Reference implementation of periodic boundary conditions for AMOEBA bonded forces

plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceBondForce.cpp

@@ -28,6 +28,13 @@
 using std::vector;
 using namespace OpenMM;
 
+void AmoebaReferenceBondForce::setPeriodic(OpenMM::RealVec* vectors) {
+    usePeriodic = true;
+    boxVectors[0] = vectors[0];
+    boxVectors[1] = vectors[1];
+    boxVectors[2] = vectors[2];
+}
+
 /**---------------------------------------------------------------------------------------
 
    Calculate Amoeba bond ixn (force and energy)
@@ -63,7 +70,10 @@ RealOpenMM AmoebaReferenceBondForce::calculateBondIxn(const RealVec& positionAto
    // get deltaR, R2, and R between 2 atoms
 
    std::vector<RealOpenMM> deltaR;
-   AmoebaReferenceForce::loadDeltaR(positionAtomA, positionAtomB, deltaR);
+   if (usePeriodic)
+       AmoebaReferenceForce::loadDeltaRPeriodic(positionAtomA, positionAtomB, deltaR, boxVectors);
+   else
+       AmoebaReferenceForce::loadDeltaR(positionAtomA, positionAtomB, deltaR);
    RealOpenMM r               = AmoebaReferenceForce::getNorm3(deltaR);
 
    // deltaIdeal = r - r_0

plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceBondForce.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
@@ -40,7 +40,7 @@ public:
        
         --------------------------------------------------------------------------------------- */
  
-    AmoebaReferenceBondForce() {};
+    AmoebaReferenceBondForce() : usePeriodic(false) {};
  
     /**---------------------------------------------------------------------------------------
        
@@ -49,7 +49,16 @@ public:
         --------------------------------------------------------------------------------------- */
  
     ~AmoebaReferenceBondForce() {};
- 
+
+    /**---------------------------------------------------------------------------------------
+
+       Set the force to use periodic boundary conditions.
+      
+       @param vectors    the vectors defining the periodic box
+      
+       --------------------------------------------------------------------------------------- */
+      
+    void setPeriodic(OpenMM::RealVec* vectors);
  
      /**---------------------------------------------------------------------------------------
      
@@ -79,6 +88,9 @@ public:
 
 private:
 
+    bool usePeriodic;
+    RealVec boxVectors[3];
+
      /**---------------------------------------------------------------------------------------
      
         Calculate Amoeba bond ixns (force and energy)

plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceForce.cpp

@@ -39,18 +39,33 @@ using namespace OpenMM;
 
 void AmoebaReferenceForce::loadDeltaR(const RealVec& xVector, const RealVec& yVector,
                                       std::vector<RealOpenMM>& deltaR) {
+    deltaR.resize(0);
+    deltaR.push_back(yVector[0] - xVector[0]);
+    deltaR.push_back(yVector[1] - xVector[1]);
+    deltaR.push_back(yVector[2] - xVector[2]);
+}
 
+/**---------------------------------------------------------------------------------------
 
-   // ---------------------------------------------------------------------------------------
+   Load delta of two vectors, applying periodic boundary conditions
 
-   //static const std::string methodName = "AmoebaReferenceForce::loadDeltaR";
+   @param xVector      first vector
+   @param yVector      second vector
+   @param deltaR       output vector: y - x
+   @param boxVectors   periodic box vectors
 
-   // ---------------------------------------------------------------------------------------
+   --------------------------------------------------------------------------------------- */
 
+void AmoebaReferenceForce::loadDeltaRPeriodic(const RealVec& xVector, const RealVec& yVector,
+                                      std::vector<RealOpenMM>& deltaR, const RealVec* boxVectors) {
+    RealVec diff = yVector-xVector;
+    diff -= boxVectors[2]*floor(diff[2]/boxVectors[2][2]+0.5);
+    diff -= boxVectors[1]*floor(diff[1]/boxVectors[1][1]+0.5);
+    diff -= boxVectors[0]*floor(diff[0]/boxVectors[0][0]+0.5);
     deltaR.resize(0);
-    deltaR.push_back(yVector[0] - xVector[0]);
-    deltaR.push_back(yVector[1] - xVector[1]);
-    deltaR.push_back(yVector[2] - xVector[2]);
+    deltaR.push_back(diff[0]);
+    deltaR.push_back(diff[1]);
+    deltaR.push_back(diff[2]);
 }
 
 /**---------------------------------------------------------------------------------------
@@ -64,13 +79,6 @@ void AmoebaReferenceForce::loadDeltaR(const RealVec& xVector, const RealVec& yVe
    --------------------------------------------------------------------------------------- */
 
 RealOpenMM AmoebaReferenceForce::getNormSquared3(const std::vector<RealOpenMM>& inputVector) {
-
-   // ---------------------------------------------------------------------------------------
-
-   //static const std::string methodName = "AmoebaReferenceForce::getNorm3";
-
-   // ---------------------------------------------------------------------------------------
-
    // get 3 norm
 
    return (inputVector[0]*inputVector[0] + inputVector[1]*inputVector[1] + inputVector[2]*inputVector[2]);
@@ -87,13 +95,6 @@ RealOpenMM AmoebaReferenceForce::getNormSquared3(const std::vector<RealOpenMM>&
    --------------------------------------------------------------------------------------- */
 
 RealOpenMM AmoebaReferenceForce::getNormSquared3(const RealOpenMM* inputVector) {
-
-   // ---------------------------------------------------------------------------------------
-
-   //static const std::string methodName = "AmoebaReferenceForce::getNorm3";
-
-   // ---------------------------------------------------------------------------------------
-
    // get 3 norm
 
    return (inputVector[0]*inputVector[0] + inputVector[1]*inputVector[1] + inputVector[2]*inputVector[2]);
@@ -110,39 +111,18 @@ RealOpenMM AmoebaReferenceForce::getNormSquared3(const RealOpenMM* inputVector)
    --------------------------------------------------------------------------------------- */
 
 RealOpenMM AmoebaReferenceForce::getNorm3(const std::vector<RealOpenMM>& inputVector) {
-
-   // ---------------------------------------------------------------------------------------
-
-   //static const std::string methodName = "AmoebaReferenceForce::getNorm3";
-
-   // ---------------------------------------------------------------------------------------
-
    // get 3 norm
 
    return SQRT(inputVector[0]*inputVector[0] + inputVector[1]*inputVector[1] + inputVector[2]*inputVector[2]);
 }
 
 RealOpenMM AmoebaReferenceForce::getNorm3(const RealOpenMM* inputVector) {
-
-   // ---------------------------------------------------------------------------------------
-
-   //static const std::string methodName = "AmoebaReferenceForce::getNorm3";
-
-   // ---------------------------------------------------------------------------------------
-
    // get 3 norm
 
    return SQRT(inputVector[0]*inputVector[0] + inputVector[1]*inputVector[1] + inputVector[2]*inputVector[2]);
 }
 
 RealOpenMM AmoebaReferenceForce::normalizeVector3(RealOpenMM* inputVector) {
-
-   // ---------------------------------------------------------------------------------------
-
-   //static const std::string methodName = "AmoebaReferenceForce::normalizeVector3";
-
-   // ---------------------------------------------------------------------------------------
-
     RealOpenMM norm   = SQRT(inputVector[0]*inputVector[0] + inputVector[1]*inputVector[1] + inputVector[2]*inputVector[2]);
     if (norm > 0.0) {
         RealOpenMM normI  = 1.0/norm;
@@ -166,13 +146,6 @@ RealOpenMM AmoebaReferenceForce::normalizeVector3(RealOpenMM* inputVector) {
    --------------------------------------------------------------------------------------- */
 
 RealOpenMM AmoebaReferenceForce::getDotProduct3(const std::vector<RealOpenMM>& xVector, const std::vector<RealOpenMM>& yVector) {
-
-   // ---------------------------------------------------------------------------------------
-
-   //static const std::string methodName = "AmoebaReferenceForce::getDotProduct3";
-
-   // ---------------------------------------------------------------------------------------
-
    // get dot product
 
    return xVector[0]*yVector[0] + xVector[1]*yVector[1] + xVector[2]*yVector[2];
@@ -190,26 +163,12 @@ RealOpenMM AmoebaReferenceForce::getDotProduct3(const std::vector<RealOpenMM>& x
    --------------------------------------------------------------------------------------- */
 
 RealOpenMM AmoebaReferenceForce::getDotProduct3(const RealOpenMM* xVector, const RealOpenMM* yVector) {
-
-   // ---------------------------------------------------------------------------------------
-
-   //static const std::string methodName = "AmoebaReferenceForce::getDotProduct3";
-
-   // ---------------------------------------------------------------------------------------
-
    // get dot product
 
    return xVector[0]*yVector[0] + xVector[1]*yVector[1] + xVector[2]*yVector[2];
 }
 
 RealOpenMM AmoebaReferenceForce::getDotProduct3(const RealOpenMM* xVector, const OpenMM::Vec3& yVector) {
-
-   // ---------------------------------------------------------------------------------------
-
-   //static const std::string methodName = "AmoebaReferenceForce::getDotProduct3";
-
-   // ---------------------------------------------------------------------------------------
-
    // get dot product
 
    return xVector[0]*yVector[0] + xVector[1]*yVector[1] + xVector[2]*yVector[2];
@@ -228,13 +187,6 @@ RealOpenMM AmoebaReferenceForce::getDotProduct3(const RealOpenMM* xVector, const
    --------------------------------------------------------------------------------------- */
 
 RealOpenMM AmoebaReferenceForce::getDotProduct3(unsigned int vectorOffset, const std::vector<RealOpenMM>& xVector, const RealOpenMM* yVector) {
-
-   // ---------------------------------------------------------------------------------------
-
-   //static const std::string methodName = "AmoebaReferenceForce::getDotProduct3";
-
-   // ---------------------------------------------------------------------------------------
-
    // get dot product
 
    return xVector[vectorOffset+0]*yVector[0] + xVector[vectorOffset+1]*yVector[1] + xVector[vectorOffset+2]*yVector[2];
@@ -253,18 +205,9 @@ RealOpenMM AmoebaReferenceForce::getDotProduct3(unsigned int vectorOffset, const
 void AmoebaReferenceForce::getCrossProduct(const std::vector<RealOpenMM>& xVector,
                                            const std::vector<RealOpenMM>& yVector,
                                            std::vector<RealOpenMM>& zVector) {
-
-   // ---------------------------------------------------------------------------------------
-
-   //static const std::string methodName = "AmoebaReferenceForce::getCrossProduct";
-
-   // ---------------------------------------------------------------------------------------
-
    zVector[0]  = xVector[1]*yVector[2] - xVector[2]*yVector[1];
    zVector[1]  = xVector[2]*yVector[0] - xVector[0]*yVector[2];
    zVector[2]  = xVector[0]*yVector[1] - xVector[1]*yVector[0];
-
-   return;
 }
 
 /**---------------------------------------------------------------------------------------
@@ -280,17 +223,8 @@ void AmoebaReferenceForce::getCrossProduct(const std::vector<RealOpenMM>& xVecto
 void AmoebaReferenceForce::getCrossProduct(const RealOpenMM* xVector,
                                            const RealOpenMM* yVector,
                                            RealOpenMM* zVector) {
-
-   // ---------------------------------------------------------------------------------------
-
-   //static const std::string methodName = "AmoebaReferenceForce::getCrossProduct";
-
-   // ---------------------------------------------------------------------------------------
-
    zVector[0]  = xVector[1]*yVector[2] - xVector[2]*yVector[1];
    zVector[1]  = xVector[2]*yVector[0] - xVector[0]*yVector[2];
    zVector[2]  = xVector[0]*yVector[1] - xVector[1]*yVector[0];
-
-   return;
 }
 

plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceForce.h

@@ -64,6 +64,18 @@ public:
     
     static void loadDeltaR(const OpenMM::RealVec& xVector, const OpenMM::RealVec& yVector,
                            std::vector<RealOpenMM>& deltaR);
+    /**---------------------------------------------------------------------------------------
+
+       Load delta of two vectors, applying periodic boundary conditions
+
+       @param xVector      first vector
+       @param yVector      second vector
+       @param deltaR       output vector: y - x
+       @param boxVectors   periodic box vectors
+
+       --------------------------------------------------------------------------------------- */
+
+    static void loadDeltaRPeriodic(const RealVec& xVector, const RealVec& yVector, std::vector<RealOpenMM>& deltaR, const RealVec* boxVectors);
     
     /**---------------------------------------------------------------------------------------
     

plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceInPlaneAngleForce.cpp

@@ -24,10 +24,18 @@
 
 #include "AmoebaReferenceForce.h"
 #include "AmoebaReferenceInPlaneAngleForce.h"
+#include "ReferenceForce.h"
 
 using std::vector;
 using namespace OpenMM;
 
+void AmoebaReferenceInPlaneAngleForce::setPeriodic(OpenMM::RealVec* vectors) {
+    usePeriodic = true;
+    boxVectors[0] = vectors[0];
+    boxVectors[1] = vectors[1];
+    boxVectors[2] = vectors[2];
+}
+
 /**---------------------------------------------------------------------------------------
 
    Get dEdT and energy prefactor given cosine of angle :: the calculation for different
@@ -120,17 +128,6 @@ RealOpenMM AmoebaReferenceInPlaneAngleForce::calculateAngleIxn(const RealVec& po
                                                                         RealOpenMM angleCubic,                 RealOpenMM angleQuartic,
                                                                         RealOpenMM anglePentic,                RealOpenMM angleSextic,
                                                                         RealVec* forces) const {
-
-   // ---------------------------------------------------------------------------------------
-
-    //static const std::string methodName = "AmoebaReferenceInPlaneAngleForce::calculateAngleIxn";
- 
-    static const RealOpenMM zero          = 0.0;
-    static const RealOpenMM one           = 1.0;
-    static const RealOpenMM two           = 2.0;
-
-   // ---------------------------------------------------------------------------------------
-
     // T   = AD x CD
     // P   = B + T*delta
     // AP  = A - P
@@ -139,40 +136,48 @@ RealOpenMM AmoebaReferenceInPlaneAngleForce::calculateAngleIxn(const RealVec& po
 
     enum { AD, BD, CD, T, AP, P, CP, M, APxM, CPxM, ADxBD, BDxCD, TxCD, ADxT, dBxAD, CDxdB, LastDeltaAtomIndex };
 
-    std::vector<RealOpenMM> deltaR[LastDeltaAtomIndex];
-    for (int ii = 0; ii < LastDeltaAtomIndex; ii++) {
-        deltaR[ii].resize(3);
+    RealVec deltaR[LastDeltaAtomIndex];
+    if (usePeriodic) {
+        deltaR[AD] = ReferenceForce::getDeltaRPeriodic(positionAtomD, positionAtomA, boxVectors);
+        deltaR[BD] = ReferenceForce::getDeltaRPeriodic(positionAtomD, positionAtomB, boxVectors);
+        deltaR[CD] = ReferenceForce::getDeltaRPeriodic(positionAtomD, positionAtomC, boxVectors);
+    }
+    else {
+        deltaR[AD] = ReferenceForce::getDeltaR(positionAtomD, positionAtomA);
+        deltaR[BD] = ReferenceForce::getDeltaR(positionAtomD, positionAtomB);
+        deltaR[CD] = ReferenceForce::getDeltaR(positionAtomD, positionAtomC);
     }
-    AmoebaReferenceForce::loadDeltaR(positionAtomD, positionAtomA, deltaR[AD]);
-    AmoebaReferenceForce::loadDeltaR(positionAtomD, positionAtomB, deltaR[BD]);
-    AmoebaReferenceForce::loadDeltaR(positionAtomD, positionAtomC, deltaR[CD]);
  
-    AmoebaReferenceForce::getCrossProduct(deltaR[AD], deltaR[CD], deltaR[T]);
+    deltaR[T] = deltaR[AD].cross(deltaR[CD]);
 
-    RealOpenMM rT2     = AmoebaReferenceForce::getNormSquared3(deltaR[T]);
-    RealOpenMM delta   = AmoebaReferenceForce::getDotProduct3(deltaR[T], deltaR[BD])/rT2;
-         delta        *= -one;
- 
-    for (int ii = 0; ii < 3; ii++) {
-       deltaR[P][ii]  = positionAtomB[ii] + deltaR[T][ii]*delta;
-       deltaR[AP][ii] = positionAtomA[ii] - deltaR[P][ii];
-       deltaR[CP][ii] = positionAtomC[ii] - deltaR[P][ii];
+    RealOpenMM rT2     = deltaR[T].dot(deltaR[T]);
+    RealOpenMM delta   = deltaR[T].dot(deltaR[BD])/rT2;
+         delta        *= -1;
+
+    deltaR[P]  = positionAtomB + deltaR[T]*delta;
+    if (usePeriodic) {
+        deltaR[AP] = ReferenceForce::getDeltaRPeriodic(deltaR[P], positionAtomA, boxVectors);
+        deltaR[CP] = ReferenceForce::getDeltaRPeriodic(deltaR[P], positionAtomC, boxVectors);
+    }
+    else {
+        deltaR[AP] = ReferenceForce::getDeltaR(deltaR[P], positionAtomA);
+        deltaR[CP] = ReferenceForce::getDeltaR(deltaR[P], positionAtomC);
     }
  
-    RealOpenMM rAp2 = AmoebaReferenceForce::getNormSquared3(deltaR[AP]);
-    RealOpenMM rCp2 = AmoebaReferenceForce::getNormSquared3(deltaR[CP]);
-    if (rAp2 <= zero && rCp2 <= zero) {
-       return zero;
+    RealOpenMM rAp2 = deltaR[AP].dot(deltaR[AP]);
+    RealOpenMM rCp2 = deltaR[CP].dot(deltaR[CP]);
+    if (rAp2 <= 0 && rCp2 <= 0) {
+       return 0;
     }
  
-    AmoebaReferenceForce::getCrossProduct(deltaR[CP], deltaR[AP], deltaR[M]);
+    deltaR[M] = deltaR[CP].cross(deltaR[AP]);
  
-    RealOpenMM rm = AmoebaReferenceForce::getNorm3(deltaR[M]);
+    RealOpenMM rm = SQRT(deltaR[M].dot(deltaR[M]));
     if (rm < 1.0e-06) {
        rm = 1.0e-06;
     }
  
-    RealOpenMM dot     = AmoebaReferenceForce::getDotProduct3(deltaR[AP], deltaR[CP]);
+    RealOpenMM dot     = deltaR[AP].dot(deltaR[CP]);
     RealOpenMM cosine  = dot/SQRT(rAp2*rCp2);
  
     RealOpenMM dEdR;
@@ -182,64 +187,47 @@ RealOpenMM AmoebaReferenceInPlaneAngleForce::calculateAngleIxn(const RealVec& po
     RealOpenMM termA   = -dEdR/(rAp2*rm);
     RealOpenMM termC   =  dEdR/(rCp2*rm);
  
-    AmoebaReferenceForce::getCrossProduct(deltaR[AP], deltaR[M], deltaR[APxM]);
-    AmoebaReferenceForce::getCrossProduct(deltaR[CP], deltaR[M], deltaR[CPxM]);
+    deltaR[APxM] = deltaR[AP].cross(deltaR[M]);
+    deltaR[CPxM] = deltaR[CP].cross(deltaR[M]);
  
     // forces will be gathered here
  
     enum { dA, dB, dC, dD, LastDIndex };
-    std::vector<RealOpenMM> forceTerm[LastDIndex];
-    for (int ii = 0; ii < LastDIndex; ii++) {
-        forceTerm[ii].resize(3);
-    }
+    RealVec forceTerm[LastDIndex];
  
-    for (int ii = 0; ii < 3; ii++) {
-       forceTerm[dA][ii] = deltaR[APxM][ii]*termA;
-       forceTerm[dC][ii] = deltaR[CPxM][ii]*termC;
-       forceTerm[dB][ii] = -one*(forceTerm[dA][ii] + forceTerm[dC][ii]);
-    }
- 
-    RealOpenMM pTrT2  = AmoebaReferenceForce::getDotProduct3(forceTerm[dB], deltaR[T]);
+    forceTerm[dA] = deltaR[APxM]*termA;
+    forceTerm[dC] = deltaR[CPxM]*termC;
+    forceTerm[dB] = -(forceTerm[dA] + forceTerm[dC]);
+
+    RealOpenMM pTrT2  = forceTerm[dB].dot(deltaR[T]);
                pTrT2 /= rT2;
  
-    AmoebaReferenceForce::getCrossProduct(deltaR[CD], forceTerm[dB], deltaR[CDxdB]);
-    AmoebaReferenceForce::getCrossProduct(forceTerm[dB], deltaR[AD], deltaR[dBxAD]);
+    deltaR[CDxdB] = deltaR[CD].cross(forceTerm[dB]);
+    deltaR[dBxAD] = forceTerm[dB].cross(deltaR[AD]);
  
     if (FABS(pTrT2) > 1.0e-08) {
  
-       RealOpenMM delta2 = delta*two;
+        RealOpenMM delta2 = delta*2;
  
-       AmoebaReferenceForce::getCrossProduct(deltaR[BD], deltaR[CD], deltaR[BDxCD]);
-       AmoebaReferenceForce::getCrossProduct(deltaR[T],  deltaR[CD], deltaR[TxCD]);
-       AmoebaReferenceForce::getCrossProduct(deltaR[AD], deltaR[BD], deltaR[ADxBD]);
-       AmoebaReferenceForce::getCrossProduct(deltaR[AD], deltaR[T],  deltaR[ADxT]);
-       for (int ii = 0; ii < 3; ii++) {
-    
-          RealOpenMM term     = deltaR[BDxCD][ii] + delta2*deltaR[TxCD][ii];
-          forceTerm[dA][ii]  += delta*deltaR[CDxdB][ii] + term*pTrT2;
-    
-               term           = deltaR[ADxBD][ii] + delta2*deltaR[ADxT][ii];
-          forceTerm[dC][ii]  += delta*deltaR[dBxAD][ii] + term*pTrT2;
-    
-          forceTerm[dD][ii]  = -(forceTerm[dA][ii] + forceTerm[dB][ii] + forceTerm[dC][ii]);
-       }
+        deltaR[BDxCD] = forceTerm[dB].cross(deltaR[CD]);
+        deltaR[TxCD] = forceTerm[T].cross(deltaR[CD]);
+        deltaR[ADxBD] = forceTerm[AD].cross(deltaR[BD]);
+        deltaR[ADxT] = forceTerm[AD].cross(deltaR[T]);
+        RealVec term = deltaR[BDxCD] + deltaR[TxCD]*delta2;
+        forceTerm[dA] += deltaR[CDxdB]*delta + term*pTrT2;
+        term = deltaR[ADxBD] + deltaR[ADxT]*delta2;
+        forceTerm[dC] += deltaR[dBxAD]*delta + term*pTrT2;
+        forceTerm[dD] = -(forceTerm[dA] + forceTerm[dB] + forceTerm[dC]);
     } else {
-       for (int ii = 0; ii < 3; ii++) {
-    
-          forceTerm[dA][ii] += delta*deltaR[CDxdB][ii];
-          forceTerm[dC][ii] += delta*deltaR[dBxAD][ii];
- 
-          forceTerm[dD][ii]  = -(forceTerm[dA][ii] + forceTerm[dB][ii] + forceTerm[dC][ii]);
-       }
+        forceTerm[dA] += deltaR[CDxdB]*delta;
+        forceTerm[dC] += deltaR[dBxAD]*delta;
+        forceTerm[dD]  = -(forceTerm[dA] + forceTerm[dB] + forceTerm[dC]);
     }
  
     // accumulate forces
  
-    for (int jj = 0; jj < 4; jj++) {
-        forces[jj][0] = forceTerm[jj][0];
-        forces[jj][1] = forceTerm[jj][1];
-        forces[jj][2] = forceTerm[jj][2];
-    }
+    for (int jj = 0; jj < 4; jj++)
+        forces[jj] = forceTerm[jj];
  
     return energy;
 

plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceInPlaneAngleForce.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
@@ -40,7 +40,7 @@ public:
        
        --------------------------------------------------------------------------------------- */
  
-    AmoebaReferenceInPlaneAngleForce() {};
+    AmoebaReferenceInPlaneAngleForce() : usePeriodic(false) {};
  
     /**---------------------------------------------------------------------------------------
        
@@ -50,6 +50,16 @@ public:
  
     ~AmoebaReferenceInPlaneAngleForce() {};
  
+    /**---------------------------------------------------------------------------------------
+
+       Set the force to use periodic boundary conditions.
+      
+       @param vectors    the vectors defining the periodic box
+      
+       --------------------------------------------------------------------------------------- */
+      
+    void setPeriodic(OpenMM::RealVec* vectors);
+
      /**---------------------------------------------------------------------------------------
      
         Calculate Amoeba in-plane angle ixns (force and energy)
@@ -88,6 +98,9 @@ public:
 
 private:
 
+    bool usePeriodic;
+    RealVec boxVectors[3];
+
     /**---------------------------------------------------------------------------------------
     
        Get dEdT and energy prefactor given cosine of angle :: the calculation for different

plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceOutOfPlaneBendForce.cpp

@@ -28,6 +28,13 @@
 using std::vector;
 using namespace OpenMM;
 
+void AmoebaReferenceOutOfPlaneBendForce::setPeriodic(OpenMM::RealVec* vectors) {
+    usePeriodic = true;
+    boxVectors[0] = vectors[0];
+    boxVectors[1] = vectors[1];
+    boxVectors[2] = vectors[2];
+}
+
 /**---------------------------------------------------------------------------------------
 
    Calculate Amoeba Out-Of-Plane-Bend  ixn (force and energy)
@@ -78,12 +85,21 @@ RealOpenMM AmoebaReferenceOutOfPlaneBendForce::calculateOutOfPlaneBendIxn(const
     std::vector<RealOpenMM> deltaR[LastDeltaIndex];
     for (int ii = 0; ii < LastDeltaIndex; ii++) {
         deltaR[ii].resize(3);
-    }   
-    AmoebaReferenceForce::loadDeltaR(positionAtomB, positionAtomA, deltaR[AB]);
-    AmoebaReferenceForce::loadDeltaR(positionAtomB, positionAtomC, deltaR[CB]);
-    AmoebaReferenceForce::loadDeltaR(positionAtomB, positionAtomD, deltaR[DB]);
-    AmoebaReferenceForce::loadDeltaR(positionAtomD, positionAtomA, deltaR[AD]);
-    AmoebaReferenceForce::loadDeltaR(positionAtomD, positionAtomC, deltaR[CD]);
+    }
+    if (usePeriodic) {
+        AmoebaReferenceForce::loadDeltaRPeriodic(positionAtomB, positionAtomA, deltaR[AB], boxVectors);
+        AmoebaReferenceForce::loadDeltaRPeriodic(positionAtomB, positionAtomC, deltaR[CB], boxVectors);
+        AmoebaReferenceForce::loadDeltaRPeriodic(positionAtomB, positionAtomD, deltaR[DB], boxVectors);
+        AmoebaReferenceForce::loadDeltaRPeriodic(positionAtomD, positionAtomA, deltaR[AD], boxVectors);
+        AmoebaReferenceForce::loadDeltaRPeriodic(positionAtomD, positionAtomC, deltaR[CD], boxVectors);
+    }
+    else {
+        AmoebaReferenceForce::loadDeltaR(positionAtomB, positionAtomA, deltaR[AB]);
+        AmoebaReferenceForce::loadDeltaR(positionAtomB, positionAtomC, deltaR[CB]);
+        AmoebaReferenceForce::loadDeltaR(positionAtomB, positionAtomD, deltaR[DB]);
+        AmoebaReferenceForce::loadDeltaR(positionAtomD, positionAtomA, deltaR[AD]);
+        AmoebaReferenceForce::loadDeltaR(positionAtomD, positionAtomC, deltaR[CD]);
+    }
 
     RealOpenMM rDB2  = AmoebaReferenceForce::getNormSquared3(deltaR[DB]);
     RealOpenMM rAD2  = AmoebaReferenceForce::getNormSquared3(deltaR[AD]);

plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceOutOfPlaneBendForce.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
@@ -40,7 +40,7 @@ public:
        
        --------------------------------------------------------------------------------------- */
  
-    AmoebaReferenceOutOfPlaneBendForce() {};
+    AmoebaReferenceOutOfPlaneBendForce() : usePeriodic(false) {};
  
     /**---------------------------------------------------------------------------------------
        
@@ -50,6 +50,16 @@ public:
  
     ~AmoebaReferenceOutOfPlaneBendForce() {};
  
+    /**---------------------------------------------------------------------------------------
+
+       Set the force to use periodic boundary conditions.
+      
+       @param vectors    the vectors defining the periodic box
+      
+       --------------------------------------------------------------------------------------- */
+      
+    void setPeriodic(OpenMM::RealVec* vectors);
+
     /**---------------------------------------------------------------------------------------
      
         Calculate Amoeba out-of-plane-bend angle (force and energy)
@@ -86,6 +96,9 @@ public:
 
 private:
 
+    bool usePeriodic;
+    RealVec boxVectors[3];
+
     /**---------------------------------------------------------------------------------------
     
        Calculate Amoeba Out-Of-Plane-Bend ixn (force and energy)

plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferencePiTorsionForce.cpp

-
-/* 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
@@ -29,6 +28,13 @@
 using std::vector;
 using namespace OpenMM;
 
+void AmoebaReferencePiTorsionForce::setPeriodic(OpenMM::RealVec* vectors) {
+    usePeriodic = true;
+    boxVectors[0] = vectors[0];
+    boxVectors[1] = vectors[1];
+    boxVectors[2] = vectors[2];
+}
+
 /**---------------------------------------------------------------------------------------
 
    Calculate Amoeba pi-torsion ixn (force and energy)
@@ -66,11 +72,19 @@ RealOpenMM AmoebaReferencePiTorsionForce::calculatePiTorsionIxn(const RealVec& p
     std::vector<RealOpenMM> deltaR[LastDeltaIndex];
     for (unsigned int ii = 0; ii < LastDeltaIndex; ii++) {
         deltaR[ii].resize(3);
-    }   
-    AmoebaReferenceForce::loadDeltaR(positionAtomD, positionAtomA, deltaR[AD]);
-    AmoebaReferenceForce::loadDeltaR(positionAtomD, positionAtomB, deltaR[BD]);
-    AmoebaReferenceForce::loadDeltaR(positionAtomC, positionAtomE, deltaR[EC]);
-    AmoebaReferenceForce::loadDeltaR(positionAtomC, positionAtomF, deltaR[FC]);
+    }
+    if (usePeriodic) {
+        AmoebaReferenceForce::loadDeltaRPeriodic(positionAtomD, positionAtomA, deltaR[AD], boxVectors);
+        AmoebaReferenceForce::loadDeltaRPeriodic(positionAtomD, positionAtomB, deltaR[BD], boxVectors);
+        AmoebaReferenceForce::loadDeltaRPeriodic(positionAtomC, positionAtomE, deltaR[EC], boxVectors);
+        AmoebaReferenceForce::loadDeltaRPeriodic(positionAtomC, positionAtomF, deltaR[FC], boxVectors);
+    }
+    else {
+        AmoebaReferenceForce::loadDeltaR(positionAtomD, positionAtomA, deltaR[AD]);
+        AmoebaReferenceForce::loadDeltaR(positionAtomD, positionAtomB, deltaR[BD]);
+        AmoebaReferenceForce::loadDeltaR(positionAtomC, positionAtomE, deltaR[EC]);
+        AmoebaReferenceForce::loadDeltaR(positionAtomC, positionAtomF, deltaR[FC]);
+    }
 
     enum { A, B, C, D, E, F, LastAtomIndex };
     std::vector<RealOpenMM> d[LastAtomIndex];

plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferencePiTorsionForce.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
@@ -40,7 +40,7 @@ public:
        
        --------------------------------------------------------------------------------------- */
  
-    AmoebaReferencePiTorsionForce() {};
+    AmoebaReferencePiTorsionForce() : usePeriodic(false) {};
  
     /**---------------------------------------------------------------------------------------
        
@@ -50,6 +50,16 @@ public:
  
     ~AmoebaReferencePiTorsionForce() {};
  
+    /**---------------------------------------------------------------------------------------
+
+       Set the force to use periodic boundary conditions.
+      
+       @param vectors    the vectors defining the periodic box
+      
+       --------------------------------------------------------------------------------------- */
+      
+    void setPeriodic(OpenMM::RealVec* vectors);
+
      /**---------------------------------------------------------------------------------------
      
         Calculate Amoeba torsion ixns (force and energy)
@@ -85,6 +95,9 @@ public:
 
 private:
 
+    bool usePeriodic;
+    RealVec boxVectors[3];
+
     /**---------------------------------------------------------------------------------------
     
        Calculate Amoeba pi-torsion ixn (force and energy)

plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceStretchBendForce.cpp

 
-/* 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
@@ -29,6 +29,13 @@
 using std::vector;
 using namespace OpenMM;
 
+void AmoebaReferenceStretchBendForce::setPeriodic(OpenMM::RealVec* vectors) {
+    usePeriodic = true;
+    boxVectors[0] = vectors[0];
+    boxVectors[1] = vectors[1];
+    boxVectors[2] = vectors[2];
+}
+
 /**---------------------------------------------------------------------------------------
 
    Calculate Amoeba stretch bend angle ixn (force and energy)
@@ -76,8 +83,14 @@ RealOpenMM AmoebaReferenceStretchBendForce::calculateStretchBendIxn(const RealVe
     for (unsigned int ii = 0; ii < LastDeltaIndex; ii++) {
         deltaR[ii].resize(3);
     }
-    AmoebaReferenceForce::loadDeltaR(positionAtomB, positionAtomA, deltaR[AB]);
-    AmoebaReferenceForce::loadDeltaR(positionAtomB, positionAtomC, deltaR[CB]);
+    if (usePeriodic) {
+        AmoebaReferenceForce::loadDeltaRPeriodic(positionAtomB, positionAtomA, deltaR[AB], boxVectors);
+        AmoebaReferenceForce::loadDeltaRPeriodic(positionAtomB, positionAtomC, deltaR[CB], boxVectors);
+    }
+    else {
+        AmoebaReferenceForce::loadDeltaR(positionAtomB, positionAtomA, deltaR[AB]);
+        AmoebaReferenceForce::loadDeltaR(positionAtomB, positionAtomC, deltaR[CB]);
+    }
     RealOpenMM  rAB2 = AmoebaReferenceForce::getNormSquared3(deltaR[AB]);
     RealOpenMM  rAB  = SQRT(rAB2);
     RealOpenMM  rCB2 = AmoebaReferenceForce::getNormSquared3(deltaR[CB]);

plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceStretchBendForce.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
@@ -40,7 +40,7 @@ public:
        
        --------------------------------------------------------------------------------------- */
  
-    AmoebaReferenceStretchBendForce() {};
+    AmoebaReferenceStretchBendForce() : usePeriodic(false) {};
  
     /**---------------------------------------------------------------------------------------
        
@@ -50,6 +50,16 @@ public:
  
     ~AmoebaReferenceStretchBendForce() {};
 
+    /**---------------------------------------------------------------------------------------
+
+       Set the force to use periodic boundary conditions.
+      
+       @param vectors    the vectors defining the periodic box
+      
+       --------------------------------------------------------------------------------------- */
+      
+    void setPeriodic(OpenMM::RealVec* vectors);
+
      /**---------------------------------------------------------------------------------------
      
         Calculate Amoeba stretch bend ixns (force and energy)
@@ -84,6 +94,9 @@ public:
 
 private:
 
+    bool usePeriodic;
+    RealVec boxVectors[3];
+
     /**---------------------------------------------------------------------------------------
     
        Calculate Amoeba stretch bend angle ixn (force and energy)

plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceTorsionTorsionForce.cpp

-
-/* 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
@@ -28,6 +27,13 @@
 using std::vector;
 using namespace OpenMM;
 
+void AmoebaReferenceTorsionTorsionForce::setPeriodic(OpenMM::RealVec* vectors) {
+    usePeriodic = true;
+    boxVectors[0] = vectors[0];
+    boxVectors[1] = vectors[1];
+    boxVectors[2] = vectors[2];
+}
+
 /**---------------------------------------------------------------------------------------
 
    Load grid values from rectenclosing angles
@@ -294,9 +300,16 @@ int AmoebaReferenceTorsionTorsionForce::checkTorsionSign(
         deltaR[ii].resize(3);
     }   
 
-    AmoebaReferenceForce::loadDeltaR(positionAtomC, positionAtomA, deltaR[CA]);
-    AmoebaReferenceForce::loadDeltaR(positionAtomC, positionAtomB, deltaR[CB]);
-    AmoebaReferenceForce::loadDeltaR(positionAtomC, positionAtomD, deltaR[CD]);
+    if (usePeriodic) {
+        AmoebaReferenceForce::loadDeltaRPeriodic(positionAtomC, positionAtomA, deltaR[CA], boxVectors);
+        AmoebaReferenceForce::loadDeltaRPeriodic(positionAtomC, positionAtomB, deltaR[CB], boxVectors);
+        AmoebaReferenceForce::loadDeltaRPeriodic(positionAtomC, positionAtomD, deltaR[CD], boxVectors);
+    }
+    else {
+        AmoebaReferenceForce::loadDeltaR(positionAtomC, positionAtomA, deltaR[CA]);
+        AmoebaReferenceForce::loadDeltaR(positionAtomC, positionAtomB, deltaR[CB]);
+        AmoebaReferenceForce::loadDeltaR(positionAtomC, positionAtomD, deltaR[CD]);
+    }
 
     RealOpenMM volume = deltaR[CA][0]*(deltaR[CB][1]*deltaR[CD][2] - deltaR[CB][2]*deltaR[CD][1]) +
                         deltaR[CB][0]*(deltaR[CD][1]*deltaR[CA][2] - deltaR[CD][2]*deltaR[CA][1]) +
@@ -351,13 +364,24 @@ RealOpenMM AmoebaReferenceTorsionTorsionForce::calculateTorsionTorsionIxn(const
         deltaR[ii].resize(3);
     }   
 
-    AmoebaReferenceForce::loadDeltaR(positionAtomA, positionAtomB, deltaR[BA]);
-    AmoebaReferenceForce::loadDeltaR(positionAtomB, positionAtomC, deltaR[CB]);
-    AmoebaReferenceForce::loadDeltaR(positionAtomC, positionAtomD, deltaR[DC]);
-    AmoebaReferenceForce::loadDeltaR(positionAtomD, positionAtomE, deltaR[ED]);
-    AmoebaReferenceForce::loadDeltaR(positionAtomA, positionAtomC, deltaR[CA]);
-    AmoebaReferenceForce::loadDeltaR(positionAtomB, positionAtomD, deltaR[DB]);
-    AmoebaReferenceForce::loadDeltaR(positionAtomC, positionAtomE, deltaR[EC]);
+    if (usePeriodic) {
+        AmoebaReferenceForce::loadDeltaRPeriodic(positionAtomA, positionAtomB, deltaR[BA], boxVectors);
+        AmoebaReferenceForce::loadDeltaRPeriodic(positionAtomB, positionAtomC, deltaR[CB], boxVectors);
+        AmoebaReferenceForce::loadDeltaRPeriodic(positionAtomC, positionAtomD, deltaR[DC], boxVectors);
+        AmoebaReferenceForce::loadDeltaRPeriodic(positionAtomD, positionAtomE, deltaR[ED], boxVectors);
+        AmoebaReferenceForce::loadDeltaRPeriodic(positionAtomA, positionAtomC, deltaR[CA], boxVectors);
+        AmoebaReferenceForce::loadDeltaRPeriodic(positionAtomB, positionAtomD, deltaR[DB], boxVectors);
+        AmoebaReferenceForce::loadDeltaRPeriodic(positionAtomC, positionAtomE, deltaR[EC], boxVectors);
+    }
+    else {
+        AmoebaReferenceForce::loadDeltaR(positionAtomA, positionAtomB, deltaR[BA]);
+        AmoebaReferenceForce::loadDeltaR(positionAtomB, positionAtomC, deltaR[CB]);
+        AmoebaReferenceForce::loadDeltaR(positionAtomC, positionAtomD, deltaR[DC]);
+        AmoebaReferenceForce::loadDeltaR(positionAtomD, positionAtomE, deltaR[ED]);
+        AmoebaReferenceForce::loadDeltaR(positionAtomA, positionAtomC, deltaR[CA]);
+        AmoebaReferenceForce::loadDeltaR(positionAtomB, positionAtomD, deltaR[DB]);
+        AmoebaReferenceForce::loadDeltaR(positionAtomC, positionAtomE, deltaR[EC]);
+    }
 
     std::vector<RealOpenMM> d[LastAtomIndex];
     for (unsigned int ii = 0; ii < LastAtomIndex; ii++) {

plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceTorsionTorsionForce.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
@@ -40,7 +40,7 @@ public:
        
        --------------------------------------------------------------------------------------- */
  
-    AmoebaReferenceTorsionTorsionForce() {};
+    AmoebaReferenceTorsionTorsionForce() : usePeriodic(false) {};
  
     /**---------------------------------------------------------------------------------------
        
@@ -50,6 +50,16 @@ public:
  
     ~AmoebaReferenceTorsionTorsionForce() {};
 
+    /**---------------------------------------------------------------------------------------
+
+       Set the force to use periodic boundary conditions.
+      
+       @param vectors    the vectors defining the periodic box
+      
+       --------------------------------------------------------------------------------------- */
+      
+    void setPeriodic(OpenMM::RealVec* vectors);
+
      /**---------------------------------------------------------------------------------------
      
         Calculate Amoeba torsion-torsion ixns (force and energy)
@@ -84,6 +94,9 @@ public:
 
 private:
 
+    bool usePeriodic;
+    RealVec boxVectors[3];
+
     /**---------------------------------------------------------------------------------------
     
        Load grid values from rectangle enclosing angles

plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaAngleForce.cpp

@@ -35,6 +35,7 @@
 
 #include "openmm/internal/AssertionUtilities.h"
 #include "openmm/Context.h"
+#include "openmm/CustomAngleForce.h"
 #include "OpenMMAmoeba.h"
 #include "openmm/System.h"
 #include "openmm/LangevinIntegrator.h"
@@ -274,12 +275,63 @@ void testOneAngle() {
     compareWithExpectedForceAndEnergy(context, *amoebaAngleForce, TOL, "testOneAngle");
 }
 
+void testPeriodic() {
+    // Create a force that uses periodic boundary conditions, then compare to an identical custom force.
+    
+    System system;
+    system.setDefaultPeriodicBoxVectors(Vec3(3, 0, 0), Vec3(0, 3, 0), Vec3(0, 0, 3));
+    int numParticles = 3;
+    for (int ii = 0; ii < numParticles; ii++)
+        system.addParticle(1.0);
+    LangevinIntegrator integrator(0.0, 0.1, 0.01);
+    AmoebaAngleForce* amoebaAngleForce = new AmoebaAngleForce();
+    double angle      = 100.0;
+    double quadraticK = 1.0;
+    double cubicK     = 1.0e-01;
+    double quarticK   = 1.0e-02;
+    double penticK    = 1.0e-03;
+    double sexticK    = 1.0e-04;
+    amoebaAngleForce->addAngle(0, 1, 2, angle, quadraticK);
+    amoebaAngleForce->setAmoebaGlobalAngleCubic(cubicK);
+    amoebaAngleForce->setAmoebaGlobalAngleQuartic(quarticK);
+    amoebaAngleForce->setAmoebaGlobalAnglePentic(penticK);
+    amoebaAngleForce->setAmoebaGlobalAngleSextic(sexticK);
+    amoebaAngleForce->setUsesPeriodicBoundaryConditions(true);
+    system.addForce(amoebaAngleForce);
+    CustomAngleForce* customForce = new CustomAngleForce("k2*delta^2 + k3*delta^3 + k4*delta^4 + k5*delta^5 + k6*delta^6; delta=theta-theta0");
+    customForce->addGlobalParameter("theta0", angle*M_PI/180);
+    customForce->addGlobalParameter("k2", quadraticK*pow(180/M_PI, 2.0));
+    customForce->addGlobalParameter("k3", cubicK*pow(180/M_PI, 3.0));
+    customForce->addGlobalParameter("k4", quarticK*pow(180/M_PI, 4.0));
+    customForce->addGlobalParameter("k5", penticK*pow(180/M_PI, 5.0));
+    customForce->addGlobalParameter("k6", sexticK*pow(180/M_PI, 6.0));
+    customForce->addAngle(0, 1, 2);
+    customForce->setUsesPeriodicBoundaryConditions(true);
+    customForce->setForceGroup(1);
+    system.addForce(customForce);
+    Context context(system, integrator, Platform::getPlatformByName("Reference"));
+
+    std::vector<Vec3> positions(numParticles);
+
+    positions[0] = Vec3(0, 1, 0);
+    positions[1] = Vec3(0, 0, 0);
+    positions[2] = Vec3(0, 0, 2);
+
+    context.setPositions(positions);
+    State s1 = context.getState(State::Forces | State::Energy, true, 1);
+    State s2 = context.getState(State::Forces | State::Energy, true, 2);
+    ASSERT_EQUAL_TOL(s2.getPotentialEnergy(), s1.getPotentialEnergy(), 1e-5);
+    for (int i = 0; i < numParticles; i++)
+        ASSERT_EQUAL_VEC(s2.getForces()[i], s1.getForces()[i], 1e-5);
+}
+
 int main(int numberOfArguments, char* argv[]) {
 
     try {
-        std::cout << "TestCudaAmoebaAngleForce running test..." << std::endl;
+        std::cout << "TestReferenceAmoebaAngleForce running test..." << std::endl;
         registerAmoebaReferenceKernelFactories();
         testOneAngle();
+        testPeriodic();
     }
     catch(const std::exception& e) {
         std::cout << "exception: " << e.what() << std::endl;

plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaBondForce.cpp

@@ -35,6 +35,7 @@
 
 #include "openmm/internal/AssertionUtilities.h"
 #include "openmm/Context.h"
+#include "openmm/CustomBondForce.h"
 #include "OpenMMAmoeba.h"
 #include "openmm/System.h"
 #include "openmm/LangevinIntegrator.h"
@@ -201,6 +202,49 @@ void testTwoBond() {
     compareWithExpectedForceAndEnergy(context, *amoebaBondForce, TOL, "testTwoBond");
 }
 
+void testPeriodic() {
+    // Create a force that uses periodic boundary conditions, then compare to an identical custom force.
+    
+    System system;
+    system.setDefaultPeriodicBoxVectors(Vec3(3, 0, 0), Vec3(0, 3, 0), Vec3(0, 0, 3));
+    int numParticles = 2;
+    for (int ii = 0; ii < numParticles; ii++)
+        system.addParticle(1.0);
+    LangevinIntegrator integrator(0.0, 0.1, 0.01);
+    AmoebaBondForce* amoebaBondForce = new AmoebaBondForce();
+    double bondLength = 1.5;
+    double quadraticK = 1.0;
+    double cubicK     = 2.0;
+    double quarticK   = 3.0;
+    amoebaBondForce->setAmoebaGlobalBondCubic(cubicK);
+    amoebaBondForce->setAmoebaGlobalBondQuartic(quarticK);
+    amoebaBondForce->addBond(0, 1, bondLength, quadraticK);
+    amoebaBondForce->setUsesPeriodicBoundaryConditions(true);
+    system.addForce(amoebaBondForce);
+    CustomBondForce* customForce = new CustomBondForce("k2*delta^2 + k3*delta^3 + k4*delta^4; delta=r-r0");
+    customForce->addGlobalParameter("r0", bondLength);
+    customForce->addGlobalParameter("k2", quadraticK);
+    customForce->addGlobalParameter("k3", cubicK);
+    customForce->addGlobalParameter("k4", quarticK);
+    customForce->addBond(0, 1);
+    customForce->setUsesPeriodicBoundaryConditions(true);
+    customForce->setForceGroup(1);
+    system.addForce(customForce);
+    Context context(system, integrator, Platform::getPlatformByName("Reference"));
+
+    std::vector<Vec3> positions(numParticles);
+
+    positions[0] = Vec3(0, 2, 0);
+    positions[1] = Vec3(0, 0, 0);
+
+    context.setPositions(positions);
+    State s1 = context.getState(State::Forces | State::Energy, true, 1);
+    State s2 = context.getState(State::Forces | State::Energy, true, 2);
+    ASSERT_EQUAL_TOL(s2.getPotentialEnergy(), s1.getPotentialEnergy(), 1e-5);
+    for (int i = 0; i < numParticles; i++)
+        ASSERT_EQUAL_VEC(s2.getForces()[i], s1.getForces()[i], 1e-5);
+}
+
 int main(int numberOfArguments, char* argv[]) {
 
     try {
@@ -208,6 +252,7 @@ int main(int numberOfArguments, char* argv[]) {
         registerAmoebaReferenceKernelFactories();
         //testOneBond();
         testTwoBond();
+        testPeriodic();
     }
     catch(const std::exception& e) {
         std::cout << "exception: " << e.what() << std::endl;

plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaInPlaneAngleForce.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 Stanford University and the Authors.           *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -354,12 +354,57 @@ void testOneAngle() {
     compareWithExpectedForceAndEnergy(context, *amoebaInPlaneAngleForce, TOL, "testOneInPlaneAngle");
 }
 
+void testPeriodic() {
+    // Create a force that uses periodic boundary conditions.
+
+    System system;
+    system.setDefaultPeriodicBoxVectors(Vec3(3, 0, 0), Vec3(0, 3, 0), Vec3(0, 0, 3));
+    int numberOfParticles = 4;
+    for (int ii = 0; ii < numberOfParticles; ii++)
+        system.addParticle(1.0);
+    LangevinIntegrator integrator(0.0, 0.1, 0.01);
+    AmoebaInPlaneAngleForce* amoebaInPlaneAngleForce = new AmoebaInPlaneAngleForce();
+    double angle      = 65.0;
+    double quadraticK = 1.0;
+    double cubicK     = 0.0e-01;
+    double quarticK   = 0.0e-02;
+    double penticK    = 0.0e-03;
+    double sexticK    = 0.0e-04;
+    amoebaInPlaneAngleForce->addAngle(0, 1, 2, 3, angle, quadraticK);
+    amoebaInPlaneAngleForce->setAmoebaGlobalInPlaneAngleCubic(cubicK);
+    amoebaInPlaneAngleForce->setAmoebaGlobalInPlaneAngleQuartic(quarticK);
+    amoebaInPlaneAngleForce->setAmoebaGlobalInPlaneAnglePentic(penticK);
+    amoebaInPlaneAngleForce->setAmoebaGlobalInPlaneAngleSextic(sexticK);
+    amoebaInPlaneAngleForce->setUsesPeriodicBoundaryConditions(true);
+    system.addForce(amoebaInPlaneAngleForce);
+    Context context(system, integrator, Platform::getPlatformByName("Reference"));
+
+    std::vector<Vec3> positions(numberOfParticles);
+    positions[0] = Vec3(0, 1, 0);
+    positions[1] = Vec3(0, 0, 0);
+    positions[2] = Vec3(0, 0, 1);
+    positions[3] = Vec3(1, 1, 1);
+
+    context.setPositions(positions);
+    State s1 = context.getState(State::Forces | State::Energy);
+    
+    // Move one atom to a position that should give identical results.
+
+    positions[2] = Vec3(0, 0, -2);
+    context.setPositions(positions);
+    State s2 = context.getState(State::Forces | State::Energy);
+    ASSERT_EQUAL_TOL(s1.getPotentialEnergy(), s2.getPotentialEnergy(), 1e-5);
+    for (int i = 0; i < numberOfParticles; i++)
+        ASSERT_EQUAL_VEC(s1.getForces()[i], s2.getForces()[i], 1e-5);
+}
+
 int main(int numberOfArguments, char* argv[]) {
 
     try {
         std::cout << "TestReferenceAmoebaInPlaneAngleForce running test..." << std::endl;
         registerAmoebaReferenceKernelFactories();
         testOneAngle();
+        testPeriodic();
     }
     catch(const std::exception& e) {
         std::cout << "exception: " << e.what() << std::endl;

plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaOutOfPlaneBendForce.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 Stanford University and the Authors.           *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -461,12 +461,50 @@ void testOneOutOfPlaneBend2(int setId) {
     }
 }
 
+void testPeriodic() {
+    // Create a force that uses periodic boundary conditions.
+
+    System system;
+    system.setDefaultPeriodicBoxVectors(Vec3(3, 0, 0), Vec3(0, 3, 0), Vec3(0, 0, 3));
+    int numberOfParticles = 4;
+    for (int ii = 0; ii < numberOfParticles; ii++)
+        system.addParticle(1.0);
+    LangevinIntegrator integrator(0.0, 0.1, 0.01);
+    AmoebaOutOfPlaneBendForce* amoebaOutOfPlaneBendForce = new AmoebaOutOfPlaneBendForce();
+    amoebaOutOfPlaneBendForce->setAmoebaGlobalOutOfPlaneBendCubic( -0.1400000E-01);
+    amoebaOutOfPlaneBendForce->setAmoebaGlobalOutOfPlaneBendQuartic(0.5600000E-04);
+    amoebaOutOfPlaneBendForce->setAmoebaGlobalOutOfPlaneBendPentic(-0.7000000E-06);
+    amoebaOutOfPlaneBendForce->setAmoebaGlobalOutOfPlaneBendSextic( 0.2200000E-07);
+    double kOutOfPlaneBend = 0.328682196E-01;
+    amoebaOutOfPlaneBendForce->addOutOfPlaneBend(0, 1, 2, 3, kOutOfPlaneBend);
+    amoebaOutOfPlaneBendForce->setUsesPeriodicBoundaryConditions(true);
+    system.addForce(amoebaOutOfPlaneBendForce);
+    Context context(system, integrator, Platform::getPlatformByName("Reference"));
+    std::vector<Vec3> positions(numberOfParticles);
+    positions[0] = Vec3(0, 0, 0);
+    positions[1] = Vec3(1, 0, 0);
+    positions[2] = Vec3(0, 1, 0);
+    positions[3] = Vec3(0, 0, 1);
+    context.setPositions(positions);
+    State s1 = context.getState(State::Forces | State::Energy);
+    
+    // Move one atom to a position that should give identical results.
+
+    positions[3] = Vec3(0, 0, -2);
+    context.setPositions(positions);
+    State s2 = context.getState(State::Forces | State::Energy);
+    ASSERT_EQUAL_TOL(s1.getPotentialEnergy(), s2.getPotentialEnergy(), 1e-5);
+    for (int i = 0; i < numberOfParticles; i++)
+        ASSERT_EQUAL_VEC(s1.getForces()[i], s2.getForces()[i], 1e-5);
+}
+
 int main(int numberOfArguments, char* argv[]) {
 
     try {
         std::cout << "TestReferenceAmoebaOutOfPlaneBendForce running test..." << std::endl;
         registerAmoebaReferenceKernelFactories();
         testOneOutOfPlaneBend();
+        testPeriodic();
         //testOneOutOfPlaneBend2(atoi(argv[1]));
         //for (int ii = 1; ii <= 6; ii++) {
         //     testOneOutOfPlaneBend2(ii);

plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaPiTorsionForce.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 Stanford University and the Authors.           *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -290,12 +290,48 @@ void testOnePiTorsion() {
     compareWithExpectedForceAndEnergy(context, *amoebaPiTorsionForce, TOL, "testOnePiTorsion");
 }
 
+void testPeriodic() {
+    // Create a force that uses periodic boundary conditions.
+
+    System system;
+    system.setDefaultPeriodicBoxVectors(Vec3(3, 0, 0), Vec3(0, 3, 0), Vec3(0, 0, 3));
+    int numberOfParticles = 6;
+    for (int ii = 0; ii < numberOfParticles; ii++)
+        system.addParticle(1.0);
+    LangevinIntegrator integrator(0.0, 0.1, 0.01);
+    AmoebaPiTorsionForce* amoebaPiTorsionForce = new AmoebaPiTorsionForce();
+    double kTorsion = 6.85;
+    amoebaPiTorsionForce->addPiTorsion(0, 1, 2, 3, 4, 5, kTorsion);
+    amoebaPiTorsionForce->setUsesPeriodicBoundaryConditions(true);
+    system.addForce(amoebaPiTorsionForce);
+    Context context(system, integrator, Platform::getPlatformByName("Reference"));
+    std::vector<Vec3> positions(numberOfParticles);
+    positions[0] = Vec3(0, 1, 0);
+    positions[1] = Vec3(0, 0, 0);
+    positions[2] = Vec3(0, 0, 0.5);
+    positions[3] = Vec3(0.4, 0.4, 0.4);
+    positions[4] = Vec3(1, 0, 1);
+    positions[5] = Vec3(1, 1, 0);
+    context.setPositions(positions);
+    State s1 = context.getState(State::Forces | State::Energy);
+    
+    // Move one atom to a position that should give identical results.
+
+    positions[0] = Vec3(0, -2, 0);
+    context.setPositions(positions);
+    State s2 = context.getState(State::Forces | State::Energy);
+    ASSERT_EQUAL_TOL(s1.getPotentialEnergy(), s2.getPotentialEnergy(), 1e-5);
+    for (int i = 0; i < numberOfParticles; i++)
+        ASSERT_EQUAL_VEC(s1.getForces()[i], s2.getForces()[i], 1e-5);
+}
+
 int main(int numberOfArguments, char* argv[]) {
 
     try {
         std::cout << "TestReferenceAmoebaPiTorsionForce running test..." << std::endl;
         registerAmoebaReferenceKernelFactories();
         testOnePiTorsion();
+        testPeriodic();
     }
     catch(const std::exception& e) {
         std::cout << "exception: " << e.what() << std::endl;

plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaStretchBendForce.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 Stanford University and the Authors.           *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -270,12 +270,48 @@ void testOneStretchBend() {
     compareWithExpectedForceAndEnergy(context, *amoebaStretchBendForce, TOL, "testOneStretchBend");
 }
 
+void testPeriodic() {
+    // Create a force that uses periodic boundary conditions.
+
+    System system;
+    system.setDefaultPeriodicBoxVectors(Vec3(3, 0, 0), Vec3(0, 3, 0), Vec3(0, 0, 3));
+    int numberOfParticles = 3;
+    for (int ii = 0; ii < numberOfParticles; ii++)
+        system.addParticle(1.0);
+    LangevinIntegrator integrator(0.0, 0.1, 0.01);
+    AmoebaStretchBendForce* amoebaStretchBendForce = new AmoebaStretchBendForce();
+    double abLength         = 0.144800000E+01;
+    double cbLength         = 0.101500000E+01;
+    double angleStretchBend = 0.108500000E+03*DegreesToRadians;
+    double kStretchBend     = 1.0;
+    amoebaStretchBendForce->addStretchBend(0, 1, 2, abLength, cbLength, angleStretchBend, kStretchBend, kStretchBend);
+    amoebaStretchBendForce->setUsesPeriodicBoundaryConditions(true);
+    system.addForce(amoebaStretchBendForce);
+    Context context(system, integrator, Platform::getPlatformByName("Reference"));
+    std::vector<Vec3> positions(numberOfParticles);
+    positions[0] = Vec3(0, 1, 0);
+    positions[1] = Vec3(0, 0, 0);
+    positions[2] = Vec3(0, 0, 1);
+    context.setPositions(positions);
+    State s1 = context.getState(State::Forces | State::Energy);
+    
+    // Move one atom to a position that should give identical results.
+
+    positions[2] = Vec3(0, 0, -2);
+    context.setPositions(positions);
+    State s2 = context.getState(State::Forces | State::Energy);
+    ASSERT_EQUAL_TOL(s1.getPotentialEnergy(), s2.getPotentialEnergy(), 1e-5);
+    for (int i = 0; i < numberOfParticles; i++)
+        ASSERT_EQUAL_VEC(s1.getForces()[i], s2.getForces()[i], 1e-5);
+}
+
 int main(int numberOfArguments, char* argv[]) {
 
     try {
         std::cout << "TestReferenceAmoebaStretchBendForce running test..." << std::endl;
         registerAmoebaReferenceKernelFactories();
         testOneStretchBend();
+        testPeriodic();
     }
     catch(const std::exception& e) {
         std::cout << "exception: " << e.what() << std::endl;