Major cleanup of the AMOEBA API

plugins/amoeba/platforms/cuda2/tests/TestCudaAmoebaGeneralizedKirkwoodForce.cpp

@@ -36,7 +36,6 @@
 #include "openmm/internal/AssertionUtilities.h"
 #include "openmm/Context.h"
 #include "OpenMMAmoeba.h"
-#include "AmoebaTinkerParameterFile.h"
 #include "openmm/System.h"
 #include "openmm/AmoebaMultipoleForce.h"
 #include "openmm/LangevinIntegrator.h"
@@ -53,9 +52,11 @@
 using namespace OpenMM;
 const double TOL = 1e-4;
+extern "C" void registerAmoebaCudaKernelFactories();
+
 // setup for 2 ammonia molecules
-static void setupAndGetForcesEnergyMultipoleAmmonia( AmoebaMultipoleForce::AmoebaPolarizationType polarizationType,
+static void setupAndGetForcesEnergyMultipoleAmmonia( AmoebaMultipoleForce::PolarizationType polarizationType,
                                                      int includeCavityTerm, std::vector<Vec3>& forces, double& energy, FILE* log ){
     // beginning of Multipole setup
@@ -316,7 +317,7 @@ static void setupAndGetForcesEnergyMultipoleAmmonia( AmoebaMultipoleForce::Amoeb
 // setup for villin
-static void setupAndGetForcesEnergyMultipoleVillin( AmoebaMultipoleForce::AmoebaPolarizationType polarizationType,
+static void setupAndGetForcesEnergyMultipoleVillin( AmoebaMultipoleForce::PolarizationType polarizationType,
                                                     int includeCavityTerm, std::vector<Vec3>& forces, double& energy, FILE* log ){
     // beginning of Multipole setup

plugins/amoeba/platforms/cuda2/tests/TestCudaAmoebaHarmonicAngleForce.cpp

@@ -34,7 +34,6 @@
  */
 
 #include "openmm/internal/AssertionUtilities.h"
-#include "AmoebaTinkerParameterFile.h"
 #include "openmm/Context.h"
 #include "OpenMMAmoeba.h"
 #include "openmm/System.h"
@@ -44,6 +43,8 @@
 
 using namespace OpenMM;
 
+extern "C" void registerAmoebaCudaKernelFactories();
+
 const double TOL = 1e-5;
 #define PI_M               3.141592653589
 #define RADIAN            57.29577951308

plugins/amoeba/platforms/cuda2/tests/TestCudaAmoebaHarmonicBondForce.cpp

@@ -35,7 +35,6 @@
 
 #include "openmm/internal/AssertionUtilities.h"
 #include "CudaPlatform.h"
-#include "AmoebaTinkerParameterFile.h"
 #include "openmm/Context.h"
 #include "OpenMMAmoeba.h"
 #include "openmm/System.h"
@@ -45,6 +44,8 @@
 
 using namespace OpenMM;
 
+extern "C" void registerAmoebaCudaKernelFactories();
+
 const double TOL = 1e-5;
 static void computeAmoebaHarmonicBondForce(int bondIndex,  std::vector<Vec3>& positions, AmoebaHarmonicBondForce& amoebaHarmonicBondForce,
                                            std::vector<Vec3>& forces, double* energy ) {

plugins/amoeba/platforms/cuda2/tests/TestCudaAmoebaHarmonicInPlaneAngleForce.cpp

@@ -34,7 +34,6 @@
  */
 
 #include "openmm/internal/AssertionUtilities.h"
-#include "AmoebaTinkerParameterFile.h"
 #include "openmm/Context.h"
 #include "OpenMMAmoeba.h"
 #include "openmm/System.h"
@@ -44,6 +43,8 @@
 
 using namespace OpenMM;
 
+extern "C" void registerAmoebaCudaKernelFactories();
+
 const double TOL = 1e-5;
 #define PI_M               3.141592653589
 #define RADIAN            57.29577951308

plugins/amoeba/platforms/cuda2/tests/TestCudaAmoebaMultipoleForce.cpp

@@ -36,7 +36,6 @@
 #include "openmm/internal/AssertionUtilities.h"
 #include "openmm/Context.h"
 #include "OpenMMAmoeba.h"
-#include "AmoebaTinkerParameterFile.h"
 #include "openmm/System.h"
 #include "openmm/AmoebaMultipoleForce.h"
 #include "openmm/LangevinIntegrator.h"
@@ -53,10 +52,12 @@
 using namespace OpenMM;
 const double TOL = 1e-4;
 
+extern "C" void registerAmoebaCudaKernelFactories();
+
 // setup for 2 ammonia molecules
 
-static void setupAndGetForcesEnergyMultipoleAmmonia( AmoebaMultipoleForce::AmoebaNonbondedMethod nonbondedMethod,
-                                                     AmoebaMultipoleForce::AmoebaPolarizationType polarizationType,
+static void setupAndGetForcesEnergyMultipoleAmmonia( AmoebaMultipoleForce::NonbondedMethod nonbondedMethod,
+                                                     AmoebaMultipoleForce::PolarizationType polarizationType,
                                                      double cutoff, int inputPmeGridDimension, std::vector<Vec3>& forces, double& energy, FILE* log ){
 
     // beginning of Multipole setup
@@ -498,8 +499,8 @@ static void testMultipoleAmmoniaMutualPolarization( FILE* log ) {
 
 // setup for box of 4 water molecules -- used to test PME
 
-static void setupAndGetForcesEnergyMultipoleWater( AmoebaMultipoleForce::AmoebaNonbondedMethod nonbondedMethod,
-                                                   AmoebaMultipoleForce::AmoebaPolarizationType polarizationType,
+static void setupAndGetForcesEnergyMultipoleWater( AmoebaMultipoleForce::NonbondedMethod nonbondedMethod,
+                                                   AmoebaMultipoleForce::PolarizationType polarizationType,
                                                    double cutoff, int inputPmeGridDimension, std::vector<Vec3>& forces,
                                                    double& energy, FILE* log ){
 
@@ -938,8 +939,8 @@ static void testQuadrupoleValidation( FILE* log ){
 // this method does too much; I tried passing the context ptr back to 
 // the tests methods, but the tests would seg fault w/ a bad_alloc error
 
-static void setupAndGetForcesEnergyMultipoleIonsAndWater( AmoebaMultipoleForce::AmoebaNonbondedMethod nonbondedMethod,
-                                                          AmoebaMultipoleForce::AmoebaPolarizationType polarizationType,
+static void setupAndGetForcesEnergyMultipoleIonsAndWater( AmoebaMultipoleForce::NonbondedMethod nonbondedMethod,
+                                                          AmoebaMultipoleForce::PolarizationType polarizationType,
                                                           double cutoff, int inputPmeGridDimension, std::string testName,
                                                           std::vector<Vec3>& forces, double& energy, FILE* log ){
 
@@ -1204,8 +1205,8 @@ static void testMultipoleIonsAndWaterPMEMutualPolarization( FILE* log ) {
 
 // setup for box of 216 water molecules -- used to test PME
 
-static void setupAndGetForcesEnergyMultipoleLargeWater( AmoebaMultipoleForce::AmoebaNonbondedMethod nonbondedMethod,
-                                                        AmoebaMultipoleForce::AmoebaPolarizationType polarizationType,
+static void setupAndGetForcesEnergyMultipoleLargeWater( AmoebaMultipoleForce::NonbondedMethod nonbondedMethod,
+                                                        AmoebaMultipoleForce::PolarizationType polarizationType,
                                                         double cutoff, int inputPmeGridDimension, std::string& testName, 
                                                         std::vector<Vec3>& forces, double& energy,
                                                         std::vector< double >& outputMultipoleMoments,
@@ -1993,8 +1994,7 @@ static void setupAndGetForcesEnergyMultipoleLargeWater( AmoebaMultipoleForce::Am
     context.setPositions(positions);
 
     if( testName == "testSystemMultipoleMoments" ){
-        Vec3 origin( 0.0, 0.0, 0.0 );
-        amoebaMultipoleForce->getSystemMultipoleMoments( origin, context, outputMultipoleMoments );
+        amoebaMultipoleForce->getSystemMultipoleMoments(context, outputMultipoleMoments );
     } else if( testName == "testMultipoleGridPotential" ){
         amoebaMultipoleForce->getElectrostaticPotential( inputGrid, context, outputGridPotential );
     } else {

plugins/amoeba/platforms/cuda2/tests/TestCudaAmoebaOutOfPlaneBendForce.cpp

@@ -34,7 +34,6 @@
  */
 
 #include "openmm/internal/AssertionUtilities.h"
-#include "AmoebaTinkerParameterFile.h"
 #include "openmm/Context.h"
 #include "OpenMMAmoeba.h"
 #include "openmm/System.h"
@@ -44,6 +43,8 @@
 
 using namespace OpenMM;
 
+extern "C" void registerAmoebaCudaKernelFactories();
+
 const double TOL = 1e-3;
 #define PI_M               3.141592653589
 #define RADIAN            57.29577951308

plugins/amoeba/platforms/cuda2/tests/TestCudaAmoebaPME.cpp

-/* -------------------------------------------------------------------------- *
- *                                   OpenMMAmoeba                             *
- * -------------------------------------------------------------------------- *
- * This is part of the OpenMM molecular simulation toolkit originating from   *
- * Simbios, the NIH National Center for Physics-Based Simulation of           *
- * Biological Structures at Stanford, funded under the NIH Roadmap for        *
- * Medical Research, grant U54 GM072970. See https://simtk.org.               *
- *                                                                            *
- * Portions copyright (c) 2008-2010 Stanford University and the Authors.      *
- * Authors: Mark Friedrichs                                                   *
- * Contributors:                                                              *
- *                                                                            *
- * Permission is hereby granted, free of charge, to any person obtaining a    *
- * copy of this software and associated documentation files (the "Software"), *
- * to deal in the Software without restriction, including without limitation  *
- * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
- * and/or sell copies of the Software, and to permit persons to whom the      *
- * Software is furnished to do so, subject to the following conditions:       *
- *                                                                            *
- * The above copyright notice and this permission notice shall be included in *
- * all copies or substantial portions of the Software.                        *
- *                                                                            *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
- * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
- * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
- * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
- * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
- * -------------------------------------------------------------------------- */
-
-/**
- * This tests the CUDA implementation of AmoebaMultipoleForce.
- */
-
-#include "openmm/internal/AssertionUtilities.h"
-#include "AmoebaTinkerParameterFile.h"
-#include "openmm/Context.h"
-#include "CudaPlatform.h"
-#include "openmm/AmoebaMultipoleForce.h"
-#include "openmm/System.h"
-#include "openmm/VerletIntegrator.h"
-#include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
-#include <iostream>
-#include <vector>
-
-using namespace OpenMM;
-using namespace std;
-
-const double TOL = 1e-5;
-
-void testPMEWater() {
-    Platform& platform = Platform::getPlatformByName("CUDA");
-    System system;
-    system.addParticle(16);
-    system.addParticle(1);
-    system.addParticle(1);
-    VerletIntegrator integrator(0.01);
-    AmoebaMultipoleForce* mp = new AmoebaMultipoleForce();
-    mp->setNonbondedMethod(AmoebaMultipoleForce::PME);
-    vector<double> dipole(3, 0.0);
-    dipole[2] = 7.556121361e-2;
-    vector<double> quadrupole(9, 0.0);
-    quadrupole[0] = 3.540307211e-2;
-    quadrupole[4] = -3.902570771e-2;
-    quadrupole[8] = 3.622635596e-3;
-    double damp = 9.707801995e-01*sqrt(0.1);
-    double polarity = 0.837*0.001;
-    mp->addParticle(-0.51966, dipole, quadrupole, 1, 1, 2, -1, 0.39, damp, polarity);
-    dipole[0] = -2.042094848e-2;
-    dipole[2] = -3.078753000e-2;
-    quadrupole[0] = -3.428482490e-3;
-    quadrupole[2] = -1.894859639e-4;
-    quadrupole[4] = -1.002408752e-2;
-    quadrupole[6] = -1.894859639e-4;
-    quadrupole[8] = 1.345257001e-2;
-    damp          = 8.897068742e-01*sqrt(0.1);
-    polarity      = 0.496*0.001;
-    mp->addParticle(0.25983, dipole, quadrupole, 0, 0, 2, -1, 0.39, damp, polarity);
-    mp->addParticle(0.25983, dipole, quadrupole, 0, 0, 1, -1, 0.39, damp, polarity);
-    mp->setCutoffDistance(1.0);
-
-    std::vector<int> intVector;
-    intVector.push_back( 0 );
-    intVector.push_back( 1 );
-    intVector.push_back( 2 );
-    mp->setCovalentMap( 0, AmoebaMultipoleForce::PolarizationCovalent11, intVector );
-    mp->setCovalentMap( 1, AmoebaMultipoleForce::PolarizationCovalent11, intVector );
-    mp->setCovalentMap( 2, AmoebaMultipoleForce::PolarizationCovalent11, intVector );
-
-    intVector.resize(0); intVector.push_back( 1 ); intVector.push_back( 2 );
-    mp->setCovalentMap( 0, AmoebaMultipoleForce::Covalent12, intVector );
-
-    intVector.resize(0); intVector.push_back( 0 ); intVector.push_back( 2 );
-    mp->setCovalentMap( 1, AmoebaMultipoleForce::Covalent12, intVector );
-
-    intVector.resize(0); intVector.push_back( 0 ); intVector.push_back( 1 );
-    mp->setCovalentMap( 2, AmoebaMultipoleForce::Covalent12, intVector );
-
-    mp->setEwaldErrorTolerance(TOL);
-    system.setDefaultPeriodicBoxVectors(Vec3(2, 0, 0), Vec3(0, 2, 0), Vec3(0, 0, 2));
-    system.addForce(mp);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(3);
-    const double angle = 109.47*M_PI/180;
-    const double dOH = 0.1;
-    positions[0] = Vec3();
-    positions[1] = Vec3(dOH, 0, 0);
-    positions[2] = Vec3(dOH*std::cos(angle), dOH*std::sin(angle), 0);
-    context.setPositions(positions);
-    State state = context.getState(State::Forces | State::Energy);
-    const vector<Vec3>& forces = state.getForces();
-
-#ifdef AMOEBA_DEBUG
-    (void) fprintf( stderr, "PME forces\n" );
-        for( unsigned int ii = 0; ii < forces.size(); ii++ ){
-            (void) fprintf( stderr, "%6u [%14.7e %14.7e %14.7e]\n", ii, 
-                            forces[ii][0], forces[ii][1], forces[ii][2] );
-    }
-    (void) fflush( stderr );
-#endif
-
-}
-
-int main() {
-    try {
-        registerAmoebaCudaKernelFactories();
-        testPMEWater();
-    } catch(const exception& e) {
-        cout << "exception: " << e.what() << endl;
-        return 1;
-    }
-    std::cout << "Done" << std::endl;
-    return 0;
-}
-

plugins/amoeba/platforms/cuda2/tests/TestCudaAmoebaPiTorsionForce.cpp

@@ -34,7 +34,6 @@
  */
 
 #include "openmm/internal/AssertionUtilities.h"
-#include "AmoebaTinkerParameterFile.h"
 #include "openmm/Context.h"
 #include "OpenMMAmoeba.h"
 #include "openmm/System.h"
@@ -44,6 +43,8 @@
 
 using namespace OpenMM;
 
+extern "C" void registerAmoebaCudaKernelFactories();
+
 const double TOL = 1e-5;
 #define PI_M               3.141592653589
 #define RADIAN            57.29577951308

plugins/amoeba/platforms/cuda2/tests/TestCudaAmoebaStretchBendForce.cpp

@@ -34,7 +34,6 @@
  */
 
 #include "openmm/internal/AssertionUtilities.h"
-#include "AmoebaTinkerParameterFile.h"
 #include "openmm/Context.h"
 #include "OpenMMAmoeba.h"
 #include "openmm/System.h"
@@ -44,9 +43,12 @@
 
 using namespace OpenMM;
 
+extern "C" void registerAmoebaCudaKernelFactories();
+
 const double TOL = 1e-5;
 #define PI_M               3.141592653589
 #define RADIAN            57.29577951308
+const double DegreesToRadians = PI_M/180.0;
 
 /* ---------------------------------------------------------------------------------------
 

plugins/amoeba/platforms/cuda2/tests/TestCudaAmoebaTorsionTorsionForce.cpp

@@ -37,13 +37,15 @@
 #include "openmm/Context.h"
 #include "OpenMMAmoeba.h"
 #include "openmm/System.h"
-#include "AmoebaTinkerParameterFile.h"
 #include "openmm/AmoebaTorsionTorsionForce.h"
 #include "openmm/LangevinIntegrator.h"
 #include <iostream>
 #include <vector>
 
 using namespace OpenMM;
+
+extern "C" void registerAmoebaCudaKernelFactories();
+
 const double TOL = 1e-4;
 
 TorsionTorsionGrid& getTorsionGrid( int gridIndex ) {

plugins/amoeba/platforms/cuda2/tests/TestCudaAmoebaVdwForce.cpp

@@ -36,7 +36,6 @@
 #include "openmm/internal/AssertionUtilities.h"
 #include "openmm/Context.h"
 #include "OpenMMAmoeba.h"
-#include "AmoebaTinkerParameterFile.h"
 #include "openmm/System.h"
 #include "openmm/AmoebaVdwForce.h"
 #include "openmm/LangevinIntegrator.h"
@@ -51,6 +50,9 @@
 
 
 using namespace OpenMM;
+
+extern "C" void registerAmoebaCudaKernelFactories();
+
 const double TOL = 1e-4;
 
 void testVdw( FILE* log ) {
@@ -63,7 +65,6 @@ void testVdw( FILE* log ) {
 
     std::string epsilonCombiningRule = std::string("HHG");
     amoebaVdwForce->setEpsilonCombiningRule( epsilonCombiningRule );
-    int classIndex = 0;
     for( int ii = 0; ii < numberOfParticles; ii++ ){
         int indexIV;
         double mass, sigma, epsilon, reduction;
@@ -94,7 +95,7 @@ void testVdw( FILE* log ) {
             exclusions.push_back ( 5 );
         }
         system.addParticle(mass);
-        amoebaVdwForce->addParticle( indexIV, classIndex, sigma, epsilon, reduction );
+        amoebaVdwForce->addParticle( indexIV, sigma, epsilon, reduction );
         amoebaVdwForce->setParticleExclusions( ii, exclusions );
     }
     LangevinIntegrator integrator(0.0, 0.1, 0.01);
@@ -136,12 +137,11 @@ void testVdw( FILE* log ) {
     }
     for( int ii = 0; ii < amoebaVdwForce->getNumParticles();  ii++ ){
         int indexIV;
-        int classIndex;
         double sigma, epsilon, reduction;
-        amoebaVdwForce->getParticleParameters( ii, indexIV, classIndex, sigma, epsilon, reduction );
+        amoebaVdwForce->getParticleParameters( ii, indexIV, sigma, epsilon, reduction );
         sigma        *= AngstromToNm;
         epsilon      *= CalToJoule;
-        amoebaVdwForce->setParticleParameters( ii, indexIV, classIndex, sigma, epsilon, reduction );
+        amoebaVdwForce->setParticleParameters( ii, indexIV, sigma, epsilon, reduction );
     }
     platformName = "CUDA";
     Context context(system, integrator, Platform::getPlatformByName( platformName ) );
@@ -186,46 +186,44 @@ void setupAndGetForcesEnergyVdwAmmonia( const std::string& sigmaCombiningRule, c
     int numberOfParticles                 = 8;
     amoebaVdwForce->setSigmaCombiningRule( sigmaCombiningRule );
     amoebaVdwForce->setEpsilonCombiningRule( epsilonCombiningRule );
-    amoebaVdwForce->setUseNeighborList( 1 );
     amoebaVdwForce->setCutoff( cutoff );
     if( boxDimension > 0.0 ){
         Vec3 a( boxDimension, 0.0, 0.0 );
         Vec3 b( 0.0, boxDimension, 0.0 );
         Vec3 c( 0.0, 0.0, boxDimension );
         system.setDefaultPeriodicBoxVectors( a, b, c );
-        amoebaVdwForce->setPBC( 1 );
+        amoebaVdwForce->setNonbondedMethod(AmoebaVdwForce::CutoffPeriodic);
         amoebaVdwForce->setUseDispersionCorrection( 1 );
     } else {
-        amoebaVdwForce->setPBC( 0 );
+        amoebaVdwForce->setNonbondedMethod(AmoebaVdwForce::NoCutoff);
         amoebaVdwForce->setUseDispersionCorrection( 0 );
     }
 
     // addParticle: ivIndex, radius, epsilon, reductionFactor
 
-    int classIndex = 0;
     system.addParticle(   1.4007000e+01 );
-    amoebaVdwForce->addParticle( 0, classIndex,   1.8550000e-01,   4.3932000e-01,   0.0000000e+00 );
+    amoebaVdwForce->addParticle( 0,   1.8550000e-01,   4.3932000e-01,   0.0000000e+00 );
 
     system.addParticle(   1.0080000e+00 );
-    amoebaVdwForce->addParticle( 0, classIndex,   1.3500000e-01,   8.3680000e-02,   9.1000000e-01 );
+    amoebaVdwForce->addParticle( 0,   1.3500000e-01,   8.3680000e-02,   9.1000000e-01 );
 
     system.addParticle(   1.0080000e+00 );
-    amoebaVdwForce->addParticle( 0, classIndex,   1.3500000e-01,   8.3680000e-02,   9.1000000e-01 );
+    amoebaVdwForce->addParticle( 0,   1.3500000e-01,   8.3680000e-02,   9.1000000e-01 );
 
     system.addParticle(   1.0080000e+00 );
-    amoebaVdwForce->addParticle( 0, classIndex,   1.3500000e-01,   8.3680000e-02,   9.1000000e-01 );
+    amoebaVdwForce->addParticle( 0,   1.3500000e-01,   8.3680000e-02,   9.1000000e-01 );
 
     system.addParticle(   1.4007000e+01 );
-    amoebaVdwForce->addParticle( 4, classIndex,   1.8550000e-01,   4.3932000e-01,   0.0000000e+00 );
+    amoebaVdwForce->addParticle( 4,   1.8550000e-01,   4.3932000e-01,   0.0000000e+00 );
 
     system.addParticle(   1.0080000e+00 );
-    amoebaVdwForce->addParticle( 4, classIndex,   1.3500000e-01,   8.3680000e-02,   9.1000000e-01 );
+    amoebaVdwForce->addParticle( 4,   1.3500000e-01,   8.3680000e-02,   9.1000000e-01 );
 
     system.addParticle(   1.0080000e+00 );
-    amoebaVdwForce->addParticle( 4, classIndex,   1.3500000e-01,   8.3680000e-02,   9.1000000e-01 );
+    amoebaVdwForce->addParticle( 4,   1.3500000e-01,   8.3680000e-02,   9.1000000e-01 );
 
     system.addParticle(   1.0080000e+00 );
-    amoebaVdwForce->addParticle( 4, classIndex,   1.3500000e-01,   8.3680000e-02,   9.1000000e-01 );
+    amoebaVdwForce->addParticle( 4,   1.3500000e-01,   8.3680000e-02,   9.1000000e-01 );
 
     // ParticleExclusions
 
@@ -463,7 +461,7 @@ void testVdwTaper( FILE* log ) {
     std::string testName      = "testVdwTaper";
 
     int numberOfParticles     = 8;
-    double boxDimension       = -1.0;
+    double boxDimension       = 50.0;
     double cutoff             = 0.25;
 
     std::vector<Vec3> forces;
@@ -532,33 +530,32 @@ void setupAndGetForcesEnergyVdwWater( const std::string& sigmaCombiningRule, con
     int numberOfParticles                 = 648;
     amoebaVdwForce->setSigmaCombiningRule( sigmaCombiningRule );
     amoebaVdwForce->setEpsilonCombiningRule( epsilonCombiningRule );
-    amoebaVdwForce->setUseNeighborList( 1 );
     amoebaVdwForce->setCutoff( cutoff );
     if( boxDimension > 0.0 ){
         Vec3 a( boxDimension, 0.0, 0.0 );
         Vec3 b( 0.0, boxDimension, 0.0 );
         Vec3 c( 0.0, 0.0, boxDimension );
         system.setDefaultPeriodicBoxVectors( a, b, c );
-        amoebaVdwForce->setPBC( 1 );
+        amoebaVdwForce->setNonbondedMethod(AmoebaVdwForce::CutoffPeriodic);
         amoebaVdwForce->setUseDispersionCorrection( includeVdwDispersionCorrection );
     } else {
-        amoebaVdwForce->setPBC( 0 );
+        amoebaVdwForce->setNonbondedMethod(AmoebaVdwForce::NoCutoff);
         amoebaVdwForce->setUseDispersionCorrection( 0 );
     }
 
-    // addParticle: ivIndex, classIndex, radius, epsilon, reductionFactor
+    // addParticle: ivIndex, radius, epsilon, reductionFactor
 
     int classIndex = 0;
     for( unsigned int ii = 0; ii < numberOfParticles; ii += 3 ){
 
        system.addParticle(   1.5995000e+01 );
-       amoebaVdwForce->addParticle( ii,  0, 1.7025000e-01,   4.6024000e-01,   0.0000000e+00 );
+       amoebaVdwForce->addParticle( ii, 1.7025000e-01,   4.6024000e-01,   0.0000000e+00 );
 
        system.addParticle(   1.0080000e+00 );
-       amoebaVdwForce->addParticle( ii, 0,   1.3275000e-01,   5.6484000e-02,   9.1000000e-01 );
+       amoebaVdwForce->addParticle( ii, 1.3275000e-01,   5.6484000e-02,   9.1000000e-01 );
 
        system.addParticle(   1.0080000e+00 );
-       amoebaVdwForce->addParticle( ii, 0,   1.3275000e-01,   5.6484000e-02,   9.1000000e-01 );
+       amoebaVdwForce->addParticle( ii, 1.3275000e-01,   5.6484000e-02,   9.1000000e-01 );
    }
 
     // exclusions

plugins/amoeba/platforms/cuda2/tests/TestCudaWcaDispersionForce.cpp

@@ -36,7 +36,6 @@
 #include "openmm/internal/AssertionUtilities.h"
 #include "openmm/Context.h"
 #include "OpenMMAmoeba.h"
-#include "AmoebaTinkerParameterFile.h"
 #include "openmm/System.h"
 #include "openmm/AmoebaWcaDispersionForce.h"
 #include "openmm/LangevinIntegrator.h"
@@ -53,6 +52,8 @@
 using namespace OpenMM;
 const double TOL = 1e-4;
 
+extern "C" void registerAmoebaCudaKernelFactories();
+
 void setupAndGetForcesEnergyWcaDispersionAmmonia( std::vector<Vec3>& forces, double& energy, FILE* log ){
 
     // beginning of WcaDispersion setup

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

@@ -53,10 +53,8 @@ extern "C" void initAmoebaReferenceKernels() {
              AmoebaReferenceKernelFactory* factory = new AmoebaReferenceKernelFactory();
 
              platform.registerKernelFactory(CalcAmoebaHarmonicBondForceKernel::Name(),          factory);
-             platform.registerKernelFactory(CalcAmoebaUreyBradleyForceKernel::Name(),           factory);
              platform.registerKernelFactory(CalcAmoebaHarmonicAngleForceKernel::Name(),         factory);
              platform.registerKernelFactory(CalcAmoebaHarmonicInPlaneAngleForceKernel::Name(),  factory);
-             platform.registerKernelFactory(CalcAmoebaTorsionForceKernel::Name(),               factory);
              platform.registerKernelFactory(CalcAmoebaPiTorsionForceKernel::Name(),             factory);
              platform.registerKernelFactory(CalcAmoebaStretchBendForceKernel::Name(),           factory);
              platform.registerKernelFactory(CalcAmoebaOutOfPlaneBendForceKernel::Name(),        factory);
@@ -79,18 +77,12 @@ KernelImpl* AmoebaReferenceKernelFactory::createKernelImpl(std::string name, con
     if (name == CalcAmoebaHarmonicBondForceKernel::Name())
         return new ReferenceCalcAmoebaHarmonicBondForceKernel(name, platform, context.getSystem());
 
-    if (name == CalcAmoebaUreyBradleyForceKernel::Name())
-        return new ReferenceCalcAmoebaUreyBradleyForceKernel(name, platform, context.getSystem());
-
     if (name == CalcAmoebaHarmonicAngleForceKernel::Name())
         return new ReferenceCalcAmoebaHarmonicAngleForceKernel(name, platform, context.getSystem());
 
     if (name == CalcAmoebaHarmonicInPlaneAngleForceKernel::Name())
         return new ReferenceCalcAmoebaHarmonicInPlaneAngleForceKernel(name, platform, context.getSystem());
 
-    if (name == CalcAmoebaTorsionForceKernel::Name())
-        return new ReferenceCalcAmoebaTorsionForceKernel(name, platform, context.getSystem());
-
     if (name == CalcAmoebaPiTorsionForceKernel::Name())
         return new ReferenceCalcAmoebaPiTorsionForceKernel(name, platform, context.getSystem());
 

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

@@ -28,7 +28,6 @@
 #include "AmoebaReferenceHarmonicBondForce.h"
 #include "AmoebaReferenceHarmonicAngleForce.h"
 #include "AmoebaReferenceHarmonicInPlaneAngleForce.h"
-#include "AmoebaReferenceTorsionForce.h"
 #include "AmoebaReferencePiTorsionForce.h"
 #include "AmoebaReferenceStretchBendForce.h"
 #include "AmoebaReferenceOutOfPlaneBendForce.h"
@@ -38,7 +37,6 @@
 #include "AmoebaReferenceWcaDispersionForce.h"
 #include "openmm/internal/AmoebaTorsionTorsionForceImpl.h"
 #include "openmm/internal/AmoebaWcaDispersionForceImpl.h"
-#include "AmoebaReferenceUreyBradleyForce.h"
 #include "ReferencePlatform.h"
 #include "openmm/internal/ContextImpl.h"
 #include "openmm/AmoebaMultipoleForce.h"
@@ -111,41 +109,6 @@ double ReferenceCalcAmoebaHarmonicBondForceKernel::execute(ContextImpl& context,
 
 // ***************************************************************************
 
-ReferenceCalcAmoebaUreyBradleyForceKernel::ReferenceCalcAmoebaUreyBradleyForceKernel(std::string name, const Platform& platform, System& system) : 
-                CalcAmoebaUreyBradleyForceKernel(name, platform), system(system) {
-}
-
-ReferenceCalcAmoebaUreyBradleyForceKernel::~ReferenceCalcAmoebaUreyBradleyForceKernel() {
-}
-
-void ReferenceCalcAmoebaUreyBradleyForceKernel::initialize(const System& system, const AmoebaUreyBradleyForce& force) {
-
-    numIxns = force.getNumInteractions();
-    for( int ii = 0; ii < numIxns; ii++) {
-
-        int particle1Index, particle2Index;
-        double lengthValue, kValue;
-        force.getUreyBradleyParameters(ii, particle1Index, particle2Index, lengthValue, kValue );
-
-        particle1.push_back( particle1Index ); 
-        particle2.push_back( particle2Index ); 
-        length.push_back(    static_cast<RealOpenMM>( lengthValue ) );
-        kQuadratic.push_back( static_cast<RealOpenMM>( kValue ) );
-    } 
-    globalUreyBradleyCubic   = static_cast<RealOpenMM>(force.getAmoebaGlobalUreyBradleyCubic());
-    globalUreyBradleyQuartic = static_cast<RealOpenMM>(force.getAmoebaGlobalUreyBradleyQuartic());
-}
-
-double ReferenceCalcAmoebaUreyBradleyForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
-    vector<RealVec>& posData   = extractPositions(context);
-    vector<RealVec>& forceData = extractForces(context);
-    AmoebaReferenceUreyBradleyForce amoebaReferenceUreyBradleyForce;
-    RealOpenMM energy      = amoebaReferenceUreyBradleyForce.calculateForceAndEnergy( numIxns, posData, particle1, particle2, length, kQuadratic,
-                                                                                      globalUreyBradleyCubic, globalUreyBradleyQuartic,
-                                                                                      forceData );
-    return static_cast<double>(energy);
-}
-
 ReferenceCalcAmoebaHarmonicAngleForceKernel::ReferenceCalcAmoebaHarmonicAngleForceKernel(std::string name, const Platform& platform, System& system) :
             CalcAmoebaHarmonicAngleForceKernel(name, platform), system(system) {
 }
@@ -220,55 +183,6 @@ double ReferenceCalcAmoebaHarmonicInPlaneAngleForceKernel::execute(ContextImpl&
     return static_cast<double>(energy);
 }
 
-ReferenceCalcAmoebaTorsionForceKernel::ReferenceCalcAmoebaTorsionForceKernel(std::string name, const Platform& platform, System& system) :
-             CalcAmoebaTorsionForceKernel(name, platform), system(system) {
-}
-
-ReferenceCalcAmoebaTorsionForceKernel::~ReferenceCalcAmoebaTorsionForceKernel() {
-}
-
-void ReferenceCalcAmoebaTorsionForceKernel::initialize(const System& system, const AmoebaTorsionForce& force) {
-
-    numTorsions = force.getNumTorsions();
-    torsionParameters1.resize( numTorsions );
-    torsionParameters2.resize( numTorsions );
-    torsionParameters3.resize( numTorsions );
-    for (int ii = 0; ii < numTorsions; ii++) {
-
-        int particle1Index, particle2Index, particle3Index, particle4Index;
-        std::vector<double> torsionParameter1;
-        std::vector<double> torsionParameter2;
-        std::vector<double> torsionParameter3;
-
-        std::vector<RealOpenMM> torsionParameters1F(3);
-        std::vector<RealOpenMM> torsionParameters2F(3);
-        std::vector<RealOpenMM> torsionParameters3F(3);
-
-        force.getTorsionParameters(ii, particle1Index, particle2Index, particle3Index, particle4Index, torsionParameter1, torsionParameter2, torsionParameter3 );
-        particle1.push_back( particle1Index ); 
-        particle2.push_back( particle2Index ); 
-        particle3.push_back( particle3Index ); 
-        particle4.push_back( particle4Index ); 
-        torsionParameters1[ii].resize( torsionParameter1.size() );
-        torsionParameters2[ii].resize( torsionParameter2.size() );
-        torsionParameters3[ii].resize( torsionParameter3.size() );
-        for ( unsigned int jj = 0; jj < torsionParameter1.size(); jj++) {
-            torsionParameters1[ii][jj] = static_cast<RealOpenMM>(torsionParameter1[jj]);
-            torsionParameters2[ii][jj] = static_cast<RealOpenMM>(torsionParameter2[jj]);
-            torsionParameters3[ii][jj] = static_cast<RealOpenMM>(torsionParameter3[jj]);
-        }
-    }
-}
-
-double ReferenceCalcAmoebaTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
-    vector<RealVec>& posData   = extractPositions(context);
-    vector<RealVec>& forceData = extractForces(context);
-    AmoebaReferenceTorsionForce amoebaReferenceTorsionForce;
-    RealOpenMM energy      = amoebaReferenceTorsionForce.calculateForceAndEnergy( numTorsions, posData, particle1, particle2, particle3, particle4,
-                                                                                  torsionParameters1, torsionParameters2, torsionParameters3, forceData );
-    return static_cast<double>(energy);
-}
-
 ReferenceCalcAmoebaPiTorsionForceKernel::ReferenceCalcAmoebaPiTorsionForceKernel(std::string name, const Platform& platform, System& system) :
          CalcAmoebaPiTorsionForceKernel(name, platform), system(system) {
 }
@@ -568,8 +482,7 @@ void ReferenceCalcAmoebaMultipoleForceKernel::getElectrostaticPotential(ContextI
     return;
 }
 
-void ReferenceCalcAmoebaMultipoleForceKernel::getSystemMultipoleMoments(ContextImpl& context, const Vec3& origin,
-                                                                        std::vector< double >& outputMultipoleMonents){
+void ReferenceCalcAmoebaMultipoleForceKernel::getSystemMultipoleMoments(ContextImpl& context, std::vector< double >& outputMultipoleMonents){
     return;
 }
 
@@ -618,7 +531,7 @@ void ReferenceCalcAmoebaMultipoleForceKernel::getSystemMultipoleMoments(ContextI
 
 ReferenceCalcAmoebaVdwForceKernel::ReferenceCalcAmoebaVdwForceKernel(std::string name, const Platform& platform, System& system) :
        CalcAmoebaVdwForceKernel(name, platform), system(system) {
-    useNeighborList = 0;
+    useCutoff = 0;
     usePBC = 0;
     cutoff = 1.0e+10;
 
@@ -634,7 +547,6 @@ void ReferenceCalcAmoebaVdwForceKernel::initialize(const System& system, const A
     numParticles = system.getNumParticles();
 
     indexIVs.resize( numParticles );
-    indexClasses.resize( numParticles );
     allExclusions.resize( numParticles );
     sigmas.resize( numParticles );
     epsilons.resize( numParticles );
@@ -642,26 +554,25 @@ void ReferenceCalcAmoebaVdwForceKernel::initialize(const System& system, const A
 
     for( int ii = 0; ii < numParticles; ii++ ){
 
-        int indexIV, indexClass;
+        int indexIV;
         double sigma, epsilon, reduction;
         std::vector<int> exclusions;
 
-        force.getParticleParameters( ii, indexIV, indexClass, sigma, epsilon, reduction );
+        force.getParticleParameters( ii, indexIV, sigma, epsilon, reduction );
         force.getParticleExclusions( ii, exclusions );
         for( unsigned int jj = 0; jj < exclusions.size(); jj++ ){
            allExclusions[ii].push_back( exclusions[jj] );
         }
 
         indexIVs[ii]      = indexIV;
-        indexClasses[ii]  = indexClass;
         sigmas[ii]        = static_cast<RealOpenMM>( sigma );
         epsilons[ii]      = static_cast<RealOpenMM>( epsilon );
         reductions[ii]    = static_cast<RealOpenMM>( reduction );
     }   
     sigmaCombiningRule   = force.getSigmaCombiningRule();
     epsilonCombiningRule = force.getEpsilonCombiningRule();
-    useNeighborList      = force.getUseNeighborList();
-    usePBC               = force.getPBC();
+    useCutoff            = (force.getNonbondedMethod() != AmoebaVdwForce::NoCutoff);
+    usePBC               = (force.getNonbondedMethod() == AmoebaVdwForce::CutoffPeriodic);
     cutoff               = force.getCutoff();
 }
 
@@ -670,7 +581,7 @@ double ReferenceCalcAmoebaVdwForceKernel::execute(ContextImpl& context, bool inc
     vector<RealVec>& posData   = extractPositions(context);
     vector<RealVec>& forceData = extractForces(context);
     AmoebaReferenceVdwForce vdwForce( sigmaCombiningRule, epsilonCombiningRule );
-    if( useNeighborList ){
+    if( useCutoff ){
         vdwForce.setCutoff( cutoff );
         if( usePBC ){
             vdwForce.setNonbondedMethod( AmoebaReferenceVdwForce::CutoffPeriodic);
@@ -680,7 +591,7 @@ double ReferenceCalcAmoebaVdwForceKernel::execute(ContextImpl& context, bool inc
     } else {
         vdwForce.setNonbondedMethod( AmoebaReferenceVdwForce::NoCutoff );
     }
-    RealOpenMM energy = vdwForce.calculateForceAndEnergy( numParticles, posData, indexIVs, indexClasses, sigmas, epsilons, reductions, allExclusions, forceData);
+    RealOpenMM energy = vdwForce.calculateForceAndEnergy( numParticles, posData, indexIVs, sigmas, epsilons, reductions, allExclusions, forceData);
     return static_cast<double>(energy);
 }
 

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

@@ -70,42 +70,6 @@ private:
     System& system;
 };
 
-/**
- * This kernel is invoked by AmoebaUreyBradleyForce to calculate the forces acting on the system and the energy of the system.
- */
-class ReferenceCalcAmoebaUreyBradleyForceKernel : public CalcAmoebaUreyBradleyForceKernel {
-public:
-    ReferenceCalcAmoebaUreyBradleyForceKernel(std::string name, 
-                                               const Platform& platform,
-                                               System& system);
-    ~ReferenceCalcAmoebaUreyBradleyForceKernel();
-    /**
-     * Initialize the kernel.
-     * 
-     * @param system     the System this kernel will be applied to
-     * @param force      the AmoebaUreyBradleyForce this kernel will be used for
-     */
-    void initialize(const System& system, const AmoebaUreyBradleyForce& force);
-    /**
-     * Execute the kernel to calculate the forces and/or energy.
-     *
-     * @param context        the context in which to execute this kernel
-     * @param includeForces  true if forces should be calculated
-     * @param includeEnergy  true if the energy should be calculated
-     * @return the potential energy due to the force
-     */
-    double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
-private:
-    int numIxns;
-    std::vector<int>   particle1;
-    std::vector<int>   particle2;
-    std::vector<RealOpenMM> length;
-    std::vector<RealOpenMM> kQuadratic;
-    RealOpenMM globalUreyBradleyCubic;
-    RealOpenMM globalUreyBradleyQuartic;
-    System& system;
-};
-
 /**
  * This kernel is invoked by AmoebaHarmonicAngleForce to calculate the forces acting on the system and the energy of the system.
  */
@@ -181,41 +145,6 @@ private:
     System& system;
 };
 
-/**
- * This kernel is invoked by AmoebaTorsionForce to calculate the forces acting on the system and the energy of the system.
- */
-class ReferenceCalcAmoebaTorsionForceKernel : public CalcAmoebaTorsionForceKernel {
-public:
-    ReferenceCalcAmoebaTorsionForceKernel(std::string name, const Platform& platform, System& system);
-    ~ReferenceCalcAmoebaTorsionForceKernel();
-    /**
-     * Initialize the kernel.
-     * 
-     * @param system     the System this kernel will be applied to
-     * @param force      the AmoebaTorsionForce this kernel will be used for
-     */
-    void initialize(const System& system, const AmoebaTorsionForce& force);
-    /**
-     * Execute the kernel to calculate the forces and/or energy.
-     *
-     * @param context        the context in which to execute this kernel
-     * @param includeForces  true if forces should be calculated
-     * @param includeEnergy  true if the energy should be calculated
-     * @return the potential energy due to the force
-     */
-    double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
-private:
-    int numTorsions;
-    std::vector<int>   particle1;
-    std::vector<int>   particle2;
-    std::vector<int>   particle3;
-    std::vector<int>   particle4;
-    std::vector< std::vector<RealOpenMM> > torsionParameters1;
-    std::vector< std::vector<RealOpenMM> > torsionParameters2;
-    std::vector< std::vector<RealOpenMM> > torsionParameters3;
-    System& system;
-};
-
 /**
  * This kernel is invoked by AmoebaPiTorsionForce to calculate the forces acting on the system and the energy of the system.
  */
@@ -398,7 +327,6 @@ public:
     /**
      * Get the system multipole moments
      *
-     * @param origin       origin
      * @param context      context
      * @param outputMultipoleMonents (charge,
                                       dipole_x, dipole_y, dipole_z,
@@ -406,7 +334,7 @@ public:
                                       quadrupole_yx, quadrupole_yy, quadrupole_yz,
                                       quadrupole_zx, quadrupole_zy, quadrupole_zz )
      */
-    void getSystemMultipoleMoments(ContextImpl& context, const Vec3& origin, std::vector< double >& outputMultipoleMonents);
+    void getSystemMultipoleMoments(ContextImpl& context, std::vector< double >& outputMultipoleMonents);
 
 private:
     int numMultipoles;
@@ -456,11 +384,10 @@ public:
     double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
 private:
     int numParticles;
-    int useNeighborList;
+    int useCutoff;
     int usePBC;
     double cutoff;
     std::vector<int> indexIVs;
-    std::vector<int> indexClasses;
     std::vector< std::vector<int> > allExclusions;
     std::vector<RealOpenMM> sigmas;
     std::vector<RealOpenMM> epsilons;

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

-/* Portions copyright (c) 2006 Stanford University and Simbios.
- * Contributors: Pande Group
- *
- * Permission is hereby granted, free of charge, to any person obtaining
- * a copy of this software and associated documentation files (the
- * "Software"), to deal in the Software without restriction, including
- * without limitation the rights to use, copy, modify, merge, publish,
- * distribute, sublicense, and/or sell copies of the Software, and to
- * permit persons to whom the Software is furnished to do so, subject
- * to the following conditions:
- *
- * The above copyright notice and this permission notice shall be included
- * in all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
- * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
- * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
- * IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE
- * LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
- * OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
- * WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
- */
-
-#include "AmoebaReferenceForce.h"
-#include "AmoebaReferenceTorsionForce.h"
-
-using std::vector;
-using OpenMM::RealVec;
-
-/**---------------------------------------------------------------------------------------
-
-   Calculate Amoeba torsion ixn (force and energy)
-
-   @param positionAtomA           Cartesian coordinates of atom A
-   @param positionAtomB           Cartesian coordinates of atom B
-   @param positionAtomC           Cartesian coordinates of atom C
-   @param positionAtomD           Cartesian coordinates of atom D
-   @param torsion1                vector of torsion params for first index (amplitude, phase, fold)
-   @param torsion2                vector of torsion params for second index (amplitude, phase, fold)
-   @param torsion3                vector of torsion params for third index (amplitude, phase, fold)
-   @param forces                  force vector
-
-   @return energy
-
-   --------------------------------------------------------------------------------------- */
-
-RealOpenMM AmoebaReferenceTorsionForce::calculateTorsionIxn( const RealVec& positionAtomA, const RealVec& positionAtomB,
-                                                             const RealVec& positionAtomC, const RealVec& positionAtomD,
-                                                             const std::vector<RealOpenMM>& torsionParameters1,
-                                                             const std::vector<RealOpenMM>& torsionParameters2,
-                                                             const std::vector<RealOpenMM>& torsionParameters3,
-                                                             RealVec* forces ) const {
-
-   // ---------------------------------------------------------------------------------------
-
-   //static const std::string methodName = "AmoebaReferenceTorsionForce::calculateHarmonicForce";
-
-   static const RealOpenMM zero          = 0.0;
-   static const RealOpenMM one           = 1.0;
-   static const RealOpenMM two           = 2.0;
-   static const RealOpenMM three         = 3.0;
-
-   // ---------------------------------------------------------------------------------------
-
-    enum { BA, CB, DC, CA, DB, LastDeltaIndex };
-    std::vector<RealOpenMM> deltaR[LastDeltaIndex];
-    AmoebaReferenceForce::loadDeltaR( positionAtomA, positionAtomB, deltaR[BA] );
-    AmoebaReferenceForce::loadDeltaR( positionAtomB, positionAtomC, deltaR[CB] );
-    AmoebaReferenceForce::loadDeltaR( positionAtomC, positionAtomD, deltaR[DC] );
-    AmoebaReferenceForce::loadDeltaR( positionAtomA, positionAtomC, deltaR[CA] );
-    AmoebaReferenceForce::loadDeltaR( positionAtomB, positionAtomD, deltaR[DB] );
-
-    enum { Xt, Xu, Xtu, LastXtIndex };
-    std::vector<RealOpenMM> crossProducts[LastXtIndex];
-    for( unsigned int ii = 0; ii < LastXtIndex; ii++ ){
-        crossProducts[ii].resize(3);
-    }
-    AmoebaReferenceForce::getCrossProduct( deltaR[BA], deltaR[CB], crossProducts[Xt] );
-    AmoebaReferenceForce::getCrossProduct( deltaR[CB], deltaR[DC], crossProducts[Xu] );
-    AmoebaReferenceForce::getCrossProduct( crossProducts[Xt], crossProducts[Xu], crossProducts[Xtu] );
- 
-    RealOpenMM rT2   = AmoebaReferenceForce::getNormSquared3( crossProducts[Xt] );
-    RealOpenMM rU2   = AmoebaReferenceForce::getNormSquared3( crossProducts[Xu] );
-    RealOpenMM rTrU  = SQRT( rT2*rU2 );
-    if( rTrU <= zero ){
-       return zero;
-    }
- 
-    RealOpenMM rCB   = AmoebaReferenceForce::getNorm3( deltaR[CB] );
- 
-    // ---------------------------------------------------------------------------------------
- 
-    // cos(w), cos(2w), cos(3w), ... 
-    // sin(w), sin(2w), sin(3w), ... 
-  
-    RealOpenMM cosine           = AmoebaReferenceForce::getDotProduct3( crossProducts[Xt], crossProducts[Xu] );
-               cosine          /= rTrU;
- 
-    RealOpenMM sine             = AmoebaReferenceForce::getDotProduct3( deltaR[CB], crossProducts[Xtu] );
-               sine            /= (rCB*rTrU);
-
-    RealOpenMM cosine2          = cosine*cosine - sine*sine;
-    RealOpenMM sine2            = two*cosine*sine;
-    RealOpenMM cosine3          = cosine*cosine2 - sine*sine2;
-    RealOpenMM sine3            = cosine*sine2 + sine*cosine2;
-
-/*
-    RealOpenMM cosine4          = cosine*cosine3 - sine*sine3;
-    RealOpenMM sine4            = cosine*sine3 + sine*cosine3;
-    RealOpenMM cosine5          = cosine*cosine4 - sine*sine4;
-    RealOpenMM sine5            = cosine*sine4 + sine*cosine4;
-    RealOpenMM cosine6          = cosine*cosine5 - sine*sine5;
-    RealOpenMM sine6            = cosine*sine5 + sine*cosine5;
-*/
- 
-    // ---------------------------------------------------------------------------------------
- 
-    // dEdPhi prefactor
-  
-    RealOpenMM dEdPhi  = torsionParameters1[0]*      (cosine* sin( torsionParameters1[1] ) - sine* cos( torsionParameters1[1] ) );
-    dEdPhi            += torsionParameters2[0]*two*  (cosine2*sin( torsionParameters2[1] ) - sine2*cos( torsionParameters2[1] ) );
-    dEdPhi            += torsionParameters3[0]*three*(cosine3*sin( torsionParameters3[1] ) - sine3*cos( torsionParameters3[1] ) );
-
-    // ---------------------------------------------------------------------------------------
-  
-    // dEdtu[0]      = dEdT
-    // dEdtu[1]      = dEdU
-  
-    // tempVector[0] == dEdA: dEdT x CB
-    // tempVector[1] == dEdB: (CA x dEdT) + (dEdU x DC)
-    // tempVector[2] == dEdC: (dEdT x BA) + (DB x dEdU)
-    // tempVector[3] == dEdD: (dEdU x CB)
-   
-    std::vector<RealOpenMM> dEdtu[2];
-    std::vector<RealOpenMM> tempVector[6];
-    for( unsigned int ii = 0; ii < 2; ii++ ){
-        dEdtu[ii].resize(3);
-    }
-    for( unsigned int ii = 0; ii < 6; ii++ ){
-        tempVector[ii].resize(3);
-    }
- 
-    // dEdT & dEdU
-  
-    AmoebaReferenceForce::getCrossProduct( crossProducts[Xt], deltaR[CB], tempVector[0] );
-    AmoebaReferenceForce::getCrossProduct( crossProducts[Xu], deltaR[CB], tempVector[1] );
-    RealOpenMM norm[2] = { dEdPhi/(rT2*rCB ), -dEdPhi/(rU2*rCB ) };
-
-    dEdtu[0][0] = norm[0]*tempVector[0][0];
-    dEdtu[0][1] = norm[0]*tempVector[0][1];
-    dEdtu[0][2] = norm[0]*tempVector[0][2];
-
-    dEdtu[1][0] = norm[1]*tempVector[1][0];
-    dEdtu[1][1] = norm[1]*tempVector[1][1];
-    dEdtu[1][2] = norm[1]*tempVector[1][2];
- 
-    // dEdA
-   
-    AmoebaReferenceForce::getCrossProduct( dEdtu[0], deltaR[CB], tempVector[0] );
- 
-    // dEdB
-  
-    AmoebaReferenceForce::getCrossProduct( deltaR[CA], dEdtu[0], tempVector[4] );
-    AmoebaReferenceForce::getCrossProduct( dEdtu[1], deltaR[DC], tempVector[1] );
- 
-    // dEdC
- 
-    AmoebaReferenceForce::getCrossProduct( dEdtu[0], deltaR[BA], tempVector[5] );
-    AmoebaReferenceForce::getCrossProduct( deltaR[DB], dEdtu[1], tempVector[2] );
-
-    tempVector[1][0] += tempVector[4][0];
-    tempVector[2][0] += tempVector[5][0];
- 
-    tempVector[1][1] += tempVector[4][1];
-    tempVector[2][1] += tempVector[5][1];
- 
-    tempVector[1][2] += tempVector[4][2];
-    tempVector[2][2] += tempVector[5][2];
- 
-    // dEdD
-  
-    AmoebaReferenceForce::getCrossProduct( dEdtu[1], deltaR[CB], tempVector[3] );
- 
-    // ---------------------------------------------------------------------------------------
-     
-    // forces
-  
-    forces[0][0] = tempVector[0][0];
-    forces[0][1] = tempVector[0][1];
-    forces[0][2] = tempVector[0][2];
- 
-    forces[1][0] = tempVector[1][0];
-    forces[1][1] = tempVector[1][1];
-    forces[1][2] = tempVector[1][2];
- 
-    forces[2][0] = tempVector[2][0];
-    forces[2][1] = tempVector[2][1];
-    forces[2][2] = tempVector[2][2];
- 
-    forces[3][0] = tempVector[3][0];
-    forces[3][1] = tempVector[3][1];
-    forces[3][2] = tempVector[3][2];
- 
-    // ---------------------------------------------------------------------------------------
- 
-    // calculate energy
-  
-    RealOpenMM energy  = torsionParameters1[0]*( one + cosine* cos( torsionParameters1[1] ) + sine *sin( torsionParameters1[1] ) );
-               energy += torsionParameters2[0]*( one + cosine2*cos( torsionParameters2[1] ) + sine2*sin( torsionParameters2[1] ) );
-               energy += torsionParameters3[0]*( one + cosine3*cos( torsionParameters3[1] ) + sine3*sin( torsionParameters3[1] ) );
-
-    return energy;
-}
-
-RealOpenMM AmoebaReferenceTorsionForce::calculateForceAndEnergy( int numTorsions, vector<RealVec>& posData,
-                                                                 const std::vector<int>&  particle1,
-                                                                 const std::vector<int>&  particle2,
-                                                                 const std::vector<int>&  particle3,
-                                                                 const std::vector<int>&  particle4,
-                                                                 const std::vector< std::vector<RealOpenMM> >& torsionParameters1,
-                                                                 const std::vector< std::vector<RealOpenMM> >& torsionParameters2,
-                                                                 const std::vector< std::vector<RealOpenMM> >& torsionParameters3,
-                                                                 vector<RealVec>& forceData ) const {
-    RealOpenMM energy      = 0.0; 
-    for (unsigned int ii = 0; ii < static_cast<unsigned int>(numTorsions); ii++) {
-        int particle1Index      = particle1[ii];
-        int particle2Index      = particle2[ii];
-        int particle3Index      = particle3[ii];
-        int particle4Index      = particle4[ii];
-        RealVec forces[4];
-        energy                 += calculateTorsionIxn( posData[particle1Index], posData[particle2Index], posData[particle3Index], posData[particle4Index],
-                                                       torsionParameters1[ii], torsionParameters2[ii], torsionParameters3[ii], forces );
-        // accumulate forces
-    
-        for( int jj = 0; jj < 3; jj++ ){
-            forceData[particle1Index][jj] -= forces[0][jj];
-            forceData[particle2Index][jj] -= forces[1][jj];
-            forceData[particle3Index][jj] -= forces[2][jj];
-            forceData[particle4Index][jj] -= forces[3][jj];
-        }
-
-    }   
-    return energy;
-}
-
-

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

-
-/* Portions copyright (c) 2006 Stanford University and Simbios.
- * Contributors: Pande Group
- *
- * Permission is hereby granted, free of charge, to any person obtaining
- * a copy of this software and associated documentation files (the
- * "Software"), to deal in the Software without restriction, including
- * without limitation the rights to use, copy, modify, merge, publish,
- * distribute, sublicense, and/or sell copies of the Software, and to
- * permit persons to whom the Software is furnished to do so, subject
- * to the following conditions:
- *
- * The above copyright notice and this permission notice shall be included
- * in all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
- * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
- * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
- * IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE
- * LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
- * OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
- * WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
- */
-
-#ifndef __AmoebaReferenceTorsionForce_H__
-#define __AmoebaReferenceTorsionForce_H__
-
-#include "SimTKUtilities/RealVec.h"
-#include <vector>
-
-// ---------------------------------------------------------------------------------------
-
-class AmoebaReferenceTorsionForce {
-
-public:
- 
-    /**---------------------------------------------------------------------------------------
-       
-       Constructor
-       
-       --------------------------------------------------------------------------------------- */
- 
-    AmoebaReferenceTorsionForce( ){};
- 
-    /**---------------------------------------------------------------------------------------
-       
-       Destructor
-       
-          --------------------------------------------------------------------------------------- */
- 
-    ~AmoebaReferenceTorsionForce( ){};
- 
-     /**---------------------------------------------------------------------------------------
-     
-        Calculate Amoeba torsion ixns (force and energy)
-     
-        @param numTorsions             number of torsions
-        @param posData                 particle positions
-        @param particle1               particle 1 indices
-        @param particle2               particle 2 indices
-        @param particle3               particle 3 indices
-        @param particle4               particle 4 indices
-        @param torsionParameters1      first  index torsion parameters (amplitude, phase, fold)
-        @param torsionParameters2      second index torsion parameters (amplitude, phase, fold)
-        @param torsionParameters3      third  index torsion parameters (amplitude, phase, fold)
-        @param forces                  output force vector
-     
-        @return total energy
-
-     
-        --------------------------------------------------------------------------------------- */
-
-    RealOpenMM calculateForceAndEnergy( int numTorsions, std::vector<OpenMM::RealVec>& posData,
-                                        const std::vector<int>&  particle1,
-                                        const std::vector<int>&  particle2,
-                                        const std::vector<int>&  particle3,
-                                        const std::vector<int>&  particle4,
-                                        const std::vector< std::vector<RealOpenMM> >& torsionParameters1,
-                                        const std::vector< std::vector<RealOpenMM> >& torsionParameters2,
-                                        const std::vector< std::vector<RealOpenMM> >& torsionParameters3,
-                                        std::vector<OpenMM::RealVec>& forceData ) const;
-
-private:
-
-    /**---------------------------------------------------------------------------------------
-    
-       Calculate Amoeba harmonic angle ixn (force and energy)
-    
-       @param positionAtomA           Cartesian coordinates of atom A
-       @param positionAtomB           Cartesian coordinates of atom B
-       @param positionAtomC           Cartesian coordinates of atom C
-       @param positionAtomD           Cartesian coordinates of atom D
-       @param torsion1                vector of torsion params for first  index (amplitude, phase, fold)
-       @param torsion2                vector of torsion params for second index (amplitude, phase, fold)
-       @param torsion3                vector of torsion params for third  index (amplitude, phase, fold)
-       @param forces                  force vector
-    
-       @return energy
-    
-       --------------------------------------------------------------------------------------- */
-    
-    RealOpenMM calculateTorsionIxn( const OpenMM::RealVec& positionAtomA, const OpenMM::RealVec& positionAtomB,
-                                               const OpenMM::RealVec& positionAtomC, const OpenMM::RealVec& positionAtomD,
-                                               const std::vector<RealOpenMM>& torsionParameters1,
-                                               const std::vector<RealOpenMM>& torsionParameters2,
-                                               const std::vector<RealOpenMM>& torsionParameters3,
-                                               OpenMM::RealVec* forces ) const;
-         
-};
-
-
-// ---------------------------------------------------------------------------------------
-
-#endif // _AmoebaReferenceTorsionForce___

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

-
-/* Portions copyright (c) 2006 Stanford University and Simbios.
- * Contributors: Pande Group
- *
- * Permission is hereby granted, free of charge, to any person obtaining
- * a copy of this software and associated documentation files (the
- * "Software"), to deal in the Software without restriction, including
- * without limitation the rights to use, copy, modify, merge, publish,
- * distribute, sublicense, and/or sell copies of the Software, and to
- * permit persons to whom the Software is furnished to do so, subject
- * to the following conditions:
- *
- * The above copyright notice and this permission notice shall be included
- * in all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
- * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
- * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
- * IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE
- * LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
- * OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
- * WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
- */
-
-#include "AmoebaReferenceUreyBradleyForce.h"
-#include "AmoebaReferenceForce.h"
-
-using std::vector;
-using OpenMM::RealVec;
-
-/**---------------------------------------------------------------------------------------
-
-   Calculate Amoeba UB ixn (force and energy)
-
-   @param positionAtomA           Cartesian coordinates of atom A
-   @param positionAtomB           Cartesian coordinates of atom B
-   @param idealLength             ideal length
-   @param kForceConstant          force constant
-   @param cubicK                  cubic force parameter
-   @param quarticK                quartic force parameter
-   @param forces                  force vector
-
-   @return energy
-
-   --------------------------------------------------------------------------------------- */
-
-RealOpenMM AmoebaReferenceUreyBradleyForce::calculateUreyBradleyIxn( const RealVec& positionAtomA, const RealVec& positionAtomB,
-                                                                     RealOpenMM idealLength, RealOpenMM kForceConstant,
-                                                                     RealOpenMM cubicK, RealOpenMM quarticK,
-                                                                     RealVec* forces ) const {
-
-   // ---------------------------------------------------------------------------------------
-
-   //static const std::string methodName = "AmoebaReferenceUreyBradleyForce::calculateHarmonicForce";
-
-   static const RealOpenMM zero          = 0.0;
-   static const RealOpenMM one           = 1.0;
-   static const RealOpenMM onePt5        = 1.5;
-   static const RealOpenMM two           = 2.0;
-
-   // ---------------------------------------------------------------------------------------
-
-   // get deltaR, R2, and R between 2 atoms
-
-   std::vector<RealOpenMM> deltaR;
-   AmoebaReferenceForce::loadDeltaR( positionAtomA, positionAtomB, deltaR );
-   RealOpenMM r               = AmoebaReferenceForce::getNorm3( deltaR );
-
-   // deltaIdeal = r - r_0
-
-   RealOpenMM deltaIdeal      = r - idealLength;
-   RealOpenMM deltaIdeal2     = deltaIdeal*deltaIdeal;
-
-   RealOpenMM dEdR            = (one + onePt5*cubicK*deltaIdeal + two*quarticK*deltaIdeal2);
-   dEdR                      *= two*kForceConstant*deltaIdeal;
-   dEdR                       = r > zero ? (dEdR/r) : zero;
-
-   forces[0][0]              = dEdR*deltaR[0];
-   forces[0][1]              = dEdR*deltaR[1];
-   forces[0][2]              = dEdR*deltaR[2];
-
-   forces[1][0]              = dEdR*deltaR[0];
-   forces[1][1]              = dEdR*deltaR[1];
-   forces[1][2]              = dEdR*deltaR[2];
-
-   RealOpenMM energy          = kForceConstant*deltaIdeal2*( one + cubicK*deltaIdeal + quarticK*deltaIdeal2 );
-   return energy;
-}
-
-RealOpenMM AmoebaReferenceUreyBradleyForce::calculateForceAndEnergy( int numIxns,
-                                                                      vector<RealVec>& particlePositions,
-                                                                      const std::vector<int>&   particle1,
-                                                                      const std::vector<int>&   particle2,
-                                                                      const std::vector<RealOpenMM>& length,
-                                                                      const std::vector<RealOpenMM>& kQuadratic,
-                                                                      RealOpenMM globalUreyBradleyCubic,
-                                                                      RealOpenMM globalUreyBradleyQuartic,
-                                                                      vector<RealVec>& forceData ) const {
-    RealOpenMM energy      = 0.0; 
-    for( int ii = 0; ii < numIxns; ii++ ){
-        int particle1Index            = particle1[ii];
-        int particle2Index            = particle2[ii];
-        RealOpenMM idealLength        = length[ii];
-        RealOpenMM kForceConstant     = kQuadratic[ii];
-        RealVec forces[2];
-        energy                       += calculateUreyBradleyIxn( particlePositions[particle1Index], particlePositions[particle2Index],
-                                                                 idealLength, kForceConstant, globalUreyBradleyCubic, globalUreyBradleyQuartic,
-                                                                 forces );
-        // accumulate forces
-    
-        for( int jj = 0; jj < 3; jj++ ){
-            forceData[particle1Index][jj] += forces[0][jj];
-            forceData[particle2Index][jj] -= forces[1][jj];
-        }
-
-    }   
-    return energy;
-}

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

-
-/* Portions copyright (c) 2006 Stanford University and Simbios.
- * Contributors: Pande Group
- *
- * Permission is hereby granted, free of charge, to any person obtaining
- * a copy of this software and associated documentation files (the
- * "Software"), to deal in the Software without restriction, including
- * without limitation the rights to use, copy, modify, merge, publish,
- * distribute, sublicense, and/or sell copies of the Software, and to
- * permit persons to whom the Software is furnished to do so, subject
- * to the following conditions:
- *
- * The above copyright notice and this permission notice shall be included
- * in all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
- * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
- * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
- * IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE
- * LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
- * OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
- * WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
- */
-
-#ifndef __AmoebaReferenceUreyBradleyForce_H__
-#define __AmoebaReferenceUreyBradleyForce_H__
-
-#include "SimTKUtilities/RealVec.h"
-#include <vector>
-
-// ---------------------------------------------------------------------------------------
-
-class AmoebaReferenceUreyBradleyForce {
-
-public:
- 
-    /**---------------------------------------------------------------------------------------
-       
-        Constructor
-       
-        --------------------------------------------------------------------------------------- */
- 
-    AmoebaReferenceUreyBradleyForce( ){};
- 
-    /**---------------------------------------------------------------------------------------
-       
-        Destructor
-       
-        --------------------------------------------------------------------------------------- */
- 
-    ~AmoebaReferenceUreyBradleyForce( ){};
- 
-     /**---------------------------------------------------------------------------------------
-     
-        Calculate Amoeba Urey-Bradley ixns (force and energy)
-     
-        @param numIxns                 number of ixns
-        @param posData                 particle positions
-        @param particle1               particle 1 indices
-        @param particle2               particle 2 indices
-        @param length                  ideal length
-        @param kForce                  force constant
-        @param cubic                   cubic force parameter
-        @param quartic                 quartic force parameter
-        @param forceDate               output force vector
-     
-        @return total energy
-     
-        --------------------------------------------------------------------------------------- */
-     
-    RealOpenMM calculateForceAndEnergy( int numIxns, std::vector<OpenMM::RealVec>& posData,
-                                        const std::vector<int>& particle1,
-                                        const std::vector<int>&  particle2,
-                                        const std::vector<RealOpenMM>& length,
-                                        const std::vector<RealOpenMM>& kForce,
-                                        RealOpenMM cubic, RealOpenMM quartic,
-                                        std::vector<OpenMM::RealVec>& forceData ) const;
-
-private:
-
-     /**---------------------------------------------------------------------------------------
-     
-        Calculate Amoeba Urey-Bradley ixns (force and energy)
-     
-        @param positionAtomA           Cartesian coordinates of atom A
-        @param positionAtomB           Cartesian coordinates of atom B
-        @param length                  ideal length
-        @param kForce                  force constant
-        @param cubic                   cubic force parameter
-        @param quartic                 quartic force parameter
-        @param forces                  force vector
-     
-        @return energy
-     
-        --------------------------------------------------------------------------------------- */
-     
-    RealOpenMM calculateUreyBradleyIxn( const OpenMM::RealVec& positionAtomA, const OpenMM::RealVec& positionAtomB,
-                                        RealOpenMM idealLength, RealOpenMM kForce,
-                                        RealOpenMM cubic, RealOpenMM quartic,
-                                        OpenMM::RealVec* forces ) const;
-     
-};
-
-// ---------------------------------------------------------------------------------------
-
-#endif // _AmoebaReferenceUreyBradleyForce___

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

@@ -210,7 +210,6 @@ RealOpenMM AmoebaReferenceVdwForce::calculatePairIxn( RealOpenMM combindedSigma,
 RealOpenMM AmoebaReferenceVdwForce::calculateForceAndEnergyNoCutoff( int numParticles,
                                                                      const vector<RealVec>& particlePositions,
                                                                      const std::vector<int>& indexIVs, 
-                                                                     const std::vector<int>& indexClasses, 
                                                                      const std::vector<RealOpenMM>& sigmas,
                                                                      const std::vector<RealOpenMM>& epsilons,
                                                                      const std::vector<RealOpenMM>& reductions,
@@ -293,7 +292,6 @@ RealOpenMM AmoebaReferenceVdwForce::calculateForceAndEnergyNoCutoff( int numPart
 RealOpenMM AmoebaReferenceVdwForce::calculateForceAndEnergyApplyCutoff( int numParticles,
                                                                         const vector<RealVec>& particlePositions,
                                                                         const std::vector<int>& indexIVs, 
-                                                                        const std::vector<int>& indexClasses, 
                                                                         const std::vector<RealOpenMM>& sigmas,
                                                                         const std::vector<RealOpenMM>& epsilons,
                                                                         const std::vector<RealOpenMM>& reductions,
@@ -376,7 +374,6 @@ RealOpenMM AmoebaReferenceVdwForce::calculateForceAndEnergyApplyCutoff( int numP
 RealOpenMM AmoebaReferenceVdwForce::calculateForceAndEnergy( int numParticles,
                                                              const vector<RealVec>& particlePositions,
                                                              const std::vector<int>& indexIVs, 
-                                                             const std::vector<int>& indexClasses, 
                                                              const std::vector<RealOpenMM>& sigmas,
                                                              const std::vector<RealOpenMM>& epsilons,
                                                              const std::vector<RealOpenMM>& reductions,
@@ -386,11 +383,11 @@ RealOpenMM AmoebaReferenceVdwForce::calculateForceAndEnergy( int numParticles,
     
     if( getNonbondedMethod() == NoCutoff ){
         return calculateForceAndEnergyNoCutoff( numParticles, particlePositions, 
-                                                indexIVs, indexClasses, sigmas, epsilons,
+                                                indexIVs, sigmas, epsilons,
                                                 reductions, allExclusions, forces );
     } else {
         return calculateForceAndEnergyApplyCutoff( numParticles, particlePositions, 
-                                                   indexIVs, indexClasses, sigmas, epsilons,
+                                                   indexIVs, sigmas, epsilons,
                                                    reductions, allExclusions, forces );
     }