextImpl& context, bo
     RealOpenMM energy = 0;
     ReferenceBondForce refBondForce;
     ReferenceProperDihedralBond periodicTorsionBond;
+    if (usePeriodic)
+        periodicTorsionBond.setPeriodic(extractBoxVectors(context));
     refBondForce.calculateForce(numTorsions, torsionIndexArray, posData, torsionParamArray, forceData, includeEnergy ? &energy : NULL, periodicTorsionBond);
     return energy;
 }
@@ -665,6 +680,7 @@ void ReferenceCalcRBTorsionForceKernel::initialize(const System& system, const R
         torsionParamArray[i][4] = (RealOpenMM) c4;
         torsionParamArray[i][5] = (RealOpenMM) c5;
     }
+    usePeriodic = force.usesPeriodicBoundaryConditions();
 }
 
 double ReferenceCalcRBTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
@@ -673,6 +689,8 @@ double ReferenceCalcRBTorsionForceKernel::execute(ContextImpl& context, bool inc
     RealOpenMM energy = 0;
     ReferenceBondForce refBondForce;
     ReferenceRbDihedralBond rbTorsionBond;
+    if (usePeriodic)
+        rbTorsionBond.setPeriodic(extractBoxVectors(context));
     refBondForce.calculateForce(numTorsions, torsionIndexArray, posData, torsionParamArray, forceData, includeEnergy ? &energy : NULL, rbTorsionBond);
     return energy;
 }
@@ -722,6 +740,7 @@ void ReferenceCalcCMAPTorsionForceKernel::initialize(const System& system, const
         force.getTorsionParameters(i, torsionMaps[i], torsionIndices[i][0], torsionIndices[i][1], torsionIndices[i][2],
             torsionIndices[i][3], torsionIndices[i][4], torsionIndices[i][5], torsionIndices[i][6], torsionIndices[i][7]);
     }
+    usePeriodic = force.usesPeriodicBoundaryConditions();
 }
 
 double ReferenceCalcCMAPTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
@@ -729,6 +748,8 @@ double ReferenceCalcCMAPTorsionForceKernel::execute(ContextImpl& context, bool i
     vector<RealVec>& forceData = extractForces(context);
     RealOpenMM totalEnergy = 0;
     ReferenceCMAPTorsionIxn torsion(coeff, torsionMaps, torsionIndices);
+    if (usePeriodic)
+        torsion.setPeriodic(extractBoxVectors(context));
     torsion.calculateIxn(posData, forceData, &totalEnergy);
     return totalEnergy;
 }
@@ -775,6 +796,7 @@ ReferenceCalcCustomTorsionForceKernel::~ReferenceCalcCustomTorsionForceKernel()
 void ReferenceCalcCustomTorsionForceKernel::initialize(const System& system, const CustomTorsionForce& force) {
     numTorsions = force.getNumTorsions();
     int numParameters = force.getNumPerTorsionParameters();
+    usePeriodic = force.usesPeriodicBoundaryConditions();
 
     // Build the arrays.
 
@@ -817,6 +839,8 @@ double ReferenceCalcCustomTorsionForceKernel::execute(ContextImpl& context, bool
         globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
     ReferenceBondForce refBondForce;
     ReferenceCustomTorsionIxn customTorsion(energyExpression, forceExpression, parameterNames, globalParameters);
+    if (usePeriodic)
+        customTorsion.setPeriodic(extractBoxVectors(context));
     refBondForce.calculateForce(numTorsions, torsionIndexArray, posData, torsionParamArray, forceData, includeEnergy ? &energy : NULL, customTorsion);
     return energy;
 }
@@ -1644,6 +1668,7 @@ ReferenceCalcCustomCentroidBondForceKernel::~ReferenceCalcCustomCentroidBondForc
 }
 
 void ReferenceCalcCustomCentroidBondForceKernel::initialize(const System& system, const CustomCentroidBondForce& force) {
+    usePeriodic = force.usesPeriodicBoundaryConditions();
 
     // Build the arrays.
 
@@ -1697,6 +1722,8 @@ double ReferenceCalcCustomCentroidBondForceKernel::execute(ContextImpl& context,
     map<string, double> globalParameters;
     for (int i = 0; i < (int) globalParameterNames.size(); i++)
         globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
+    if (usePeriodic)
+        ixn->setPeriodic(extractBoxVectors(context));
     ixn->calculatePairIxn(posData, bondParamArray, globalParameters, forceData, includeEnergy ? &energy : NULL);
     return energy;
 }
@@ -1728,6 +1755,7 @@ ReferenceCalcCustomCompoundBondForceKernel::~ReferenceCalcCustomCompoundBondForc
 }
 
 void ReferenceCalcCustomCompoundBondForceKernel::initialize(const System& system, const CustomCompoundBondForce& force) {
+    usePeriodic = force.usesPeriodicBoundaryConditions();
 
     // Build the arrays.
 
@@ -1774,6 +1802,8 @@ double ReferenceCalcCustomCompoundBondForceKernel::execute(ContextImpl& context,
     map<string, double> globalParameters;
     for (int i = 0; i < (int) globalParameterNames.size(); i++)
         globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
+    if (usePeriodic)
+        ixn->setPeriodic(extractBoxVectors(context));
     ixn->calculatePairIxn(posData, bondParamArray, globalParameters, forceData, includeEnergy ? &energy : NULL);
     return energy;
 }

platforms/reference/src/ReferenceTabulatedFunction.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) 2014 Stanford University and the Authors.           *
+ * Portions copyright (c) 2014-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -80,6 +80,13 @@ ReferenceContinuous1DFunction::ReferenceContinuous1DFunction(const Continuous1DF
     SplineFitter::createNaturalSpline(x, values, derivs);
 }
 
+ReferenceContinuous1DFunction::ReferenceContinuous1DFunction(const ReferenceContinuous1DFunction& other) : function(other.function) {
+    function.getFunctionParameters(values, min, max);
+    x = other.x;
+    values = other.values;
+    derivs = other.derivs;
+}
+
 int ReferenceContinuous1DFunction::getNumArguments() const {
     return 1;
 }
@@ -99,7 +106,7 @@ double ReferenceContinuous1DFunction::evaluateDerivative(const double* arguments
 }
 
 CustomFunction* ReferenceContinuous1DFunction::clone() const {
-    return new ReferenceContinuous1DFunction(function);
+    return new ReferenceContinuous1DFunction(*this);
 }
 
 ReferenceContinuous2DFunction::ReferenceContinuous2DFunction(const Continuous2DFunction& function) : function(function) {
@@ -113,6 +120,14 @@ ReferenceContinuous2DFunction::ReferenceContinuous2DFunction(const Continuous2DF
     SplineFitter::create2DNaturalSpline(x, y, values, c);
 }
 
+ReferenceContinuous2DFunction::ReferenceContinuous2DFunction(const ReferenceContinuous2DFunction& other) : function(other.function) {
+    function.getFunctionParameters(xsize, ysize, values, xmin, xmax, ymin, ymax);
+    x = other.x;
+    y = other.y;
+    values = other.values;
+    c = other.c;
+}
+
 int ReferenceContinuous2DFunction::getNumArguments() const {
     return 2;
 }
@@ -144,7 +159,7 @@ double ReferenceContinuous2DFunction::evaluateDerivative(const double* arguments
 }
 
 CustomFunction* ReferenceContinuous2DFunction::clone() const {
-    return new ReferenceContinuous2DFunction(function);
+    return new ReferenceContinuous2DFunction(*this);
 }
 
 ReferenceContinuous3DFunction::ReferenceContinuous3DFunction(const Continuous3DFunction& function) : function(function) {
@@ -161,6 +176,15 @@ ReferenceContinuous3DFunction::ReferenceContinuous3DFunction(const Continuous3DF
     SplineFitter::create3DNaturalSpline(x, y, z, values, c);
 }
 
+ReferenceContinuous3DFunction::ReferenceContinuous3DFunction(const ReferenceContinuous3DFunction& other) : function(other.function) {
+    function.getFunctionParameters(xsize, ysize, zsize, values, xmin, xmax, ymin, ymax, zmin, zmax);
+    x = other.x;
+    y = other.y;
+    z = other.z;
+    values = other.values;
+    c = other.c;
+}
+
 int ReferenceContinuous3DFunction::getNumArguments() const {
     return 3;
 }
@@ -200,7 +224,7 @@ double ReferenceContinuous3DFunction::evaluateDerivative(const double* arguments
 }
 
 CustomFunction* ReferenceContinuous3DFunction::clone() const {
-    return new ReferenceContinuous3DFunction(function);
+    return new ReferenceContinuous3DFunction(*this);
 }
 
 ReferenceDiscrete1DFunction::ReferenceDiscrete1DFunction(const Discrete1DFunction& function) : function(function) {

platforms/reference/src/SimTKReference/ReferenceAngleBondIxn.cpp

@@ -38,7 +38,7 @@ using namespace OpenMM;
 
    --------------------------------------------------------------------------------------- */
 
-ReferenceAngleBondIxn::ReferenceAngleBondIxn() {
+ReferenceAngleBondIxn::ReferenceAngleBondIxn() : usePeriodic(false) {
 
    // ---------------------------------------------------------------------------------------
 
@@ -64,6 +64,13 @@ ReferenceAngleBondIxn::~ReferenceAngleBondIxn() {
 
 }
 
+void ReferenceAngleBondIxn::setPeriodic(OpenMM::RealVec* vectors) {
+    usePeriodic = true;
+    boxVectors[0] = vectors[0];
+    boxVectors[1] = vectors[1];
+    boxVectors[2] = vectors[2];
+}
+
 /**---------------------------------------------------------------------------------------
 
    Get dEdR and energy term for angle bond
@@ -145,8 +152,14 @@ void ReferenceAngleBondIxn::calculateBondIxn(int* atomIndices,
    int atomAIndex = atomIndices[0];
    int atomBIndex = atomIndices[1];
    int atomCIndex = atomIndices[2];
-   ReferenceForce::getDeltaR(atomCoordinates[atomAIndex], atomCoordinates[atomBIndex], deltaR[0]);  
-   ReferenceForce::getDeltaR(atomCoordinates[atomCIndex], atomCoordinates[atomBIndex], deltaR[1]);  
+   if (usePeriodic) {
+      ReferenceForce::getDeltaRPeriodic(atomCoordinates[atomAIndex], atomCoordinates[atomBIndex], boxVectors, deltaR[0]);  
+      ReferenceForce::getDeltaRPeriodic(atomCoordinates[atomCIndex], atomCoordinates[atomBIndex], boxVectors, deltaR[1]);  
+   }
+   else {
+      ReferenceForce::getDeltaR(atomCoordinates[atomAIndex], atomCoordinates[atomBIndex], deltaR[0]);  
+      ReferenceForce::getDeltaR(atomCoordinates[atomCIndex], atomCoordinates[atomBIndex], deltaR[1]);  
+   }
 
    RealOpenMM pVector[threeI];
    SimTKOpenMMUtilities::crossProductVector3(deltaR[0], deltaR[1], pVector);

platforms/reference/src/SimTKReference/ReferenceCMAPTorsionIxn.cpp

 
-/* Portions copyright (c) 2010 Stanford University and Simbios.
+/* Portions copyright (c) 2010-2016 Stanford University and Simbios.
  * Contributors: Peter Eastman
  *
  * Permission is hereby granted, free of charge, to any person obtaining
@@ -36,7 +36,14 @@ using namespace OpenMM;
 
 ReferenceCMAPTorsionIxn::ReferenceCMAPTorsionIxn(const vector<vector<vector<RealOpenMM> > >& coeff,
         const vector<int>& torsionMaps, const vector<vector<int> >& torsionIndices) :
-        coeff(coeff), torsionMaps(torsionMaps), torsionIndices(torsionIndices) {
+        coeff(coeff), torsionMaps(torsionMaps), torsionIndices(torsionIndices), usePeriodic(false) {
+}
+
+void ReferenceCMAPTorsionIxn::setPeriodic(OpenMM::RealVec* vectors) {
+    usePeriodic = true;
+    boxVectors[0] = vectors[0];
+    boxVectors[1] = vectors[1];
+    boxVectors[2] = vectors[2];
 }
 
 /**---------------------------------------------------------------------------------------
@@ -83,13 +90,23 @@ void ReferenceCMAPTorsionIxn::calculateOneIxn(int index, vector<RealVec>& atomCo
     // Compute deltas between the various atoms involved.
 
     RealOpenMM deltaA[3][ReferenceForce::LastDeltaRIndex];
-    ReferenceForce::getDeltaR(atomCoordinates[a2], atomCoordinates[a1], deltaA[0]);
-    ReferenceForce::getDeltaR(atomCoordinates[a2], atomCoordinates[a3], deltaA[1]);
-    ReferenceForce::getDeltaR(atomCoordinates[a4], atomCoordinates[a3], deltaA[2]);
     RealOpenMM deltaB[3][ReferenceForce::LastDeltaRIndex];
-    ReferenceForce::getDeltaR(atomCoordinates[b2], atomCoordinates[b1], deltaB[0]);
-    ReferenceForce::getDeltaR(atomCoordinates[b2], atomCoordinates[b3], deltaB[1]);
-    ReferenceForce::getDeltaR(atomCoordinates[b4], atomCoordinates[b3], deltaB[2]);
+    if (usePeriodic) {
+        ReferenceForce::getDeltaRPeriodic(atomCoordinates[a2], atomCoordinates[a1], boxVectors, deltaA[0]);
+        ReferenceForce::getDeltaRPeriodic(atomCoordinates[a2], atomCoordinates[a3], boxVectors, deltaA[1]);
+        ReferenceForce::getDeltaRPeriodic(atomCoordinates[a4], atomCoordinates[a3], boxVectors, deltaA[2]);
+        ReferenceForce::getDeltaRPeriodic(atomCoordinates[b2], atomCoordinates[b1], boxVectors, deltaB[0]);
+        ReferenceForce::getDeltaRPeriodic(atomCoordinates[b2], atomCoordinates[b3], boxVectors, deltaB[1]);
+        ReferenceForce::getDeltaRPeriodic(atomCoordinates[b4], atomCoordinates[b3], boxVectors, deltaB[2]);
+    }
+    else {
+        ReferenceForce::getDeltaR(atomCoordinates[a2], atomCoordinates[a1], deltaA[0]);
+        ReferenceForce::getDeltaR(atomCoordinates[a2], atomCoordinates[a3], deltaA[1]);
+        ReferenceForce::getDeltaR(atomCoordinates[a4], atomCoordinates[a3], deltaA[2]);
+        ReferenceForce::getDeltaR(atomCoordinates[b2], atomCoordinates[b1], deltaB[0]);
+        ReferenceForce::getDeltaR(atomCoordinates[b2], atomCoordinates[b3], deltaB[1]);
+        ReferenceForce::getDeltaR(atomCoordinates[b4], atomCoordinates[b3], deltaB[2]);
+    }
 
     // Visual Studio complains if crossProduct declared as 'crossProduct[2][3]'
 

platforms/reference/src/SimTKReference/ReferenceCustomAngleIxn.cpp

-/* Portions copyright (c) 2010-2013 Stanford University and Simbios.
+/* Portions copyright (c) 2010-2016 Stanford University and Simbios.
  * Contributors: Peter Eastman
  *
  * Permission is hereby granted, free of charge, to any person obtaining
@@ -39,7 +39,7 @@ using namespace std;
 
 ReferenceCustomAngleIxn::ReferenceCustomAngleIxn(const Lepton::CompiledExpression& energyExpression,
         const Lepton::CompiledExpression& forceExpression, const vector<string>& parameterNames, map<string, double> globalParameters) :
-        energyExpression(energyExpression), forceExpression(forceExpression) {
+        energyExpression(energyExpression), forceExpression(forceExpression), usePeriodic(false) {
     
     energyTheta = ReferenceForce::getVariablePointer(this->energyExpression, "theta");
     forceTheta = ReferenceForce::getVariablePointer(this->forceExpression, "theta");
@@ -61,13 +61,13 @@ ReferenceCustomAngleIxn::ReferenceCustomAngleIxn(const Lepton::CompiledExpressio
    --------------------------------------------------------------------------------------- */
 
 ReferenceCustomAngleIxn::~ReferenceCustomAngleIxn() {
+}
 
-   // ---------------------------------------------------------------------------------------
-
-   // static const char* methodName = "\nReferenceCustomAngleIxn::~ReferenceCustomAngleIxn";
-
-   // ---------------------------------------------------------------------------------------
-
+void ReferenceCustomAngleIxn::setPeriodic(OpenMM::RealVec* vectors) {
+    usePeriodic = true;
+    boxVectors[0] = vectors[0];
+    boxVectors[1] = vectors[1];
+    boxVectors[2] = vectors[2];
 }
 
 /**---------------------------------------------------------------------------------------
@@ -106,8 +106,14 @@ void ReferenceCustomAngleIxn::calculateBondIxn(int* atomIndices,
    int atomAIndex = atomIndices[0];
    int atomBIndex = atomIndices[1];
    int atomCIndex = atomIndices[2];
-   ReferenceForce::getDeltaR(atomCoordinates[atomAIndex], atomCoordinates[atomBIndex], deltaR[0]);
-   ReferenceForce::getDeltaR(atomCoordinates[atomCIndex], atomCoordinates[atomBIndex], deltaR[1]);
+   if (usePeriodic) {
+      ReferenceForce::getDeltaRPeriodic(atomCoordinates[atomAIndex], atomCoordinates[atomBIndex], boxVectors, deltaR[0]);
+      ReferenceForce::getDeltaRPeriodic(atomCoordinates[atomCIndex], atomCoordinates[atomBIndex], boxVectors, deltaR[1]);
+   }
+   else {
+      ReferenceForce::getDeltaR(atomCoordinates[atomAIndex], atomCoordinates[atomBIndex], deltaR[0]);
+      ReferenceForce::getDeltaR(atomCoordinates[atomCIndex], atomCoordinates[atomBIndex], deltaR[1]);
+   }
    RealOpenMM pVector[3];
    SimTKOpenMMUtilities::crossProductVector3(deltaR[0], deltaR[1], pVector);
    RealOpenMM rp = SQRT(DOT3(pVector, pVector));

platforms/reference/src/SimTKReference/ReferenceCustomBondIxn.cpp

 
-/* Portions copyright (c) 2009-2013 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
@@ -40,7 +40,7 @@ using namespace OpenMM;
 
 ReferenceCustomBondIxn::ReferenceCustomBondIxn(const Lepton::CompiledExpression& energyExpression,
         const Lepton::CompiledExpression& forceExpression, const vector<string>& parameterNames, map<string, double> globalParameters) :
-        energyExpression(energyExpression), forceExpression(forceExpression) {
+        energyExpression(energyExpression), forceExpression(forceExpression), usePeriodic(false) {
     energyR = ReferenceForce::getVariablePointer(this->energyExpression, "r");
     forceR = ReferenceForce::getVariablePointer(this->forceExpression, "r");
     numParameters = parameterNames.size();
@@ -61,13 +61,13 @@ ReferenceCustomBondIxn::ReferenceCustomBondIxn(const Lepton::CompiledExpression&
    --------------------------------------------------------------------------------------- */
 
 ReferenceCustomBondIxn::~ReferenceCustomBondIxn() {
+}
 
-   // ---------------------------------------------------------------------------------------
-
-   // static const char* methodName = "\nReferenceCustomBondIxn::~ReferenceCustomBondIxn";
-
-   // ---------------------------------------------------------------------------------------
-
+void ReferenceCustomBondIxn::setPeriodic(OpenMM::RealVec* vectors) {
+    usePeriodic = true;
+    boxVectors[0] = vectors[0];
+    boxVectors[1] = vectors[1];
+    boxVectors[2] = vectors[2];
 }
 
 /**---------------------------------------------------------------------------------------
@@ -108,7 +108,10 @@ void ReferenceCustomBondIxn::calculateBondIxn(int* atomIndices,
 
    int atomAIndex = atomIndices[0];
    int atomBIndex = atomIndices[1];
-   ReferenceForce::getDeltaR(atomCoordinates[atomAIndex], atomCoordinates[atomBIndex], deltaR);
+   if (usePeriodic)
+       ReferenceForce::getDeltaRPeriodic(atomCoordinates[atomAIndex], atomCoordinates[atomBIndex], boxVectors, deltaR);
+   else
+       ReferenceForce::getDeltaR(atomCoordinates[atomAIndex], atomCoordinates[atomBIndex], deltaR);
    
    ReferenceForce::setVariable(energyR, deltaR[ReferenceForce::RIndex]);
    ReferenceForce::setVariable(forceR, deltaR[ReferenceForce::RIndex]);