Merge pull request #1467 from peastman/amoebaperiodic

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/cuda/src/AmoebaCudaKernels.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) 2008-2015 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman, Mark Friedrichs                                    *
  * Contributors:                                                              *
  *                                                                            *
@@ -117,7 +117,7 @@ void CudaCalcAmoebaBondForceKernel::initialize(const System& system, const Amoeb
     }
     params->upload(paramVector);
     map<string, string> replacements;
-    replacements["APPLY_PERIODIC"] = "0";
+    replacements["APPLY_PERIODIC"] = (force.usesPeriodicBoundaryConditions() ? "1" : "0");
     replacements["COMPUTE_FORCE"] = CudaAmoebaKernelSources::amoebaBondForce;
     replacements["PARAMS"] = cu.getBondedUtilities().addArgument(params->getDevicePointer(), "float2");
     replacements["CUBIC_K"] = cu.doubleToString(force.getAmoebaGlobalBondCubic());
@@ -215,7 +215,7 @@ void CudaCalcAmoebaAngleForceKernel::initialize(const System& system, const Amoe
     }
     params->upload(paramVector);
     map<string, string> replacements;
-    replacements["APPLY_PERIODIC"] = "0";
+    replacements["APPLY_PERIODIC"] = (force.usesPeriodicBoundaryConditions() ? "1" : "0");
     replacements["COMPUTE_FORCE"] = CudaAmoebaKernelSources::amoebaAngleForce;
     replacements["PARAMS"] = cu.getBondedUtilities().addArgument(params->getDevicePointer(), "float2");
     replacements["CUBIC_K"] = cu.doubleToString(force.getAmoebaGlobalAngleCubic());
@@ -317,6 +317,7 @@ void CudaCalcAmoebaInPlaneAngleForceKernel::initialize(const System& system, con
     }
     params->upload(paramVector);
     map<string, string> replacements;
+    replacements["APPLY_PERIODIC"] = (force.usesPeriodicBoundaryConditions() ? "1" : "0");
     replacements["PARAMS"] = cu.getBondedUtilities().addArgument(params->getDevicePointer(), "float2");
     replacements["CUBIC_K"] = cu.doubleToString(force.getAmoebaGlobalInPlaneAngleCubic());
     replacements["QUARTIC_K"] = cu.doubleToString(force.getAmoebaGlobalInPlaneAngleQuartic());
@@ -419,6 +420,7 @@ void CudaCalcAmoebaPiTorsionForceKernel::initialize(const System& system, const
     }
     params->upload(paramVector);
     map<string, string> replacements;
+    replacements["APPLY_PERIODIC"] = (force.usesPeriodicBoundaryConditions() ? "1" : "0");
     replacements["PARAMS"] = cu.getBondedUtilities().addArgument(params->getDevicePointer(), "float");
     cu.getBondedUtilities().addInteraction(atoms, cu.replaceStrings(CudaAmoebaKernelSources::amoebaPiTorsionForce, replacements), force.getForceGroup());
     cu.addForce(new ForceInfo(force));
@@ -519,6 +521,7 @@ void CudaCalcAmoebaStretchBendForceKernel::initialize(const System& system, cons
     params1->upload(paramVector);
     params2->upload(paramVectorK);
     map<string, string> replacements;
+    replacements["APPLY_PERIODIC"] = (force.usesPeriodicBoundaryConditions() ? "1" : "0");
     replacements["PARAMS"] = cu.getBondedUtilities().addArgument(params1->getDevicePointer(), "float3");
     replacements["FORCE_CONSTANTS"] = cu.getBondedUtilities().addArgument(params2->getDevicePointer(), "float2");
     replacements["RAD_TO_DEG"] = cu.doubleToString(180/M_PI);
@@ -619,6 +622,7 @@ void CudaCalcAmoebaOutOfPlaneBendForceKernel::initialize(const System& system, c
     }
     params->upload(paramVector);
     map<string, string> replacements;
+    replacements["APPLY_PERIODIC"] = (force.usesPeriodicBoundaryConditions() ? "1" : "0");
     replacements["PARAMS"] = cu.getBondedUtilities().addArgument(params->getDevicePointer(), "float");
     replacements["CUBIC_K"] = cu.doubleToString(force.getAmoebaGlobalOutOfPlaneBendCubic());
     replacements["QUARTIC_K"] = cu.doubleToString(force.getAmoebaGlobalOutOfPlaneBendQuartic());
@@ -750,6 +754,7 @@ void CudaCalcAmoebaTorsionTorsionForceKernel::initialize(const System& system, c
     gridValues->upload(gridValuesVec);
     gridParams->upload(gridParamsVec);
     map<string, string> replacements;
+    replacements["APPLY_PERIODIC"] = (force.usesPeriodicBoundaryConditions() ? "1" : "0");
     replacements["GRID_VALUES"] = cu.getBondedUtilities().addArgument(gridValues->getDevicePointer(), "float4");
     replacements["GRID_PARAMS"] = cu.getBondedUtilities().addArgument(gridParams->getDevicePointer(), "float4");
     replacements["TORSION_PARAMS"] = cu.getBondedUtilities().addArgument(torsionParams->getDevicePointer(), "int2");

plugins/amoeba/platforms/cuda/src/kernels/amoebaInPlaneForce.cu

 float2 angleParams = PARAMS[index];
-real xad = pos1.x - pos4.x;
-real yad = pos1.y - pos4.y;
-real zad = pos1.z - pos4.z;
+real3 ad = make_real3(pos1.x-pos4.x, pos1.y-pos4.y, pos1.z-pos4.z);
+real3 bd = make_real3(pos2.x-pos4.x, pos2.y-pos4.y, pos2.z-pos4.z);
+real3 cd = make_real3(pos3.x-pos4.x, pos3.y-pos4.y, pos3.z-pos4.z);
 
-real xbd = pos2.x - pos4.x;
-real ybd = pos2.y - pos4.y;
-real zbd = pos2.z - pos4.z;
+#if APPLY_PERIODIC
+APPLY_PERIODIC_TO_DELTA(ad)
+APPLY_PERIODIC_TO_DELTA(bd)
+APPLY_PERIODIC_TO_DELTA(cd)
+#endif
 
-real xcd = pos3.x - pos4.x;
-real ycd = pos3.y - pos4.y;
-real zcd = pos3.z - pos4.z;
-
-real xt = yad*zcd - zad*ycd;
-real yt = zad*xcd - xad*zcd;
-real zt = xad*ycd - yad*xcd;
+real xt = ad.y*cd.z - ad.z*cd.y;
+real yt = ad.z*cd.x - ad.x*cd.z;
+real zt = ad.x*cd.y - ad.y*cd.x;
 
 real rt2 = xt*xt + yt*yt + zt*zt;
 
-real delta = -(xt*xbd + yt*ybd + zt*zbd) / rt2;
+real delta = -(xt*bd.x + yt*bd.y + zt*bd.z) / rt2;
 
 real xip = pos2.x + xt*delta;
 real yip = pos2.y + yt*delta;
 real zip = pos2.z + zt*delta;
 
-real xap = pos1.x - xip;
-real yap = pos1.y - yip;
-real zap = pos1.z - zip;
+real3 ap = make_real3(pos1.x-xip, pos1.y-yip, pos1.z-zip);
+real3 cp = make_real3(pos3.x-xip, pos3.y-yip, pos3.z-zip);
 
-real xcp = pos3.x - xip;
-real ycp = pos3.y - yip;
-real zcp = pos3.z - zip;
+#if APPLY_PERIODIC
+APPLY_PERIODIC_TO_DELTA(ap)
+APPLY_PERIODIC_TO_DELTA(cp)
+#endif
 
-real rap2 = xap*xap + yap*yap + zap*zap;
-real rcp2 = xcp*xcp + ycp*ycp + zcp*zcp;
+real rap2 = ap.x*ap.x + ap.y*ap.y + ap.z*ap.z;
+real rcp2 = cp.x*cp.x + cp.y*cp.y + cp.z*cp.z;
 
-real xm = ycp*zap - zcp*yap;
-real ym = zcp*xap - xcp*zap;
-real zm = xcp*yap - ycp*xap;
+real xm = cp.y*ap.z - cp.z*ap.y;
+real ym = cp.z*ap.x - cp.x*ap.z;
+real zm = cp.x*ap.y - cp.y*ap.x;
 
 real rm = max(SQRT(xm*xm + ym*ym + zm*zm), (real) 1e-6f);
-real dotp = xap*xcp + yap*ycp + zap*zcp;
+real dotp = ap.x*cp.x + ap.y*cp.y + ap.z*cp.z;
 real product = SQRT(rap2*rcp2);
 real cosine = (product > 0 ? (dotp/product) : 0);
 cosine = max(min(cosine, (real) 1), (real) -1);
 real angle;
 if (cosine > 0.99f || cosine < -0.99f) {
-    real3 cross_prod = cross(make_real3(xap, yap, zap), make_real3(xcp, ycp, zcp));
+    real3 cross_prod = cross(ap, cp);
     angle = ASIN(SQRT(dot(cross_prod, cross_prod)/(rap2*rcp2)))*RAD_TO_DEG;
     if (cosine < 0.0f)
         angle = 180-angle;
@@ -67,13 +65,13 @@ dEdAngle *= RAD_TO_DEG;
 real terma = -dEdAngle/(rap2*rm);
 real termc = dEdAngle/(rcp2*rm);
 
-real dedxia = terma * (yap*zm-zap*ym);
-real dedyia = terma * (zap*xm-xap*zm);
-real dedzia = terma * (xap*ym-yap*xm);
+real dedxia = terma * (ap.y*zm-ap.z*ym);
+real dedyia = terma * (ap.z*xm-ap.x*zm);
+real dedzia = terma * (ap.x*ym-ap.y*xm);
 
-real dedxic = termc * (ycp*zm-zcp*ym);
-real dedyic = termc * (zcp*xm-xcp*zm);
-real dedzic = termc * (xcp*ym-ycp*xm);
+real dedxic = termc * (cp.y*zm-cp.z*ym);
+real dedyic = termc * (cp.z*xm-cp.x*zm);
+real dedzic = termc * (cp.x*ym-cp.y*xm);
 
 real dedxip = -dedxia - dedxic;
 real dedyip = -dedyia - dedyic;
@@ -82,23 +80,23 @@ real dedzip = -dedzia - dedzic;
 real delta2 = 2.0f*delta;
 real ptrt2 = (dedxip*xt + dedyip*yt + dedzip*zt) / rt2;
 
-real term = (zcd*ybd-ycd*zbd) + delta2*(yt*zcd-zt*ycd);
-real dpdxia = delta*(ycd*dedzip-zcd*dedyip) + term*ptrt2;
+real term = (cd.z*bd.y-cd.y*bd.z) + delta2*(yt*cd.z-zt*cd.y);
+real dpdxia = delta*(cd.y*dedzip-cd.z*dedyip) + term*ptrt2;
 
-term = (xcd*zbd-zcd*xbd) + delta2*(zt*xcd-xt*zcd);
-real dpdyia = delta*(zcd*dedxip-xcd*dedzip) + term*ptrt2;
+term = (cd.x*bd.z-cd.z*bd.x) + delta2*(zt*cd.x-xt*cd.z);
+real dpdyia = delta*(cd.z*dedxip-cd.x*dedzip) + term*ptrt2;
 
-term = (ycd*xbd-xcd*ybd) + delta2*(xt*ycd-yt*xcd);
-real dpdzia = delta*(xcd*dedyip-ycd*dedxip) + term*ptrt2;
+term = (cd.y*bd.x-cd.x*bd.y) + delta2*(xt*cd.y-yt*cd.x);
+real dpdzia = delta*(cd.x*dedyip-cd.y*dedxip) + term*ptrt2;
 
-term = (yad*zbd-zad*ybd) + delta2*(zt*yad-yt*zad);
-real dpdxic = delta*(zad*dedyip-yad*dedzip) + term*ptrt2;
+term = (ad.y*bd.z-ad.z*bd.y) + delta2*(zt*ad.y-yt*ad.z);
+real dpdxic = delta*(ad.z*dedyip-ad.y*dedzip) + term*ptrt2;
 
-term = (zad*xbd-xad*zbd) + delta2*(xt*zad-zt*xad);
-real dpdyic = delta*(xad*dedzip-zad*dedxip) + term*ptrt2;
+term = (ad.z*bd.x-ad.x*bd.z) + delta2*(xt*ad.z-zt*ad.x);
+real dpdyic = delta*(ad.x*dedzip-ad.z*dedxip) + term*ptrt2;
 
-term = (xad*ybd-yad*xbd) + delta2*(yt*xad-xt*yad);
-real dpdzic = delta*(yad*dedxip-xad*dedyip) + term*ptrt2;
+term = (ad.x*bd.y-ad.y*bd.x) + delta2*(yt*ad.x-xt*ad.y);
+real dpdzic = delta*(ad.y*dedxip-ad.x*dedyip) + term*ptrt2;
 
 dedxia = dedxia + dpdxia;
 dedyia = dedyia + dpdyia;

plugins/amoeba/platforms/cuda/src/kernels/amoebaOutOfPlaneBendForce.cu

 // compute the value of the bond angle
 
-real xab = pos1.x - pos2.x;
-real yab = pos1.y - pos2.y;
-real zab = pos1.z - pos2.z;
-
-real xcb = pos3.x - pos2.x;
-real ycb = pos3.y - pos2.y;
-real zcb = pos3.z - pos2.z;
-
-// compute the out-of-plane bending angle
-
-real xdb = pos4.x - pos2.x;
-real ydb = pos4.y - pos2.y;
-real zdb = pos4.z - pos2.z;
-
-real xad = pos1.x - pos4.x;
-real yad = pos1.y - pos4.y;
-real zad = pos1.z - pos4.z;
-
-real xcd = pos3.x - pos4.x;
-real ycd = pos3.y - pos4.y;
-real zcd = pos3.z - pos4.z;
-
-real rdb2 = xdb*xdb + ydb*ydb + zdb*zdb;
-real rad2 = xad*xad + yad*yad + zad*zad;
-real rcd2 = xcd*xcd + ycd*ycd + zcd*zcd;
-
-real ee = xab*(ycb*zdb-zcb*ydb) + yab*(zcb*xdb-xcb*zdb) + zab*(xcb*ydb-ycb*xdb);
-
-real dot = xad*xcd + yad*ycd + zad*zcd;
+real3 ab = make_real3(pos1.x-pos2.x, pos1.y-pos2.y, pos1.z-pos2.z);
+real3 cb = make_real3(pos3.x-pos2.x, pos3.y-pos2.y, pos3.z-pos2.z);
+real3 db = make_real3(pos4.x-pos2.x, pos4.y-pos2.y, pos4.z-pos2.z);
+real3 ad = make_real3(pos1.x-pos4.x, pos1.y-pos4.y, pos1.z-pos4.z);
+real3 cd = make_real3(pos3.x-pos4.x, pos3.y-pos4.y, pos3.z-pos4.z);
+
+#if APPLY_PERIODIC
+APPLY_PERIODIC_TO_DELTA(ab)
+APPLY_PERIODIC_TO_DELTA(cb)
+APPLY_PERIODIC_TO_DELTA(db)
+APPLY_PERIODIC_TO_DELTA(ad)
+APPLY_PERIODIC_TO_DELTA(cd)
+#endif
+
+real rdb2 = db.x*db.x + db.y*db.y + db.z*db.z;
+real rad2 = ad.x*ad.x + ad.y*ad.y + ad.z*ad.z;
+real rcd2 = cd.x*cd.x + cd.y*cd.y + cd.z*cd.z;
+
+real ee = ab.x*(cb.y*db.z-cb.z*db.y) + ab.y*(cb.z*db.x-cb.x*db.z) + ab.z*(cb.x*db.y-cb.y*db.x);
+
+real dot = ad.x*cd.x + ad.y*cd.y + ad.z*cd.z;
 real cc = rad2*rcd2 - dot*dot;
 real bkk2 = (cc != 0 ? (ee*ee)/(cc) : (real) 0);
 bkk2 = rdb2 - bkk2;
 
-real adXcd_0 = yad*zcd - zad*ycd;
-real adXcd_1 = zad*xcd - xad*zcd;
-real adXcd_2 = xad*ycd - yad*xcd;
+real adXcd_0 = ad.y*cd.z - ad.z*cd.y;
+real adXcd_1 = ad.z*cd.x - ad.x*cd.z;
+real adXcd_2 = ad.x*cd.y - ad.y*cd.x;
 real adXcd_nrm2 = adXcd_0*adXcd_0 + adXcd_1*adXcd_1 + adXcd_2*adXcd_2;
 
-real adXcd_dot_db = xdb*adXcd_0 + ydb*adXcd_1 + zdb*adXcd_2;
+real adXcd_dot_db = db.x*adXcd_0 + db.y*adXcd_1 + db.z*adXcd_2;
 adXcd_dot_db /= SQRT(rdb2*adXcd_nrm2);
 
 real angle = abs(ASIN(adXcd_dot_db));
@@ -62,13 +54,13 @@ real dedcos = -deddt*eeSign/SQRT(cc*bkk2);
 
 real term = ee / cc;
 
-real dccdxia = (xad*rcd2-xcd*dot) * term;
-real dccdyia = (yad*rcd2-ycd*dot) * term;
-real dccdzia = (zad*rcd2-zcd*dot) * term;
+real dccdxia = (ad.x*rcd2-cd.x*dot) * term;
+real dccdyia = (ad.y*rcd2-cd.y*dot) * term;
+real dccdzia = (ad.z*rcd2-cd.z*dot) * term;
 
-real dccdxic = (xcd*rad2-xad*dot) * term;
-real dccdyic = (ycd*rad2-yad*dot) * term;
-real dccdzic = (zcd*rad2-zad*dot) * term;
+real dccdxic = (cd.x*rad2-ad.x*dot) * term;
+real dccdyic = (cd.y*rad2-ad.y*dot) * term;
+real dccdzic = (cd.z*rad2-ad.z*dot) * term;
 
 real dccdxid = -dccdxia - dccdxic;
 real dccdyid = -dccdyia - dccdyic;
@@ -76,17 +68,17 @@ real dccdzid = -dccdzia - dccdzic;
 
 term = ee / rdb2;
 
-real deedxia = ydb*zcb - zdb*ycb;
-real deedyia = zdb*xcb - xdb*zcb;
-real deedzia = xdb*ycb - ydb*xcb;
+real deedxia = db.y*cb.z - db.z*cb.y;
+real deedyia = db.z*cb.x - db.x*cb.z;
+real deedzia = db.x*cb.y - db.y*cb.x;
 
-real deedxic = yab*zdb - zab*ydb;
-real deedyic = zab*xdb - xab*zdb;
-real deedzic = xab*ydb - yab*xdb;
+real deedxic = ab.y*db.z - ab.z*db.y;
+real deedyic = ab.z*db.x - ab.x*db.z;
+real deedzic = ab.x*db.y - ab.y*db.x;
 
-real deedxid = ycb*zab - zcb*yab + xdb*term;
-real deedyid = zcb*xab - xcb*zab + ydb*term;
-real deedzid = xcb*yab - ycb*xab + zdb*term;
+real deedxid = cb.y*ab.z - cb.z*ab.y + db.x*term;
+real deedyid = cb.z*ab.x - cb.x*ab.z + db.y*term;
+real deedzid = cb.x*ab.y - cb.y*ab.x + db.z*term;
 
 // compute first derivative components for this angle
 

plugins/amoeba/platforms/cuda/src/kernels/amoebaPiTorsionForce.cu

 // compute the value of the pi-orbital torsion angle
 
-real xad = pos1.x - pos4.x;
-real yad = pos1.y - pos4.y;
-real zad = pos1.z - pos4.z;
-
-real xbd = pos2.x - pos4.x;
-real ybd = pos2.y - pos4.y;
-real zbd = pos2.z - pos4.z;
-
-real xec = pos5.x - pos3.x;
-real yec = pos5.y - pos3.y;
-real zec = pos5.z - pos3.z;
-
-real xgc = pos6.x - pos3.x;
-real ygc = pos6.y - pos3.y;
-real zgc = pos6.z - pos3.z;
-
-real xip = yad*zbd - ybd*zad + pos3.x;
-real yip = zad*xbd - zbd*xad + pos3.y;
-real zip = xad*ybd - xbd*yad + pos3.z;
-
-real xiq = yec*zgc - ygc*zec + pos4.x;
-real yiq = zec*xgc - zgc*xec + pos4.y;
-real ziq = xec*ygc - xgc*yec + pos4.z;
+real3 ad = make_real3(pos1.x-pos4.x, pos1.y-pos4.y, pos1.z-pos4.z);
+real3 bd = make_real3(pos2.x-pos4.x, pos2.y-pos4.y, pos2.z-pos4.z);
+real3 ec = make_real3(pos5.x-pos3.x, pos5.y-pos3.y, pos5.z-pos3.z);
+real3 gc = make_real3(pos6.x-pos3.x, pos6.y-pos3.y, pos6.z-pos3.z);
+
+#if APPLY_PERIODIC
+APPLY_PERIODIC_TO_DELTA(ad)
+APPLY_PERIODIC_TO_DELTA(bd)
+APPLY_PERIODIC_TO_DELTA(ec)
+APPLY_PERIODIC_TO_DELTA(gc)
+#endif
+
+real xip = ad.y*bd.z - bd.y*ad.z + pos3.x;
+real yip = ad.z*bd.x - bd.z*ad.x + pos3.y;
+real zip = ad.x*bd.y - bd.x*ad.y + pos3.z;
+
+real xiq = ec.y*gc.z - gc.y*ec.z + pos4.x;
+real yiq = ec.z*gc.x - gc.z*ec.x + pos4.y;
+real ziq = ec.x*gc.y - gc.x*ec.y + pos4.z;
 
 real xcp = pos3.x - xip;
 real ycp = pos3.y - yip;
@@ -112,21 +108,21 @@ real dedziq = ydc*dedxu - xdc*dedyu;
 
 // compute first derivative components for individual atoms
 
-real dedxia = ybd*dedzip - zbd*dedyip;
-real dedyia = zbd*dedxip - xbd*dedzip;
-real dedzia = xbd*dedyip - ybd*dedxip;
+real dedxia = bd.y*dedzip - bd.z*dedyip;
+real dedyia = bd.z*dedxip - bd.x*dedzip;
+real dedzia = bd.x*dedyip - bd.y*dedxip;
 
-real dedxib = zad*dedyip - yad*dedzip;
-real dedyib = xad*dedzip - zad*dedxip;
-real dedzib = yad*dedxip - xad*dedyip;
+real dedxib = ad.z*dedyip - ad.y*dedzip;
+real dedyib = ad.x*dedzip - ad.z*dedxip;
+real dedzib = ad.y*dedxip - ad.x*dedyip;
 
-real dedxie = ygc*dedziq - zgc*dedyiq;
-real dedyie = zgc*dedxiq - xgc*dedziq;
-real dedzie = xgc*dedyiq - ygc*dedxiq;
+real dedxie = gc.y*dedziq - gc.z*dedyiq;
+real dedyie = gc.z*dedxiq - gc.x*dedziq;
+real dedzie = gc.x*dedyiq - gc.y*dedxiq;
 
-real dedxig = zec*dedyiq - yec*dedziq;
-real dedyig = xec*dedziq - zec*dedxiq;
-real dedzig = yec*dedxiq - xec*dedyiq;
+real dedxig = ec.z*dedyiq - ec.y*dedziq;
+real dedyig = ec.x*dedziq - ec.z*dedxiq;
+real dedzig = ec.y*dedxiq - ec.x*dedyiq;
 
 dedxic = dedxic + dedxip - dedxie - dedxig;
 dedyic = dedyic + dedyip - dedyie - dedyig;