Removed unnecessary functions and variables which were redundant/already commented out

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

@@ -332,10 +332,10 @@ public:
     void getInducedDipoles(Context& context, std::vector<Vec3>& dipoles);
 
     /**
-     * Get the total dipole moments of all particles.
+     * Get the total dipole moments (fixed plus induced) 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
+     * @param context         the Context for which to get the total dipoles
+     * @param[out] dipoles    the total dipole moment of particle i is stored into the i'th element
      */
     void getTotalDipoles(Context& context, std::vector<Vec3>& dipoles);
 

plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.cpp

@@ -1822,34 +1822,34 @@ void CudaCalcAmoebaMultipoleForceKernel::getTotalDipoles(ContextImpl& context, v
         vector<double4> posqVec;
         vector<double> labDipoleVec;
         vector<double> inducedDipoleVec;
-        vector<double> totalDipoleVecX(numParticles);
-        vector<double> totalDipoleVecY(numParticles);
-        vector<double> totalDipoleVecZ(numParticles);
+        double totalDipoleVecX;
+        double totalDipoleVecY;
+        double totalDipoleVecZ;
         inducedDipole->download(inducedDipoleVec);
         labFrameDipoles->download(labDipoleVec);
         cu.getPosq().download(posqVec);
         for (int i = 0; i < numParticles; i++) {
-            totalDipoleVecX[i] = posqVec[i].x * posqVec[i].w + labDipoleVec[3*i] + inducedDipoleVec[3*i];
-            totalDipoleVecY[i] = posqVec[i].y * posqVec[i].w + labDipoleVec[3*i+1] + inducedDipoleVec[3*i+1];
-            totalDipoleVecZ[i] = posqVec[i].z * posqVec[i].w + labDipoleVec[3*i+2] + inducedDipoleVec[3*i+2];
-            dipoles[order[i]] = Vec3(totalDipoleVecX[i], totalDipoleVecY[i], totalDipoleVecZ[i]);
+            totalDipoleVecX = posqVec[i].x * posqVec[i].w + labDipoleVec[3*i] + inducedDipoleVec[3*i];
+            totalDipoleVecY = posqVec[i].y * posqVec[i].w + labDipoleVec[3*i+1] + inducedDipoleVec[3*i+1];
+            totalDipoleVecZ = posqVec[i].z * posqVec[i].w + labDipoleVec[3*i+2] + inducedDipoleVec[3*i+2];
+            dipoles[order[i]] = Vec3(totalDipoleVecX, totalDipoleVecY, totalDipoleVecZ);
         }
     }
     else {
         vector<float4> posqVec;
         vector<float> labDipoleVec;
         vector<float> inducedDipoleVec;
-        vector<float> totalDipoleVecX(numParticles);
-        vector<float> totalDipoleVecY(numParticles);
-        vector<float> totalDipoleVecZ(numParticles);
+        float totalDipoleVecX;
+        float totalDipoleVecY;
+        float totalDipoleVecZ;
         inducedDipole->download(inducedDipoleVec);
         labFrameDipoles->download(labDipoleVec);
         cu.getPosq().download(posqVec);
         for (int i = 0; i < numParticles; i++) {
-            totalDipoleVecX[i] = posqVec[i].x * posqVec[i].w + labDipoleVec[3*i] + inducedDipoleVec[3*i];
-            totalDipoleVecY[i] = posqVec[i].y * posqVec[i].w + labDipoleVec[3*i+1] + inducedDipoleVec[3*i+1];
-            totalDipoleVecZ[i] = posqVec[i].z * posqVec[i].w + labDipoleVec[3*i+2] + inducedDipoleVec[3*i+2];
-            dipoles[order[i]] = Vec3(totalDipoleVecX[i], totalDipoleVecY[i], totalDipoleVecZ[i]);
+            totalDipoleVecX = posqVec[i].x * posqVec[i].w + labDipoleVec[3*i] + inducedDipoleVec[3*i];
+            totalDipoleVecY = posqVec[i].y * posqVec[i].w + labDipoleVec[3*i+1] + inducedDipoleVec[3*i+1];
+            totalDipoleVecZ = posqVec[i].z * posqVec[i].w + labDipoleVec[3*i+2] + inducedDipoleVec[3*i+2];
+            dipoles[order[i]] = Vec3(totalDipoleVecX, totalDipoleVecY, totalDipoleVecZ);
         }
     }
 }

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

@@ -647,21 +647,6 @@ void AmoebaReferenceMultipoleForce::applyRotationMatrix(vector<MultipoleParticle
     }
 }
 
-//void AmoebaReferenceMultipoleForce::applyRotationMatrixPublic(vector<MultipoleParticleData>& particleData,
-//                                                        const vector<int>& multipoleAtomXs,
-//                                                        const vector<int>& multipoleAtomYs,
-//                                                        const vector<int>& multipoleAtomZs,
-//                                                        const vector<int>& axisTypes) const
-//{
-//
-//    for (unsigned int ii = 0; ii < _numParticles; ii++) {
-//        if (multipoleAtomZs[ii] >= 0 && multipoleAtomXs[ii] >= 0) {
-//            applyRotationMatrixToParticle(particleData[ii], particleData[multipoleAtomZs[ii]], particleData[multipoleAtomXs[ii]],
-//                                           multipoleAtomYs[ii] > -1 ? &particleData[multipoleAtomYs[ii]] : NULL, axisTypes[ii]);
-//        }
-//    }
-//}
-
 void AmoebaReferenceMultipoleForce::getAndScaleInverseRs(RealOpenMM dampI, RealOpenMM dampJ,
                                                          RealOpenMM tholeI, RealOpenMM tholeJ,
                                                          RealOpenMM r, vector<RealOpenMM>& rrI) const

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

@@ -674,13 +674,6 @@ protected:
             RealOpenMM quadrupole[6];
             RealVec sphericalDipole;
             RealOpenMM sphericalQuadrupole[5];
-            RealOpenMM thole;
-            RealOpenMM dampingFactor;
-            RealOpenMM polarity;
-
-            std::vector<RealOpenMM> xDipoleTraj;
-            std::vector<RealOpenMM> yDipoleTraj;
-            std::vector<RealOpenMM> zDipoleTraj;
     };
     
     /**
@@ -720,10 +713,6 @@ protected:
     RealOpenMM _uScale[5];
 
     std::vector<TransformedMultipole> _transformed;
-    std::vector<RealVec> _fixedMultipoleField;
-    std::vector<RealVec> _fixedMultipoleFieldPolar;
-    std::vector<RealVec> _inducedDipole;
-    std::vector<RealVec> _labFramePermanentDipole;
     std::vector<RealVec> _inducedDipolePolar;
 
     int _mutualInducedDipoleConverged;
@@ -1048,13 +1037,6 @@ protected:
      */
     virtual void calculateInducedDipoles(const std::vector<MultipoleParticleData>& particleData);
 
-    /*
-     * Calculate permanent dipoles rotated in the lab frame.
-     * 
-     * @param particleData      vector of particle positions and parameters (charge, labFrame dipoles, quadrupoles, ...)
-     */
- //   virtual void calculateLabFramePermanentDipoles(const std::vector<MultipoleParticleData>& particleData);
-
     /**
      * Setup: 
      *        if needed invert multipole moments at chiral centers
@@ -1303,13 +1285,6 @@ private:
      */
     void calculateInducedDipoles(const std::vector<MultipoleParticleData>& particleData);
 
-    /*
-     * Calculate fixed dipoles rotated in the lab frame.
-     * 
-     * @param particleData      vector of particle positions and parameters (charge, labFrame dipoles, quadrupoles, ...)
-     */
- //   void calculateLabFramePermanentDipoles(const std::vector<MultipoleParticleData>& particleData);
-
     /**
      * Calculate fields due induced dipoles at each site.
      *