Removed unused accessors; set missing initializations in AmoebaVdwForce

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

@@ -126,12 +126,12 @@ public:
     /**
      * Get the dielectric offset (nm) used in OBC
      */
-    double getDielectricOffset() const;
+    //double getDielectricOffset() const;
 
     /**
      * Set the dielectric offset (nm) used in OBC
      */
-    void setDielectricOffset(double dielectricOffset);
+    //void setDielectricOffset(double dielectricOffset);
 
     /**
      * Get the flag signalling whether the cavity term should be included

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

@@ -165,7 +165,7 @@ public:
      *		 
      * @param the B-spline order parameter
      */		 
-    void setPmeBSplineOrder(int inputBSplineOrder);
+    //void setPmeBSplineOrder(int inputBSplineOrder);
      
    /**		   
      * Get the PME grid dimensions		 
@@ -265,14 +265,14 @@ public:
      * 
      * @return iteration method to be used for calculating the mutual induced dipole
      */
-    MutualInducedIterationMethod getMutualInducedIterationMethod( void ) const;
+    //MutualInducedIterationMethod getMutualInducedIterationMethod( void ) const;
     
     /**
      * Set the iteration method to be used for calculating the mutual induced dipoles
      * 
      * @param iteration method to be used for calculating the mutual induced dipole
      */
-    void setMutualInducedIterationMethod( MutualInducedIterationMethod inputMutualInducedIterationMethod ); 
+    //void setMutualInducedIterationMethod( MutualInducedIterationMethod inputMutualInducedIterationMethod ); 
     
     /**
      * Get the max number of iterations to be used in calculating the mutual induced dipoles
@@ -307,28 +307,29 @@ public:
      * 
      * @return scaling distance cutoff
      */
-    double getScalingDistanceCutoff( void ) const;
+    //double getScalingDistanceCutoff( void ) const;
     
     /**
      * Set the scaling distance cutoff
      * 
      * @param scaling distance cutoff
      */
-    void setScalingDistanceCutoff( double inputScalingDistanceCutoff ); 
+    //void setScalingDistanceCutoff( double inputScalingDistanceCutoff ); 
     
     /**
      * Get the electric constant
       
      * @return the electric constant
      */
-    double getElectricConstant( void ) const;
+    //double getElectricConstant( void ) const;
     
     /**
      * Set the electric constant
      * 
      * @param the electric constant
      */
-    void setElectricConstant( double inputElectricConstant ); 
+    //void setElectricConstant( double inputElectricConstant ); 
+
     /**
      * Get the error tolerance for Ewald summation.  This corresponds to the fractional error in the forces
      * which is acceptable.  This value is used to select the reciprocal space cutoff and separation

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

@@ -118,7 +118,7 @@ public:
     /**
      * Set epsilon combining rule
      * 
-     * @param epsilonCombiningRule   epsilon combining rule:  'ARITHMETIC', 'GEOMETRIC'. 'CUBIC-MEAN'
+     * @param epsilonCombiningRule   epsilon combining rule:   'ARITHMETIC', 'GEOMETRIC'. 'HARMONIC', 'HHG'
      */
     void setEpsilonCombiningRule( const std::string& epsilonCombiningRule );
 
@@ -193,9 +193,12 @@ private:
 
     class VdwInfo;
     int usePBC;
-    int useNeighborList; double cutoff;
+    int useNeighborList;
+    double cutoff;
+
     std::string sigmaCombiningRule;
     std::string epsilonCombiningRule;
+
     std::vector< std::vector<int> > exclusions;
 
 // Retarded visual studio compiler complains about being unable to 

plugins/amoeba/openmmapi/src/AmoebaGeneralizedKirkwoodForce.cpp

@@ -57,14 +57,14 @@ void AmoebaGeneralizedKirkwoodForce::setParticleParameters(int index, double cha
     particles[index].radius = radius;
     particles[index].scalingFactor = scalingFactor;
 }
-
+/*
 double AmoebaGeneralizedKirkwoodForce::getDielectricOffset() const {
     return dielectricOffset;
 }
 
 void AmoebaGeneralizedKirkwoodForce::setDielectricOffset(double inputDielectricOffset ) {
     dielectricOffset = inputDielectricOffset;
-}
+} */
 
 int AmoebaGeneralizedKirkwoodForce::getIncludeCavityTerm() const {
     return includeCavityTerm;

plugins/amoeba/openmmapi/src/AmoebaMultipoleForce.cpp

@@ -78,9 +78,10 @@ int AmoebaMultipoleForce::getPmeBSplineOrder( void ) const {
     return pmeBSplineOrder;		 
 }		 
 		 
+/*
 void AmoebaMultipoleForce::setPmeBSplineOrder(int inputBSplineOrder) {			 
     pmeBSplineOrder = inputBSplineOrder;		 
-}		 
+}	*/	 
  
 void AmoebaMultipoleForce::getPmeGridDimensions( std::vector<int>& gridDimension ) const {		 
     if( gridDimension.size() < 3 ){
@@ -103,14 +104,14 @@ void AmoebaMultipoleForce::setPmeGridDimensions( const std::vector<int>& gridDim
     pmeGridDimension[2] = gridDimension[2];
     return;
 }		 
- 
+/* 
 AmoebaMultipoleForce::MutualInducedIterationMethod AmoebaMultipoleForce::getMutualInducedIterationMethod( void ) const {
     return mutualInducedIterationMethod;
 }
 
 void AmoebaMultipoleForce::setMutualInducedIterationMethod( AmoebaMultipoleForce::MutualInducedIterationMethod inputMutualInducedIterationMethod ) {
     mutualInducedIterationMethod = inputMutualInducedIterationMethod;
-}
+} */
 
 int AmoebaMultipoleForce::getMutualInducedMaxIterations( void ) const {
     return mutualInducedMaxIterations;
@@ -127,7 +128,7 @@ double AmoebaMultipoleForce::getMutualInducedTargetEpsilon( void ) const {
 void AmoebaMultipoleForce::setMutualInducedTargetEpsilon( double inputMutualInducedTargetEpsilon ) {
     mutualInducedTargetEpsilon = inputMutualInducedTargetEpsilon;
 }
-
+/*
 double AmoebaMultipoleForce::getScalingDistanceCutoff( void ) const {
     return scalingDistanceCutoff;
 }
@@ -142,7 +143,7 @@ double AmoebaMultipoleForce::getElectricConstant( void ) const {
 
 void AmoebaMultipoleForce::setElectricConstant( double inputElectricConstant ) {
     electricConstant = inputElectricConstant;
-}
+} */
 
 double AmoebaMultipoleForce::getEwaldErrorTolerance() const {
     return ewaldErrorTol;

plugins/amoeba/openmmapi/src/AmoebaVdwForce.cpp

@@ -38,7 +38,7 @@ using namespace OpenMM;
 using std::string;
 using std::vector;
 
-AmoebaVdwForce::AmoebaVdwForce() : usePBC(0), cutoff(1.0e+10), useNeighborList(0) {
+AmoebaVdwForce::AmoebaVdwForce() : sigmaCombiningRule("CUBIC-MEAN"), epsilonCombiningRule("HHG"), usePBC(0), cutoff(1.0e+10), useNeighborList(0) {
 }
 
 int AmoebaVdwForce::addParticle(int ivIndex, int classIndex, double sigma, double epsilon, double reductionFactor ) {