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/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());