Created a public verison of the applyRotationMatrix function so that it can be...

Created a public verison of the applyRotationMatrix function so that it can be accessed from outside

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

@@ -722,7 +722,7 @@ void ReferenceCalcAmoebaMultipoleForceKernel::getLabFramePermanentDipoles(Contex
     // Retrieve the permanent dipoles in the lab frame.
     
     vector<RealVec> labFramePermanentDipoles;
-    amoebaReferenceMultipoleForce->applyRotationMatrix(particleData, multipoleAtomsXs, multipoleAtomsYs, multipoleAtomsZs, axisTypes);
+    amoebaReferenceMultipoleForce->applyRotationMatrixPublic(particleData, multipoleAtomsXs, multipoleAtomsYs, multipoleAtomsZs, axisTypes);
     for (int i = 0; i < numParticles; i++)
         outputDipoles[i] = labFramePermanentDipoles[i];
     delete amoebaReferenceMultipoleForce;

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

@@ -647,6 +647,21 @@ 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

@@ -585,6 +585,25 @@ public:
                                          const std::vector<RealVec>& inputGrid,
                                          std::vector<RealOpenMM>& outputPotential);
 
+
+    /**
+     * Apply rotation matrix to molecular dipole/quadrupoles to get corresponding lab frame values.
+     * This is the public redeclaration of the original applyRotationMatrix function which is protected, since
+     * I need to access it from outside.
+     * 
+     * @param particleData            vector of parameters (charge, labFrame dipoles, quadrupoles, ...) for particles
+     *                                dipole and quadrupole entries are modified
+     * @param multipoleAtomXs         vector of z-particle indices used to map molecular frame to lab frame
+     * @param multipoleAtomYs         vector of x-particle indices used to map molecular frame to lab frame
+     * @param multipoleAtomZs         vector of y-particle indices used to map molecular frame to lab frame
+     * @param axisType                axis type
+     */
+    void applyRotationMatrixPublic(std::vector<MultipoleParticleData>& particleData, 
+                             const std::vector<int>& multipoleAtomXs,
+                             const std::vector<int>& multipoleAtomYs,
+                             const std::vector<int>& multipoleAtomZs,
+                             const std::vector<int>& axisTypes) const;
+
 protected:
 
     enum MultipoleParticleDataEnum { PARTICLE_POSITION, PARTICLE_CHARGE, PARTICLE_DIPOLE, PARTICLE_QUADRUPOLE,