Added required headers. Still need to actually implement the functions

plugins/amoeba/openmmapi/include/openmm/AmoebaMultipoleForce.h

@@ -316,15 +316,6 @@ public:
      * This can be overridden by explicitly setting an alpha parameter and grid dimensions to use.
      */
     void setEwaldErrorTolerance(double tol);
-
-    /**
-     * Get the induced dipole moments of all particles.
-     *
-     * @param context         the Context for which to get the induced dipoles
-     * @param[out] dipoles    the induced dipole moment of particle i is stored into the i'th element
-     */
-    void getInducedDipoles(Context& context, std::vector<Vec3>& dipoles);
-
     /**
      * Get the fixed dipole moments of all particles in the global reference frame.
      *
@@ -332,6 +323,13 @@ public:
      * @param[out] dipoles    the fixed dipole moment of particle i is stored into the i'th element
      */
     void getLabFramePermanentDipoles(Context& context, std::vector<Vec3>& dipoles);
+    /**
+     * Get the induced dipole moments of all particles.
+     *
+     * @param context         the Context for which to get the induced dipoles
+     * @param[out] dipoles    the induced dipole moment of particle i is stored into the i'th element
+     */
+    void getInducedDipoles(Context& context, std::vector<Vec3>& dipoles);
 
     /**
      * Get the electrostatic potential.

plugins/amoeba/openmmapi/include/openmm/amoebaKernels.h

@@ -59,7 +59,7 @@ public:
 
     /**
      * Initialize the kernel.
-     * 
+     *
      * @param system     the System this kernel will be applied to
      * @param force      the AmoebaBondForce this kernel will be used for
      */
@@ -99,7 +99,7 @@ public:
 
     /**
      * Initialize the kernel.
-     * 
+     *
      * @param system     the System this kernel will be applied to
      * @param force      the AmoebaAngleForce this kernel will be used for
      */
@@ -139,7 +139,7 @@ public:
 
     /**
      * Initialize the kernel.
-     * 
+     *
      * @param system     the System this kernel will be applied to
      * @param force      the AmoebaInPlaneAngleForce this kernel will be used for
      */
@@ -179,7 +179,7 @@ public:
 
     /**
      * Initialize the kernel.
-     * 
+     *
      * @param system     the System this kernel will be applied to
      * @param force      the PiTorsionForce this kernel will be used for
      */
@@ -219,7 +219,7 @@ public:
 
     /**
      * Initialize the kernel.
-     * 
+     *
      * @param system     the System this kernel will be applied to
      * @param force      the StretchBendForce this kernel will be used for
      */
@@ -259,7 +259,7 @@ public:
 
     /**
      * Initialize the kernel.
-     * 
+     *
      * @param system     the System this kernel will be applied to
      * @param force      the OutOfPlaneBendForce this kernel will be used for
      */
@@ -299,7 +299,7 @@ public:
 
     /**
      * Initialize the kernel.
-     * 
+     *
      * @param system     the System this kernel will be applied to
      * @param force      the TorsionTorsionForce this kernel will be used for
      */
@@ -332,7 +332,7 @@ public:
 
     /**
      * Initialize the kernel.
-     * 
+     *
      * @param system     the System this kernel will be applied to
      * @param force      the MultipoleForce this kernel will be used for
      */
@@ -348,6 +348,7 @@ public:
      */
     virtual double execute(ContextImpl& context, bool includeForces, bool includeEnergy) = 0;
 
+    virtual void getLabFramePermanentDipoles(ContextImpl& context, std::vector<Vec3>& dipoles) = 0;
     virtual void getInducedDipoles(ContextImpl& context, std::vector<Vec3>& dipoles) = 0;
 
     virtual void getElectrostaticPotential(ContextImpl& context, const std::vector< Vec3 >& inputGrid,
@@ -364,7 +365,7 @@ public:
 
     /**
      * Get the parameters being used for PME.
-     * 
+     *
      * @param alpha   the separation parameter
      * @param nx      the number of grid points along the X axis
      * @param ny      the number of grid points along the Y axis
@@ -389,7 +390,7 @@ public:
 
     /**
      * Initialize the kernel.
-     * 
+     *
      * @param system     the System this kernel will be applied to
      * @param force      the GBSAOBCForce this kernel will be used for
      */
@@ -429,7 +430,7 @@ public:
 
     /**
      * Initialize the kernel.
-     * 
+     *
      * @param system     the System this kernel will be applied to
      * @param force      the GBSAOBCForce this kernel will be used for
      */
@@ -469,7 +470,7 @@ public:
 
     /**
      * Initialize the kernel.
-     * 
+     *
      * @param system     the System this kernel will be applied to
      * @param force      the GBSAOBCForce this kernel will be used for
      */

plugins/amoeba/openmmapi/include/openmm/internal/AmoebaMultipoleForceImpl.h

@@ -64,7 +64,7 @@ public:
 
     /**
      * Get the CovalentMap for an atom
-     * 
+     *
      * @param force                AmoebaMultipoleForce force reference
      * @param index                the index of the atom for which to set parameters
      * @param minCovalentIndex     minimum covalent index
@@ -76,15 +76,13 @@ public:
 
     /**
      * Get the covalent degree for the  CovalentEnd lists
-     * 
+     *
      * @param force                AmoebaMultipoleForce force reference
      * @param covalentDegree      covalent degrees for the CovalentEnd lists
      */
     static void getCovalentDegree(const AmoebaMultipoleForce& force, std::vector<int>& covalentDegree);
-
-    void getInducedDipoles(ContextImpl& context, std::vector<Vec3>& dipoles);
-    
     void getLabFramePermanentDipoles(ContextImpl& context, std::vector<Vec3>& dipoles);
+    void getInducedDipoles(ContextImpl& context, std::vector<Vec3>& dipoles);
 
     void getElectrostaticPotential(ContextImpl& context, const std::vector< Vec3 >& inputGrid,
                                    std::vector< double >& outputElectrostaticPotential);
@@ -92,7 +90,7 @@ public:
     void getSystemMultipoleMoments(ContextImpl& context, std::vector< double >& outputMultipoleMoments);
     void updateParametersInContext(ContextImpl& context);
     void getPMEParameters(double& alpha, int& nx, int& ny, int& nz) const;
- 
+
 
 private:
     const AmoebaMultipoleForce& owner;

plugins/amoeba/openmmapi/src/AmoebaMultipoleForce.cpp

@@ -69,19 +69,19 @@ void AmoebaMultipoleForce::setCutoffDistance(double distance) {
     cutoffDistance = distance;
 }
 
-double AmoebaMultipoleForce::getAEwald() const { 
-    return aewald; 
-} 
- 
-void AmoebaMultipoleForce::setAEwald(double inputAewald) { 
-    aewald = inputAewald; 
-} 
- 
-int AmoebaMultipoleForce::getPmeBSplineOrder() const { 
-    return pmeBSplineOrder; 
-} 
- 
-void AmoebaMultipoleForce::getPmeGridDimensions(std::vector<int>& gridDimension) const { 
+double AmoebaMultipoleForce::getAEwald() const {
+    return aewald;
+}
+
+void AmoebaMultipoleForce::setAEwald(double inputAewald) {
+    aewald = inputAewald;
+}
+
+int AmoebaMultipoleForce::getPmeBSplineOrder() const {
+    return pmeBSplineOrder;
+}
+
+void AmoebaMultipoleForce::getPmeGridDimensions(std::vector<int>& gridDimension) const {
     if (gridDimension.size() < 3) {
         gridDimension.resize(3);
     }
@@ -93,15 +93,15 @@ void AmoebaMultipoleForce::getPmeGridDimensions(std::vector<int>& gridDimension)
         gridDimension[0] = gridDimension[1] = gridDimension[2] = 0;
     }
     return;
-} 
- 
+}
+
 void AmoebaMultipoleForce::setPmeGridDimensions(const std::vector<int>& gridDimension) {
     pmeGridDimension.resize(3);
     pmeGridDimension[0] = gridDimension[0];
     pmeGridDimension[1] = gridDimension[1];
     pmeGridDimension[2] = gridDimension[2];
     return;
-} 
+}
 
 void AmoebaMultipoleForce::getPMEParametersInContext(const Context& context, double& alpha, int& nx, int& ny, int& nz) const {
     dynamic_cast<const AmoebaMultipoleForceImpl&>(getImplInContext(context)).getPMEParameters(alpha, nx, ny, nz);
@@ -131,13 +131,13 @@ void AmoebaMultipoleForce::setEwaldErrorTolerance(double tol) {
     ewaldErrorTol = tol;
 }
 
-int AmoebaMultipoleForce::addMultipole(double charge, const std::vector<double>& molecularDipole, const std::vector<double>& molecularQuadrupole, int axisType, 
+int AmoebaMultipoleForce::addMultipole(double charge, const std::vector<double>& molecularDipole, const std::vector<double>& molecularQuadrupole, int axisType,
                                        int multipoleAtomZ, int multipoleAtomX, int multipoleAtomY, double thole, double dampingFactor, double polarity) {
     multipoles.push_back(MultipoleInfo(charge, molecularDipole, molecularQuadrupole,  axisType, multipoleAtomZ,  multipoleAtomX, multipoleAtomY, thole, dampingFactor, polarity));
     return multipoles.size()-1;
 }
 
-void AmoebaMultipoleForce::getMultipoleParameters(int index, double& charge, std::vector<double>& molecularDipole, std::vector<double>& molecularQuadrupole, 
+void AmoebaMultipoleForce::getMultipoleParameters(int index, double& charge, std::vector<double>& molecularDipole, std::vector<double>& molecularQuadrupole,
                                                   int& axisType, int& multipoleAtomZ, int& multipoleAtomX, int& multipoleAtomY, double& thole, double& dampingFactor, double& polarity) const {
     charge                      = multipoles[index].charge;
 
@@ -167,7 +167,7 @@ void AmoebaMultipoleForce::getMultipoleParameters(int index, double& charge, std
     polarity                    = multipoles[index].polarity;
 }
 
-void AmoebaMultipoleForce::setMultipoleParameters(int index, double charge, const std::vector<double>& molecularDipole, const std::vector<double>& molecularQuadrupole, 
+void AmoebaMultipoleForce::setMultipoleParameters(int index, double charge, const std::vector<double>& molecularDipole, const std::vector<double>& molecularQuadrupole,
                                                   int axisType, int multipoleAtomZ, int multipoleAtomX, int multipoleAtomY, double thole, double dampingFactor, double polarity) {
 
     multipoles[index].charge                      = charge;
@@ -230,8 +230,12 @@ void AmoebaMultipoleForce::getCovalentMaps(int index, std::vector< std::vector<i
     }
 }
 
-void AmoebaMultipoleForce::getInducedDipoles(Context& context, vector<Vec3>& dipoles) {
-    dynamic_cast<AmoebaMultipoleForceImpl&>(getImplInContext(context)).getInducedDipoles(getContextImpl(context), dipoles);
+void AmoebaMultipoleForce::getLabFramePermanentDipoles(Context& context, vector<Vec3>& dipoles) {
+    dynamic_cast<AmoebaMultipoleForceImpl&>(getImplInContext(context)).getLabFramePermanentDipoles(getContextImpl(context), dipoles);
+}
+
+void AmoebaMultipoleForce::getLabFramePermanentDipoles(Context& context, vector<Vec3>& dipoles) {
+    dynamic_cast<AmoebaMultipoleForceImpl&>(getImplInContext(context)).getLabFramePermanentDipoles(getContextImpl(context), dipoles);
 }
 
 void AmoebaMultipoleForce::getElectrostaticPotential(const std::vector< Vec3 >& inputGrid, Context& context, std::vector< double >& outputElectrostaticPotential) {

plugins/amoeba/openmmapi/src/AmoebaMultipoleForceImpl.cpp

@@ -61,7 +61,7 @@ void AmoebaMultipoleForceImpl::initialize(ContextImpl& context) {
         double cutoff = owner.getCutoffDistance();
         if (cutoff > 0.5*boxVectors[0][0] || cutoff > 0.5*boxVectors[1][1] || cutoff > 0.5*boxVectors[2][2])
             throw OpenMMException("AmoebaMultipoleForce: The cutoff distance cannot be greater than half the periodic box size.");
-    }   
+    }
 
     double quadrupoleValidationTolerance = 1.0e-05;
     for (int ii = 0; ii < system.getNumParticles(); ii++) {
@@ -170,7 +170,7 @@ void AmoebaMultipoleForceImpl::getCovalentRange(const AmoebaMultipoleForce& forc
                *maxCovalentIndex = covalentList[ii];
             }
         }
-    }   
+    }
     return;
 }
 
@@ -179,10 +179,14 @@ void AmoebaMultipoleForceImpl::getCovalentDegree(const AmoebaMultipoleForce& for
     const int* CovalentDegrees = AmoebaMultipoleForceImpl::getCovalentDegrees();
     for (unsigned int kk = 0; kk < AmoebaMultipoleForce::CovalentEnd; kk++) {
         covalentDegree[kk] = CovalentDegrees[kk];
-    }   
+    }
     return;
 }
 
+void AmoebaMultipoleForceImpl::getLabFramePermanentDipoles(ContextImpl& context, vector<Vec3>& dipoles) {
+    kernel.getAs<CalcAmoebaMultipoleForceKernel>().getLabFramePermanentDipoles(context, dipoles);
+}
+
 void AmoebaMultipoleForceImpl::getInducedDipoles(ContextImpl& context, vector<Vec3>& dipoles) {
     kernel.getAs<CalcAmoebaMultipoleForceKernel>().getInducedDipoles(context, dipoles);
 }