Reference implementation of periodic boundary conditions for AMOEBA bonded forces

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/src/SimTKReference/ReferenceForce.cpp

@@ -73,6 +73,10 @@ void ReferenceForce::getDeltaR(const RealVec& atomCoordinatesI, const RealVec& a
    deltaR[RIndex]    = (RealOpenMM) SQRT(deltaR[R2Index]);
 }
 
+RealVec ReferenceForce::getDeltaR(const RealVec& atomCoordinatesI, const RealVec& atomCoordinatesJ) {
+    return atomCoordinatesJ-atomCoordinatesI;
+}
+
 void ReferenceForce::getDeltaRPeriodic(const RealVec& atomCoordinatesI, const RealVec& atomCoordinatesJ,
                                const RealOpenMM* boxSize, RealOpenMM* deltaR) {
    deltaR[XIndex]    = periodicDifference(atomCoordinatesJ[0], atomCoordinatesI[0], boxSize[0]);
@@ -96,6 +100,15 @@ void ReferenceForce::getDeltaRPeriodic(const RealVec& atomCoordinatesI, const Re
     deltaR[RIndex] = SQRT(deltaR[R2Index]);
 }
 
+RealVec ReferenceForce::getDeltaRPeriodic(const RealVec& atomCoordinatesI, const RealVec& atomCoordinatesJ,
+                               const RealVec* boxVectors) {
+    RealVec diff = atomCoordinatesJ-atomCoordinatesI;
+    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);
+    return diff;
+}
+
 double* ReferenceForce::getVariablePointer(Lepton::CompiledExpression& expression, const std::string& name) {
     if (expression.getVariables().find(name) == expression.getVariables().end())
         return NULL;

plugins/amoeba/openmmapi/include/openmm/AmoebaAngleForce.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) 2008-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Mark Friedrichs, Peter Eastman                                    *
  * Contributors:                                                              *
  *                                                                            *
@@ -166,21 +166,25 @@ public:
      * in an angle cannot be changed, nor can new angles be added.
      */
     void updateParametersInContext(Context& context);
+    /**
+     * Set whether this force should apply periodic boundary conditions when calculating displacements.
+     * Usually this is not appropriate for bonded forces, but there are situations when it can be useful.
+     */
+    void setUsesPeriodicBoundaryConditions(bool periodic);
     /**
      * Returns whether or not this force makes use of periodic boundary
      * conditions.
      *
-     * @returns true if nonbondedMethod uses PBC and false otherwise
+     * @returns true if force uses PBC and false otherwise
      */
-    bool usesPeriodicBoundaryConditions() const {
-        return false;
-    }
+    bool usesPeriodicBoundaryConditions() const;
 protected:
     ForceImpl* createImpl() const;
     double _globalCubicK, _globalQuarticK, _globalPenticK, _globalSexticK;
 private:
     class AngleInfo;
     std::vector<AngleInfo> angles;
+    bool usePeriodic;
 };
 
 /**

plugins/amoeba/openmmapi/include/openmm/AmoebaBondForce.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) 2008-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Mark Friedrichs, Peter Eastman                                    *
  * Contributors:                                                              *
  *                                                                            *
@@ -138,21 +138,25 @@ public:
      * in a bond cannot be changed, nor can new bonds be added.
      */
     void updateParametersInContext(Context& context);
+    /**
+     * Set whether this force should apply periodic boundary conditions when calculating displacements.
+     * Usually this is not appropriate for bonded forces, but there are situations when it can be useful.
+     */
+    void setUsesPeriodicBoundaryConditions(bool periodic);
     /**
      * Returns whether or not this force makes use of periodic boundary
      * conditions.
      *
-     * @returns true if nonbondedMethod uses PBC and false otherwise
+     * @returns true if force uses PBC and false otherwise
      */
-    bool usesPeriodicBoundaryConditions() const {
-        return false;
-    }
+    bool usesPeriodicBoundaryConditions() const;
 protected:
     double _globalQuarticK, _globalCubicK;
     ForceImpl* createImpl() const;
 private:
     class BondInfo;
     std::vector<BondInfo> bonds;
+    bool usePeriodic;
 };
 
 /**

plugins/amoeba/openmmapi/include/openmm/AmoebaInPlaneAngleForce.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) 2008-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Mark Friedrichs, Peter Eastman                                    *
  * Contributors:                                                              *
  *                                                                            *
@@ -171,21 +171,25 @@ public:
      * in an angle cannot be changed, nor can new angles be added.
      */
     void updateParametersInContext(Context& context);
+    /**
+     * Set whether this force should apply periodic boundary conditions when calculating displacements.
+     * Usually this is not appropriate for bonded forces, but there are situations when it can be useful.
+     */
+    void setUsesPeriodicBoundaryConditions(bool periodic);
     /**
      * Returns whether or not this force makes use of periodic boundary
      * conditions.
      *
-     * @returns true if nonbondedMethod uses PBC and false otherwise
+     * @returns true if force uses PBC and false otherwise
      */
-    bool usesPeriodicBoundaryConditions() const {
-        return false;
-    }
+    bool usesPeriodicBoundaryConditions() const;
 protected:
     ForceImpl* createImpl() const;
     double _globalCubicK, _globalQuarticK, _globalPenticK, _globalSexticK;
 private:
     class AngleInfo;
     std::vector<AngleInfo> angles;
+    bool usePeriodic;
 };
 
 /**

plugins/amoeba/openmmapi/include/openmm/AmoebaOutOfPlaneBendForce.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) 2008-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Mark Friedrichs, Peter Eastman                                    *
  * Contributors:                                                              *
  *                                                                            *
@@ -163,21 +163,25 @@ public:
      * in a term cannot be changed, nor can new terms be added.
      */
     void updateParametersInContext(Context& context);
+    /**
+     * Set whether this force should apply periodic boundary conditions when calculating displacements.
+     * Usually this is not appropriate for bonded forces, but there are situations when it can be useful.
+     */
+    void setUsesPeriodicBoundaryConditions(bool periodic);
     /**
      * Returns whether or not this force makes use of periodic boundary
      * conditions.
      *
-     * @returns true if nonbondedMethod uses PBC and false otherwise
+     * @returns true if force uses PBC and false otherwise
      */
-    bool usesPeriodicBoundaryConditions() const {
-        return false;
-    }
+    bool usesPeriodicBoundaryConditions() const;
 protected:
     ForceImpl* createImpl() const;
     double _globalCubicK, _globalQuarticK, _globalPenticK, _globalSexticK;
 private:
     class OutOfPlaneBendInfo;
     std::vector<OutOfPlaneBendInfo> outOfPlaneBends;
+    bool usePeriodic;
 };
 
 /**

plugins/amoeba/openmmapi/include/openmm/AmoebaPiTorsionForce.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) 2008-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Mark Friedrichs, Peter Eastman                                    *
  * Contributors:                                                              *
  *                                                                            *
@@ -113,20 +113,24 @@ public:
      * in a torsion cannot be changed, nor can new torsions be added.
      */
     void updateParametersInContext(Context& context);
+    /**
+     * Set whether this force should apply periodic boundary conditions when calculating displacements.
+     * Usually this is not appropriate for bonded forces, but there are situations when it can be useful.
+     */
+    void setUsesPeriodicBoundaryConditions(bool periodic);
     /**
      * Returns whether or not this force makes use of periodic boundary
      * conditions.
      *
-     * @returns true if nonbondedMethod uses PBC and false otherwise
+     * @returns true if force uses PBC and false otherwise
      */
-    bool usesPeriodicBoundaryConditions() const {
-        return false;
-    }
+    bool usesPeriodicBoundaryConditions() const;
 protected:
     ForceImpl* createImpl() const;
 private:
     class PiTorsionInfo;
     std::vector<PiTorsionInfo> piTorsions;
+    bool usePeriodic;
 };
 
 /**

plugins/amoeba/openmmapi/include/openmm/AmoebaStretchBendForce.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) 2008-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Mark Friedrichs, Peter Eastman                                    *
  * Contributors:                                                              *
  *                                                                            *
@@ -119,20 +119,24 @@ public:
      * in a term cannot be changed, nor can new terms be added.
      */
     void updateParametersInContext(Context& context);
+    /**
+     * Set whether this force should apply periodic boundary conditions when calculating displacements.
+     * Usually this is not appropriate for bonded forces, but there are situations when it can be useful.
+     */
+    void setUsesPeriodicBoundaryConditions(bool periodic);
     /**
      * Returns whether or not this force makes use of periodic boundary
      * conditions.
      *
-     * @returns true if nonbondedMethod uses PBC and false otherwise
+     * @returns true if force uses PBC and false otherwise
      */
-    bool usesPeriodicBoundaryConditions() const {
-        return false;
-    }
+    bool usesPeriodicBoundaryConditions() const;
 protected:
     ForceImpl* createImpl() const;
 private:
     class StretchBendInfo;
     std::vector<StretchBendInfo> stretchBends;
+    bool usePeriodic;
 };
 
 /**

plugins/amoeba/openmmapi/include/openmm/AmoebaTorsionTorsionForce.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) 2008-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Mark Friedrichs, Peter Eastman                                    *
  * Contributors:                                                              *
  *                                                                            *
@@ -137,15 +137,18 @@ public:
      *                         grid[x][y][5] = dEd(xy) value
      */
     void setTorsionTorsionGrid(int index, const std::vector<std::vector<std::vector<double> > >& grid);
+    /**
+     * Set whether this force should apply periodic boundary conditions when calculating displacements.
+     * Usually this is not appropriate for bonded forces, but there are situations when it can be useful.
+     */
+    void setUsesPeriodicBoundaryConditions(bool periodic);
     /**
      * Returns whether or not this force makes use of periodic boundary
      * conditions.
      *
-     * @returns true if nonbondedMethod uses PBC and false otherwise
+     * @returns true if force uses PBC and false otherwise
      */
-    bool usesPeriodicBoundaryConditions() const {
-        return false;
-    }
+    bool usesPeriodicBoundaryConditions() const;
 protected:
     ForceImpl* createImpl() const;
 private:
@@ -153,6 +156,7 @@ private:
     class TorsionTorsionGridInfo;
     std::vector<TorsionTorsionInfo> torsionTorsions;
     std::vector<TorsionTorsionGridInfo> torsionTorsionGrids;
+    bool usePeriodic;
 };
 
 /**

plugins/amoeba/openmmapi/src/AmoebaAngleForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2009 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors:                                                                   *
  * Contributors:                                                              *
  *                                                                            *
@@ -36,7 +36,7 @@
 
 using namespace OpenMM;
 
-AmoebaAngleForce::AmoebaAngleForce() {
+AmoebaAngleForce::AmoebaAngleForce() : usePeriodic(false) {
     _globalCubicK = _globalQuarticK = _globalPenticK = _globalSexticK = 0.0;
 }
 
@@ -102,3 +102,11 @@ ForceImpl* AmoebaAngleForce::createImpl() const {
 void AmoebaAngleForce::updateParametersInContext(Context& context) {
     dynamic_cast<AmoebaAngleForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
 }
+
+void AmoebaAngleForce::setUsesPeriodicBoundaryConditions(bool periodic) {
+    usePeriodic = periodic;
+}
+
+bool AmoebaAngleForce::usesPeriodicBoundaryConditions() const {
+    return usePeriodic;
+}

plugins/amoeba/openmmapi/src/AmoebaBondForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2009 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors:                                                                   *
  * Contributors:                                                              *
  *                                                                            *
@@ -36,7 +36,7 @@
 
 using namespace OpenMM;
 
-AmoebaBondForce::AmoebaBondForce() {
+AmoebaBondForce::AmoebaBondForce() : usePeriodic(false) {
    _globalCubicK = _globalQuarticK = 0.0;
 }
 
@@ -82,3 +82,11 @@ ForceImpl* AmoebaBondForce::createImpl() const {
 void AmoebaBondForce::updateParametersInContext(Context& context) {
     dynamic_cast<AmoebaBondForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
 }
+
+void AmoebaBondForce::setUsesPeriodicBoundaryConditions(bool periodic) {
+    usePeriodic = periodic;
+}
+
+bool AmoebaBondForce::usesPeriodicBoundaryConditions() const {
+    return usePeriodic;
+}

plugins/amoeba/openmmapi/src/AmoebaInPlaneAngleForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2009 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors:                                                                   *
  * Contributors:                                                              *
  *                                                                            *
@@ -36,7 +36,7 @@
 
 using namespace OpenMM;
 
-AmoebaInPlaneAngleForce::AmoebaInPlaneAngleForce() {
+AmoebaInPlaneAngleForce::AmoebaInPlaneAngleForce() : usePeriodic(false) {
     _globalCubicK = _globalQuarticK = _globalPenticK = _globalSexticK = 0.0;
 }
 
@@ -104,3 +104,11 @@ ForceImpl* AmoebaInPlaneAngleForce::createImpl() const {
 void AmoebaInPlaneAngleForce::updateParametersInContext(Context& context) {
     dynamic_cast<AmoebaInPlaneAngleForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
 }
+
+void AmoebaInPlaneAngleForce::setUsesPeriodicBoundaryConditions(bool periodic) {
+    usePeriodic = periodic;
+}
+
+bool AmoebaInPlaneAngleForce::usesPeriodicBoundaryConditions() const {
+    return usePeriodic;
+}

plugins/amoeba/openmmapi/src/AmoebaOutOfPlaneBendForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2009 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors:                                                                   *
  * Contributors:                                                              *
  *                                                                            *
@@ -36,7 +36,7 @@
 
 using namespace OpenMM;
 
-AmoebaOutOfPlaneBendForce::AmoebaOutOfPlaneBendForce() {
+AmoebaOutOfPlaneBendForce::AmoebaOutOfPlaneBendForce() : usePeriodic(false) {
     _globalCubicK     = -0.1400000E-01;
     _globalQuarticK   =  0.5600000E-04;
     _globalPenticK    = -0.7000000E-06;
@@ -106,3 +106,11 @@ ForceImpl* AmoebaOutOfPlaneBendForce::createImpl() const {
 void AmoebaOutOfPlaneBendForce::updateParametersInContext(Context& context) {
     dynamic_cast<AmoebaOutOfPlaneBendForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
 }
+
+void AmoebaOutOfPlaneBendForce::setUsesPeriodicBoundaryConditions(bool periodic) {
+    usePeriodic = periodic;
+}
+
+bool AmoebaOutOfPlaneBendForce::usesPeriodicBoundaryConditions() const {
+    return usePeriodic;
+}

plugins/amoeba/openmmapi/src/AmoebaPiTorsionForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2009 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors:                                                                   *
  * Contributors:                                                              *
  *                                                                            *
@@ -36,7 +36,7 @@
 
 using namespace OpenMM;
 
-AmoebaPiTorsionForce::AmoebaPiTorsionForce() {
+AmoebaPiTorsionForce::AmoebaPiTorsionForce() : usePeriodic(false) {
 }
 
 int AmoebaPiTorsionForce::addPiTorsion(int particle1, int particle2, int particle3, int particle4, int particle5, int particle6,  double k) {
@@ -71,3 +71,11 @@ ForceImpl* AmoebaPiTorsionForce::createImpl() const {
 void AmoebaPiTorsionForce::updateParametersInContext(Context& context) {
     dynamic_cast<AmoebaPiTorsionForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
 }
+
+void AmoebaPiTorsionForce::setUsesPeriodicBoundaryConditions(bool periodic) {
+    usePeriodic = periodic;
+}
+
+bool AmoebaPiTorsionForce::usesPeriodicBoundaryConditions() const {
+    return usePeriodic;
+}

plugins/amoeba/openmmapi/src/AmoebaStretchBendForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2009 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors:                                                                   *
  * Contributors:                                                              *
  *                                                                            *
@@ -36,7 +36,7 @@
 
 using namespace OpenMM;
 
-AmoebaStretchBendForce::AmoebaStretchBendForce() {
+AmoebaStretchBendForce::AmoebaStretchBendForce() : usePeriodic(false) {
 }
 
 int AmoebaStretchBendForce::addStretchBend(int particle1, int particle2, int particle3,
@@ -76,3 +76,11 @@ ForceImpl* AmoebaStretchBendForce::createImpl() const {
 void AmoebaStretchBendForce::updateParametersInContext(Context& context) {
     dynamic_cast<AmoebaStretchBendForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
 }
+
+void AmoebaStretchBendForce::setUsesPeriodicBoundaryConditions(bool periodic) {
+    usePeriodic = periodic;
+}
+
+bool AmoebaStretchBendForce::usesPeriodicBoundaryConditions() const {
+    return usePeriodic;
+}

plugins/amoeba/openmmapi/src/AmoebaTorsionTorsionForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors:                                                                   *
  * Contributors:                                                              *
  *                                                                            *
@@ -38,7 +38,7 @@
 using namespace OpenMM;
 using namespace std;
 
-AmoebaTorsionTorsionForce::AmoebaTorsionTorsionForce() {
+AmoebaTorsionTorsionForce::AmoebaTorsionTorsionForce() : usePeriodic(false) {
 }
 
 int AmoebaTorsionTorsionForce::addTorsionTorsion(int particle1, int particle2, int particle3,
@@ -183,3 +183,11 @@ AmoebaTorsionTorsionForce::TorsionTorsionGridInfo::TorsionTorsionGridInfo(const
             }
     }
 }
+
+void AmoebaTorsionTorsionForce::setUsesPeriodicBoundaryConditions(bool periodic) {
+    usePeriodic = periodic;
+}
+
+bool AmoebaTorsionTorsionForce::usesPeriodicBoundaryConditions() const {
+    return usePeriodic;
+}

plugins/amoeba/platforms/reference/src/AmoebaReferenceKernels.cpp

@@ -104,12 +104,15 @@ void ReferenceCalcAmoebaBondForceKernel::initialize(const System& system, const
     } 
     globalBondCubic   = static_cast<RealOpenMM>(force.getAmoebaGlobalBondCubic());
     globalBondQuartic = static_cast<RealOpenMM>(force.getAmoebaGlobalBondQuartic());
+    usePeriodic = force.usesPeriodicBoundaryConditions();
 }
 
 double ReferenceCalcAmoebaBondForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
     vector<RealVec>& posData   = extractPositions(context);
     vector<RealVec>& forceData = extractForces(context);
     AmoebaReferenceBondForce amoebaReferenceBondForce;
+    if (usePeriodic)
+        amoebaReferenceBondForce.setPeriodic(extractBoxVectors(context));
     RealOpenMM energy      = amoebaReferenceBondForce.calculateForceAndEnergy(numBonds, posData, particle1, particle2, length, kQuadratic,
                                                                                        globalBondCubic, globalBondQuartic,
                                                                                        forceData);
@@ -160,12 +163,15 @@ void ReferenceCalcAmoebaAngleForceKernel::initialize(const System& system, const
     globalAngleQuartic  = static_cast<RealOpenMM>(force.getAmoebaGlobalAngleQuartic());
     globalAnglePentic   = static_cast<RealOpenMM>(force.getAmoebaGlobalAnglePentic());
     globalAngleSextic   = static_cast<RealOpenMM>(force.getAmoebaGlobalAngleSextic());
+    usePeriodic = force.usesPeriodicBoundaryConditions();
 }
 
 double ReferenceCalcAmoebaAngleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
     vector<RealVec>& posData   = extractPositions(context);
     vector<RealVec>& forceData = extractForces(context);
     AmoebaReferenceAngleForce amoebaReferenceAngleForce;
+    if (usePeriodic)
+        amoebaReferenceAngleForce.setPeriodic(extractBoxVectors(context));
     RealOpenMM energy      = amoebaReferenceAngleForce.calculateForceAndEnergy(numAngles, 
                                        posData, particle1, particle2, particle3, angle, kQuadratic, globalAngleCubic, globalAngleQuartic, globalAnglePentic, globalAngleSextic, forceData);
     return static_cast<double>(energy);
@@ -213,6 +219,7 @@ void ReferenceCalcAmoebaInPlaneAngleForceKernel::initialize(const System& system
     globalInPlaneAngleQuartic  = static_cast<RealOpenMM>(force.getAmoebaGlobalInPlaneAngleQuartic());
     globalInPlaneAnglePentic   = static_cast<RealOpenMM>(force.getAmoebaGlobalInPlaneAnglePentic());
     globalInPlaneAngleSextic   = static_cast<RealOpenMM>(force.getAmoebaGlobalInPlaneAngleSextic());
+    usePeriodic = force.usesPeriodicBoundaryConditions();
 }
 
 double ReferenceCalcAmoebaInPlaneAngleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
@@ -220,6 +227,8 @@ double ReferenceCalcAmoebaInPlaneAngleForceKernel::execute(ContextImpl& context,
     vector<RealVec>& posData   = extractPositions(context);
     vector<RealVec>& forceData = extractForces(context);
     AmoebaReferenceInPlaneAngleForce amoebaReferenceInPlaneAngleForce;
+    if (usePeriodic)
+        amoebaReferenceInPlaneAngleForce.setPeriodic(extractBoxVectors(context));
     RealOpenMM energy      = amoebaReferenceInPlaneAngleForce.calculateForceAndEnergy(numAngles, posData, particle1, particle2, particle3, particle4, 
                                                                                                angle, kQuadratic, globalInPlaneAngleCubic, globalInPlaneAngleQuartic,
                                                                                                globalInPlaneAnglePentic, globalInPlaneAngleSextic, forceData);
@@ -266,12 +275,15 @@ void ReferenceCalcAmoebaPiTorsionForceKernel::initialize(const System& system, c
         particle6.push_back(particle6Index); 
         kTorsion.push_back(static_cast<RealOpenMM>(kTorsionParameter));
     }
+    usePeriodic = force.usesPeriodicBoundaryConditions();
 }
 
 double ReferenceCalcAmoebaPiTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
     vector<RealVec>& posData   = extractPositions(context);
     vector<RealVec>& forceData = extractForces(context);
     AmoebaReferencePiTorsionForce amoebaReferencePiTorsionForce;
+    if (usePeriodic)
+        amoebaReferencePiTorsionForce.setPeriodic(extractBoxVectors(context));
     RealOpenMM energy      = amoebaReferencePiTorsionForce.calculateForceAndEnergy(numPiTorsions, posData, particle1, particle2,
                                                                                     particle3, particle4, particle5, particle6,
                                                                                     kTorsion, forceData);
@@ -318,12 +330,15 @@ void ReferenceCalcAmoebaStretchBendForceKernel::initialize(const System& system,
         k1Parameters.push_back(static_cast<RealOpenMM>(k1));
         k2Parameters.push_back(static_cast<RealOpenMM>(k2));
     }
+    usePeriodic = force.usesPeriodicBoundaryConditions();
 }
 
 double ReferenceCalcAmoebaStretchBendForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
     vector<RealVec>& posData   = extractPositions(context);
     vector<RealVec>& forceData = extractForces(context);
     AmoebaReferenceStretchBendForce amoebaReferenceStretchBendForce;
+    if (usePeriodic)
+        amoebaReferenceStretchBendForce.setPeriodic(extractBoxVectors(context));
     RealOpenMM energy      = amoebaReferenceStretchBendForce.calculateForceAndEnergy(numStretchBends, posData, particle1, particle2, particle3,
                                                                                       lengthABParameters, lengthCBParameters, angleParameters, k1Parameters,
                                                                                       k2Parameters, forceData);
@@ -376,13 +391,15 @@ void ReferenceCalcAmoebaOutOfPlaneBendForceKernel::initialize(const System& syst
     globalOutOfPlaneBendAngleQuartic    = static_cast<RealOpenMM>(force.getAmoebaGlobalOutOfPlaneBendQuartic());
     globalOutOfPlaneBendAnglePentic     = static_cast<RealOpenMM>(force.getAmoebaGlobalOutOfPlaneBendPentic());
     globalOutOfPlaneBendAngleSextic     = static_cast<RealOpenMM>(force.getAmoebaGlobalOutOfPlaneBendSextic());
-
+    usePeriodic = force.usesPeriodicBoundaryConditions();
 }
 
 double ReferenceCalcAmoebaOutOfPlaneBendForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
     vector<RealVec>& posData   = extractPositions(context);
     vector<RealVec>& forceData = extractForces(context);
     AmoebaReferenceOutOfPlaneBendForce amoebaReferenceOutOfPlaneBendForce;
+    if (usePeriodic)
+        amoebaReferenceOutOfPlaneBendForce.setPeriodic(extractBoxVectors(context));
     RealOpenMM energy      = amoebaReferenceOutOfPlaneBendForce.calculateForceAndEnergy(numOutOfPlaneBends, posData,
                                                                                          particle1, particle2, particle3, particle4,
                                                                                          kParameters, 
@@ -434,6 +451,7 @@ void ReferenceCalcAmoebaTorsionTorsionForceKernel::initialize(const System& syst
         chiralCheckAtom.push_back(chiralCheckAtomIndex); 
         gridIndices.push_back(gridIndex); 
     }
+    usePeriodic = force.usesPeriodicBoundaryConditions();
 
     // torsion-torsion grids
 
@@ -478,6 +496,8 @@ double ReferenceCalcAmoebaTorsionTorsionForceKernel::execute(ContextImpl& contex
     vector<RealVec>& posData   = extractPositions(context);
     vector<RealVec>& forceData = extractForces(context);
     AmoebaReferenceTorsionTorsionForce amoebaReferenceTorsionTorsionForce;
+    if (usePeriodic)
+        amoebaReferenceTorsionTorsionForce.setPeriodic(extractBoxVectors(context));
     RealOpenMM energy      = amoebaReferenceTorsionTorsionForce.calculateForceAndEnergy(numTorsionTorsions, posData,
                                                                                          particle1, particle2, particle3, particle4, particle5,
                                                                                          chiralCheckAtom, gridIndices, torsionTorsionGrids, forceData);

plugins/amoeba/platforms/reference/src/AmoebaReferenceKernels.h

@@ -77,6 +77,7 @@ private:
     RealOpenMM globalBondCubic;
     RealOpenMM globalBondQuartic;
     const System& system;
+    bool usePeriodic;
 };
 
 /**
@@ -121,6 +122,7 @@ private:
     RealOpenMM globalAnglePentic;
     RealOpenMM globalAngleSextic;
     const System& system;
+    bool usePeriodic;
 };
 
 /**
@@ -166,6 +168,7 @@ private:
     RealOpenMM globalInPlaneAnglePentic;
     RealOpenMM globalInPlaneAngleSextic;
     const System& system;
+    bool usePeriodic;
 };
 
 /**
@@ -208,6 +211,7 @@ private:
     std::vector<int>   particle6;
     std::vector<RealOpenMM> kTorsion;
     const System& system;
+    bool usePeriodic;
 };
 
 /**
@@ -251,6 +255,7 @@ private:
     std::vector<RealOpenMM> k1Parameters;
     std::vector<RealOpenMM> k2Parameters;
     const System& system;
+    bool usePeriodic;
 };
 
 /**
@@ -295,6 +300,7 @@ private:
     RealOpenMM globalOutOfPlaneBendAnglePentic;
     RealOpenMM globalOutOfPlaneBendAngleSextic;
     const System& system;
+    bool usePeriodic;
 };
 
 /**
@@ -334,6 +340,7 @@ private:
     std::vector< std::vector< std::vector< std::vector<RealOpenMM> > > > torsionTorsionGrids;
 
     const System& system;
+    bool usePeriodic;
 };
 
 /**

plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceAngleForce.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 +28,13 @@
 using std::vector;
 using namespace OpenMM;
 
+void AmoebaReferenceAngleForce::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
@@ -132,11 +139,17 @@ RealOpenMM AmoebaReferenceAngleForce::calculateAngleIxn(const RealVec& positionA
    // ---------------------------------------------------------------------------------------
 
     std::vector<RealOpenMM> deltaR[2];
-    AmoebaReferenceForce::loadDeltaR(positionAtomA, positionAtomB, deltaR[0]);
+    if (usePeriodic)
+        AmoebaReferenceForce::loadDeltaRPeriodic(positionAtomA, positionAtomB, deltaR[0], boxVectors);
+    else
+        AmoebaReferenceForce::loadDeltaR(positionAtomA, positionAtomB, deltaR[0]);
     RealOpenMM rAB2      = AmoebaReferenceForce::getNormSquared3(deltaR[0]);
     RealOpenMM rAB       = SQRT(rAB2);
  
-    AmoebaReferenceForce::loadDeltaR(positionAtomC, positionAtomB, deltaR[1]);
+    if (usePeriodic)
+        AmoebaReferenceForce::loadDeltaRPeriodic(positionAtomC, positionAtomB, deltaR[1], boxVectors);
+    else
+        AmoebaReferenceForce::loadDeltaR(positionAtomC, positionAtomB, deltaR[1]);
     RealOpenMM rCB2      = AmoebaReferenceForce::getNormSquared3(deltaR[1]);
     RealOpenMM rCB       = SQRT(rCB2);
  

plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceAngleForce.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:
        
        --------------------------------------------------------------------------------------- */
  
-    AmoebaReferenceAngleForce() {};
+    AmoebaReferenceAngleForce() : usePeriodic(false) {};
  
     /**---------------------------------------------------------------------------------------
        
@@ -50,6 +50,16 @@ public:
  
     ~AmoebaReferenceAngleForce() {};
  
+    /**---------------------------------------------------------------------------------------
+
+       Set the force to use periodic boundary conditions.
+      
+       @param vectors    the vectors defining the periodic box
+      
+       --------------------------------------------------------------------------------------- */
+      
+    void setPeriodic(OpenMM::RealVec* vectors);
+
      /**---------------------------------------------------------------------------------------
      
         Calculate Amoeba angle ixns (force and energy)
@@ -86,6 +96,9 @@ public:
 
 private:
 
+    bool usePeriodic;
+    RealVec boxVectors[3];
+
     /**---------------------------------------------------------------------------------------
     
        Get dEdT and energy prefactor given cosine of angle :: the calculation for different