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/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/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());