Removed unused accessors

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

@@ -893,7 +893,8 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
     std::vector<int> minCovalentIndices(numMultipoles);
     std::vector<int> minCovalentPolarizationIndices(numMultipoles);
 
-    float scalingDistanceCutoff = static_cast<float>(force.getScalingDistanceCutoff());
+    //float scalingDistanceCutoff = static_cast<float>(force.getScalingDistanceCutoff());
+    float scalingDistanceCutoff = 50.0f;
 
     std::vector<AmoebaMultipoleForce::CovalentType> covalentList;
     covalentList.push_back( AmoebaMultipoleForce::Covalent12 );
@@ -970,11 +971,6 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
     }
 
     int polarizationType = static_cast<int>(force.getPolarizationType());
-    int iterativeMethod = static_cast<int>(force.getMutualInducedIterationMethod());
-    if( iterativeMethod != 0 && polarizationType == 0 ){
-         throw OpenMMException("Iterative method for mutual induced dipoles not recognized.\n");
-    }
-
     int nonbondedMethod = static_cast<int>(force.getNonbondedMethod());
     if( nonbondedMethod != 0 && nonbondedMethod != 1 ){
          throw OpenMMException("AmoebaMultipoleForce nonbonded method not recognized.\n");
@@ -987,13 +983,11 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
     gpuSetAmoebaMultipoleParameters(data.getAmoebaGpu(), charges, dipoles, quadrupoles, axisTypes, multipoleAtomZs, multipoleAtomXs, multipoleAtomYs,
                                     tholes, scalingDistanceCutoff, dampingFactors, polarity,
                                     multipoleAtomCovalentInfo, covalentDegree, minCovalentIndices, minCovalentPolarizationIndices, (maxCovalentRange+2),
-                                    static_cast<int>(force.getMutualInducedIterationMethod()),
-                                    force.getMutualInducedMaxIterations(),
+                                    0, force.getMutualInducedMaxIterations(),
                                     static_cast<float>( force.getMutualInducedTargetEpsilon()),
                                     nonbondedMethod, polarizationType,
                                     static_cast<float>( force.getCutoffDistance()),
-                                    static_cast<float>( force.getAEwald()),
-                                    static_cast<float>( force.getElectricConstant()) );
+                                    static_cast<float>( force.getAEwald()) );
     if (nonbondedMethod == AmoebaMultipoleForce::PME) {
         double alpha;
         int xsize, ysize, zsize;
@@ -1098,7 +1092,7 @@ void CudaCalcAmoebaGeneralizedKirkwoodForceKernel::initialize(const System& syst
 
         gpuSetAmoebaGrycukParameters( data.getAmoebaGpu(), static_cast<float>(force.getSoluteDielectric() ), 
                                       static_cast<float>( force.getSolventDielectric() ), 
-                                      static_cast<float>( force.getDielectricOffset() ), radius, scale, charge,
+                                      radius, scale, charge,
                                       force.getIncludeCavityTerm(),
                                       static_cast<float>( force.getProbeRadius() ), 
                                       static_cast<float>( force.getSurfaceAreaFactor() ) ); 
@@ -1107,7 +1101,7 @@ void CudaCalcAmoebaGeneralizedKirkwoodForceKernel::initialize(const System& syst
 
         gpuSetAmoebaObcParameters( data.getAmoebaGpu(), static_cast<float>(force.getSoluteDielectric() ), 
                                    static_cast<float>( force.getSolventDielectric() ), 
-                                   static_cast<float>( force.getDielectricOffset() ), radius, scale, charge,
+                                   radius, scale, charge,
                                    force.getIncludeCavityTerm(),
                                    static_cast<float>( force.getProbeRadius() ), 
                                    static_cast<float>( force.getSurfaceAreaFactor() ) ); 

plugins/amoeba/platforms/cuda/src/kernels/amoebaCudaGpu.cpp

@@ -1699,7 +1699,7 @@ void gpuSetAmoebaMultipoleParameters(amoebaGpuContext amoebaGpu, const std::vect
                                      const std::vector< std::vector< std::vector<int> > >& multipoleParticleCovalentInfo, const std::vector<int>& covalentDegree,
                                      const std::vector<int>& minCovalentIndices,  const std::vector<int>& minCovalentPolarizationIndices, int maxCovalentRange, 
                                      int mutualInducedIterativeMethod, int mutualInducedMaxIterations, float mutualInducedTargetEpsilon,
-                                     int nonbondedMethod, int polarizationType, float cutoffDistance, float alphaEwald, float electricConstant ) {
+                                     int nonbondedMethod, int polarizationType, float cutoffDistance, float alphaEwald ) {
 
 // ---------------------------------------------------------------------------------------
 
@@ -1743,7 +1743,7 @@ void gpuSetAmoebaMultipoleParameters(amoebaGpuContext amoebaGpu, const std::vect
     }
 
     amoebaGpu->amoebaSim.sqrtPi                      = std::sqrt( 3.14159265358f );
-    amoebaGpu->amoebaSim.electric                    = electricConstant;
+    amoebaGpu->amoebaSim.electric                    = 138.9354558456f;
     amoebaGpu->gpuContext->sim.alphaEwald            = alphaEwald;
     amoebaGpu->gpuContext->sim.nonbondedCutoff       = cutoffDistance;
 
@@ -2078,14 +2078,14 @@ void gpuSetAmoebaMultipoleParameters(amoebaGpuContext amoebaGpu, const std::vect
 }
 
 extern "C"
-void gpuSetAmoebaObcParameters( amoebaGpuContext amoebaGpu, float innerDielectric, float solventDielectric, float dielectricOffset,
+void gpuSetAmoebaObcParameters( amoebaGpuContext amoebaGpu, float innerDielectric, float solventDielectric,
                                 const std::vector<float>& radius, const std::vector<float>& scale, const std::vector<float>& charge,
                                 int includeCavityTerm, float probeRadius, float surfaceAreaFactor )
 {
 
     gpuContext gpu                         = amoebaGpu->gpuContext;
     int paddedNumberOfAtoms                = gpu->sim.paddedNumberOfAtoms;
-    gpu->sim.dielectricOffset              = dielectricOffset;
+    gpu->sim.dielectricOffset              = 0.009f;
     amoebaGpu->includeObcCavityTerm        = includeCavityTerm;
     gpu->sim.probeRadius                   = probeRadius;
     gpu->sim.surfaceAreaFactor             = surfaceAreaFactor;
@@ -2093,7 +2093,7 @@ void gpuSetAmoebaObcParameters( amoebaGpuContext amoebaGpu, float innerDielectri
 
     for (unsigned int i = 0; i < particles; i++) 
     {    
-            (*gpu->psObcData)[i].x = radius[i] - dielectricOffset;
+            (*gpu->psObcData)[i].x = radius[i] - gpu->sim.dielectricOffset;
             (*gpu->psObcData)[i].y = scale[i] * (*gpu->psObcData)[i].x;
             (*gpu->psPosq4)[i].w   = charge[i];
     }    
@@ -2122,7 +2122,7 @@ void gpuSetAmoebaObcParameters( amoebaGpuContext amoebaGpu, float innerDielectri
 
     if( amoebaGpu->log ){
         (void) fprintf( amoebaGpu->log,"gpuSetAmoebaObcParameters: cavity=%d dielectricOffset=%15.7e probeRadius=%15.7e surfaceAreaFactor=%15.7e\n", 
-                        includeCavityTerm, dielectricOffset, probeRadius, surfaceAreaFactor );
+                        includeCavityTerm, gpu->sim.dielectricOffset, probeRadius, surfaceAreaFactor );
         (void) fprintf( amoebaGpu->log,"                           gkc=%12.3f solventDielectric=%15.7e innerDielectric=%15.7e sim.preFactor=%15.7e\n", 
                         amoebaGpu->amoebaSim.gkc, amoebaGpu->amoebaSim.dwater, amoebaGpu->amoebaSim.dielec, gpu->sim.preFactor );
         (void) fprintf( amoebaGpu->log,"                           fc=%15.7e fd=%15.7e fq=%15.7e\n",
@@ -2143,14 +2143,13 @@ void gpuSetAmoebaObcParameters( amoebaGpuContext amoebaGpu, float innerDielectri
 }
 
 extern "C"
-void gpuSetAmoebaGrycukParameters( amoebaGpuContext amoebaGpu, float innerDielectric, float solventDielectric, float dielectricOffset,
+void gpuSetAmoebaGrycukParameters( amoebaGpuContext amoebaGpu, float innerDielectric, float solventDielectric,
                                    const std::vector<float>& radius, const std::vector<float>& scale, const std::vector<float>& charge,
                                    int includeCavityTerm, float probeRadius, float surfaceAreaFactor )
 {
 
     gpuContext gpu                         = amoebaGpu->gpuContext;
     int paddedNumberOfAtoms                = gpu->sim.paddedNumberOfAtoms;
-    gpu->sim.dielectricOffset              = dielectricOffset;
     amoebaGpu->includeObcCavityTerm        = includeCavityTerm;
     gpu->sim.probeRadius                   = probeRadius;
     gpu->sim.surfaceAreaFactor             = surfaceAreaFactor;
@@ -2191,8 +2190,8 @@ void gpuSetAmoebaGrycukParameters( amoebaGpuContext amoebaGpu, float innerDielec
     if( amoebaGpu->log ){
         unsigned int maxPrint = MAX_PARAMETER_PRINT;
         unsigned int maxIndex = particles;
-        (void) fprintf( amoebaGpu->log,"gpuSetAmoebaGrycukParameters: cavity=%d dielectricOffset=%15.7e probeRadius=%15.7e surfaceAreaFactor=%15.7e\n", 
-                        includeCavityTerm, dielectricOffset, probeRadius, surfaceAreaFactor );
+        (void) fprintf( amoebaGpu->log,"gpuSetAmoebaGrycukParameters: cavity=%d probeRadius=%15.7e surfaceAreaFactor=%15.7e\n", 
+                        includeCavityTerm, probeRadius, surfaceAreaFactor );
         (void) fprintf( amoebaGpu->log,"                           gkc=%12.3f solventDielectric=%15.7e innerDielectric=%15.7e sim.preFactor=%15.7e\n", 
                         amoebaGpu->amoebaSim.gkc, amoebaGpu->amoebaSim.dwater, amoebaGpu->amoebaSim.dielec, gpu->sim.preFactor );
         (void) fprintf( amoebaGpu->log,"                           fc=%15.7e fd=%15.7e fq=%15.7e\n",

plugins/amoeba/platforms/cuda/src/kernels/amoebaGpuTypes.h

@@ -280,16 +280,16 @@ void gpuSetAmoebaMultipoleParameters(amoebaGpuContext amoebaGpu, const std::vect
                                      const std::vector< std::vector< std::vector<int> > >& multipoleAtomCovalentInfo, const std::vector<int>& covalentDegree,
                                      const std::vector<int>& minCovalentIndices,  const std::vector<int>& minCovalentPolarizationIndices, int maxCovalentRange,
                                      int mutualInducedIterationMethod, int mutualInducedMaxIterations, float mutualInducedTargetEpsilon,
-                                     int nonbondedMethod, int polarizationType, float cutoffDistance,  float alphaEwald, float electricConstant );
+                                     int nonbondedMethod, int polarizationType, float cutoffDistance,  float alphaEwald );
 
 
 extern "C"
-void gpuSetAmoebaObcParameters( amoebaGpuContext amoebaGpu , float innerDielectric, float solventDielectric, float dielectricOffset,
+void gpuSetAmoebaObcParameters( amoebaGpuContext amoebaGpu , float innerDielectric, float solventDielectric,
                                 const std::vector<float>& radius, const std::vector<float>& scale, const std::vector<float>& charge,
                                 int includeCavityTerm, float probeRadius, float surfaceAreaFactor);
 
 extern "C"
-void gpuSetAmoebaGrycukParameters( amoebaGpuContext amoebaGpu , float innerDielectric, float solventDielectric, float dielectricOffset,
+void gpuSetAmoebaGrycukParameters( amoebaGpuContext amoebaGpu , float innerDielectric, float solventDielectric,
                                    const std::vector<float>& radius, const std::vector<float>& scale, const std::vector<float>& charge,
                                    int includeCavityTerm, float probeRadius, float surfaceAreaFactor);
 

plugins/amoeba/platforms/cuda/tests/AmoebaTinkerParameterFile.cpp

@@ -2216,7 +2216,7 @@ static int readAmoebaMultipoleParameters( FILE* filePtr, int version, MapStringI
         multipoleForce->setNonbondedMethod( AmoebaMultipoleForce::PME );
         multipoleForce->setCutoffDistance( cutoffDistance );
         multipoleForce->setAEwald( aewald );
-        multipoleForce->setPmeBSplineOrder( bsOrder );
+        //multipoleForce->setPmeBSplineOrder( bsOrder );
         multipoleForce->setPmeGridDimensions( grid );
         system.setDefaultPeriodicBoxVectors( Vec3(box[0], 0.0, 0.0), Vec3(0.0, box[1], 0.0), Vec3(0.0, 0.0, box[2]) );
     } else {
@@ -2334,7 +2334,7 @@ static int readAmoebaMultipoleParameters( FILE* filePtr, int version, MapStringI
       
         multipoleForce->setAEwald(                multipoleForce->getAEwald()/AngstromToNm );
         multipoleForce->setCutoffDistance(        multipoleForce->getCutoffDistance()*AngstromToNm );
-        multipoleForce->setScalingDistanceCutoff( multipoleForce->getScalingDistanceCutoff()*AngstromToNm );
+        //multipoleForce->setScalingDistanceCutoff( multipoleForce->getScalingDistanceCutoff()*AngstromToNm );
 
         Vec3 a,b,c;
         system.getDefaultPeriodicBoxVectors( a, b, c);
@@ -2374,9 +2374,11 @@ static int readAmoebaMultipoleParameters( FILE* filePtr, int version, MapStringI
 
         }
     } else {
+/*
         float electricConstant         = static_cast<float>(multipoleForce->getElectricConstant());
               electricConstant        /= static_cast<float>(AngstromToNm*CalToJoule);
         multipoleForce->setElectricConstant( electricConstant );
+*/
     }
 
     // diagnostics
@@ -2597,7 +2599,7 @@ static int readAmoebaGeneralizedKirkwoodParameters( FILE* filePtr, MapStringInt&
     // convert to OpenMM units
 
     if( useOpenMMUnits ){
-        gbsaObcForce->setDielectricOffset( 0.009 );
+        //gbsaObcForce->setDielectricOffset( 0.009 );
         for( int ii = 0; ii < gbsaObcForce->getNumParticles(); ii++ ){
             double charge, radius, scalingFactor;
             gbsaObcForce->getParticleParameters( ii, charge, radius, scalingFactor );
@@ -2605,7 +2607,7 @@ static int readAmoebaGeneralizedKirkwoodParameters( FILE* filePtr, MapStringInt&
             gbsaObcForce->setParticleParameters( ii, charge, radius, scalingFactor );
         }
     } else {
-        gbsaObcForce->setDielectricOffset( 0.09 );
+        //gbsaObcForce->setDielectricOffset( 0.09 );
         gbsaObcForce->setProbeRadius( 1.4 );
         double surfaceAreaFactor = gbsaObcForce->getSurfaceAreaFactor( );
         surfaceAreaFactor       *= (AngstromToNm*AngstromToNm)/CalToJoule;